rpoB Family assigned · medium auto-curated
H37Rv Rv0667 · MTBC0 mtbc0_000705 ·
1172 aa · 763893–767411 (+) ·
RefSeq NP_215181.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA-directed RNA polymerase subunit beta |
|---|---|
| MTBC0 PGAP re-annotation | DNA-directed RNA polymerase subunit beta |
| Revised (this work) | DNA-directed RNA polymerase subunit beta. Pfam: RNA_pol_Rpb2_1 (PF04563.21), RNA_pol_Rpb2_2 (PF04561.20), RNA_pol_Rpb2_3 (PF04565.22), RNA_pol_Rpb2_45 (PF10385.15), RNA_pol_Rpb2_6 (PF00562.34), RNA_pol_Rpb2_7 (PF04560.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGY9
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 | rpoB |
| eggNOG description | DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates |
| Orthologous group | COG0085 |
| EC number |
EC 2.7.7.6
|
| KEGG orthology |
K03043
|
| KEGG pathways |
map00230, map00240, map01100, map03020
|
| KEGG modules |
M00183
|
| Gene Ontology (21) |
GO:0000428, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0008150, GO:0016020, GO:0030312, GO:0030880 +9 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 | 1.043 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 29 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_Rpb2_1 | PF04563.21 | 4.0e-16 | 111–417 | RNA polymerase beta subunit |
RNA_pol_Rpb2_2 | PF04561.20 | 2.1e-27 | 175–373 | RNA polymerase Rpb2, domain 2 |
RNA_pol_Rpb2_3 | PF04565.22 | 6.0e-28 | 432–500 | RNA polymerase Rpb2, domain 3 |
RNA_pol_Rpb2_45 | PF10385.15 | 4.4e-28 | 510–576 | RNA polymerase beta subunit external 1 domain |
RNA_pol_Rpb2_6 | PF00562.34 | 1.8e-125 | 637–1056 | RNA polymerase Rpb2, domain 6 |
RNA_pol_Rpb2_7 | PF04560.26 | 1.7e-27 | 1058–1132 | RNA polymerase Rpb2, domain 7 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpoC (DNA-directed RNA polymerase subunit beta'), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 999 | 1000 ctx | neighborhood:817 fusion:900 cooccurence:767 coexpression:962 experimental:999 database:844 textmining:959 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 999 | 1000 ctx | cooccurence:481 coexpression:970 experimental:999 database:844 textmining:973 |
Rv2703 sigA |
RNA polymerase sigma factor SigA | 999 | 1000 | experimental:999 textmining:514 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 999 | 1000 | coexpression:655 experimental:999 database:844 textmining:850 |
Rv2710 sigB |
RNA polymerase sigma factor SigB | 999 | 1000 | experimental:999 |
Rv0735 sigL |
ECF RNA polymerase sigma factor SigL | 999 | 999 | experimental:999 |
Rv3583c carD |
RNA polymerase-binding transcription factor CarD | 999 | 999 | experimental:999 |
Rv3223c sigH |
ECF RNA polymerase sigma factor SigH | 999 | 999 | experimental:999 |
Rv0640 rplK |
50S ribosomal protein L11 | 998 | 997 ctx | cooccurence:621 coexpression:918 experimental:908 |
Rv0719 rplF |
50S ribosomal protein L6 | 997 | 996 | coexpression:958 experimental:902 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 997 | 995 | coexpression:955 experimental:820 textmining:586 |
Rv0721 rpsE |
30S ribosomal protein S5 | 996 | 995 | coexpression:962 experimental:812 textmining:409 |
Rv0701 rplC |
50S ribosomal protein L3 | 998 | 994 | coexpression:968 experimental:771 textmining:701 |
Rv0706 rplV |
50S ribosomal protein L22 | 994 | 993 | coexpression:958 experimental:785 |
Rv0704 rplB |
50S ribosomal protein L2 | 997 | 992 | coexpression:967 experimental:707 textmining:665 |
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
- Legacy H37Rv annotation: DNA-directed RNA polymerase subunit beta
- MTBC0 PGAP product: DNA-directed RNA polymerase subunit beta
- Pfam (hmmscan --cut_ga): RNA_pol_Rpb2_1 PF04563.21 (E=4e-16), RNA_pol_Rpb2_2 PF04561.20 (E=2e-27), RNA_pol_Rpb2_3 PF04565.22 (E=6e-28), RNA_pol_Rpb2_45 PF10385.15 (E=4e-28), RNA_pol_Rpb2_6 PF00562.34 (E=2e-125), RNA_pol_Rpb2_7 PF04560.26 (E=2e-27)
- (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_215181.1)
- Domains: Pfam-A via hmmscan --cut_ga — RNA_pol_Rpb2_1 (PF04563.21), RNA_pol_Rpb2_2 (PF04561.20), RNA_pol_Rpb2_3 (PF04565.22), RNA_pol_Rpb2_45 (PF10385.15), RNA_pol_Rpb2_6 (PF00562.34), RNA_pol_Rpb2_7 (PF04560.26)
- 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
COG0085 - Curated reference: UniProt P9WGY9 (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 —
387 functional partner(s); context anchor
rpoC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000705|Rv0667|rpoB MADSRQSKTAASPSPSRPQSSSNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIGQILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEAQPNAIVSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGINLSRNESASVEDLA