Rv2617c Family assigned · medium auto-curated
H37Rv Rv2617c · MTBC0 mtbc0_002786 ·
146 aa · 2969409–2969849 (-) ·
RefSeq NP_217133.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | DoxX family membrane protein |
| Revised (this work) | DoxX family membrane 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 |
I6XER9
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | DoxX |
| Orthologous group | 2BVXR |
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, 1 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 |
|---|---|---|---|---|
DoxX | PF07681.18 | 5.2e-05 | 24–106 | DoxX |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccD2 (ESX-2 secretion system protein EccD), medium confidence from genomic context alone (score 418 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2618 hyp |
hypothetical protein | 873 | 873 ctx | neighborhood:581 cooccurence:706 |
Rv3887c eccD2 |
ESX-2 secretion system protein EccD | 418 | 418 ctx | cooccurence:418 |
Rv3604c |
transmembrane protein | 411 | 411 ctx | cooccurence:408 |
Rv3810 pirG |
cell surface protein | 828 | 161 | textmining:804 |
Rv1625c cya |
adenylate cyclase | 699 | 50 | textmining:697 |
Rv1417 |
membrane protein | 870 | 47 | textmining:870 |
Rv1416 ribH |
6,7-dimethyl-8-ribityllumazine synthase | 804 | 47 | textmining:803 |
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: transmembrane protein
- MTBC0 PGAP product: DoxX family membrane protein
- Pfam (hmmscan --cut_ga): DoxX PF07681.18 (E=5e-05)
- (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_217133.1)
- 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
2BVXR - Curated reference: UniProt I6XER9 (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 —
7 functional partner(s); context anchor
eccD2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002786|Rv2617c| MSIRPTTSPALADQLKDPAYSAYVLLRTLFTVAPILFGLDKFFNLLTHPQHWNMYLAGWINDLVPGTADQCMYLVGAIEIVAGVLVAVAPRIGAWVVAAWLAGIILNLVTGPGFYDIALRDFGLLVGAIALARLAQGVHSGGIGRP