sigC Resolved · high auto-curated
H37Rv Rv2069 · MTBC0 mtbc0_002203 ·
185 aa · 2355557–2356114 (+) ·
RefSeq NP_216585.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ECF RNA polymerase sigma factor SigC |
|---|---|
| MTBC0 PGAP re-annotation | RNA polymerase sigma factor SigC |
| Revised (this work) | RNA polymerase sigma factor SigC. Pfam: Sigma70_r2 (PF04542.21), Sigma70_ECF (PF07638.18), Sigma70_r4_2 (PF08281.19), Sigma70_r4 (PF04545.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGH1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ECF RNA polymerase sigma factor SigC |
| Curated function | Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. Extracytoplasmic function (ECF) sigma factors are usually held in an inactive form by an anti-sigma factor until released by regulated intramembrane proteolysis; this sigma factor does not seem to have a cognate anti-sigma factor however. It has been suggested that the sigma domains 2 and 4 may interact via polar residues in this protein to autoregulate. Positively regulates expression of a small regulon of genes. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | sigC |
| eggNOG description | Belongs to the sigma-70 factor family. ECF subfamily |
| Orthologous group | COG1595 |
| KEGG orthology |
K03088
|
| Gene Ontology (36) |
GO:0001101, GO:0001666, GO:0006355, GO:0006950, GO:0008150, GO:0009266, GO:0009405, GO:0009408, GO:0009410, GO:0009415, GO:0009628, GO:0009889 +24 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 2 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 |
|---|---|---|---|---|
Sigma70_r2 | PF04542.21 | 6.4e-15 | 30–93 | Sigma-70 region 2 |
Sigma70_ECF | PF07638.18 | 8.6e-05 | 53–174 | ECF sigma factor |
Sigma70_r4_2 | PF08281.19 | 4.7e-16 | 122–174 | Sigma-70, region 4 |
Sigma70_r4 | PF04545.23 | 8.9e-06 | 128–174 | Sigma-70, region 4 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0093c (membrane protein), high confidence from genomic context alone (score 891 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0093c |
membrane protein | 891 | 891 ctx | fusion:734 cooccurence:462 |
Rv3223c sigH |
ECF RNA polymerase sigma factor SigH | 939 | 752 ctx | cooccurence:752 textmining:766 |
Rv3911 sigM |
ECF RNA polymerase sigma factor SigM | 903 | 704 ctx | cooccurence:702 textmining:687 |
Rv2068c blaC |
beta-lactamase | 663 | 655 ctx | neighborhood:589 |
Rv0735 sigL |
ECF RNA polymerase sigma factor SigL | 945 | 628 ctx | cooccurence:627 textmining:859 |
Rv2067c hyp |
hypothetical protein | 556 | 556 ctx | neighborhood:550 |
Rv3221A rshA |
anti-sigma factor RshA | 580 | 484 | |
Rv0736 rslA |
anti-sigma-L factor RslA | 515 | 484 | |
Rv1222 rseA |
anti-sigma E factor RseA | 558 | 473 | |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 486 | 457 | experimental:456 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 482 | 454 | experimental:451 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 465 | 436 | experimental:431 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 462 | 433 | experimental:431 |
Rv3909 hyp |
hypothetical protein | 417 | 418 | |
Rv3372 otsB2 |
trehalose 6-phosphate phosphatase | 412 | 413 | coexpression:413 |
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: ECF RNA polymerase sigma factor SigC
- MTBC0 PGAP product: RNA polymerase sigma factor SigC
- Pfam (hmmscan --cut_ga): Sigma70_r2 PF04542.21 (E=6e-15), Sigma70_ECF PF07638.18 (E=9e-05), Sigma70_r4_2 PF08281.19 (E=5e-16), Sigma70_r4 PF04545.23 (E=9e-06)
- (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_216585.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sigma70_r2 (PF04542.21), Sigma70_ECF (PF07638.18), Sigma70_r4_2 (PF08281.19), Sigma70_r4 (PF04545.23)
- 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
COG1595 - Curated reference: UniProt P9WGH1 (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 —
28 functional partner(s); context anchor
Rv0093c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002203|Rv2069|sigC MTATASDDEAVTALALSAAKGNGRALEAFIKATQQDVWRFVAYLSDVGSADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHVVADHIRHVRSRPRTTRGARPEHLIDGDRHARGFEDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDALLADAEPDDLTG