rpoC Family assigned · medium auto-curated
H37Rv Rv0668 · MTBC0 - ·
1316 aa · 763370–767320 (+) ·
RefSeq NP_215182.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA-directed RNA polymerase subunit beta' |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | DNA-directed RNA polymerase subunit beta'. Pfam: RNA_pol_Rpb1_1 (PF04997.18), RNA_pol_Rpb1_2 (PF00623.26), RNA_pol_Rpb1_3 (PF04983.24), RNA_pol_Rpb1_4 (PF05000.23), RNA_pol_Rpb1_5 (PF04998.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WGY7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DNA-directed RNA polymerase subunit beta' |
| EC (curated) |
EC 2.7.7.6
|
| Curated function | DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | rpoC |
| eggNOG description | DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates |
| Orthologous group | COG0086 |
| EC number |
EC 2.7.7.6
|
| KEGG orthology |
K03046
|
| KEGG pathways |
map00230, map00240, map01100, map03020
|
| KEGG modules |
M00183
|
| Gene Ontology (18) |
GO:0000428, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0030312, GO:0030880, GO:0032991, GO:0040007 +6 more
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.769 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 14 synonymous, 33 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
RNA_pol_Rpb1_1 | PF04997.18 | 1.1e-78 | 6–417 | RNA polymerase Rpb1, domain 1 |
RNA_pol_Rpb1_2 | PF00623.26 | 3.1e-36 | 419–560 | RNA polymerase Rpb1, domain 2 |
RNA_pol_Rpb1_3 | PF04983.24 | 6.5e-23 | 564–736 | RNA polymerase Rpb1, domain 3 |
RNA_pol_Rpb1_4 | PF05000.23 | 2.8e-09 | 751–829 | RNA polymerase Rpb1, domain 4 |
RNA_pol_Rpb1_5 | PF04998.23 | 1.3e-63 | 843–1216 | RNA polymerase Rpb1, domain 5 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpoA (DNA-directed RNA polymerase subunit alpha), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 999 | 1000 ctx | cooccurence:575 coexpression:957 experimental:999 database:844 textmining:970 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 999 | 1000 | experimental:999 database:844 textmining:856 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 999 | 1000 ctx | neighborhood:817 fusion:900 cooccurence:767 coexpression:962 experimental:999 database:844 textmining:959 |
Rv3197A whiB7 |
transcriptional regulator WhiB7 | 999 | 999 | experimental:999 |
Rv2703 sigA |
RNA polymerase sigma factor SigA | 999 | 999 | experimental:999 |
Rv0735 sigL |
ECF RNA polymerase sigma factor SigL | 999 | 999 | experimental:999 |
Rv2710 sigB |
RNA polymerase sigma factor SigB | 999 | 999 | experimental:999 |
Rv3223c sigH |
ECF RNA polymerase sigma factor SigH | 999 | 999 | experimental:999 |
Rv0721 rpsE |
30S ribosomal protein S5 | 995 | 994 | coexpression:953 experimental:818 |
Rv3456c rplQ |
50S ribosomal protein L17 | 991 | 990 | coexpression:962 experimental:699 |
Rv0705 rpsS |
30S ribosomal protein S19 | 989 | 989 | coexpression:957 experimental:725 |
Rv2841c nusA |
transcription termination/antitermination protein NusA | 988 | 986 ctx | cooccurence:442 coexpression:681 experimental:919 |
Rv0707 rpsC |
30S ribosomal protein S3 | 988 | 986 ctx | cooccurence:458 coexpression:908 experimental:718 |
Rv0706 rplV |
50S ribosomal protein L22 | 986 | 985 | coexpression:905 experimental:832 |
Rv0723 rplO |
50S ribosomal protein L15 | 987 | 983 | coexpression:967 experimental:478 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): DNA-directed RNA polymerase subunit beta'
- Pfam (hmmscan --cut_ga): RNA_pol_Rpb1_1 PF04997.18 (E=1e-78), RNA_pol_Rpb1_2 PF00623.26 (E=3e-36), RNA_pol_Rpb1_3 PF04983.24 (E=6e-23), RNA_pol_Rpb1_4 PF05000.23 (E=3e-09), RNA_pol_Rpb1_5 PF04998.23 (E=1e-63)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_215182.1)
- Domains: Pfam-A via hmmscan --cut_ga — RNA_pol_Rpb1_1 (PF04997.18), RNA_pol_Rpb1_2 (PF00623.26), RNA_pol_Rpb1_3 (PF04983.24), RNA_pol_Rpb1_4 (PF05000.23), RNA_pol_Rpb1_5 (PF04998.23)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG0086 - Curated reference: UniProt P9WGY7 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
273 functional partner(s); context anchor
rpoA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0668|rpoC MLDVNFFDELRIGLATAEDIRQWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDEEMRHNELSTLEAEMAVERKAVEDQRDGELEARAQKLEADLAELEAEGAKADARRKVRDGGEREMRQIRDRAQRELDRLEDIWSTFTKLAPKQLIVDENLYRELVDRYGEYFTGAMGAESIQKLIENFDIDAEAESLRDVIRNGKGQKKLRALKRLKVVAAFQQSGNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKSLSDLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFVMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLLNRAPTLHRLGIQAFEPMLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQAEARILMLSSNNILSPASGRPLAMPRLDMVTGLYYLTTEVPGDTGEYQPASGDHPETGVYSSPAEAIMAADRGVLSVRAKIKVRLTQLRPPVEIEAELFGHSGWQPGDAWMAETTLGRVMFNELLPLGYPFVNKQMHKKVQAAIINDLAERYPMIVVAQTVDKLKDAGFYWATRSGVTVSMADVLVPPRKKEILDHYEERADKVEKQFQRGALNHDERNEALVEIWKEATDEVGQALREHYPDDNPIITIVDSGATGNFTQTRTLAGMKGLVTNPKGEFIPRPVKSSFREGLTVLEYFINTHGARKGLADTALRTADSGYLTRRLVDVSQDVIVREHDCQTERGIVVELAERAPDGTLIRDPYIETSAYARTLGTDAVDEAGNVIVERGQDLGDPEIDALLAAGITQVKVRSVLTCATSTGVCATCYGRSMATGKLVDIGEAVGIVAAQSIGEPGTQLTMRTFHQGGVGEDITGGLPRVQELFEARVPRGKAPIADVTGRVRLEDGERFYKITIVPDDGGEEVVYDKISKRQRLRVFKHEDGSERVLSDGDHVEVGQQLMEGSADPHEVLRVQGPREVQIHLVREVQEVYRAQGVSIHDKHIEVIVRQMLRRVTIIDSGSTEFLPGSLIDRAEFEAENRRVVAEGGEPAAGRPVLMGITKASLATDSWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGINRYRNIAVQPTEEARAAAYTIPSYEDQYYSPDFGAATGAAVPLDDYGYSDYR