Column descriptions:
Rank CDD Gene context Motif Rank Score Weight Species Len Score Conserved Energy BP Seq_id GC RFAM
0 9904 IlvB Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] [Amino acid transport and metabolism / Coenzyme metabolism] context 0 3400.62 366.96 37.00 82.60 53.99 23.00 -19.75 14.09 0.42 0.44 RF00230 T-box 147
22646 YqgFc Likely ribonuclease with RNase H fold. YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions. context 1 2057.05 317.93 36.00 78.00 46.89 21.00 -6.15 6.25 0.41 0.45 RF00230 T-box 143
9941 LeuD 3-isopropylmalate dehydratase small subunit [Amino acid transport and metabolism] context 2 1701.86 243.00 32.00 53.40 40.16 18.00 -5.89 7.97 0.47 0.48 RF00230 T-box 108
10418 TrpD Anthranilate phosphoribosyltransferase [Amino acid transport and metabolism] context 3 1627.07 384.00 41.00 50.50 39.08 5.00 -19.44 11.85 0.41 0.46 RF00230 T-box 129
27056 DUF1292 Protein of unknown function (DUF1292). This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown. context 4 1356.65 289.00 31.00 55.70 42.07 15.00 -3.90 6.15 0.51 0.47 RF00230 T-box 138
10619 GlyS Glycyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis] context 5 1231.63 111.00 31.00 156.70 52.15 20.00 0.40 4.98 0.33 0.42 RF00230 T-box 45
24864 DUF901 Protein of unknown function (DUF901). This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown. context 6 909.69 107.00 29.00 56.20 42.60 10.00 -2.73 8.53 0.47 0.48 RF00230 T-box 32
10383 PabA Anthranilate/para-aminobenzoate synthases component II [Amino acid transport and metabolism / Coenzyme metabolism] context 7 801.06 65.98 24.00 49.10 38.07 9.00 -19.35 11.97 0.40 0.49 RF00230 T-box 30
9892 PheS Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis] context 8 662.42 29.00 29.00 87.40 68.70 23.00 -10.08 10.57 0.47 0.41 RF00230 T-box 10
10297 GRS1 Glycyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis] context 9 600.97 27.37 19.00 62.10 50.41 15.00 -8.82 13.98 0.43 0.50 RF00230 T-box 10
10034 TrpA Tryptophan synthase alpha chain [Amino acid transport and metabolism] context 10 296.58 19.00 12.00 136.50 46.27 6.00 -13.18 14.80 0.32 0.44 RF00230 T-box 10
10490 MetE Methionine synthase II (cobalamin-independent) [Amino acid transport and metabolism] context 11 291.54 11.92 11.00 116.40 81.50 11.00 -21.71 20.17 0.38 0.38 RF00162 S_box 1 RF00230 T-box 3
10619 GlyS Glycyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis] context 12 267.53 15.00 15.00 91.50 71.36 23.00 -6.33 6.17 0.45 0.47 RF00230 T-box 3
27671 HisRS-like_core Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ. HisZ along with HisG catalyze the first reaction in histidine biosynthesis. HisZ is found only in a subset of bacteria and differs from HisRS in lacking a C-terminal anti-codon binding domain. context 13 239.76 21.00 20.00 55.20 45.86 10.00 -6.52 6.02 0.47 0.47 RF00230 T-box 6
10055 TrpS Tryptophanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] context 14 239.61 17.00 16.00 52.50 51.79 11.00 -9.51 8.90 0.50 0.46 RF00230 T-box 11
10772 CysE Serine acetyltransferase [Amino acid transport and metabolism] context 15 234.41 14.00 14.00 80.90 70.46 12.00 -20.91 11.26 0.49 0.47
27671 HisRS-like_core Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ. HisZ along with HisG catalyze the first reaction in histidine biosynthesis. HisZ is found only in a subset of bacteria and differs from HisRS in lacking a C-terminal anti-codon binding domain. context 16 218.34 5.00 5.00 111.60 160.45 84.00 -10.25 18.57 0.82 0.24
10008 TrpB Tryptophan synthase beta chain [Amino acid transport and metabolism] context 17 199.66 17.99 18.00 44.90 31.88 4.00 -13.31 9.96 0.34 0.52 RF00230 T-box 9
10048 AspS Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] context 18 192.25 19.45 20.00 53.20 22.28 4.00 -2.67 7.92 0.36 0.37 RF00230 T-box 3
22646 YqgFc Likely ribonuclease with RNase H fold. YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions. context 19 185.78 22.52 21.00 42.00 21.35 6.00 -5.60 4.03 0.38 0.39 RF00230 T-box 8
24821 DUF880 Protein of unknown function (DUF880). This family consists of a number of hypothetical bacterial and plant proteins. The family also contains the C terminal region of a Cysteinyl-tRNA synthetase from Staphylococcus epidermidis. The function of this family is unknown. context 20 174.83 15.00 15.00 48.10 41.58 9.00 -12.75 6.94 0.47 0.49
9941 LeuD 3-isopropylmalate dehydratase small subunit [Amino acid transport and metabolism] context 21 147.60 10.00 10.00 141.20 59.24 4.00 -18.27 16.08 0.31 0.50 RF00230 T-box 3
24821 DUF880 Protein of unknown function (DUF880). This family consists of a number of hypothetical bacterial and plant proteins. The family also contains the C terminal region of a Cysteinyl-tRNA synthetase from Staphylococcus epidermidis. The function of this family is unknown. context 22 121.35 84.00 33.00 47.20 35.87 0.00 -16.16 7.59 0.42 0.47 RF00230 T-box 17
16655 Iso_dh Isocitrate/isopropylmalate dehydrogenase. context 23 113.05 10.00 10.00 74.10 53.46 11.00 -2.10 3.88 0.34 0.54 RF00230 T-box 4
27671 HisRS-like_core Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ. HisZ along with HisG catalyze the first reaction in histidine biosynthesis. HisZ is found only in a subset of bacteria and differs from HisRS in lacking a C-terminal anti-codon binding domain. context 24 89.13 7.73 8.00 57.70 28.39 6.00 -8.02 7.21 0.45 0.33
1 13174 COG3859 Predicted membrane protein [Function unknown] context 0 3115.11 96.00 35.00 150.40 95.52 44.00 -17.98 18.65 0.42 0.42 RF00059 THI 71
13872 COG4732 Predicted membrane protein [Function unknown] context 1 922.74 47.00 21.00 126.60 66.44 28.00 -14.15 8.40 0.40 0.41 RF00059 THI 36
10225 ThiD Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase [Coenzyme metabolism] context 2 878.54 54.00 22.00 97.10 44.09 18.00 -14.69 9.00 0.37 0.41 RF00059 THI 37 RF00230 T-box 1
11812 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism] context 3 277.42 25.00 15.00 46.10 41.76 8.00 -7.88 9.32 0.51 0.48 RF00059 THI 17
11812 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism] context 4 146.89 11.95 11.00 45.70 38.45 8.00 -5.79 8.65 0.47 0.49 RF00059 THI 6
10534 DadA Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism] context 5 112.13 15.95 12.00 47.60 25.61 4.00 -5.79 5.14 0.41 0.37 RF00059 THI 2
11171 CodB Purine-cytosine permease and related proteins [Nucleotide transport and metabolism] context 6 96.41 4.00 3.00 196.60 119.75 8.00 -13.10 15.95 0.21 0.41 RF00059 THI 1
2 11125 MetH Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism] context 0 2376.06 112.00 18.00 158.00 130.19 42.00 -32.16 24.78 0.48 0.44 RF00162 S_box 71
10057 COG0182 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis] context 1 667.22 50.00 17.00 78.10 80.62 32.00 -7.62 6.31 0.57 0.52 RF00162 S_box 34
28024 MTHFR Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase to convert homocysteine to methionine. The enzymatic mechanism is a ping-pong bi-bi mechanism, in which NAD(P)+ release precedes the binding of methylenetetrahydrofolate and the acceptor is free FAD. The family includes the 5,10-methylenetetrahydrofolate reductase EC:1.7.99.5 from prokaryotes and methylenetetrahydrofolate reductase EC: 1.5.1.20 from eukaryotes. The bacterial enzyme is a homotetramer and NADH is the preferred reductant while the eukaryotic enzyme is a homodimer and NADPH is the preferred reductant. In humans, there are several clinically significant mutations in MTHFR that result in hyperhomocysteinemia, which is a risk factor for the development of cardiovascular disease. context 2 483.05 95.98 22.00 93.40 43.84 4.00 -9.82 6.38 0.34 0.43 RF00162 S_box 43 RF00230 T-box 14
11719 AbcD ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism] context 3 460.06 42.93 24.00 53.70 26.55 5.00 -14.62 10.15 0.36 0.37 RF00230 T-box 1
10516 MetH Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism] context 4 243.75 15.00 15.00 136.10 66.80 4.00 -13.53 14.46 0.23 0.39 RF00162 S_box 1 RF00230 T-box 2
11501 COG1791 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown] context 5 234.48 11.00 7.00 94.60 71.48 20.00 -22.92 12.12 0.46 0.44 RF00162 S_box 5
10057 COG0182 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis] context 6 174.59 4.00 4.00 105.90 144.03 65.00 -21.80 17.24 0.59 0.55 RF00162 S_box 2
10050 CysH 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism] context 7 134.34 5.00 5.00 246.80 151.61 9.00 -9.55 20.40 0.26 0.35 RF00162 S_box 2
9266 Cys_Met_Meta_PP Cys/Met metabolism PLP-dependent enzyme. This family includes enzymes involved in cysteine and methionine metabolism. The following are members: Cystathionine gamma-lyase, Cystathionine gamma-synthase, Cystathionine beta-lyase, Methionine gamma-lyase, OAH/OAS sulfhydrylase, O-succinylhomoserine sulfhydrylase All of these members participate is slightly different reactions. All these enzymes use PLP (pyridoxal-5'-phosphate) as a cofactor. context 8 92.25 3.00 3.00 168.10 185.21 23.00 -21.26 16.71 0.41 0.47 RF00162 S_box 2
11178 NlpA ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism] context 9 89.15 39.27 25.00 33.80 19.52 0.00 -15.70 9.71 0.33 0.38 RF00230 T-box 1
10057 COG0182 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis] context 10 69.84 6.00 6.00 48.90 33.28 4.00 -16.38 12.26 0.38 0.40
9266 Cys_Met_Meta_PP Cys/Met metabolism PLP-dependent enzyme. This family includes enzymes involved in cysteine and methionine metabolism. The following are members: Cystathionine gamma-lyase, Cystathionine gamma-synthase, Cystathionine beta-lyase, Methionine gamma-lyase, OAH/OAS sulfhydrylase, O-succinylhomoserine sulfhydrylase All of these members participate is slightly different reactions. All these enzymes use PLP (pyridoxal-5'-phosphate) as a cofactor. context 11 64.99 4.00 4.00 90.80 85.83 6.00 -15.14 15.33 0.36 0.43 RF00162 S_box 1
3 9991 COG0116 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair] context 0 2327.63 30.00 30.00 241.10 290.82 122.00 -45.62 30.05 0.61 0.46 RF00011 RNaseP_bact_b 24
4 4383 DHBP_synthase 3,4-dihydroxy-2-butanone 4-phosphate synthase. 3,4-Dihydroxy-2-butanone 4-phosphate is biosynthesised from ribulose 5-phosphate and serves as the biosynthetic precursor for the xylene ring of riboflavin. Sometimes found as a bifunctional enzyme with pfam00925. context 0 2228.37 49.00 34.00 204.80 155.20 58.00 -27.45 16.23 0.41 0.45 RF00050 RFN 41
10675 RibA GTP cyclohydrolase II [Coenzyme metabolism] context 1 1347.86 51.00 34.00 126.30 138.80 61.00 -11.10 7.54 0.58 0.50 RF00050 RFN 41
7812 DMRL_synthase 6,7-dimethyl-8-ribityllumazine synthase. This family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase EC:2.5.1.9, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function. context 2 528.41 18.00 18.00 129.00 154.59 52.00 -14.74 9.08 0.55 0.51 RF00050 RFN 13
10960 COG1242 Predicted Fe-S oxidoreductase [General function prediction only] context 3 462.65 21.00 17.00 91.30 85.22 27.00 -5.03 7.98 0.43 0.45 RF00050 RFN 17
5 28287 PEPCK_ATP Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity, this model describes the ATP-dependent groups. context 0 1640.05 112.00 17.00 112.30 110.96 43.00 -13.61 15.01 0.58 0.47 RF00162 S_box 78
28287 PEPCK_ATP Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity, this model describes the ATP-dependent groups. context 1 616.78 105.00 17.00 132.20 95.02 35.00 -0.79 2.35 0.50 0.46 RF00162 S_box 79
28287 PEPCK_ATP Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity, this model describes the ATP-dependent groups. context 2 276.58 16.00 11.00 85.50 69.58 21.00 -0.64 7.89 0.50 0.45 RF00162 S_box 9
6 28178 DHOase_IIa Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C.elegans protein involved in axon growth. context 0 1539.74 69.00 31.00 119.00 62.97 24.00 -15.23 11.64 0.37 0.42
10331 CarB Carbamoylphosphate synthase large subunit (split gene in MJ) [Amino acid transport and metabolism / Nucleotide transport and metabolism] context 1 1118.83 68.00 26.00 106.40 50.93 15.00 -11.97 10.45 0.33 0.44
9919 PyrC Dihydroorotase and related cyclic amidohydrolases [Nucleotide transport and metabolism] context 2 1058.63 46.00 22.00 107.60 57.38 19.00 -23.09 13.98 0.35 0.46
11939 UraA Xanthine/uracil permeases [Nucleotide transport and metabolism] context 3 857.05 58.00 24.00 103.60 52.47 13.00 -13.10 9.27 0.34 0.45 RF00167 Purine 10
10411 PyrB Aspartate carbamoyltransferase, catalytic chain [Nucleotide transport and metabolism] context 4 843.80 61.00 28.00 107.40 51.28 15.00 -7.31 6.61 0.35 0.44
10411 PyrB Aspartate carbamoyltransferase, catalytic chain [Nucleotide transport and metabolism] context 5 719.55 30.00 28.00 104.40 55.88 14.00 -17.16 13.43 0.33 0.42
23373 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. context 6 406.48 27.97 22.00 78.20 31.99 5.00 -12.06 11.08 0.26 0.39
7 10390 GuaA GMP synthase, PP-ATPase domain/subunit [Nucleotide transport and metabolism] context 0 1429.50 51.00 21.00 145.70 99.22 33.00 -22.61 14.89 0.38 0.39 RF00167 Purine 33 RF00442 ykkC-yxkD 1
9916 PurE Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism] context 1 165.32 14.00 14.00 31.80 34.99 17.00 -2.34 4.54 0.56 0.44 RF00167 Purine 6
10025 PurM Phosphoribosylaminoimidazole (AIR) synthetase [Nucleotide transport and metabolism] context 2 70.99 4.00 4.00 240.90 158.48 8.00 7.99 9.22 0.24 0.39 RF00167 Purine 2
8 10732 GcvP Glycine cleavage system protein P (pyridoxal-binding), C-terminal domain [Amino acid transport and metabolism] context 0 1322.64 29.00 26.00 174.60 105.26 37.00 -28.18 19.79 0.35 0.44 RF00504 gcvT 24
10837 AlsT Na+/alanine symporter [Amino acid transport and metabolism] context 1 653.63 17.98 16.00 155.50 80.36 36.00 -9.19 14.39 0.39 0.45 RF00504 gcvT 15
16987 Cation_efflux Cation efflux family. Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are thought to be efflux pumps that remove these ions from cells. context 2 279.45 7.00 7.00 160.90 101.90 40.00 -6.05 17.84 0.45 0.40 RF00504 gcvT 6
9928 MMT1 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism] context 3 79.63 4.00 4.00 99.90 121.29 11.00 -19.03 18.40 0.52 0.32
9 24631 DUF149 Uncharacterised BCR, YbaB family COG0718. context 0 1235.55 28.00 28.00 165.70 136.77 29.00 -31.64 25.34 0.38 0.43 RF00169 SRP_bact 21
10 10986 CbiB Cobalamin biosynthesis protein CobD/CbiB [Coenzyme metabolism] context 0 1222.14 36.00 13.00 230.60 144.06 46.00 -17.97 18.31 0.39 0.43 RF00174 Cobalamin 30
10739 CobJ Precorrin-3B methylase [Coenzyme metabolism] context 1 143.29 4.00 4.00 135.10 132.82 39.00 -14.83 16.04 0.49 0.50 RF00174 Cobalamin 2
25922 CbiN Cobalt transport protein component CbiN. CbiN is part of the active cobalt transport system involved in uptake of cobalt in to the cell involved with cobalamin biosynthesis (vitamin B12). It has been suggested that CbiN may function as the periplasmic binding protein component of the active cobalt transport system. context 2 126.85 4.00 4.00 248.00 178.83 22.00 -4.73 14.95 0.33 0.46 RF00174 Cobalamin 2
11507 CobB Cobyrinic acid a,c-diamide synthase [Coenzyme metabolism] context 3 51.25 4.00 4.00 136.00 114.51 10.00 -0.77 5.15 0.32 0.50 RF00174 Cobalamin 3
11 12678 COG3344 Retron-type reverse transcriptase [DNA replication, recombination, and repair] context 0 1211.97 16.00 5.00 428.30 460.65 142.00 -45.55 46.80 0.53 0.46
12 13194 COG3880 Uncharacterized protein with conserved CXXC pairs [Function unknown] context 0 1151.59 56.00 9.00 152.70 202.41 98.00 -23.62 14.80 0.71 0.43
13 6339 GrpE GrpE. context 0 1126.14 87.00 40.00 37.70 35.84 17.00 -10.88 8.61 0.59 0.36
14 1427 Transposase_mut Transposase, Mutator family. context 0 1060.45 29.00 6.00 129.00 230.78 118.00 -30.92 37.45 0.94 0.35
15 10097 RplL Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis] context 0 967.83 33.00 33.00 158.40 88.43 35.00 -2.63 9.53 0.39 0.41
10119 RplJ Ribosomal protein L10 [Translation, ribosomal structure and biogenesis] context 1 929.86 35.00 35.00 108.80 64.98 24.00 -15.57 10.50 0.36 0.41
16 25808 DUF28 Domain of unknown function DUF28. This domain is found in bacterial and yeast proteins it compromises the entire length or central region of most of the proteins in the family, all of which are hypothetical with no known function. The average length of this domain is approximately 230 amino acids long. context 0 965.63 78.92 34.00 40.30 31.17 9.00 -18.77 10.84 0.42 0.31
17 5361 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. context 0 959.37 84.00 29.00 36.10 32.29 12.00 -17.07 9.48 0.45 0.32
18 10141 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair] context 0 944.83 94.00 35.00 39.80 31.66 8.00 -19.04 9.22 0.41 0.27
19 10234 RpsF Ribosomal protein S6 [Translation, ribosomal structure and biogenesis] context 0 911.41 36.00 36.00 139.80 65.84 21.00 -6.89 9.07 0.30 0.33
1634 Ribosomal_S18 Ribosomal protein S18. context 1 493.35 34.88 35.00 46.20 40.69 12.00 -5.23 7.98 0.49 0.45
1634 Ribosomal_S18 Ribosomal protein S18. context 2 58.51 26.49 27.00 99.00 35.38 0.00 -2.44 5.40 0.23 0.34
20 9895 LysA Diaminopimelate decarboxylase [Amino acid transport and metabolism] context 0 899.11 32.00 17.00 121.10 69.03 22.00 -23.25 17.02 0.36 0.42 RF00168 Lysine 21
21 10727 TerC Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism] context 0 896.97 22.00 17.00 112.00 92.37 32.00 -25.02 26.23 0.48 0.42 RF00080 yybP-ykoY 14
22 10897 COG1179 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism] context 0 859.15 32.00 25.00 156.70 100.57 21.00 -23.26 15.05 0.42 0.47
23 10478 RecJ Single-stranded DNA-specific exonuclease [DNA replication, recombination, and repair] context 0 858.69 91.00 34.00 38.10 32.41 5.00 -18.05 12.77 0.41 0.36 RF00230 T-box 1
10700 LysP Amino acid transporters [Amino acid transport and metabolism] context 1 89.54 4.00 4.00 72.80 71.12 22.00 -19.98 13.77 0.61 0.29
24 10835 AnsP Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism] context 0 849.56 100.00 34.00 34.50 30.16 8.00 -17.26 7.40 0.42 0.34
25 10272 COG0398 Uncharacterized conserved protein [Function unknown] context 0 847.52 56.00 35.00 74.30 47.80 16.00 -8.29 6.70 0.40 0.46
26 16802 Ribosomal_L1 Ribosomal protein L1p/L10e family. This family includes prokaryotic L1 and eukaryotic L10. context 0 823.93 48.00 40.00 65.20 40.30 21.00 -6.99 5.87 0.41 0.40
27 9926 RpsJ Ribosomal protein S10 [Translation, ribosomal structure and biogenesis] context 0 812.00 27.00 27.00 145.80 148.81 49.00 -13.44 11.03 0.60 0.45
803 Ribosomal_L22 Ribosomal protein L22p/L17e. This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. context 1 272.79 26.00 26.00 30.30 50.22 17.00 -5.40 5.12 0.80 0.64
24417 Ribosomal_S8 Ribosomal protein S8. context 2 251.21 28.98 22.00 59.10 31.83 4.00 -9.38 6.48 0.34 0.38
803 Ribosomal_L22 Ribosomal protein L22p/L17e. This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. context 3 221.20 19.00 19.00 85.00 88.26 16.00 2.31 5.02 0.60 0.49
24393 Ribosomal_L14 Ribosomal protein L14p/L23e. context 4 179.06 23.95 24.00 28.40 28.63 7.00 -1.74 4.02 0.52 0.63
803 Ribosomal_L22 Ribosomal protein L22p/L17e. This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. context 5 164.97 26.80 18.00 45.50 29.45 4.00 -7.39 4.05 0.40 0.57
22970 Ribosomal_L3 Ribosomal protein L3. context 6 89.91 14.43 15.00 53.90 37.80 6.00 -0.44 2.55 0.44 0.39
28 10357 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones] context 0 803.57 87.00 33.00 35.90 32.26 5.00 -17.15 13.23 0.45 0.28
29 15150 Resolvase Resolvase, N terminal domain. The N-terminal domain of the resolvase family (this family) contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase - see pfam02796. context 0 794.78 11.00 9.00 281.80 349.07 176.00 -19.51 23.64 0.77 0.26
15150 Resolvase Resolvase, N terminal domain. The N-terminal domain of the resolvase family (this family) contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase - see pfam02796. context 1 148.02 3.00 1.00 185.80 285.01 160.00 -33.23 28.26 0.91 0.28
30 25645 EF_TS Elongation factor TS. context 0 775.70 61.00 30.00 39.80 33.92 11.00 -18.43 9.19 0.45 0.37
31 10164 InfC Translation initiation factor 3 (IF-3) [Translation, ribosomal structure and biogenesis] context 0 765.60 31.00 31.00 110.80 65.22 16.00 -19.30 15.06 0.40 0.44
32 11690 LdcC Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism] context 0 752.85 91.00 33.00 31.40 28.77 5.00 -16.97 10.36 0.42 0.42
33 10700 LysP Amino acid transporters [Amino acid transport and metabolism] context 0 736.51 27.00 20.00 115.30 76.37 14.00 -23.27 20.34 0.36 0.44 RF00168 Lysine 18
34 13857 COG4716 Myosin-crossreactive antigen [Function unknown] context 0 718.33 80.00 28.00 34.00 33.47 8.00 -18.59 9.36 0.49 0.40
35 14730 COG5646 Uncharacterized conserved protein [Function unknown] context 0 717.01 72.65 28.00 36.00 30.13 8.00 -19.08 8.55 0.41 0.36 RF00230 T-box 1
36 11491 NrdI Protein involved in ribonucleotide reduction [Nucleotide transport and metabolism] context 0 713.62 63.00 22.00 35.60 35.81 12.00 -20.01 10.24 0.50 0.39
37 11135 HrcA Transcriptional regulator of heat shock gene [Transcription] context 0 691.60 93.39 40.00 25.00 31.04 16.00 -8.70 3.81 0.71 0.40
38 9976 TruA Pseudouridylate synthase [Translation, ribosomal structure and biogenesis] context 0 666.26 71.00 28.00 36.90 34.71 5.00 -18.50 13.44 0.46 0.39
39 11945 MgtE Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism] context 0 664.55 25.00 15.00 123.30 149.99 34.00 -28.04 15.84 0.63 0.46 RF00380 ykoK 21
40 10323 GlmS Glucosamine 6-phosphate synthetase, contains amidotransferase and phosphosugar isomerase domains [Cell envelope biogenesis, outer membrane] context 0 645.35 19.00 19.00 98.00 102.45 27.00 -28.15 22.48 0.53 0.48 RF00234 glmS 13
41 10393 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis] context 0 639.42 26.00 26.00 177.60 114.08 30.00 4.63 7.41 0.37 0.37
42 12166 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair] context 0 632.76 24.00 24.00 142.10 133.67 34.00 -16.34 8.13 0.40 0.42 RF00169 SRP_bact 20
43 10561 Ung Uracil DNA glycosylase [DNA replication, recombination, and repair] context 0 618.67 60.00 26.00 41.60 23.88 8.00 -16.60 9.42 0.46 0.34
44 10332 GroL Chaperonin GroEL (HSP60 family) [Posttranslational modification, protein turnover, chaperones] context 0 617.72 30.00 30.00 107.90 60.13 23.00 -10.95 7.31 0.40 0.29
45 25346 RL11 Ribosomal protein L11/L12; context 0 613.36 36.99 37.00 57.20 37.91 12.00 -8.78 9.01 0.40 0.40
46 25629 Ribosomal_L21p Ribosomal prokaryotic L21 protein. context 0 586.79 33.97 34.00 94.10 58.94 21.00 -3.08 5.62 0.40 0.44
47 11419 COG1708 Predicted nucleotidyltransferases [General function prediction only] context 0 585.51 9.00 3.00 228.00 402.02 228.00 -35.20 37.90 1.00 0.28
48 25197 PrmA Ribosomal protein L11 methyltransferase (PrmA). This family consists of several Ribosomal protein L11 methyltransferase (EC:2.1.1.-) sequences. context 0 583.33 56.00 24.00 38.70 34.61 8.00 -20.21 9.50 0.45 0.35
49 2325 Transposase_17 Transposase IS200 like. Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS200 from E. coli. context 0 581.90 31.00 11.00 115.20 87.84 18.00 -18.54 16.69 0.45 0.40
50 5638 Cad Cadmium resistance transporter. context 0 581.49 11.00 11.00 287.80 272.41 57.00 -16.31 26.87 0.55 0.32 RF00240 RNA-OUT 1
5638 Cad Cadmium resistance transporter. context 1 420.03 13.00 13.00 125.40 105.06 31.00 -10.92 16.73 0.50 0.29
51 9965 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis] context 0 575.42 19.00 19.00 185.60 107.82 37.00 -7.23 7.89 0.32 0.38
52 10724 RbfA Ribosome-binding factor A [Translation, ribosomal structure and biogenesis] context 0 573.36 75.00 30.00 27.00 27.36 8.00 -16.60 5.58 0.46 0.52
53 10892 OpuBB ABC-type proline/glycine betaine transport systems, permease component [Amino acid transport and metabolism] context 0 561.87 21.00 3.00 232.40 352.30 131.00 -8.03 24.03 0.78 0.36 RF00005 tRNA 6
10892 OpuBB ABC-type proline/glycine betaine transport systems, permease component [Amino acid transport and metabolism] context 1 510.06 21.00 3.00 180.00 298.96 142.00 -21.90 21.55 0.92 0.37
54 11436 COG1725 Predicted transcriptional regulators [Transcription] context 0 554.34 61.00 29.00 31.30 28.06 5.00 -14.07 10.17 0.44 0.35 RF00230 T-box 2
11436 COG1725 Predicted transcriptional regulators [Transcription] context 1 170.69 11.30 7.00 55.30 29.44 11.00 -13.07 9.19 0.41 0.33
55 26270 RNA_pol_Rpb2_1 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain. context 0 553.44 7.00 7.00 197.50 232.13 129.00 -15.90 32.90 0.68 0.30
9960 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] context 1 258.91 17.00 17.00 79.60 62.05 6.00 -14.15 12.72 0.34 0.33
9961 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] context 2 186.52 14.00 14.00 76.30 45.66 5.00 -14.89 10.24 0.30 0.38
56 10448 GlpA Glycerol-3-phosphate dehydrogenase [Energy production and conversion] context 0 552.95 33.60 19.00 61.50 40.10 8.00 -18.18 16.51 0.40 0.33
57 4036 HSP70 Hsp70 protein. Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region. context 0 550.14 32.99 32.00 75.10 42.94 16.00 -8.37 6.01 0.35 0.31
58 14028 COG4894 Uncharacterized conserved protein [Function unknown] context 0 548.26 17.00 9.00 183.60 162.23 28.00 -26.31 23.60 0.48 0.38
15771 DUF554 Protein of unknown function (DUF554). Family of uncharacterised prokaryotic proteins. Multiple predicted transmembrane regions suggest that the region is membrane associated. context 1 60.36 4.00 4.00 77.00 80.48 10.00 -9.06 13.62 0.61 0.29
59 25846 DUF81 Domain of unknown function DUF81. This integral membrane protein family has no known function. The alignment appears to contain two duplicated modules of three transmembrane helices. context 0 541.08 76.67 32.00 34.90 28.09 4.00 -17.42 7.72 0.40 0.37
60 11180 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair] context 0 538.52 43.00 21.00 43.80 37.97 9.00 -14.96 11.40 0.47 0.29
61 10467 LspA Lipoprotein signal peptidase [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion] context 0 535.70 66.00 23.00 38.10 35.02 5.00 -15.60 11.62 0.47 0.33 RF00230 T-box 1
62 16544 PTS_IIA_lac PTS_IIA, PTS system, lactose/cellobiose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. This family of proteins normally function as a homotrimer, stabilized by a centrally located metal ion. Separation into subunits is thought to occur after phosphorylation. context 0 532.77 71.00 27.00 27.60 26.66 5.00 -12.80 8.71 0.45 0.36
63 14105 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair] context 0 528.52 48.00 23.00 39.10 27.31 8.00 -18.57 10.26 0.48 0.30
64 27792 HPPK 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after uptake by a carrier-mediated active transport system. Most microbes and plants lack this system and must synthesize folates de novo from guanosine triphosphate. One enzyme from this pathway is HPPK which catalyzes pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP). The functional enzyme is a monomer. Mammals lack many of the enzymes in the folate pathway including, HPPK. context 0 518.28 87.00 36.00 37.60 0.00 4.00 1.84 5.71 0.41 0.31
65 9584 DUF370 Domain of unknown function (DUF370). Bacterial domain of unknown function. context 0 517.96 36.00 17.00 36.10 31.98 13.00 -18.23 10.33 0.45 0.33
66 17117 PA PA domain. The PA (Protease associated) domain is found as an insert domain in diverse proteases. The PA domain is also found in a plant vacuolar sorting receptor and members of the RZF family. context 0 514.75 62.00 21.00 31.70 25.93 8.00 -20.39 7.94 0.47 0.45
67 10070 NusA Transcription elongation factor [Transcription] context 0 513.35 33.94 34.00 68.50 34.53 10.00 -10.75 8.94 0.40 0.33
68 9886 SpeB Arginase/agmatinase/formimionoglutamate hydrolase, arginase family [Amino acid transport and metabolism] context 0 513.32 55.00 21.00 35.10 30.44 5.00 -16.81 11.93 0.40 0.46
69 13148 COG3830 ACT domain-containing protein [Signal transduction mechanisms] context 0 501.64 9.00 9.00 120.90 164.08 72.00 -43.31 30.12 0.70 0.40
70 10331 CarB Carbamoylphosphate synthase large subunit (split gene in MJ) [Amino acid transport and metabolism / Nucleotide transport and metabolism] context 0 499.67 66.98 25.00 30.70 27.88 4.00 -16.88 10.13 0.42 0.51 RF00230 T-box 1
71 7866 Ribosomal_L27 Ribosomal L27 protein. context 0 498.47 34.91 35.00 119.60 63.18 19.00 0.07 4.12 0.39 0.39
72 4174 Ribosomal_S2 Ribosomal protein S2. context 0 494.43 28.75 29.00 133.10 61.31 5.00 -11.03 16.77 0.30 0.36
73 15625 DUF464 Protein of unknown function (DUF464). context 0 488.02 8.00 8.00 212.80 275.69 142.00 -16.66 18.58 0.71 0.38
12220 COG2868 Predicted ribosomal protein [Translation, ribosomal structure and biogenesis] context 1 460.72 23.00 23.00 69.00 63.31 16.00 -5.84 12.88 0.52 0.46
15625 DUF464 Protein of unknown function (DUF464). context 2 190.49 9.00 9.00 58.70 53.17 12.00 -5.26 11.75 0.32 0.44
12220 COG2868 Predicted ribosomal protein [Translation, ribosomal structure and biogenesis] context 3 98.51 12.00 12.00 87.80 48.24 6.00 3.75 4.13 0.38 0.37
74 9924 RpsG Ribosomal protein S7 [Translation, ribosomal structure and biogenesis] context 0 487.93 9.00 9.00 138.10 190.16 79.00 -20.32 20.04 0.54 0.38
75 10232 DnaG DNA primase (bacterial type) [DNA replication, recombination, and repair] context 0 486.60 50.00 20.00 33.80 36.73 10.00 -18.47 8.06 0.51 0.36
76 11710 AbrB Regulators of stationary/sporulation gene expression [Transcription] context 0 486.53 35.00 24.00 39.30 36.03 9.00 -21.87 9.89 0.42 0.39 RF00230 T-box 1
77 10339 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones] context 0 486.38 38.00 25.00 41.60 26.90 8.00 -16.73 10.32 0.45 0.38
78 11369 COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair] context 0 484.13 51.00 21.00 32.40 29.38 7.00 -12.95 9.74 0.47 0.35
79 10534 DadA Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism] context 0 482.06 50.00 19.00 35.30 32.12 6.00 -18.49 11.80 0.44 0.43 RF00230 T-box 7
80 10407 Obg Predicted GTPase [General function prediction only] context 0 480.21 50.00 19.00 35.50 34.76 8.00 -19.78 9.86 0.49 0.42
81 9906 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis] context 0 476.60 52.00 28.00 30.30 29.48 5.00 -15.33 9.99 0.47 0.44
82 10691 FcbC Predicted thioesterase [General function prediction only] context 0 473.25 48.00 23.00 38.90 30.83 5.00 -19.45 10.81 0.40 0.31 RF00230 T-box 1
83 23505 Gln-synt_N Glutamine synthetase, beta-Grasp domain. context 0 472.62 50.00 18.00 32.10 37.13 10.00 -18.94 8.93 0.54 0.40
84 9425 GidB Glucose inhibited division protein. This is a family of bacterial Glucose inhibited division proteins these are probably involved in the regulation of cell devision. context 0 470.62 8.00 2.00 258.00 464.80 258.00 -58.30 37.66 1.00 0.31
85 10797 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair] context 0 470.51 56.00 23.00 41.60 38.25 5.00 -20.61 10.14 0.45 0.31
86 12328 COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only] context 0 469.27 6.00 5.00 246.60 231.19 95.00 -44.33 31.11 0.47 0.39
13419 BtuD ABC-type cobalamin transport system, ATPase component [Coenzyme metabolism] context 1 323.99 4.00 4.00 225.80 275.22 106.00 -54.43 38.30 0.62 0.36
12328 COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only] context 2 211.54 6.76 7.00 151.60 92.06 26.00 -12.75 12.20 0.35 0.40
13402 COG4120 ABC-type uncharacterized transport system, permease component [General function prediction only] context 3 180.20 7.00 7.00 149.50 96.24 8.00 -21.82 25.86 0.32 0.40
13402 COG4120 ABC-type uncharacterized transport system, permease component [General function prediction only] context 4 156.73 10.00 7.00 148.90 94.48 5.00 -20.84 15.19 0.29 0.38
10890 AraH Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components [Carbohydrate transport and metabolism] context 5 108.65 4.00 4.00 176.20 188.63 18.00 -11.91 17.43 0.43 0.43
87 28272 Alkanesulfonate_monoxygenase Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin mononucleotide (FMNH2), which is provided by the NADPH-dependent FMN oxidoreductase (SsuE). context 0 467.61 50.00 22.00 60.30 35.14 4.00 -11.55 13.30 0.41 0.30 RF00230 T-box 2
88 24072 CtsR Firmicute transcriptional repressor of class III stress genes (CtsR). This family consists of several Firmicute transcriptional repressor of class III stress genes (CtsR) proteins. CtsR of L. monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon. context 0 466.68 19.98 20.00 159.10 58.57 15.00 -6.12 10.03 0.28 0.29
24072 CtsR Firmicute transcriptional repressor of class III stress genes (CtsR). This family consists of several Firmicute transcriptional repressor of class III stress genes (CtsR) proteins. CtsR of L. monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon. context 1 200.03 16.45 16.00 50.30 26.33 5.00 -9.46 8.55 0.32 0.34
89 11260 CinA Uncharacterized protein (competence- and mitomycin-induced) [General function prediction only] context 0 465.09 42.00 17.00 38.00 33.24 8.00 -21.89 10.57 0.42 0.43 RF00230 T-box 1
90 10375 PyrG CTP synthase (UTP-ammonia lyase) [Nucleotide transport and metabolism] context 0 464.15 43.00 21.00 64.50 30.62 6.00 -13.21 10.16 0.38 0.40 RF00230 T-box 4
91 12009 ComEC Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only] context 0 463.63 45.00 16.00 36.50 38.51 9.00 -20.95 11.25 0.51 0.42
92 10398 LysC Aspartokinases [Amino acid transport and metabolism] context 0 463.07 12.00 10.00 162.70 131.07 23.00 -38.49 27.77 0.42 0.42 RF00168 Lysine 7
93 10443 PstC ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism] context 0 462.19 43.00 25.00 36.10 30.78 8.00 -16.09 7.71 0.44 0.24
94 10036 BioA Adenosylmethionine-8-amino-7-oxononanoate aminotransferase [Coenzyme metabolism] context 0 462.06 62.00 21.00 36.70 32.22 5.00 -19.33 9.23 0.43 0.36
95 22970 Ribosomal_L3 Ribosomal protein L3. context 0 459.45 47.00 15.00 33.30 37.68 12.00 -19.67 9.05 0.54 0.42
96 12511 COG3173 Predicted aminoglycoside phosphotransferase [General function prediction only] context 0 457.60 54.68 20.00 30.70 26.79 5.00 -16.53 10.20 0.41 0.47
97 24564 PAP2 PAP2 superfamily. This family includes the enzyme type 2 phosphatidic acid phosphatase (PAP2), Glucose-6-phosphatase EC:3.1.3.9, Phosphatidylglycerophosphatase B EC:3.1.3.27 and bacterial acid phosphatase EC:3.1.3.2. context 0 457.24 59.86 25.00 26.50 23.90 5.00 -12.96 8.23 0.45 0.45
98 10147 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair] context 0 454.80 31.35 28.00 41.40 20.99 6.00 -14.18 11.26 0.34 0.34
99 10169 Cdd Cytidine deaminase [Nucleotide transport and metabolism] context 0 452.98 48.49 17.00 38.90 29.45 8.00 -22.63 8.99 0.44 0.42
100 23019 Formyl_trans_N Formyl transferase. This family includes the following members. Glycinamide ribonucleotide transformylase catalyses the third step in de novo purine biosynthesis, the transfer of a formyl group to 5'-phosphoribosylglycinamide. Formyltetrahydrofolate deformylase produces formate from formyl- tetrahydrofolate. Methionyl-tRNA formyltransferase transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA. Inclusion of the following members is supported by PSI-blast. HOXX_BRAJA (P31907) contains a related domain of unknown function. PRTH_PORGI (P46071) contains a related domain of unknown function. Y09P_MYCTU (Q50721) contains a related domain of unknown function. context 0 451.27 21.00 9.00 104.50 106.44 16.00 -7.19 20.92 0.46 0.40
101 9965 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis] context 0 449.91 46.00 20.00 34.60 36.16 9.00 -17.40 8.35 0.51 0.38
102 12235 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning] context 0 443.40 57.00 23.00 30.00 34.53 5.00 -17.49 10.41 0.53 0.44
103 9916 PurE Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism] context 0 442.05 8.00 6.00 244.30 265.95 82.00 -14.11 22.70 0.57 0.42
104 10263 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair] context 0 440.73 49.00 14.00 31.30 35.34 9.00 -14.61 11.25 0.53 0.46
105 10290 PlsX Fatty acid/phospholipid biosynthesis enzyme [Lipid metabolism] context 0 440.45 37.98 21.00 56.50 31.44 5.00 -6.13 12.00 0.36 0.37
106 10101 PstS ABC-type phosphate transport system, periplasmic component [Inorganic ion transport and metabolism] context 0 439.49 29.83 27.00 69.20 21.81 5.00 -9.87 10.62 0.27 0.30
10443 PstC ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism] context 1 287.18 15.90 15.00 106.40 40.94 14.00 -5.52 6.15 0.27 0.27
10443 PstC ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism] context 2 152.32 9.92 10.00 107.50 34.24 4.00 -13.12 10.13 0.22 0.31
107 10320 HcaD Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only] context 0 434.33 45.00 23.00 33.20 37.28 8.00 -19.93 7.63 0.49 0.38
108 10448 GlpA Glycerol-3-phosphate dehydrogenase [Energy production and conversion] context 0 433.00 35.00 19.00 55.90 41.15 5.00 -25.80 15.01 0.39 0.40
109 10937 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones] context 0 431.88 39.00 17.00 38.60 38.34 9.00 -19.65 10.47 0.50 0.36
110 10674 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis] context 0 430.47 36.87 27.00 32.10 19.65 6.00 -8.90 8.06 0.34 0.38
24586 tRNA_m1G_MT tRNA (Guanine-1)-methyltransferase. This is a family of tRNA (Guanine-1)-methyltransferases EC:2.1.1.31. In E.coli K12 this enzyme catalyses the conversion of a guanosine residue to N1-methylguanine in position 37, next to the anticodon, in tRNA. context 1 389.65 37.72 30.00 57.40 22.78 4.00 -8.06 7.62 0.29 0.32
24586 tRNA_m1G_MT tRNA (Guanine-1)-methyltransferase. This is a family of tRNA (Guanine-1)-methyltransferases EC:2.1.1.31. In E.coli K12 this enzyme catalyses the conversion of a guanosine residue to N1-methylguanine in position 37, next to the anticodon, in tRNA. context 2 95.18 37.83 30.00 62.30 22.45 0.00 -10.55 8.56 0.26 0.33
1790 Ribosomal_L19 Ribosomal protein L19. context 3 92.61 9.90 8.00 30.50 20.78 4.00 -10.35 8.26 0.45 0.22
111 10648 COG0780 Enzyme related to GTP cyclohydrolase I [General function prediction only] context 0 429.20 42.00 18.00 40.60 36.83 6.00 -19.45 12.63 0.47 0.43
112 12166 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair] context 0 426.90 48.00 19.00 32.00 33.83 8.00 -20.05 7.96 0.48 0.45 RF00230 T-box 3
113 10398 LysC Aspartokinases [Amino acid transport and metabolism] context 0 426.75 30.00 15.00 37.00 38.76 10.00 -19.40 13.84 0.50 0.34
114 10470 TauC ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism] context 0 424.38 42.00 19.00 35.60 29.72 7.00 -19.23 9.05 0.42 0.47 RF00230 T-box 2
28272 Alkanesulfonate_monoxygenase Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin mononucleotide (FMNH2), which is provided by the NADPH-dependent FMN oxidoreductase (SsuE). context 1 82.35 7.00 4.00 61.50 38.02 4.00 -14.75 14.52 0.35 0.38
115 11371 COG1660 Predicted P-loop-containing kinase [General function prediction only] context 0 424.05 23.59 23.00 88.20 33.29 6.00 -15.07 12.61 0.25 0.31
17072 UPF0052 Uncharacterized protein family UPF0052. context 1 368.13 31.22 28.00 51.60 21.58 5.00 -6.24 8.02 0.31 0.35
11195 COG1481 Uncharacterized protein conserved in bacteria [Function unknown] context 2 241.13 26.62 23.00 39.60 19.17 4.00 -7.31 6.22 0.32 0.34
11195 COG1481 Uncharacterized protein conserved in bacteria [Function unknown] context 3 113.28 12.97 11.00 39.30 24.68 4.00 -9.14 6.86 0.37 0.36
116 24072 CtsR Firmicute transcriptional repressor of class III stress genes (CtsR). This family consists of several Firmicute transcriptional repressor of class III stress genes (CtsR) proteins. CtsR of L. monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon. context 0 421.50 28.00 9.00 123.00 40.43 20.00 -5.82 6.67 0.28 0.28
117 13411 COG4129 Predicted membrane protein [Function unknown] context 0 421.08 5.00 5.00 216.00 353.71 201.00 -33.86 33.84 0.96 0.28
23505 Gln-synt_N Glutamine synthetase, beta-Grasp domain. context 1 158.45 5.00 5.00 84.00 130.86 75.00 -7.88 12.82 0.96 0.22
118 12610 COG3274 Uncharacterized protein conserved in bacteria [Function unknown] context 0 420.22 9.00 9.00 214.00 243.05 97.00 -8.76 14.13 0.63 0.39
119 10375 PyrG CTP synthase (UTP-ammonia lyase) [Nucleotide transport and metabolism] context 0 417.64 41.00 25.00 34.60 28.27 5.00 -17.80 10.57 0.44 0.46 RF00230 T-box 2
120 10075 RplO Ribosomal protein L15 [Translation, ribosomal structure and biogenesis] context 0 415.63 10.00 10.00 114.20 124.79 41.00 -16.75 23.48 0.56 0.38
121 10132 RpmJ Ribosomal protein L36 [Translation, ribosomal structure and biogenesis] context 0 414.66 9.00 9.00 143.80 189.83 98.00 -5.96 15.78 0.73 0.36
10235 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis] context 1 125.76 10.00 10.00 59.40 65.28 19.00 2.51 4.86 0.59 0.32
9974 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis] context 2 101.22 10.78 11.00 53.60 52.08 8.00 4.38 5.06 0.49 0.32
10078 RplQ Ribosomal protein L17 [Translation, ribosomal structure and biogenesis] context 3 96.64 11.00 11.00 59.30 50.03 12.00 3.43 3.29 0.52 0.30
9974 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis] context 4 80.26 11.00 11.00 36.70 39.35 8.00 1.07 3.96 0.61 0.30
1005 Ribosomal_L36 Ribosomal protein L36. context 5 80.01 4.00 4.00 130.90 144.76 51.00 -5.63 5.08 0.65 0.31
9974 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis] context 6 77.82 9.83 10.00 43.30 30.75 4.00 -5.47 6.20 0.43 0.39
122 11784 EmrE Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism] context 0 413.27 10.00 7.00 127.30 132.74 56.00 -31.41 18.87 0.56 0.51 RF00442 ykkC-yxkD 5
123 23615 MecA Negative regulator of genetic competence (MecA). This family contains several bacterial MecA proteins. The development of competence in Bacillus subtilis is regulated by growth conditions and several regulatory genes. In complex media competence development is poor, and there is little or no expression of late competence genes. Mec mutations permit competence development and late competence gene expression in complex media, bypassing the requirements for many of the competence regulatory genes. The mecA gene product acts negatively in the development of competence. Null mutations in mecA allow expression of a late competence gene comG, under conditions where it is not normally expressed, including in complex media and in cells mutant for several competence regulatory genes. Overexpression of MecA inhibits comG transcription. context 0 413.01 29.00 22.00 41.30 34.25 10.00 -15.45 9.97 0.47 0.32
124 9774 SgaT_UlaA Putative sugar-specific permease, SgaT/UlaA. This family consists of bacterial transmembrane proteins with a putative sugar-specific permease function, analogous to the IIC component of the PTS system (pfam02378). It has been suggested that this permease may form part of an L-ascorbate utilisation pathway, with proposed specificity for 3-keto-L-gulonate (formed by hydrolysis of L-ascorbate). context 0 411.46 22.93 17.00 90.20 34.29 8.00 -12.89 10.11 0.24 0.30
12745 SgaB Phosphotransferase system, galactitol-specific IIB component [Carbohydrate transport and metabolism] context 1 309.88 24.89 16.00 57.90 23.85 4.00 -17.34 13.76 0.34 0.32
12745 SgaB Phosphotransferase system, galactitol-specific IIB component [Carbohydrate transport and metabolism] context 2 81.65 28.34 15.00 109.70 40.77 0.00 -15.22 11.30 0.21 0.32
125 11709 COG2001 Uncharacterized protein conserved in bacteria [Function unknown] context 0 409.99 24.97 25.00 124.20 49.90 13.00 -9.44 6.52 0.32 0.30
23269 Methyltransf_5 MraW methylase family. Members of this family are probably SAM dependent methyltransferases. This family appears to be related to pfam01596. context 1 62.44 27.89 28.00 70.30 24.40 0.00 -9.62 7.46 0.30 0.30
126 10878 Era GTPase [General function prediction only] context 0 409.27 32.64 23.00 53.20 25.21 4.00 -16.06 12.21 0.30 0.37
23165 DAGK_prokar Prokaryotic diacylglycerol kinase. context 1 317.65 28.58 22.00 41.30 20.99 5.00 -10.60 7.63 0.31 0.39
10193 COG0319 Predicted metal-dependent hydrolase [General function prediction only] context 2 92.17 34.24 29.00 40.60 21.38 0.00 -11.63 10.02 0.28 0.39
127 25413 Beta-lactamase Beta-lactamase. This family appears to be distantly related to pfam00905 and pfam00768 D-alanyl-D-alanine carboxypeptidase. context 0 404.07 39.00 18.00 37.00 37.17 8.00 -22.10 8.60 0.44 0.41
128 10464 RnpA RNase P protein component [Translation, ribosomal structure and biogenesis] context 0 403.90 60.00 26.00 25.70 27.37 4.00 -13.63 8.35 0.49 0.49
129 23962 Cna_B Cna protein B-type domain. This domain is found in Staphylococcus aureus collagen-binding surface protein. However, this region does not mediate collagen binding, the pfam05737 region carries out that function. The structure of the repetitive B-region has been solved and forms a beta sandwich structure. It is thought that this region forms a stalk in Staphylococcus aureus collagen-binding protein that presents the ligand binding domain away from the bacterial cell surface. context 0 402.17 4.00 3.00 283.50 471.78 278.00 -28.93 38.18 0.98 0.24
130 25424 Ribosomal_S12 Ribosomal protein S12. context 0 399.26 9.00 9.00 92.30 154.83 78.00 -17.16 19.63 0.78 0.42
25424 Ribosomal_S12 Ribosomal protein S12. context 1 315.82 9.00 9.00 79.10 134.11 71.00 -11.51 13.49 0.78 0.44
131 16769 Ribosomal_L4 Ribosomal protein L4/L1 family. This family includes Ribosomal L4/L1 from eukaryotes and archaebacteria and L4 from eubacteria. L4 from yeast has been shown to bind rRNA. context 0 397.52 9.00 9.00 153.20 232.45 129.00 -11.42 12.08 0.80 0.29
9964 RplW Ribosomal protein L23 [Translation, ribosomal structure and biogenesis] context 1 386.34 9.00 9.00 145.60 223.40 132.00 -10.97 11.43 0.82 0.28
9965 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis] context 2 240.36 10.00 10.00 67.80 59.74 30.00 -8.08 10.33 0.54 0.20
9965 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis] context 3 173.65 9.00 9.00 73.60 89.16 27.00 -0.77 6.98 0.51 0.24
132 10042 PyrD Dihydroorotate dehydrogenase [Nucleotide transport and metabolism] context 0 395.56 39.00 20.00 41.90 34.09 6.00 -18.52 9.98 0.44 0.44 RF00230 T-box 3
133 12243 ManX Phosphotransferase system, mannose/fructose-specific component IIA [Carbohydrate transport and metabolism] context 0 394.15 35.00 15.00 42.10 39.86 8.00 -22.99 10.61 0.43 0.37
134 13242 DnaD Putative primosome component and related proteins [DNA replication, recombination, and repair] context 0 393.96 30.98 26.00 66.80 25.18 5.00 -11.06 9.26 0.29 0.39
9763 HTS Homoserine O-succinyltransferase. context 1 92.64 4.00 4.00 134.40 129.77 28.00 -4.28 8.75 0.46 0.27
9763 HTS Homoserine O-succinyltransferase. context 2 89.48 4.00 4.00 107.00 110.49 32.00 2.40 9.48 0.61 0.24
135 11971 TrmA SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis] context 0 392.69 34.00 13.00 36.70 37.82 9.00 -21.07 12.89 0.50 0.43
136 10610 COG0742 N6-adenine-specific methylase [DNA replication, recombination, and repair] context 0 391.39 7.00 7.00 188.70 190.11 57.00 -29.46 28.42 0.52 0.46
26115 Cons_hypoth95 Conserved hypothetical protein 95. context 1 200.40 7.00 7.00 72.30 111.60 62.00 -8.00 11.20 0.85 0.50
137 9896 UppS Undecaprenyl pyrophosphate synthase [Lipid metabolism] context 0 390.97 31.00 26.00 70.80 27.27 5.00 -8.01 9.12 0.29 0.33
10618 COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane] context 1 326.71 26.58 22.00 48.30 19.37 5.00 -7.80 9.35 0.32 0.36
138 3916 53EXOc 5'-3' exonuclease; context 0 388.51 23.98 20.00 114.30 31.93 5.00 -11.70 11.94 0.23 0.32
25690 CoaE Dephospho-CoA kinase. This family catalyses the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form Coenzyme A EC:2.7.1.24. This enzyme uses ATP in its reaction. context 1 177.02 9.00 9.00 119.20 50.03 11.00 -9.26 8.29 0.24 0.32
3916 53EXOc 5'-3' exonuclease; context 2 75.96 27.88 23.00 72.50 26.60 0.00 -12.88 9.52 0.25 0.34
3916 53EXOc 5'-3' exonuclease; context 3 72.42 34.68 28.00 31.30 16.78 0.00 -10.09 6.26 0.28 0.40
139 10410 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] context 0 386.70 7.00 7.00 124.00 153.77 83.00 -20.02 26.41 0.72 0.38 RF00005 tRNA 7
10410 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] context 1 249.09 6.00 6.00 125.50 177.92 38.00 -23.10 26.62 0.59 0.38
140 8892 Pencillinase_R Penicillinase repressor. The penicillinase repressor negatively regulates expression of the penicillinase gene. The N-terminal region of this protein is involved in operator recognition, while the C-terminal is responsible for dimerisation of the protein. context 0 384.32 12.00 10.00 194.60 207.03 40.00 -11.87 17.61 0.67 0.23
13469 MecR1 Antirepressor regulating drug resistance, predicted signal transduction N-terminal membrane component [Transcription / Signal transduction mechanisms] context 1 363.66 17.00 13.00 61.10 50.03 24.00 -6.72 11.66 0.58 0.23
8892 Pencillinase_R Penicillinase repressor. The penicillinase repressor negatively regulates expression of the penicillinase gene. The N-terminal region of this protein is involved in operator recognition, while the C-terminal is responsible for dimerisation of the protein. context 2 109.06 4.00 3.00 99.60 114.57 35.00 -7.56 15.85 0.70 0.24
141 25130 DUF1021 Protein of unknown function (DUF1021). This family consists of several hypothetical bacterial proteins of unknown function. context 0 381.78 9.00 9.00 115.10 110.95 43.00 -20.07 21.66 0.52 0.33
10319 GidA NAD/FAD-utilizing enzyme apparently involved in cell division [Cell division and chromosome partitioning] context 1 138.34 8.00 8.00 66.10 66.02 28.00 -0.78 5.09 0.48 0.31
13201 COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms] context 2 97.26 5.00 5.00 65.30 78.67 25.00 -1.27 9.76 0.65 0.27
142 24927 CoiA Competence protein CoiA-like family. Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterised protein. context 0 381.50 26.00 20.00 49.00 35.40 9.00 -17.19 10.92 0.44 0.37
143 27979 thiolase Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and eukaryotes (cytosol, microbodies and mitochondria). There are 2 functional different classes: thiolase-I (3-ketoacyl-CoA thiolase) and thiolase-II (acetoacetyl-CoA thiolase). Thiolase-I can cleave longer fatty acid molecules and plays an important role in the beta-oxidative degradation of fatty acids. Thiolase-II has a high substrate specificity. Although it can cleave acetoacyl-CoA, its main function is the synthesis of acetoacyl-CoA from two molecules of acetyl-CoA, which gives it importance in several biosynthetic pathways. context 0 381.40 42.00 12.00 34.40 37.35 8.00 -20.46 12.38 0.51 0.44
144 11277 THI80 Thiamine pyrophosphokinase [Coenzyme metabolism] context 0 379.81 33.00 19.00 48.20 35.44 6.00 -13.70 10.97 0.41 0.40 RF00230 T-box 1
145 25520 IMPDH IMP dehydrogenase / GMP reductase domain. This family is involved in biosynthesis of guanosine nucleotide. Members of this family contain a TIM barrel structure. In the inosine monophosphate dehydrogenases 2 CBS domains pfam00571 are inserted in the TIM barrel. This family is a member of the common phosphate binding site TIM barrel family. context 0 379.20 39.00 15.00 35.00 38.47 10.00 -18.80 8.52 0.52 0.31
146 27740 INT_Tn1545_C Tn1545-related conjugative transposon integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes bacterial (gram positive) and phage integrases, including those similar to Tn1545, Tn5252, and Tn5276 conjugative transposon integrases and Lactobacillus phage phi adh integrase. context 0 378.39 15.00 6.00 107.00 123.80 31.00 -18.90 21.87 0.63 0.40
147 10876 FliI Flagellar biosynthesis/type III secretory pathway ATPase [Cell motility and secretion / Intracellular trafficking and secretion] context 0 377.60 49.81 23.00 26.50 25.55 4.00 -14.34 8.54 0.42 0.49
148 10585 FldA Flavodoxins [Energy production and conversion] context 0 377.02 37.00 17.00 34.20 26.30 8.00 -20.51 9.30 0.49 0.39
149 10109 GroS Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones] context 0 375.56 16.00 16.00 111.30 84.96 18.00 -13.26 13.32 0.44 0.29
150 28024 MTHFR Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase to convert homocysteine to methionine. The enzymatic mechanism is a ping-pong bi-bi mechanism, in which NAD(P)+ release precedes the binding of methylenetetrahydrofolate and the acceptor is free FAD. The family includes the 5,10-methylenetetrahydrofolate reductase EC:1.7.99.5 from prokaryotes and methylenetetrahydrofolate reductase EC: 1.5.1.20 from eukaryotes. The bacterial enzyme is a homotetramer and NADH is the preferred reductant while the eukaryotic enzyme is a homodimer and NADPH is the preferred reductant. In humans, there are several clinically significant mutations in MTHFR that result in hyperhomocysteinemia, which is a risk factor for the development of cardiovascular disease. context 0 373.47 38.00 12.00 34.00 35.03 9.00 -19.42 11.36 0.50 0.43
151 13279 COG3973 Superfamily I DNA and RNA helicases [General function prediction only] context 0 370.49 45.00 21.00 31.20 29.67 4.00 -16.27 10.74 0.45 0.39
152 12009 ComEC Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only] context 0 365.77 28.79 22.00 50.70 25.21 6.00 -9.70 9.58 0.35 0.30
12009 ComEC Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only] context 1 241.43 21.65 15.00 41.80 22.71 6.00 -9.49 8.52 0.39 0.31
11269 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair] context 2 64.14 24.82 18.00 38.90 21.84 0.00 -14.22 11.51 0.32 0.32
153 10227 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair] context 0 365.38 11.00 11.00 194.60 161.46 28.00 -22.85 15.65 0.40 0.42 RF00169 SRP_bact 9
27548 BofA SigmaK-factor processing regulatory protein BofA. This family contains the sigmaK-factor processing regulatory protein BofA (Bypass-of-forespore protein A) (approximately 80 residues long). During sporulation in Bacillus subtilis, transcription is controlled in the developing sporangium by a cascade of sporulation-specific transcription factors (sigma factors). Following engulfment, processing of sigmaK is inhibited by BofA. It has been suggested that this effect is exerted by alteration of the level of the SpoIVFA protein. context 1 217.02 8.00 7.00 99.60 85.81 26.00 -7.38 13.42 0.47 0.38
154 10270 SufC ABC-type transport system involved in Fe-S cluster assembly, ATPase component [Posttranslational modification, protein turnover, chaperones] context 0 364.41 35.83 27.00 45.90 20.68 4.00 -9.59 8.37 0.32 0.33
10391 CsdB Selenocysteine lyase [Amino acid transport and metabolism] context 1 297.16 23.46 20.00 68.10 25.03 4.00 -7.56 9.40 0.25 0.33
10689 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion] context 2 220.35 22.64 22.00 42.90 21.28 5.00 -5.91 6.72 0.38 0.28
10689 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion] context 3 218.61 15.97 13.00 77.90 26.15 4.00 -9.67 11.08 0.24 0.30
155 12248 COG2898 Uncharacterized conserved protein [Function unknown] context 0 362.68 35.00 10.00 35.60 34.02 12.00 -16.83 10.41 0.49 0.43
156 14517 COG5433 Transposase [DNA replication, recombination, and repair] context 0 362.65 12.00 2.00 144.00 260.13 142.00 -27.65 29.37 0.99 0.32
157 24415 Ribosomal_S9 Ribosomal protein S9/S16. This family includes small ribosomal subunit S9 from prokaryotes and S16 from eukaryotes. context 0 361.28 25.00 25.00 57.50 56.09 19.00 -3.02 6.20 0.57 0.43
24415 Ribosomal_S9 Ribosomal protein S9/S16. This family includes small ribosomal subunit S9 from prokaryotes and S16 from eukaryotes. context 1 333.71 26.00 25.00 64.20 51.79 9.00 3.86 8.07 0.45 0.40
24440 Ribosomal_L13 Ribosomal protein L13. context 2 244.06 12.00 12.00 104.50 112.48 41.00 -1.27 5.02 0.50 0.42
24440 Ribosomal_L13 Ribosomal protein L13. context 3 136.33 23.00 23.00 34.10 28.12 10.00 0.79 1.86 0.54 0.39
158 10845 COG1123 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only] context 0 360.43 34.00 18.00 32.60 31.35 6.00 -16.93 10.39 0.43 0.46 RF00230 T-box 3
159 5655 EIID-AGA PTS system mannose/fructose/sorbose family IID component. context 0 357.81 25.39 17.00 89.00 26.38 5.00 -11.79 10.91 0.26 0.26
14750 PTS_IIB_man PTS_IIB, PTS system, Mannose/sorbose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. The active site histidine receives a phosphate group from the IIA subunit and transfers it to the substrate. context 1 324.06 27.90 16.00 101.00 30.98 7.00 -6.02 6.09 0.26 0.28
12243 ManX Phosphotransferase system, mannose/fructose-specific component IIA [Carbohydrate transport and metabolism] context 2 178.74 19.00 15.00 93.90 39.84 4.00 -4.83 5.75 0.26 0.29
5655 EIID-AGA PTS system mannose/fructose/sorbose family IID component. context 3 87.94 8.00 6.00 154.30 143.27 9.00 1.46 5.21 0.37 0.24
7110 EII-Sor PTS system sorbose-specific iic component. context 4 85.21 9.51 9.00 74.90 45.00 4.00 2.18 5.59 0.32 0.32
12243 ManX Phosphotransferase system, mannose/fructose-specific component IIA [Carbohydrate transport and metabolism] context 5 67.78 27.68 18.00 41.80 23.31 0.00 -13.20 10.23 0.30 0.36 RF00001 5S_rRNA 1
14750 PTS_IIB_man PTS_IIB, PTS system, Mannose/sorbose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. The active site histidine receives a phosphate group from the IIA subunit and transfers it to the substrate. context 6 67.06 7.00 5.00 152.10 116.68 4.00 5.65 11.75 0.49 0.26
160 1790 Ribosomal_L19 Ribosomal protein L19. context 0 357.61 27.94 28.00 94.40 58.29 13.00 0.68 5.19 0.42 0.41
1790 Ribosomal_L19 Ribosomal protein L19. context 1 285.76 27.00 27.00 87.30 57.32 15.00 -2.20 3.39 0.46 0.42
161 9913 EriC Chloride channel protein EriC [Inorganic ion transport and metabolism] context 0 355.43 25.10 13.00 49.50 25.02 8.00 -13.03 11.13 0.35 0.30
9913 EriC Chloride channel protein EriC [Inorganic ion transport and metabolism] context 1 317.32 25.00 14.00 37.60 25.79 8.00 -13.40 9.79 0.39 0.33
9995 RpiA Ribose 5-phosphate isomerase [Carbohydrate transport and metabolism] context 2 74.96 4.00 4.00 56.40 74.68 22.00 -11.88 9.65 0.61 0.30
162 9953 ArgF Ornithine carbamoyltransferase [Amino acid transport and metabolism] context 0 354.05 25.76 17.00 105.40 30.72 5.00 -5.31 9.86 0.24 0.27
9953 ArgF Ornithine carbamoyltransferase [Amino acid transport and metabolism] context 1 99.54 4.00 4.00 184.80 203.31 9.00 -12.72 26.25 0.39 0.32
11941 ArcA Arginine deiminase [Amino acid transport and metabolism] context 2 89.95 8.00 8.00 76.00 46.57 4.00 -14.58 12.04 0.40 0.27
163 16550 YlxR Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation context 0 353.47 22.99 15.00 68.00 32.03 10.00 -12.56 10.42 0.39 0.36
15753 DUF503 Protein of unknown function (DUF503). Family of hypothetical bacterial proteins. context 1 276.86 11.00 9.00 128.70 74.37 26.00 -17.91 9.27 0.37 0.40
24605 RBFA Ribosome-binding factor A. context 2 86.84 7.00 6.00 58.10 50.01 16.00 -16.06 4.66 0.48 0.45
164 9932 GapA Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism] context 0 352.39 6.79 7.00 177.30 157.89 69.00 -7.73 19.41 0.53 0.28
9932 GapA Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism] context 1 137.74 9.94 10.00 43.10 38.44 10.00 -5.36 9.30 0.50 0.34
165 11324 COG1611 Predicted Rossmann fold nucleotide-binding protein [General function prediction only] context 0 350.04 33.00 16.00 33.60 29.16 6.00 -18.72 10.65 0.41 0.49 RF00230 T-box 1
166 17134 CbiQ Cobalt transport protein. This family consists of various cobalt transport proteins Most of which are found in Cobalamin (Vitamin B12) biosynthesis operons. In Salmonella the cbiN cbiQ (product CbiQ in this family) and cbiO are likely to form an active cobalt transport system. context 0 349.63 41.00 18.00 34.00 27.89 4.00 -17.52 10.81 0.40 0.49 RF00230 T-box 1
167 28005 D-AAT_like D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and D-glutamate in addition to other D-amino acids. The enzyme like other members of this superfamily requires PLP as a cofactor. Members of this subgroup are found in all three forms of life. context 0 347.06 24.00 13.00 44.80 29.99 9.00 -19.88 13.10 0.44 0.31 RF00230 T-box 1
168 9932 GapA Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism] context 0 346.69 42.00 20.00 39.70 29.69 4.00 -20.34 10.61 0.45 0.38
169 4036 HSP70 Hsp70 protein. Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region. context 0 343.99 5.00 5.00 162.00 269.90 160.00 -26.30 29.25 0.99 0.27
4036 HSP70 Hsp70 protein. Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region. context 1 186.48 8.00 8.00 49.50 39.67 20.00 -10.61 10.76 0.40 0.44
4036 HSP70 Hsp70 protein. Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region. context 2 144.61 10.00 10.00 54.50 56.16 18.00 -1.10 6.32 0.55 0.37
170 10346 LeuB Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism] context 0 342.44 29.00 13.00 38.50 37.18 8.00 -23.37 10.68 0.41 0.43
171 10399 PyrH Uridylate kinase [Nucleotide transport and metabolism] context 0 342.00 34.96 29.00 49.60 23.12 5.00 -9.04 7.39 0.39 0.34
10399 PyrH Uridylate kinase [Nucleotide transport and metabolism] context 1 93.62 41.93 30.00 34.20 22.03 0.00 -10.47 8.95 0.34 0.37
172 10125 NusG Transcription antiterminator [Transcription] context 0 341.93 30.00 27.00 52.20 25.51 5.00 -10.45 8.33 0.33 0.37
10125 NusG Transcription antiterminator [Transcription] context 1 164.82 16.00 16.00 47.50 34.89 13.00 -3.17 4.10 0.51 0.30
10125 NusG Transcription antiterminator [Transcription] context 2 122.29 17.52 17.00 31.10 18.19 4.00 1.15 4.63 0.42 0.37
173 15348 Amidase Amidase. context 0 340.62 31.37 19.00 37.90 22.36 5.00 -11.79 9.08 0.34 0.31
15348 Amidase Amidase. context 1 53.88 7.00 7.00 65.50 47.63 5.00 0.98 4.90 0.43 0.25
174 13849 COG4708 Predicted membrane protein [Function unknown] context 0 337.62 8.00 8.00 104.30 135.83 71.00 -10.83 17.26 0.69 0.38
13849 COG4708 Predicted membrane protein [Function unknown] context 1 71.42 7.97 8.00 54.10 50.03 4.00 -2.26 7.97 0.42 0.34
175 25501 RrnaAD Ribosomal RNA adenine dimethylase. context 0 337.56 8.00 2.00 166.00 302.74 166.00 -31.51 30.10 1.00 0.32
176 10199 COG0325 Predicted enzyme with a TIM-barrel fold [General function prediction only] context 0 336.33 7.00 7.00 145.20 181.46 80.00 -13.56 14.68 0.51 0.22
10199 COG0325 Predicted enzyme with a TIM-barrel fold [General function prediction only] context 1 331.71 7.00 7.00 120.30 154.11 100.00 -6.75 17.48 0.78 0.25
16398 DivIVA DivIVA protein. The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate minicells. Inactivation of divIVA produces a minicell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype. These proteins appear to contain coiled-coils. context 2 228.98 6.00 6.00 120.50 153.92 58.00 -7.47 19.77 0.79 0.21
25898 YGGT YGGT family. This family consists of a repeat found in conserved hypothetical integral membrane proteins. The function of this region and the proteins which possess it is unknown. context 3 171.72 4.00 4.00 116.50 139.39 56.00 -12.64 20.66 0.63 0.22
10199 COG0325 Predicted enzyme with a TIM-barrel fold [General function prediction only] context 4 161.80 9.00 9.00 92.30 91.18 16.00 -2.07 12.17 0.61 0.24
11509 COG1799 Uncharacterized protein conserved in bacteria [Function unknown] context 5 67.63 8.00 8.00 89.70 95.24 4.00 -4.36 10.04 0.59 0.23
10199 COG0325 Predicted enzyme with a TIM-barrel fold [General function prediction only] context 6 61.96 4.00 4.00 80.70 87.39 7.00 -18.89 19.33 0.58 0.31
177 10424 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair] context 0 335.92 9.00 8.00 154.20 134.68 43.00 -7.80 15.68 0.48 0.48 RF00504 gcvT 9
178 24886 DUF909 Bacterial protein of unknown function (DUF909). This family consists of several short bacterial proteins of unknown function. context 0 335.63 3.00 3.00 307.40 426.47 213.00 -25.42 49.90 0.85 0.26
24886 DUF909 Bacterial protein of unknown function (DUF909). This family consists of several short bacterial proteins of unknown function. context 1 134.41 6.00 3.00 138.20 133.28 18.00 -11.87 20.39 0.53 0.22
24886 DUF909 Bacterial protein of unknown function (DUF909). This family consists of several short bacterial proteins of unknown function. context 2 115.85 5.00 3.00 119.40 132.85 18.00 -14.98 21.18 0.59 0.23
179 10472 NrdG Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones] context 0 335.37 27.95 24.00 76.10 28.02 6.00 -8.88 6.62 0.28 0.32
10472 NrdG Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones] context 1 262.06 15.00 15.00 150.40 78.36 24.00 -2.33 3.91 0.31 0.34
10473 COG0603 Predicted PP-loop superfamily ATPase [General function prediction only] context 2 245.40 13.00 13.00 100.30 67.19 17.00 -0.39 8.08 0.39 0.38
10648 COG0780 Enzyme related to GTP cyclohydrolase I [General function prediction only] context 3 210.37 13.00 13.00 88.20 63.57 27.00 -1.81 4.14 0.43 0.39
10589 COG0720 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism] context 4 128.32 9.97 10.00 41.60 29.19 8.00 -5.74 7.43 0.37 0.46
10648 COG0780 Enzyme related to GTP cyclohydrolase I [General function prediction only] context 5 125.37 10.00 10.00 85.70 62.93 13.00 -3.66 5.12 0.43 0.40
180 10492 COG0622 Predicted phosphoesterase [General function prediction only] context 0 333.21 38.00 16.00 44.00 37.40 5.00 -18.24 11.51 0.48 0.35
181 10233 RplI Ribosomal protein L9 [Translation, ribosomal structure and biogenesis] context 0 326.38 33.63 31.00 41.90 21.20 4.00 -10.01 7.52 0.34 0.35
25130 DUF1021 Protein of unknown function (DUF1021). This family consists of several hypothetical bacterial proteins of unknown function. context 1 149.43 18.00 13.00 75.30 36.67 4.00 -5.23 5.73 0.32 0.34
10179 DnaB Replicative DNA helicase [DNA replication, recombination, and repair] context 2 85.17 33.24 29.00 40.30 20.31 0.00 -12.53 8.86 0.29 0.39
10233 RplI Ribosomal protein L9 [Translation, ribosomal structure and biogenesis] context 3 53.73 24.78 22.00 59.60 26.44 0.00 -11.24 8.44 0.36 0.34
182 10207 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis] context 0 325.51 9.00 9.00 123.80 111.32 45.00 -10.69 14.76 0.51 0.26
10207 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis] context 1 138.52 11.97 11.00 47.00 34.18 12.00 -1.38 4.62 0.42 0.20
183 10335 PrsA Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism] context 0 324.86 21.56 20.00 116.20 31.68 5.00 -9.65 10.15 0.24 0.34
10335 PrsA Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism] context 1 76.35 29.76 24.00 84.50 20.61 0.00 -6.95 8.02 0.25 0.32
184 9911 Rpe Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism] context 0 324.29 29.78 26.00 35.70 18.10 4.00 -11.04 8.84 0.33 0.37
185 10504 Hpt Hypoxanthine-guanine phosphoribosyltransferase [Nucleotide transport and metabolism] context 0 324.28 28.41 24.00 48.80 23.12 4.00 -9.45 10.45 0.34 0.31
186 10065 FolD 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism] context 0 321.87 30.92 29.00 48.80 24.72 4.00 -12.00 9.28 0.36 0.34
10065 FolD 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism] context 1 121.16 8.00 7.00 93.70 65.61 8.00 -4.11 11.09 0.39 0.33
187 27850 LDH L-lactate dehydrogenases (LDH); member of the family of NAD-dependent 2-hydroxycarboxylate dehydrogenases. LDHs are tetrameric enzymes catalyzing the last step of glycolysis in which pyruvate is converted to L-lactate. Vertebrate LDHs are non-allosteric, but some bacterial LDHs are activated by an allosteric effector, fructose-1,6-bisphosphate. L-2-hydroxyisocaproate dehydrogenases and tetrameric LDH-like MDHs are also included in this group. context 0 320.30 11.43 11.00 125.50 52.01 15.00 -7.90 11.33 0.24 0.30
27850 LDH L-lactate dehydrogenases (LDH); member of the family of NAD-dependent 2-hydroxycarboxylate dehydrogenases. LDHs are tetrameric enzymes catalyzing the last step of glycolysis in which pyruvate is converted to L-lactate. Vertebrate LDHs are non-allosteric, but some bacterial LDHs are activated by an allosteric effector, fructose-1,6-bisphosphate. L-2-hydroxyisocaproate dehydrogenases and tetrameric LDH-like MDHs are also included in this group. context 1 111.56 10.30 8.00 53.90 29.01 5.00 -0.82 7.96 0.37 0.32
188 11385 FtsK DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning] context 0 319.31 32.00 17.00 40.30 36.22 5.00 -20.47 11.71 0.46 0.42
189 25707 Pept_tRNA_hydro Peptidyl-tRNA hydrolase. context 0 318.45 31.88 28.00 48.80 23.14 4.00 -6.21 7.91 0.33 0.38
10915 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription] context 1 167.02 20.99 17.00 46.90 25.30 5.00 -1.10 5.44 0.43 0.38
10915 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription] context 2 126.01 18.24 17.00 56.10 19.95 4.00 -2.60 3.92 0.37 0.36
10915 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription] context 3 120.89 14.00 13.00 74.90 40.80 4.00 -5.80 6.96 0.39 0.32
25707 Pept_tRNA_hydro Peptidyl-tRNA hydrolase. context 4 94.09 7.00 7.00 62.50 51.67 7.00 -14.58 10.79 0.43 0.32
25707 Pept_tRNA_hydro Peptidyl-tRNA hydrolase. context 5 77.74 9.00 9.00 52.90 44.13 5.00 -8.12 7.03 0.49 0.35
16272 DivIC Septum formation initiator. DivIC from B. subtilis is necessary for both vegetative and sporulation septum formation. These proteins are mainly composed of an amino terminal coiled-coil. context 6 73.51 4.00 4.00 127.30 93.43 8.00 -4.42 13.59 0.33 0.27
13262 COG3956 Protein containing tetrapyrrole methyltransferase domain and MazG-like (predicted pyrophosphatase) domain [General function prediction only] context 7 68.71 4.00 4.00 167.40 115.11 4.00 -9.66 18.97 0.27 0.27
190 10094 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis] context 0 317.72 11.00 11.00 118.80 127.34 14.00 -21.53 28.20 0.48 0.38
10094 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis] context 1 206.76 18.00 16.00 53.50 46.89 5.00 -16.35 12.08 0.47 0.44
191 10354 LepA Membrane GTPase LepA [Cell envelope biogenesis, outer membrane] context 0 317.58 26.00 17.00 37.30 30.66 8.00 -19.22 10.90 0.52 0.33
192 10343 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair] context 0 317.03 31.62 25.00 57.20 23.64 4.00 -8.50 8.62 0.35 0.28
11485 COG1774 Uncharacterized homolog of PSP1 [Function unknown] context 1 68.46 5.61 6.00 55.80 24.38 4.00 -6.65 10.23 0.33 0.31
10187 COG0313 Predicted methyltransferases [General function prediction only] context 2 64.32 4.00 4.00 49.70 57.05 9.00 -11.38 13.77 0.49 0.34
193 9976 TruA Pseudouridylate synthase [Translation, ribosomal structure and biogenesis] context 0 316.35 27.82 24.00 35.50 17.99 4.00 -8.90 9.36 0.32 0.34
194 10353 FusA Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis] context 0 315.67 9.00 9.00 170.60 139.89 38.00 -3.77 14.17 0.44 0.33
195 12745 SgaB Phosphotransferase system, galactitol-specific IIB component [Carbohydrate transport and metabolism] context 0 314.23 28.46 18.00 52.30 24.76 4.00 -14.87 11.31 0.34 0.33
196 9904 IlvB Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] [Amino acid transport and metabolism / Coenzyme metabolism] context 0 312.81 21.54 17.00 94.90 36.45 4.00 -9.92 10.70 0.21 0.45 RF00230 T-box 4 RF00379 ydaO-yuaA 1
197 10425 GlpK Glycerol kinase [Energy production and conversion] context 0 310.98 20.83 20.00 96.10 35.16 4.00 -14.94 12.56 0.24 0.34
198 10067 MetK S-adenosylmethionine synthetase [Coenzyme metabolism] context 0 310.52 30.65 30.00 43.60 21.36 4.00 -10.78 8.37 0.35 0.32
199 11631 Hfq Uncharacterized host factor I protein [General function prediction only] context 0 309.88 27.00 16.00 35.00 32.34 8.00 -17.27 8.28 0.42 0.43
200 12169 COG2815 Uncharacterized protein conserved in bacteria [Function unknown] context 0 308.70 38.00 17.00 44.50 34.55 4.00 -16.65 10.61 0.44 0.42
201 10193 COG0319 Predicted metal-dependent hydrolase [General function prediction only] context 0 307.22 38.00 19.00 40.40 26.10 4.00 -13.85 9.12 0.42 0.43
202 5373 POL3Bc DNA polymerase III beta subunit; the processivity factor of the holoenzyme forms a ring shaped dimer that encircles dsDNA (sliding clamp) context 0 305.62 32.00 32.00 108.20 76.26 30.00 -1.53 1.48 0.49 0.33
5373 POL3Bc DNA polymerase III beta subunit; the processivity factor of the holoenzyme forms a ring shaped dimer that encircles dsDNA (sliding clamp) context 1 258.71 32.00 32.00 158.60 96.33 34.00 2.77 0.86 0.45 0.30
5373 POL3Bc DNA polymerase III beta subunit; the processivity factor of the holoenzyme forms a ring shaped dimer that encircles dsDNA (sliding clamp) context 2 223.08 33.98 34.00 82.20 48.49 25.00 2.88 0.82 0.48 0.27
24980 DUF951 Bacterial protein of unknown function (DUF951). This family consists of several short hypothetical bacterial proteins of unknown function. context 3 102.78 5.00 5.00 129.40 147.09 39.00 -0.01 7.33 0.68 0.28
203 11222 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription] context 0 305.33 34.00 15.00 38.60 33.58 5.00 -18.58 9.64 0.40 0.36
204 2564 ArsB Arsenical pump membrane protein. context 0 303.38 11.00 10.00 150.10 74.03 16.00 -6.69 13.26 0.28 0.31
205 24456 HAMP HAMP domain. context 0 303.32 26.00 19.00 32.50 27.48 7.00 -14.81 9.23 0.45 0.40 RF00230 T-box 1
206 11152 ArgR Arginine repressor [Transcription] context 0 303.20 32.38 20.00 98.40 24.97 6.00 -3.56 3.95 0.24 0.30
10368 RecN ATPase involved in DNA repair [DNA replication, recombination, and repair] context 1 157.65 8.00 8.00 84.60 67.37 17.00 -2.86 8.58 0.38 0.32
10907 COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis] context 2 60.03 4.00 4.00 84.50 98.91 11.00 -9.00 11.26 0.56 0.39
207 17796 Adenylsucc_synt Adenylosuccinate synthetase. The enzyme (also known as IMP:L-aspartate ligase (GDP forming)) catalyzes the first committed step in the biosynthesis of AMP. It forms adenylosuccinate from IMP and L-aspartate, converting GTP to GDP and Pi in the process. Adenylosuccinate synthetase along with adenylosuccinate lyase and AMP deaminase form the functional unit of purine nucleotide cycle, which interconverts IMP and AMP via the formation of adenylosuccinate. The enzyme is present in diverse organisms and tissues. In leishmanial and trypanosomal parasites, which lack a de novo pathway for the synthesis of purine nucleotides, adenylosuccinate synthetase still plays a prominent role in nucleotide salvage pathways. context 0 302.87 5.00 5.00 250.30 331.33 89.00 -19.85 30.85 0.75 0.28
17796 Adenylsucc_synt Adenylosuccinate synthetase. The enzyme (also known as IMP:L-aspartate ligase (GDP forming)) catalyzes the first committed step in the biosynthesis of AMP. It forms adenylosuccinate from IMP and L-aspartate, converting GTP to GDP and Pi in the process. Adenylosuccinate synthetase along with adenylosuccinate lyase and AMP deaminase form the functional unit of purine nucleotide cycle, which interconverts IMP and AMP via the formation of adenylosuccinate. The enzyme is present in diverse organisms and tissues. In leishmanial and trypanosomal parasites, which lack a de novo pathway for the synthesis of purine nucleotides, adenylosuccinate synthetase still plays a prominent role in nucleotide salvage pathways. context 1 226.01 7.00 7.00 201.30 232.03 39.00 1.12 17.02 0.64 0.27
17796 Adenylsucc_synt Adenylosuccinate synthetase. The enzyme (also known as IMP:L-aspartate ligase (GDP forming)) catalyzes the first committed step in the biosynthesis of AMP. It forms adenylosuccinate from IMP and L-aspartate, converting GTP to GDP and Pi in the process. Adenylosuccinate synthetase along with adenylosuccinate lyase and AMP deaminase form the functional unit of purine nucleotide cycle, which interconverts IMP and AMP via the formation of adenylosuccinate. The enzyme is present in diverse organisms and tissues. In leishmanial and trypanosomal parasites, which lack a de novo pathway for the synthesis of purine nucleotides, adenylosuccinate synthetase still plays a prominent role in nucleotide salvage pathways. context 2 96.86 9.24 10.00 66.00 59.78 5.00 -6.94 8.48 0.47 0.33
17796 Adenylsucc_synt Adenylosuccinate synthetase. The enzyme (also known as IMP:L-aspartate ligase (GDP forming)) catalyzes the first committed step in the biosynthesis of AMP. It forms adenylosuccinate from IMP and L-aspartate, converting GTP to GDP and Pi in the process. Adenylosuccinate synthetase along with adenylosuccinate lyase and AMP deaminase form the functional unit of purine nucleotide cycle, which interconverts IMP and AMP via the formation of adenylosuccinate. The enzyme is present in diverse organisms and tissues. In leishmanial and trypanosomal parasites, which lack a de novo pathway for the synthesis of purine nucleotides, adenylosuccinate synthetase still plays a prominent role in nucleotide salvage pathways. context 3 82.88 5.41 6.00 65.40 47.45 6.00 -14.97 15.08 0.49 0.26
208 14106 GlcU Putative glucose uptake permease [Carbohydrate transport and metabolism] context 0 302.84 25.87 17.00 44.30 23.10 5.00 -14.07 10.22 0.34 0.34
209 6281 Ribosomal_S16 Ribosomal protein S16. context 0 301.85 37.00 36.00 50.70 30.64 5.00 -5.81 6.02 0.47 0.27
11547 COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only] context 1 253.31 18.89 17.00 59.10 30.60 8.00 -8.00 8.99 0.41 0.32
11547 COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only] context 2 184.98 7.00 7.00 83.90 85.55 29.00 -5.40 13.87 0.58 0.31
26230 UPF0122 Putative helix-turn-helix protein, YlxM / p13 like. Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13. Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway. context 3 138.30 9.00 9.00 72.00 47.14 19.00 0.50 5.78 0.47 0.32
210 11436 COG1725 Predicted transcriptional regulators [Transcription] context 0 301.62 22.44 16.00 78.60 27.34 4.00 -15.45 13.21 0.29 0.29
211 9885 SUA5 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis] context 0 301.13 25.99 21.00 49.50 25.04 4.00 -13.78 10.97 0.33 0.30
212 12281 COG2932 Predicted transcriptional regulator [Transcription] context 0 301.11 4.00 3.00 245.00 333.38 113.00 -42.04 40.79 0.76 0.38
213 10903 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis] context 0 300.22 28.00 12.00 34.40 37.70 12.00 -16.06 8.87 0.59 0.43
214 12550 COG3212 Predicted membrane protein [Function unknown] context 0 299.81 3.00 3.00 305.80 421.47 235.00 -22.98 34.82 0.82 0.24
12550 COG3212 Predicted membrane protein [Function unknown] context 1 70.05 4.00 4.00 108.00 84.54 13.00 -0.07 9.06 0.39 0.23
215 10197 MutL DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair] context 0 299.04 14.99 15.00 108.90 33.44 15.00 -9.27 7.06 0.27 0.34
10124 MutS Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair] context 1 58.40 19.99 19.00 52.60 24.39 0.00 -14.55 12.82 0.30 0.34
216 11044 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism] context 0 295.97 18.97 19.00 46.40 30.23 13.00 -5.16 8.64 0.47 0.22
217 10018 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] context 0 295.70 31.00 14.00 38.60 36.14 6.00 -20.40 10.72 0.48 0.43 RF00230 T-box 2
218 11230 FliS Flagellin-specific chaperone FliS [Cell motility and secretion / Intracellular trafficking and secretion / Posttranslational modification, protein turnover, chaperones] context 0 295.54 36.00 20.00 34.00 31.48 4.00 -18.85 9.28 0.45 0.40 RF00230 T-box 1
219 10000 Tmk Thymidylate kinase [Nucleotide transport and metabolism] context 0 294.67 37.00 19.00 71.80 27.66 5.00 -3.66 4.83 0.29 0.31
11690 LdcC Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism] context 1 90.59 9.00 8.00 44.00 30.84 4.00 -9.24 7.82 0.32 0.40
220 22990 ADK Adenylate kinase. context 0 294.40 15.00 12.00 50.90 45.92 12.00 -15.68 13.85 0.42 0.33
221 10464 RnpA RNase P protein component [Translation, ribosomal structure and biogenesis] context 0 294.20 32.59 27.00 30.00 17.24 5.00 -6.97 5.86 0.37 0.37
222 9969 RplE Ribosomal protein L5 [Translation, ribosomal structure and biogenesis] context 0 294.06 8.00 8.00 94.90 131.62 62.00 -14.19 15.64 0.72 0.41
223 10129 RpmE Ribosomal protein L31 [Translation, ribosomal structure and biogenesis] context 0 293.49 23.00 23.00 79.00 55.37 14.00 -4.15 5.16 0.45 0.38
224 25044 DUF984 Protein of unknown function (DUF984). Family of bacterial proteins with unknown function. context 0 292.56 32.00 15.00 34.50 32.62 6.00 -16.16 9.93 0.50 0.43
225 12978 COG3655 Predicted transcriptional regulator [Transcription] context 0 291.86 15.00 14.00 96.60 47.52 10.00 -7.38 10.44 0.28 0.27
12978 COG3655 Predicted transcriptional regulator [Transcription] context 1 179.42 13.89 14.00 96.40 47.25 8.00 -4.23 6.61 0.33 0.26
226 11044 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism] context 0 291.20 24.00 10.00 53.00 46.67 20.00 -2.85 7.28 0.61 0.23
227 10314 IlvH Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism] context 0 289.91 5.00 5.00 147.40 133.05 57.00 -33.43 31.15 0.53 0.32
228 11491 NrdI Protein involved in ribonucleotide reduction [Nucleotide transport and metabolism] context 0 289.82 29.00 11.00 37.10 36.44 8.00 -19.96 10.04 0.46 0.42
229 26138 Competence Competence protein. Members of this family are integral membrane proteins with 6 predicted transmembrane helices. Some members of this family have been shown to be essential for bacterial competence in uptake of extracellular DNA. These proteins may transport DNA across the cell membrane. These proteins contain a highly conserved motif in the amino terminal transmembrane region that has two histidines that may form a metal binding site. context 0 289.34 20.00 11.00 44.80 39.05 10.00 -19.63 11.69 0.44 0.37
230 27833 AdcA Metal binding protein AcdA. These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion. The AcdA proteins belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and they bind their ligand in the cleft between these domains. In addition, many of these proteins have a low complexity region containing metal binding histidine-rich motif (repetitive HDH sequence). context 0 288.91 16.00 8.00 151.90 86.28 14.00 -9.76 8.33 0.26 0.28 RF00029 Intron_gpII 1
12772 COG3443 Predicted periplasmic or secreted protein [General function prediction only] context 1 165.12 7.00 7.00 98.70 100.73 34.00 1.08 8.46 0.52 0.26
231 24611 MGS MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes inosicase. The known structures in this family show a common phosphate binding site. context 0 287.69 56.00 9.00 85.60 66.57 22.00 6.77 3.05 0.53 0.44
232 9932 GapA Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism] context 0 284.95 24.68 21.00 35.60 22.40 4.00 -13.89 10.49 0.33 0.36
233 16565 DHPS DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and protein biosynthesis. Prokaryotes (and some lower eukaryotes) must synthesize folate de novo, while higher eukaryotes are able to utilize dietary folate and therefore lack DHPS. Sulfonamide drugs, which are substrate analogs of pABA, target DHPS. context 0 284.82 32.00 15.00 41.60 26.98 5.00 -16.84 9.65 0.43 0.42
234 10911 COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair] context 0 283.87 20.87 19.00 58.20 25.13 6.00 -13.71 9.52 0.32 0.37
10911 COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair] context 1 269.95 19.76 18.00 71.90 29.16 5.00 -12.56 8.85 0.25 0.38
235 5654 EIIBC-GUT Sorbitol phosphotransferase enzyme II. context 0 283.17 41.00 22.00 32.50 25.60 5.00 -15.53 5.93 0.49 0.45
236 10039 RnhB Ribonuclease HII [DNA replication, recombination, and repair] context 0 282.72 23.00 20.00 59.20 28.73 5.00 -12.70 9.17 0.31 0.36
237 25266 Hsp33 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat shock), the Cys are reversibly oxidized to disulfide bonds, which causes the chaperone activity to be turned on. Hsp33 is homodimeric in its functional form. context 0 281.37 21.82 20.00 52.90 25.77 5.00 -10.41 10.47 0.33 0.35 RF00005 tRNA 2 RF00029 Intron_gpII 1
25266 Hsp33 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat shock), the Cys are reversibly oxidized to disulfide bonds, which causes the chaperone activity to be turned on. Hsp33 is homodimeric in its functional form. context 1 167.68 13.97 14.00 117.80 44.37 4.00 -11.73 8.88 0.26 0.33
238 12060 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription] context 0 280.36 30.00 17.00 39.10 33.99 8.00 -8.78 7.15 0.53 0.43
239 11277 THI80 Thiamine pyrophosphokinase [Coenzyme metabolism] context 0 280.30 25.00 15.00 38.00 32.01 6.00 -18.46 9.87 0.40 0.41
240 13380 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair] context 0 279.81 14.00 11.00 48.70 29.23 13.00 -18.94 12.41 0.39 0.42
241 11468 NhaC Na+/H+ antiporter [Energy production and conversion] context 0 279.58 25.99 17.00 44.40 23.38 5.00 -14.16 8.71 0.34 0.39 RF00230 T-box 3
242 11682 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms] context 0 279.04 17.00 17.00 131.20 79.46 22.00 1.23 5.34 0.44 0.30
11682 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms] context 1 131.04 22.98 22.00 31.10 20.85 10.00 -0.18 1.69 0.53 0.30
243 27389 Transposase_35 Putative transposase DNA-binding domain. This putative domain is found at the C-terminus of a large number of transposase proteins. This domain contains four conserved cysteines suggestive of a zinc binding domain. Given the need for transposases to bind DNA as well as the large number of DNA-binding zinc fingers we hypothesise this domain is DNA-binding. context 0 277.90 3.00 1.00 340.00 550.23 288.00 -63.06 54.76 0.90 0.37
244 10293 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair] context 0 276.58 16.00 13.00 59.20 42.02 8.00 -22.41 15.14 0.40 0.28 RF00230 T-box 2
245 8704 ADP_ribosyl_GH ADP-ribosylglycohydrolase. This family includes enzymes that ADP-ribosylations, for example ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves ADP-ribose-L-arginine. The family also includes dinitrogenase reductase activating glycohydrolase. Most surprisingly the family also includes jellyfish crystallins, these proteins appear to have lost the presumed active site residues. context 0 276.43 8.00 6.00 318.30 309.75 34.00 -19.38 21.71 0.58 0.33
246 27792 HPPK 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after uptake by a carrier-mediated active transport system. Most microbes and plants lack this system and must synthesize folates de novo from guanosine triphosphate. One enzyme from this pathway is HPPK which catalyzes pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP). The functional enzyme is a monomer. Mammals lack many of the enzymes in the folate pathway including, HPPK. context 0 275.18 28.00 16.00 35.70 31.87 4.00 -17.18 12.45 0.43 0.34
247 11591 PflD Pyruvate-formate lyase [Energy production and conversion] context 0 273.29 7.00 7.00 147.70 121.14 40.00 -7.38 17.82 0.47 0.27
10245 GldA Glycerol dehydrogenase and related enzymes [Energy production and conversion] context 1 101.83 7.00 7.00 104.40 94.60 15.00 1.23 7.10 0.51 0.26
10245 GldA Glycerol dehydrogenase and related enzymes [Energy production and conversion] context 2 54.64 4.00 4.00 82.50 84.91 10.00 -8.96 10.61 0.58 0.22
248 11667 COG1959 Predicted transcriptional regulator [Transcription] context 0 272.55 23.81 15.00 88.80 28.06 9.00 -2.32 4.65 0.28 0.29
11667 COG1959 Predicted transcriptional regulator [Transcription] context 1 224.38 27.20 21.00 30.70 19.46 10.00 3.42 3.51 0.52 0.26
249 12650 COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair] context 0 272.32 64.00 20.00 47.20 41.70 15.00 3.54 1.59 0.61 0.25 RF00388 QaRNA 3
250 25825 5-FTHF_cyc-lig 5-formyltetrahydrofolate cyclo-ligase family. 5-formyltetrahydrofolate cyclo-ligase or methenyl-THF synthetase EC:6.3.3.2 catalyses the interchange of 5-formyltetrahydrofolate (5-FTHF) to 5-10-methenyltetrahydrofolate, this requires ATP and Mg2+. 5-FTHF is used in chemotherapy where it is clinically known as Leucovorin. context 0 271.34 4.00 4.00 279.50 366.98 90.00 -27.94 32.14 0.63 0.30
251 10803 PtsA Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism] context 0 271.29 9.00 9.00 236.70 188.69 33.00 3.08 10.40 0.38 0.25
252 9925 TufB GTPases - translation elongation factors [Translation, ribosomal structure and biogenesis] context 0 269.64 9.00 9.00 72.60 118.64 66.00 -11.05 12.61 0.93 0.29
9925 TufB GTPases - translation elongation factors [Translation, ribosomal structure and biogenesis] context 1 101.93 10.00 10.00 66.70 72.20 4.00 -12.04 13.11 0.53 0.35
253 11216 Cls Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthases and related enzymes [Lipid metabolism] context 0 269.63 30.96 13.00 32.50 31.51 5.00 -18.14 10.42 0.44 0.49 RF00230 T-box 2
254 9184 UvrD-helicase UvrD/REP helicase. The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. Some members have large insertions near to the carboxy-terminus relative to other members of the family. context 0 268.40 11.00 3.00 109.30 179.53 89.00 -19.72 13.07 0.77 0.42
255 10272 COG0398 Uncharacterized conserved protein [Function unknown] context 0 268.32 8.00 8.00 136.70 169.56 63.00 -10.11 12.46 0.70 0.42 RF00023 tmRNA 10
256 10984 BioY Uncharacterized conserved protein [General function prediction only] context 0 267.40 34.99 27.00 58.40 29.46 4.00 -5.30 6.33 0.43 0.26
13598 COG4357 Uncharacterized conserved protein [Function unknown] context 1 78.60 4.00 4.00 73.90 69.41 16.00 -15.98 12.87 0.54 0.31
257 11232 COG1518 Uncharacterized protein predicted to be involved in DNA repair [DNA replication, recombination, and repair] context 0 266.65 7.00 7.00 156.00 195.43 73.00 -10.90 13.48 0.68 0.33
258 13892 COG4753 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms] context 0 266.41 27.00 19.00 39.00 31.32 4.00 -14.89 9.74 0.38 0.28
259 10026 PurD Phosphoribosylamine-glycine ligase [Nucleotide transport and metabolism] context 0 265.52 3.00 3.00 233.90 331.86 202.00 -26.62 36.03 0.93 0.21
260 4580 Transposase_12 Transposase. Transposase proteins are necessary for efficient DNA transposition. Contains transposases for IS204, IS1001, IS1096 and IS1165. context 0 265.50 49.95 5.00 51.10 47.25 18.00 -1.85 7.67 0.54 0.37
261 11471 SdaA L-serine deaminase [Amino acid transport and metabolism] context 0 262.18 5.00 5.00 192.00 249.85 53.00 -22.85 32.56 0.63 0.26
262 16550 YlxR Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation context 0 260.89 40.98 27.00 24.50 27.50 4.00 -15.42 5.53 0.50 0.47
263 27335 SpoIIE Stage II sporulation protein E (SpoIIE). This family contains a number of bacterial stage II sporulation E proteins (EC:3.1.3.16). These are required for formation of a normal polar septum during sporulation. The N-terminal region is hydrophobic and is expected to contain up to 12 membrane-spanning segments. context 0 256.92 13.93 11.00 112.20 37.44 7.00 -12.24 10.82 0.22 0.33
264 10626 Smf Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion] context 0 255.60 25.76 24.00 56.30 23.98 4.00 -10.32 7.64 0.33 0.34
10626 Smf Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion] context 1 70.59 29.65 26.00 36.80 19.94 0.00 -11.19 9.59 0.34 0.34
265 10263 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair] context 0 255.37 18.00 12.00 39.30 40.17 11.00 -20.00 10.03 0.49 0.43
266 24057 FbpA Fibronectin-binding protein A N-terminus (FbpA). This family consists of the N-terminal region of the prokaryotic fibronectin-binding protein. Fibronectin binding is considered to be an important virulence factor in streptococcal infections. Fibronectin is a dimeric glycoprotein that is present in a soluble form in plasma and extracellular fluids; it is also present in a fibrillar form on cell surfaces. Both the soluble and cellular forms of fibronectin may be incorporated into the extracellular tissue matrix. While fibronectin has critical roles in eukaryotic cellular processes, such as adhesion, migration and differentiation, it is also a substrate for the attachment of bacteria. The binding of pathogenic Streptococcus pyogenes and Staphylococcus aureus to epithelial cells via fibronectin facilitates their internalisation and systemic spread within the host. context 0 254.62 5.00 5.00 137.00 207.00 90.00 -25.15 24.15 0.84 0.35
267 13405 COG4123 Predicted O-methyltransferase [General function prediction only] context 0 251.57 21.54 17.00 73.50 22.10 4.00 -7.81 7.25 0.22 0.37
268 12669 COG3335 Transposase and inactivated derivatives [DNA replication, recombination, and repair] context 0 250.31 14.00 2.00 192.50 249.23 100.00 -10.50 13.69 0.76 0.37
12669 COG3335 Transposase and inactivated derivatives [DNA replication, recombination, and repair] context 1 98.16 14.00 2.00 234.00 309.43 100.00 3.13 2.05 0.74 0.37
12669 COG3335 Transposase and inactivated derivatives [DNA replication, recombination, and repair] context 2 55.19 15.00 2.00 43.80 35.84 6.00 -5.19 5.81 0.43 0.35
269 10191 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription] context 0 249.37 17.00 16.00 108.60 47.01 8.00 -10.70 7.90 0.30 0.31
25267 Dtyr_deacylase D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not in archea; beta barrel-like fold structure; forms homodimers in which two surface cavities serve as the active site for tRNA binding context 1 125.93 7.97 8.00 53.70 37.88 8.00 -13.71 11.18 0.37 0.30
270 11070 COG1354 Uncharacterized conserved protein [Function unknown] context 0 249.35 22.99 19.00 48.10 23.15 4.00 -11.61 9.25 0.32 0.30
271 10095 COG0220 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only] context 0 249.30 24.98 22.00 65.10 25.47 5.00 -7.39 5.63 0.29 0.31
272 11903 PepD Di- and tripeptidases [Amino acid transport and metabolism] context 0 248.51 15.35 15.00 132.10 37.49 4.00 -15.80 13.84 0.24 0.27
11903 PepD Di- and tripeptidases [Amino acid transport and metabolism] context 1 75.06 13.67 14.00 33.50 25.79 4.00 1.86 3.08 0.45 0.27
273 10297 GRS1 Glycyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis] context 0 248.34 19.00 17.00 49.10 26.51 5.00 -11.88 9.97 0.30 0.33
274 10019 Sun tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis] context 0 246.56 35.79 20.00 42.90 19.97 4.00 -1.65 4.88 0.34 0.37
12606 COG3270 Uncharacterized conserved protein [Function unknown] context 1 76.07 10.00 4.00 47.10 33.09 4.00 -9.45 9.85 0.42 0.31
275 12060 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription] context 0 245.85 12.00 8.00 58.00 45.86 16.00 -15.21 12.69 0.43 0.31
276 10948 CzcD Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism] context 0 245.75 12.00 11.00 120.60 62.82 13.00 -6.00 7.68 0.24 0.28
10948 CzcD Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism] context 1 150.59 16.57 16.00 32.20 21.42 5.00 -5.79 7.42 0.49 0.25
277 14485 COG5401 Spore germination protein [General function prediction only] context 0 245.53 8.00 7.00 125.70 64.60 30.00 -4.14 10.78 0.34 0.40
278 10285 LivG ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism] context 0 242.40 9.00 2.00 162.70 233.19 96.00 -19.65 17.29 0.71 0.42
279 10937 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones] context 0 241.94 31.00 23.00 32.80 33.94 4.00 -17.53 7.50 0.48 0.38
280 13200 COG3886 Predicted HKD family nuclease [DNA replication, recombination, and repair] context 0 240.91 28.00 17.00 38.00 35.57 4.00 -21.38 9.15 0.43 0.41
281 23225 Transposase_8 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family. context 0 239.99 8.00 5.00 128.90 175.44 63.00 -0.72 12.82 0.76 0.31
282 10053 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair] context 0 239.94 16.51 15.00 78.50 23.21 6.00 -9.75 8.15 0.25 0.35
283 25928 DUF163 Uncharacterized ACR, COG1576. context 0 236.85 26.00 25.00 118.50 54.48 13.00 -2.16 1.70 0.27 0.30
284 27265 MatC_N Dicarboxylate carrier protein MatC N-terminus. This family represents the N-terminal region of the bacterial dicarboxylate carrier protein MatC. The MatC protein is an integral membrane protein that could function as a malonate carrier. context 0 236.33 4.00 4.00 166.40 272.56 139.00 -30.24 22.57 0.90 0.35
285 25575 Rotamase PPIC-type PPIASE domain. Rotamases increase the rate of protein folding by catalysing the interconversion of cis-proline and trans-proline. context 0 236.07 15.00 10.00 57.70 32.57 9.00 -17.44 12.88 0.42 0.31
286 12160 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion] context 0 235.77 20.58 18.00 52.10 23.85 5.00 -6.74 9.66 0.39 0.27
13709 ComGC Competence protein ComGC [Intracellular trafficking and secretion] context 1 213.58 20.81 15.00 41.10 25.23 4.00 -12.51 10.27 0.38 0.26
12160 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion] context 2 162.65 21.63 20.00 41.00 20.33 4.00 -5.61 5.25 0.40 0.26
11173 PulF Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion] context 3 72.94 4.00 4.00 68.70 92.59 18.00 -11.41 10.23 0.56 0.28
287 10423 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion] context 0 235.47 18.63 15.00 50.80 28.15 5.00 -9.72 9.30 0.30 0.34
288 10953 PhnP Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only] context 0 235.45 22.81 22.00 50.00 21.52 4.00 -9.46 8.25 0.33 0.37
289 12345 COG3002 Uncharacterized protein conserved in bacteria [Function unknown] context 0 234.96 7.00 7.00 130.60 89.21 13.00 -21.23 29.02 0.34 0.35
290 27833 AdcA Metal binding protein AcdA. These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion. The AcdA proteins belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and they bind their ligand in the cleft between these domains. In addition, many of these proteins have a low complexity region containing metal binding histidine-rich motif (repetitive HDH sequence). context 0 232.72 22.00 17.00 50.90 37.01 5.00 -14.70 10.25 0.45 0.34
291 7263 Spore_permease Spore germination protein. context 0 231.11 28.00 12.00 31.90 37.58 8.00 -19.09 6.76 0.51 0.43
292 10904 PrfB Protein chain release factor B [Translation, ribosomal structure and biogenesis] context 0 231.02 18.83 19.00 140.40 93.43 26.00 -2.33 2.37 0.42 0.35
10904 PrfB Protein chain release factor B [Translation, ribosomal structure and biogenesis] context 1 206.31 21.00 21.00 110.00 75.36 21.00 2.98 1.73 0.38 0.34
11885 FtsX Cell division protein [Cell division and chromosome partitioning] context 2 164.94 7.00 7.00 125.90 136.71 37.00 4.56 7.91 0.53 0.33
293 10789 AdhP Zn-dependent alcohol dehydrogenases [General function prediction only] context 0 230.55 28.00 17.00 34.30 31.86 4.00 -18.52 8.77 0.45 0.33
294 10419 ArgB Acetylglutamate kinase [Amino acid transport and metabolism] context 0 230.38 14.00 14.00 106.80 39.99 11.00 -7.72 6.77 0.28 0.23
295 10467 LspA Lipoprotein signal peptidase [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion] context 0 228.38 12.99 13.00 92.80 45.72 9.00 -4.80 7.38 0.22 0.33 RF00230 T-box 2
10467 LspA Lipoprotein signal peptidase [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion] context 1 152.15 17.61 17.00 41.00 23.67 5.00 -6.15 5.10 0.37 0.33 RF00230 T-box 2
296 10783 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only] context 0 228.34 22.97 10.00 32.60 29.56 7.00 -12.72 9.70 0.45 0.46
297 10890 AraH Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components [Carbohydrate transport and metabolism] context 0 227.38 16.99 10.00 60.70 27.79 6.00 -9.87 13.17 0.37 0.34
298 24199 PBPb Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in PBPe context 0 227.37 20.00 13.00 36.60 31.67 8.00 -16.56 8.20 0.45 0.24
299 5341 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop andWalker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. context 0 225.89 25.00 9.00 35.00 35.67 8.00 -18.74 9.21 0.49 0.43
300 9413 PTS_IIB_fruc PTS system, Fructose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The sugar-specific permease of the PTS consists of three domains (IIA, IIB and IIC). IIB is is phosphorylated by phospho-IIA, before the phosphoryl group is transferred to the sugar substrate. context 0 225.74 21.69 21.00 142.90 46.67 4.00 -6.12 6.28 0.25 0.28
11473 PtsN Phosphotransferase system mannitol/fructose-specific IIA domain (Ntr-type) [Carbohydrate transport and metabolism / Signal transduction mechanisms] context 1 183.20 26.00 23.00 102.90 41.33 10.00 0.51 1.53 0.31 0.26
301 15338 Tautomerase Tautomerase enzyme. This family includes the enzyme 4-oxalocrotonate tautomerase that catalyses the ketonisation of 2-hydroxymuconate to 2-oxo-3-hexenedioate. context 0 224.85 5.00 5.00 133.00 235.60 131.00 -18.30 15.26 0.99 0.34
15338 Tautomerase Tautomerase enzyme. This family includes the enzyme 4-oxalocrotonate tautomerase that catalyses the ketonisation of 2-hydroxymuconate to 2-oxo-3-hexenedioate. context 1 156.87 5.00 5.00 81.00 146.69 80.00 -10.80 12.15 0.99 0.38
302 10460 CumB Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis] context 0 224.44 5.00 5.00 207.20 255.80 44.00 -24.83 31.00 0.68 0.31
303 10220 GloA Lactoylglutathione lyase and related lyases [Amino acid transport and metabolism] context 0 224.10 17.00 8.00 91.30 38.54 17.00 -3.94 4.45 0.30 0.29
304 10649 NusB Transcription termination factor [Transcription] context 0 224.04 22.53 20.00 49.20 20.35 4.00 -9.39 7.59 0.33 0.32
305 10205 FabD (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism] context 0 223.96 10.79 8.00 70.60 62.20 18.00 -12.08 10.90 0.44 0.33
7889 ABC2_membrane ABC-2 type transporter. context 1 141.70 4.00 4.00 122.00 128.57 21.00 -14.60 30.19 0.51 0.29
10205 FabD (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism] context 2 136.58 4.00 4.00 170.50 187.96 20.00 -25.33 32.32 0.56 0.21
7889 ABC2_membrane ABC-2 type transporter. context 3 118.45 4.00 4.00 113.00 114.46 22.00 -15.90 22.91 0.58 0.22
11529 COG1819 Glycosyl transferases, related to UDP-glucuronosyltransferase [Carbohydrate transport and metabolism / Signal transduction mechanisms] context 4 111.45 6.00 6.00 96.40 55.64 8.00 0.20 10.94 0.26 0.29
11529 COG1819 Glycosyl transferases, related to UDP-glucuronosyltransferase [Carbohydrate transport and metabolism / Signal transduction mechanisms] context 5 54.42 4.00 4.00 136.00 84.66 13.00 1.38 5.75 0.41 0.27
306 26076 Relaxase Relaxase/Mobilisation nuclease domain. Relaxases/mobilisation proteins are required for the horizontal transfer of genetic information contained on plasmids that occurs during bacterial conjugation. The relaxase, in conjunction with several auxiliary proteins, forms the relaxation complex or relaxosome. Relaxases nick duplex DNA in a specific manner by catalysing trans-esterification. context 0 223.49 7.00 7.00 135.60 146.42 21.00 -34.00 28.85 0.60 0.45
307 11491 NrdI Protein involved in ribonucleotide reduction [Nucleotide transport and metabolism] context 0 222.91 16.00 11.00 32.30 37.83 14.00 -18.27 8.57 0.56 0.43
308 16563 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions. context 0 220.69 13.00 11.00 66.40 38.47 11.00 -7.86 8.18 0.31 0.37
309 10607 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane] context 0 219.03 27.00 17.00 31.60 25.46 4.00 -13.37 7.76 0.42 0.50 RF00230 T-box 1
310 10237 NagB 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism] context 0 218.28 10.00 10.00 95.30 67.46 14.00 -5.38 12.75 0.38 0.30
311 10892 OpuBB ABC-type proline/glycine betaine transport systems, permease component [Amino acid transport and metabolism] context 0 217.55 8.00 6.00 124.40 58.69 22.00 -1.16 10.00 0.28 0.35
10892 OpuBB ABC-type proline/glycine betaine transport systems, permease component [Amino acid transport and metabolism] context 1 204.86 5.00 3.00 114.00 194.30 109.00 -16.00 18.52 0.99 0.26
312 11102 HIS2 Histidinol phosphatase and related hydrolases of the PHP family [Amino acid transport and metabolism / General function prediction only] context 0 217.11 26.00 11.00 47.70 33.84 5.00 -14.64 8.66 0.40 0.44 RF00230 T-box 3
313 10324 AhpC Peroxiredoxin [Posttranslational modification, protein turnover, chaperones] context 0 215.30 6.00 6.00 111.80 65.18 25.00 -6.57 16.35 0.32 0.29
12957 AhpF Alkyl hydroperoxide reductase, large subunit [Posttranslational modification, protein turnover, chaperones] context 1 99.66 5.00 5.00 141.00 154.37 32.00 -3.23 7.65 0.62 0.26
314 12909 COG3584 Uncharacterized protein conserved in bacteria [Function unknown] context 0 214.43 38.92 13.00 86.40 20.33 4.00 -2.60 3.53 0.24 0.34
315 13004 COG3682 Predicted transcriptional regulator [Transcription] context 0 214.33 13.00 12.00 94.90 57.94 13.00 -8.52 8.08 0.39 0.25
13004 COG3682 Predicted transcriptional regulator [Transcription] context 1 202.65 18.98 18.00 41.70 22.99 10.00 -1.82 4.25 0.38 0.28
16563 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions. context 2 197.47 5.00 5.00 148.50 186.24 62.00 -9.83 19.31 0.77 0.20
13004 COG3682 Predicted transcriptional regulator [Transcription] context 3 164.02 8.00 7.00 119.90 89.85 48.00 4.83 4.61 0.52 0.19
316 10314 IlvH Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism] context 0 214.29 14.00 12.00 71.50 51.07 6.00 -21.89 13.90 0.36 0.40 RF00230 T-box 1
317 11596 TagB Putative glycosyl/glycerophosphate transferases involved in teichoic acid biosynthesis TagF/TagB/EpsJ/RodC [Cell envelope biogenesis, outer membrane] context 0 213.86 20.96 12.00 40.90 24.39 4.00 -11.28 10.57 0.34 0.35
318 10694 COG0827 Adenine-specific DNA methylase [DNA replication, recombination, and repair] context 0 213.44 20.80 17.00 39.80 22.84 4.00 -10.58 9.72 0.38 0.41
319 11175 COG1461 Predicted kinase related to dihydroxyacetone kinase [General function prediction only] context 0 213.31 14.00 14.00 114.90 62.07 15.00 7.79 5.04 0.33 0.29
320 12240 HemK Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis] context 0 212.78 5.00 5.00 89.00 160.50 87.00 -19.30 20.56 0.99 0.36
9987 GlyA Glycine/serine hydroxymethyltransferase [Amino acid transport and metabolism] context 1 72.43 8.82 8.00 92.00 40.99 8.00 4.99 2.80 0.35 0.34
27995 LT_GEWL Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), as do "goose-type" lysozymes. However, in addition to this, they also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue. context 2 55.94 4.00 4.00 100.00 101.73 14.00 -4.55 7.85 0.57 0.28
321 27719 INT_XerDC XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily. In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites. context 0 212.60 10.00 10.00 64.10 66.28 33.00 -0.10 7.76 0.57 0.27
27719 INT_XerDC XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily. In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites. context 1 167.15 10.00 10.00 60.20 72.73 36.00 -1.69 6.02 0.78 0.25
322 10935 TypA Predicted membrane GTPase involved in stress response [Signal transduction mechanisms] context 0 212.56 8.00 8.00 124.50 125.85 37.00 -3.95 8.54 0.45 0.26
323 10404 QRI7 Metal-dependent proteases with possible chaperone activity [Posttranslational modification, protein turnover, chaperones] context 0 211.65 24.00 14.00 37.10 32.55 4.00 -18.34 9.19 0.40 0.35
324 11591 PflD Pyruvate-formate lyase [Energy production and conversion] context 0 211.14 7.00 7.00 69.90 63.67 50.00 -7.13 10.33 0.57 0.26
11591 PflD Pyruvate-formate lyase [Energy production and conversion] context 1 149.75 5.00 5.00 99.50 141.80 59.00 -5.25 13.03 0.86 0.26
325 11920 MtlA Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism] context 0 210.61 9.00 9.00 111.00 52.47 9.00 -6.65 13.69 0.23 0.33
11920 MtlA Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism] context 1 137.58 15.00 15.00 101.50 46.09 4.00 -4.87 6.61 0.33 0.33
11920 MtlA Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism] context 2 119.68 12.98 13.00 82.20 41.23 4.00 -5.13 5.65 0.28 0.35
326 9972 RplF Ribosomal protein L6P/L9E [Translation, ribosomal structure and biogenesis] context 0 209.63 9.98 10.00 90.70 96.25 27.00 1.73 8.24 0.51 0.38
327 12662 COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair] context 0 209.08 9.00 1.00 147.80 272.41 147.00 -33.24 28.76 0.99 0.38
328 27389 Transposase_35 Putative transposase DNA-binding domain. This putative domain is found at the C-terminus of a large number of transposase proteins. This domain contains four conserved cysteines suggestive of a zinc binding domain. Given the need for transposases to bind DNA as well as the large number of DNA-binding zinc fingers we hypothesise this domain is DNA-binding. context 0 208.63 8.00 3.00 142.30 152.89 30.00 -9.64 22.04 0.54 0.30
329 14588 COG5504 Predicted Zn-dependent protease [Posttranslational modification, protein turnover, chaperones] context 0 208.32 18.00 11.00 85.00 42.40 6.00 -11.07 8.83 0.34 0.30
330 12228 AroA 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism] context 0 208.26 15.84 15.00 83.80 35.73 4.00 -6.67 9.72 0.24 0.32 RF00230 T-box 1
331 24417 Ribosomal_S8 Ribosomal protein S8. context 0 207.95 21.00 17.00 63.90 29.66 6.00 -5.61 4.77 0.29 0.44
9973 RpsE Ribosomal protein S5 [Translation, ribosomal structure and biogenesis] context 1 137.50 9.00 9.00 52.90 48.43 9.00 -10.44 10.91 0.43 0.50
10061 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis] context 2 76.94 11.00 10.00 101.20 109.57 39.00 0.96 0.73 0.58 0.46
332 13015 COG3694 ABC-type uncharacterized transport system, permease component [General function prediction only] context 0 206.57 5.00 5.00 136.40 183.44 64.00 -4.72 16.75 0.63 0.29
13750 COG4587 ABC-type uncharacterized transport system, permease component [General function prediction only] context 1 190.25 7.00 7.00 150.80 104.03 27.00 0.76 10.32 0.38 0.30
333 10952 ElaC Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only] context 0 206.47 22.87 18.00 60.60 25.18 4.00 -9.48 6.87 0.34 0.36
334 10232 DnaG DNA primase (bacterial type) [DNA replication, recombination, and repair] context 0 206.31 17.00 13.00 34.80 33.42 6.00 -16.89 10.86 0.43 0.39 RF00230 T-box 3
335 10900 AcpD Acyl carrier protein phosphodiesterase [Lipid metabolism] context 0 205.98 16.00 12.00 39.40 36.40 5.00 -18.70 14.01 0.41 0.38 RF00230 T-box 1
336 10430 LivH Branched-chain amino acid ABC-type transport system, permease components [Amino acid transport and metabolism] context 0 205.12 19.00 13.00 50.70 34.65 5.00 -15.32 9.56 0.38 0.39
337 25927 DUF150 Uncharacterised BCR, YhbC family COG0779. context 0 204.67 7.00 7.00 152.90 135.35 15.00 -13.07 18.56 0.33 0.31
338 10965 COG1247 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane] context 0 204.32 19.78 13.00 50.90 26.03 5.00 -7.92 7.89 0.34 0.36
339 9958 ThrB Homoserine kinase [Amino acid transport and metabolism] context 0 202.59 13.00 8.00 54.30 46.12 8.00 -13.44 14.53 0.41 0.36
11253 FolB Dihydroneopterin aldolase [Coenzyme metabolism] context 1 82.41 4.00 4.00 143.60 97.95 11.00 -12.18 15.54 0.41 0.34 RF00059 THI 1
11253 FolB Dihydroneopterin aldolase [Coenzyme metabolism] context 2 52.46 4.00 4.00 62.10 79.47 9.00 -9.68 11.03 0.59 0.35
340 24627 cobW Cobalamin synthesis protein/P47K. This family of proteins contains P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the cobW gene product, which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans. context 0 202.04 16.75 9.00 75.40 40.00 17.00 0.34 4.16 0.38 0.28
341 10802 COG1079 Uncharacterized ABC-type transport system, permease component [General function prediction only] context 0 201.45 24.89 25.00 29.80 17.75 4.00 -5.10 5.01 0.35 0.46
13759 COG4603 ABC-type uncharacterized transport system, permease component [General function prediction only] context 1 126.37 13.74 13.00 43.20 29.30 4.00 -11.82 7.41 0.38 0.45
342 10316 ProS Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] context 0 200.55 29.00 15.00 29.90 30.40 4.00 -15.47 7.73 0.50 0.43
343 10231 GidB Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane] context 0 200.50 20.89 16.00 41.50 18.86 5.00 -6.20 6.16 0.33 0.36
344 9931 AtpA F0F1-type ATP synthase, alpha subunit [Energy production and conversion] context 0 200.45 18.00 16.00 46.10 39.00 8.00 -8.90 7.20 0.47 0.42
25446 OSCP ATP synthase delta (OSCP) subunit. The ATP D subunit from E. coli is the same as the OSCP subunit which is this family. The ATP D subunit from metazoa are found in family pfam00401. context 1 139.86 10.83 11.00 37.90 28.36 8.00 -9.25 8.28 0.42 0.45
345 10217 Tgt Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis] context 0 199.83 8.00 8.00 113.80 116.04 40.00 -10.23 7.45 0.48 0.36
10217 Tgt Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis] context 1 122.48 6.00 6.00 152.40 160.40 13.00 3.66 13.89 0.44 0.36
346 10373 BioB Biotin synthase and related enzymes [Coenzyme metabolism] context 0 199.54 12.00 12.00 126.80 70.43 5.00 -17.11 15.42 0.29 0.30
347 25795 PMSR Peptide methionine sulfoxide reductase. This enzyme repairs damaged proteins. Methionine sulfoxide in proteins is reduced to methionine. context 0 199.48 22.54 16.00 50.00 22.86 4.00 -9.43 7.77 0.39 0.31
348 10354 LepA Membrane GTPase LepA [Cell envelope biogenesis, outer membrane] context 0 198.74 20.66 15.00 31.90 25.42 5.00 -12.79 7.56 0.40 0.38
349 10724 RbfA Ribosome-binding factor A [Translation, ribosomal structure and biogenesis] context 0 198.50 19.86 20.00 83.90 37.32 4.00 -13.03 7.74 0.33 0.35
350 10953 PhnP Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only] context 0 198.19 3.00 3.00 180.50 265.96 127.00 -31.60 26.42 0.77 0.29
12185 COG2832 Uncharacterized protein conserved in bacteria [Function unknown] context 1 82.32 4.00 4.00 82.50 90.94 20.00 -15.70 12.79 0.61 0.27
351 10668 Eda 2-keto-3-deoxy-6-phosphogluconate aldolase [Carbohydrate transport and metabolism] context 0 197.77 5.00 5.00 214.80 160.13 68.00 -1.51 7.80 0.34 0.25
10668 Eda 2-keto-3-deoxy-6-phosphogluconate aldolase [Carbohydrate transport and metabolism] context 1 185.95 3.00 3.00 263.20 241.43 60.00 -4.38 21.06 0.33 0.27
26674 DUF1124 Putative ribose 5-phosphate isomerase (DUF1124). This family consists of several hypothetical and putative bacterial ribose 5-phosphate isomerase proteins. context 2 107.96 6.00 6.00 87.00 81.31 15.00 -3.73 10.65 0.50 0.27
352 11194 COG1480 Predicted membrane-associated HD superfamily hydrolase [General function prediction only] context 0 197.75 12.99 9.00 60.60 36.29 4.00 -20.72 16.59 0.27 0.43
353 26891 UPF0236 Uncharacterised protein family (UPF0236). context 0 196.92 25.00 3.00 150.40 142.22 18.00 -6.15 13.13 0.54 0.36
354 10287 PanB Ketopantoate hydroxymethyltransferase [Coenzyme metabolism] context 0 196.83 6.00 6.00 113.20 75.78 24.00 -10.91 15.12 0.34 0.48
355 28159 ATZ_TRZ_like TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are catalyzed by atrazine chlorohydrolase (AtzA), hydroxyatrazine ethylaminohydrolase (AtzB), and N-isopropylammelide N-isopropylaminohydrolase (AtzC). All three enzymes belong to the superfamily of metal dependent hydrolases. AtzA and AtzB, beside other related enzymes are represented in this CD. context 0 196.53 15.00 9.00 62.40 24.72 5.00 -4.04 9.24 0.23 0.36
356 3793 PTS_IIB_lac PTS system, lactose/cellobiose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation context 0 196.37 7.00 5.00 79.10 67.97 26.00 -8.37 17.14 0.52 0.26
3793 PTS_IIB_lac PTS system, lactose/cellobiose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation context 1 174.17 5.00 3.00 126.50 147.95 31.00 -18.30 26.03 0.55 0.30
357 10777 LdhA Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only] context 0 196.27 19.46 15.00 46.60 23.14 5.00 -9.80 6.95 0.35 0.34
10777 LdhA Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only] context 1 187.90 15.25 12.00 88.10 25.00 5.00 -8.78 6.54 0.23 0.36
358 11645 COG1937 Uncharacterized protein conserved in bacteria [Function unknown] context 0 196.17 8.57 7.00 124.10 73.28 16.00 -9.32 8.05 0.26 0.31
359 17140 PTS_EIIC Phosphotransferase system, EIIC. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The sugar-specific permease of the PTS consists of three domains (IIA, IIB and IIC). The IIC domain catalyses the transfer of a phosphoryl group from IIB to the sugar substrate. context 0 196.00 10.00 7.00 55.10 47.71 15.00 -11.88 12.33 0.44 0.40
360 25355 AAA ATPase family associated with various cellular activities (AAA). AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes. context 0 195.27 15.00 8.00 39.90 38.98 11.00 -16.65 10.63 0.53 0.43
361 9969 RplE Ribosomal protein L5 [Translation, ribosomal structure and biogenesis] context 0 194.81 10.00 10.00 69.90 82.22 31.00 -16.45 8.15 0.67 0.42
10073 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis] context 1 108.65 15.52 12.00 33.80 28.03 4.00 -6.50 5.65 0.48 0.54
362 10925 GlmU N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane] context 0 194.69 3.00 3.00 146.00 229.00 138.00 -29.00 28.95 0.95 0.29
10925 GlmU N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane] context 1 66.92 5.00 5.00 142.70 98.87 5.00 -16.33 13.09 0.38 0.30
363 16741 SBP_bac_5 Bacterial extracellular solute-binding proteins, family 5. context 0 194.68 18.98 12.00 56.40 29.11 4.00 -13.30 10.59 0.36 0.30
364 11952 COG2246 Predicted membrane protein [Function unknown] context 0 194.64 6.00 6.00 150.60 179.21 43.00 -17.69 14.86 0.61 0.35
365 10429 PgsA Phosphatidylglycerophosphate synthase [Lipid metabolism] context 0 193.95 16.93 14.00 92.80 32.71 4.00 -7.32 7.37 0.23 0.36
10783 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only] context 1 155.26 11.79 12.00 59.20 31.87 6.00 -7.45 7.56 0.28 0.36
366 5361 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. context 0 193.83 16.91 13.00 63.00 30.54 4.00 -10.76 10.53 0.32 0.35
5361 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. context 1 144.97 16.43 13.00 71.00 22.49 4.00 -7.53 4.97 0.27 0.38
367 10528 ComEC Predicted membrane metal-binding protein [General function prediction only] context 0 193.55 9.00 6.00 74.80 65.78 21.00 -4.05 11.43 0.46 0.28
10079 PlsC 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism] context 1 92.27 4.00 4.00 121.00 123.02 26.00 -5.45 11.17 0.55 0.30
368 12624 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms] context 0 193.05 5.00 5.00 124.60 165.87 49.00 -9.45 21.21 0.70 0.27
13728 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms] context 1 154.83 5.00 5.00 73.50 107.77 43.00 -3.60 15.76 0.71 0.19
12624 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms] context 2 64.57 4.00 4.00 57.00 71.16 9.00 -16.45 15.86 0.56 0.38
369 10835 AnsP Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism] context 0 192.85 22.42 13.00 36.10 21.53 4.00 -10.83 7.86 0.37 0.39
370 26480 DUF972 Protein of unknown function (DUF972). This family consists of several hypothetical bacterial and one Caenorhabditis elegans sequence. The function of this family is unknown. context 0 192.73 14.00 10.00 33.20 33.05 9.00 -14.94 10.85 0.48 0.37
371 11406 COG1695 Predicted transcriptional regulators [Transcription] context 0 189.69 20.00 2.00 128.50 146.70 66.00 -11.90 7.60 0.61 0.38
372 16990 Transposase_9 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes an amino-terminal region of the pilin gene inverting protein (PIVML) and members of the IS111A/IS1328/IS1533 family of transposases. context 0 189.62 8.00 2.00 220.00 201.46 76.00 -10.18 10.98 0.53 0.32
373 23729 Spore_GerAC Spore germination B3/ GerAC like, C-terminal. The GerAC protein of the Bacillus subtilis spore is required for the germination response to L-alanine. Members of this family are thought to be located in the inner spore membrane. Although the function of this family is unclear, they are likely to encode the components of the germination apparatus that respond directly to this germinant, mediating the spore's response. context 0 188.35 19.98 10.00 94.30 27.96 4.00 -7.98 8.25 0.28 0.30
5081 GerA Bacillus/Clostridium GerA spore germination protein. context 1 100.49 15.16 8.00 31.90 18.90 4.00 -0.75 4.98 0.38 0.40
374 11413 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms] context 0 187.77 8.00 8.00 93.30 69.28 20.00 -12.25 9.00 0.33 0.30
375 9933 GlgP Glucan phosphorylase [Carbohydrate transport and metabolism] context 0 186.73 11.00 10.00 84.50 47.12 8.00 -12.67 12.76 0.36 0.35
2956 4a_glucanotrans 4-alpha-glucanotransferase. These enzymes EC:2.4.1.25 transfer a segment of a (1,4)-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose or (1,4)-alpha-D-glucan. context 1 103.57 8.00 8.00 126.60 55.66 4.00 -13.09 13.17 0.33 0.32
376 11980 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms] context 0 185.87 20.67 16.00 34.30 19.67 4.00 -9.33 7.15 0.36 0.29
377 10988 COG1272 Predicted membrane protein, hemolysin III homolog [General function prediction only] context 0 184.99 9.50 10.00 65.20 63.04 28.00 -1.97 6.31 0.52 0.25
378 16696 CSD 'Cold-shock' DNA-binding domain. context 0 184.80 21.00 13.00 85.30 40.32 8.00 0.76 3.94 0.35 0.29
379 10463 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair] context 0 182.51 16.00 16.00 97.70 51.76 8.00 -1.69 6.03 0.38 0.31
10463 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair] context 1 103.39 17.00 17.00 115.50 61.61 4.00 -0.40 2.73 0.31 0.29
380 11582 COG1873 Uncharacterized conserved protein [Function unknown] context 0 182.06 16.00 10.00 102.40 34.80 6.00 -10.73 6.68 0.27 0.36
11582 COG1873 Uncharacterized conserved protein [Function unknown] context 1 149.51 10.97 7.00 81.40 27.46 4.00 -16.21 12.88 0.25 0.38
11582 COG1873 Uncharacterized conserved protein [Function unknown] context 2 138.14 11.95 8.00 48.50 26.87 5.00 -9.44 10.45 0.36 0.34
381 10804 IolE Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism] context 0 181.64 3.00 3.00 168.90 239.57 129.00 -18.11 24.97 0.88 0.27
382 11889 NarI Nitrate reductase gamma subunit [Energy production and conversion] context 0 181.02 5.00 5.00 184.50 103.55 29.00 -13.39 12.12 0.27 0.35
11889 NarI Nitrate reductase gamma subunit [Energy production and conversion] context 1 165.02 5.00 5.00 182.90 105.08 26.00 -4.97 10.81 0.26 0.35
11889 NarI Nitrate reductase gamma subunit [Energy production and conversion] context 2 124.26 7.00 6.00 93.10 47.14 8.00 -15.38 11.78 0.30 0.38
11888 NarJ Nitrate reductase delta subunit [Energy production and conversion] context 3 124.04 5.00 5.00 110.70 79.59 14.00 -19.68 15.17 0.35 0.39
383 12627 COG3293 Transposase and inactivated derivatives [DNA replication, recombination, and repair] context 0 180.98 5.00 2.00 105.00 184.54 99.00 -17.85 21.58 0.96 0.38
384 12808 SdrC Predicted secreted protein containing a PDZ domain [Signal transduction mechanisms] context 0 180.72 13.00 12.00 66.10 34.98 5.00 -12.29 10.47 0.28 0.30
385 25346 RL11 Ribosomal protein L11/L12; context 0 179.99 9.00 9.00 119.20 90.91 23.00 -3.53 7.93 0.46 0.29
386 10085 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair] context 0 179.69 22.76 20.00 36.00 17.80 4.00 -6.47 5.01 0.39 0.34
387 10903 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis] context 0 179.03 6.00 6.00 201.30 171.31 19.00 -6.37 21.33 0.46 0.34
388 11821 ProX ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism] context 0 178.34 5.00 5.00 144.30 204.93 77.00 0.44 12.03 0.73 0.31
13441 ProW ABC-type proline/glycine betaine transport system, permease component [Amino acid transport and metabolism] context 1 160.07 5.00 5.00 135.10 190.22 68.00 -1.79 11.12 0.74 0.31
11821 ProX ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism] context 2 155.04 5.00 5.00 76.00 114.64 55.00 -8.65 13.76 0.79 0.31
389 5177 Peptidase_U4 Sporulation factor SpoIIGA. context 0 176.91 9.00 9.00 119.90 57.01 7.00 -16.34 12.88 0.24 0.33
390 11645 COG1937 Uncharacterized protein conserved in bacteria [Function unknown] context 0 176.50 20.83 14.00 30.20 21.97 10.00 -2.47 4.26 0.54 0.35
391 7590 SLH S-layer homology domain. context 0 174.60 16.00 10.00 44.50 38.73 5.00 -15.05 12.48 0.46 0.41
392 11764 COG2056 Predicted permease [General function prediction only] context 0 174.33 9.00 9.00 138.10 66.37 9.00 -9.41 9.38 0.23 0.32
393 26344 Phage_prot_Gp6 Phage portal protein, SPP1 Gp6-like. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. During SPP1 morphogenesis, Gp6 participates in the procapsid assembly reaction. context 0 173.81 18.00 12.00 42.50 36.85 4.00 -21.51 10.62 0.42 0.42
394 2898 FemAB FemAB family. The femAB operon codes for two nearly identical approximately 50-kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan. These proteins are also considered as a factor influencing the level of methicillin resistance. context 0 173.18 7.00 6.00 120.60 56.14 15.00 -17.62 13.99 0.34 0.25
395 27775 DHFR Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5,10-methylenetetrahydrofolate which is then utilized by thymidylate synthase. Inhibition of DHFR interrupts thymidilate synthesis and DNA replication, inhibitors of DHFR (such as Methotrexate) are used in cancer chemotherapy. 5,6,7,8-tetrahydrofolate also is involved in glycine, serine, and threonine metabolism and aminoacyl-tRNA biosynthesis. context 0 173.13 20.00 18.00 46.30 24.33 4.00 -7.69 6.67 0.37 0.34 RF00230 T-box 1
396 10430 LivH Branched-chain amino acid ABC-type transport system, permease components [Amino acid transport and metabolism] context 0 173.10 8.00 7.00 139.50 92.21 8.00 -19.69 13.93 0.24 0.40
397 23047 UBA UBA/TS-N domain. This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280. context 0 173.00 16.00 14.00 94.90 37.90 4.00 -9.05 7.64 0.27 0.30
398 10333 ThrA Homoserine dehydrogenase [Amino acid transport and metabolism] context 0 172.46 15.00 13.00 73.40 34.48 4.00 -10.93 9.62 0.30 0.36 RF00230 T-box 1
10333 ThrA Homoserine dehydrogenase [Amino acid transport and metabolism] context 1 87.00 8.00 8.00 124.50 73.26 4.00 -5.73 9.01 0.32 0.25
399 10615 DdpA ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism] context 0 172.28 3.94 4.00 153.30 198.82 24.00 -24.62 29.13 0.38 0.25
400 27348 DUF1429 Protein of unknown function (DUF1429). This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown. context 0 172.03 11.00 10.00 79.70 35.17 6.00 -18.23 11.14 0.28 0.36
401 23475 FlaG FlaG protein. Although important for flagella the exact function of this protein is unknown. context 0 170.77 17.00 10.00 46.50 38.07 5.00 -17.95 11.49 0.48 0.41
402 13672 CoiA Competence protein [General function prediction only] context 0 170.73 16.02 13.00 33.90 15.28 4.00 -14.05 8.17 0.32 0.38
403 14387 ATM1 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones] context 0 170.59 13.00 10.00 84.40 36.27 5.00 -10.51 8.78 0.25 0.30
404 26218 DUF419 Protein of unknown function (DUF419). context 0 170.26 3.00 3.00 156.00 234.40 118.00 -23.09 22.89 0.84 0.32
26218 DUF419 Protein of unknown function (DUF419). context 1 139.73 3.00 3.00 143.00 222.73 124.00 -16.95 15.37 0.88 0.33
405 10284 LivF ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism] context 0 170.02 90.00 32.00 45.40 33.12 0.00 -22.40 14.67 0.43 0.37
406 11679 COG1971 Predicted membrane protein [Function unknown] context 0 168.67 15.00 10.00 56.40 27.61 4.00 -12.43 10.63 0.31 0.37
407 12166 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair] context 0 168.56 17.79 19.00 42.90 19.35 5.00 1.64 5.60 0.37 0.29
408 11711 RadC DNA repair proteins [DNA replication, recombination, and repair] context 0 168.53 6.00 6.00 91.20 51.15 22.00 -14.91 13.86 0.39 0.32
409 11207 HprK Serine kinase of the HPr protein, regulates carbohydrate metabolism [Signal transduction mechanisms] context 0 168.20 14.00 14.00 47.90 26.36 6.00 -9.20 9.08 0.39 0.31
11207 HprK Serine kinase of the HPr protein, regulates carbohydrate metabolism [Signal transduction mechanisms] context 1 104.59 12.87 13.00 50.60 29.33 4.00 -4.49 5.24 0.34 0.36
410 10970 TlyC Hemolysins and related proteins containing CBS domains [General function prediction only] context 0 168.19 4.00 4.00 188.50 178.90 48.00 -10.46 19.44 0.53 0.33
10970 TlyC Hemolysins and related proteins containing CBS domains [General function prediction only] context 1 143.76 8.00 8.00 58.20 55.95 15.00 -5.80 10.41 0.49 0.46
411 11225 COG1511 Predicted membrane protein [Function unknown] context 0 167.56 15.84 14.00 45.50 23.28 4.00 -13.71 8.76 0.33 0.39
412 10502 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair] context 0 167.37 13.72 14.00 49.00 26.44 5.00 -10.57 9.62 0.35 0.30 RF00050 RFN 2
413 25939 AdoMet_dc S-adenosylmethionine decarboxylase. This family contains several S-adenosylmethionine decarboxylase proteins from bacterial and archaebacterial species. S-adenosylmethionine decarboxylase (AdoMetDC), a key enzyme in the biosynthesis of spermidine and spermine, is first synthesised as a proenzyme, which is cleaved post translationally to form alpha and beta subunits. The alpha subunit contains a covalently bound pyruvoyl group derived from serine that is essential for activity. context 0 167.23 6.00 6.00 115.40 132.46 47.00 -3.30 9.71 0.59 0.44
414 15551 ATP-cone ATP cone domain. context 0 167.17 22.95 20.00 45.70 23.50 4.00 -6.16 4.61 0.36 0.35
12935 DnaB Replication initiation/membrane attachment protein [DNA replication, recombination, and repair] context 1 72.62 6.00 6.00 72.50 84.31 13.00 -0.76 5.66 0.51 0.27
415 26027 HGTP_anticodon Anticodon binding domain. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases; it is probably the anticodon binding domain. context 0 167.15 14.00 8.00 35.90 39.06 12.00 -15.36 7.65 0.52 0.43
416 11551 RpmD Ribosomal protein L30/L7E [Translation, ribosomal structure and biogenesis] context 0 166.61 15.00 10.00 52.10 39.43 4.00 -17.37 12.38 0.37 0.43
417 27838 FeuA Periplasmic binding protein FeuA. These proteins have predicted to function as initial receptors in ABC transport of metal ions in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains. context 0 166.41 5.00 5.00 133.90 167.83 53.00 -5.42 13.95 0.67 0.24
418 10560 SmpB tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones] context 0 165.86 23.93 22.00 39.60 18.87 4.00 -4.88 3.83 0.36 0.44
419 24891 CodY GTP-sensing transcriptional pleiotropic repressor CodY. This family consists of several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk. context 0 165.33 10.00 10.00 114.00 79.47 13.00 -1.50 8.49 0.41 0.25
27793 cysteine_hydrolases Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It also contains isochorismatase, an enzyme that catalyzes the conversion of isochorismate to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of the vinyl ether bond, and other related enzymes with unknown function. context 1 63.57 5.00 5.00 87.90 62.86 4.00 -6.90 18.09 0.47 0.25
420 10319 GidA NAD/FAD-utilizing enzyme apparently involved in cell division [Cell division and chromosome partitioning] context 0 165.32 5.00 5.00 157.70 113.06 28.00 -8.11 11.63 0.30 0.33
421 17181 DUF177 Uncharacterized ACR, COG1399. context 0 165.29 14.00 14.00 124.80 72.46 30.00 -0.70 1.80 0.39 0.33
17181 DUF177 Uncharacterized ACR, COG1399. context 1 155.09 21.00 21.00 92.10 33.79 16.00 3.83 1.01 0.30 0.32
17181 DUF177 Uncharacterized ACR, COG1399. context 2 147.21 16.98 17.00 32.20 28.24 16.00 -2.01 2.87 0.62 0.28
422 9885 SUA5 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis] context 0 165.27 12.77 13.00 64.40 26.12 5.00 -4.17 7.77 0.25 0.35
423 10042 PyrD Dihydroorotate dehydrogenase [Nucleotide transport and metabolism] context 0 164.87 8.00 8.00 102.50 73.83 20.00 -1.67 8.20 0.39 0.29
424 10873 Dxs Deoxyxylulose-5-phosphate synthase [Coenzyme metabolism / Lipid metabolism] context 0 164.68 5.00 5.00 75.20 107.03 43.00 -20.94 15.82 0.63 0.51
425 27392 DUF1444 Protein of unknown function (DUF1444). This family contains several hypothetical bacterial proteins of unknown function that are approximately 250 residues long. context 0 164.66 10.00 10.00 88.90 55.23 12.00 -9.61 8.89 0.40 0.32
426 11375 CcmA Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane] context 0 164.44 5.00 5.00 101.60 74.76 28.00 -12.09 11.89 0.31 0.33
427 27985 KAS_III Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl carrier protein (ACP) with acyl-ACP. KASIII initiates this process by specifically using acetyl-CoA over acyl-CoA. context 0 163.47 12.00 10.00 37.40 0.00 5.00 -20.45 13.97 0.38 0.38
27985 KAS_III Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl carrier protein (ACP) with acyl-ACP. KASIII initiates this process by specifically using acetyl-CoA over acyl-CoA. context 1 99.41 7.78 7.00 66.20 37.03 4.00 -16.00 13.08 0.35 0.36
428 25520 IMPDH IMP dehydrogenase / GMP reductase domain. This family is involved in biosynthesis of guanosine nucleotide. Members of this family contain a TIM barrel structure. In the inosine monophosphate dehydrogenases 2 CBS domains pfam00571 are inserted in the TIM barrel. This family is a member of the common phosphate binding site TIM barrel family. context 0 163.38 7.00 7.00 127.70 86.22 39.00 1.45 5.42 0.39 0.28
429 13444 COG4181 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism] context 0 162.90 5.00 5.00 148.50 126.13 27.00 -10.77 17.95 0.46 0.30
430 13686 COG4487 Uncharacterized protein conserved in bacteria [Function unknown] context 0 162.88 8.00 7.00 56.50 43.58 20.00 -2.90 8.97 0.43 0.31
431 11037 TroR Mn-dependent transcriptional regulator [Transcription] context 0 162.79 5.00 5.00 137.00 181.49 54.00 0.29 15.06 0.77 0.21
11037 TroR Mn-dependent transcriptional regulator [Transcription] context 1 125.84 7.90 8.00 70.00 49.17 19.00 3.19 6.83 0.53 0.21
26173 FeoA FeoA domain. This family includes FeoA a small protein, probably involved in Fe2+ transport. This presumed short domain is also found at the C-terminus of a variety of metal dependent transcriptional regulators. This suggests that this domain may be metal-binding. In most cases this is likely to be either iron or manganese. context 2 74.68 4.00 4.00 82.50 79.82 15.00 -8.46 13.53 0.59 0.27
432 10415 Tig FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) [Posttranslational modification, protein turnover, chaperones] context 0 162.79 13.00 13.00 129.20 51.88 6.00 -3.45 6.07 0.24 0.35
433 26128 PUD Bacterial pullanase-associated domain. Domain is found in pullanase - carbohydrate de-branching - proteins. It is found both to the N or the C terminii of of the alpha-amylase active site region. This domain contains several conserved aromatic residues that are suggestive of a carbohydrate binding function. context 0 162.72 5.00 5.00 162.00 209.15 28.00 -25.17 22.91 0.61 0.33
26128 PUD Bacterial pullanase-associated domain. Domain is found in pullanase - carbohydrate de-branching - proteins. It is found both to the N or the C terminii of of the alpha-amylase active site region. This domain contains several conserved aromatic residues that are suggestive of a carbohydrate binding function. context 1 113.87 5.00 5.00 113.10 145.60 15.00 -13.42 19.79 0.58 0.34
434 13161 COG3845 ABC-type uncharacterized transport systems, ATPase components [General function prediction only] context 0 162.67 11.51 12.00 111.90 48.78 4.00 -9.87 14.00 0.32 0.30
435 10496 MetC Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism] context 0 162.34 4.00 4.00 104.40 169.05 89.00 -19.09 16.25 0.88 0.43 RF00230 T-box 2
10496 MetC Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism] context 1 85.51 7.00 7.00 45.80 48.78 10.00 -9.18 6.73 0.46 0.49 RF00230 T-box 3
436 12649 COG3315 O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism] context 0 162.27 8.00 8.00 71.20 48.88 14.00 -11.89 11.88 0.41 0.31
437 11535 RplY Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and biogenesis] context 0 161.81 4.00 4.00 112.30 136.02 61.00 -21.17 17.38 0.65 0.36
438 26397 Peptidase_S55 SpoIVB peptidase S55. The protein SpoIVB plays a key role in signaling in the final sigma-K checkpoint of Bacillus subtilis. context 0 161.47 7.00 6.00 133.30 82.13 25.00 -8.69 7.12 0.33 0.41
27592 PDZ_metalloprotease PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins. context 1 126.29 9.00 9.00 95.10 44.50 6.00 -7.76 9.21 0.29 0.32
26397 Peptidase_S55 SpoIVB peptidase S55. The protein SpoIVB plays a key role in signaling in the final sigma-K checkpoint of Bacillus subtilis. context 2 100.05 8.00 8.00 79.60 42.75 4.00 -13.20 10.80 0.29 0.28
439 27785 SAICAR_synt_Tm Prokaryotic and archaeal group of SAICAR synthetases represented by the Thermotoga maritima (Tm) SAICAR synthetase and E. coli PurC. SAICAR synthetase catalyzes the seventh step of the de novo biosynthesis of purine nucleotides. context 0 161.41 14.00 14.00 56.30 29.81 4.00 -15.05 10.76 0.34 0.32
440 27985 KAS_III Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl carrier protein (ACP) with acyl-ACP. KASIII initiates this process by specifically using acetyl-CoA over acyl-CoA. context 0 161.05 17.00 14.00 128.50 43.13 11.00 2.40 2.32 0.28 0.25
441 10670 COG0802 Predicted ATPase or kinase [General function prediction only] context 0 159.42 6.00 6.00 87.70 91.44 19.00 -23.09 19.12 0.52 0.37
442 26846 Transglycosylas Transglycosylase-like domain. This family of proteins are very likely to act as transglycosylase enzymes related to pfam00062 and pfam01464. These other families are weakly matched by this family, and include the known active site residues. context 0 158.88 7.00 7.00 117.50 86.12 16.00 -4.36 9.54 0.30 0.23
443 10895 PotC ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism] context 0 158.80 17.00 14.00 89.60 35.20 4.00 -7.27 5.80 0.27 0.29
13158 PotA ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism] context 1 136.93 5.00 5.00 116.80 151.88 50.00 -4.52 10.01 0.67 0.29
10679 MurB UDP-N-acetylmuramate dehydrogenase [Cell envelope biogenesis, outer membrane] context 2 116.16 6.00 6.00 79.30 86.50 30.00 -3.42 8.44 0.68 0.26
10679 MurB UDP-N-acetylmuramate dehydrogenase [Cell envelope biogenesis, outer membrane] context 3 65.58 7.99 8.00 42.40 31.59 4.00 -1.43 7.68 0.48 0.32
10556 PotD Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism] context 4 56.66 7.49 7.00 31.20 22.27 4.00 -2.13 6.07 0.50 0.30
444 24456 HAMP HAMP domain. context 0 158.08 5.00 5.00 108.00 145.39 29.00 -18.40 22.25 0.65 0.29
445 27838 FeuA Periplasmic binding protein FeuA. These proteins have predicted to function as initial receptors in ABC transport of metal ions in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains. context 0 157.87 33.99 16.00 37.80 23.38 7.00 2.31 2.33 0.53 0.24
446 10415 Tig FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) [Posttranslational modification, protein turnover, chaperones] context 0 157.68 17.00 16.00 90.20 33.17 4.00 -6.70 5.55 0.27 0.36
10415 Tig FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) [Posttranslational modification, protein turnover, chaperones] context 1 108.58 6.00 6.00 120.50 140.78 26.00 2.74 6.50 0.52 0.26
447 10355 TrmU Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis] context 0 157.67 11.00 11.00 60.30 59.94 7.00 -6.33 12.27 0.43 0.36
448 10338 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones] context 0 157.25 11.81 11.00 123.50 46.41 5.00 -8.17 7.65 0.23 0.29
449 10910 Soj ATPases involved in chromosome partitioning [Cell division and chromosome partitioning] context 0 157.19 16.65 14.00 39.90 23.15 5.00 -7.24 6.29 0.37 0.35
10910 Soj ATPases involved in chromosome partitioning [Cell division and chromosome partitioning] context 1 85.52 15.88 13.00 59.60 26.01 4.00 2.37 2.19 0.31 0.33
450 10434 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism] context 0 156.72 12.95 12.00 43.80 24.61 6.00 -7.94 8.49 0.36 0.36
451 1248 dUTPase dUTPase. dUTPase hydrolyses dUTP to dUMP and pyrophosphate. context 0 156.71 9.79 9.00 48.20 25.20 9.00 -11.96 10.25 0.38 0.28
452 11189 Spo0J Predicted transcriptional regulators [Transcription] context 0 156.54 19.02 15.00 31.50 20.48 4.00 -7.91 5.63 0.36 0.38
453 10653 CcdA Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones] context 0 155.61 10.00 8.00 91.40 56.71 8.00 -4.18 7.71 0.25 0.36
454 25650 Transgly Transglycosylase. The penicillin-binding proteins are bifunctional proteins consisting of transglycosylase and transpeptidase in the N- and C-terminus respectively. The transglycosylase domain catalyses the polymerisation of murein glycan chains. context 0 155.15 5.00 5.00 125.00 109.56 34.00 0.19 10.98 0.39 0.32 RF00230 T-box 1
455 14020 COG4886 Leucine-rich repeat (LRR) protein [Function unknown] context 0 154.92 19.95 7.00 53.90 26.20 5.00 -8.52 8.07 0.36 0.29
14020 COG4886 Leucine-rich repeat (LRR) protein [Function unknown] context 1 87.48 9.81 3.00 91.90 49.71 4.00 -13.20 10.42 0.25 0.33
456 9997 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair] context 0 154.92 12.00 9.00 35.50 35.67 8.00 -19.01 9.37 0.43 0.48
457 10843 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism] context 0 153.87 12.85 11.00 41.70 21.14 6.00 -4.57 7.99 0.39 0.33
458 10789 AdhP Zn-dependent alcohol dehydrogenases [General function prediction only] context 0 152.59 7.00 7.00 91.70 77.00 13.00 -13.42 12.60 0.35 0.32
459 12497 Kup K+ transporter [Inorganic ion transport and metabolism] context 0 151.74 5.00 5.00 118.00 154.22 40.00 -5.41 15.12 0.66 0.28
12497 Kup K+ transporter [Inorganic ion transport and metabolism] context 1 85.91 8.00 7.00 68.00 47.91 4.00 -9.03 12.28 0.44 0.29
460 10906 COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis] context 0 151.65 96.00 38.00 34.20 28.42 0.00 -16.95 8.58 0.40 0.36 RF00230 T-box 1
461 10138 ProB Glutamate 5-kinase [Amino acid transport and metabolism] context 0 151.56 10.00 10.00 88.00 44.60 5.00 -14.38 10.16 0.23 0.30 RF00230 T-box 2
462 10320 HcaD Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only] context 0 151.37 18.97 15.00 53.70 27.33 4.00 -2.69 5.71 0.36 0.35
463 10917 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair] context 0 151.19 5.00 5.00 101.50 156.68 79.00 -16.45 10.39 0.90 0.31
10917 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair] context 1 150.13 7.96 8.00 43.00 33.66 12.00 -7.33 10.97 0.38 0.35
464 28278 Ribosomal_L30 Ribosomal protein L30 (known as L7 in eukaryotes) is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome. In eukaryotes and archaea, L7 has an additional C-terminal extension that protrudes out from the large subunit toward the subunit interface along with subunit L12 and the 23S rRNA which together form a region referred to as the L7/L12 stalk. context 0 150.97 14.00 11.00 91.90 57.53 5.00 4.25 8.23 0.35 0.35
28278 Ribosomal_L30 Ribosomal protein L30 (known as L7 in eukaryotes) is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome. In eukaryotes and archaea, L7 has an additional C-terminal extension that protrudes out from the large subunit toward the subunit interface along with subunit L12 and the 23S rRNA which together form a region referred to as the L7/L12 stalk. context 1 111.35 12.00 9.00 81.50 64.91 4.00 1.25 10.33 0.47 0.35
465 15609 IucA_IucC IucA / IucC family. IucA and IucC catalyse discrete steps in biosynthesis of the siderophore aerobactin from N epsilon-acetyl-N epsilon-hydroxylysine and citrate. context 0 150.77 11.00 6.00 71.40 59.92 23.00 -4.24 5.17 0.49 0.22
15609 IucA_IucC IucA / IucC family. IucA and IucC catalyse discrete steps in biosynthesis of the siderophore aerobactin from N epsilon-acetyl-N epsilon-hydroxylysine and citrate. context 1 136.54 9.97 6.00 54.50 28.98 11.00 -5.90 7.90 0.39 0.27
466 2596 Peptidase_M29 Thermophilic metalloprotease (M29). context 0 150.71 3.00 3.00 151.30 232.64 145.00 -9.59 15.99 0.92 0.24
467 10320 HcaD Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only] context 0 150.60 10.91 12.00 112.30 38.35 4.00 -12.95 9.00 0.24 0.29
468 8774 SecG Preprotein translocase SecG subunit. context 0 150.50 4.00 4.00 154.50 221.43 92.00 -1.14 12.59 0.82 0.35
8774 SecG Preprotein translocase SecG subunit. context 1 126.51 4.00 4.00 150.50 196.63 47.00 0.55 14.20 0.67 0.34
469 25948 Dak2 DAK2 domain. This domain is the predicted phosphatase domain of the dihydroxyacetone kinase family. context 0 150.19 16.00 10.00 33.90 36.08 4.00 -19.04 11.93 0.48 0.43
470 15753 DUF503 Protein of unknown function (DUF503). Family of hypothetical bacterial proteins. context 0 149.97 18.00 12.00 26.40 28.01 8.00 -13.80 5.40 0.56 0.45
471 25457 Ribosomal_S14 Ribosomal protein S14p/S29e. This family includes both ribosomal S14 from prokaryotes and S29 from eukaryotes. context 0 149.77 8.00 8.00 133.20 70.15 20.00 3.20 6.42 0.37 0.31
472 10084 NrdA Ribonucleotide reductase, alpha subunit [Nucleotide transport and metabolism] context 0 149.47 20.34 16.00 34.90 22.09 4.00 1.49 5.78 0.45 0.29
473 11936 Cfa Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane] context 0 149.41 3.00 3.00 119.70 171.27 104.00 -14.92 21.90 0.92 0.24
474 28017 QPRTase Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide. QPRTase functions as a homodimer with two active sites, each formed by the C-terminal region of one subunit and the N-terminal region of the other. context 0 149.08 4.00 4.00 76.00 126.12 62.00 -17.74 20.77 0.93 0.36
475 13188 COG3874 Uncharacterized conserved protein [Function unknown] context 0 149.02 7.00 7.00 113.00 44.70 13.00 -5.56 8.24 0.24 0.38
13188 COG3874 Uncharacterized conserved protein [Function unknown] context 1 72.49 7.00 6.00 66.90 43.90 4.00 -14.58 8.87 0.34 0.42
476 13391 COG4109 Predicted transcriptional regulator containing CBS domains [Transcription] context 0 147.59 11.00 10.00 89.30 53.76 4.00 -13.95 11.24 0.26 0.28
8660 Ribonuclease_BN Ribonuclease BN-like family. This family contains integral membrane proteins with 5 to 6 predicted transmembrane spans. The family include ribonuclease BN that is involved in tRNA maturation. This family of proteins does not seem to contain any completely conserved polar residues that would be expected in a nuclease enzyme, suggesting that many members of this family may not have this catalytic activity. context 1 66.98 4.00 4.00 79.50 74.27 9.00 -13.86 14.02 0.46 0.29
9900 Map Methionine aminopeptidase [Translation, ribosomal structure and biogenesis] context 2 60.99 6.00 6.00 65.10 54.25 4.00 -4.69 13.04 0.53 0.28
477 11873 PulG Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion] context 0 147.59 13.00 9.00 60.10 30.94 6.00 -10.22 6.26 0.27 0.38
478 26068 Na_citrate Bacterial sodium:citrate symporter. The sodium:citrate symporter is found on the boundary membrane, and allows the uptake of citrate for its utilisation as a source of carbon and energy. context 0 147.50 5.00 5.00 141.50 202.77 63.00 -1.47 8.95 0.65 0.27
479 11084 MdoB Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane] context 0 147.41 19.00 11.00 27.60 30.60 4.00 -15.76 8.76 0.49 0.50
480 26368 CHAP CHAP domain. This domain corresponds to an amidase function. Many of these proteins are involved in cell wall metabolism of bacteria. This domain is found at the N-terminus of proteins, where is functions as a glutathionylspermidine amidase EC:3.5.1.78. context 0 145.91 22.76 12.00 42.80 25.24 4.00 -6.23 4.91 0.38 0.30
26368 CHAP CHAP domain. This domain corresponds to an amidase function. Many of these proteins are involved in cell wall metabolism of bacteria. This domain is found at the N-terminus of proteins, where is functions as a glutathionylspermidine amidase EC:3.5.1.78. context 1 93.80 4.00 2.00 139.50 123.44 21.00 -15.30 17.01 0.47 0.30
481 11318 PheA Chorismate mutase [Amino acid transport and metabolism] context 0 145.52 13.89 12.00 33.10 23.69 4.00 -13.37 9.20 0.35 0.35 RF00230 T-box 2
482 10081 FtsZ Cell division GTPase [Cell division and chromosome partitioning] context 0 145.26 15.99 16.00 39.10 24.89 5.00 -8.91 6.34 0.40 0.28
483 24417 Ribosomal_S8 Ribosomal protein S8. context 0 145.22 10.00 10.00 46.00 51.75 20.00 -2.46 6.16 0.59 0.34
484 11530 NagA N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism] context 0 144.87 7.00 7.00 106.10 123.54 23.00 -8.19 9.97 0.54 0.29
485 12294 COG2946 Putative phage replication protein RstA [DNA replication, recombination, and repair] context 0 144.42 6.96 4.00 177.50 88.75 8.00 -23.65 20.26 0.31 0.47
12294 COG2946 Putative phage replication protein RstA [DNA replication, recombination, and repair] context 1 64.57 5.00 3.00 120.40 64.19 4.00 -19.37 12.08 0.25 0.43
486 11915 RsbU Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription] context 0 144.37 14.00 9.00 34.20 39.51 5.00 -21.10 12.14 0.51 0.46
487 25153 DUF1034 Domain of Unknown Function (DUF1034). This family consists of several domains of unknown function which are present in several bacterial and plant peptidases. This domain is found in conjunction with pfam00082, pfam02225 and is often found with pfam00746. context 0 144.15 8.00 5.00 240.20 260.96 13.00 -17.84 16.61 0.57 0.29
25153 DUF1034 Domain of Unknown Function (DUF1034). This family consists of several domains of unknown function which are present in several bacterial and plant peptidases. This domain is found in conjunction with pfam00082, pfam02225 and is often found with pfam00746. context 1 126.88 7.00 5.00 146.90 155.35 14.00 -4.36 13.71 0.54 0.29
488 10293 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair] context 0 144.11 15.00 10.00 31.50 32.41 5.00 -13.53 9.30 0.46 0.47
489 10128 DapF Diaminopimelate epimerase [Amino acid transport and metabolism] context 0 143.11 5.00 5.00 114.80 89.06 22.00 -11.17 14.76 0.40 0.39
10128 DapF Diaminopimelate epimerase [Amino acid transport and metabolism] context 1 106.91 8.00 7.00 64.60 46.53 5.00 -13.87 12.22 0.35 0.42
490 13786 COG4642 Uncharacterized protein conserved in bacteria [Function unknown] context 0 143.01 7.00 7.00 84.30 53.91 14.00 -10.59 11.17 0.38 0.29
11545 COG1835 Predicted acyltransferases [Lipid metabolism] context 1 103.67 6.00 6.00 97.10 58.02 11.00 -6.10 8.53 0.32 0.28
491 10559 SecE Preprotein translocase subunit SecE [Intracellular trafficking and secretion] context 0 142.91 7.00 7.00 242.90 251.63 42.00 -2.59 5.63 0.57 0.38
492 13837 COG4696 Uncharacterized protein conserved in bacteria [Function unknown] context 0 142.59 8.00 8.00 57.40 60.32 19.00 -8.18 9.10 0.55 0.25
493 11917 COG2210 Uncharacterized conserved protein [Function unknown] context 0 142.28 13.00 7.00 74.10 46.32 15.00 -3.81 3.94 0.38 0.30
11917 COG2210 Uncharacterized conserved protein [Function unknown] context 1 106.13 5.00 3.00 119.70 102.33 23.00 -7.41 12.29 0.52 0.29
1754 UPF0033 Uncharacterized protein family UPF0033. context 2 93.32 5.00 4.00 99.40 64.12 14.00 -7.53 7.43 0.29 0.29
494 11758 PaaI Uncharacterized protein, possibly involved in aromatic compounds catabolism [Secondary metabolites biosynthesis, transport, and catabolism] context 0 141.73 15.94 12.00 40.50 23.28 4.00 -11.50 6.81 0.34 0.41
495 16440 AmoA Putative ammonia monooxygenase. This family are annotated by COGS as putative ammonia monooxygenase enzymes. context 0 141.31 11.00 9.00 36.90 36.74 6.00 -19.13 11.86 0.43 0.42
496 25404 ATP-synt_A ATP synthase A chain. context 0 141.23 14.00 14.00 82.90 33.55 4.00 -7.05 6.30 0.26 0.28
25404 ATP-synt_A ATP synthase A chain. context 1 124.34 12.69 12.00 52.50 24.18 6.00 -5.79 5.79 0.39 0.33
10580 AtpF F0F1-type ATP synthase, subunit b [Energy production and conversion] context 2 94.39 4.00 4.00 126.00 125.41 18.00 -8.05 17.44 0.57 0.22
10099 AtpG F0F1-type ATP synthase, gamma subunit [Energy production and conversion] context 3 86.72 6.80 7.00 54.20 29.12 4.00 -12.22 11.66 0.41 0.24
497 10011 Asd Aspartate-semialdehyde dehydrogenase [Amino acid transport and metabolism] context 0 141.10 7.00 7.00 171.70 169.05 10.00 -12.64 14.34 0.36 0.33
10011 Asd Aspartate-semialdehyde dehydrogenase [Amino acid transport and metabolism] context 1 137.97 9.00 9.00 99.20 99.87 22.00 -0.70 4.34 0.41 0.26
498 12311 COG2966 Uncharacterized conserved protein [Function unknown] context 0 141.10 4.00 4.00 93.80 104.40 50.00 -5.90 17.35 0.70 0.23
499 10431 SerB Phosphoserine phosphatase [Amino acid transport and metabolism] context 0 140.05 11.99 10.00 37.90 24.74 4.00 -10.56 12.36 0.37 0.27
500 10083 NrdF Ribonucleotide reductase, beta subunit [Nucleotide transport and metabolism] context 0 140.03 8.80 9.00 173.00 69.44 4.00 -6.58 12.68 0.22 0.36
501 17466 LacD Tagatose 1,6-diphosphate aldolase, (LacD). Tagatose 1,6-diphosphate aldolase (EC:4.1.2.40) is part of the tagatose-6-phosphate pathway of galactose-6-phosphate degradation. context 0 139.37 5.00 5.00 116.50 150.59 34.00 -9.01 10.45 0.46 0.24
11725 GalM Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism] context 1 93.56 4.00 4.00 68.30 88.90 18.00 -19.00 19.24 0.64 0.30
17466 LacD Tagatose 1,6-diphosphate aldolase, (LacD). Tagatose 1,6-diphosphate aldolase (EC:4.1.2.40) is part of the tagatose-6-phosphate pathway of galactose-6-phosphate degradation. context 2 59.77 4.00 4.00 107.80 116.86 10.00 -3.92 11.60 0.53 0.21
502 11717 SdhC Succinate dehydrogenase/fumarate reductase, cytochrome b subunit [Energy production and conversion] context 0 139.21 6.90 7.00 80.40 60.92 16.00 -9.55 10.01 0.41 0.31
503 12309 COG2964 Uncharacterized protein conserved in bacteria [Function unknown] context 0 138.95 5.00 5.00 166.30 212.65 64.00 8.43 8.06 0.67 0.21
504 11579 RbsD ABC-type ribose transport system, auxiliary component [Carbohydrate transport and metabolism] context 0 138.87 9.00 9.00 120.30 61.20 6.00 -11.77 11.52 0.30 0.28
505 26196 DFP DNA / pantothenate metabolism flavoprotein. The DNA/pantothenate metabolism flavoprotein (EC:4.1.1.36) affects synthesis of DNA, and pantothenate metabolism. context 0 138.82 3.00 3.00 113.70 176.08 105.00 -10.20 18.93 0.93 0.26
506 10501 PTC1 Serine/threonine protein phosphatase [Signal transduction mechanisms] context 0 138.32 8.00 8.00 59.00 64.99 35.00 0.03 5.69 0.67 0.27
10098 Fmt Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis] context 1 86.22 4.00 4.00 128.50 117.66 20.00 -7.30 12.88 0.56 0.31
507 25448 Bac_DNA_binding Bacterial DNA-binding protein. context 0 138.31 42.85 29.00 32.60 14.59 4.00 2.45 1.16 0.43 0.28
25448 Bac_DNA_binding Bacterial DNA-binding protein. context 1 135.96 14.93 10.00 42.50 26.51 6.00 -4.88 6.49 0.43 0.27
508 28313 EAL EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second messenger, cyclic di-GMP, and is a good candidate for a diguanylate phosphodiesterase function. Together with the GGDEF domain, EAL might be involved in regulating cell surface adhesiveness in bacteria. context 0 137.24 11.91 9.00 108.20 37.34 4.00 -5.70 7.68 0.23 0.34 RF00167 Purine 1
509 11796 SpoVG Uncharacterized protein, involved in the regulation of septum location [Cell envelope biogenesis, outer membrane] context 0 136.72 6.00 6.00 151.80 107.49 24.00 1.35 7.51 0.35 0.31
510 15551 ATP-cone ATP cone domain. context 0 136.24 10.00 8.00 114.80 58.83 6.00 -10.52 9.38 0.30 0.27
511 10446 GrpE Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones] context 0 136.02 10.00 9.00 31.80 35.18 10.00 -16.19 10.08 0.55 0.43
512 27467 DUF1483 Protein of unknown function (DUF1483). This family consists of several bacterial and phage proteins of around 410 residues in length. Bacterial members of this family seem to be found exclusively in Streptococcus species. The function of this family is unknown. context 0 135.61 4.00 4.00 125.80 178.44 48.00 -22.00 13.83 0.58 0.41
513 2301 Nucleoside_tra2 Na+ dependent nucleoside transporter. This family consists of nucleoside transport proteins. One member is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. One member is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. context 0 135.41 5.00 5.00 93.10 131.36 55.00 -8.48 10.63 0.80 0.28
514 10490 MetE Methionine synthase II (cobalamin-independent) [Amino acid transport and metabolism] context 0 135.40 5.00 5.00 78.10 80.35 24.00 0.80 13.03 0.43 0.21
10516 MetH Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism] context 1 77.38 5.00 5.00 103.90 69.61 4.00 -9.42 19.39 0.34 0.16
515 11665 URH1 Inosine-uridine nucleoside N-ribohydrolase [Nucleotide transport and metabolism] context 0 135.25 13.00 11.00 64.70 29.99 4.00 -8.56 7.40 0.28 0.30
516 10458 GpmA Phosphoglycerate mutase 1 [Carbohydrate transport and metabolism] context 0 135.12 8.00 8.00 110.30 76.77 12.00 1.38 6.08 0.26 0.30
10458 GpmA Phosphoglycerate mutase 1 [Carbohydrate transport and metabolism] context 1 56.69 4.00 4.00 95.50 112.04 4.00 -16.55 23.91 0.50 0.37
517 14522 COG5438 Predicted multitransmembrane protein [Function unknown] context 0 134.88 10.00 7.00 59.40 48.28 6.00 -21.24 13.34 0.41 0.33
518 16361 RNA_pol_delta DNA-directed RNA polymerase delta subunit. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich carboxyl-terminal region. context 0 134.55 4.00 4.00 118.00 123.01 27.00 -4.95 22.88 0.55 0.27
519 10801 COG1078 HD superfamily phosphohydrolases [General function prediction only] context 0 134.39 14.00 11.00 29.40 26.60 5.00 -11.42 7.64 0.41 0.40
520 25520 IMPDH IMP dehydrogenase / GMP reductase domain. This family is involved in biosynthesis of guanosine nucleotide. Members of this family contain a TIM barrel structure. In the inosine monophosphate dehydrogenases 2 CBS domains pfam00571 are inserted in the TIM barrel. This family is a member of the common phosphate binding site TIM barrel family. context 0 133.97 7.00 7.00 145.10 106.13 9.00 -14.00 14.73 0.37 0.25
521 14590 COG5506 Uncharacterized conserved protein [Function unknown] context 0 133.88 8.00 8.00 123.20 133.78 42.00 4.96 3.65 0.55 0.27
522 10590 GatC Asp-tRNAAsn/Glu-tRNAGln amidotransferase C subunit [Translation, ribosomal structure and biogenesis] context 0 133.51 5.00 5.00 113.70 148.31 15.00 -22.59 25.33 0.54 0.32
523 13761 CeuC ABC-type enterochelin transport system, permease component [Inorganic ion transport and metabolism] context 0 132.85 13.00 13.00 79.30 34.00 15.00 4.72 2.13 0.31 0.25
13760 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism] context 1 114.01 13.00 13.00 116.50 41.51 5.00 -1.06 3.55 0.24 0.29
524 11449 COG1738 Uncharacterized conserved protein [Function unknown] context 0 132.67 5.00 5.00 86.00 58.67 18.00 -4.01 13.54 0.35 0.36
525 7560 Bac_DnaA Bacterial dnaA protein. context 0 132.30 6.00 6.00 91.00 95.64 30.00 -2.04 9.66 0.60 0.35
526 13218 COG3906 Uncharacterized protein conserved in bacteria [Function unknown] context 0 131.98 5.00 5.00 84.40 107.62 33.00 -6.48 14.90 0.71 0.24
527 10970 TlyC Hemolysins and related proteins containing CBS domains [General function prediction only] context 0 131.70 19.00 18.00 79.00 35.53 9.00 1.58 1.99 0.38 0.27
528 11165 COG1451 Predicted metal-dependent hydrolase [General function prediction only] context 0 131.37 11.00 7.00 38.30 26.44 9.00 -9.19 7.99 0.44 0.26
529 11084 MdoB Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane] context 0 131.31 7.00 7.00 49.00 38.47 19.00 -1.88 8.98 0.49 0.22
11084 MdoB Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane] context 1 60.96 4.00 4.00 105.00 76.36 21.00 7.03 5.04 0.46 0.27
530 11224 COG1510 Predicted transcriptional regulators [Transcription] context 0 131.03 10.00 7.00 53.30 45.54 14.00 -4.80 7.91 0.59 0.17
531 11796 SpoVG Uncharacterized protein, involved in the regulation of septum location [Cell envelope biogenesis, outer membrane] context 0 130.28 11.00 10.00 61.90 33.97 5.00 -11.77 9.25 0.34 0.29
532 10948 CzcD Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism] context 0 130.23 5.00 5.00 114.50 148.35 40.00 -1.58 12.32 0.73 0.27
533 11148 COG1434 Uncharacterized conserved protein [Function unknown] context 0 129.26 10.69 7.00 56.20 27.67 6.00 -12.29 9.13 0.35 0.33
534 8742 DnaB_C DnaB-like helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerisation of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. context 0 128.78 4.00 1.00 277.50 355.81 167.00 -4.90 14.11 0.81 0.26
535 8105 Rep_2 Plasmid replication protein. This family consists of various bacterial plasmid replication (Rep) proteins. These proteins are essential for replication of plasmids, the Rep proteins are topoisomerases that nick the positive stand at the plus origin of replication and also at the single-strand conversion sequence. context 0 128.60 4.97 3.00 160.60 126.37 14.00 -11.84 16.44 0.29 0.39
536 10562 ThiJ Putative intracellular protease/amidase [General function prediction only] context 0 128.33 12.00 11.00 33.80 34.44 5.00 -17.02 10.19 0.46 0.44
537 12715 COG3383 Uncharacterized anaerobic dehydrogenase [General function prediction only] context 0 127.61 4.00 4.00 122.60 120.26 22.00 -19.16 23.38 0.51 0.32
12080 COG2427 Uncharacterized conserved protein [Function unknown] context 1 89.92 5.00 5.00 82.20 75.54 4.00 -30.56 25.41 0.33 0.40
538 13897 COG4758 Predicted membrane protein [Function unknown] context 0 127.55 9.00 9.00 40.50 33.64 11.00 -10.16 8.07 0.45 0.37
539 3189 AHS1 Allophanate hydrolase subunit 1. This family is the first subunit of allophanate hydrolase. context 0 127.12 5.00 5.00 171.30 102.28 14.00 -12.10 12.29 0.27 0.34
540 27837 PsaA Metal binding protein PsaA. These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence). context 0 126.51 6.00 6.00 136.20 122.00 18.00 -2.00 11.48 0.47 0.22
541 10427 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair] context 0 126.30 14.71 15.00 76.70 24.76 4.00 -1.86 4.22 0.25 0.33
542 27761 HTH_MERR_2 Helix-turn-helix MERR transcription regulator, subgroup 2. Based on sequence similarity, these proteins were predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MERR suoerfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MERR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH (helix-turn-helix) motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. context 0 126.24 5.00 5.00 132.00 155.59 40.00 -0.55 9.99 0.63 0.35
27761 HTH_MERR_2 Helix-turn-helix MERR transcription regulator, subgroup 2. Based on sequence similarity, these proteins were predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MERR suoerfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MERR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH (helix-turn-helix) motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. context 1 81.95 6.00 6.00 99.10 120.57 12.00 -1.50 7.34 0.48 0.37
543 23941 Transposase_34 IS66 Orf2 like protein. This protein is found in insertion sequences related to IS66. The function of these proteins is uncertain, but they are probably essential for transposition. context 0 126.03 11.00 3.00 116.00 126.53 39.00 -3.10 5.28 0.62 0.35
544 10444 PpsA Phosphoenolpyruvate synthase/pyruvate phosphate dikinase [Carbohydrate transport and metabolism] context 0 125.98 12.00 7.00 73.40 49.75 5.00 -12.64 9.73 0.37 0.41
545 11890 MalE Maltose-binding periplasmic proteins/domains [Carbohydrate transport and metabolism] context 0 125.85 13.00 13.00 188.60 85.08 17.00 4.78 1.58 0.29 0.29
13151 MalG ABC-type maltose transport systems, permease component [Carbohydrate transport and metabolism] context 1 120.72 5.00 5.00 151.80 135.59 34.00 -3.20 7.67 0.45 0.25
11890 MalE Maltose-binding periplasmic proteins/domains [Carbohydrate transport and metabolism] context 2 114.56 9.88 10.00 64.20 47.59 18.00 -0.73 3.75 0.52 0.27
11890 MalE Maltose-binding periplasmic proteins/domains [Carbohydrate transport and metabolism] context 3 89.62 14.00 14.00 147.90 72.89 4.00 0.36 3.22 0.33 0.28
11583 LacA Beta-galactosidase [Carbohydrate transport and metabolism] context 4 68.72 5.00 4.00 50.30 38.63 9.00 -3.02 7.72 0.36 0.33
546 12259 COG2910 Putative NADH-flavin reductase [General function prediction only] context 0 125.72 13.00 9.00 34.00 24.69 13.00 -2.27 4.03 0.51 0.26
547 11665 URH1 Inosine-uridine nucleoside N-ribohydrolase [Nucleotide transport and metabolism] context 0 125.63 7.00 7.00 98.50 82.16 34.00 -2.79 4.05 0.43 0.37
548 26027 HGTP_anticodon Anticodon binding domain. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases; it is probably the anticodon binding domain. context 0 125.63 12.81 12.00 34.60 22.45 4.00 -9.55 7.83 0.35 0.31
549 11060 FlgL Flagellin and related hook-associated proteins [Cell motility and secretion] context 0 125.23 5.00 5.00 176.10 103.39 34.00 5.12 6.42 0.35 0.34
550 11524 COG1814 Uncharacterized membrane protein [Function unknown] context 0 125.09 5.89 6.00 77.60 51.70 12.00 -23.87 14.25 0.40 0.29
551 13438 COG4172 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only] context 0 125.08 8.00 6.00 93.70 51.67 8.00 -1.93 8.63 0.27 0.32 RF00230 T-box 2
552 27577 Glyco_hydro_88 Glycosyl Hydrolase Family 88. Unsaturated glucuronyl hydrolase catalyses the hydrolytic release of unsaturated glucuronic acids from oligosaccharides (EC:3.2.1.-) produced by the reactions of polysaccharide lyases. context 0 125.00 5.00 5.00 212.40 149.43 43.00 3.02 4.63 0.32 0.24
27577 Glyco_hydro_88 Glycosyl Hydrolase Family 88. Unsaturated glucuronyl hydrolase catalyses the hydrolytic release of unsaturated glucuronic acids from oligosaccharides (EC:3.2.1.-) produced by the reactions of polysaccharide lyases. context 1 124.80 6.00 6.00 166.60 114.22 17.00 1.52 8.30 0.33 0.25
27577 Glyco_hydro_88 Glycosyl Hydrolase Family 88. Unsaturated glucuronyl hydrolase catalyses the hydrolytic release of unsaturated glucuronic acids from oligosaccharides (EC:3.2.1.-) produced by the reactions of polysaccharide lyases. context 2 88.50 9.00 8.00 118.30 53.59 4.00 -5.25 6.53 0.28 0.28
553 10608 ClpP Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion] context 0 124.86 8.97 9.00 62.50 55.99 26.00 -0.37 3.82 0.52 0.26
554 17788 Bacterial_PFK Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include bacterial ATP-dependent phosphofructokinases. These are allosrterically regulated homotetramers; the subunits are of about 320 amino acids. context 0 124.64 7.00 7.00 44.70 41.34 24.00 -4.03 7.86 0.60 0.24
555 8034 PTA_PTB Phosphate acetyl/butaryl transferase. This family contains both phosphate acetyltransferase and phosphate butaryltransferase. These enzymes catalyse the transfer of an acetyl or butaryl group to orthophosphate. context 0 124.33 5.00 5.00 152.90 69.40 14.00 0.93 10.45 0.24 0.23
556 12603 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion] context 0 124.33 7.00 1.00 209.60 237.39 90.00 -9.65 12.44 0.63 0.46
557 10002 COG0127 Xanthosine triphosphate pyrophosphatase [Nucleotide transport and metabolism] context 0 123.94 7.00 7.00 72.80 58.68 9.00 -7.66 13.29 0.39 0.38
2337 DUF37 Domain of unknown function DUF37. This domain is found in short (70 amino acid) hypothetical proteins from various bacteria. The domain contains three conserved cysteine residues. A member from Aeromonas hydrophila has been found to have hemolytic activity (unpublished). context 1 81.23 4.00 4.00 140.50 116.81 18.00 -5.84 11.33 0.50 0.33
10558 Rph RNase PH [Translation, ribosomal structure and biogenesis] context 2 50.32 5.00 5.00 73.00 59.86 4.00 -11.38 10.61 0.44 0.41
558 14752 Sortase Sortase domain; transpeptidase of Gram-positive bacteria, cleaves surface proteins at the LPXTG motif between Thr and Gly and catalyzes the formation of an amide bond between the carboxyl group of Thr and the amino group of cell-wall crossbridges. In two different classes of sortases the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. context 0 123.87 11.99 10.00 52.90 27.43 4.00 -9.46 11.76 0.45 0.26
559 9882 PepP Xaa-Pro aminopeptidase [Amino acid transport and metabolism] context 0 123.85 9.93 10.00 85.70 73.15 6.00 -6.49 7.67 0.31 0.29
9882 PepP Xaa-Pro aminopeptidase [Amino acid transport and metabolism] context 1 109.07 11.82 12.00 32.30 22.06 10.00 -1.53 4.05 0.50 0.32
9882 PepP Xaa-Pro aminopeptidase [Amino acid transport and metabolism] context 2 107.39 12.00 12.00 66.70 46.78 12.00 -0.35 2.56 0.39 0.26
9882 PepP Xaa-Pro aminopeptidase [Amino acid transport and metabolism] context 3 97.05 7.00 7.00 93.00 82.29 15.00 5.88 6.07 0.48 0.25
560 10861 Fer Ferredoxin [Energy production and conversion] context 0 123.84 9.00 7.00 53.80 31.21 8.00 -7.52 9.75 0.40 0.30
561 28024 MTHFR Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase to convert homocysteine to methionine. The enzymatic mechanism is a ping-pong bi-bi mechanism, in which NAD(P)+ release precedes the binding of methylenetetrahydrofolate and the acceptor is free FAD. The family includes the 5,10-methylenetetrahydrofolate reductase EC:1.7.99.5 from prokaryotes and methylenetetrahydrofolate reductase EC: 1.5.1.20 from eukaryotes. The bacterial enzyme is a homotetramer and NADH is the preferred reductant while the eukaryotic enzyme is a homodimer and NADPH is the preferred reductant. In humans, there are several clinically significant mutations in MTHFR that result in hyperhomocysteinemia, which is a risk factor for the development of cardiovascular disease. context 0 123.44 13.68 14.00 34.90 25.04 4.00 -8.37 8.33 0.45 0.31 RF00230 T-box 1
562 14473 COG5386 Cell surface protein [Cell envelope biogenesis, outer membrane] context 0 123.15 8.00 6.00 101.40 55.14 17.00 0.69 5.17 0.35 0.23
563 13863 COG4722 Phage-related protein [Function unknown] context 0 123.08 15.85 8.00 39.10 26.39 4.00 -10.89 8.06 0.41 0.36
564 11473 PtsN Phosphotransferase system mannitol/fructose-specific IIA domain (Ntr-type) [Carbohydrate transport and metabolism / Signal transduction mechanisms] context 0 122.55 49.23 25.00 73.60 23.49 0.00 -11.63 9.64 0.23 0.31
9413 PTS_IIB_fruc PTS system, Fructose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The sugar-specific permease of the PTS consists of three domains (IIA, IIB and IIC). IIB is is phosphorylated by phospho-IIA, before the phosphoryl group is transferred to the sugar substrate. context 1 62.66 26.92 24.00 49.80 22.01 0.00 -8.76 8.70 0.34 0.33
565 11270 COG1556 Uncharacterized conserved protein [Function unknown] context 0 122.31 7.00 7.00 88.50 55.77 17.00 0.60 7.10 0.40 0.31
10859 COG1139 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion] context 1 96.44 6.00 6.00 142.40 81.49 13.00 2.86 6.85 0.35 0.32
10122 GlpC Fe-S oxidoreductase [Energy production and conversion] context 2 86.61 9.00 8.00 37.60 28.99 12.00 -0.61 3.46 0.45 0.34
566 12904 PepC Aminopeptidase C [Amino acid transport and metabolism] context 0 122.30 5.00 5.00 80.50 114.94 26.00 -9.30 15.30 0.67 0.24
567 11008 BetT Choline-glycine betaine transporter [Cell envelope biogenesis, outer membrane] context 0 122.24 5.00 4.00 127.20 91.59 38.00 1.98 7.19 0.44 0.22
568 11260 CinA Uncharacterized protein (competence- and mitomycin-induced) [General function prediction only] context 0 122.17 10.91 8.00 90.30 37.74 5.00 2.11 6.45 0.25 0.33
11260 CinA Uncharacterized protein (competence- and mitomycin-induced) [General function prediction only] context 1 96.56 7.53 7.00 36.10 19.11 4.00 -15.44 12.34 0.35 0.31
569 11455 Med Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only] context 0 121.79 4.00 4.00 117.10 133.35 36.00 -11.71 13.83 0.54 0.35
570 10745 Hmp Hemoglobin-like flavoprotein [Energy production and conversion] context 0 121.78 7.00 7.00 39.20 32.85 17.00 -4.66 10.03 0.57 0.24
571 11909 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms] context 0 121.23 11.97 6.00 126.40 40.85 4.00 -9.35 7.12 0.21 0.33
572 11650 COG1942 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only] context 0 121.19 4.00 4.00 91.00 92.47 58.00 -10.69 10.41 0.66 0.23
573 10843 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism] context 0 120.81 23.82 16.00 29.90 20.49 4.00 -2.18 3.23 0.47 0.30
4391 ABC-3 ABC 3 transport family. context 1 57.73 8.00 7.00 37.90 35.13 4.00 -4.70 5.42 0.43 0.41
574 10066 Fba Fructose/tagatose bisphosphate aldolase [Carbohydrate transport and metabolism] context 0 120.77 9.00 9.00 80.50 71.24 22.00 -1.75 4.38 0.54 0.34
575 12902 COG3576 Predicted flavin-nucleotide-binding protein structurally related to pyridoxine 5'-phosphate oxidase [General function prediction only] context 0 120.72 5.00 5.00 72.70 99.87 51.00 -10.15 9.45 0.83 0.29
576 10244 FeoB Fe2+ transport system protein B [Inorganic ion transport and metabolism] context 0 120.48 6.00 6.00 159.10 96.77 11.00 -1.18 11.52 0.32 0.26
577 23505 Gln-synt_N Glutamine synthetase, beta-Grasp domain. context 0 119.84 13.98 12.00 32.20 25.72 6.00 -7.93 6.40 0.53 0.30
578 10906 COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis] context 0 119.47 4.22 5.00 60.90 42.50 12.00 -17.10 13.57 0.29 0.39
579 11269 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair] context 0 119.38 10.00 10.00 100.10 44.39 4.00 -6.19 10.18 0.30 0.27
580 10040 ArgH Argininosuccinate lyase [Amino acid transport and metabolism] context 0 119.25 11.45 12.00 33.20 20.69 4.00 -14.21 8.70 0.37 0.37
10012 ArgG Argininosuccinate synthase [Amino acid transport and metabolism] context 1 110.26 12.59 13.00 35.10 18.53 4.00 -3.04 6.68 0.39 0.30
581 13390 PrfC Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis] context 0 118.65 6.00 6.00 104.10 74.52 11.00 -5.82 12.22 0.35 0.32
13390 PrfC Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis] context 1 59.54 4.00 4.00 86.50 60.27 11.00 -14.20 8.11 0.41 0.33
582 25982 Lyase_8_C Polysaccharide lyase family 8, C-terminal beta-sandwich domain. This family consists of a group of secreted bacterial lyase enzymes EC:4.2.2.1 capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen. context 0 118.54 5.00 5.00 178.80 193.02 13.00 -9.76 23.42 0.55 0.28
23324 Lyase_8 Polysaccharide lyase family 8, super-sandwich domain. This family consists of a group of secreted bacterial lyase enzymes EC:4.2.2.1 capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen. context 1 89.00 5.00 5.00 128.60 148.17 12.00 -0.34 16.10 0.62 0.25
23324 Lyase_8 Polysaccharide lyase family 8, super-sandwich domain. This family consists of a group of secreted bacterial lyase enzymes EC:4.2.2.1 capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen. context 2 62.19 4.00 4.00 85.50 95.63 9.00 -8.40 15.24 0.58 0.28
23324 Lyase_8 Polysaccharide lyase family 8, super-sandwich domain. This family consists of a group of secreted bacterial lyase enzymes EC:4.2.2.1 capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen. context 3 53.89 4.00 4.00 132.50 118.68 4.00 -11.40 21.61 0.50 0.27
583 1464 Ammonium_transp Ammonium Transporter Family. context 0 118.39 7.47 7.00 31.60 15.99 9.00 -13.87 8.47 0.35 0.32
584 10967 FadB 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism] context 0 117.87 10.00 7.00 45.40 39.31 15.00 -1.34 5.27 0.52 0.32
27636 VLCAD Very long chain acyl-CoA dehydrogenase (VLCAD). VLCAD acyl-CoA dehydrogenases (ACAD), which is found in the mitochondria of eukaryotes and in some bacteria. It catalyzes the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. VLCAD, which is a homodimer. context 1 96.61 6.96 6.00 45.70 37.83 11.00 -7.74 7.82 0.45 0.39
7739 3HCDH 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain. This family also includes lambda crystallin. Some proteins include two copies of this domain. context 2 85.55 4.00 4.00 104.70 79.88 21.00 -5.58 10.14 0.47 0.28
27636 VLCAD Very long chain acyl-CoA dehydrogenase (VLCAD). VLCAD acyl-CoA dehydrogenases (ACAD), which is found in the mitochondria of eukaryotes and in some bacteria. It catalyzes the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. VLCAD, which is a homodimer. context 3 58.56 6.92 6.00 34.00 23.95 5.00 -3.13 6.05 0.44 0.40
585 4290 Voltage_CLC Voltage gated chloride channel. This family of ion channels contains 10 or 12 transmembrane helices. Each protein forms a single pore. It has been shown that some members of this family form homodimers. These proteins contain two pfam00571 domains. context 0 117.53 4.00 4.00 260.50 320.31 12.00 -26.69 33.26 0.47 0.38
586 26076 Relaxase Relaxase/Mobilisation nuclease domain. Relaxases/mobilisation proteins are required for the horizontal transfer of genetic information contained on plasmids that occurs during bacterial conjugation. The relaxase, in conjunction with several auxiliary proteins, forms the relaxation complex or relaxosome. Relaxases nick duplex DNA in a specific manner by catalysing trans-esterification. context 0 117.40 4.00 4.00 113.60 131.27 16.00 -39.23 27.12 0.51 0.44
587 10945 PPX1 Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion] context 0 117.32 10.00 10.00 137.10 51.35 6.00 3.42 5.55 0.25 0.27
588 10749 EntE Peptide arylation enzymes [Secondary metabolites biosynthesis, transport, and catabolism] context 0 116.87 5.00 5.00 71.00 44.43 22.00 -5.50 11.32 0.46 0.25
10749 EntE Peptide arylation enzymes [Secondary metabolites biosynthesis, transport, and catabolism] context 1 76.27 3.00 3.00 162.70 105.18 18.00 -1.74 13.14 0.37 0.29
12764 COG3433 Aryl carrier domain [Secondary metabolites biosynthesis, transport, and catabolism] context 2 72.50 4.00 4.00 88.00 65.24 20.00 4.28 7.97 0.49 0.26
589 10479 FepD ABC-type Fe3+-siderophore transport system, permease component [Inorganic ion transport and metabolism] context 0 116.11 6.00 3.00 81.60 44.14 13.00 -11.64 13.46 0.34 0.30
590 27942 vWA_ywmD_type VWA ywmD type:Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains. Not much is known about the function of the members of this subgroup. All members of this subgroup however have a conserved MIDAS motif. context 0 116.10 4.00 2.00 283.80 158.69 24.00 0.23 13.60 0.28 0.39
591 13634 LcnDR2 Lantibiotic modifying enzyme [Defense mechanisms] context 0 116.00 4.00 4.00 137.70 166.66 21.00 -15.38 20.63 0.52 0.27
592 25324 HTH_LUXR helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon context 0 115.81 6.00 1.00 114.90 135.30 67.00 -8.02 16.39 0.64 0.27
25324 HTH_LUXR helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon context 1 87.35 6.00 3.00 50.20 46.83 14.00 -1.50 9.58 0.46 0.26
593 10031 BioF 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism] context 0 115.74 12.00 10.00 38.60 25.75 8.00 -2.92 5.96 0.51 0.21
594 12756 PksG 3-hydroxy-3-methylglutaryl CoA synthase [Lipid metabolism] context 0 115.68 8.00 8.00 64.30 48.09 10.00 -5.04 8.61 0.42 0.29
595 12152 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism] context 0 115.56 12.00 9.00 108.70 46.23 6.00 -5.23 4.33 0.27 0.40
596 24157 Sialidase Sialidases or neuraminidases function to bind and hydrolyze terminal sialic acid residues from various glycoconjugates as well as playing roles in pathogenesis, bacterial nutrition and cellular interactions. They have a six-bladed, beta-propeller fold with the non-viral sialidases containing 2-5 Asp-box motifs (most commonly Ser/Thr-X-Asp-[X]-Gly-X-Thr- Trp/Phe). This CD includes eubacterial, eukaryotic, and viral sialidases. context 0 115.43 4.00 4.00 108.30 121.10 23.00 -6.98 16.87 0.47 0.26
597 13998 COG4864 Uncharacterized protein conserved in bacteria [Function unknown] context 0 115.06 7.00 7.00 138.90 62.91 5.00 -12.15 12.47 0.24 0.29
13998 COG4864 Uncharacterized protein conserved in bacteria [Function unknown] context 1 113.76 3.00 3.00 212.10 196.66 55.00 -15.37 10.16 0.39 0.26
13998 COG4864 Uncharacterized protein conserved in bacteria [Function unknown] context 2 62.48 4.00 4.00 119.70 51.22 4.00 -10.83 13.36 0.23 0.29
598 12125 CopZ Copper chaperone [Inorganic ion transport and metabolism] context 0 114.96 12.00 10.00 80.50 39.79 18.00 -1.84 1.87 0.36 0.34
599 27811 DnaB_C DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. context 0 114.78 9.00 1.00 198.10 218.54 72.00 -2.77 11.96 0.67 0.25
27811 DnaB_C DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. context 1 64.63 4.00 1.00 83.20 107.20 39.00 -10.25 14.22 0.76 0.29
600 11258 COG1544 Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis] context 0 114.75 10.00 10.00 51.60 46.00 20.00 1.32 3.52 0.54 0.31
601 11142 COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism] context 0 114.68 13.82 10.00 38.20 22.04 5.00 -6.43 6.23 0.44 0.25
11142 COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism] context 1 94.88 10.68 7.00 50.30 33.60 4.00 -3.88 9.13 0.44 0.23
602 28126 DHQase_I Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase.) Catalyzes the cis-dehydration of 3-dehydroquinate via a covalent imine intermediate to produce dehydroshikimate. Dehydroquinase is the third enzyme in the shikimate pathway, which is involved in the biosynthesis of aromatic amino acids. Type I DHQase exists as a homodimer. Type II 3-dehydroquinase also catalyzes the same overall reaction, but is unrelated in terms of sequence and structure, and utilizes a completely different reaction mechanism. context 0 114.61 5.00 5.00 123.30 147.06 65.00 1.21 5.56 0.69 0.23
603 26065 DUF285 Mycoplasma protein of unknown function, DUF285. context 0 114.06 7.00 1.00 124.20 157.52 57.00 -5.94 16.25 0.62 0.18
604 1464 Ammonium_transp Ammonium Transporter Family. context 0 113.68 12.00 12.00 45.20 29.87 6.00 -3.81 5.79 0.40 0.31
605 11962 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair] context 0 113.68 10.00 9.00 62.90 30.99 4.00 -12.06 10.57 0.34 0.29
606 12895 ElsH Metal-dependent hydrolase [General function prediction only] context 0 113.57 10.00 9.00 121.70 78.63 11.00 -0.16 3.84 0.33 0.28
607 25583 Flagellin_N Bacterial flagellin N-terminus. Flagellins polymerise to form bacterial flagella. This family includes flagellins and hook associated protein 3. context 0 113.43 6.00 6.00 76.90 67.30 11.00 -6.68 10.85 0.34 0.39
25583 Flagellin_N Bacterial flagellin N-terminus. Flagellins polymerise to form bacterial flagella. This family includes flagellins and hook associated protein 3. context 1 95.95 5.00 5.00 85.20 66.63 18.00 -11.76 8.70 0.43 0.41
608 10948 CzcD Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism] context 0 113.42 12.81 11.00 31.10 22.26 7.00 -2.87 4.12 0.38 0.37
609 10024 TpiA Triosephosphate isomerase [Carbohydrate transport and metabolism] context 0 113.31 5.00 5.00 98.10 76.95 13.00 -13.26 12.06 0.31 0.33
610 15690 DUF534 Protein of unknown function (DUF534). Putative secreted protein of unknown function. context 0 113.25 7.00 7.00 74.40 76.62 5.00 -26.67 26.68 0.53 0.38 RF00230 T-box 2
15690 DUF534 Protein of unknown function (DUF534). Putative secreted protein of unknown function. context 1 86.87 7.00 7.00 120.80 122.43 4.00 -18.26 17.60 0.48 0.32 RF00230 T-box 2
611 26805 Sm_multidrug_ex Putative small multi-drug export protein. This family contains a small number of putative small multi-drug export proteins. context 0 112.55 4.00 4.00 130.70 154.61 42.00 -7.18 12.57 0.67 0.28
26805 Sm_multidrug_ex Putative small multi-drug export protein. This family contains a small number of putative small multi-drug export proteins. context 1 108.82 3.69 4.00 142.90 138.11 49.00 -4.44 10.53 0.70 0.26
26805 Sm_multidrug_ex Putative small multi-drug export protein. This family contains a small number of putative small multi-drug export proteins. context 2 81.72 4.00 4.00 104.10 118.32 35.00 -1.65 7.47 0.63 0.28
612 10968 NirB NAD(P)H-nitrite reductase [Energy production and conversion] context 0 112.35 8.00 8.00 125.20 57.73 4.00 -14.54 11.74 0.25 0.33 RF00162 S_box 1
613 10854 TagH ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane] context 0 112.32 41.96 27.00 57.80 23.10 0.00 -8.79 9.99 0.24 0.36
11393 TagG ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane] context 1 72.69 5.00 5.00 66.20 36.99 5.00 -13.84 13.82 0.34 0.30
614 27838 FeuA Periplasmic binding protein FeuA. These proteins have predicted to function as initial receptors in ABC transport of metal ions in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains. context 0 112.24 32.00 15.00 103.30 31.82 7.00 1.13 0.73 0.29 0.27
615 12955 COG3631 Ketosteroid isomerase-related protein [General function prediction only] context 0 112.19 5.00 3.00 77.60 61.61 17.00 -16.73 14.96 0.42 0.36
616 25724 Chorismate_synt Chorismate synthase. context 0 112.04 14.43 14.00 36.30 18.07 5.00 -1.76 3.88 0.36 0.44 RF00230 T-box 1
617 10324 AhpC Peroxiredoxin [Posttranslational modification, protein turnover, chaperones] context 0 112.01 11.00 11.00 81.70 40.31 4.00 -2.92 7.16 0.29 0.24
618 10913 RecF Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair] context 0 111.96 5.00 5.00 118.00 153.56 34.00 -0.72 8.65 0.59 0.25
619 11789 COG2081 Predicted flavoproteins [General function prediction only] context 0 111.37 9.00 9.00 82.30 51.22 23.00 2.72 2.31 0.35 0.31
620 12012 MazE Growth regulator [Signal transduction mechanisms] context 0 111.11 6.00 5.00 159.80 93.03 13.00 -2.71 6.69 0.25 0.31
12012 MazE Growth regulator [Signal transduction mechanisms] context 1 106.48 4.00 3.00 232.10 126.34 9.00 -12.68 15.69 0.19 0.31
621 12989 COG3666 Transposase and inactivated derivatives [DNA replication, recombination, and repair] context 0 111.08 28.00 3.00 42.40 39.53 17.00 -4.22 4.65 0.61 0.37
622 25050 DUF988 Protein of unknown function (DUF988). This family consists of several hypothetical bacterial proteins of unknown function. context 0 110.89 9.00 9.00 53.40 41.48 9.00 -4.18 6.93 0.42 0.38
25050 DUF988 Protein of unknown function (DUF988). This family consists of several hypothetical bacterial proteins of unknown function. context 1 100.53 8.00 8.00 69.50 55.99 19.00 -0.53 4.03 0.49 0.38
623 8772 RecU Recombination protein U. context 0 110.70 7.00 7.00 72.00 64.97 35.00 0.49 4.05 0.57 0.26
624 8104 Methionine_synt Methionine synthase, vitamin-B12 independent. This is a family of vitamin-B12 independent methionine synthases or 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferases, EC:2.1.1.14 from bacteria and plants. Plants are the only higher eukaryotes that have the required enzymes for methionine synthesis. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to homocysteine. The aligned region makes up the carboxy region of the approximately 750 amino acid protein except in some hypothetical archaeal proteins present in the family, where this region corresponds to the entire length. context 0 110.12 4.00 4.00 125.20 149.53 13.00 -30.80 26.41 0.46 0.36
625 13095 GatC Phosphotransferase system, galactitol-specific IIC component [Carbohydrate transport and metabolism] context 0 110.01 8.00 4.00 66.30 46.58 9.00 -14.74 13.48 0.47 0.28
13095 GatC Phosphotransferase system, galactitol-specific IIC component [Carbohydrate transport and metabolism] context 1 78.92 4.00 3.00 67.00 75.92 12.00 -15.85 19.50 0.57 0.29
626 11879 DapD Tetrahydrodipicolinate N-succinyltransferase [Amino acid transport and metabolism] context 0 109.43 10.00 10.00 51.30 31.77 4.00 -11.85 9.98 0.35 0.35 RF00168 Lysine 2
627 22916 Gln-synt_C Glutamine synthetase, catalytic domain. context 0 108.72 20.83 20.00 27.30 20.80 4.00 0.92 3.39 0.53 0.23
628 28171 TatD_DNAse TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity. context 0 108.60 7.97 5.00 45.70 28.37 6.00 -13.76 9.86 0.28 0.43 RF00230 T-box 1
629 15353 UPF0051 Uncharacterized protein family (UPF0051). context 0 108.44 17.96 15.00 30.80 20.10 7.00 1.80 2.70 0.52 0.24
630 26240 PAD_porph Porphyromonas-type peptidyl-arginine deiminase. Peptidyl-arginine deiminase (PAD) enzymes catalyse the deimination of the guanidino group from carboxy-terminal arginine residues of various peptides to produce ammonia. PAD from Porphyromonas gingivalis (PPAD) appears to be evolutionarily unrelated to mammalian PAD (pfam03068), which is a metalloenzyme. PPAD is thought to belong to the same superfamily as aminotransferase and arginine deiminase, and to form an alpha/beta propeller structure. This family has previously been named PPADH (Porphyromonas peptidyl-arginine deiminase homologues). The predicted catalytic residues in PPAD are Asp130, Asp187, His236, Asp238 and Cys351. These are absolutely conserved with the exception of Asp187 which is absent in two family members. PPAD is also able to catalyse the deimination of free L-arginine, but has primarily peptidyl-arginine specificity. It may have a FMN cofactor. context 0 107.91 8.00 5.00 83.60 36.55 4.00 -18.44 12.83 0.25 0.36
631 12779 VirB4 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion] context 0 107.80 12.99 8.00 76.80 34.77 4.00 -5.36 5.29 0.27 0.31
12779 VirB4 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion] context 1 98.64 8.00 4.00 97.30 46.82 8.00 -0.34 5.95 0.23 0.32
12779 VirB4 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion] context 2 87.52 14.00 6.00 42.60 27.01 4.00 -7.30 5.79 0.39 0.33
632 11323 COG1610 Uncharacterized conserved protein [Function unknown] context 0 107.09 9.97 10.00 100.00 52.23 13.00 7.64 2.78 0.32 0.37
633 28241 KdgK 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the glycolysis and therefore use polymers, like pectin and xylan as carbon sources. context 0 107.08 10.62 11.00 63.40 29.12 11.00 7.02 3.30 0.39 0.22
634 12586 LacZ Beta-galactosidase/beta-glucuronidase [Carbohydrate transport and metabolism] context 0 107.00 9.00 6.00 66.00 49.13 7.00 -12.88 8.72 0.39 0.30
635 12353 COG3011 Uncharacterized protein conserved in bacteria [Function unknown] context 0 106.82 7.00 7.00 115.10 50.02 6.00 -9.14 9.39 0.25 0.26
636 12403 TolA Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane] context 0 106.59 6.00 1.00 129.00 204.35 56.00 -20.61 16.34 0.63 0.35
637 10272 COG0398 Uncharacterized conserved protein [Function unknown] context 0 106.50 8.98 9.00 40.20 33.89 7.00 -10.65 7.78 0.40 0.47 RF00023 tmRNA 6
638 11168 EutG Alcohol dehydrogenase, class IV [Energy production and conversion] context 0 106.49 22.52 20.00 35.30 22.88 6.00 0.94 1.57 0.48 0.20
639 9905 NadB Aspartate oxidase [Coenzyme metabolism] context 0 106.46 8.00 7.00 44.00 48.87 15.00 -0.62 7.58 0.64 0.36
8307 NadA Quinolinate synthetase A protein. Quinolinate synthetase catalyses the second step of the de novo biosynthetic pathway of pyridine nucleotide formation. In particular, quinolinate synthetase is involved in the condensation of dihydroxyacetone phosphate and iminoaspartate to form quinolinic acid. This synthesis requires two enzymes, a FAD-containing "B protein" and an "A protein". context 1 68.05 8.98 9.00 56.70 35.14 4.00 -0.54 5.99 0.44 0.24
640 10441 Rnc dsRNA-specific ribonuclease [Transcription] context 0 106.21 35.96 32.00 86.30 26.73 0.00 -13.14 10.58 0.24 0.33
10441 Rnc dsRNA-specific ribonuclease [Transcription] context 1 81.15 7.00 7.00 125.30 81.37 4.00 -8.05 10.24 0.32 0.47
641 10912 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair] context 0 106.12 5.00 5.00 101.70 122.46 38.00 -0.39 8.49 0.72 0.30
642 12793 COG3465 Uncharacterized conserved protein [Function unknown] context 0 106.05 7.00 6.00 110.70 71.92 12.00 -8.89 7.69 0.40 0.40
643 13083 COG3763 Uncharacterized protein conserved in bacteria [Function unknown] context 0 106.04 5.00 5.00 62.50 82.72 36.00 -2.96 9.94 0.80 0.26
644 11605 COG1896 Predicted hydrolases of HD superfamily [General function prediction only] context 0 105.84 8.00 8.00 56.80 33.32 4.00 -15.81 12.92 0.31 0.36
645 11655 IspE 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate synthase [Lipid metabolism] context 0 105.81 9.92 10.00 51.80 33.57 4.00 -9.99 9.33 0.35 0.41
646 9952 PheA Prephenate dehydratase [Amino acid transport and metabolism] context 0 105.67 66.00 25.00 31.70 25.98 0.00 -18.33 8.05 0.35 0.44
647 10451 PstA ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism] context 0 105.34 37.98 29.00 63.90 24.17 0.00 -13.33 10.63 0.26 0.36
648 11436 COG1725 Predicted transcriptional regulators [Transcription] context 0 105.30 17.00 16.00 54.90 36.33 4.00 -4.20 4.40 0.48 0.25
649 12650 COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair] context 0 105.08 7.00 1.00 128.50 234.89 124.00 6.91 10.04 0.98 0.39
12650 COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair] context 1 81.74 11.00 2.00 126.20 166.20 10.00 -2.34 12.76 0.57 0.43
650 11075 COG1359 Uncharacterized conserved protein [Function unknown] context 0 104.66 8.00 8.00 95.80 42.70 6.00 -6.54 7.73 0.28 0.31
651 13580 COG4333 Uncharacterized protein conserved in bacteria [Function unknown] context 0 104.66 5.90 4.00 110.10 73.09 12.00 1.22 9.09 0.32 0.31
652 26139 MinC_C Septum formation inhibitor MinC, C-terminal domain. In Escherichia coli ftsZ assembles into a Z ring at midcell while assembly at polar sites is prevented by the min system. MinC, a component of this system, is an inhibitor of FtsZ assembly that is positioned within the cell by interaction with MinDE. MinC is an oligomer, probably a dimer. The C terminal half of MinC is the most conserved and interacts with MinD. The N terminal half is thought interact with FtsZ. context 0 104.54 11.00 8.00 86.20 35.26 7.00 -5.24 3.82 0.28 0.30
653 9897 TktA Transketolase [Carbohydrate transport and metabolism] context 0 104.27 8.39 7.00 53.70 24.70 5.00 -9.09 10.90 0.40 0.28
654 8034 PTA_PTB Phosphate acetyl/butaryl transferase. This family contains both phosphate acetyltransferase and phosphate butaryltransferase. These enzymes catalyse the transfer of an acetyl or butaryl group to orthophosphate. context 0 104.17 9.77 8.00 49.90 24.54 5.00 -9.48 7.41 0.34 0.32
655 14606 COG5522 Predicted integral membrane protein [Function unknown] context 0 104.06 7.00 7.00 69.80 47.79 11.00 -1.31 7.30 0.37 0.31
656 11020 LldD L-lactate dehydrogenase (FMN-dependent) and related alpha-hydroxy acid dehydrogenases [Energy production and conversion] context 0 104.00 9.84 10.00 53.10 49.20 8.00 -3.51 4.88 0.37 0.26
657 7555 CAT Chloramphenicol acetyltransferase. context 0 103.39 3.00 3.00 149.00 127.87 16.00 -15.96 20.53 0.28 0.33
658 9413 PTS_IIB_fruc PTS system, Fructose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The sugar-specific permease of the PTS consists of three domains (IIA, IIB and IIC). IIB is is phosphorylated by phospho-IIA, before the phosphoryl group is transferred to the sugar substrate. context 0 103.24 10.35 11.00 44.40 24.79 4.00 -5.45 7.10 0.40 0.34
659 11864 KdpC K+-transporting ATPase, c chain [Inorganic ion transport and metabolism] context 0 103.04 3.00 2.00 195.00 223.51 78.00 -8.34 12.20 0.71 0.27
7232 KdpA Potassium-transporting ATPase A subunit. context 1 68.93 3.90 3.00 128.90 133.60 28.00 1.01 5.42 0.48 0.27
660 10566 RhaT Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only] context 0 102.84 13.00 7.00 26.00 27.24 4.00 -14.07 8.43 0.43 0.56
661 15000 GIYc GIY-YIG type nucleases (URI domain); context 0 102.65 5.00 5.00 81.10 92.12 13.00 -11.18 17.56 0.55 0.29
662 9890 ProA Gamma-glutamyl phosphate reductase [Amino acid transport and metabolism] context 0 102.53 9.38 10.00 41.20 28.47 4.00 -11.21 8.51 0.34 0.46 RF00230 T-box 3
663 10215 SecF Preprotein translocase subunit SecF [Intracellular trafficking and secretion] context 0 102.50 4.73 5.00 114.90 69.46 13.00 -7.71 9.87 0.31 0.41
664 12021 COG2348 Uncharacterized protein involved in methicillin resistance [Defense mechanisms] context 0 102.40 9.00 6.00 45.10 36.71 6.00 -4.17 10.94 0.46 0.28
665 10711 AcrA Membrane-fusion protein [Cell envelope biogenesis, outer membrane] context 0 101.73 7.00 7.00 72.60 50.14 28.00 7.20 3.82 0.51 0.19
10447 SalY ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms] context 1 92.06 3.90 4.00 111.00 125.80 13.00 -3.51 15.25 0.38 0.23
10711 AcrA Membrane-fusion protein [Cell envelope biogenesis, outer membrane] context 2 84.80 7.00 5.00 157.50 125.42 4.00 0.54 14.57 0.38 0.28
666 25501 RrnaAD Ribosomal RNA adenine dimethylase. context 0 101.58 10.00 3.00 129.00 199.07 92.00 -0.56 1.92 0.75 0.29
667 27077 RepA_N Replication initiator protein A (RepA) N-terminus. This family represents the N-terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids. Most proteins in this family are bacterial, but archaeal and eukaryotic members are also included. context 0 101.49 7.00 4.00 72.60 72.87 10.00 -10.56 9.86 0.38 0.38
668 10431 SerB Phosphoserine phosphatase [Amino acid transport and metabolism] context 0 101.36 9.00 6.00 90.60 43.67 4.00 -11.90 10.32 0.30 0.30
25033 EzrA Septation ring formation regulator, EzrA. During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation. context 1 59.62 10.00 7.00 56.20 55.38 4.00 0.66 4.41 0.47 0.23
10431 SerB Phosphoserine phosphatase [Amino acid transport and metabolism] context 2 54.83 4.00 4.00 97.50 91.96 11.00 8.10 8.22 0.49 0.33
669 28282 HCP Hybrid cluster protein (HCP), formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. HCP has three structural domains, an N-terminal alpha-helical domain, and two similar domains comprising a central beta-sheet flanked by alpha-helices. HCP contains two iron-sulfur clusters, one of which is a [Fe4-S4] cubane cluster similar to that of carbon monoxide dehydrogenase (CODH). The second cluster, referred to as the hybrid cluster, is a hybrid [Fe4-S2-O2] center located at the interface of the three domains. Although the hybrid cluster is buried within the protein, it is accessible through a large hydrophobic cavity. context 0 101.19 5.00 4.00 55.70 37.90 10.00 -12.10 14.26 0.34 0.22
670 11017 GltP Na+/H+-dicarboxylate symporters [Energy production and conversion] context 0 101.17 7.00 6.00 92.50 39.52 14.00 -1.20 4.66 0.31 0.35
671 10537 MscS Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane] context 0 101.17 4.00 4.00 110.50 104.96 36.00 -1.90 10.78 0.61 0.23
672 13027 AmiR Response regulator with putative antiterminator output domain [Signal transduction mechanisms] context 0 101.10 6.00 5.00 90.30 68.00 5.00 -25.33 18.56 0.33 0.41
25005 EutS Ethanolamine utilisation protein EutS. This family consists of several bacterial EutS ethanolamine utilisation proteins. The eut operon of Salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. The exact function of EutS is unknown. context 1 68.24 4.00 4.00 76.00 43.15 4.00 -17.68 18.71 0.27 0.34
673 14496 COG5412 Phage-related protein [Function unknown] context 0 100.95 9.00 6.00 156.90 49.03 4.00 -8.66 5.80 0.17 0.38
674 11633 FruB Phosphotransferase system, HPr-related proteins [Carbohydrate transport and metabolism] context 0 100.85 11.81 10.00 46.10 29.46 4.00 -9.39 6.41 0.37 0.38
675 23291 Polysacc_synt Polysaccharide biosynthesis protein. Members of this family are integral membrane proteins. Many members of the family are implicated in production of polysaccharide. The family includes RfbX part of the O antigen biosynthesis operon. The family includes SpoVB from Bacillus subtilis, which is involved in spore cortex biosynthesis. context 0 100.83 7.00 6.00 54.30 37.90 8.00 -14.44 10.86 0.42 0.32
676 5369 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction. context 0 100.80 9.00 6.00 140.70 53.78 5.00 -9.36 6.87 0.25 0.31 RF00169 SRP_bact 1
677 25753 Methylase_S Type I restriction modification DNA specificity domain. This domain is also known as the target recognition domain (TRD). Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity subunit (this family), two modification (M) subunits and two restriction (R) subunits. context 0 100.77 12.00 9.00 70.80 30.13 4.00 -2.92 4.50 0.25 0.34
678 10961 ELP3 Histone acetyltransferase [Transcription / Chromatin structure and dynamics] context 0 100.47 5.00 5.00 73.70 47.81 13.00 -9.35 11.93 0.39 0.30
679 9505 PadR Transcriptional regulator PadR-like family. Members of this family are transcriptional regulators that appear to be related to the pfam01047 family. This family includes PadR, a protein that is involved in negative regulation of phenolic acid metabolism. context 0 100.27 4.00 4.00 80.00 87.89 21.00 -6.90 17.19 0.58 0.24
680 10783 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only] context 0 100.22 12.81 11.00 43.50 27.53 4.00 -4.87 5.95 0.41 0.33
681 13724 NatA ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism] context 0 100.19 8.00 7.00 79.20 35.95 4.00 -14.18 10.63 0.28 0.29
682 27994 Ala_racemase Alanine racemase. This CD corresponds to alanine racemases, the prototype of the alanine racemase superfamily. Other proteins in this superfamily, such as, eukaryotic ornithine decarboxylases, bacterial diaminopimelate decarboxylases and biosynthetic arginine decarboxylases are not included in this CD. Alanine racemases have been classified as PyridoxaL 5'-phosphate Dependent Enzymes class III (PLPDE_III) and catalyzes the interconversion between L- and D-alanine. Homodimer formation is required for catalytic activity. context 0 100.17 4.00 4.00 84.00 97.93 18.00 -16.21 17.23 0.50 0.44
683 10928 GalU UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane] context 0 100.13 6.00 6.00 34.80 30.37 20.00 -6.05 7.17 0.52 0.28
684 26398 Peptidase_U57 YabG peptidase U57. YabG is a protease involved in the proteolysis and maturation of SpoIVA and YrbA proteins, conserved with the cortex and/or coat assembly by Bacillus subtilis. context 0 100.09 9.00 7.00 46.70 23.75 6.00 -10.04 6.95 0.33 0.36
685 23522 ICMT Isoprenylcysteine carboxyl methyltransferase (ICMT) family. The isoprenylcysteine o-methyltransferase (EC:2.1.1.100) family carry out carboxyl methylation of cleaved eukaryotic proteins that terminate in a CaaX motif. In Saccharomyces cerevisiae this methylation is carried out by Ste14p, an integral endoplasmic reticulum membrane protein. Ste14p is the founding member of the isoprenylcysteine carboxyl methyltransferase (ICMT) family, whose members share significant sequence homology. context 0 99.63 5.00 5.00 133.60 110.40 10.00 -8.68 16.35 0.42 0.28 RF00167 Purine 1
23522 ICMT Isoprenylcysteine carboxyl methyltransferase (ICMT) family. The isoprenylcysteine o-methyltransferase (EC:2.1.1.100) family carry out carboxyl methylation of cleaved eukaryotic proteins that terminate in a CaaX motif. In Saccharomyces cerevisiae this methylation is carried out by Ste14p, an integral endoplasmic reticulum membrane protein. Ste14p is the founding member of the isoprenylcysteine carboxyl methyltransferase (ICMT) family, whose members share significant sequence homology. context 1 73.62 6.00 6.00 83.30 51.51 5.00 -11.44 11.29 0.39 0.28
686 9907 CysK Cysteine synthase [Amino acid transport and metabolism] context 0 99.36 39.54 24.00 93.20 26.34 0.00 -8.14 8.26 0.22 0.32 RF00029 Intron_gpII 1 RF00230 T-box 1
687 9511 UPF0153 Uncharacterised protein family (UPF0153). This family of proteins contain 8 conserved cysteines that may form a metal binding site. The function of these proteins is unknown but might be an Fe-S cluster as part of an oxidoreductase complex. context 0 99.22 4.00 4.00 89.00 98.71 13.00 -31.96 25.17 0.54 0.29
688 13872 COG4732 Predicted membrane protein [Function unknown] context 0 99.20 6.95 7.00 66.70 50.84 15.00 3.40 6.21 0.47 0.34
689 24315 Glyco_32 Glycosyl hydrolases family 32; context 0 99.08 16.90 17.00 40.40 27.73 12.00 -1.30 1.42 0.51 0.29
24315 Glyco_32 Glycosyl hydrolases family 32; context 1 87.46 16.87 17.00 35.30 27.41 8.00 -0.29 1.84 0.57 0.28 RF00005 tRNA 1
690 1427 Transposase_mut Transposase, Mutator family. context 0 99.04 20.00 5.00 49.70 62.58 24.00 3.25 2.05 0.72 0.26
691 10969 Ndh NADH dehydrogenase, FAD-containing subunit [Energy production and conversion] context 0 99.03 6.00 6.00 115.90 84.61 11.00 -6.16 6.81 0.28 0.26
11288 MenA 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism] context 1 89.38 5.77 5.00 76.30 52.07 4.00 -26.35 21.77 0.40 0.39
11288 MenA 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism] context 2 80.94 7.66 7.00 40.60 21.40 4.00 -20.18 8.92 0.36 0.38
11288 MenA 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism] context 3 66.93 4.00 4.00 68.00 64.25 9.00 -21.00 16.13 0.53 0.28
692 10497 COG0627 Predicted esterase [General function prediction only] context 0 98.84 8.00 8.00 56.80 42.76 11.00 -5.09 6.27 0.46 0.35
693 10185 PDX2 Predicted glutamine amidotransferase involved in pyridoxine biosynthesis [Coenzyme metabolism] context 0 98.74 5.00 5.00 108.20 83.31 8.00 -16.81 12.84 0.27 0.31
694 9633 DUF386 Domain of unknown function (DUF386). This family consists of conserved hypothetical proteins, typically about 150 amino acids in length, with no known function. context 0 98.70 5.00 5.00 138.00 165.21 19.00 -2.89 10.35 0.51 0.32
695 24639 Cache Cache domain. context 0 98.68 13.92 9.00 31.60 18.77 5.00 -5.76 3.95 0.39 0.42
696 13747 COG4584 Transposase and inactivated derivatives [DNA replication, recombination, and repair] context 0 98.56 8.00 3.00 46.00 46.42 14.00 -8.91 9.88 0.51 0.46
697 27030 GutM Glucitol operon activator protein (GutM). This family consists of several glucitol operon activator (GutM) proteins. Expression of the glucitol (gut) operon in Escherichia coli is regulated by an unusual, complex system which consists of an activator (encoded by the gutM gene) and a repressor (encoded by the gutR gene) in addition to the cAMP-CRP complex (CRP, cAMP receptor protein). Synthesis of the mRNA, which initiates at the promoter specific to the gutR gene, occurs within the gutM gene. Expressional control of the gut operon appears to occur as a consequence of the antagonistic action of the products of the autogenously regulated gutM and gutR genes. context 0 98.42 4.00 4.00 184.70 120.20 4.00 -19.69 28.83 0.20 0.29
8655 EII-GUT PTS system enzyme II sorbitol-specific factor. context 1 60.13 4.00 3.00 174.40 100.90 4.00 -7.45 13.27 0.23 0.31
698 10046 NadE NAD synthase [Coenzyme metabolism] context 0 98.41 4.00 4.00 109.50 109.70 29.00 -2.70 11.40 0.55 0.35
28015 NAPRTase_A Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products. This subgroup is present in bacteria and eukaryota (except funghi). context 1 52.01 4.00 4.00 129.00 127.46 4.00 -16.97 20.93 0.52 0.32
28015 NAPRTase_A Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products. This subgroup is present in bacteria and eukaryota (except funghi). context 2 51.91 4.00 4.00 76.50 90.34 5.00 -3.30 18.14 0.56 0.32
699 10085 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair] context 0 97.98 38.04 28.00 86.80 20.64 0.00 -11.67 8.98 0.26 0.29 RF00162 S_box 1
10085 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair] context 1 80.14 31.04 23.00 87.60 27.04 0.00 -10.28 8.92 0.26 0.23
10085 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair] context 2 76.93 21.48 14.00 35.40 18.53 4.00 -0.24 1.33 0.39 0.45 RF00162 S_box 1
700 12118 COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription] context 0 97.68 11.00 9.00 31.10 22.32 6.00 -6.22 5.14 0.39 0.38
701 10917 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair] context 0 97.34 9.00 7.00 45.60 43.11 5.00 -15.13 10.45 0.44 0.43
702 10198 MiaA tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis] context 0 97.20 7.00 7.00 80.70 63.87 12.00 -4.55 6.48 0.41 0.29
703 24988 DUF956 Domain of unknown function (DUF956). Family of bacterial sequences with undetermined function. context 0 96.76 8.00 8.00 103.40 70.82 4.00 -9.60 12.19 0.35 0.31
704 10726 AmiC N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane] context 0 96.67 20.00 12.00 54.40 24.45 6.00 1.16 1.88 0.41 0.25
705 13897 COG4758 Predicted membrane protein [Function unknown] context 0 96.29 56.99 22.00 44.20 31.49 0.00 -16.40 11.06 0.44 0.40
706 10174 DltE Short-chain dehydrogenases of various substrate specificities [General function prediction only] context 0 96.20 6.61 7.00 54.50 30.51 5.00 -8.71 11.26 0.31 0.33 RF00230 T-box 1
707 5491 Colicin_V Colicin V production protein. Colicin V production protein is required in E. Coli for colicin V production from plasmid pColV-K30. This protein is coded for in the purF operon. context 0 95.88 7.00 7.00 136.50 102.16 40.00 6.55 2.10 0.45 0.26
5491 Colicin_V Colicin V production protein. Colicin V production protein is required in E. Coli for colicin V production from plasmid pColV-K30. This protein is coded for in the purF operon. context 1 92.95 9.00 9.00 119.40 91.31 26.00 7.16 1.71 0.42 0.26
708 11733 FixB Electron transfer flavoprotein, alpha subunit [Energy production and conversion] context 0 95.62 8.00 7.00 31.70 28.06 15.00 -3.17 5.35 0.56 0.23
709 13857 COG4716 Myosin-crossreactive antigen [Function unknown] context 0 95.20 10.00 10.00 36.20 28.92 4.00 -12.58 8.20 0.38 0.31
710 25724 Chorismate_synt Chorismate synthase. context 0 95.02 6.56 7.00 48.30 36.52 9.00 -6.39 7.61 0.38 0.37
711 27994 Ala_racemase Alanine racemase. This CD corresponds to alanine racemases, the prototype of the alanine racemase superfamily. Other proteins in this superfamily, such as, eukaryotic ornithine decarboxylases, bacterial diaminopimelate decarboxylases and biosynthetic arginine decarboxylases are not included in this CD. Alanine racemases have been classified as PyridoxaL 5'-phosphate Dependent Enzymes class III (PLPDE_III) and catalyzes the interconversion between L- and D-alanine. Homodimer formation is required for catalytic activity. context 0 94.71 39.97 29.00 47.00 21.58 0.00 -11.54 9.16 0.30 0.37
712 11861 ElaA Predicted acyltransferase [General function prediction only] context 0 94.60 8.58 8.00 46.70 22.85 5.00 -8.90 7.01 0.39 0.37
713 17162 TRAG TraG/TraD family. The TraG/TraD family are bacterial conjugation proteins. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome although the exact mechanism of action is unknown. These proteins contain a P-loop and walker-B site for nucleotide binding. context 0 94.40 5.00 3.00 106.90 78.70 12.00 -5.71 13.51 0.38 0.22
714 10571 COG0702 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism] context 0 94.12 6.00 4.00 62.10 44.03 13.00 -9.30 9.13 0.43 0.24
715 28293 PVA Penicillin V acylase (PVA), also known as conjugated bile salt acid hydrolase (CBAH), catalyzes the hydrolysis of penicillin V to yield 6-amino penicillanic acid (6-APA), an important key intermediate of semisynthetic penicillins. PVA has an N-terminal nucleophilic cysteine as do other Ntn Hydrolases which is exposed by prossessing of the PVA precursor. PVA forms a homotetramer. context 0 93.99 6.75 6.00 51.50 30.18 6.00 -12.49 10.40 0.35 0.29
716 10639 MurD UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane] context 0 93.98 7.00 7.00 62.50 66.37 24.00 3.06 3.65 0.49 0.25
717 10102 RpmB Ribosomal protein L28 [Translation, ribosomal structure and biogenesis] context 0 93.73 8.00 8.00 61.00 87.13 36.00 0.12 2.73 0.72 0.38
718 12383 COG3044 Predicted ATPase of the ABC class [General function prediction only] context 0 93.71 47.00 20.00 41.80 30.95 0.00 -22.21 11.81 0.37 0.34
719 11658 COG1950 Predicted membrane protein [Function unknown] context 0 93.70 10.91 9.00 31.20 17.95 4.00 -8.98 5.55 0.31 0.43
720 13250 COG3944 Capsular polysaccharide biosynthesis protein [Cell envelope biogenesis, outer membrane] context 0 93.52 10.00 7.00 33.70 26.25 4.00 -14.63 7.85 0.34 0.41
721 10070 NusA Transcription elongation factor [Transcription] context 0 93.50 84.00 28.00 23.40 24.47 0.00 -14.34 5.95 0.47 0.52
722 11667 COG1959 Predicted transcriptional regulator [Transcription] context 0 93.40 14.97 11.00 102.10 36.37 4.00 0.14 2.70 0.27 0.25
723 13404 COG4122 Predicted O-methyltransferase [General function prediction only] context 0 93.13 37.23 24.00 44.80 20.38 0.00 -12.61 10.25 0.29 0.38
724 9930 AtpD F0F1-type ATP synthase, beta subunit [Energy production and conversion] context 0 92.97 57.88 31.00 30.80 26.95 0.00 -15.58 7.14 0.42 0.40
725 26232 DUF457 Predicted membrane-bound metal-dependent hydrolase (DUF457). Family of predicted membrane-bound metal-dependent