rsfA Resolved · high auto-curated
H37Rv Rv1365c · MTBC0 mtbc0_001467 ·
128 aa · 1548485–1548871 (-) ·
RefSeq NP_215881.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | anti-sigma-F factor antagonist RsfA |
|---|---|
| MTBC0 PGAP re-annotation | anti-sigma-F factor antagonist RsfA |
| Revised (this work) | Anti-sigma-F factor antagonist RsfA. Pfam: STAS (PF01740.27), STAS_2 (PF13466.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGE3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Anti-sigma-F factor antagonist RsfA |
| Curated function | Positive, redox-sensitive regulator of sigma-F (SigF) activity. When reduced binds to anti-sigma-F factor RsbW (UsfX) preventing its binding to SigF, thus activating transcription. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | rsfA |
| eggNOG description | STAS domain |
| Orthologous group | COG1366 |
| Gene Ontology (39) |
GO:0000988, GO:0000989, GO:0003674, GO:0006355, GO:0008150, GO:0009889, GO:0009891, GO:0009893, GO:0010468, GO:0010556, GO:0010557, GO:0010604 +27 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 | 1.045 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 |
|---|---|---|---|---|
STAS | PF01740.27 | 7.4e-24 | 20–124 | STAS domain |
STAS_2 | PF13466.13 | 2.3e-10 | 20–115 | Mlab, STAS domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1364c (sigma factor regulatory protein), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1364c |
sigma factor regulatory protein | 998 | 998 ctx | neighborhood:545 coexpression:928 experimental:912 |
Rv3287c rsbW |
anti-sigma factor RsbW | 952 | 901 ctx | cooccurence:441 coexpression:507 experimental:658 textmining:538 |
Rv1354c hyp |
hypothetical protein | 750 | 735 | coexpression:648 |
Rv1173 fbiC |
FO synthase | 658 | 659 | coexpression:648 |
Rv0655 mkl |
ABC transporter ATP-binding protein | 644 | 645 | experimental:629 |
Rv3899c hyp |
hypothetical protein | 632 | 633 ctx | cooccurence:561 |
Rv3687c rsfB |
anti-anti-sigma factor RsfB | 920 | 613 ctx | cooccurence:611 textmining:803 |
Rv1752 hyp |
hypothetical protein | 611 | 612 ctx | cooccurence:607 |
Rv2079 hyp |
hypothetical protein | 590 | 591 ctx | cooccurence:587 |
Rv3912 rsmA |
anti-sigma-M factor RsmA | 560 | 561 ctx | cooccurence:547 |
Rv1366 hyp |
hypothetical protein | 829 | 559 ctx | neighborhood:496 textmining:630 |
Rv0497 |
transmembrane protein | 556 | 557 ctx | cooccurence:554 |
Rv2721c hyp |
hypothetical protein | 552 | 552 ctx | cooccurence:551 |
Rv0020c fhaA |
FHA domain-containing protein FhaA | 542 | 542 | |
Rv0172 mce1D |
Mce family protein Mce1D | 536 | 536 |
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: anti-sigma-F factor antagonist RsfA
- MTBC0 PGAP product: anti-sigma-F factor antagonist RsfA
- Pfam (hmmscan --cut_ga): STAS PF01740.27 (E=7e-24), STAS_2 PF13466.13 (E=2e-10)
- (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_215881.1)
- Domains: Pfam-A via hmmscan --cut_ga — STAS (PF01740.27), STAS_2 (PF13466.13)
- 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
COG1366 - Curated reference: UniProt P9WGE3 (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 —
92 functional partner(s); context anchor
Rv1364c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001467|Rv1365c|rsfA MNPTQAGSFTTPVSNALKATIQHHDSAVIIHARGEIDAANEHTWQDLVTKAAAATTAPEPLVVNLNGLDFMGCCAVAVLAHEAERCRRRGVDVRLVSRDRAVARIIHACGYGDVLPVHPTTESALSAT