sigE Resolved · high auto-curated
H37Rv Rv1221 · MTBC0 mtbc0_001309 ·
257 aa · 1372855–1373628 (+) ·
RefSeq NP_215737.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ECF RNA polymerase sigma factor SigE |
|---|---|
| MTBC0 PGAP re-annotation | RNA polymerase sigma factor SigE |
| Revised (this work) | RNA polymerase sigma factor SigE. 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 |
P9WGG7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ECF RNA polymerase sigma factor SigE |
| 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. Responds to heat shock and surface stress (detergent exposure). When combined with isolated core RNA polymerase from M.smegmatis is able to guide initiation from the sigB promoter. Required for full expression of sigB, and for sigB induction after detergent exposure but not after heat shock. Controls a regulon of about 38 genes in culture and about. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | sigE |
| eggNOG description | Belongs to the sigma-70 factor family. ECF subfamily |
| Orthologous group | COG1595 |
| KEGG orthology |
K03088
|
| Gene Ontology (68) |
GO:0000302, GO:0000988, GO:0000990, GO:0003674, GO:0003676, GO:0003677, GO:0005488, GO:0006355, GO:0006950, GO:0006979, GO:0008150, GO:0009266 +56 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 | 0.108 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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_r2 | PF04542.21 | 1.4e-22 | 87–153 | Sigma-70 region 2 |
Sigma70_r4_2 | PF08281.19 | 3.1e-17 | 186–236 | Sigma-70, region 4 |
Sigma70_r4 | PF04545.23 | 6.2e-14 | 189–237 | Sigma-70, region 4 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rseA (anti-sigma E factor RseA), high confidence from genomic context alone (score 789 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1222 rseA |
anti-sigma E factor RseA | 859 | 789 ctx | neighborhood:614 |
Rv2710 sigB |
RNA polymerase sigma factor SigB | 837 | 739 | coexpression:738 textmining:402 |
Rv3414c sigD |
ECF RNA polymerase sigma factor SigD | 551 | 552 ctx | cooccurence:549 |
Rv1220c |
methyltransferase | 550 | 551 ctx | neighborhood:551 |
Rv1223 htrA |
serine protease HtrA | 535 | 517 ctx | neighborhood:490 |
Rv1224 tatB |
Sec-independent protein translocase protein TatB | 509 | 509 ctx | neighborhood:490 |
Rv3221A rshA |
anti-sigma factor RshA | 701 | 492 | textmining:437 |
Rv0736 rslA |
anti-sigma-L factor RslA | 510 | 487 | |
Rv2782c pepR |
zinc protease | 483 | 483 ctx | cooccurence:468 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 488 | 460 | experimental:456 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 484 | 456 | experimental:451 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 473 | 443 | experimental:431 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 464 | 435 | experimental:431 |
Rv0445c sigK |
ECF RNA polymerase sigma factor SigK | 415 | 415 ctx | cooccurence:413 |
Rv2006 otsB1 |
trehalose-6-phosphate phosphatase OtsB | 412 | 413 | coexpression:413 |
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 SigE
- MTBC0 PGAP product: RNA polymerase sigma factor SigE
- Pfam (hmmscan --cut_ga): Sigma70_r2 PF04542.21 (E=1e-22), Sigma70_r4_2 PF08281.19 (E=3e-17), Sigma70_r4 PF04545.23 (E=6e-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_215737.1)
- 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 P9WGG7 (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 —
24 functional partner(s); context anchor
rseA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001309|Rv1221|sigE MELLGGPRVGNTESQLCVADGDDLPTYCSANSEDLNITTITTLSPTSMSHPQQVRDDQWVEPSDQLQGTAVFDATGDKATMPSWDELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSVQNYQPGTFEGWLHRITTNLFLDMVRRRARIRMEALPEDYDRVPADEPNPEQIYHDARLGPDLQAALASLPPEFRAAVVLCDIEGLSYEEIGATLGVKLGTVRSRIHRGRQALRDYLAAHPEHGECAVHVNPVR