Rv1489A Family assigned · medium auto-curated
H37Rv Rv1489A · MTBC0 - ·
76 aa · 1678942–1679172 (+) ·
RefSeq YP_177646.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains MM_CoA_mutase (PF01642.29) 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.
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 |
L7N6A8
TrEMBL · unreviewed
· Predicted
|
|---|---|
| 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 |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | mutA |
| eggNOG description | cobalamin binding |
| Orthologous group | COG2185 |
| EC number |
EC 5.4.99.2
|
| KEGG orthology |
K01847
|
| KEGG pathways |
map00280, map00630, map00640, map00720, map01100, map01120, map01200
|
| KEGG modules |
M00373, M00376, M00741
|
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, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.39% of strains (569) · 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 |
|---|---|---|---|---|
MM_CoA_mutase | PF01642.29 | 9.2e-06 | 5–55 | Methylmalonyl-CoA mutase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0513 (transmembrane protein), high confidence from genomic context alone (score 705 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) |
|---|---|---|---|---|
Rv1492 mutA |
methylmalonyl-CoA mutase small subunit | 998 | 999 | coexpression:688 experimental:994 |
Rv1493 mutB |
methylmalonyl-CoA mutase large subunit | 875 | 863 | experimental:782 |
Rv1496 meaB |
transport system kinase | 751 | 727 | coexpression:690 |
Rv1489 hyp |
hypothetical protein | 705 | 705 ctx | neighborhood:691 |
Rv0513 |
transmembrane protein | 704 | 705 ctx | cooccurence:704 |
Rv3802c |
membrane protein | 703 | 704 ctx | cooccurence:691 |
Rv1488 hyp |
hypothetical protein | 667 | 667 ctx | neighborhood:663 |
Rv1487 hyp |
hypothetical protein | 665 | 665 ctx | neighborhood:608 |
Rv2673 aftC |
alpha-(1->3)-arabinofuranosyltransferase | 657 | 657 ctx | cooccurence:657 |
Rv3346c |
transmembrane protein | 615 | 615 ctx | cooccurence:615 |
Rv0227c |
membrane protein | 613 | 613 ctx | cooccurence:613 |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 599 | 600 ctx | cooccurence:596 |
Rv3668c |
protease | 585 | 586 ctx | cooccurence:583 |
Rv0226c |
transmembrane protein | 580 | 580 ctx | cooccurence:579 |
Rv2876 |
transmembrane protein | 580 | 580 ctx | cooccurence:579 |
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): hypothetical protein
- Pfam (hmmscan --cut_ga): MM_CoA_mutase PF01642.29 (E=9e-06)
- (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_177646.1)
- Domains: Pfam-A via hmmscan --cut_ga — MM_CoA_mutase (PF01642.29)
- 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
COG2185 - Curated reference: UniProt L7N6A8 (TrEMBL, unreviewed; 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 —
49 functional partner(s); context anchor
Rv0513 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1489A| MSVGEVEVLKVENSRVRAEQLAKLYELRSSRDRVRVDAALAELSRAAAARGCAGTSGLGNNLMAPGPPHSLLGRDR