Rv3064c Family assigned · medium auto-curated
H37Rv Rv3064c · MTBC0 mtbc0_003256 ·
141 aa · 3451189–3451614 (-) ·
RefSeq NP_217580.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | DoxX family protein |
| Revised (this work) | DoxX family protein. Pfam: DoxX (PF07681.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6XG31
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable conserved integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | membrane |
| Orthologous group | COG2259 |
| KEGG orthology |
K15977
|
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 | 0.118 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.45% of strains (656) · 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 |
|---|---|---|---|---|
DoxX | PF07681.18 | 3.5e-13 | 17–94 | DoxX |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mmr (multidrug resistance protein Mmr), medium confidence from genomic context alone (score 594 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3065 mmr |
multidrug resistance protein Mmr | 593 | 594 ctx | neighborhood:577 |
Rv3868 eccA1 |
ESX-1 secretion system protein EccA1 | 578 | 579 | database:576 |
Rv0282 eccA3 |
ESX-3 secretion system protein EccA | 577 | 578 | database:576 |
Rv0435c |
ATPase | 576 | 576 | database:576 |
Rv3066 |
DeoR family transcriptional regulator | 551 | 551 ctx | neighborhood:550 |
Rv0908 ctpE |
metal cation transporter ATPase E | 481 | 481 | |
Rv0425c ctpH |
metal cation transporting ATPase H | 481 | 481 | |
Rv1997 ctpF |
cation transporter ATPase F | 479 | 480 | |
Rv0107c ctpI |
cation-transporter ATPase I | 479 | 480 | |
Rv3413c rsdA |
anti-sigma-D factor RsdA | 470 | 470 ctx | cooccurence:470 |
Rv1305 atpE |
ATP synthase subunit C | 433 | 433 | database:417 |
Rv0732 secY |
preprotein translocase SecY | 402 | 365 | |
Rv2182c |
1-acylglycerol-3-phosphate O-acyltransferase | 575 | 282 | textmining:434 |
Rv3484 cpsA hyp |
hypothetical protein | 576 | 159 | textmining:517 |
Rv3483c hyp |
hypothetical protein | 687 | 142 | textmining:651 |
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: integral membrane protein
- MTBC0 PGAP product: DoxX family protein
- Pfam (hmmscan --cut_ga): DoxX PF07681.18 (E=4e-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_217580.1)
- Domains: Pfam-A via hmmscan --cut_ga — DoxX (PF07681.18)
- 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
COG2259 - Curated reference: UniProt I6XG31 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
30 functional partner(s); context anchor
mmr - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003256|Rv3064c| MVKDLDRRLAGCLPAVLSLFRLVYGLLFAGYGSMILFGWPVTSAQPVEFGSWPGWYAGVIELVAGLLIATGLFTRAVAFVASGEMAVAYFWMHQPYALWPIGGPPDGNGGTPAILFCFGFFLLVFTGGGIYSIDARRTVTA