# UBCG Set

This document describes the gene set included in the current version of the UBCG phylogenomics pipeline \[[Learn more](/home/science-blogs/profile/ubcg-technical-guide.md)].

| Gene | COG category | COG ID  | HMM profile       | Function                                               |
| ---- | ------------ | ------- | ----------------- | ------------------------------------------------------ |
| alaS | J            | COG0013 | TIGR00344         | Alanine-tRNA ligase                                    |
| argS | J            | COG0018 | TIGR00456         | Arginine-tRNA ligase                                   |
| aspS | J            | COG0173 | TIGR00459         | Aspartate-tRNA ligase                                  |
| cgtA | DL           | COG0536 | TIGR02729/PF01018 | GTPase ObgE/CgtA                                       |
| coaE | H            | COG0237 | TIGR00152         | Dephospho-CoA kinase                                   |
| cysS | J            | COG0215 | TIGR00435         | Cysteine-tRNA ligase                                   |
| dnaA | L            | COG0593 | TIGR00362/PF00308 | Chromosomal replication initiator protein DnaA         |
| dnaG | L            | COG0358 | TIGR01391         | DNA primase                                            |
| dnaX | L            | COG2812 | TIGR02397         | DNA polymerase III subunit gamma                       |
| engA | R            | COG1160 | TIGR03594         | GTPase Der                                             |
| ffh  | U            | COG0541 | TIGR00959         | Signal recognition particle protein                    |
| fmt  | J            | COG0223 | TIGR00460         | Methionyl-tRNA formyltransferase                       |
| frr  | J            | COG0233 | TIGR00496         | Ribosome-recycling factor                              |
| ftsY | U            | COG0552 | TIGR00064         | Signal recognition particle receptor FtsY              |
| gmk  | F            | COG0194 | TIGR03263/PF00625 | Guanylate kinase                                       |
| hisS | J            | COG0124 | TIGR00442         | Histidine-tRNA ligase                                  |
| ileS | J            | COG0060 | TIGR00392         | Isoleucine-tRNA ligase 1                               |
| infB | J            | COG0532 | TIGR00487         | Translation initiation factor IF-2                     |
| infC | J            | COG0290 | TIGR00168         | Translation initiation factor IF-3                     |
| ksgA | J            | COG0030 | TIGR00755         | Ribosomal RNA small subunit methyltransferase A        |
| lepA | J            | COG0481 | TIGR01393         | Elongation factor 4                                    |
| leuS | J            | COG0495 | TIGR00396         | Leucine-tRNA ligase                                    |
| ligA | L            | COG0272 | TIGR00575         | DNA ligase                                             |
| nusA | K            | COG0195 | TIGR01953         | Transcription termination/antitermination protein NusA |
| nusG | K            | COG0250 | TIGR00922         | Transcription termination/antitermination protein NusG |
| pgk  | G            | COG0126 | PF00162           | Phosphoglycerate kinase                                |
| pheS | J            | COG0016 | TIGR00468         | Phenylalanine-tRNA ligase alpha subunit                |
| pheT | J            | COG0073 | TIGR00472         | Phenylalanine-tRNA ligase beta subunit                 |
| prfA | J            | COG0216 | TIGR00019         | Peptide chain release factor 1                         |
| pyrG | F            | COG0504 | TIGR00337         | CTP synthase                                           |
| recA | L            | COG0468 | TIGR02012         | DNA recombination and repair protein                   |
| rbfA | J            | COG0858 | TIGR00082         | 30S ribosome-binding factor                            |
| rnc  | K            | COG0571 | TIGR02191         | Ribonuclease 3                                         |
| rplA | J            | COG0081 | TIGR01169         | 50S ribosomal protein L1                               |
| rplB | J            | COG0090 | TIGR01171         | 50S ribosomal protein L2                               |
| rplC | J            | COG0087 | TIGR03625/PF00297 | 50S ribosomal protein L3                               |
| rplD | J            | COG0088 | TIGR03953         | 50S ribosomal protein L4                               |
| rplE | J            | COG0094 | PF00281           | 50S ribosomal protein L5                               |
| rplF | J            | COG0097 | TIGR03654/PF00347 | 50S ribosomal protein L6                               |
| rplI | J            | COG0359 | TIGR00158/PF01281 | 50S ribosomal protein L9                               |
| rplJ | J            | COG0244 | PF00466           | 50S ribosomal protein L10                              |
| rplK | J            | COG0080 | TIGR01632         | 50S ribosomal protein L11                              |
| rplL | J            | COG0222 | TIGR00855         | 50S ribosomal protein L7/L12                           |
| rplM | J            | COG0102 | TIGR01066         | 50S ribosomal protein L13                              |
| rplN | J            | COG0093 | TIGR01067         | 50S ribosomal protein L14                              |
| rplO | J            | COG0200 | TIGR01071         | 50S ribosomal protein L15                              |
| rplP | J            | COG0197 | TIGR01164         | 50S ribosomal protein L16                              |
| rplQ | J            | COG0203 | TIGR00059         | 50S ribosomal protein L17                              |
| rplR | J            | COG0256 | TIGR00060         | 50S ribosomal protein L18                              |
| rplS | J            | COG0335 | TIGR01024         | 50S ribosomal protein L19                              |
| rplT | J            | COG0292 | TIGR01032         | 50S ribosomal protein L20                              |
| rplU | J            | COG0261 | TIGR00061         | 50S ribosomal protein L21                              |
| rplV | J            | COG0091 | TIGR01044         | 50S ribosomal protein L22                              |
| rplW | J            | COG0089 | PF00276           | 50S ribosomal protein L23                              |
| rplX | J            | COG0198 | TIGR01079         | 50S ribosomal protein L24                              |
| rpmA | J            | COG0211 | TIGR00062         | 50S ribosomal protein L27                              |
| rpmC | J            | COG0255 | TIGR00012         | 50S ribosomal protein L29                              |
| rpmI | J            | COG0291 | TIGR00001         | 50S ribosomal protein L35                              |
| rpoA | K            | COG0202 | TIGR02027         | DNA-directed RNA polymerase subunit alpha              |
| rpoB | K            | COG0085 | TIGR02013         | DNA-directed RNA polymerase subunit beta               |
| rpoC | K            | COG0086 | TIGR02386         | DNA-directed RNA polymerase subunit beta’              |
| rpsB | J            | COG0052 | TIGR01011         | 30S ribosomal protein S2                               |
| rpsC | J            | COG0092 | TIGR01009         | 30S ribosomal protein S3                               |
| rpsD | J            | COG0522 | TIGR01017         | 30S ribosomal protein S4                               |
| rpsE | J            | COG0098 | TIGR01021         | 30S ribosomal protein S5                               |
| rpsF | J            | COG0360 | TIGR00166/PF01250 | 30S ribosomal protein S6                               |
| rpsG | J            | COG0049 | TIGR01029         | 30S ribosomal protein S7                               |
| rpsH | J            | COG0096 | PF00410           | 30S ribosomal protein S8                               |
| rpsI | J            | COG0103 | PF00380           | 30S ribosomal protein S9                               |
| rpsJ | J            | COG0051 | TIGR01049         | 30S ribosomal protein S10                              |
| rpsK | J            | COG0100 | TIGR03632         | 30S ribosomal protein S11                              |
| rpsL | J            | COG0048 | TIGR00981         | 30S ribosomal protein S12                              |
| rpsM | J            | COG0099 | TIGR03631         | 30S ribosomal protein S13                              |
| rpsO | J            | COG0184 | TIGR00952         | 30S ribosomal protein S15                              |
| rpsP | J            | COG0228 | TIGR00002         | 30S ribosomal protein S16                              |
| rpsQ | J            | COG0186 | TIGR03635         | 30S ribosomal protein S17                              |
| rpsR | J            | COG0238 | TIGR00165         | 30S ribosomal protein S18                              |
| rpsS | J            | COG0185 | TIGR01050         | 30S ribosomal protein S19                              |
| rpsT | J            | COG0268 | TIGR00029         | 30S ribosomal protein S20                              |
| secA | U            | COG0653 | TIGR00963         | Protein translocase subunit SecA                       |
| secG | U            | COG1314 | TIGR00810         | Protein-export membrane protein SecG                   |
| secY | U            | COG0201 | TIGR00967         | Protein translocase subunit SecY                       |
| serS | J            | COG0172 | TIGR00414         | Serine-tRNA ligase                                     |
| smpB | O            | COG0691 | TIGR00086         | SsrA-binding protein                                   |
| tig  | O            | COG0544 | TIGR00115         | Trigger factor                                         |
| tilS | J            | COG0037 | TIGR02432         | tRNA(Ile)-lysidine synthase                            |
| truB | J            | COG0130 | TIGR00431         | tRNA pseudouridine synthase B                          |
| tsaD | J            | COG0533 | TIGR03723         | tRNA N6-adenosine threonylcarbamoyltransferase         |
| tsf  | J            | COG0264 | TIGR00116/PF00889 | Elongation factor Ts                                   |
| uvrB | L            | COG0556 | TIGR00631         | UvrABC system protein B                                |
| ybeY | J            | COG0319 | TIGR00043         | Endoribonuclease YbeY                                  |
| ychF | J            | COG0012 | TIGR00092         | Ribosome-binding ATPase YchF                           |

<figure><img src="/files/uIkhQIfwYIPtVSzX3gUv" alt=""><figcaption><p><strong>Location of UBCG genes on </strong><em><strong>Escherichia coli</strong></em><strong> K12 genome</strong></p></figcaption></figure>


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