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 COG0736 holo-[acyl-carrier-protein] synthase activity -0.038030
2 COG0221 Catalyzes the hydrolysis of inorganic pyrophosphate (PPi) forming two phosphate ions -0.027039
3 348N2 -0.024588
4 COG0185 Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA -0.024466
5 COG0102 This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly -0.023435
6 COG0465 Acts as a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. Plays a role in the quality control of integral membrane proteins -0.022798
7 COG0344 acyl-phosphate glycerol-3-phosphate acyltransferase activity -0.022790
8 COG2423 ornithine cyclodeaminase activity 0.022635
9 COG0052 Belongs to the universal ribosomal protein uS2 family -0.022106
10 COG0096 One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit -0.022106
11 COG0097 This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7 L12 stalk, and near the tRNA binding site of the peptidyltransferase center -0.022106
12 COG0319 Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA -0.022036
13 COG1984 allophanate hydrolase subunit 2 0.021996
14 COG0775 Catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S- adenosylhomocysteine (SAH AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively -0.021428
15 COG0441 Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr) -0.021151
16 COG0733 neurotransmitter:sodium symporter activity 0.020473
17 COG0125 Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis -0.020112
18 COG3169 Protein conserved in bacteria -0.020079
19 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 -0.020050
20 COG0080 Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors -0.020050
21 COG0564 pseudouridine synthase activity -0.020050
22 COG0592 DNA-directed DNA polymerase activity -0.020050
23 COG0629 single-stranded DNA binding -0.020050
24 COG0653 protein targeting -0.020050
25 COG0691 Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene -0.020050
26 COG2812 DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity -0.020050
27 COG0571 ribonuclease III activity -0.020050
28 COG0706 membrane insertase activity -0.020050
29 COG0435 Glutathione S-transferase 0.019893
30 COG2091 lysine biosynthetic process via aminoadipic acid 0.019861
31 COG3485 protocatechuate 3,4-dioxygenase -0.019847
32 COG0623 enoyl-[acyl-carrier-protein] reductase (NADH) activity -0.019830
33 COG1979 alcohol dehydrogenase 0.019786
34 COG0816 Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA -0.019495
35 COG0255 Belongs to the universal ribosomal protein uL29 family -0.019313
36 COG1108 ABC-type Mn2 Zn2 transport systems permease components -0.019306
37 COG0267 Belongs to the bacterial ribosomal protein bL33 family -0.019297
38 COG2232 ATP-grasp domain 0.019262
39 COG0469 pyruvate kinase activity -0.019076
40 COG0594 ribonuclease P activity -0.019073
41 COG1540 5-oxoprolinase (ATP-hydrolyzing) activity 0.019043
42 COG5239 Endonuclease/Exonuclease/phosphatase family 0.018546
43 COG2049 5-oxoprolinase (ATP-hydrolyzing) activity 0.018436
44 COG3228 Belongs to the MtfA family 0.018389
45 COG3977 Valine--pyruvate aminotransferase 0.018356
46 COG4390 Protein conserved in bacteria 0.018267
47 COG0363 glucosamine-6-phosphate deaminase activity -0.018088
48 COG3513 CRISPR (clustered regularly interspaced short palindromic repeat) is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein. The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA. Subsequently Cas9 crRNA tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer 0.018077
49 COG1284 Uncharacterised 5xTM membrane BCR, YitT family COG1284 -0.018038
50 COG0069 glutamate synthase activity 0.018021
51 32RZ1 0.017982
52 COG0791 NLP P60 protein -0.017694
53 COG1944 ATP diphosphatase activity 0.017606
54 COG0728 peptidoglycan biosynthetic process -0.017577
55 COG0783 Belongs to the Dps family -0.017492
56 COG4758 membrane 0.017448
57 COG1106 Psort location Cytoplasmic, score -0.017399
58 2Z9E6 Capsule assembly protein Wzi 0.017384
59 COG0813 purine-nucleoside phosphorylase activity -0.017266
60 COG0286 site-specific DNA-methyltransferase (adenine-specific) activity -0.017193
61 COG4446 Protein conserved in bacteria 0.017188
62 COG3240 lipase activity 0.017101
63 COG0282 Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction -0.017089
64 COG0416 fatty acid biosynthetic process -0.016916
65 COG1418 mRNA catabolic process -0.016892
66 COG2947 Ubiquinol--cytochrome c reductase -0.016716
67 COG3129 Specifically methylates the adenine in position 1618 of 23S rRNA 0.016707
68 COG0459 protein refolding -0.016701
69 COG2764 glyoxalase bleomycin resistance protein dioxygenase -0.016680
70 COG0471 metal ion transport 0.016667
71 COG0154 amidase activity -0.016599
72 COG5572 integral membrane protein 0.016503
73 COG4125 Chlorhexidine efflux transporter 0.016501
74 COG3316 Transposase and inactivated derivatives 0.016433
75 COG1943 Transposase 0.016392
76 32QYJ 0.016295
77 COG4728 Protein conserved in bacteria 0.016251
78 COG2076 Multidrug Resistance protein -0.016189
79 COG2366 antibiotic biosynthetic process 0.016048
80 COG4584 PFAM Integrase catalytic -0.016010
81 COG3125 oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor -0.016006
82 COG2079 MmgE PrpD family protein 0.015861
83 COG0053 Belongs to the cation diffusion facilitator (CDF) transporter (TC 2.A.4) family -0.015822
84 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 -0.015753
85 COG0450 alkyl hydroperoxide reductase -0.015746
86 COG0103 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) -0.015732
87 COG0366 Alpha amylase catalytic -0.015728
88 COG2255 four-way junction helicase activity -0.015602
89 COG3146 Protein conserved in bacteria 0.015592
90 COG0737 Belongs to the 5'-nucleotidase family -0.015562
91 COG3595 metallopeptidase activity 0.015550
92 COG1502 Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol -0.015528
93 COG0064 Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp- tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln) -0.015510
94 2Z7NN Protein of unknown function (DUF1538) 0.015505
95 COG0071 Belongs to the small heat shock protein (HSP20) family -0.015446
96 33T1G 0.015419
97 COG2918 glutathione biosynthetic process 0.015410
98 COG2865 translation initiation factor activity -0.015393
99 COG2078 PFAM AMMECR1 domain protein 0.015258
100 COG0544 peptidyl-prolyl cis-trans isomerase activity -0.015252
101 COG4843 Uncharacterized protein conserved in bacteria (DUF2179) 0.015208
102 314ZU 0.015160
103 COG2928 Conserved Protein -0.015109
104 COG3230 heme oxygenase -0.015040
105 COG3707 response regulator -0.014993
106 346DU GDSL-like Lipase/Acylhydrolase 0.014913
107 COG4552 Acetyltransferase involved in intracellular survival and related -0.014867
108 COG5625 HemY protein N-terminus 0.014850
109 33MJX Antitoxin to bacterial toxin RNase LS or RnlA 0.014814
110 COG1738 Involved in the import of queuosine (Q) precursors, required for Q precursor salvage -0.014802
111 COG3641 Membrane 0.014789
112 COG1401 restriction endodeoxyribonuclease activity 0.014774
113 COG3710 Transcriptional regulator -0.014732
114 COG1408 metallophosphoesterase 0.014717
115 COG3774 pathogenesis 0.014701
116 COG3616 Alanine racemase, N-terminal domain 0.014696
117 32RT7 0.014677
118 COG0393 Putative heavy-metal-binding 0.014674
119 COG0428 transporter -0.014663
120 COG2944 sequence-specific DNA binding -0.014636
121 33HA8 0.014597
122 COG2962 Rard protein 0.014582
123 COG5325 Glycosyltransferase like family 0.014564
124 COG3486 L-lysine 6-monooxygenase (NADPH) activity -0.014536
125 COG0595 An RNase that has 5'-3' exonuclease and possibly endonuclease activity. Involved in maturation of rRNA and in some organisms also mRNA maturation and or decay -0.014533
126 COG1355 regulation of microtubule-based process 0.014533
127 331QF 0.014531
128 COG4895 conserved protein (DUF2196) 0.014466
129 COG0822 iron-sulfur transferase activity -0.014459
130 COG2208 phosphoserine phosphatase activity -0.014427
131 COG4719 TIGRFAM conserved repeat domain 0.014396
132 COG5416 Lipopolysaccharide assembly protein A domain -0.014343
133 COG0496 Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates -0.014259
134 COG0235 Class ii aldolase -0.014258
135 COG5217 Protein of unknown function (DUF3086) 0.014203
136 COG1183 phosphatidylcholine synthase activity -0.014193
137 COG0561 phosphatase activity -0.014134
138 COG1669 hydrolase activity, acting on ester bonds -0.014126
139 COG4731 Uncharacterized protein conserved in bacteria (DUF2147) 0.014052
140 COG3241 Transfers electrons from cytochrome c551 to cytochrome oxidase -0.014048
141 3417T 0.014041
142 COG1324 tolerance protein -0.014003
143 COG3025 triphosphatase activity 0.013970
144 COG3284 Transcriptional regulator -0.013951
145 33YJW Ankyrin repeat -0.013941
146 COG3568 Endonuclease Exonuclease Phosphatase -0.013941
147 32XSE 0.013937
148 32ZD1 Late competence development protein ComFB 0.013896
149 2Z8W3 Protein of unknown function (DUF1538) 0.013894
150 3368N 0.013894
151 3349Y 0.013883
152 COG1556 Lactate utilization protein 0.013880
153 COG2220 Zn-dependent hydrolases of the beta-lactamase fold -0.013864
154 COG4618 COG4618 ABC-type protease lipase transport system, ATPase and permease components -0.013841
155 COG0398 Pfam SNARE associated Golgi protein -0.013755
156 3027T 0.013748
157 32RP0 type III effector 0.013733
158 COG0474 ATPase, P-type transporting, HAD superfamily, subfamily IC -0.013694
159 COG0803 Belongs to the bacterial solute-binding protein 9 family -0.013620
160 COG2898 Catalyzes the transfer of a lysyl group from L-lysyl- tRNA(Lys) to membrane-bound phosphatidylglycerol (PG), which produces lysylphosphatidylglycerol (LPG), a major component of the bacterial membrane with a positive net charge. LPG synthesis contributes to bacterial virulence as it is involved in the resistance mechanism against cationic antimicrobial peptides (CAMP) produces by the host's immune system (defensins, cathelicidins) and by the competing microorganisms -0.013539
161 COG1412 self proteolysis -0.013491
162 COG3789 protein conserved in bacteria 0.013433
163 COG4890 Cyd operon protein YbgT 0.013411
164 COG4321 Ribbon-helix-helix domain -0.013408
165 32U2Y 0.013371
166 32AXC Prokaryotic dksA/traR C4-type zinc finger 0.013363
167 COG3142 Participates in the control of copper homeostasis -0.013333
168 COG0538 isocitrate dehydrogenase activity 0.013331
169 COG0636 F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation -0.013299
170 32UZ7 Protein of unknown function (DUF2933) 0.013263
171 COG1760 l-serine dehydratase 0.013260
172 COG5527 Initiator Replication protein 0.013222
173 COG4259 (LipO)protein 0.013220
174 COG0656 L-ascorbic acid biosynthetic process -0.013092
175 31CX3 COG0457 FOG TPR repeat 0.013088
176 COG2032 superoxide dismutase activity -0.013067
177 COG4171 peptide transport system, permease 0.013053
178 COG1235 May be involved in the transport of PQQ or its precursor to the periplasm -0.013049
179 309NR 0.013040
180 COG0312 modulator of DNA gyrase -0.013023
181 COG0586 Pfam SNARE associated Golgi protein -0.013017
182 COG3837 Cupin domain -0.013015
183 COG4327 Domain of unknown function (DUF4212) 0.012993
184 COG2119 membrane -0.012933
185 32TMV Bacterial inner membrane protein 0.012931
186 COG3152 Membrane -0.012916
187 COG3198 Protein conserved in bacteria 0.012886
188 32WZC HlyD family secretion protein 0.012882
189 COG1142 4fe-4S ferredoxin, iron-sulfur binding domain protein -0.012836
190 COG4445 tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE) 0.012744
191 COG1680 COG1680 Beta-lactamase class C and other penicillin binding 0.012723
192 COG1898 dTDP-4-dehydrorhamnose 3,5-epimerase activity -0.012710
193 COG2900 Belongs to the SlyX family 0.012692
194 32W8D Protein of unknown function (DUF3108) 0.012677
195 COG3202 ADP transmembrane transporter activity -0.012601
196 COG0647 UMP catabolic process -0.012590
197 32KGU 0.012580
198 COG3007 enoyl-[acyl-carrier-protein] reductase (NADH) activity 0.012579
199 2ZH66 PFAM Propeptide, PepSY amd peptidase M4 0.012569
200 2ZCF6 0.012551
201 COG2162 N-hydroxyarylamine O-acetyltransferase activity 0.012549
202 COG2346 COG2346, Truncated hemoglobins 0.012545
203 336ZM 0.012529
204 COG4262 Catalyzes the irreversible transfer of a propylamine group from the amino donor S-adenosylmethioninamine (decarboxy- AdoMet) to putrescine (1,4-diaminobutane) to yield spermidine 0.012528
205 COG3667 copper resistance 0.012519
206 COG4579 [isocitrate dehydrogenase (NADP+)] phosphatase activity 0.012504
207 2Z86E Protein of unknown function (DUF2927) -0.012491
208 COG2821 murein-degrading enzyme. may play a role in recycling of muropeptides during cell elongation and or cell division -0.012453
209 COG3021 interspecies interaction between organisms 0.012434
210 32X54 Domain of unknown function (DUF4377) 0.012416
211 COG5278 phosphoserine phosphatase activity 0.012402
212 COG4655 Putative Flp pilus-assembly TadE/G-like 0.012376
213 33HUF -0.012347
214 COG1597 lipid kinase activity -0.012339
215 COG2904 Catalyzes the NADPH-dependent reduction of 7-cyano-7- deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) 0.012312
216 330EN 23S rRNA-intervening sequence protein 0.012294
217 COG3655 Transcriptional regulator -0.012291
218 COG1711 Protein of unknown function (DUF3014) 0.012291
219 COG1925 phosphoenolpyruvate-dependent sugar phosphotransferase system -0.012285
220 33B4X 0.012229
221 COG3884 Acyl-ACP thioesterase -0.012186
222 COG3428 Bacterial PH domain 0.012169
223 COG4976 Methyltransferase -0.012134
224 COG4242 Belongs to the peptidase S51 family 0.012100
225 2ZADV 0.012097
226 2ZI89 0.012097
227 313BQ 0.012097
228 COG1211 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity -0.012077
229 COG0403 The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor 0.012062
230 COG2077 Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, respectively. Plays a role in cell protection against oxidative stress by detoxifying peroxides -0.012045
231 COG2180 nitrate reductase molybdenum cofactor assembly chaperone 0.012040
232 COG1420 regulation of RNA biosynthetic process -0.012018
233 33V6Z 0.012009
234 COG3402 PFAM membrane-flanked domain 0.012006
235 COG0287 Prephenate dehydrogenase -0.011981
236 33BUY 0.011978
237 COG1509 lysine 2,3-aminomutase activity 0.011972
238 31M4A 0.011972
239 30Q80 0.011965
240 COG2013 TIGRFAM TIGR00266 family protein -0.011952
241 COG0860 N-Acetylmuramoyl-L-alanine amidase -0.011952
242 33BAR 0.011942
243 COG5571 outer membrane autotransporter 0.011912
244 2ZE4B Protein of unknown function (DUF3187) -0.011860
245 COG3488 Thiol oxidoreductase 0.011859
246 32STP 0.011857
247 COG1964 Radical SAM superfamily 0.011836
248 2Z9JY 0.011821
249 COG3197 Cytochrome oxidase maturation protein 0.011803
250 COG3415 Transposase 0.011711