Rv1531 Family assigned · medium auto-curated
H37Rv Rv1531 · MTBC0 mtbc0_001638 ·
188 aa · 1742282–1742848 (+) ·
RefSeq NP_216047.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | carboxymuconolactone decarboxylase family protein |
| Revised (this work) | Carboxymuconolactone decarboxylase family protein. Pfam: CMD (PF02627.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53905
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 |
S Function unknown
|
|---|---|
| eggNOG description | carboxymuconolactone decarboxylase |
| Orthologous group | COG2128 |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 4 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 |
|---|---|---|---|---|
CMD | PF02627.26 | 1.6e-17 | 40–122 | Carboxymuconolactone decarboxylase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: adh (alcohol dehydrogenase), high confidence from genomic context alone (score 833 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) |
|---|---|---|---|---|
Rv1530 adh |
alcohol dehydrogenase | 833 | 833 ctx | neighborhood:801 |
Rv2423 hyp |
hypothetical protein | 542 | 542 ctx | cooccurence:540 |
Rv2067c hyp |
hypothetical protein | 536 | 537 ctx | cooccurence:534 |
Rv1529 fadD24 |
fatty-acid--CoA ligase FadD24 | 524 | 525 ctx | neighborhood:513 |
Rv0943c |
monooxygenase | 524 | 524 ctx | cooccurence:512 |
Rv3899c hyp |
hypothetical protein | 495 | 495 ctx | cooccurence:491 |
Rv1286 cysC |
adenylyl-sulfate kinase | 476 | 476 | coexpression:476 |
Rv3060c |
GntR family transcriptional regulator | 452 | 452 ctx | cooccurence:452 |
Rv3435c |
transmembrane protein | 541 | 448 ctx | cooccurence:448 |
Rv1868 hyp |
hypothetical protein | 432 | 433 ctx | cooccurence:431 |
Rv3773c hyp |
hypothetical protein | 408 | 408 ctx | cooccurence:407 |
Rv2399c cysT |
sulfate ABC transporter permease CysT | 403 | 404 | coexpression:404 |
Rv0433 |
carboxylate-amine ligase | 402 | 402 | coexpression:402 |
Rv0771 |
4-carboxymuconolactone decarboxylase | 668 | 205 | textmining:600 |
Rv3833 |
AraC family transcriptional regulator | 483 | 130 | textmining:431 |
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: carboxymuconolactone decarboxylase family protein
- Pfam (hmmscan --cut_ga): CMD PF02627.26 (E=2e-17)
- (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_216047.1)
- Domains: Pfam-A via hmmscan --cut_ga — CMD (PF02627.26)
- 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
COG2128 - Curated reference: UniProt O53905 (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 —
36 functional partner(s); context anchor
adh - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001638|Rv1531| MTTSRVPLLPVDEAKAAADEAGVPDYMAELSIFQVLLNHPRLARTFNDLLATMLWHGTLDSRLRELVIMRIGWLTDCDYEWTQHWRVASGLGVSADDLLGVRDWQGYNGFGPAEQAVLAATDDVVREGAVSAQSWSACERELHCDKVVLIELVTVISAWRMVASILHSLEVPLEDGVSSWPPDGLSPR