sigF Resolved · high auto-curated
H37Rv Rv3286c · MTBC0 mtbc0_003494 ·
261 aa · 3690249–3691034 (-) ·
RefSeq NP_217803.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | RNA polymerase sigma factor SigF |
|---|---|
| MTBC0 PGAP re-annotation | RNA polymerase sigma factor SigF |
| Revised (this work) | RNA polymerase sigma factor SigF. Pfam: Sigma70_r2 (PF04542.21), Sigma70_r3 (PF04539.23), 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 |
P9WGI3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | RNA polymerase sigma factor SigF |
| Curated function | Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. Held in an inactive form by a cognate anti-sigma factor RsbW (UsfX) until released. Increased expression decreases growth rate, and after 3 days increases the expression of 51 loci encoding 33 protein-coding genes as well as some non-coding RNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | sigF |
| eggNOG description | Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released |
| Orthologous group | COG1191 |
| KEGG orthology |
K03090
|
| Gene Ontology (78) |
GO:0000988, GO:0000990, GO:0003674, GO:0005488, GO:0005515, GO:0006355, GO:0006629, GO:0006950, GO:0006979, GO:0006995, GO:0007154, GO:0008150 +66 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 | 0.354 · 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 |
|---|---|---|---|---|
Sigma70_r2 | PF04542.21 | 5.6e-14 | 43–112 | Sigma-70 region 2 |
Sigma70_r3 | PF04539.23 | 7.9e-11 | 126–188 | Sigma-70 region 3 |
Sigma70_r4_2 | PF08281.19 | 2.0e-10 | 206–256 | Sigma-70, region 4 |
Sigma70_r4 | PF04545.23 | 3.7e-17 | 209–257 | Sigma-70, region 4 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rsbW (anti-sigma factor RsbW), high confidence from genomic context alone (score 989 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3287c rsbW |
anti-sigma factor RsbW | 998 | 989 ctx | neighborhood:802 cooccurence:407 coexpression:840 experimental:471 textmining:859 |
Rv1364c |
sigma factor regulatory protein | 976 | 935 ctx | neighborhood:544 coexpression:713 experimental:471 textmining:643 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 937 | 919 | experimental:904 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 931 | 911 | experimental:897 |
Rv3288c usfY hyp |
hypothetical protein | 805 | 805 ctx | neighborhood:701 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 839 | 790 | experimental:789 |
Rv1904 hyp |
hypothetical protein | 715 | 595 | |
Rv0516c oprA |
anti-anti-sigma factor | 891 | 592 | textmining:745 |
Rv3289c |
transmembrane protein | 568 | 569 ctx | neighborhood:462 |
Rv3660c ssd hyp |
hypothetical protein | 545 | 505 | coexpression:420 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 559 | 495 | experimental:474 |
Rv2588c yajC |
membrane protein secretion factor YajC | 488 | 489 | experimental:458 |
Rv2785c rpsO |
30S ribosomal protein S15 | 478 | 478 | experimental:458 |
Rv1107c xseB |
exodeoxyribonuclease VII small subunit | 461 | 461 | experimental:458 |
Rv0714 rplN |
50S ribosomal protein L14 | 460 | 461 | experimental:458 |
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: RNA polymerase sigma factor SigF
- MTBC0 PGAP product: RNA polymerase sigma factor SigF
- Pfam (hmmscan --cut_ga): Sigma70_r2 PF04542.21 (E=6e-14), Sigma70_r3 PF04539.23 (E=8e-11), Sigma70_r4_2 PF08281.19 (E=2e-10), Sigma70_r4 PF04545.23 (E=4e-17)
- (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_217803.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sigma70_r2 (PF04542.21), Sigma70_r3 (PF04539.23), 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
COG1191 - Curated reference: UniProt P9WGI3 (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 —
63 functional partner(s); context anchor
rsbW - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003494|Rv3286c|sigF MTARAAGGSASRANEYADVPEMFRELVGLPAGSPEFQRHRDKIVQRCLPLADHIARRFEGRGEPRDDLIQVARVGLVNAAVRFDVKTGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGTATADLSQRLGRAPSASELAAELGMDRAEVIEGLLAGSSYHTLSIDSGGGSDDDARAITDTLGDVDAGLDQIENREVLRPLLEALPERERTVLVLRFFDSMTQTQIAERVGISQMHVSRLLAKSLARLRDQLE