Rv1364c Family assigned · medium auto-curated
H37Rv Rv1364c · MTBC0 - ·
653 aa · 1535683–1537644 (-) ·
RefSeq YP_177802.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | sigma factor regulatory protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Sigma factor regulatory protein. Pfam: PAS_4 (PF08448.17), SpoIIE (PF07228.18), HATPase_c_2 (PF13581.13), STAS_2 (PF13466.13), STAS (PF01740.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WLZ7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Multidomain regulatory protein Rv1364c |
| EC (curated) |
EC 2.7.11.1, EC 3.1.3.16
|
| Curated function | Primarily acts as an independent SigF regulator that is sensitive to the osmosensory signal, mediating the cross talk of PknD with the SigF regulon. Possesses both phosphatase and kinase activities. The kinase domain functions as a classic anti-sigma factor-like kinase to phosphorylate the anti-anti-sigma factor domain at the canonical regulatory site, and the phosphatase domain antagonizes this activity. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| Preferred name | rsbU |
| eggNOG description | Stage II sporulation protein E |
| Orthologous group | COG1366 |
| Gene Ontology (41) |
GO:0000287, GO:0003674, GO:0003824, GO:0004035, GO:0005488, GO:0005515, GO:0006355, GO:0006793, GO:0006796, GO:0008150, GO:0008152, GO:0009889 +29 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 | 0.406 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 8 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 |
|---|---|---|---|---|
PAS_4 | PF08448.17 | 1.7e-11 | 21–135 | PAS fold |
SpoIIE | PF07228.18 | 3.8e-41 | 203–396 | Stage II sporulation protein E (SpoIIE) |
HATPase_c_2 | PF13581.13 | 1.2e-16 | 409–522 | Histidine kinase-like ATPase domain |
STAS_2 | PF13466.13 | 1.5e-09 | 555–637 | Mlab, STAS domain |
STAS | PF01740.27 | 4.4e-13 | 560–632 | STAS domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rsfA (anti-sigma-F factor antagonist RsfA), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1354c hyp |
hypothetical protein | 999 | 1000 ctx | neighborhood:544 coexpression:999 textmining:735 |
Rv1173 fbiC |
FO synthase | 999 | 999 | coexpression:999 |
Rv1365c rsfA |
anti-sigma-F factor antagonist RsfA | 998 | 998 ctx | neighborhood:545 coexpression:928 experimental:912 |
Rv3687c rsfB |
anti-anti-sigma factor RsfB | 996 | 996 ctx | cooccurence:569 coexpression:929 experimental:859 |
Rv1904 hyp |
hypothetical protein | 996 | 996 | coexpression:928 experimental:912 |
Rv2638 hyp |
hypothetical protein | 995 | 994 | coexpression:929 experimental:859 |
Rv0516c oprA |
anti-anti-sigma factor | 992 | 991 | coexpression:928 experimental:859 |
Rv3287c rsbW |
anti-sigma factor RsbW | 990 | 987 | coexpression:959 experimental:658 |
Rv1876 bfrA |
bacterioferritin BfrA | 959 | 944 | coexpression:944 |
Rv3286c sigF |
RNA polymerase sigma factor SigF | 976 | 935 ctx | neighborhood:544 coexpression:713 experimental:471 textmining:643 |
Rv0990c hyp |
hypothetical protein | 931 | 931 | coexpression:931 |
Rv3657c |
membrane protein | 930 | 931 | coexpression:920 |
Rv2896c dprA hyp |
hypothetical protein | 922 | 922 | coexpression:918 |
Rv3658c |
transmembrane protein | 919 | 920 | coexpression:920 |
Rv3242c hyp |
hypothetical protein | 892 | 889 | coexpression:874 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): sigma factor regulatory protein
- Pfam (hmmscan --cut_ga): PAS_4 PF08448.17 (E=2e-11), SpoIIE PF07228.18 (E=4e-41), HATPase_c_2 PF13581.13 (E=1e-16), STAS_2 PF13466.13 (E=1e-09), STAS PF01740.27 (E=4e-13)
- (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 YP_177802.1)
- Domains: Pfam-A via hmmscan --cut_ga — PAS_4 (PF08448.17), SpoIIE (PF07228.18), HATPase_c_2 (PF13581.13), STAS_2 (PF13466.13), STAS (PF01740.27)
- 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
COG1366 - Curated reference: UniProt P9WLZ7 (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 —
175 functional partner(s); context anchor
rsfA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1364c| MAAEMDWDKTVGAAEDVRRIFEHIPAILVGLEGPDHRFVAVNAAYRGFSPLLDTVGQPAREVYPELEGQQIYEMLDRVYQTGEPQSGSEWRLQTDYDGSGVEERYFDFVVTPRRRADGSIEGVQLIVDDVTSRVRARQAAEARVEELSERYRNVRDSATVMQQALLAASVPVVPGADIAAEYLVAAEDTAAGGDWFDALALGDRLVLVVGDVVGHGVEAAAVMSQLRTALRMQISAGYTVVEALEAVDRFHKQVPGSKSATMCVGSLDFTSGEFQYCTAGHPPPLLVTADASARYVEPTGAGPLGSGTGFPVRSEVLNIGDAILFYTDGLIERPGRPLEASTAEFADLAASIASGSGGFVLDAPARPIDRLCSDTLELLLRSTGYNDDVTLLAMQRRAPTPPLHITLDATINAARTVRAQLREWLAEIGADHSDIADIVHAISEFVENAVEHGYATDVSKGIVVAAALAGDGNVRASVIDRGQWKDHRDGARGRGRGLAMAEALVSEARIMHGAGGTTATLTHRLSRPARFVTDTMVRRAAFQQTIDSEFVSLVESGRIVVRGDVDSTTAATLDRQIAVESRSGIAPVTIDLSAVTHLGSAGVGALAAACDRARKQGTECVLVAPPGSPAHHVLSLVQLPVVGADTEDIFAQE