sigM Resolved · high auto-curated
H37Rv Rv3911 · MTBC0 - ·
222 aa · 4400186–4400854 (+) ·
RefSeq NP_218428.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ECF RNA polymerase sigma factor SigM |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | ECF RNA polymerase sigma factor SigM. Pfam: Sigma70_r2 (PF04542.21). |
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 |
O53590
SwissProt · reviewed
· Evidence at transcript level
|
|---|---|
| UniProt name | ECF RNA polymerase sigma factor SigM |
| 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 held in an inactive form by an anti-sigma factor (RsaM, AC L7N5D7) until released by regulated intramembrane proteolysis (Probable). This sigma factor is required for the synthesis of surface or secreted molecules. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | sigM |
| eggNOG description | Belongs to the sigma-70 factor family. ECF subfamily |
| Orthologous group | COG1595 |
| KEGG orthology |
K03088
|
| Gene Ontology (48) |
GO:0001101, GO:0005575, GO:0005623, GO:0005886, GO:0006355, GO:0008150, GO:0009410, GO:0009415, GO:0009628, GO:0009889, GO:0009891, GO:0009893 +36 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 | 0.613 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 98.21% of strains (142603) · reference-fixed |
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 | 2.6e-16 | 39–105 | Sigma-70 region 2 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rsmA (anti-sigma-M factor RsmA), high confidence from genomic context alone (score 878 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3912 rsmA |
anti-sigma-M factor RsmA | 885 | 878 ctx | neighborhood:807 |
Rv3909 hyp |
hypothetical protein | 827 | 828 ctx | neighborhood:724 |
Rv3910 murJ |
peptidoglycan biosynthesis protein | 746 | 737 ctx | neighborhood:724 |
Rv3908 mutT4 |
mutator protein MutT | 730 | 731 ctx | neighborhood:724 |
Rv2069 sigC |
ECF RNA polymerase sigma factor SigC | 903 | 704 ctx | cooccurence:702 textmining:687 |
Rv3913 trxB2 |
thioredoxin reductase | 722 | 612 ctx | neighborhood:603 |
Rv3914 trxC |
thioredoxin TrxC | 704 | 605 ctx | neighborhood:603 |
Rv0735 sigL |
ECF RNA polymerase sigma factor SigL | 914 | 560 ctx | cooccurence:498 textmining:814 |
Rv0445c sigK |
ECF RNA polymerase sigma factor SigK | 884 | 524 ctx | cooccurence:506 textmining:768 |
Rv3414c sigD |
ECF RNA polymerase sigma factor SigD | 894 | 513 ctx | cooccurence:510 textmining:792 |
Rv0736 rslA |
anti-sigma-L factor RslA | 673 | 506 | |
Rv0182c sigG |
ECF RNA polymerase sigma factor SigG | 748 | 503 ctx | cooccurence:492 textmining:515 |
Rv3915 cwlM |
peptidoglycan hydrolase | 522 | 500 ctx | neighborhood:482 |
Rv2181 |
alpha-(1-2)-phosphatidylinositol mannoside mannosyltransferase | 495 | 495 | |
Rv3221A rshA |
anti-sigma factor RshA | 558 | 486 |
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): ECF RNA polymerase sigma factor SigM
- Pfam (hmmscan --cut_ga): Sigma70_r2 PF04542.21 (E=3e-16)
- (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_218428.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sigma70_r2 (PF04542.21)
- 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 O53590 (SwissProt, reviewed; Evidence at transcript 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 —
40 functional partner(s); context anchor
rsmA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3911|sigM MPPPIGYCPAVGFGGRHERSDAELLAAHVAGDRYAFDQLFRRHHRQLHRLARLTSRTSEDADDALQDAMLSAHRGAGSFRYDAAVSSWLHRIVVNACLDRLRRAKAHPTAPLEDVYPVADRTAQVETAIAVQRALMRLPVEQRAAVVAVDMQGYSIADTRPDAGRGRGHRQEPLRPGAGPPSAAAGLSQHRGEHPALTPLPVRRSIDPRARRYPTSGYCHRA