Rv2913c Family assigned · medium auto-curated
H37Rv Rv2913c · MTBC0 mtbc0_003095 ·
611 aa · 3240692–3242527 (-) ·
RefSeq NP_217429.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | D-amino acid aminohydrolase |
|---|---|
| MTBC0 PGAP re-annotation | amidohydrolase family protein |
| Revised (this work) | Amidohydrolase family protein. Pfam: Amidohydro_3 (PF07969.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJH9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2913c |
UniProt still lists this protein as Uncharacterized protein Rv2913c; 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 catabolism
|
|---|---|
| eggNOG description | N-acyl-D-aspartate D-glutamate deacylase |
| Orthologous group | COG3653 |
| Gene Ontology (8) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, 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 | 0.252 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 11 synonymous, 7 missense, 1 nonsense, 2 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 3.08% of strains (4466) · 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 |
|---|---|---|---|---|
Amidohydro_3 | PF07969.18 | 7.0e-11 | 60–213 | Amidohydrolase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2912c (TetR family HTH-type transcriptional regulator), high confidence from genomic context alone (score 922 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2912c |
TetR family HTH-type transcriptional regulator | 972 | 922 ctx | neighborhood:881 textmining:653 |
Rv2914c pknI |
serine/threonine-protein kinase PknI | 661 | 589 ctx | neighborhood:588 |
Rv0293c hyp |
hypothetical protein | 560 | 560 ctx | cooccurence:558 |
Rv2916c ffh |
signal recognition particle protein | 542 | 542 ctx | neighborhood:540 |
Rv2915c hyp |
hypothetical protein | 831 | 537 ctx | neighborhood:537 textmining:650 |
Rv3775 lipE |
lipase LipE | 497 | 498 ctx | cooccurence:481 |
Rv1393c |
monoxygenase | 423 | 424 ctx | cooccurence:419 |
Rv1923 lipD |
lipase LipD | 417 | 417 | |
Rv1497 lipL |
esterase LipL | 414 | 414 | |
Rv2911 dacB2 |
penicillin-binding protein DacB2 | 471 | 96 | textmining:439 |
Rv3330 dacB1 |
penicillin-binding protein DacB | 466 | 93 | textmining:436 |
Rv1367c hyp |
hypothetical protein | 529 | 77 | textmining:511 |
Rv3332 nagA |
N-acetylglucosamine-6-phosphate deacetylase NagA | 674 | 51 | textmining:671 |
Rv2970c lipN |
lipase/esterase LipN | 522 | 48 | textmining:519 |
Rv3451 cut3 |
cutinase | 652 | 47 | textmining:651 |
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: D-amino acid aminohydrolase
- MTBC0 PGAP product: amidohydrolase family protein
- Pfam (hmmscan --cut_ga): Amidohydro_3 PF07969.18 (E=7e-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_217429.1)
- Domains: Pfam-A via hmmscan --cut_ga — Amidohydro_3 (PF07969.18)
- 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
COG3653 - Curated reference: UniProt P9WJH9 (SwissProt, reviewed; 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 —
25 functional partner(s); context anchor
Rv2912c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003095|Rv2913c| MLAWRQLNDLEETVTYDVIIRDGLWFDGTGNAPLTRTLGIRDGVVATVAAGALDETGCPEVVDAAGKWVVPGFIDVHTHYDAEVLLDPGLRESVRHGVTTVLLGNCSLSTVYANSEDAADLFSRVEAVPREFVLGALRDNQTWSTPAEYIEAIDALPLGPNVSSLLGHSDLRTAVLGLDRATDDTVRPTEAELAKMAKLLDEALEAGMLGMSGMDAAIDKLDGDRFRSRALPSTFATWRERRKLISVLRHRGRILQSAPDVDNPVSALLFFLASSRIFNRRKGVRMSMLVSADAKSMPLAVHVFGLGTRVLNKLLGSQVRFQHLPVPFELYSDGIDLPVFEEFGAGTAALHLRDQLQRNELLADRSYRRSFRREFDRIKLGPSLWHRDFHDAVIVECPDKSLIGKSFGAIADERGLHPLDAFLDVLVDNGERNVRWTTIVANHRPNQLNKLAAEPSVHMGFSDAGAHLRNMAFYNFGLRLLKRARDADRAGQPFLSIERAVYRLTGELAEWFGIGAGTLRQGDRADFAVIDPTHLDESVDGYHEEAVPYYGGLRRMVNRNDATVVATGVGGTVVFRGGQFGGQFRDGYGQNVKSGRYLRAGELGAALSRSA