rslA Resolved · high auto-curated
H37Rv Rv0736 · MTBC0 mtbc0_000778 ·
250 aa · 832333–833085 (+) ·
RefSeq NP_215250.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | anti-sigma-L factor RslA |
|---|---|
| MTBC0 PGAP re-annotation | anti-sigma-L factor RslA |
| Revised (this work) | Anti-sigma-L factor RslA. Pfam: zf-HC2 (PF13490.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJ67
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Anti-sigma-L factor RslA |
| Curated function | An anti-sigma factor for extracytoplasmic function (ECF) sigma factor SigL. ECF sigma factors are held in an inactive form by an anti-sigma factor until released by regulated intramembrane proteolysis (RIP). RIP occurs when an extracytoplasmic signal triggers a concerted proteolytic cascade to transmit information and elicit cellular responses. The membrane-spanning regulatory substrate protein is first cut extracytoplasmically (site-1 protease, S1P), then within the membrane itself (site-2 protease, S2P, Rip1), while cytoplasmic proteases finish degrading the regulatory protein, liberating th. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Putative zinc-finger |
| Orthologous group | COG1595 |
| Gene Ontology (28) |
GO:0000988, GO:0000989, GO:0003674, GO:0005488, GO:0008150, GO:0008270, GO:0009889, GO:0010556, GO:0016989, 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 | 0.767 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 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 |
|---|---|---|---|---|
zf-HC2 | PF13490.12 | 1.7e-09 | 33–58 | Putative zinc-finger |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sigL (ECF RNA polymerase sigma factor SigL), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0735 sigL |
ECF RNA polymerase sigma factor SigL | 999 | 1000 ctx | neighborhood:664 fusion:446 cooccurence:573 coexpression:821 experimental:997 textmining:619 |
Rv1145 mmpL13a |
transmembrane transport protein | 791 | 791 | coexpression:791 |
Rv0737 |
transcriptional regulator | 786 | 778 ctx | neighborhood:656 |
Rv1138c |
oxidoreductase | 791 | 767 | coexpression:767 |
Rv1660 pks10 |
chalcone synthase | 758 | 747 | coexpression:746 |
Rv1146 mmpL13b |
transmembrane transport protein | 746 | 746 | coexpression:746 |
Rv3773c hyp |
hypothetical protein | 711 | 712 ctx | cooccurence:701 |
Rv0048c |
membrane protein | 624 | 625 ctx | cooccurence:624 |
Rv2079 hyp |
hypothetical protein | 606 | 606 ctx | cooccurence:588 |
Rv1189 sigI |
ECF RNA polymerase sigma factor SigI | 622 | 604 | |
Rv2423 hyp |
hypothetical protein | 585 | 585 ctx | cooccurence:583 |
Rv3779 |
transmembrane protein | 535 | 535 ctx | cooccurence:534 |
Rv0142 hyp |
hypothetical protein | 535 | 535 ctx | cooccurence:521 |
Rv1816 |
HTH-type transcriptional regulator | 531 | 531 ctx | cooccurence:523 |
Rv0738 hyp |
hypothetical protein | 515 | 515 |
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-L factor RslA
- MTBC0 PGAP product: anti-sigma-L factor RslA
- Pfam (hmmscan --cut_ga): zf-HC2 PF13490.12 (E=2e-09)
- (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_215250.1)
- Domains: Pfam-A via hmmscan --cut_ga — zf-HC2 (PF13490.12)
- 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 P9WJ67 (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 —
47 functional partner(s); context anchor
sigL - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000778|Rv0736|rslA MTMPLRGLGPPDDTGVREVSTGDDHHYAMWDAAYVLGALSAADRREFEAHLAGCPECRGAVTELCGVPALLSQLDRDEVAAISESAPTVVASGLSPELLPSLLAAVHRRRRRTRLITWVASSAAAAVLAIGVLVGVQGHSAAPQRAAVSALPMAQVGTQLLASTVSISGEPWGTFINLRCVCLAPPYASHDTLAMVVVGRDGSQTRLATWLAEPGHTATPAGSISTPVDQIAAVQVVAADTGQVLLQRSL