Rv3040c Resolved · medium auto-curated
H37Rv Rv3040c · MTBC0 mtbc0_003232 ·
288 aa · 3421502–3422368 (-) ·
RefSeq NP_217556.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | NUDIX hydrolase |
| Revised (this work) | NUDIX hydrolase. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53287
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 |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | Nudix hydrolase |
| Orthologous group | COG0494 |
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 | 0.7 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: echA17 (enoyl-CoA hydratase EchA17), high confidence from genomic context alone (score 913 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) |
|---|---|---|---|---|
Rv3039c echA17 |
enoyl-CoA hydratase EchA17 | 913 | 913 ctx | neighborhood:881 |
Rv3041c |
ABC transporter ATP-binding protein | 905 | 905 ctx | neighborhood:881 |
Rv3038c hyp |
hypothetical protein | 878 | 879 ctx | neighborhood:879 |
Rv3042c serB2 |
phosphoserine phosphatase SerB | 872 | 872 ctx | neighborhood:869 |
Rv3043c ctaD |
cytochrome C oxidase cytochrome 1 | 803 | 804 ctx | neighborhood:803 |
Rv3036c TB22.2 hyp |
hypothetical protein | 659 | 659 ctx | neighborhood:647 |
Rv3677c |
beta lactamase | 656 | 656 ctx | cooccurence:445 |
Rv0331 |
dehydrogenase/reductase | 651 | 636 | database:583 |
Rv0737 |
transcriptional regulator | 540 | 541 ctx | cooccurence:534 |
Rv3680 |
anion transporter ATPase | 522 | 505 ctx | cooccurence:417 |
Rv3037c |
S-adenosylmethionine-dependent methyltransferase | 491 | 492 ctx | neighborhood:490 |
Rv3679 |
anion transporter ATPase | 462 | 442 | |
Rv3234c tgs3 |
diacyglycerol O-acyltransferase | 438 | 439 ctx | cooccurence:426 |
Rv3044 fecB |
FeIII-dicitrate-binding periplasmic lipoprotein | 434 | 433 ctx | neighborhood:425 |
Rv0998 |
acetyltransferase Pat | 417 | 418 ctx | cooccurence:413 |
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: NUDIX hydrolase
- (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_217556.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG0494 - Curated reference: UniProt O53287 (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 —
27 functional partner(s); context anchor
echA17 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003232|Rv3040c| MNSPREPLVPPPTPRPAATVMLVRDPDAGSASGLAVFLMRRHAAMDFAAGVMVFPGGGVDDRDRDADLGRLGAWAGPPPQWWAQRFGIEPDLAEALVCAAARETFEESGVLFAGPVDQDHSAPNSIVSDASVYGDARRALADRTLSFADFLQREKLVLRSDLLRPWANWVTPEAELTRRYDTYFFVGALPEGQRADGENTESDRAGWVLPADAIADFAAGRNFLLPPTWTQLDSLAGHTVADVLAVERQIVPVQPQLARNGDNWEIEFFDSDRYNQARRSGGSTGWPL