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 COG1850 ribulose-bisphosphate carboxylase activity 0.030230
2 COG1969 Ni Fe-hydrogenase, b-type cytochrome subunit 0.026399
3 COG2723 6-phospho-beta-galactosidase activity -0.026337
4 COG0375 protein maturation 0.024789
5 COG0378 Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG 0.023158
6 COG0374 Belongs to the NiFe NiFeSe hydrogenase large subunit family 0.023050
7 COG0349 Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides -0.022868
8 COG1435 thymidine kinase activity -0.022743
9 COG1740 oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor 0.022635
10 COG0298 carbon dioxide binding 0.021989
11 COG0409 Hydrogenase expression formation protein 0.021989
12 COG0068 Along with HypE, it catalyzes the synthesis of the CN ligands of the active site iron of NiFe -hydrogenases using carbamoylphosphate as a substrate. It functions as a carbamoyl transferase using carbamoylphosphate as a substrate and transferring the carboxamido moiety in an ATP-dependent reaction to the thiolate of the C-terminal cysteine of HypE yielding a protein-S-carboxamide 0.021682
13 COG4451 ribulose bisphosphate carboxylase, small 0.021403
14 COG2962 Rard protein -0.021290
15 COG0295 cytidine deaminase activity -0.020900
16 COG2008 Catalyzes the cleavage of L-allo-threonine and L- threonine to glycine and acetaldehyde -0.020720
17 COG1533 DNA photolyase activity 0.020715
18 COG1773 rubredoxin 0.020559
19 COG2862 Uncharacterized protein family, UPF0114 0.019902
20 COG1633 Catalyzes the formation of the isocyclic ring in chlorophyll biosynthesis. Mediates the cyclase reaction, which results in the formation of divinylprotochlorophyllide (Pchlide) characteristic of all chlorophylls from magnesium-protoporphyrin IX 13-monomethyl ester (MgPMME) 0.019681
21 COG3666 COG3666 Transposase and inactivated derivatives 0.019050
22 COG0644 oxidoreductase 0.018668
23 COG0843 Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Subunits 1- 3 form the functional core of the enzyme complex. CO I is the catalytic subunit of the enzyme. Electrons originating in cytochrome c are transferred via the copper A center of subunit 2 and heme A of subunit 1 to the bimetallic center formed by heme A3 and copper B -0.018619
24 COG0680 Initiates the rapid degradation of small, acid-soluble proteins during spore germination 0.018566
25 COG0602 queuosine metabolic process 0.018553
26 COG0017 Asparaginyl-tRNA synthetase -0.018505
27 COG2020 methyltransferase activity 0.018480
28 COG0584 glycerophosphoryl diester phosphodiesterase -0.018479
29 COG0247 lactate metabolic process 0.018438
30 COG2818 Glycosylase -0.018428
31 COG3743 rRNA binding -0.018345
32 COG2195 Cleaves the N-terminal amino acid of tripeptides -0.018325
33 COG0309 Hydrogenase expression formation protein (HypE) 0.018158
34 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 0.017942
35 COG0851 Prevents the cell division inhibition by proteins MinC and MinD at internal division sites while permitting inhibition at polar sites. This ensures cell division at the proper site by restricting the formation of a division septum at the midpoint of the long axis of the cell 0.017895
36 COG3883 PFAM NLP P60 protein -0.017739
37 COG0011 TIGRFAM Protein of 0.017500
38 COG3005 denitrification pathway 0.017450
39 COG3344 reverse transcriptase -0.017349
40 COG0561 phosphatase activity -0.017267
41 COG2348 transferase activity, transferring amino-acyl groups -0.017131
42 339P0 KaiB 0.016885
43 COG2986 histidine ammonia-lyase -0.016623
44 COG1145 4fe-4S ferredoxin, iron-sulfur binding domain protein 0.016620
45 COG1566 PFAM secretion protein HlyD family protein 0.016582
46 COG0058 SHG alpha-glucan phosphorylase activity 0.016441
47 COG0580 Belongs to the MIP aquaporin (TC 1.A.8) family -0.016212
48 COG3533 Beta-L-arabinofuranosidase, GH127 -0.016167
49 COG4907 membrane protein (DUF2207) -0.016139
50 COG0371 Dehydrogenase 0.016127
51 COG4785 May be involved in cell division -0.016126
52 COG2076 Multidrug Resistance protein 0.016076
53 COG3865 3-Demethylubiquinone-9 3-methyltransferase 0.016069
54 COG5424 Ring cyclization and eight-electron oxidation of 3a-(2- amino-2-carboxyethyl)-4,5-dioxo-4,5,6,7,8,9-hexahydroquinoline- 7,9-dicarboxylic-acid to PQQ 0.016047
55 COG2187 AAA domain 0.015974
56 COG1438 arginine binding -0.015894
57 COG1979 alcohol dehydrogenase -0.015881
58 COG1738 Involved in the import of queuosine (Q) precursors, required for Q precursor salvage -0.015826
59 COG1926 phosphoribosyltransferase 0.015824
60 COG1289 transmembrane transporter activity 0.015785
61 COG4091 Methyl-accepting Chemotaxis protein 0.015754
62 COG2115 Belongs to the xylose isomerase family -0.015727
63 COG3940 Belongs to the glycosyl hydrolase 43 family -0.015713
64 COG1652 LysM domain -0.015623
65 COG1950 PFAM Membrane protein of 0.015595
66 COG0384 phenazine biosynthesis protein PhzF -0.015576
67 COG4695 Portal protein -0.015555
68 COG0620 Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation 0.015541
69 COG0075 2-aminoethylphosphonate-pyruvate transaminase activity 0.015520
70 COG1054 Belongs to the UPF0176 family -0.015519
71 COG1820 Belongs to the metallo-dependent hydrolases superfamily. NagA family -0.015468
72 COG1236 Exonuclease of the beta-lactamase fold involved in RNA processing 0.015448
73 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 0.015434
74 COG0738 Major facilitator superfamily -0.015413
75 COG4916 TIR domain 0.015382
76 COG1011 Hydrolase -0.015324
77 COG1429 ligase activity, forming nitrogen-metal bonds 0.015260
78 COG4260 virion core protein, lumpy skin disease virus -0.015196
79 COG2379 hydroxypyruvate reductase 0.015152
80 COG2049 5-oxoprolinase (ATP-hydrolyzing) activity 0.015099
81 COG0850 regulation of cytokinetic process 0.015076
82 COG0589 response to stress 0.015047
83 COG1434 Gram-negative-bacterium-type cell wall biogenesis 0.014960
84 COG2055 Belongs to the LDH2 MDH2 oxidoreductase family -0.014928
85 COG4325 translation initiation factor activity -0.014928
86 COG3395 kinase activity 0.014761
87 COG4309 conserved protein (DUF2249) -0.014580
88 COG5405 Protease subunit of a proteasome-like degradation complex believed to be a general protein degrading machinery 0.014566
89 COG0287 Prephenate dehydrogenase 0.014503
90 COG0657 acetylesterase activity -0.014492
91 COG4301 Catalyzes the SAM-dependent triple methylation of the alpha-amino group of histidine to form hercynine, a step in the biosynthesis pathway of ergothioneine 0.014441
92 COG1981 membrane 0.014437
93 COG1416 DNA-binding transcription factor activity 0.014424
94 COG1144 Oxidoreductase 0.014367
95 COG3507 Belongs to the glycosyl hydrolase 43 family -0.014355
96 COG2191 Formylmethanofuran dehydrogenase, subunit e 0.014352
97 COG1501 Belongs to the glycosyl hydrolase 31 family -0.014287
98 COG1487 ribonuclease activity 0.014266
99 COG4989 oxidoreductase activity -0.014227
100 COG3712 iron ion homeostasis 0.014224
101 COG1733 regulation of RNA biosynthetic process -0.014115
102 COG1151 hydroxylamine reductase activity 0.014105
103 COG4181 ATPase activity -0.014088
104 COG1898 dTDP-4-dehydrorhamnose 3,5-epimerase activity 0.014049
105 COG1366 Belongs to the anti-sigma-factor antagonist family -0.014046
106 2ZCCT Glyoxalase-like domain -0.013990
107 COG0189 ligase activity 0.013978
108 COG4185 zeta toxin -0.013953
109 COG0860 N-Acetylmuramoyl-L-alanine amidase 0.013883
110 2ZMC1 -0.013867
111 COG3358 COGs COG3358 conserved -0.013858
112 COG1594 Catalyzes the reduction of ribonucleotides to deoxyribonucleotides. May function to provide a pool of deoxyribonucleotide precursors for DNA repair during oxygen limitation and or for immediate growth after restoration of oxygen -0.013852
113 COG3521 Type VI secretion 0.013791
114 COG0814 amino acid -0.013783
115 COG5283 actin binding -0.013779
116 COG3705 Required for the first step of histidine biosynthesis. May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine 0.013766
117 COG4912 Dna alkylation repair -0.013742
118 COG3185 4-Hydroxyphenylpyruvate dioxygenase -0.013710
119 COG0535 radical SAM domain protein 0.013702
120 COG2932 Transcriptional regulator 0.013698
121 COG2257 FlhB HrpN YscU SpaS Family 0.013669
122 33D9H Peptidase propeptide and YPEB domain 0.013650
123 COG5330 Evidence 4 Homologs of previously reported genes of 0.013611
124 COG2069 CO dehydrogenase acetyl-CoA synthase delta subunit 0.013521
125 COG2391 methyltransferase activity 0.013494
126 32YPT -0.013448
127 COG0338 D12 class N6 adenine-specific DNA methyltransferase -0.013443
128 2Z9II PEGA domain -0.013439
129 COG0214 Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by the PdxT subunit. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively -0.013429
130 COG1393 Belongs to the ArsC family 0.013425
131 COG0134 indole-3-glycerol-phosphate synthase activity 0.013417
132 COG4972 Pilus assembly protein -0.013358
133 COG1058 Belongs to the CinA family 0.013352
134 32STP 0.013335
135 COG3954 Phosphoribulokinase 0.013326
136 COG2025 fatty acid beta-oxidation using acyl-CoA dehydrogenase -0.013312
137 COG2086 electron transfer activity -0.013312
138 COG2166 iron-sulfur cluster assembly -0.013268
139 COG2936 dipeptidyl-peptidase activity -0.013253
140 COG3642 lipopolysaccharide core region biosynthetic process 0.013248
141 COG1443 Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP) -0.013241
142 COG0035 Catalyzes the conversion of uracil and 5-phospho-alpha- D-ribose 1-diphosphate (PRPP) to UMP and diphosphate -0.013216
143 COG1609 Transcriptional regulator -0.013210
144 COG0396 ATPase activity -0.013190
145 COG0719 Fe-S assembly protein -0.013190
146 COG4774 siderophore transport 0.013164
147 COG1433 Dinitrogenase iron-molybdenum cofactor 0.013141
148 COG3345 alpha-galactosidase -0.013140
149 COG1474 Belongs to the peptidase S16 family -0.013107
150 COG0474 ATPase, P-type transporting, HAD superfamily, subfamily IC 0.013067
151 COG2222 sugar isomerase -0.013060
152 COG3381 protein complex oligomerization 0.013002
153 COG3342 major pilin protein fima -0.012986
154 COG2220 Zn-dependent hydrolases of the beta-lactamase fold -0.012979
155 COG5501 0.012954
156 COG1972 Belongs to the concentrative nucleoside transporter (CNT) (TC 2.A.41) family -0.012950
157 COG2356 endonuclease I -0.012890
158 COG2893 phosphoenolpyruvate-dependent sugar phosphotransferase system 0.012866
159 COG1956 GAF domain-containing protein -0.012816
160 COG5403 PFAM Bacterial protein of -0.012814
161 COG0311 Catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the biosynthesis of pyridoxal 5'-phosphate. The resulting ammonia molecule is channeled to the active site of PdxS -0.012792
162 COG0146 N-methylhydantoinase B acetone carboxylase alpha subunit 0.012785
163 COG2603 Catalyzes the transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA 0.012770
164 COG4653 Phage capsid family -0.012768
165 COG3886 PLD-like domain -0.012756
166 COG1514 Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'- phosphomonoester 0.012721
167 COG0423 glycine-tRNA ligase activity -0.012718
168 COG1092 Specifically methylates the guanine in position 2445 (m2G2445) and the guanine in position 2069 (m7G2069) of 23S rRNA -0.012700
169 COG3349 Catalyzes the conversion of zeta-carotene to lycopene via the intermediary of neurosporene. It carries out two consecutive desaturations (introduction of double bonds) at positions C-7 and C-7' 0.012690
170 COG1538 Outer membrane efflux protein 0.012679
171 COG5271 translation initiation factor activity 0.012650
172 COG5646 InterPro IPR014922 -0.012646
173 COG2048 Heterodisulfide reductase, subunit B 0.012645
174 COG3104 oligopeptide transport -0.012643
175 COG1739 Uncharacterized protein family UPF0029 -0.012571
176 COG1723 PFAM Uncharacterised ACR, YagE family COG1723 0.012567
177 COG2138 Cobalamin (vitamin B12) biosynthesis CbiX protein 0.012550
178 COG1209 Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis 0.012537
179 COG4799 Acetyl-CoA carboxylase, carboxyltransferase component subunits alpha and beta -0.012519
180 COG1018 Is involved in NO detoxification in an aerobic process, termed nitric oxide dioxygenase (NOD) reaction that utilizes O(2) and NAD(P)H to convert NO to nitrate, which protects the bacterium from various noxious nitrogen compounds. Therefore, plays a central role in the inducible response to nitrosative stress -0.012486
181 COG5625 HemY protein N-terminus 0.012462
182 COG0627 Serine hydrolase involved in the detoxification of formaldehyde -0.012450
183 COG2313 pseudouridylate synthase activity -0.012449
184 COG1764 response to oxidative stress -0.012442
185 COG0400 carboxylic ester hydrolase activity -0.012433
186 COG3921 Protein conserved in bacteria 0.012425
187 COG2866 Carboxypeptidase -0.012411
188 COG2937 Belongs to the GPAT DAPAT family -0.012409
189 COG3246 L-lysine catabolic process to acetate 0.012371
190 COG2353 YceI-like domain -0.012367
191 COG4067 protein conserved in archaea -0.012343
192 COG1492 cobalamin metabolic process 0.012340
193 COG0001 glutamate-1-semialdehyde 2,1-aminomutase activity 0.012323
194 32SEB 0.012298
195 2ZITU Cupin domain 0.012266
196 COG1618 nucleotide phosphatase activity, acting on free nucleotides 0.012254
197 COG5107 Psort location Cytoplasmic, score 8.96 -0.012254
198 COG3809 Transcription factor zinc-finger -0.012252
199 33N16 -0.012241
200 COG3093 addiction module antidote protein HigA 0.012238
201 COG1273 With LigD forms a non-homologous end joining (NHEJ) DNA repair enzyme, which repairs dsDNA breaks with reduced fidelity. Binds linear dsDNA with 5'- and 3'- overhangs but not closed circular dsDNA nor ssDNA. Recruits and stimulates the ligase activity of LigD 0.012236
202 COG5153 cell wall organization 0.012234
203 COG2963 transposase activity -0.012231
204 COG5470 NIPSNAP family containing protein 0.012180
205 2ZBES 0.012174
206 30ICB -0.012172
207 COG1760 l-serine dehydratase -0.012172
208 COG2221 Nitrite and sulphite reductase 4Fe-4S 0.012162
209 COG4764 Protein conserved in bacteria -0.012161
210 COG1560 Kdo2-lipid A biosynthetic process -0.012135
211 COG1742 UPF0060 membrane protein 0.012111
212 32YVX Protein of unknown function (DUF2905) 0.012103
213 COG3000 fatty acid hydroxylase -0.012102
214 COG4174 ABC transporter (Permease) -0.012081
215 COG1641 Involved in the biosynthesis of a nickel-pincer cofactor ((SCS)Ni(II) pincer complex). Binds Ni(2 ), and functions in nickel delivery to pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN), to form the mature cofactor. Is thus probably required for the activation of nickel-pincer cofactor- dependent enzymes 0.012060
216 COG0550 Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone -0.012048
217 COG0158 D-fructose-1,6-bisphosphate 1-phosphohydrolase class 1 0.012021
218 COG3402 PFAM membrane-flanked domain -0.011949
219 COG5483 Protein of unknown function, DUF488 0.011943
220 COG0705 Rhomboid family 0.011942
221 COG3914 O-linked N-acetylglucosamine transferase SPINDLY family 0.011911
222 COG4630 Xanthine dehydrogenase iron-sulfur cluster and FAD-binding subunit A 0.011904
223 COG1270 Converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group 0.011888
224 COG2175 clavaminate synthase activity -0.011885
225 COG0852 NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient 0.011857
226 COG1476 TRANSCRIPTIONal -0.011841
227 COG4196 transglutaminase domain protein 0.011832
228 COG0780 Catalyzes the NADPH-dependent reduction of 7-cyano-7- deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) 0.011813
229 COG1239 Involved in chlorophyll biosynthesis. Catalyzes the insertion of magnesium ion into protoporphyrin IX to yield Mg- protoporphyrin IX 0.011797
230 COG0661 Is probably a protein kinase regulator of UbiI activity which is involved in aerobic coenzyme Q (ubiquinone) biosynthesis 0.011790
231 COG3975 serine-type endopeptidase activity 0.011740
232 COG2185 Catalyzes the reversible interconversion of isobutyryl- CoA and n-butyryl-CoA, using radical chemistry. Also exhibits GTPase activity, associated with its G-protein domain (MeaI) that functions as a chaperone that assists cofactor delivery and proper holo-enzyme assembly -0.011726
233 COG2233 PERMEase -0.011708
234 2ZC4V -0.011705
235 COG3222 Protein conserved in bacteria -0.011695
236 COG2894 cell division 0.011685
237 COG3913 Uncharacterized protein conserved in bacteria (DUF2094) 0.011673
238 COG1320 monovalent cation:proton antiporter activity 0.011621
239 COG1863 multisubunit Na H antiporter MnhE subunit 0.011621
240 COG2089 acid synthase 0.011535
241 COG1364 Catalyzes two activities which are involved in the cyclic version of arginine biosynthesis the synthesis of N- acetylglutamate from glutamate and acetyl-CoA as the acetyl donor, and of ornithine by transacetylation between N(2)-acetylornithine and glutamate 0.011527
242 COG0759 Could be involved in insertion of integral membrane proteins into the membrane 0.011524
243 COG3646 Phage regulatory protein -0.011517
244 COG0176 Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway 0.011514
245 30BPJ -0.011474
246 COG1032 radical SAM domain protein 0.011474
247 COG1865 Adenosylcobinamide amidohydrolase 0.011470
248 344FT Cupin domain 0.011453
249 COG1284 Uncharacterised 5xTM membrane BCR, YitT family COG1284 -0.011439
250 COG1622 oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor -0.011421