sigH Family assigned · medium auto-curated
H37Rv Rv3223c · MTBC0 mtbc0_003430 ·
216 aa · 3621043–3621693 (-) ·
RefSeq NP_217739.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ECF RNA polymerase sigma factor SigH |
|---|---|
| MTBC0 PGAP re-annotation | sigma-70 family RNA polymerase sigma factor SigH |
| Revised (this work) | Sigma-70 family RNA polymerase sigma factor SigH. 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 |
P9WGH9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ECF RNA polymerase sigma factor SigH |
| 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 a cognate anti-sigma factor (RshA) until released. This sigma factor is involved in heat shock and oxidative stress responses; it positively regulates the expression of itself, sigE, sigB and a number of transcriptional regulators as well as other effectors of heat and oxidative stress, leading to direct and indirect control of up to 25% of the bacterial genome. Modulates expression o. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | sigH |
| eggNOG description | Belongs to the sigma-70 factor family. ECF subfamily |
| Orthologous group | COG1595 |
| KEGG orthology |
K03088
|
| Gene Ontology (45) |
GO:0000988, GO:0000990, GO:0003674, GO:0005575, GO:0005618, GO:0005623, GO:0006355, GO:0006950, GO:0006979, GO:0008150, GO:0009266, GO:0009408 +33 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 | 0.63 · 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_r2 | PF04542.21 | 8.9e-18 | 37–99 | Sigma-70 region 2 |
Sigma70_r4_2 | PF08281.19 | 1.7e-16 | 140–191 | Sigma-70, region 4 |
Sigma70_r4 | PF04545.23 | 2.1e-10 | 144–192 | Sigma-70, region 4 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rshA (anti-sigma factor RshA), high confidence from genomic context alone (score 983 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 999 | 999 | experimental:999 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 999 | 999 | experimental:999 |
Rv3221A rshA |
anti-sigma factor RshA | 999 | 983 ctx | neighborhood:882 experimental:800 textmining:953 |
Rv3222c hyp |
hypothetical protein | 970 | 967 ctx | neighborhood:882 coexpression:732 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 915 | 911 | experimental:898 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 904 | 899 | experimental:898 |
Rv2069 sigC |
ECF RNA polymerase sigma factor SigC | 939 | 752 ctx | cooccurence:752 textmining:766 |
Rv3221c TB7.3 |
acetyl-CoA carboxylase biotin carboxyl carrier protein subunit | 743 | 743 ctx | neighborhood:720 |
Rv3224 |
iron-regulated short-chain dehydrogenase/reductase | 722 | 723 ctx | neighborhood:717 |
Rv3224B |
Rv3224B, len: 72 aa. Conserved hypothetical protein (possibly gene fragment), similar to C-terminal part of ML0799|AL583919_131 conserved hy | 718 | 718 ctx | neighborhood:717 |
Rv3220c pdtaS |
two component sensor kinase | 599 | 578 ctx | neighborhood:508 |
Rv0014c pknB |
serine/threonine-protein kinase PknB | 843 | 565 | experimental:554 textmining:655 |
Rv3206c moeB1 |
adenylyltransferase/sulfurtransferase MoeZ | 532 | 520 | coexpression:518 |
Rv0018c pstP |
phosphoserine/threonine phosphatase PstP | 528 | 516 | experimental:500 |
Rv3907c pcnA |
poly(A) polymerase PcnA | 523 | 506 ctx | cooccurence:492 |
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 SigH
- MTBC0 PGAP product: sigma-70 family RNA polymerase sigma factor SigH
- Pfam (hmmscan --cut_ga): Sigma70_r2 PF04542.21 (E=9e-18), Sigma70_r4_2 PF08281.19 (E=2e-16), Sigma70_r4 PF04545.23 (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_217739.1)
- 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 P9WGH9 (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 —
61 functional partner(s); context anchor
rshA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003430|Rv3223c|sigH MADIDGVTGSAGLQPGPSEETDEELTARFERDAIPLLDQLYGGALRMTRNPADAEDLLQETMVKAYAGFRSFRHGTNLKAWLYRILTNTYINSYRKKQRQPAEYPTEQITDWQLASNAEHSSTGLRSAEVEALEALPDTEIKEALQALPEEFRMAVYYADVEGFPYKEIAEIMDTPIGTVMSRLHRGRRQLRGLLADVARDRGFARGEQAHEGVSS