Rv0180c Family assigned · medium auto-curated
H37Rv Rv0180c · MTBC0 mtbc0_000193 ·
452 aa · 211240–212598 (-) ·
RefSeq NP_214694.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | YhgE/Pip domain-containing protein |
| Revised (this work) | YhgE/Pip domain-containing protein. Pfam: ABC2_membrane_3 (PF12698.14), DUF3533 (PF12051.15). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07424
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF3533) |
| Orthologous group | COG1511 |
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) pseudogene candidate
| pN/pS | 0.367 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 14 synonymous, 13 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 5.05% of strains (7330) · 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 |
|---|---|---|---|---|
ABC2_membrane_3 | PF12698.14 | 3.9e-17 | 34–407 | ABC-2 family transporter protein |
DUF3533 | PF12051.15 | 1.5e-24 | 36–381 | Protein of unknown function (DUF3533) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3434c (transmembrane protein), high confidence from genomic context alone (score 707 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0181c hyp |
hypothetical protein | 968 | 848 ctx | neighborhood:846 textmining:803 |
Rv1006 hyp |
hypothetical protein | 741 | 741 ctx | cooccurence:741 |
Rv1435c hyp |
hypothetical protein | 707 | 708 ctx | cooccurence:706 |
Rv3434c |
transmembrane protein | 706 | 707 ctx | cooccurence:705 |
Rv2598 hyp |
hypothetical protein | 694 | 695 ctx | cooccurence:690 |
Rv1868 hyp |
hypothetical protein | 692 | 692 ctx | cooccurence:692 |
Rv0090 |
membrane protein | 686 | 687 ctx | cooccurence:685 |
Rv0182c sigG |
ECF RNA polymerase sigma factor SigG | 740 | 674 ctx | neighborhood:662 |
Rv0185 hyp |
hypothetical protein | 662 | 663 ctx | neighborhood:418 cooccurence:439 |
Rv1748 hyp |
hypothetical protein | 661 | 661 ctx | cooccurence:659 |
Rv0179c lprO |
lipoprotein LprO | 764 | 641 ctx | neighborhood:639 |
Rv0184 hyp |
hypothetical protein | 628 | 628 ctx | neighborhood:423 |
Rv3166c hyp |
hypothetical protein | 627 | 627 ctx | cooccurence:627 |
Rv2937 drrB |
daunorubicin ABC transporter permease DrrB | 618 | 618 ctx | cooccurence:543 |
Rv2114 hyp |
hypothetical protein | 611 | 611 ctx | cooccurence:610 |
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: YhgE/Pip domain-containing protein
- Pfam (hmmscan --cut_ga): ABC2_membrane_3 PF12698.14 (E=4e-17), DUF3533 PF12051.15 (E=1e-24)
- (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_214694.1)
- Domains: Pfam-A via hmmscan --cut_ga — ABC2_membrane_3 (PF12698.14), DUF3533 (PF12051.15)
- 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
COG1511 - Curated reference: UniProt O07424 (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 —
66 functional partner(s); context anchor
Rv3434c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000193|Rv0180c| MSQAQPRPAAPNPKRNVKAIRTVRFWMAPIATTLALMSALAALYLGGILNPMTNLRHFPIALVNEDAGPAGQQIVDGLVSGLDKNKFDIRVVSPDEARRLLDTAAVYGSALIPPTFSSQLRDFGASAVTPTRTDRPAITISTNPRAGTLAASIAGQTLTRALTVVNGKVGERLTAEVAAQTGGVALAGAAAAGLASPIDVKSTAYNPLPNGTGNGLSAFYYALLLLLAGFTGSIVVSTLVDSMLGYVPAEFGPVYRFAEQVNISRFRTLLVKWAVMVVLALLTSGVYLAIAHGLGMPIPLGWQVWLYGVFAIIAVGVTSSSLIAVLGSMGLLVSMLIFVILGLPSAGATVPLEAVPAFFRWLAQFEPMHQVFLGVRSLLYLNGNADAGLSQALTMTSIGLIIGLLLGGFITHLYDRSSFHRIPGAVEMAIAVEHQAQYQARQSARESSSEQP