Rv1375 Family assigned · medium auto-curated
H37Rv Rv1375 · MTBC0 mtbc0_001476 ·
439 aa · 1557176–1558495 (+) ·
RefSeq NP_215891.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | YcaO-like family protein |
| Revised (this work) | YcaO-like family protein. Pfam: YcaO (PF02624.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WF27
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv1375 |
UniProt still lists this protein as Uncharacterized protein Rv1375; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | YcaO cyclodehydratase, ATP-ad Mg2+-binding |
| Orthologous group | COG1944 |
| KEGG orthology |
K09136
|
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 | 0.27 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 7 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.77% of strains (1111) · 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 |
|---|---|---|---|---|
YcaO | PF02624.22 | 2.2e-57 | 115–423 | YcaO cyclodehydratase, ATP-ad Mg2+-binding |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: csm5 (CRISPR type III-associated RAMP protein Csm5), medium confidence from genomic context alone (score 475 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) |
|---|---|---|---|---|
Rv1376 hyp |
hypothetical protein | 988 | 986 ctx | neighborhood:882 cooccurence:774 coexpression:533 |
Rv1863c |
integral membrane protein | 656 | 636 | coexpression:623 |
Rv1140 |
integral membrane protein | 654 | 633 | coexpression:620 |
Rv0658c |
integral membrane protein | 654 | 633 | coexpression:620 |
Rv0804 hyp |
hypothetical protein | 653 | 632 | coexpression:619 |
Rv1747 |
ABC transporter ATP-binding protein/permease | 631 | 571 | coexpression:488 |
Rv3262 fbiB |
coenzyme F420:L-glutamate ligase | 535 | 505 | coexpression:476 |
Rv2337c hyp |
hypothetical protein | 532 | 502 ctx | cooccurence:484 |
Rv3127 hyp |
hypothetical protein | 523 | 493 | coexpression:476 |
Rv3131 |
NAD(P)H nitroreductase | 523 | 493 | coexpression:476 |
Rv3368c |
oxidoreductase | 522 | 492 | coexpression:475 |
Rv2032 acg |
NAD(P)H nitroreductase | 522 | 492 | coexpression:475 |
Rv0306 bluB |
oxidoreductase | 520 | 490 | coexpression:473 |
Rv2819c csm5 |
CRISPR type III-associated RAMP protein Csm5 | 474 | 475 ctx | cooccurence:468 |
Rv1457c |
antibiotic ABC transporter permease | 491 | 460 | coexpression:442 |
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: YcaO-like family protein
- Pfam (hmmscan --cut_ga): YcaO PF02624.22 (E=2e-57)
- (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_215891.1)
- Domains: Pfam-A via hmmscan --cut_ga — YcaO (PF02624.22)
- 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
COG1944 - Curated reference: UniProt P9WF27 (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 —
26 functional partner(s); context anchor
csm5 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001476|Rv1375| MTGRRLARFPAFRAGVAQDDDVGSTLSQGSTTGVLSGPNWSYWPSRVLGSADPTTIAHRHGTHRITSPDETWLALQPFLAPAGITRVADVTWLDCLGIPTVQAVRPASLTLSVSQGKAASYRAAQVSAVMESLEGWHAENVTADLWSATARDLEADLTYDPAQLRHRPGSLYHAGVKLDWMVATTLLTGRRTWVPWTAVLVNVATRDCWEPPMFEMDTTGLASGNCYDEATLHALYEVMERHSVAAAVAGETMFEVPTDDVAGSDSAHLVEMIRDAGDDVDLARIDVWDGYYCFAAELTSATLEVTFGGFGLHHDPNVALSRAITEAAQSRITAISGAREDLPSAIYHRFGRVHTYAKARKTSLRLNRARPTPWRVPDVDSLPELVASAATAVANRSGTEPLAVVCDFADACVPVVKVLAPGLVLSSASPMRTPLQEAE