sigA Resolved · high auto-curated
H37Rv Rv2703 · MTBC0 mtbc0_002877 ·
528 aa · 3040250–3041836 (+) ·
RefSeq NP_217219.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | RNA polymerase sigma factor SigA |
|---|---|
| MTBC0 PGAP re-annotation | RNA polymerase sigma factor |
| Revised (this work) | RNA polymerase sigma factor. Pfam: Sigma70_r1_2 (PF00140.26), Sigma70_r2 (PF04542.21), Sigma70_r3 (PF04539.23), 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 |
P9WGI1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | RNA polymerase sigma factor SigA |
| Curated function | Sigma factors are initiation factors that promote the attachment of RNA polymerase (RNAP) to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth (Probable). RNAP reconstituted with SigA or SigB is equally susceptible to rifampicin. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | sigA |
| eggNOG description | Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth |
| Orthologous group | COG0568 |
| KEGG orthology |
K03086
|
| Gene Ontology (52) |
GO:0000988, GO:0000990, GO:0001101, GO:0003674, GO:0003676, GO:0003677, GO:0005488, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006355 +40 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 | 0.651 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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_r1_2 | PF00140.26 | 1.7e-15 | 226–259 | Sigma-70 factor, region 1.2 |
Sigma70_r2 | PF04542.21 | 6.5e-24 | 295–365 | Sigma-70 region 2 |
Sigma70_r3 | PF04539.23 | 1.0e-28 | 374–450 | Sigma-70 region 3 |
Sigma70_r4 | PF04545.23 | 2.8e-18 | 463–516 | Sigma-70, region 4 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpoA (DNA-directed RNA polymerase subunit alpha), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 999 | 1000 | experimental:999 textmining:514 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 999 | 1000 ctx | cooccurence:508 experimental:999 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 999 | 999 | experimental:999 |
Rv3197A whiB7 |
transcriptional regulator WhiB7 | 999 | 999 | experimental:999 |
Rv3219 whiB1 |
transcriptional regulator WhiB1 | 999 | 999 | experimental:999 textmining:504 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 999 | 999 | experimental:999 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 995 | 995 | experimental:995 |
Rv3583c carD |
RNA polymerase-binding transcription factor CarD | 974 | 973 | experimental:971 |
Rv2095c pafC |
proteasome accessory factor C | 871 | 871 | experimental:870 |
Rv2359 zur |
zinc uptake regulation protein | 852 | 820 | experimental:767 |
Rv2704 hyp |
hypothetical protein | 900 | 819 ctx | neighborhood:815 textmining:469 |
Rv2343c dnaG |
DNA primase | 833 | 811 ctx | cooccurence:426 coexpression:646 |
Rv2702 ppgK |
polyphosphate glucokinase | 752 | 742 ctx | neighborhood:741 |
Rv3833 |
AraC family transcriptional regulator | 766 | 732 | experimental:722 |
Rv2841c nusA |
transcription termination/antitermination protein NusA | 723 | 689 | experimental:446 |
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 SigA
- MTBC0 PGAP product: RNA polymerase sigma factor
- Pfam (hmmscan --cut_ga): Sigma70_r1_2 PF00140.26 (E=2e-15), Sigma70_r2 PF04542.21 (E=6e-24), Sigma70_r3 PF04539.23 (E=1e-28), Sigma70_r4 PF04545.23 (E=3e-18)
- (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_217219.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sigma70_r1_2 (PF00140.26), Sigma70_r2 (PF04542.21), Sigma70_r3 (PF04539.23), 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
COG0568 - Curated reference: UniProt P9WGI1 (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 —
114 functional partner(s); context anchor
rpoA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002877|Rv2703|sigA MAATKASTATDEPVKRTATKSPAASASGAKTGAKRTAAKSASGSPPAKRATKPAARSVKPASAPQDTTTSTIPKRKTRAAAKSAAAKAPSARGHATKPRAPKDAQHEAATDPEDALDSVEELDAEPDLDVEPGEDLDLDAADLNLDDLEDDVAPDADDDLDSGDDEDHEDLEAEAAVAPGQTADDDEEIAEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD