rseA Resolved · medium auto-curated
H37Rv Rv1222 · MTBC0 mtbc0_001310 ·
154 aa · 1373786–1374250 (+) ·
RefSeq NP_215738.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | anti-sigma E factor RseA |
|---|---|
| MTBC0 PGAP re-annotation | anti-sigma E factor RseA |
| Revised (this work) | Anti-sigma E factor RseA. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
L0T905
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Anti-sigma-E factor RseA |
| Curated function | An anti-sigma factor for extracytoplasmic function (ECF) sigma factor SigE. ECF sigma factors are held in an inactive form by an anti-sigma factor. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | rseA |
| eggNOG description | nucleic acid-templated transcription |
| Orthologous group | COG5662 |
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 | 0.356 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.12% of strains (178) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: tatB (Sec-independent protein translocase protein TatB), high confidence from genomic context alone (score 804 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1224 tatB |
Sec-independent protein translocase protein TatB | 804 | 804 ctx | neighborhood:659 |
Rv1221 sigE |
ECF RNA polymerase sigma factor SigE | 859 | 789 ctx | neighborhood:614 |
Rv1223 htrA |
serine protease HtrA | 776 | 773 ctx | neighborhood:659 |
Rv1109c hyp |
hypothetical protein | 770 | 770 ctx | cooccurence:769 |
Rv2520c |
membrane protein | 770 | 770 ctx | cooccurence:770 |
Rv1083 hyp |
hypothetical protein | 761 | 761 ctx | cooccurence:760 |
Rv0475 hbhA |
heparin binding hemagglutinin HbhA | 753 | 754 ctx | cooccurence:750 |
Rv3004 cfp6 |
low molecular weight protein antigen 6 | 753 | 754 ctx | cooccurence:751 |
Rv2468c hyp |
hypothetical protein | 749 | 749 ctx | cooccurence:740 |
Rv3311 hyp |
hypothetical protein | 748 | 749 ctx | cooccurence:748 |
Rv2091c |
membrane protein | 744 | 745 ctx | cooccurence:741 |
Rv3212 hyp |
hypothetical protein | 736 | 736 ctx | cooccurence:734 |
Rv0876c |
transmembrane protein | 735 | 736 ctx | cooccurence:732 |
Rv1111c hyp |
hypothetical protein | 724 | 724 ctx | cooccurence:724 |
Rv2700 cei hyp |
hypothetical protein | 718 | 718 ctx | cooccurence:718 |
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 E factor RseA
- MTBC0 PGAP product: anti-sigma E factor RseA
- (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_215738.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG5662 - Curated reference: UniProt L0T905 (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 —
122 functional partner(s); context anchor
tatB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001310|Rv1222|rseA MADPGSVGHVFRRAFSWLPAQFASQSDAPVGAPRQFRSTEHLSIEAIAAFVDGELRMNAHLRAAHHLSLCAQCAAEVDDQSRARAALRDSHPIRIPSTLLGLLSEIPRCPPEGPSKGSSGGSSQGPPDGAAAGFGDRFADGDGGNRGRQSRVRR