Rv1194c Family assigned · medium auto-curated
H37Rv Rv1194c · MTBC0 mtbc0_001282 ·
421 aa · 1345690–1346955 (-) ·
RefSeq NP_215710.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | PucR family transcriptional regulator |
| Revised (this work) | PucR family transcriptional regulator. Pfam: GGDEF_2 (PF17853.7), HTH_30 (PF13556.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05296
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolismT Signal transduction mechanisms
|
|---|---|
| eggNOG description | transcriptional |
| Orthologous group | COG2508 |
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 | 0.585 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 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 |
|---|---|---|---|---|
GGDEF_2 | PF17853.7 | 6.0e-13 | 187–294 | GGDEF-like domain |
HTH_30 | PF13556.13 | 1.7e-11 | 345–396 | PucR C-terminal helix-turn-helix domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PE_PGRS36 (PE-PGRS family protein PE_PGRS36; Rv2098c, (MTCY49.38c), len: 434 aa. PE_PGRS36,Member of the Mycobacterium tuberculosis PE family, PGRS sub), medium confidence from genomic context alone (score 448 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2098c PE_PGRS36 |
PE-PGRS family protein PE_PGRS36; Rv2098c, (MTCY49.38c), len: 434 aa. PE_PGRS36,Member of the Mycobacterium tuberculosis PE family, PGRS sub | 447 | 448 ctx | cooccurence:445 |
Rv3726 |
dehydrogenase | 438 | 439 ctx | cooccurence:436 |
Rv2945c lppX |
lipoprotein LppX | 431 | 432 ctx | cooccurence:426 |
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: hypothetical protein
- MTBC0 PGAP product: PucR family transcriptional regulator
- Pfam (hmmscan --cut_ga): GGDEF_2 PF17853.7 (E=6e-13), HTH_30 PF13556.13 (E=2e-11)
- (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_215710.1)
- Domains: Pfam-A via hmmscan --cut_ga — GGDEF_2 (PF17853.7), HTH_30 (PF13556.13)
- 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
COG2508 - Curated reference: UniProt O05296 (TrEMBL, unreviewed; 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 —
3 functional partner(s); context anchor
PE_PGRS36 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001282|Rv1194c| MAWQQPSPRIRELIREGARIALNPSPEWIEELDRATIAANPAIANDPVLAKVVQTANRANLVYWAAANLRDPGARVPANLGTEPLRMARDLVRRGLDTVAFNIYRTGEHIGWRFWMGIAFELTSDPQELRELLDVSARSVNDFIEATLTGIAAQVQSEHDELTRSTHAERLEVVGLILDGAPISPERAEAKLGYPLSRAHTAAIIWSDELDGDHSYLDRAADLFCHAVGSTRPLTVVAGAASRWAWVTDADGLDIDTVQAAVDNAPGARIAIGTTANGVEGFRRSHLEALITQRTLSRLRSTQRVAFFADVKMVALISQNPDAASEFITSTLGDLESASPDLQTALLTFINEQCNASRAAKRLHTHRNTFLRRLESAQRLLPRPLDHTSVHVAVALEALQWRGNKAHALSSPGRRSNSVPA