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 COG0633 Ferredoxin -0.016082
2 2Z96N monooxygenase activity 0.015205
3 2ZCU4 0.015205
4 32XR3 0.015205
5 3310K 0.015205
6 COG2372 response to copper ion 0.013676
7 COG0847 DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The epsilon subunit contain the editing function and is a proofreading 3'-5' exonuclease -0.012445
8 32SMX Cytochrome c554 and c-prime 0.011530
9 34453 0.011381
10 COG0040 Catalyzes the condensation of ATP and 5-phosphoribose 1- diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of hisG enzymatic activity -0.011256
11 2ZI48 Ammonia monooxygenase 0.011206
12 30TCX PFAM Ammonia monooxygenase particulate methane monooxygenase, subunit C 0.011206
13 2ZBMT Protein of unknown function (DUF2959) 0.010877
14 3320J Domain of unknown function (DUF2024) 0.010683
15 COG4258 3-demethylubiquinone-9 3-O-methyltransferase activity 0.010626
16 COG1585 Membrane protein implicated in regulation of membrane protease activity -0.010606
17 COG1838 Catalyzes the reversible hydration of fumarate to (S)- malate -0.010510
18 334XP 0.010403
19 349B3 0.010403
20 COG4520 surface antigen 0.010382
21 2Z7UJ Alginate export 0.010366
22 COG2189 Belongs to the N(4) N(6)-methyltransferase family 0.010126
23 COG3784 Protein of unknown function (DUF1318) 0.010110
24 COG1138 Cytochrome C-type biogenesis protein 0.010065
25 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 0.010065
26 COG2386 Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes 0.010065
27 COG3088 subunit of a heme lyase 0.010065
28 COG3114 Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes 0.010065
29 COG2025 fatty acid beta-oxidation using acyl-CoA dehydrogenase -0.010061
30 COG2086 electron transfer activity -0.010061
31 COG1213 nucleotidyl transferase 0.010036
32 COG1146 Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions -0.010034
33 COG3749 Protein conserved in bacteria -0.009999
34 32YQV copG family 0.009971
35 COG4133 protoheme IX ABC transporter activity 0.009819
36 COG1277 ABC-type transport system involved in multi-copper enzyme maturation permease component 0.009810
37 COG0048 Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit -0.009747
38 COG0049 tRNA binding -0.009747
39 COG0051 transcription antitermination factor activity, RNA binding -0.009747
40 COG0052 Belongs to the universal ribosomal protein uS2 family -0.009747
41 COG0080 Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors -0.009747
42 COG0085 RNA polymerase activity -0.009747
43 COG0087 One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit -0.009747
44 COG0088 Forms part of the polypeptide exit tunnel -0.009747
45 COG0090 One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity -0.009747
46 COG0092 Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation -0.009747
47 COG0093 Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome -0.009747
48 COG0094 This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits -0.009747
49 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 -0.009747
50 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 -0.009747
51 COG0099 Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits -0.009747
52 COG0100 Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome -0.009747
53 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 -0.009747
54 COG0184 Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome -0.009747
55 COG0185 Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA -0.009747
56 COG0186 One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA -0.009747
57 COG0197 Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs -0.009747
58 COG0199 Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site -0.009747
59 COG0200 Binds to the 23S rRNA -0.009747
60 COG0202 RNA polymerase activity -0.009747
61 COG0203 ribosomal protein L17 -0.009747
62 COG0211 Belongs to the bacterial ribosomal protein bL27 family -0.009747
63 COG0238 Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit -0.009747
64 COG0257 Belongs to the bacterial ribosomal protein bL36 family -0.009747
65 COG0261 This protein binds to 23S rRNA in the presence of protein L20 -0.009747
66 COG0267 Belongs to the bacterial ribosomal protein bL33 family -0.009747
67 COG0290 IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins -0.009747
68 COG0292 Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit -0.009747
69 COG0305 Participates in initiation and elongation during chromosome replication -0.009747
70 COG0360 Binds together with S18 to 16S ribosomal RNA -0.009747
71 COG0361 One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre- initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initation complex -0.009747
72 COG0443 Heat shock 70 kDa protein -0.009747
73 COG0445 tRNA wobble uridine modification -0.009747
74 COG0459 protein refolding -0.009747
75 COG0480 Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post- translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome -0.009747
76 COG0482 sulfurtransferase activity -0.009747
77 COG0522 One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit -0.009747
78 COG0539 negative regulation of cytoplasmic translation -0.009747
79 COG0568 sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released -0.009747
80 COG0576 Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins, in association with DnaK and GrpE. It is the nucleotide exchange factor for DnaK and may function as a thermosensor. Unfolded proteins bind initially to DnaJ -0.009747
81 COG0629 single-stranded DNA binding -0.009747
82 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 -0.009747
83 COG0740 serine-type endopeptidase activity -0.009747
84 COG1104 cysteine desulfurase activity -0.009747
85 COG1160 GTP binding -0.009747
86 COG1219 ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP -0.009747
87 COG1825 This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance -0.009747
88 COG0484 heat shock protein binding -0.009723
89 COG0385 Bile acid 0.009688
90 COG0050 This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis -0.009680
91 33AM4 0.009648
92 COG0348 domain, Protein -0.009619
93 COG3360 Dodecin 0.009578
94 33AAQ Protein of unknown function (DUF2909) 0.009571
95 COG0098 Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body -0.009547
96 COG1276 copper resistance 0.009490
97 COG0650 Formate hydrogenlyase subunit 4 -0.009304
98 COG3260 NADH ubiquinone oxidoreductase 20 -0.009304
99 COG3262 NADH dehydrogenase (ubiquinone), 30 kDa subunit -0.009304
100 COG4237 Hydrogenase 4 membrane -0.009304
101 COG2732 (Barnase) inhibitor -0.009295
102 COG1797 cobyrinic acid a,c-diamide synthase activity -0.009277
103 COG0755 Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes -0.009257
104 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 -0.009231
105 32RTT 0.009230
106 COG3004 Na( ) H( ) antiporter that extrudes sodium in exchange for external protons 0.009223
107 COG1278 Cold shock -0.009151
108 32VR7 Protein of unknown function (DUF2490) 0.009119
109 COG1392 Phosphate transport regulator -0.009085
110 COG1030 water channel activity 0.009066
111 COG3273 potassium ion transport 0.009005
112 COG3189 MarR family transcriptional regulator 0.008928
113 COG1537 nuclear-transcribed mRNA catabolic process, no-go decay 0.008857
114 COG3916 Acyl-homoserine-lactone synthase 0.008852
115 COG0579 oxidoreductase -0.008847
116 317EK 0.008845
117 32T3N PEP-CTERM motif 0.008844
118 COG0411 ABC transporter -0.008832
119 COG3338 carbonate dehydratase activity 0.008829
120 COG1657 PFAM Prenyltransferase squalene oxidase 0.008806
121 COG0435 Glutathione S-transferase 0.008777
122 COG2141 COG2141 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases -0.008769
123 33M9A 0.008720
124 COG1993 acr, cog1993 0.008681
125 COG0426 domain, Protein 0.008651
126 COG1485 Reduces the stability of FtsZ polymers in the presence of ATP -0.008648
127 COG3585 molybdate ion transport -0.008607
128 COG5483 Protein of unknown function, DUF488 0.008571
129 COG4290 ribonuclease -0.008560
130 317ND 0.008522
131 2ZSRZ 0.008472
132 COG1179 involved in molybdopterin and THIamine biosynthesis family 1 -0.008472
133 303WG 0.008444
134 30SQC PFAM UspA 0.008435
135 COG1280 lysine exporter protein (LysE YggA) -0.008434
136 COG3857 The heterodimer acts as both an ATP-dependent DNA helicase and an ATP-dependent, dual-direction single-stranded exonuclease. Recognizes the chi site generating a DNA molecule suitable for the initiation of homologous recombination 0.008363
137 COG3025 triphosphatase activity 0.008350
138 COG1662 PFAM IS1 transposase 0.008268
139 COG3545 Serine hydrolase -0.008260
140 32YHH 0.008229
141 COG1522 sequence-specific DNA binding -0.008208
142 COG3531 Protein-disulfide isomerase 0.008205
143 33C4N Putative beta-barrel porin-2, OmpL-like. bbp2 0.008183
144 COG2363 Small membrane protein 0.008167
145 COG1282 The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane 0.008099
146 COG3288 NAD(P)+ transhydrogenase (AB-specific) activity 0.008099
147 33FM5 0.008098
148 COG2519 Catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenine at position 58 (m1A58) in tRNA 0.008077
149 31EPY 0.007993
150 32JNV 0.007993
151 COG3576 pyridoxamine 5-phosphate -0.007955
152 COG2128 Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity -0.007955
153 COG3485 protocatechuate 3,4-dioxygenase 0.007947
154 COG2440 electron transfer flavoprotein-ubiquinone oxidoreductase -0.007946
155 COG1793 dna ligase -0.007904
156 COG1492 cobalamin metabolic process -0.007899
157 COG2832 Protein of unknown function (DUF454) 0.007887
158 COG0622 Phosphoesterase -0.007878
159 COG1853 conserved protein domain typically associated with flavoprotein oxygenases, DIM6 NTAB family -0.007865
160 COG1333 cytochrome c biogenesis protein -0.007846
161 COG0086 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates -0.007796
162 COG4487 mechanosensitive ion channel activity 0.007782
163 COG3002 Belongs to the UPF0753 family 0.007781
164 COG1499 amine dehydrogenase activity 0.007674
165 COG2186 Transcriptional regulator -0.007619
166 32Z5Z MerR HTH family regulatory protein 0.007618
167 339KM Lipoprotein 0.007610
168 3351P 0.007610
169 337YY Cytochrome P460 0.007610
170 32SHD 0.007608
171 33JAB 0.007604
172 COG0069 glutamate synthase activity 0.007594
173 32RKS Glycine-zipper domain 0.007593
174 COG2249 NAD(P)H dehydrogenase (quinone) activity -0.007587
175 COG3218 ABC-type transport auxiliary lipoprotein component 0.007554
176 COG3065 identical protein binding 0.007543
177 301FE 0.007526
178 COG2334 A protein kinase that phosphorylates Ser and Thr residues. Probably acts to suppress the effects of stress linked to accumulation of reactive oxygen species. Probably involved in the extracytoplasmic stress response -0.007517
179 COG2234 aminopeptidase activity 0.007517
180 COG3303 Catalyzes the reduction of nitrite to ammonia, consuming six electrons in the process 0.007511
181 COG1010 Tetrapyrrole (Corrin/Porphyrin) Methylases -0.007484
182 COG2082 Precorrin-8x methylmutase -0.007484
183 COG2241 protein methyltransferase activity -0.007484
184 COG2243 precorrin-2 c20-methyltransferase -0.007484
185 2ZFCZ 0.007481
186 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 0.007477
187 2ZGH7 0.007473
188 302MZ 0.007473
189 3162Q 0.007473
190 COG3094 Invasion gene expression up-regulator, SirB 0.007467
191 33AS4 Protein of unknown function (DUF2970) 0.007451
192 2Z92U Domain of unknown function (DUF4105) 0.007449
193 COG2847 Copper chaperone PCu(A)C -0.007447
194 COG1322 Protein conserved in bacteria -0.007444
195 COG5653 Protein involved in cellulose biosynthesis 0.007434
196 COG5590 rpsU-divergently transcribed protein 0.007433
197 COG1376 ErfK ybiS ycfS ynhG family protein 0.007431
198 2ZC93 Sugar-transfer associated ATP-grasp 0.007401
199 COG3658 cytochrome -0.007386
200 COG0288 reversible hydration of carbon dioxide 0.007385
201 COG2875 Belongs to the precorrin methyltransferase family -0.007381
202 COG1648 precorrin-2 dehydrogenase activity 0.007372
203 COG2876 3-deoxy-7-phosphoheptulonate synthase activity 0.007358
204 COG0600 ABC-type nitrate sulfonate bicarbonate transport system permease component -0.007354
205 COG1116 anion transmembrane transporter activity -0.007354
206 2ZA5V 0.007325
207 335PY 0.007325
208 33XM3 0.007324
209 COG2094 Belongs to the DNA glycosylase MPG family 0.007291
210 COG4089 membrane 0.007260
211 COG1451 nucleotide metabolic process 0.007257
212 COG0514 ATP-dependent DNA helicase (RecQ) -0.007244
213 338N4 Protein of unknown function (DUF1566) -0.007239
214 COG0475 glutathione-regulated potassium exporter activity 0.007233
215 331R8 Protein of unknown function VcgC/VcgE (DUF2780) 0.007211
216 33KRU 0.007211
217 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 0.007175
218 COG3302 dmso reductase anchor subunit -0.007173
219 COG0584 glycerophosphoryl diester phosphodiesterase 0.007167
220 COG3111 PFAM Bacterial OB fold (BOF) protein 0.007167
221 COG3453 Protein conserved in bacteria 0.007163
222 COG1752 Esterase of the alpha-beta hydrolase superfamily 0.007154
223 3393N 0.007146
224 COG0663 COG0663 Carbonic anhydrases acetyltransferases, isoleucine patch superfamily -0.007146
225 2ZC3I 0.007133
226 COG3328 transposase activity 0.007131
227 COG2073 Cobalamin biosynthesis protein cbiG -0.007126
228 COG0415 Belongs to the DNA photolyase family -0.007125
229 COG3225 cell adhesion 0.007119
230 COG1003 The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor 0.007108
231 COG1694 Mazg nucleotide pyrophosphohydrolase -0.007106
232 300UA Cytochrome P460 0.007093
233 COG2964 Protein conserved in bacteria -0.007092
234 COG2150 ACT domain 0.007088
235 COG4095 Psort location CytoplasmicMembrane, score -0.007085
236 COG4446 Protein conserved in bacteria 0.007073
237 COG3300 MHYT domain 0.007057
238 COG3339 Conserved Protein 0.007033
239 COG0683 leucine binding -0.007011
240 COG5621 secreted hydrolase 0.006918
241 COG2133 pyrroloquinoline quinone binding 0.006913
242 COG3547 Transposase (IS116 IS110 IS902 family) -0.006899
243 COG3222 Protein conserved in bacteria 0.006894
244 COG0518 GMP synthase (glutamine-hydrolyzing) activity 0.006878
245 COG1999 signal sequence binding 0.006876
246 332F0 Domain of unknown function (DUF4389) 0.006867
247 COG1310 metal-dependent protease of the Pad1 Jab1 superfamily 0.006855
248 2Z8P8 -0.006824
249 COG4263 nitrous-oxide reductase activity 0.006790
250 2Z8UN Protoglobin 0.006770