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 | COG3520 | type VI secretion protein | 0.093477 |
2 | COG3455 | Type IV VI secretion system protein, DotU family | 0.091595 |
3 | COG3517 | type VI secretion protein | 0.090988 |
4 | COG3523 | ImpA, N-terminal, type VI secretion system | 0.090538 |
5 | COG3516 | type VI secretion protein | 0.087710 |
6 | COG3522 | type VI secretion protein | 0.084804 |
7 | COG3518 | anti-sigma factor antagonist activity | 0.079786 |
8 | COG3515 | Protein conserved in bacteria | 0.074923 |
9 | COG3519 | Type VI secretion system, TssF | 0.073947 |
10 | COG3157 | Type VI secretion system effector, Hcp | 0.072735 |
11 | COG3521 | Type VI secretion | 0.059650 |
12 | COG3501 | Rhs element vgr protein | 0.057794 |
13 | COG3913 | Uncharacterized protein conserved in bacteria (DUF2094) | 0.054289 |
14 | COG4104 | PAAR repeat-containing protein | 0.050529 |
15 | COG3456 | conserved protein contains FHA domain | 0.036269 |
16 | COG4455 | Protein of avirulence locus involved in temperature-dependent protein secretion | 0.033480 |
17 | COG4249 | Peptidase C14 caspase catalytic subunit p20 | 0.031837 |
18 | COG2268 | Band 7 protein | 0.030176 |
19 | COG2603 | Catalyzes the transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA | 0.029360 |
20 | COG2216 | Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit is responsible for energy coupling to the transport system | 0.029017 |
21 | COG4968 | Prepilin-type N-terminal cleavage methylation domain | 0.028732 |
22 | COG3299 | homolog of phage Mu protein gp47 | 0.027918 |
23 | COG2055 | Belongs to the LDH2 MDH2 oxidoreductase family | -0.027557 |
24 | COG3034 | peptidoglycan biosynthetic process | 0.027278 |
25 | COG1113 | amino acid transport | 0.026977 |
26 | COG2156 | Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit acts as a catalytic chaperone that increases the ATP- binding affinity of the ATP-hydrolyzing subunit KdpB by the formation of a transient KdpB KdpC ATP ternary complex | 0.026674 |
27 | COG1262 | PFAM Formylglycine-generating sulfatase enzyme | -0.026461 |
28 | COG0300 | oxidoreductase activity | 0.026261 |
29 | COG4799 | Acetyl-CoA carboxylase, carboxyltransferase component subunits alpha and beta | -0.026206 |
30 | COG4695 | Portal protein | -0.025614 |
31 | COG1213 | nucleotidyl transferase | 0.025449 |
32 | COG2045 | Belongs to the ComB family | -0.024774 |
33 | COG0392 | lysyltransferase activity | -0.024610 |
34 | COG5435 | protein kinase activity | 0.024394 |
35 | COG1285 | pathogenesis | 0.023963 |
36 | COG4461 | 4-amino-4-deoxy-alpha-L-arabinopyranosyl undecaprenyl phosphate biosynthetic process | 0.023194 |
37 | COG3448 | diguanylate cyclase activity | 0.022822 |
38 | COG0591 | Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family | 0.022806 |
39 | COG1027 | Aspartate ammonia-lyase | 0.022750 |
40 | COG4579 | [isocitrate dehydrogenase (NADP+)] phosphatase activity | -0.022581 |
41 | COG3072 | Adenylate cyclase | 0.022444 |
42 | COG4555 | ABC transporter | -0.022329 |
43 | COG0538 | isocitrate dehydrogenase activity | -0.022170 |
44 | COG1135 | Part of the ABC transporter complex MetNIQ involved in methionine import. Responsible for energy coupling to the transport system | 0.022118 |
45 | COG4970 | Tfp pilus assembly protein FimT | 0.021813 |
46 | COG0672 | )-iron permease | -0.021679 |
47 | COG2838 | Isocitrate dehydrogenase | 0.021580 |
48 | COG3600 | Phage-associated protein | -0.021523 |
49 | COG5615 | integral membrane protein | -0.021476 |
50 | COG4252 | Chase2 domain | -0.021242 |
51 | COG4607 | ABC-type enterochelin transport system periplasmic component | 0.021132 |
52 | COG2011 | ABC-type metal ion transport system permease component | 0.021003 |
53 | COG3831 | ATPase activity | 0.020952 |
54 | COG1607 | acyl-coa hydrolase | -0.020935 |
55 | COG4307 | Protein conserved in bacteria | 0.020654 |
56 | COG0724 | RNA recognition motif | 0.020642 |
57 | COG3619 | membrane | 0.020612 |
58 | COG4857 | Catalyzes the phosphorylation of methylthioribose into methylthioribose-1-phosphate | -0.020608 |
59 | COG2461 | Hemerythrin HHE cation binding domain protein | -0.020545 |
60 | COG2831 | hemolysin activation secretion protein | 0.020491 |
61 | COG0388 | Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source | 0.020439 |
62 | COG2801 | Transposase and inactivated derivatives | 0.020425 |
63 | COG1232 | Catalyzes the 6-electron oxidation of protoporphyrinogen-IX to form protoporphyrin-IX | -0.020309 |
64 | COG3011 | Protein conserved in bacteria | 0.020242 |
65 | COG3915 | nitrate assimilation | 0.020212 |
66 | COG4253 | self proteolysis | 0.020144 |
67 | COG2895 | sulfate adenylyltransferase (ATP) activity | 0.019944 |
68 | COG0715 | COG0715 ABC-type nitrate sulfonate bicarbonate transport systems periplasmic components | -0.019933 |
69 | COG4924 | 0.019863 | |
70 | COG1636 | Catalyzes the conversion of epoxyqueuosine (oQ) to queuosine (Q), which is a hypermodified base found in the wobble positions of tRNA(Asp), tRNA(Asn), tRNA(His) and tRNA(Tyr) | -0.019670 |
71 | 32H4Q | Bacterial regulatory proteins, tetR family | 0.019490 |
72 | COG2104 | thiamine diphosphate biosynthetic process | 0.019453 |
73 | COG0428 | transporter | 0.019400 |
74 | COG1434 | Gram-negative-bacterium-type cell wall biogenesis | -0.019356 |
75 | COG3033 | Beta-eliminating lyase | -0.019303 |
76 | 32AXC | Prokaryotic dksA/traR C4-type zinc finger | -0.019205 |
77 | COG4675 | tail collar domain protein | 0.019203 |
78 | COG0402 | S-adenosylhomocysteine deaminase activity | 0.019159 |
79 | COG3172 | ATPase kinase involved in NAD metabolism | -0.019139 |
80 | COG3154 | lipid carrier protein | 0.018930 |
81 | COG4269 | membrane | -0.018865 |
82 | COG0627 | Serine hydrolase involved in the detoxification of formaldehyde | 0.018860 |
83 | COG1416 | DNA-binding transcription factor activity | -0.018846 |
84 | COG5654 | RES domain protein | -0.018845 |
85 | COG0601 | transmembrane transport | 0.018762 |
86 | COG0618 | 3'(2'),5'-bisphosphate nucleotidase activity | -0.018757 |
87 | COG2862 | Uncharacterized protein family, UPF0114 | 0.018633 |
88 | COG4692 | amylo-alpha-1,6-glucosidase activity | 0.018579 |
89 | COG2978 | secondary active p-aminobenzoyl-glutamate transmembrane transporter activity | -0.018573 |
90 | COG4254 | PFAM FecR protein | -0.018545 |
91 | COG1635 | Involved in the biosynthesis of the thiazole moiety of thiamine. Catalyzes the conversion of NAD and glycine to adenosine diphosphate 5-(2-hydroxyethyl)-4-methylthiazole-2-carboxylate (ADT), an adenylated thiazole intermediate, using free sulfide as a source of sulfur | -0.018524 |
92 | COG1984 | allophanate hydrolase subunit 2 | 0.018521 |
93 | COG0553 | Transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA. Does not activate transcription on linear DNA. Probably not involved in DNA repair | -0.018506 |
94 | COG1423 | dna ligase | 0.018504 |
95 | COG3004 | Na( ) H( ) antiporter that extrudes sodium in exchange for external protons | 0.018457 |
96 | COG3192 | ethanolamine utilization protein | 0.018444 |
97 | 32Y12 | ParD-like antitoxin of type II bacterial toxin-antitoxin system | -0.018366 |
98 | COG0826 | peptidase U32 | 0.018324 |
99 | COG3485 | protocatechuate 3,4-dioxygenase | 0.018229 |
100 | COG3469 | chitinase activity | 0.018181 |
101 | 2ZNS7 | 0.018175 | |
102 | COG1419 | protein localization to endoplasmic reticulum | 0.018102 |
103 | COG2020 | methyltransferase activity | -0.018080 |
104 | COG0683 | leucine binding | -0.018068 |
105 | COG2026 | Addiction module toxin, RelE StbE family | -0.018062 |
106 | COG2704 | Responsible for the transport of C4-dicarboxylates from the periplasm across the inner membrane | 0.017995 |
107 | COG2210 | Belongs to the sulfur carrier protein TusA family | 0.017990 |
108 | COG1765 | OsmC-like protein | -0.017898 |
109 | COG3969 | phosphoadenosine phosphosulfate | 0.017892 |
110 | COG0530 | calcium, potassium:sodium antiporter activity | -0.017865 |
111 | 32TJX | 0.017850 | |
112 | COG2610 | gluconate transmembrane transporter activity | 0.017825 |
113 | COG0154 | amidase activity | -0.017735 |
114 | COG1352 | Methylation of the membrane-bound methyl-accepting chemotaxis proteins (MCP) to form gamma-glutamyl methyl ester residues in MCP | 0.017723 |
115 | COG0327 | Belongs to the GTP cyclohydrolase I type 2 NIF3 family | -0.017703 |
116 | COG3797 | Protein conserved in bacteria | 0.017689 |
117 | COG4567 | Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain | 0.017597 |
118 | COG4978 | Transcriptional regulator | 0.017589 |
119 | COG3760 | aminoacyl-tRNA metabolism involved in translational fidelity | -0.017588 |
120 | COG2110 | phosphatase homologous to the C-terminal domain of histone macroH2A1 | 0.017561 |
121 | COG2060 | Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit binds and transports the potassium across the cytoplasmic membrane | 0.017559 |
122 | COG2356 | endonuclease I | -0.017540 |
123 | COG2040 | homocysteine | 0.017531 |
124 | COG1816 | Catalyzes the hydrolytic deamination of adenine to hypoxanthine. Plays an important role in the purine salvage pathway and in nitrogen catabolism | 0.017525 |
125 | COG3476 | COG3476 Tryptophan-rich sensory protein (mitochondrial benzodiazepine receptor homolog) | 0.017500 |
126 | COG2323 | membrane | 0.017491 |
127 | COG2854 | intermembrane phospholipid transfer | 0.017448 |
128 | COG4658 | electron transport chain | -0.017427 |
129 | COG0308 | aminopeptidase N | 0.017385 |
130 | COG1989 | Cleaves type-4 fimbrial leader sequence and methylates the N-terminal (generally Phe) residue | 0.017336 |
131 | COG1173 | ABC-type dipeptide oligopeptide nickel transport systems, permease components | 0.017319 |
132 | COG3073 | An anti-sigma factor for extracytoplasmic function (ECF) sigma factor sigma-E (RpoE). ECF sigma factors are held in an inactive form by an anti-sigma factor until released by regulated intramembrane proteolysis (RIP). RIP occurs when an extracytoplasmic signal triggers a concerted proteolytic cascade to transmit information and elicit cellular responses. The membrane-spanning regulatory substrate protein is first cut periplasmically (site-1 protease, S1P, DegS), then within the membrane itself (site-2 protease, S2P, RseP), while cytoplasmic proteases finish degrading the anti-sigma factor, liberating sigma-E | 0.017265 |
133 | COG1773 | rubredoxin | 0.017111 |
134 | COG0004 | ammonium transporteR | -0.017091 |
135 | COG2826 | transposase and inactivated derivatives, IS30 family | 0.017072 |
136 | 2Z9D2 | Psort location CytoplasmicMembrane, score | -0.017051 |
137 | COG1459 | type II secretion system | 0.017049 |
138 | COG3534 | alpha-L-arabinofuranosidase | 0.017016 |
139 | COG2962 | Rard protein | 0.016985 |
140 | COG2912 | Transglutaminase-like superfamily | -0.016981 |
141 | COG3178 | 'Phosphotransferase | -0.016968 |
142 | COG0252 | asparaginase activity | 0.016947 |
143 | 33968 | 0.016918 | |
144 | 33VRK | GDSL-like Lipase/Acylhydrolase family | -0.016873 |
145 | COG3572 | ergothioneine biosynthetic process | 0.016867 |
146 | COG1540 | 5-oxoprolinase (ATP-hydrolyzing) activity | 0.016849 |
147 | COG1823 | symporter activity | 0.016836 |
148 | COG1030 | water channel activity | 0.016827 |
149 | COG1021 | 2,3-dihydroxybenzoate-AMP ligase | 0.016801 |
150 | COG1464 | Belongs to the NlpA lipoprotein family | 0.016780 |
151 | COG2115 | Belongs to the xylose isomerase family | 0.016747 |
152 | COG3465 | dGTPase activity | 0.016733 |
153 | COG1457 | Belongs to the purine-cytosine permease (2.A.39) family | 0.016721 |
154 | COG3093 | addiction module antidote protein HigA | -0.016699 |
155 | COG3876 | Protein conserved in bacteria | -0.016634 |
156 | 34AQQ | 0.016605 | |
157 | COG2808 | Putative FMN-binding domain | 0.016581 |
158 | COG3284 | Transcriptional regulator | 0.016578 |
159 | COG1929 | Belongs to the glycerate kinase type-1 family | 0.016527 |
160 | COG0520 | Catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L- selenocystine to produce L-alanine | 0.016523 |
161 | COG2135 | peptidase activity | 0.016513 |
162 | 349CY | COG1670 acetyltransferases, including N-acetylases of ribosomal proteins | -0.016461 |
163 | 33JYX | 0.016415 | |
164 | COG2804 | Type II secretory pathway, ATPase PulE Tfp pilus assembly pathway, ATPase PilB | 0.016407 |
165 | 33BQB | cellular response to cell envelope stress | 0.016402 |
166 | 32YM4 | -0.016371 | |
167 | 32SEB | 0.016341 | |
168 | COG4133 | protoheme IX ABC transporter activity | -0.016273 |
169 | COG4742 | methyltransferase activity | 0.016269 |
170 | COG2853 | Lipoprotein | 0.016234 |
171 | COG3975 | serine-type endopeptidase activity | -0.016204 |
172 | COG0709 | Synthesizes selenophosphate from selenide and ATP | 0.016119 |
173 | COG1378 | Sugar-specific transcriptional regulator TrmB | 0.016070 |
174 | COG0347 | Belongs to the P(II) protein family | -0.016024 |
175 | 30JKP | 0.015969 | |
176 | COG0797 | Lytic transglycosylase with a strong preference for naked glycan strands that lack stem peptides | -0.015963 |
177 | COG1518 | maintenance of DNA repeat elements | 0.015872 |
178 | COG3540 | Alkaline phosphatase | -0.015856 |
179 | COG1473 | amidohydrolase | 0.015799 |
180 | COG3919 | ATP-grasp | 0.015766 |
181 | COG5361 | Conserved Protein | 0.015758 |
182 | COG0555 | PFAM binding-protein-dependent transport systems inner membrane component | 0.015754 |
183 | COG4392 | branched-chain amino acid | 0.015666 |
184 | COG1592 | Rubrerythrin | -0.015650 |
185 | COG3710 | Transcriptional regulator | 0.015585 |
186 | COG1708 | protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity | 0.015579 |
187 | 32RR9 | Type VI secretion-associated protein, VC_A0118 family | 0.015577 |
188 | COG1796 | DNA polymerase | -0.015575 |
189 | COG3668 | Plasmid stabilization system | 0.015571 |
190 | COG4653 | Phage capsid family | -0.015565 |
191 | COG1961 | COG1961 Site-specific recombinases, DNA invertase Pin homologs | 0.015549 |
192 | COG0213 | The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis | 0.015531 |
193 | COG4459 | periplasmic nitrate reductase | 0.015523 |
194 | COG1166 | arginine decarboxylase activity | 0.015496 |
195 | COG0529 | Catalyzes the synthesis of activated sulfate | 0.015484 |
196 | COG4390 | Protein conserved in bacteria | -0.015474 |
197 | 2ZUKB | PAS domain | 0.015464 |
198 | 32ZJ3 | -0.015460 | |
199 | COG3049 | Linear amide C-N hydrolases, choloylglycine hydrolase family | 0.015451 |
200 | COG3039 | Transposase | 0.015442 |
201 | COG1237 | beta-lactamase domain protein | 0.015407 |
202 | COG0027 | Involved in the de novo purine biosynthesis. Catalyzes the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR). Formate is provided by PurU via hydrolysis of 10-formyl-tetrahydrofolate | 0.015405 |
203 | COG3310 | Protein conserved in bacteria | 0.015385 |
204 | COG2022 | thiamine diphosphate biosynthetic process | 0.015372 |
205 | COG4421 | COG4421 Capsular polysaccharide biosynthesis protein | -0.015367 |
206 | COG0634 | Belongs to the purine pyrimidine phosphoribosyltransferase family | 0.015361 |
207 | COG3751 | 2OG-Fe(II) oxygenase superfamily | -0.015345 |
208 | COG0689 | Phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates | 0.015339 |
209 | COG4605 | iron ion homeostasis | 0.015324 |
210 | COG5018 | Exonuclease | 0.015311 |
211 | COG1288 | antiporter activity | -0.015267 |
212 | COG0369 | Component of the sulfite reductase complex that catalyzes the 6-electron reduction of sulfite to sulfide. This is one of several activities required for the biosynthesis of L- cysteine from sulfate. The flavoprotein component catalyzes the electron flow from NADPH - FAD - FMN to the hemoprotein component | 0.015260 |
213 | 32DP5 | -0.015257 | |
214 | COG3916 | Acyl-homoserine-lactone synthase | 0.015243 |
215 | COG0157 | Belongs to the NadC ModD family | 0.015243 |
216 | 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 | -0.015224 |
217 | 32THI | PFAM SapC family protein | -0.015210 |
218 | 30TX1 | -0.015210 | |
219 | 33492 | 0.015197 | |
220 | COG4706 | dehydratase | 0.015196 |
221 | COG4258 | 3-demethylubiquinone-9 3-O-methyltransferase activity | 0.015150 |
222 | COG3549 | Plasmid maintenance system killer | -0.015138 |
223 | 32YCB | Plasmid maintenance protein CcdB | 0.015123 |
224 | COG0371 | Dehydrogenase | -0.015120 |
225 | COG3055 | Converts alpha-N-acetylneuranimic acid (Neu5Ac) to the beta-anomer, accelerating the equilibrium between the alpha- and beta-anomers. Probably facilitates sialidase-negative bacteria to compete sucessfully for limited amounts of extracellular Neu5Ac, which is likely taken up in the beta-anomer. In addition, the rapid removal of sialic acid from solution might be advantageous to the bacterium to damp down host responses | 0.015114 |
226 | 32XFJ | 0.015100 | |
227 | COG3019 | metal-binding protein | 0.015073 |
228 | COG4941 | Belongs to the sigma-70 factor family | -0.015059 |
229 | COG3166 | PFAM Fimbrial assembly family protein | 0.015014 |
230 | COG3271 | cysteine-type peptidase activity | 0.015001 |
231 | COG0235 | Class ii aldolase | 0.014906 |
232 | COG3506 | Protein of unknown function (DUF1349) | 0.014863 |
233 | COG2821 | murein-degrading enzyme. may play a role in recycling of muropeptides during cell elongation and or cell division | -0.014851 |
234 | COG0739 | heme binding | -0.014849 |
235 | COG5505 | Protein of unknown function (DUF819) | -0.014843 |
236 | COG5270 | sulfate reduction | -0.014815 |
237 | COG2240 | Pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate (PLP). Catalyzes the phosphorylation of pyridoxal to PLP | 0.014812 |
238 | COG1574 | metal-dependent hydrolase with the TIM-barrel fold | -0.014798 |
239 | 33NXX | Transposase | 0.014783 |
240 | COG4763 | Acyl-transferase | -0.014777 |
241 | COG4425 | Alpha/beta-hydrolase family | 0.014767 |
242 | COG4566 | intracellular signal transduction | -0.014749 |
243 | COG2375 | cellular response to nickel ion | 0.014739 |
244 | COG3555 | Aspartyl Asparaginyl beta-hydroxylase | 0.014724 |
245 | COG1522 | sequence-specific DNA binding | -0.014688 |
246 | COG3395 | kinase activity | 0.014684 |
247 | COG4737 | Cytotoxic translational repressor of toxin-antitoxin stability system | -0.014671 |
248 | COG5330 | Evidence 4 Homologs of previously reported genes of | -0.014663 |
249 | COG1754 | DNA topoisomerase type I activity | -0.014644 |
250 | COG2332 | Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH | -0.014624 |