Rv0128 Family assigned · low auto-curated
H37Rv Rv0128 · MTBC0 mtbc0_000139 ·
259 aa · 156013–156792 (+) ·
RefSeq NP_214642.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | YoaK family protein |
| Revised (this work) | YoaK family 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 |
P96805
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 (DUF1275) |
| Orthologous group | COG3619 |
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 | 1.398 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.34% of strains (487) · 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 |
|---|---|---|---|---|
DUF1275 | PF06912.17 | 1.6e-30 | 12–212 | Protein of unknown function (DUF1275) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mak (maltokinase), high confidence from genomic context alone (score 795 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0127 mak |
maltokinase | 795 | 795 ctx | neighborhood:794 |
Rv0126 treS |
trehalose synthase/amylase TreS | 717 | 718 ctx | neighborhood:716 |
Rv0204c |
transmembrane protein | 716 | 717 ctx | cooccurence:706 |
Rv3820c papA2 |
trehalose-2-sulfate acyltransferase | 690 | 691 ctx | cooccurence:686 |
Rv3824c papA1 |
acyltransferase | 684 | 685 ctx | cooccurence:684 |
Rv1182 papA3 |
acyltransferase papA3 | 654 | 654 ctx | cooccurence:652 |
Rv3779 |
transmembrane protein | 634 | 634 ctx | cooccurence:634 |
Rv0048c |
membrane protein | 604 | 604 ctx | cooccurence:602 |
Rv0125 pepA |
serine protease PepA | 595 | 595 ctx | neighborhood:593 |
Rv0507 mmpL2 |
transmembrane transport protein MmpL2 | 580 | 580 ctx | cooccurence:580 |
Rv2942 mmpL7 |
transmembrane transport protein MmpL7 | 552 | 552 ctx | cooccurence:552 |
Rv0402c mmpL1 |
transmembrane transport protein MmpL1 | 551 | 551 ctx | cooccurence:550 |
Rv0450c mmpL4 |
transmembrane transport protein MmpL4 | 551 | 551 ctx | cooccurence:551 |
Rv1065 hyp |
hypothetical protein | 547 | 547 ctx | cooccurence:547 |
Rv2945c lppX |
lipoprotein LppX | 543 | 544 ctx | cooccurence:539 |
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: YoaK family protein
- Pfam (hmmscan --cut_ga): DUF1275 PF06912.17 (E=2e-30)
- (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_214642.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF1275 (PF06912.17)
- 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
COG3619 - Curated reference: UniProt P96805 (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 —
35 functional partner(s); context anchor
mak - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000139|Rv0128| MQREIYDGEARLSWVLAALAGILGATAFTHSAGYFVTFMTGNSQRAVLGLFGDDAWMSVTASLLILFFVAGVVIASVCRRHFWAAHPHGPTVLTTFSLIFAAGVDIMLGGWHESMLDFVPILFVVFGIGALNTSFVKDGEVSVPLSYVTGTLVKMGQGIERHLAGGKVEDWLGYFLLHASFVLGAAAGGAISMVVTGPQMLAVAAVVCAATTGYTYLHADRRGLVNQKRPQPGKRLFRALRRGELDSGTSTPATNYGSS