Rv1624c Family assigned · low auto-curated
H37Rv Rv1624c · MTBC0 mtbc0_001731 ·
195 aa · 1837962–1838549 (-) ·
RefSeq NP_216140.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | HdeD family acid-resistance protein |
| Revised (this work) | HdeD family acid-resistance protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06141
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable conserved membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Short repeat of unknown function (DUF308) |
| Orthologous group | COG3247 |
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 | 0.369 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
DUF308 | PF03729.19 | 1.0e-11 | 30–99 | Short repeat of unknown function (DUF308) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cya (adenylate cyclase), high confidence from genomic context alone (score 842 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1625c cya |
adenylate cyclase | 842 | 842 ctx | neighborhood:840 |
Rv1623c cydA |
cytochrome D ubiquinol oxidase subunit I CydA | 781 | 781 ctx | neighborhood:768 |
Rv1622c cydB |
cytochrome D ubiquinol oxidase subunit II CydB | 761 | 761 ctx | neighborhood:743 |
Rv1621c cydD |
cytochrome biosyntheisis ABC transporter ATP-binding protein/permease CydD | 691 | 691 ctx | neighborhood:688 |
Rv1620c cydC |
cytochrome biosyntheisis ABC transporter ATP-binding protein/permease CydC | 690 | 690 ctx | neighborhood:688 |
Rv1811 mgtC |
Mg2+ transport P-type ATPase MgtC | 689 | 659 | coexpression:648 |
Rv3008 hyp |
hypothetical protein | 687 | 657 | coexpression:646 |
Rv3432c gadB |
glutamate decarboxylase GadB | 624 | 593 | coexpression:447 |
Rv0185 hyp |
hypothetical protein | 522 | 522 ctx | cooccurence:522 |
Rv3035 hyp |
hypothetical protein | 489 | 490 ctx | cooccurence:487 |
Rv1125 hyp |
hypothetical protein | 468 | 469 ctx | cooccurence:466 |
Rv3481c |
integral membrane protein | 459 | 460 ctx | cooccurence:458 |
Rv1626 pdtaR |
two-component system transcriptional regulator | 449 | 448 ctx | neighborhood:440 |
Rv0184 hyp |
hypothetical protein | 434 | 434 ctx | cooccurence:434 |
Rv1780 hyp |
hypothetical protein | 431 | 432 ctx | cooccurence:428 |
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: membrane protein
- MTBC0 PGAP product: HdeD family acid-resistance protein
- Pfam (hmmscan --cut_ga): DUF308 PF03729.19 (E=1e-11)
- (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_216140.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF308 (PF03729.19)
- 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
COG3247 - Curated reference: UniProt O06141 (TrEMBL, unreviewed; Predicted)
- 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
cya - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001731|Rv1624c| MCHTAPMEPSPVVSPLPRLLPHLWKSTLASGILSLILGVLVLAWPGISILVAAMAFGVYLLITGVAQVAFAFSLHVSAGGRILLFISGAASLILAVLAFRHFGDAVLLLAIWIGIGFIFRGVATTVSAISDPMLPGRGWSIFVGVISLIAGIVVMASPFESIWILALVVGIWLVVIGACEIASSFAIRKASQTLG