Rv0894 Family assigned · medium auto-curated
H37Rv Rv0894 · MTBC0 mtbc0_000948 ·
393 aa · 999738–1000919 (+) ·
RefSeq NP_215409.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Contains HTH_77 (PF25872.1) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKP9
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv0894 |
UniProt still lists this protein as Uncharacterized protein Rv0894; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | involved in signal transduction (via phosphorylation) involved in transcriptional regulatory mechanism and in the regulation of secondary metabolites catalytic activity ATP a protein ADP a phosphoprotein |
| Orthologous group | COG3903 |
| Gene Ontology (10) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0008150, GO:0040007, GO:0044424, GO:0044444, GO:0044464
|
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) pseudogene candidate
| pN/pS | 0.278 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 5.92% of strains (8597) · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
HTH_77 | PF25872.1 | 7.3e-10 | 284–360 | Winged helix-turn-helix domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: moaR1 (transcriptional regulator MoaR), high confidence from genomic context alone (score 989 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3124 moaR1 |
transcriptional regulator MoaR | 996 | 989 ctx | fusion:899 cooccurence:489 coexpression:802 textmining:663 |
Rv1267c embR |
transcriptional regulator EmbR | 968 | 967 ctx | fusion:774 coexpression:800 |
Rv0891c hyp |
hypothetical protein | 965 | 965 ctx | fusion:756 coexpression:801 |
Rv0895 |
diacyglycerol O-acyltransferase | 908 | 908 ctx | neighborhood:559 coexpression:801 |
Rv1359 |
transcriptional regulator | 893 | 894 | coexpression:860 |
Rv3167c |
TetR family transcriptional regulator | 861 | 861 | coexpression:834 |
Rv0602c tcrA |
two component DNA binding transcriptional regulator TcrA | 850 | 845 | coexpression:845 |
Rv3263 |
DNA methylase | 841 | 841 | coexpression:841 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 841 | 841 | coexpression:841 |
Rv3840 |
transcriptional regulator | 834 | 834 | coexpression:834 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 834 | 834 | coexpression:834 |
Rv1189 sigI |
ECF RNA polymerase sigma factor SigI | 833 | 833 | coexpression:791 |
Rv3736 |
AraC/XylS family transcriptional regulator | 833 | 833 | coexpression:833 |
Rv1931c |
transcriptional regulator | 828 | 829 | coexpression:801 |
Rv1725c hyp |
hypothetical protein | 826 | 826 | coexpression:800 |
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: transcriptional regulator
- MTBC0 PGAP product: hypothetical protein
- Pfam (hmmscan --cut_ga): HTH_77 PF25872.1 (E=7e-10)
- (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_215409.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_77 (PF25872.1)
- 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
COG3903 - Curated reference: UniProt P9WKP9 (SwissProt, reviewed; Predicted)
- 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 —
79 functional partner(s); context anchor
moaR1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000948|Rv0894| MPSRATVQEFSDSYPFCHNGFRPIMMPKIVSVQHSTRRHLTSFVGRKAELNDVRRLLSDKRLVTLTGPDGMGKSRLALQIGAQIAHEFTYGRWDCDLATVTDRDCVSISMLNALGLPVQPGLSAIDTLVGVINDARVLLVLDHCEHLLDACAAIIDSLLRSCPRLTILTTSTEAIGLAGELTWRVPPLSLTNDAIELFVDRARRVRSDFAINADTAVTVGEICRRLDGVPLAIELAAARTDTLSPVEILAGLNDRFRLVAGAAGNAVRPEQTLCATVQWSHALLSGPERALLHRLAVFAGGFDLDGAQAVGANDEDFEGYQTLGRFAELVDKAFVVVENNRGRAGYRLLYSVRQYALEKLSESGEADAVLARYRKHLKQPNQVVRAGSGGVRY