Rv1339 Family assigned · medium auto-curated
H37Rv Rv1339 · MTBC0 - ·
273 aa · 1505917–1506738 (+) ·
RefSeq NP_215855.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Anti-Pycsar_Apyc1 (PF23023.2), Lactamase_B (PF00753.34), Lactamase_B_2 (PF12706.14) 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 |
P9WGC1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1339 |
UniProt still lists this protein as Uncharacterized protein Rv1339; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | yhfI |
| eggNOG description | Metal-dependent hydrolases of the beta-lactamase superfamily III |
| Orthologous group | COG1234 |
| Gene Ontology (49) |
GO:0003674, GO:0003824, GO:0004518, GO:0004519, GO:0004521, GO:0004540, GO:0005575, GO:0005623, GO:0005886, GO:0006139, GO:0006396, GO:0006399 +37 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)
| pN/pS | 0.354 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Anti-Pycsar_Apyc1 | PF23023.2 | 2.9e-09 | 20–203 | Anti-Pycsar protein Apyc1 |
Lactamase_B | PF00753.34 | 9.0e-06 | 35–182 | Metallo-beta-lactamase superfamily |
Lactamase_B_2 | PF12706.14 | 1.4e-17 | 67–237 | Beta-lactamase superfamily domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rphA (ribonuclease PH), high confidence from genomic context alone (score 896 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) |
|---|---|---|---|---|
Rv1340 rphA |
ribonuclease PH | 906 | 896 ctx | neighborhood:861 |
Rv1336 cysM |
O-phosphoserine sulfhydrylase | 844 | 845 ctx | neighborhood:843 |
Rv1335 cysO |
sulfur carrier protein CysO | 840 | 840 ctx | neighborhood:838 |
Rv1334 mec |
[CysO | 825 | 825 ctx | neighborhood:813 |
Rv1341 rdgB |
non-canonical purine NTP pyrophosphatase | 821 | 821 ctx | neighborhood:808 |
Rv1333 |
hydrolase | 815 | 816 ctx | neighborhood:813 |
Rv1332 |
transcriptional regulator | 800 | 800 ctx | neighborhood:797 |
Rv1331 clpS |
ATP-dependent Clp protease adapter protein ClpS | 798 | 798 ctx | neighborhood:797 |
Rv1338 murI |
glutamate racemase | 756 | 757 ctx | neighborhood:746 |
Rv1337 |
integral membrane protein | 752 | 753 ctx | neighborhood:746 |
Rv1330c pncB1 |
nicotinic acid phosphoribosyltransferase PncB1 | 743 | 726 ctx | neighborhood:725 |
Rv1329c dinG |
ATP-dependent helicase DinG | 647 | 634 ctx | neighborhood:555 |
Rv3676 crp |
cAMP receptor protein | 655 | 615 ctx | cooccurence:601 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 468 | 469 | |
Rv2239c hyp |
hypothetical protein | 414 | 415 ctx | cooccurence:408 |
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): Anti-Pycsar_Apyc1 PF23023.2 (E=3e-09), Lactamase_B PF00753.34 (E=9e-06), Lactamase_B_2 PF12706.14 (E=1e-17)
- (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_215855.1)
- Domains: Pfam-A via hmmscan --cut_ga — Anti-Pycsar_Apyc1 (PF23023.2), Lactamase_B (PF00753.34), Lactamase_B_2 (PF12706.14)
- 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
COG1234 - Curated reference: UniProt P9WGC1 (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 —
21 functional partner(s); context anchor
rphA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1339| MRRCIPHRCIGHGTVVSVRITVLGCSGSVVGPDSPASGYLLRAPHTPPLVIDFGGGVLGALQRHADPASVHVLLSHLHADHCLDLPGLFVWRRYHPSRPSGKALLYGPSDTWSRLGAASSPYGGEIDDCSDIFDVHHWADSEPVTLGALTIVPRLVAHPTESFGLRITDPSGASLAYSGDTGICDQLVELARGVDVFLCEASWTHSPKHPPDLHLSGTEAGMVAAQAGVRELLLTHIPPWTSREDVISEAKAEFDGPVHAVVCDETFEVRRAG