Table 2 COGs conserved in the acidic cluster of the multimodal distribution. P(a) and P(b) are the frequency of occurance in the acidic and basic clusters respectively, F is the function group. The COGs are listed with their P(v) which is score of their variability between the acidic and basic clusters of the pI distribution weighted by their frequency of occurance across all genomes in the dataset. pI values of four organisms – the extremophiles Buchnera (environment bacteriocyte), Halobacterium (highly acidic – high salt), and E. coli and H. pylori – intestinal bacteria with different environmental pH.
COGs with pI conserved in Acidic Cluster | |||||||||
|---|---|---|---|---|---|---|---|---|---|
COG | P(a) | P(b) | P(v) | F | Role | Hbs | Eco | Hpy | Buc |
COG2890 | 0.80 | 0.18 | 0.35 | J | Predicted rRNA or tRNA methylase | 4.23 | 4.99 | 5.61 | 9.38 |
COG0021 | 0.81 | 0.00 | 0.05 | G | Transketolase | - | 5.61 | 6.23 | 7.98 |
COG0215 | 0.82 | 0.11 | 0.24 | J | Cysteinyl-tRNA synthetase | 4.47 | 5.29 | 5.88 | 9.33 |
COG0016 | 0.82 | 0.14 | 0.32 | J | Phenylalanyl-tRNA synthetase alpha subunit | 4.14 | 5.71 | 6.35 | 9.51 |
COG0449 | 0.82 | 0.04 | 0.08 | M | Glucosamine 6-phosphate synthetase, contains amidotransferase and phosphosugar isomerase | 5.08 | 5.52 | 6.05 | 9.52 |
COG0206 | 0.82 | 0.08 | 0.16 | D | Cell division GTPase | 4.35 | 4.63 | 5.26 | 5.08 |
COG0436 | 0.82 | 0.04 | 0.10 | E | PLP-dependent aminotransferases | 4.41 | 6.15 | 7.41 | - |
COG0468 | 0.83 | 0.15 | 0.31 | L | RecA/RadA recombinase | 4.44 | 5.06 | 5.47 | - |
COG0125 | 0.83 | 0.17 | 0.35 | F | Thymidylate kinase | 4.32 | 5.26 | 8.97 | 10.01 |
COG0084 | 0.84 | 0.03 | 0.09 | L | Mg-dependent DNase | - | 5.44 | 5.43 | 8.81 |
COG0504 | 0.84 | 0.07 | 0.18 | F | CTP synthase (UTP-ammonia lyase) | 4.47 | 5.58 | 7.55 | 9.01 |
COG0495 | 0.84 | 0.11 | 0.27 | J | Leucyl-tRNA synthetase | 4.18 | 5.14 | 7.51 | 9.53 |
COG0124 | 0.86 | 0.12 | 0.27 | J | Histidyl-tRNA synthetase | 4.29 | 5.57 | 5.54 | 9.28 |
COG0443 | 0.86 | 0.02 | 0.04 | O | Molecular chaperone | 3.95 | 5.08 | 5.02 | 7.44 |
COG0024 | 0.86 | 0.08 | 0.22 | J | Methionine aminopeptidase | 4.05 | 5.55 | 5.89 | 8.70 |
COG0209 | 0.87 | 0.03 | 0.10 | F | Ribonucleotide reductase alpha subunit | 4.39 | 5.89 | 5.73 | 9.11 |
COG0142 | 0.87 | 0.06 | 0.13 | H | Geranylgeranyl pyrophosphate synthase | 4.31 | 4.96 | 5.94 | 9.58 |
COG0441 | 0.88 | 0.10 | 0.23 | J | Threonyl-tRNA synthetase | 4.35 | 5.76 | 5.93 | 8.86 |
COG0112 | 0.88 | 0.10 | 0.19 | E | Glycine hydroxymethyltransferase | 4.30 | 5.95 | 6.41 | 9.22 |
COG0525 | 0.88 | 0.12 | 0.23 | J | Valyl-tRNA synthetase | 4.09 | 5.19 | 6.12 | 9.38 |
COG0060 | 0.89 | 0.11 | 0.23 | J | Isoleucyl-tRNA synthetase | 4.13 | 5.63 | 6.15 | 9.22 |
COG0073 | 0.89 | 0.08 | 0.19 | R | EMAP domain | 4.04 | 5.29 | 5.42 | 8.90 |
COG0172 | 0.89 | 0.09 | 0.21 | J | Seryl-tRNA synthetase | 4.60 | 5.30 | 6.70 | 9.42 |
COG0018 | 0.89 | 0.09 | 0.20 | J | Arginyl-tRNA synthetase | 4.18 | 5.29 | 5.94 | 9.72 |
COG0143 | 0.89 | 0.09 | 0.20 | J | Methionyl-tRNA synthetase | 4.16 | 5.39 | 6.00 | 9.27 |
COG1109 | 0.89 | 0.09 | 0.21 | G | Phosphomannomutase | 4.43 | 5.55 | 6.18 | 9.03 |
COG0006 | 0.90 | 0.04 | 0.11 | E | Xaa-Pro aminopeptidase | 4.42 | 5.35 | 5.73 | - |
COG0442 | 0.91 | 0.09 | 0.18 | J | Prolyl-tRNA synthetase | 4.45 | 5.11 | 5.90 | 9.51 |
COG0126 | 0.91 | 0.07 | 0.14 | G | 3-phosphoglycerate kinase | 4.29 | 5.06 | 6.18 | 9.37 |
COG0012 | 0.91 | 0.09 | 0.17 | R | Predicted GTPase | 4.15 | 4.86 | 5.50 | 9.07 |
COG0149 | 0.91 | 0.02 | 0.09 | G | Triosephosphate isomerase | 4.15 | 5.55 | 7.58 | 9.23 |
COG0492 | 0.92 | 0.08 | 0.16 | O | Thioredoxin reductase | 4.27 | 5.24 | 6.02 | 9.36 |
COG0072 | 0.93 | 0.07 | 0.14 | J | Phenylalanyl-tRNA synthetase beta subunit | 4.33 | 5.26 | 6.63 | 8.30 |
COG0085 | 0.94 | 0.02 | 0.08 | K | DNA-directed RNA polymerase beta subunit/140 kD subunit (split gene in Mjan, Mthe, Aful) | 4.77 | 5.14 | 6.14 | 7.81 |
COG0231 | 0.94 | 0.02 | 0.08 | J | Translation elongation factor P/translation initiation factor eIF-5A | 4.78 | 5.28 | 5.34 | 9.40 |
COG0459 | 0.95 | 0.01 | 0.04 | O | Chaperonin GroEL (HSP60 family) | 4.16 | 4.84 | 5.51 | 5.04 |
COG0013 | 0.95 | 0.05 | 0.09 | J | Alanyl-tRNA synthetase | 4.29 | 5.51 | 5.96 | 9.42 |
COG0592 | 0.96 | 0.04 | 0.09 | L | DNA polymerase sliding clamp subunit (PCNA homolog) | 3.97 | 5.20 | 5.45 | 8.93 |
COG0202 | 0.98 | 0.02 | 0.05 | K | DNA-directed RNA polymerase alpha subunit/40 kD subunit | 4.11 | 4.95 | 4.95 | 5.03 |
COG0148 | 0.98 | 0.00 | 0.00 | G | Enolase | 4.38 | 5.28 | 5.42 | 6.93 |
COG0480 | 0.99 | 0.01 | 0.03 | J | Translation elongation and release factors (GTPases) | 4.41 | 5.41 | 5.23 | 7.61 |