Rv1738 Family assigned · medium auto-curated
H37Rv Rv1738 · MTBC0 mtbc0_001851 ·
94 aa · 1977729–1978013 (+) ·
RefSeq NP_216254.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF1876 domain-containing protein |
| Revised (this work) | DUF1876 domain-containing protein. Pfam: Rv2632c-like (PF08962.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLS3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1738 |
UniProt still lists this protein as Uncharacterized protein Rv1738; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Domain of unknown function (DUF1876) |
| Orthologous group | 2EH65 |
| Gene Ontology (27) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0008150, GO:0009605, GO:0009607, GO:0016020, GO:0040007, GO:0043207 +15 more
|
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 | 0.635 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 6.16% of strains (8951) · 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 |
|---|---|---|---|---|
Rv2632c-like | PF08962.17 | 2.2e-32 | 11–90 | Rv2632c-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3131 (NAD(P)H nitroreductase), high confidence from genomic context alone (score 915 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) |
|---|---|---|---|---|
Rv3127 hyp |
hypothetical protein | 954 | 922 ctx | cooccurence:465 coexpression:860 textmining:436 |
Rv3131 |
NAD(P)H nitroreductase | 937 | 915 ctx | cooccurence:419 coexpression:860 |
Rv2031c hspX |
alpha-crystallin | 963 | 906 | coexpression:860 textmining:630 |
Rv1996 |
universal stress protein | 922 | 906 | coexpression:861 |
Rv2032 acg |
NAD(P)H nitroreductase | 979 | 900 ctx | cooccurence:438 coexpression:829 textmining:804 |
Rv3134c |
universal stress protein | 975 | 882 ctx | cooccurence:424 coexpression:803 textmining:803 |
Rv1737c narK2 |
nitrate/nitrite transporter | 925 | 872 ctx | neighborhood:449 coexpression:778 textmining:436 |
Rv0080 hyp |
hypothetical protein | 895 | 867 | coexpression:804 |
Rv3130c tgs1 |
diacyglycerol O-acyltransferase | 909 | 861 | coexpression:861 |
Rv0079 hyp |
hypothetical protein | 949 | 860 | coexpression:860 textmining:654 |
Rv2007c fdxA |
ferredoxin | 933 | 845 | coexpression:845 textmining:586 |
Rv1733c |
transmembrane protein | 922 | 845 | coexpression:797 textmining:518 |
Rv2626c hrp1 |
hypoxic response protein | 960 | 806 | coexpression:805 textmining:803 |
Rv2623 TB31.7 |
universal stress protein | 926 | 800 | coexpression:735 textmining:650 |
Rv2627c hyp |
hypothetical protein | 797 | 797 | coexpression:797 |
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: DUF1876 domain-containing protein
- Pfam (hmmscan --cut_ga): Rv2632c-like PF08962.17 (E=2e-32)
- (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_216254.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rv2632c-like (PF08962.17)
- 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
2EH65 - Curated reference: UniProt P9WLS3 (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 —
31 functional partner(s); context anchor
Rv3131 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001851|Rv1738| MCGDQSDHVLQHWTVDISIDEHEGLTRAKARLRWREKELVGVGLARLNPADRNVPEIGDELSVARALSDLGKRMLKVSTHDIEAVTHQPARLLY