Rv3277 Resolved · high auto-curated
H37Rv Rv3277 · MTBC0 - ·
272 aa · 3659878–3660696 (+) ·
RefSeq NP_217794.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transmembrane protein. Pfam: GtrA_DPMS_TM (PF04138.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P96882
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | membrane |
| Orthologous group | COG2246 |
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 | 0.84 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.48% of strains (697) · 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 |
|---|---|---|---|---|
GtrA_DPMS_TM | PF04138.21 | 2.0e-23 | 76–206 | GtrA/DPMS, transmembrane domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: purK (5-(carboxyamino)imidazole ribonucleotide synthase), medium confidence from genomic context alone (score 660 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3276c purK |
5-(carboxyamino)imidazole ribonucleotide synthase | 660 | 660 ctx | neighborhood:655 |
Rv3275c purE |
5-(carboxyamino)imidazole ribonucleotide mutase | 659 | 660 ctx | neighborhood:655 |
Rv1632c hyp |
hypothetical protein | 671 | 659 ctx | cooccurence:643 |
Rv1109c hyp |
hypothetical protein | 626 | 627 ctx | cooccurence:625 |
Rv3205c hyp |
hypothetical protein | 591 | 592 ctx | cooccurence:587 |
Rv3274c fadE25 |
acyl-CoA dehydrogenase | 589 | 590 ctx | neighborhood:584 |
Rv0876c |
transmembrane protein | 572 | 572 ctx | cooccurence:572 |
Rv2091c |
membrane protein | 568 | 568 ctx | cooccurence:567 |
Rv2418c octT hyp |
hypothetical protein | 564 | 564 ctx | cooccurence:558 |
Rv2732c |
transmembrane protein | 562 | 563 ctx | cooccurence:560 |
Rv3415c hyp |
hypothetical protein | 561 | 561 ctx | cooccurence:560 |
Rv0475 hbhA |
heparin binding hemagglutinin HbhA | 558 | 558 ctx | cooccurence:557 |
Rv0383c ttfA hyp |
hypothetical protein | 555 | 556 ctx | cooccurence:542 |
Rv1083 hyp |
hypothetical protein | 541 | 541 ctx | cooccurence:541 |
Rv2206 |
transmembrane protein | 538 | 538 ctx | cooccurence:538 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): transmembrane protein
- Pfam (hmmscan --cut_ga): GtrA_DPMS_TM PF04138.21 (E=2e-23)
- (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_217794.1)
- Domains: Pfam-A via hmmscan --cut_ga — GtrA_DPMS_TM (PF04138.21)
- 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
COG2246 - Curated reference: UniProt P96882 (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 —
33 functional partner(s); context anchor
purK - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3277| MNEVTAGVRELATAIMVSRHLTGVLAGHGSQTVTYHFASILCSSVHSLVVSFADATIARLPGVVQPYAQRHHELIKFAIVGGTTFIIDTAIFYTLKLTVLEPKPVTAKVIAGIVAVIASYVLNREWSFRDRGGRERHHEALLFFAFSGVGVLLSMAPLWFSSYILQLRVPTVSLTMENIADFISAYIIGNLLQMAFRFWAFRRWVFPDEFARNPDKALESALTAGGIAEVFEDVLEGGFEDGNVTLLRAWRNRANRFAQLGDSSEPRVSKTS