sigI Resolved · high auto-curated
H37Rv Rv1189 · MTBC0 mtbc0_001277 ·
290 aa · 1340534–1341406 (+) ·
RefSeq NP_215705.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ECF RNA polymerase sigma factor SigI |
|---|---|
| MTBC0 PGAP re-annotation | RNA polymerase sigma factor SigI |
| Revised (this work) | RNA polymerase sigma factor SigI. Pfam: Sigma70_r2 (PF04542.21), Sigma70_r4_2 (PF08281.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGH3
SwissProt · reviewed
· Evidence at transcript level
|
|---|---|
| UniProt name | Probable ECF RNA polymerase sigma factor SigI |
| 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 until released, although no anti-sigma factor is known for this protein (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | sigI |
| eggNOG description | Belongs to the sigma-70 factor family. ECF subfamily |
| Orthologous group | COG1595 |
| KEGG orthology |
K03088
|
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) pseudogene candidate
| pN/pS | 0.593 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 1.53% of strains (2225) · clonal |
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 | 1.0e-08 | 12–74 | Sigma-70 region 2 |
Sigma70_r4_2 | PF08281.19 | 1.8e-11 | 111–162 | Sigma-70, region 4 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1931c (transcriptional regulator), high confidence from genomic context alone (score 905 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1190 hyp |
hypothetical protein | 971 | 972 ctx | neighborhood:741 coexpression:860 |
Rv1931c |
transcriptional regulator | 908 | 905 ctx | cooccurence:489 coexpression:822 |
Rv1725c hyp |
hypothetical protein | 871 | 872 | coexpression:833 |
Rv3167c |
TetR family transcriptional regulator | 868 | 868 | coexpression:834 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 870 | 865 | coexpression:845 |
Rv2488c |
LuxR family transcriptional regulator | 868 | 860 | coexpression:829 |
Rv3082c virS |
HTH-type transcriptional regulator VirS | 844 | 838 | coexpression:804 |
Rv3736 |
AraC/XylS family transcriptional regulator | 842 | 836 | coexpression:806 |
Rv0894 |
transcriptional regulator | 833 | 833 | coexpression:791 |
Rv3124 moaR1 |
transcriptional regulator MoaR | 833 | 833 | coexpression:833 |
Rv3055 |
TetR family transcriptional regulator | 832 | 832 | coexpression:803 |
Rv3840 |
transcriptional regulator | 831 | 832 | coexpression:831 |
Rv0887c hyp |
hypothetical protein | 831 | 831 ctx | cooccurence:431 coexpression:716 |
Rv1556 |
HTH-type transcriptional regulator | 828 | 829 | coexpression:797 |
Rv1460 sufR |
transcriptional regulator | 825 | 826 | coexpression:800 |
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 SigI
- MTBC0 PGAP product: RNA polymerase sigma factor SigI
- Pfam (hmmscan --cut_ga): Sigma70_r2 PF04542.21 (E=1e-08), Sigma70_r4_2 PF08281.19 (E=2e-11)
- (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_215705.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sigma70_r2 (PF04542.21), Sigma70_r4_2 (PF08281.19)
- 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 P9WGH3 (SwissProt, reviewed; Evidence at transcript 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 —
97 functional partner(s); context anchor
Rv1931c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001277|Rv1189|sigI MSQHDPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGDIDDERGWLIVVTSRLCLDHIKSASTRRERPQDIAAWHDGDASVSSVDPADRVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKINESRIAASVEPAQHRVVTRAFIEACSNGDLDTLLEVLDPGVAGEIDARKGVVVVGADRVGPTILRHWSHPATVLVAQPVCGQPAVLAFVNRALAGVLALSIEAGKITKIHVLVQPSTLDPLRAELGGG