Table 1.
Families evaluated in this work. Columns are as follows: PFAM ID, PFAM Name and PFAM Description: R-value (correlation between genome size and PFAM distribution); Total number of members in the bacterial and archaeal genomes; Proportion of the PFAM (%) relative to the complete collection; PFAM Coefficient of Variation (CV); Number of total of domains; Number of different domains (NR); PFAM Distribution (%) among all the organisms.
| PFAM ID | PFAM Name | PFAM Description | Correlation (R value) | Total No. of Proteins | Proportion | CV | Domains (Total) | Domains (NR) | Genomic Distribution (%) |
|---|---|---|---|---|---|---|---|---|---|
| PF00096 | zf-C2H2 | Zinc finger, C2H2 type | −0.04 | 59 | 0.00 | 6.82 | 105 | 24 | 0.03 |
| PF00126 | HTH_1 | Bacterial regulatory helix-turn-helix protein, lysR family | 0.57 | 21320 | 0.09 | 1.70 | 42400 | 98 | 0.87 |
| PF00165 | HTH_AraC | Bacterial regulatory helix-turn-helix proteins, AraC family | 0.05 | 47 | 0.00 | 6.85 | 86 | 27 | 0.03 |
| PF00170 | bZIP_1 | bZIP transcription factor | 0.03 | 248 | 0.00 | 3.11 | 4587 | 341 | 0.12 |
| PF00196 | GerE | Bacterial regulatory proteins, luxR family | 0.71 | 12932 | 0.06 | 1.53 | 25020 | 290 | 0.79 |
| PF00216 | Bac_DNA_binding | Bacterial DNA-binding protein | 0.24 | 3276 | 0.01 | 0.95 | 4731 | 40 | 0.88 |
| PF00313 | CSD | ’Cold-shock’ DNA-binding domain | 0.62 | 3651 | 0.02 | 0.91 | 3866 | 39 | 0.79 |
| PF00325 | Crp | Bacterial regulatory proteins, crp family | 0.18 | 186 | 0.00 | 2.70 | 377 | 24 | 0.13 |
| PF00356 | LacI | Bacterial regulatory proteins, lacI family | 0.43 | 7083 | 0.03 | 1.71 | 14525 | 108 | 0.61 |
| PF00376 | MerR | MerR family regulatory protein | 0.54 | 1506 | 0.01 | 1.65 | 2885 | 66 | 0.43 |
| PF00392 | GntR | Bacterial regulatory proteins, gntR family | 0.70 | 13263 | 0.06 | 1.33 | 25478 | 205 | 0.79 |
| PF00440 | TetR_N | Bacterial regulatory proteins, tetR family | 0.67 | 23839 | 0.11 | 2.62 | 33009 | 197 | 0.87 |
| PF00486 | Trans_reg_C | Transcriptional regulatory protein, C terminal | 0.74 | 14446 | 0.06 | 1.01 | 31282 | 163 | 0.87 |
| PF00816 | Histone_HNS | H-NS histone family | 0.24 | 434 | 0.00 | 3.68 | 537 | 37 | 0.16 |
| PF00847 | AP2 | AP2 domain | 0.08 | 77 | 0.00 | 5.50 | 105 | 13 | 0.04 |
| PF01022 | HTH_5 | Bacterial regulatory protein, arsR family | 0.43 | 3940 | 0.02 | 0.93 | 4683 | 138 | 0.84 |
| PF01047 | MarR | MarR family | 0.66 | 5880 | 0.03 | 1.15 | 6384 | 142 | 0.81 |
| PF01258 | zf-dskA_traR | Prokaryotic dksA/traR C4-type zinc finger | 0.31 | 1564 | 0.01 | 1.02 | 1744 | 25 | 0.67 |
| PF01316 | Arg_repressor | Arginine repressor, DNA binding domain | 0.10 | 631 | 0.00 | 1.33 | 1287 | 26 | 0.41 |
| PF01325 | Fe_dep_repress | Iron dependent repressor, N-terminal DNA binding domain | 0.11 | 1076 | 0.00 | 1.23 | 2675 | 43 | 0.53 |
| PF01340 | MetJ | Met Apo-repressor, MetJ | 0.05 | 72 | 0.00 | 4.27 | 73 | 2 | 0.05 |
| PF01371 | Trp_repressor | Trp repressor protein | 0.04 | 299 | 0.00 | 2.00 | 330 | 20 | 0.21 |
| PF01381 | HTH_3 | Helix-turn-helix | 0.50 | 12084 | 0.05 | 0.82 | 16741 | 394 | 0.94 |
| PF01402 | RHH_1 | Ribbon-helix-helix protein, copG family | 0.17 | 1714 | 0.01 | 1.56 | 2228 | 93 | 0.52 |
| PF01418 | HTH_6 | Helix-turn-helix domain, rpiR family | 0.27 | 1802 | 0.01 | 1.74 | 3574 | 48 | 0.43 |
| PF01475 | FUR | Ferric uptake regulator family | 0.51 | 2891 | 0.01 | 0.64 | 2992 | 45 | 0.87 |
| PF01638 | HxlR | HxlR-like helix-turn-helix | 0.64 | 3255 | 0.01 | 1.65 | 3389 | 37 | 0.64 |
| PF01722 | BolA | BolA-like protein | 0.20 | 898 | 0.00 | 1.36 | 905 | 5 | 0.37 |
| PF01726 | LexA_DNA_bind | LexA DNA binding domain | 0.44 | 1015 | 0.00 | 0.91 | 1988 | 33 | 0.64 |
| PF01978 | TrmB | Sugar-specific transcriptional regulator TrmB | 0.04 | 1436 | 0.01 | 2.47 | 2475 | 164 | 0.38 |
| PF02082 | Rrf2 | Transcriptional regulator | 0.48 | 2531 | 0.01 | 0.85 | 2644 | 51 | 0.78 |
| PF02257 | RFX_DNA_binding | RFX DNA-binding domain | 0.03 | 12 | 0.00 | 13.56 | 28 | 7 | 0.01 |
| PF02467 | Whib | Transcription factor WhiB | 0.38 | 947 | 0.00 | 2.92 | 1000 | 18 | 0.14 |
| PF02604 | PhdYeFM_antitox | Antitoxin Phd_YefM, type II toxin-antitoxin system | 0.29 | 2020 | 0.01 | 1.58 | 2104 | 30 | 0.52 |
| PF02892 | zf-BED | BED zinc finger | −0.01 | 17 | 0.00 | 11.11 | 30 | 11 | 0.01 |
| PF02954 | HTH_8 | Bacterial regulatory protein, Fis family | 0.42 | 7162 | 0.03 | 1.51 | 20550 | 157 | 0.61 |
| PF03333 | PapB | Adhesin biosynthesis transcription regulatory protein | 0.05 | 14 | 0.00 | 11.01 | 22 | 5 | 0.01 |
| PF03551 | PadR | Transcriptional regulator PadR-like family | 0.49 | 3098 | 0.01 | 1.62 | 3782 | 52 | 0.62 |
| PF03749 | SfsA | Sugar fermentation stimulation protein | 0.07 | 458 | 0.00 | 1.46 | 475 | 7 | 0.33 |
| PF03869 | Arc | Arc-like DNA binding domain | 0.20 | 171 | 0.00 | 3.50 | 174 | 3 | 0.10 |
| PF03965 | Penicillinase_R | Penicillinase repressor | 0.39 | 1013 | 0.00 | 1.88 | 1081 | 39 | 0.37 |
| PF04014 | MazE_antitoxin | Antidote-toxin recognition MazE, bacterial antitoxin | 0.07 | 1798 | 0.01 | 1.72 | 2321 | 59 | 0.46 |
| PF04024 | PspC | PspC domain | 0.34 | 1004 | 0.00 | 1.47 | 1300 | 34 | 0.41 |
| PF04221 | RelB | RelB antitoxin | -0.08 | 466 | 0.00 | 2.96 | 499 | 18 | 0.17 |
| PF04247 | SirB | Invasion gene expression up-regulator, SirB | 0.12 | 213 | 0.00 | 2.56 | 291 | 26 | 0.14 |
| PF04299 | FMN_bind_2 | Putative FMN-binding domain | 0.41 | 325 | 0.00 | 2.04 | 325 | 1 | 0.22 |
| PF04353 | Rsd_AlgQ | Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ | 0.11 | 98 | 0.00 | 3.74 | 112 | 4 | 0.07 |
| PF04383 | KilA-N | KilA-N domain | 0.06 | 136 | 0.00 | 4.19 | 160 | 14 | 0.08 |
| PF04397 | LytTR | LytTr DNA-binding domain | 0.25 | 2649 | 0.01 | 2.13 | 4836 | 47 | 0.53 |
| PF04606 | Ogr_Delta | Ogr/Delta-like zinc finger | 0.11 | 80 | 0.00 | 4.94 | 94 | 10 | 0.05 |
| PF04761 | Phage_Treg | Lactococcus bacteriophage putative transcription regulator | −0.01 | 1 | 0.00 | 36.47 | 1 | 1 | 0.00 |
| PF04947 | Pox_VLTF3 | Poxvirus Late Transcription Factor VLTF3 like | −0.02 | 14 | 0.00 | 12.86 | 25 | 12 | 0.01 |
| PF04967 | HTH_10 | HTH DNA binding domain | 0.02 | 704 | 0.00 | 7.47 | 1610 | 61 | 0.07 |
| PF05016 | ParE_toxin | ParE toxin of type II toxin-antitoxin system, parDE | 0.22 | 1808 | 0.01 | 1.63 | 1839 | 10 | 0.48 |
| PF05043 | Mga | Mga helix-turn-helix domain | −0.01 | 695 | 0.00 | 5.32 | 2544 | 41 | 0.13 |
| PF05068 | MtlR | Mannitol repressor | 0.06 | 37 | 0.00 | 6.54 | 38 | 2 | 0.02 |
| PF05225 | HTH_psq | helix-turn-helix, Psq domain | 0.08 | 50 | 0.00 | 6.45 | 139 | 45 | 0.03 |
| PF05247 | FlhD | Flagellar transcriptional activator (FlhD) | 0.18 | 114 | 0.00 | 4.44 | 167 | 2 | 0.06 |
| PF05280 | FlhC | Flagellar transcriptional activator (FlhC) | 0.19 | 116 | 0.00 | 4.12 | 118 | 3 | 0.07 |
| PF05321 | HHA | Haemolysin expression modulating protein | 0.03 | 33 | 0.00 | 8.72 | 34 | 2 | 0.02 |
| PF05443 | ROS_MUCR | ROS/MUCR transcriptional regulator protein | 0.16 | 362 | 0.00 | 6.11 | 416 | 20 | 0.10 |
| PF05764 | YL1 | YL1 nuclear protein | 0.08 | 12 | 0.00 | 10.48 | 41 | 20 | 0.01 |
| PF05848 | CtsR | Firmicute transcriptional repressor of class III stress genes (CtsR) | −0.04 | 191 | 0.00 | 2.50 | 202 | 8 | 0.14 |
| PF05930 | Phage_AlpA | Prophage CP4-57 regulatory protein (AlpA) | 0.18 | 431 | 0.00 | 2.74 | 482 | 11 | 0.18 |
| PF06018 | CodY | CodY GAF-like domain | 0.01 | 188 | 0.00 | 2.85 | 398 | 17 | 0.12 |
| PF06054 | CoiA | Competence protein CoiA-like family | 0.04 | 182 | 0.00 | 2.81 | 198 | 9 | 0.12 |
| PF06069 | PerC | PerC transcriptional activator | 0.02 | 7 | 0.00 | 14.86 | 9 | 3 | 0.01 |
| PF06116 | RinB | Transcriptional activator RinB | −0.02 | 9 | 0.00 | 19.41 | 9 | 1 | 0.00 |
| PF06320 | GCN5L1 | GCN5-like protein 1 (GCN5L1) | −0.03 | 34 | 0.00 | 8.39 | 214 | 71 | 0.02 |
| PF06338 | ComK | ComK protein | 0.01 | 93 | 0.00 | 4.85 | 96 | 4 | 0.05 |
| PF06769 | YoeB_toxin | YoeB-like toxin of bacterial type II toxin-antitoxin system | 0.10 | 350 | 0.00 | 2.49 | 356 | 4 | 0.18 |
| PF06818 | Fez1 | Fez1 | 0.07 | 399 | 0.00 | 2.77 | 8316 | 400 | 0.16 |
| PF06839 | zf-GRF | GRF zinc finger | 0.05 | 4 | 0.00 | 28.82 | 7 | 4 | 0.00 |
| PF06923 | GutM | Glucitol operon activator protein (GutM) | 0.02 | 76 | 0.00 | 4.71 | 81 | 6 | 0.05 |
| PF06943 | zf-LSD1 | LSD1 zinc finger | 0.02 | 5 | 0.00 | 16.28 | 16 | 6 | 0.00 |
| PF07180 | CaiF_GrlA | CaiF/GrlA transcriptional regulator | 0.00 | 6 | 0.00 | 17.17 | 9 | 3 | 0.00 |
| PF07417 | Crl | Transcriptional regulator Crl | 0.08 | 31 | 0.00 | 6.48 | 31 | 1 | 0.02 |
| PF07704 | PSK_trans_fac | Rv0623-like transcription factor | 0.24 | 142 | 0.00 | 4.38 | 293 | 16 | 0.07 |
| PF07716 | bZIP_2 | Basic region leucine zipper | 0.00 | 35 | 0.00 | 7.38 | 901 | 152 | 0.02 |
| PF07750 | GcrA | GcrA cell cycle regulator | 0.19 | 211 | 0.00 | 3.58 | 232 | 12 | 0.10 |
| PF07764 | Omega_Repress | Omega Transcriptional Repressor | -0.03 | 4 | 0.00 | 18.21 | 4 | 1 | 0.00 |
| PF07804 | HipA_C | HipA-like C-terminal domain | 0.29 | 814 | 0.00 | 1.85 | 1436 | 10 | 0.32 |
| PF07848 | PaaX | PaaX-like protein | 0.48 | 272 | 0.00 | 2.68 | 530 | 19 | 0.15 |
| PF07879 | PHB_acc_N | PHB/PHA accumulation regulator DNA-binding domain | 0.31 | 251 | 0.00 | 2.13 | 553 | 17 | 0.18 |
| PF08220 | HTH_DeoR | DeoR-like helix-turn-helix domain | 0.45 | 2567 | 0.01 | 1.35 | 5238 | 87 | 0.60 |
| PF08222 | HTH_CodY | CodY helix-turn-helix domain | −0.01 | 173 | 0.00 | 2.76 | 340 | 3 | 0.12 |
| PF08270 | PRD_Mga | M protein trans-acting positive regulator (MGA) PRD domain | −0.06 | 20 | 0.00 | 10.59 | 57 | 5 | 0.01 |
| PF08279 | HTH_11 | HTH domain | 0.35 | 3290 | 0.01 | 1.36 | 8331 | 183 | 0.72 |
| PF08280 | HTH_Mga | M protein trans-acting positive regulator (MGA) HTH domain | −0.02 | 98 | 0.00 | 7.17 | 325 | 13 | 0.04 |
| PF08299 | Bac_DnaA_C | Bacterial dnaA protein helix-turn-helix | 0.20 | 1385 | 0.01 | 0.56 | 3716 | 23 | 0.90 |
| PF09278 | MerR-DNA-bind | MerR, DNA binding | 0.44 | 981 | 0.00 | 1.75 | 1988 | 39 | 0.35 |
| PF09339 | HTH_IclR | IclR helix-turn-helix domain | 0.56 | 4383 | 0.02 | 1.85 | 8834 | 158 | 0.58 |
| PF11046 | HycA_repressor | Transcriptional repressor of hyc and hyp operons | 0.06 | 5 | 0.00 | 16.28 | 5 | 1 | 0.00 |
| PF12324 | HTH_15 | Helix-turn-helix domain of alkylmercury lyase | 0.17 | 42 | 0.00 | 7.61 | 83 | 20 | 0.03 |
| PF12431 | CitT | Transcriptional regulator | 0.17 | 82 | 0.00 | 5.06 | 186 | 8 | 0.05 |
| PF12793 | SgrR_N | Sugar transport-related sRNA regulator N-term | 0.14 | 102 | 0.00 | 5.68 | 215 | 5 | 0.04 |
| PF12833 | HTH_18 | Helix-turn-helix domain | 0.62 | 16065 | 0.07 | 1.63 | 32766 | 236 | 0.75 |
| PF13384 | HTH_23 | Homeodomain-like domain | 0.37 | 2261 | 0.01 | 1.55 | 4836 | 274 | 0.63 |
| PF13404 | HTH_AsnC-type | AsnC-type helix-turn-helix domain | 0.59 | 2324 | 0.01 | 1.68 | 4460 | 88 | 0.52 |
| PF13411 | MerR_1 | MerR HTH family regulatory protein | 0.64 | 5468 | 0.02 | 1.23 | 7255 | 206 | 0.82 |
| PF13412 | HTH_24 | Winged helix-turn-helix DNA-binding | 0.41 | 4567 | 0.02 | 1.12 | 8874 | 260 | 0.81 |
| PF13413 | HTH_25 | Helix-turn-helix domain | 0.23 | 817 | 0.00 | 1.05 | 1559 | 60 | 0.54 |
| PF13545 | HTH_Crp_2 | Crp-like helix-turn-helix domain | 0.57 | 4228 | 0.02 | 1.02 | 8248 | 122 | 0.82 |
| PF13556 | HTH_30 | PucR C-terminal helix-turn-helix domain | 0.47 | 2065 | 0.01 | 2.50 | 3180 | 69 | 0.36 |
| PF13693 | HTH_35 | Winged helix-turn-helix DNA-binding | 0.04 | 111 | 0.00 | 6.64 | 135 | 17 | 0.05 |
| PF13936 | HTH_38 | Helix-turn-helix domain | 0.13 | 1350 | 0.01 | 2.40 | 2872 | 165 | 0.40 |
| PF14549 | P22_Cro | DNA-binding transcriptional regulator Cro | 0.06 | 41 | 0.00 | 6.64 | 51 | 10 | 0.03 |
| PF14850 | Pro_dh-DNA_bdg | DNA-binding domain of Proline dehydrogenase | 0.24 | 315 | 0.00 | 1.87 | 967 | 4 | 0.23 |
| PF15723 | MqsR_toxin | Motility quorum-sensing regulator, toxin of MqsA | 0.11 | 72 | 0.00 | 4.54 | 103 | 7 | 0.05 |
| PF15731 | MqsA_antitoxin | Antitoxin component of bacterial toxin-antitoxin system, MqsA | 0.06 | 199 | 0.00 | 3.13 | 271 | 20 | 0.12 |
| PF15943 | YdaS_antitoxin | Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT | 0.08 | 171 | 0.00 | 3.87 | 231 | 29 | 0.09 |