Rv3672c Resolved · high auto-curated
H37Rv Rv3672c · MTBC0 mtbc0_003891 ·
273 aa · 4137351–4138172 (-) ·
RefSeq NP_218189.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | CoA pyrophosphatase |
| Revised (this work) | CoA pyrophosphatase. Pfam: NUDIX (PF00293.35). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6XHX8
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Nudix hydrolase domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | nudL |
| eggNOG description | Nudix hydrolase |
| Orthologous group | COG0494 |
| KEGG orthology |
K18568
|
| KEGG pathways |
map00332, map01130
|
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 0 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.48% of strains (699) · 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 |
|---|---|---|---|---|
NUDIX | PF00293.35 | 6.4e-13 | 97–200 | NUDIX domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: marP (serine protease), high confidence from genomic context alone (score 929 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) |
|---|---|---|---|---|
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 941 | 933 | experimental:787 database:643 |
Rv3671c marP |
serine protease | 930 | 929 ctx | neighborhood:816 database:530 |
Rv3673c |
membrane-anchored thioredoxin-like protein | 921 | 919 ctx | neighborhood:591 coexpression:771 |
Rv3211 rhlE |
ATP-dependent RNA helicase RhlE | 787 | 774 | experimental:403 database:615 |
Rv1253 deaD |
ATP-dependent RNA helicase DeaD | 781 | 768 | experimental:403 database:615 |
Rv2888c amiC |
amidase AmiC | 761 | 762 | coexpression:735 |
Rv1677 dsbF |
lipoprotein DsbF | 734 | 724 | coexpression:649 |
Rv2878c mpt53 |
soluble secreted antigen Mpt53 | 733 | 724 | coexpression:648 |
Rv2524c fas |
fatty acid synthase | 676 | 665 | database:406 |
Rv1340 rphA |
ribonuclease PH | 689 | 658 | database:636 |
Rv0118c oxcA |
oxalyl-CoA decarboxylase OxcA | 602 | 601 | database:520 |
Rv3674c nth |
endonuclease III | 617 | 597 ctx | neighborhood:591 |
Rv3339c icd1 |
isocitrate dehydrogenase | 594 | 595 | database:581 |
Rv1391 dfp |
bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase | 588 | 589 | database:556 |
Rv1043c hyp |
hypothetical protein | 594 | 584 | database:530 |
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: CoA pyrophosphatase
- Pfam (hmmscan --cut_ga): NUDIX PF00293.35 (E=6e-13)
- (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_218189.1)
- Domains: Pfam-A via hmmscan --cut_ga — NUDIX (PF00293.35)
- 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 I6XHX8 (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 —
103 functional partner(s); context anchor
marP - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003891|Rv3672c| MSAGGTPLQAGATPTGSRGTVALRPDAGPSWLRPLVDNVGQIPDAYRRRLPADVLAMVTAAGAVSAMTSSRRDHREAAVLVLFSGPEAGPGDGGVPDDADLLLTVRASTLRHHAGQAAFPGGVVDPADDGPVATALREANEETGIDPSRLHPLATMERTFIAPSRFHVVPVLAYSPDPGPVAVVNEAETAIVARVPVRAFINPANRLMVYRRPHTRRWAGPAFLLNQMLVWGFTGQVISAVLDVAGWAQPWDTGDIRELDAAMVLIDDESDPR