sigL Family assigned · medium auto-curated
H37Rv Rv0735 · MTBC0 mtbc0_000777 ·
177 aa · 831736–832269 (+) ·
RefSeq NP_215249.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ECF RNA polymerase sigma factor SigL |
|---|---|
| MTBC0 PGAP re-annotation | sigma-70 family RNA polymerase sigma factor SigL |
| Revised (this work) | Sigma-70 family RNA polymerase sigma factor SigL. Pfam: Sigma70_ECF (PF07638.18), Sigma70_r2 (PF04542.21), PhyR_sigma2 (PF22029.3), 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 |
P9WGH5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ECF RNA polymerase sigma factor SigL |
| 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 an anti-sigma factor until released by regulated intramembrane proteolysis. Over-expression of SigL induces 19-28 genes including polyketide synthases, secreted and membrane proteins. Might play a minor role in regulating SigB. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | sigL |
| eggNOG description | Belongs to the sigma-70 factor family. ECF subfamily |
| Orthologous group | COG1595 |
| KEGG orthology |
K03088
|
| Gene Ontology (28) |
GO:0000988, GO:0000990, GO:0003674, GO:0006355, GO:0008150, GO:0009889, GO:0010468, GO:0010556, GO:0016987, GO:0019219, GO:0019222, GO:0031323 +16 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 | 0.359 · 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_ECF | PF07638.18 | 3.5e-05 | 6–163 | ECF sigma factor |
Sigma70_r2 | PF04542.21 | 2.6e-18 | 18–85 | Sigma-70 region 2 |
PhyR_sigma2 | PF22029.3 | 8.7e-09 | 23–72 | Sigma2 domain of PhyR |
Sigma70_r4_2 | PF08281.19 | 1.7e-12 | 114–166 | Sigma-70, region 4 |
Sigma70_r4 | PF04545.23 | 3.4e-14 | 119–167 | Sigma-70, region 4 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rslA (anti-sigma-L factor RslA), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0736 rslA |
anti-sigma-L factor RslA | 999 | 1000 ctx | neighborhood:664 fusion:446 cooccurence:573 coexpression:821 experimental:997 textmining:619 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 999 | 999 | experimental:999 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 999 | 999 | experimental:999 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 904 | 899 | experimental:898 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 903 | 899 | experimental:898 |
Rv0734 mapA |
methionine aminopeptidase | 826 | 826 ctx | neighborhood:790 |
Rv1137c |
Hypothetical protein; Rv1137c, (MTCI65.04c), len: 122 aa. Hypothetical unknown protein. | 798 | 798 | coexpression:798 |
Rv0733 adk |
adenylate kinase | 791 | 791 ctx | neighborhood:790 |
Rv0732 secY |
preprotein translocase SecY | 781 | 781 ctx | neighborhood:780 |
Rv2488c |
LuxR family transcriptional regulator | 676 | 656 | coexpression:655 |
Rv2069 sigC |
ECF RNA polymerase sigma factor SigC | 945 | 628 ctx | cooccurence:627 textmining:859 |
Rv3911 sigM |
ECF RNA polymerase sigma factor SigM | 914 | 560 ctx | cooccurence:498 textmining:814 |
Rv0737 |
transcriptional regulator | 548 | 531 | |
Rv1138c |
oxidoreductase | 514 | 514 | coexpression:514 |
Rv3221A rshA |
anti-sigma factor RshA | 567 | 485 |
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 SigL
- MTBC0 PGAP product: sigma-70 family RNA polymerase sigma factor SigL
- Pfam (hmmscan --cut_ga): Sigma70_ECF PF07638.18 (E=3e-05), Sigma70_r2 PF04542.21 (E=3e-18), PhyR_sigma2 PF22029.3 (E=9e-09), Sigma70_r4_2 PF08281.19 (E=2e-12), Sigma70_r4 PF04545.23 (E=3e-14)
- (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_215249.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sigma70_ECF (PF07638.18), Sigma70_r2 (PF04542.21), PhyR_sigma2 (PF22029.3), 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 P9WGH5 (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 —
38 functional partner(s); context anchor
rslA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000777|Rv0735|sigL MARVSGAAAAEAALMRALYDEHAAVLWRYALRLTGDAAQAEDVVQETLLRAWQHPEVIGDTARPARAWLFTVARNMIIDERRSARFRNVVGSTDQSGTPEQSTPDEVNAALDRLLIADALAQLSAEHRAVIQRSYYRGWSTAQIATDLGIAEGTVKSRLHYAVRALRLTLQELGVTR