Rv1382 Resolved · high auto-curated
H37Rv Rv1382 · MTBC0 mtbc0_001483 ·
165 aa · 1564821–1565318 (+) ·
RefSeq NP_215898.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | transporter |
| Revised (this work) | Transporter. Pfam: bPH_11 (PF25362.2). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71810
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable export or membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolismF Nucleotide transport and metabolism
|
|---|---|
| eggNOG description | Belongs to the CarA family |
| Orthologous group | COG0505 |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 3 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 |
|---|---|---|---|---|
bPH_11 | PF25362.2 | 1.6e-48 | 43–163 | Bacterial PH domain-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: carB (carbamoyl-phosphate synthase large subunit), high confidence from genomic context alone (score 995 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) |
|---|---|---|---|---|
Rv1384 carB |
carbamoyl-phosphate synthase large subunit | 996 | 995 ctx | neighborhood:882 coexpression:793 experimental:829 |
Rv1381 pyrC |
dihydroorotase | 994 | 994 ctx | neighborhood:882 coexpression:953 |
Rv1383 carA |
carbamoyl-phosphate synthase small subunit | 977 | 976 ctx | neighborhood:882 coexpression:805 |
Rv1380 pyrB |
aspartate carbamoyltransferase | 981 | 975 ctx | neighborhood:882 coexpression:794 |
Rv1385 pyrF |
orotidine 5'-phosphate decarboxylase | 974 | 971 ctx | neighborhood:881 coexpression:764 |
Rv1379 pyrR |
bifunctional pyrimidine operon regulatory protein/uracil phosphoribosyltransferase | 964 | 960 ctx | neighborhood:882 coexpression:676 |
Rv2670c zapE hyp |
hypothetical protein | 794 | 794 ctx | cooccurence:770 |
Rv2772c |
transmembrane protein | 774 | 774 ctx | cooccurence:773 |
Rv3317 sdhD |
succinate dehydrogenase hydrophobic membrane anchor subunit | 773 | 774 ctx | cooccurence:771 |
Rv3316 sdhC |
succinate dehydrogenase cytochrome B-556 subunit | 769 | 770 ctx | cooccurence:768 |
Rv2139 pyrD |
dihydroorotate dehydrogenase | 795 | 768 | coexpression:729 |
Rv0383c ttfA hyp |
hypothetical protein | 757 | 735 | coexpression:668 |
Rv0385 |
monooxygenase | 719 | 690 | coexpression:676 |
Rv1937 |
oxygenase | 784 | 685 | coexpression:667 |
Rv0382c pyrE |
orotate phosphoribosyltransferase | 707 | 681 | coexpression:670 |
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: transporter
- Pfam (hmmscan --cut_ga): bPH_11 PF25362.2 (E=2e-48)
- (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_215898.1)
- Domains: Pfam-A via hmmscan --cut_ga — bPH_11 (PF25362.2)
- 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
COG0505 - Curated reference: UniProt P71810 (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 —
74 functional partner(s); context anchor
carB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001483|Rv1382| MNSGTLAGSLIFAAVLVMLIAVLARLMMRGWRRRSERQAELLGDLPDVPEHVSSATVTTRGLYVGATLSPAWNERVTVGDLGYRSKAVLTRYPSGIMVERARAQPIWIPTESIAAIRMERGVAGKVVAGIGILAIRWRLPSGTEIDVGFRADNRDEYQEWLEEPV