Metamenu

Model Internals

Each PhenDB model is trained on sets of bacterial ENOGs (orthologous groups from EggNOG 4.5), which have or have not been identified in the training genomes. Each ENOG is given a weight, with the magnitude of the weight being the importance of that ENOG for the final prediction. The sign of the weight indicates whether the presence (positive weight) or absence (negative weight) of this ENOG is indicative of the trait.

This table lists the 250 highest-ranking ENOGs of this model.

rank in model enog name enog description weight in model
1 COG0568 sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released -0.037607
2 COG0513 Belongs to the DEAD box helicase family -0.035810
3 COG1514 Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'- phosphomonoester 0.032125
4 COG2110 phosphatase homologous to the C-terminal domain of histone macroH2A1 0.030432
5 COG4591 ABC-type transport system involved in lipoprotein release permease component -0.029408
6 COG0692 Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine -0.028234
7 COG0514 ATP-dependent DNA helicase (RecQ) -0.027489
8 COG0736 holo-[acyl-carrier-protein] synthase activity -0.027374
9 COG0358 DNA primase activity -0.027257
10 COG2249 NAD(P)H dehydrogenase (quinone) activity -0.027129
11 COG4106 trans-aconitate 2-methyltransferase activity -0.027058
12 COG3973 AAA domain -0.026750
13 COG1272 protein, Hemolysin III -0.026109
14 COG3591 Belongs to the peptidase S1B family -0.026014
15 COG0489 protein tyrosine kinase activity -0.025722
16 COG1353 crispr-associated protein 0.025713
17 COG0207 Catalyzes the reductive methylation of 2'-deoxyuridine- 5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor and reductant in the reaction, yielding dihydrofolate (DHF) as a by-product. This enzymatic reaction provides an intracellular de novo source of dTMP, an essential precursor for DNA biosynthesis -0.024767
18 COG2018 Roadblock/LC7 domain 0.024375
19 COG1857 crispr-associated protein 0.024145
20 COG2391 methyltransferase activity 0.023729
21 COG0342 Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA -0.023649
22 COG1180 Activation of pyruvate formate-lyase under anaerobic conditions by generation of an organic free radical, using S- adenosylmethionine and reduced flavodoxin as cosubstrates to produce 5'-deoxy-adenosine 0.023612
23 COG3270 Specifically methylates the cytosine at position 1407 (m5C1407) of 16S rRNA 0.023442
24 COG0571 ribonuclease III activity -0.023006
25 COG1704 LemA family -0.022844
26 COG0230 Belongs to the bacterial ribosomal protein bL34 family -0.022813
27 COG1547 Domain of unknown function (DUF309) 0.022808
28 COG0270 DNA (cytosine-5-)-methyltransferase activity -0.022794
29 COG0488 (ABC) transporter -0.022679
30 COG0389 Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII -0.022641
31 COG4942 peptidase -0.022583
32 COG3638 Part of the ABC transporter complex PhnCDE involved in phosphonates import. Responsible for energy coupling to the transport system -0.022534
33 COG0326 Molecular chaperone. Has ATPase activity -0.022492
34 COG1301 dicarboxylic acid transport -0.022462
35 COG1434 Gram-negative-bacterium-type cell wall biogenesis 0.022401
36 COG2105 PFAM AIG2 family protein 0.022338
37 COG1647 Serine aminopeptidase, S33 -0.022060
38 COG2046 Belongs to the sulfate adenylyltransferase family 0.022030
39 COG3344 reverse transcriptase -0.022017
40 COG2223 nitrite transmembrane transporter activity -0.021973
41 COG1974 Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. In the presence of single-stranded DNA, RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon and eventually DNA repair -0.021973
42 COG0262 Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis -0.021894
43 COG0370 Transporter of a GTP-driven Fe(2 ) uptake system 0.021875
44 COG2964 Protein conserved in bacteria -0.021843
45 COG2723 6-phospho-beta-galactosidase activity 0.021750
46 COG1253 flavin adenine dinucleotide binding -0.021687
47 COG3328 transposase activity 0.021587
48 COG0532 One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex -0.021579
49 COG4572 Cation transport regulator 0.021496
50 COG2152 Converts 4-O-beta-D-mannopyranosyl-D-glucopyranose (Man- Glc) to mannose 1-phosphate (Man1P) and glucose 0.021383
51 COG3462 membrane protein (DUF2078) 0.021211
52 COG1733 regulation of RNA biosynthetic process -0.021170
53 COG0782 Necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus -0.021132
54 COG1961 COG1961 Site-specific recombinases, DNA invertase Pin homologs -0.020900
55 COG0149 triose-phosphate isomerase activity -0.020880
56 COG3212 peptidase 0.020875
57 COG1129 ABC transporter 0.020728
58 COG0594 ribonuclease P activity -0.020717
59 COG1993 acr, cog1993 0.020659
60 COG0398 Pfam SNARE associated Golgi protein -0.020628
61 COG1832 CoA-binding protein 0.020599
62 COG1428 Deoxynucleoside kinase -0.020472
63 COG1331 Highly conserved protein containing a thioredoxin domain 0.020433
64 COG5377 YqaJ viral recombinase family -0.020190
65 COG3639 organic phosphonate transmembrane transporter activity -0.020180
66 COG0558 Belongs to the CDP-alcohol phosphatidyltransferase class-I family -0.020064
67 COG0013 Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction alanine is first activated by ATP to form Ala- AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain -0.019933
68 COG1609 Transcriptional regulator 0.019777
69 COG1355 regulation of microtubule-based process 0.019704
70 COG1517 CRISPR-associated protein, TM1812 family 0.019650
71 COG1230 cation diffusion facilitator family transporter 0.019546
72 COG0148 phosphopyruvate hydratase activity -0.019486
73 COG2378 regulation of single-species biofilm formation -0.019473
74 COG3711 transcriptional antiterminator -0.019302
75 COG0834 ABC-type amino acid transport signal transduction systems periplasmic component domain -0.019199
76 COG3937 granule-associated protein 0.019172
77 COG1367 TIGRFAM CRISPR-associated RAMP protein, Cmr1 family 0.019016
78 COG1721 protein (some members contain a von Willebrand factor type A (vWA) domain 0.019013
79 COG2151 metal-sulfur cluster biosynthetic enzyme 0.018997
80 COG2177 Part of the ABC transporter FtsEX involved in 0.018961
81 COG4627 Pfam Methyltransferase -0.018952
82 COG0466 ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner -0.018896
83 COG1801 Protein of unknown function DUF72 0.018826
84 COG3387 PFAM Glycoside hydrolase 15-related 0.018730
85 COG3883 PFAM NLP P60 protein 0.018720
86 COG2771 luxR family -0.018601
87 COG1553 Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions. Accepts sulfur from TusA and transfers it in turn to TusE 0.018573
88 COG1328 CTP reductase activity 0.018546
89 COG2154 pterin-4-alpha-carbinolamine dehydratase 0.018524
90 COG2840 Smr protein MutS2 -0.018432
91 COG1190 Belongs to the class-II aminoacyl-tRNA synthetase family -0.018281
92 COG1774 PSP1 C-terminal conserved region 0.018192
93 COG0300 oxidoreductase activity -0.018186
94 COG3031 protein transport across the cell outer membrane 0.018071
95 COG4916 TIR domain 0.018033
96 COG0236 Carrier of the growing fatty acid chain in fatty acid biosynthesis 0.017973
97 COG2945 thiolester hydrolase activity 0.017965
98 COG0260 Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides -0.017959
99 COG0194 GDP metabolic process -0.017891
100 COG0760 Chaperone involved in the correct folding and assembly of outer membrane proteins. Recognizes specific patterns of aromatic residues and the orientation of their side chains, which are found more frequently in integral outer membrane proteins. May act in both early periplasmic and late outer membrane-associated steps of protein maturation -0.017861
101 COG0017 Asparaginyl-tRNA synthetase -0.017815
102 COG2240 Pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate (PLP). Catalyzes the phosphorylation of pyridoxal to PLP -0.017781
103 COG0266 class I DNA-(apurinic or apyrimidinic site) endonuclease activity -0.017750
104 COG0591 Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family -0.017716
105 COG1074 ATP-dependent DNA helicase activity -0.017673
106 COG0698 ribose 5-phosphate isomerase -0.017453
107 COG1924 4 iron, 4 sulfur cluster binding -0.017424
108 COG2344 Modulates transcription in response to changes in cellular NADH NAD( ) redox state 0.017385
109 COG3474 cytochrome 0.017356
110 COG1293 RNA-binding protein homologous to eukaryotic snRNP 0.017347
111 33BH1 0.017345
112 COG2274 protein secretion by the type I secretion system -0.017294
113 COG1669 hydrolase activity, acting on ester bonds 0.017270
114 COG3221 ABC-type phosphate phosphonate transport system periplasmic component -0.017266
115 COG3041 Addiction module toxin RelE StbE family -0.017230
116 COG2524 Domain in cystathionine beta-synthase and other proteins. 0.017228
117 COG3113 response to antibiotic 0.017178
118 COG1794 racemase activity, acting on amino acids and derivatives -0.017093
119 COG1619 proteins homologs of microcin C7 resistance protein MccF -0.017063
120 COG1959 2 iron, 2 sulfur cluster binding 0.017058
121 COG1454 alcohol dehydrogenase 0.017050
122 COG2310 stress, protein -0.017035
123 COG1054 Belongs to the UPF0176 family -0.017005
124 COG3797 Protein conserved in bacteria -0.016990
125 COG1683 Conserved Protein 0.016958
126 COG3568 Endonuclease Exonuclease Phosphatase -0.016864
127 COG4766 ethanolamine catabolic process -0.016820
128 COG1085 galactose-1-phosphate uridylyltransferase 0.016705
129 COG5438 YibE/F-like protein -0.016695
130 COG3550 peptidyl-serine autophosphorylation -0.016689
131 COG4268 DNA restriction-modification system -0.016656
132 3373B 0.016630
133 COG1690 Belongs to the RtcB family 0.016602
134 COG0702 epimerase -0.016585
135 COG3087 Lytic transglycosylase with a strong preference for naked glycan strands that lack stem peptides -0.016575
136 COG1564 THIamine pyrophosphokinase 0.016569
137 COG0716 FMN binding -0.016466
138 COG1741 Belongs to the pirin family -0.016456
139 COG2254 TIGRFAM CRISPR-associated helicase Cas3 0.016451
140 COG2382 esterase 0.016439
141 COG4105 Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane -0.016363
142 32YVX Protein of unknown function (DUF2905) 0.016361
143 COG4176 ABC-type proline glycine betaine transport system permease component -0.016327
144 COG4175 Glycine betaine -0.016327
145 COG1336 Crispr-associated ramp protein, Cmr4 family 0.016303
146 COG3668 Plasmid stabilization system -0.016252
147 COG0696 Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate -0.016178
148 COG1183 phosphatidylcholine synthase activity -0.016175
149 COG2246 polysaccharide biosynthetic process 0.016148
150 COG0560 Phosphoserine phosphatase -0.016126
151 COG3693 PFAM glycoside hydrolase, family 10 0.016124
152 COG2314 TM2 domain -0.016094
153 COG0308 aminopeptidase N -0.016082
154 COG1393 Belongs to the ArsC family -0.016063
155 COG1928 C-terminal four TMM region of protein-O-mannosyltransferase 0.016042
156 COG0421 Catalyzes the irreversible transfer of a propylamine group from the amino donor S-adenosylmethioninamine (decarboxy- AdoMet) to putrescine (1,4-diaminobutane) to yield spermidine 0.016037
157 COG4753 response regulator -0.016023
158 COG1186 Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA -0.016017
159 COG0586 Pfam SNARE associated Golgi protein -0.016012
160 COG1235 May be involved in the transport of PQQ or its precursor to the periplasm -0.016009
161 COG2041 Part of the MsrPQ system that repairs oxidized periplasmic proteins containing methionine sulfoxide residues (Met-O), using respiratory chain electrons. Thus protects these proteins from oxidative-stress damage caused by reactive species of oxygen and chlorine generated by the host defense mechanisms. MsrPQ is essential for the maintenance of envelope integrity under bleach stress, rescuing a wide series of structurally unrelated periplasmic proteins from methionine oxidation. The catalytic subunit MsrP is non-stereospecific, being able to reduce both (R-) and (S-) diastereoisomers of methionine sulfoxide 0.015983
162 COG1626 Provides the cells with the ability to utilize trehalose at high osmolarity by splitting it into glucose molecules that can subsequently be taken up by the phosphotransferase-mediated uptake system 0.015982
163 COG1144 Oxidoreductase 0.015932
164 COG1769 CRISPR-associated protein (Cas_Cmr3) 0.015895
165 COG2308 Evidence 4 Homologs of previously reported genes of -0.015888
166 COG0310 cobalt ion transport 0.015807
167 COG0627 Serine hydrolase involved in the detoxification of formaldehyde -0.015800
168 2ZESX 0.015760
169 COG4214 carbohydrate transport 0.015737
170 COG0476 Involved in molybdopterin and thiamine biosynthesis, family 2 0.015714
171 COG1918 ferrous iron import across plasma membrane 0.015695
172 COG2045 Belongs to the ComB family 0.015633
173 COG0387 Pfam Sodium calcium exchanger 0.015566
174 COG0391 Required for morphogenesis under gluconeogenic growth conditions 0.015566
175 COG1335 isochorismatase 0.015560
176 COG1332 CRISPR-associated RAMP protein, Csm5 family 0.015545
177 COG0046 Part of the phosphoribosylformylglycinamidine synthase complex involved in the purines biosynthetic pathway. Catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to yield formylglycinamidine ribonucleotide (FGAM) and glutamate. The FGAM synthase complex is composed of three subunits. PurQ produces an ammonia molecule by converting glutamine to glutamate. PurL transfers the ammonia molecule to FGAR to form FGAM in an ATP-dependent manner. PurS interacts with PurQ and PurL and is thought to assist in the transfer of the ammonia molecule from PurQ to PurL 0.015545
178 COG1132 (ABC) transporter -0.015526
179 COG3476 COG3476 Tryptophan-rich sensory protein (mitochondrial benzodiazepine receptor homolog) -0.015448
180 COG2358 TRAP transporter, solute receptor (TAXI family -0.015447
181 COG0756 dUTP diphosphatase activity -0.015441
182 COG2929 Ribonuclease toxin, BrnT, of type II toxin-antitoxin system 0.015416
183 COG2359 stage V sporulation protein S 0.015416
184 COG1076 Co-chaperone involved in the maturation of iron-sulfur cluster-containing proteins. Seems to help targeting proteins to be folded toward HscA -0.015355
185 COG0153 Catalyzes the transfer of the gamma-phosphate of ATP to D-galactose to form alpha-D-galactose-1-phosphate (Gal-1-P) 0.015340
186 COG1796 DNA polymerase 0.015309
187 COG1122 ATPase activity -0.015298
188 COG3757 hydrolase, family 25 -0.015277
189 COG1288 antiporter activity -0.015235
190 COG1321 iron dependent repressor 0.015209
191 COG2072 flavoprotein involved in K transport -0.015196
192 2ZCN4 0.015191
193 COG0672 )-iron permease 0.015146
194 COG1811 Na channel or pump 0.015142
195 COG1566 PFAM secretion protein HlyD family protein -0.015118
196 COG1490 D-aminoacyl-tRNA deacylase activity 0.015089
197 COG2884 Cell division ATP-binding protein ftsE 0.015038
198 COG4181 ATPase activity -0.014986
199 COG5350 Protein tyrosine phosphatase -0.014969
200 COG3576 pyridoxamine 5-phosphate -0.014967
201 COG0288 reversible hydration of carbon dioxide -0.014942
202 COG5547 Small integral membrane protein 0.014931
203 COG0714 Associated with various cellular activities 0.014882
204 COG0584 glycerophosphoryl diester phosphodiesterase -0.014881
205 COG4823 Abi-like protein -0.014868
206 3432K Helix-turn-helix domain 0.014823
207 COG1878 Catalyzes the hydrolysis of N-formyl-L-kynurenine to L- kynurenine, the second step in the kynurenine pathway of tryptophan degradation 0.014803
208 COG3448 diguanylate cyclase activity -0.014803
209 COG1567 CRISPR-associated RAMP protein, Csm4 family 0.014744
210 COG4866 Psort location Cytoplasmic, score -0.014735
211 COG2153 protein acetylation -0.014728
212 COG1836 PFAM Integral membrane protein DUF92 0.014719
213 COG1476 TRANSCRIPTIONal -0.014714
214 COG1748 Saccharopine dehydrogenase -0.014711
215 COG0802 atpase or kinase -0.014699
216 COG3337 CRISPR-associated protein (Cas_Cmr5) 0.014689
217 COG0733 neurotransmitter:sodium symporter activity -0.014665
218 COG2827 Endonuclease containing a URI domain -0.014598
219 COG1238 metal cluster binding -0.014597
220 COG3411 Ferredoxin 0.014578
221 COG0694 Involved in iron-sulfur cluster biogenesis. Binds a 4Fe- 4S cluster, can transfer this cluster to apoproteins, and thereby intervenes in the maturation of Fe S proteins. Could also act as a scaffold chaperone for damaged Fe S proteins -0.014578
222 COG1038 Catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second -0.014569
223 COG0639 Hydrolyzes diadenosine 5',5'''-P1,P4-tetraphosphate to yield ADP -0.014547
224 COG2350 Protein conserved in bacteria -0.014547
225 COG2320 Catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A -0.014499
226 COG4115 mRNA cleavage -0.014483
227 33BVW 0.014442
228 COG1643 Atp-dependent helicase -0.014427
229 COG5184 regulator of chromosome condensation, RCC1 0.014424
230 COG0220 tRNA (guanine-N7-)-methyltransferase activity -0.014410
231 COG1814 membrane 0.014395
232 COG0641 radical SAM 0.014394
233 COG2313 pseudouridylate synthase activity 0.014350
234 COG2191 Formylmethanofuran dehydrogenase, subunit e 0.014328
235 COG4123 Specifically methylates the adenine in position 37 of tRNA(1)(Val) (anticodon cmo5UAC) -0.014319
236 COG1193 negative regulation of DNA recombination 0.014318
237 COG5635 Nacht domain -0.014314
238 COG5542 integral membrane protein 0.014309
239 COG4405 Protein conserved in bacteria -0.014291
240 COG0425 Belongs to the sulfur carrier protein TusA family 0.014261
241 COG3525 Glycosyl hydrolase, family 20, catalytic domain 0.014218
242 COG2264 protein methyltransferase activity 0.014205
243 COG3381 protein complex oligomerization 0.014161
244 COG1292 Belongs to the BCCT transporter (TC 2.A.15) family -0.014151
245 COG1217 gtp-binding protein TYPA -0.014140
246 COG0235 Class ii aldolase -0.014128
247 COG3636 A helicase nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit has ssDNA-dependent ATPase and 5'-3' helicase activity. When added to pre-assembled RecBC greatly stimulates nuclease activity and augments holoenzyme processivity. Negatively regulates the RecA-loading ability of RecBCD -0.014108
248 COG0688 phosphatidylethanolamine metabolic process -0.014044
249 2ZUM9 0.014039
250 COG1330 A helicase nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit recognizes the wild- type Chi sequence, and when added to isolated RecB increases its ATP-dependent helicase processivity -0.014035