rpoZ Family assigned · medium auto-curated
H37Rv Rv1390 · MTBC0 mtbc0_001491 ·
110 aa · 1574437–1574769 (+) ·
RefSeq NP_215906.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA-directed RNA polymerase subunit omega |
|---|---|
| MTBC0 PGAP re-annotation | DNA-directed RNA polymerase subunit omega |
| Revised (this work) | DNA-directed RNA polymerase subunit omega. Pfam: RNA_pol_Rpb6 (PF01192.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGY5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DNA-directed RNA polymerase subunit omega |
| EC (curated) |
EC 2.7.7.6
|
| Curated function | Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | rpoZ |
| eggNOG description | Promotes RNA polymerase assembly. Latches the N- and C- terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits |
| Orthologous group | COG1758 |
| EC number |
EC 2.7.7.6
|
| KEGG orthology |
K03060
|
| KEGG pathways |
map00230, map00240, map01100, map03020
|
| KEGG modules |
M00183
|
| Gene Ontology (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0008150, GO:0030312, GO:0040007, GO:0044464, GO:0071944
|
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 | 0.325 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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_Rpb6 | PF01192.28 | 1.7e-13 | 42–104 | RNA polymerase Rpb6 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rbpA (RNA polymerase-binding protein RbpA), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 999 | 1000 | coexpression:805 experimental:999 database:844 textmining:878 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 999 | 1000 | experimental:999 database:844 textmining:856 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 999 | 1000 | coexpression:655 experimental:999 database:844 textmining:850 |
Rv2703 sigA |
RNA polymerase sigma factor SigA | 999 | 999 | experimental:999 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 998 | 999 ctx | cooccurence:729 experimental:995 |
Rv2101 helZ |
helicase HelZ | 986 | 986 | experimental:910 database:843 |
Rv2710 sigB |
RNA polymerase sigma factor SigB | 985 | 984 | experimental:983 |
Rv1329c dinG |
ATP-dependent helicase DinG | 977 | 976 | experimental:854 database:844 |
Rv3583c carD |
RNA polymerase-binding transcription factor CarD | 976 | 974 | experimental:960 |
Rv1389 gmk |
guanylate kinase | 997 | 970 ctx | neighborhood:796 coexpression:861 textmining:914 |
Rv0719 rplF |
50S ribosomal protein L6 | 962 | 961 | coexpression:671 experimental:885 |
Rv1388 mihF |
integration host factor MihF | 979 | 956 ctx | neighborhood:706 coexpression:686 experimental:449 textmining:560 |
Rv2890c rpsB |
30S ribosomal protein S2 | 958 | 946 | coexpression:731 experimental:792 |
Rv2841c nusA |
transcription termination/antitermination protein NusA | 981 | 944 | coexpression:413 experimental:882 textmining:675 |
Rv0651 rplJ |
50S ribosomal protein L10 | 917 | 907 | coexpression:796 experimental:474 |
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 omega
- MTBC0 PGAP product: DNA-directed RNA polymerase subunit omega
- Pfam (hmmscan --cut_ga): RNA_pol_Rpb6 PF01192.28 (E=2e-13)
- (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_215906.1)
- Domains: Pfam-A via hmmscan --cut_ga — RNA_pol_Rpb6 (PF01192.28)
- 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
COG1758 - Curated reference: UniProt P9WGY5 (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 —
255 functional partner(s); context anchor
rbpA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001491|Rv1390|rpoZ MSISQSDASLAAVPAVDQFDPSSGASGGYDTPLGITNPPIDELLDRVSSKYALVIYAAKRARQINDYYNQLGEGILEYVGPLVEPGLQEKPLSIALREIHADLLEHTEGE