sigK Family assigned · medium auto-curated
H37Rv Rv0445c · MTBC0 mtbc0_000467 ·
187 aa · 537198–537761 (-) ·
RefSeq NP_214959.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ECF RNA polymerase sigma factor SigK |
|---|---|
| MTBC0 PGAP re-annotation | sigma-70 family RNA polymerase sigma factor SigK |
| Revised (this work) | Sigma-70 family RNA polymerase sigma factor SigK. Pfam: Sigma70_r2 (PF04542.21), 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 |
P9WGH7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ECF RNA polymerase sigma factor SigK |
| 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 until released by regulated intramembrane proteolysis. Sigma-K controls genes such as mpt70 and mpt83. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | sigK |
| eggNOG description | Belongs to the sigma-70 factor family. ECF subfamily |
| Orthologous group | COG1595 |
| KEGG orthology |
K03088
|
| Gene Ontology (21) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0008150, GO:0010468, GO:0010565, GO:0016020, GO:0019216, GO:0019217, GO:0019222, GO:0030312 +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 | 0.343 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 | 1.2e-14 | 30–96 | Sigma-70 region 2 |
Sigma70_r4_2 | PF08281.19 | 1.2e-10 | 128–180 | Sigma-70, region 4 |
Sigma70_r4 | PF04545.23 | 1.3e-13 | 133–182 | Sigma-70, region 4 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rskA (anti-sigma-K factor RskA), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0444c rskA |
anti-sigma-K factor RskA | 999 | 999 ctx | neighborhood:706 cooccurence:636 experimental:987 textmining:906 |
Rv0448c hyp |
hypothetical protein | 828 | 827 ctx | neighborhood:726 |
Rv0446c |
transmembrane protein | 763 | 763 ctx | neighborhood:694 |
Rv0447c ufaA1 |
cyclopropane-fatty-acyl-phospholipid synthase UfaA | 749 | 738 ctx | neighborhood:696 |
Rv0449c hyp |
hypothetical protein | 897 | 712 ctx | neighborhood:586 textmining:657 |
Rv3911 sigM |
ECF RNA polymerase sigma factor SigM | 884 | 524 ctx | cooccurence:506 textmining:768 |
Rv2873 mpt83 |
cell surface lipoprotein | 911 | 501 ctx | cooccurence:429 textmining:831 |
Rv2875 mpt70 |
major secreted immunogenic protein Mpt70 | 914 | 490 ctx | cooccurence:413 textmining:840 |
Rv0736 rslA |
anti-sigma-L factor RslA | 634 | 489 | |
Rv3221A rshA |
anti-sigma factor RshA | 516 | 486 | |
Rv1222 rseA |
anti-sigma E factor RseA | 605 | 471 | |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 489 | 461 | experimental:456 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 487 | 458 | experimental:451 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 477 | 448 | experimental:431 |
Rv0451c mmpS4 |
membrane protein MmpS4 | 440 | 440 ctx | neighborhood:436 |
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 SigK
- MTBC0 PGAP product: sigma-70 family RNA polymerase sigma factor SigK
- Pfam (hmmscan --cut_ga): Sigma70_r2 PF04542.21 (E=1e-14), Sigma70_r4_2 PF08281.19 (E=1e-10), Sigma70_r4 PF04545.23 (E=1e-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_214959.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sigma70_r2 (PF04542.21), 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 P9WGH7 (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 —
36 functional partner(s); context anchor
rskA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000467|Rv0445c|sigK MTGPPRLSSDLDALLRRVAGHDQAAFAEFYDHTKSRVYGLVMRVLRDTGYSEETTQEIYLEVWRNASEFDSAKGSALAWLLTMAHRRAVDRVRCEQAGNQREVRYGAANVDPASDVVADLAIAGDERRRVTECLKALTDTQRQCIELAYYGGLTYVEVSRRLAANLSTIKSRMRDALRSLRNCLDVS