Rv0064 Family assigned · low auto-curated
H37Rv Rv0064 · MTBC0 mtbc0_000070 ·
979 aa · 68728–71667 (+) ·
RefSeq NP_214578.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | UPF0182 family protein |
| Revised (this work) | UPF0182 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 |
P9WFL5
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | UPF0182 protein Rv0064 |
UniProt still lists this protein as UPF0182 protein Rv0064; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Uncharacterised protein family (UPF0182) |
| Orthologous group | COG1615 |
| KEGG orthology |
K09118
|
| Gene Ontology (9) |
GO:0005575, GO:0005576, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.796 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 11 synonymous, 24 missense, 1 nonsense, 5 frameshift |
| Disruption | 6 distinct premature-stop/frameshift site(s); most common in 1.66% of strains (2411) · convergent |
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 |
|---|---|---|---|---|
UPF0182 | PF03699.19 | 6.4e-277 | 24–819 | Uncharacterised protein family (UPF0182) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC1 (ribonuclease VapC1), high confidence from genomic context alone (score 711 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0065 vapC1 |
ribonuclease VapC1 | 711 | 711 ctx | neighborhood:682 |
Rv0064A vapB1 |
antitoxin VapB1 | 686 | 686 ctx | neighborhood:686 |
Rv0063 |
oxidoreductase | 426 | 426 ctx | neighborhood:419 |
Rv0293c hyp |
hypothetical protein | 404 | 404 | coexpression:404 |
Rv0095c hyp |
hypothetical protein | 539 | 84 | textmining:518 |
Rv0590 mce2B |
Mce-family protein Mce2B; Rv0590, (MTCY19H5.32c), len: 275 aa. Mce2B; belongs to 24-membered Mycobacterium tuberculosis Mce protein family ( | 441 | 55 | textmining:433 |
Rv2954c hyp |
hypothetical protein | 525 | 54 | textmining:519 |
Rv0240 vapC24 |
ribonuclease VapC24 | 657 | 50 | textmining:654 |
Rv3087 |
diacyglycerol O-acyltransferase | 445 | 50 | textmining:440 |
Rv3376 |
phosphatase | 632 | 47 | textmining:630 |
Rv1359 |
transcriptional regulator | 542 | 47 | textmining:540 |
Rv3378c |
diterpene synthase | 525 | 47 | textmining:523 |
Rv1288 hyp |
hypothetical protein | 733 | 46 | textmining:732 |
Rv0895 |
diacyglycerol O-acyltransferase | 612 | 46 | textmining:610 |
Rv3826 fadD23 |
long-chain-fatty-acid--CoA ligase FadD23 | 435 | 46 | textmining:433 |
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: UPF0182 family protein
- Pfam (hmmscan --cut_ga): UPF0182 PF03699.19 (E=6e-277)
- (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_214578.1)
- Domains: Pfam-A via hmmscan --cut_ga — UPF0182 (PF03699.19)
- 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
COG1615 - Curated reference: UniProt P9WFL5 (SwissProt, reviewed; 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 —
24 functional partner(s); context anchor
vapC1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000070|Rv0064| METGSPGKRPVLPKRARLLVTAGMGMLALLLFGPRLVDIYVDWLWFGEVGFRSVWITVLLTRLAIVAAVALVVAGIVLAALLLAYRSRPFFVPDEPQRDPVAPLRSAVMRRPRLFGWGIAVTLGVVCGLIASFDWVKVQLFVHGGTFGIVDPEFGYDIGFFVFDLPFYRSVLNWLFVAVVLAFLASLLTHYLFGGLRLTTGRGMLTQAARVQLAVFAGAVVLLKAVAYWLDRYELLSSGRKEPTFTGAGYTDIHAELPAKLVLVAIAVLCAVSFFTAIFLRDLRIPAMAAALLVLSAILVGGLWPLLMEQFSVRPNAADVERPYIQRNIEATREAYRIGGDWVQYRSYPGIGTKQPRDVPVDVTTIAKVRLLDPHILSRTFTQQQQLKNFFSFAEILDIDRYRIDGELQDYIVGVRELSPKSLTGNQTDWINKHTVYTHGNGFVAAPANRVNAAARDAENISDSNSGYPIYAVSDIASLGSGRQVIPVEQPRVYYGEVIAQADPDYAIVGGAPGSAPREYDTDTSKYTYTGAGGVSIGNWFNRTVFATKFAQHKFLFSREIGSESKVLIHRDPKERVQRVAPWLTTDDNPYPVVVNGRIVWIVDAYTTLDTYPYAQRSSLEGPVTSPTGIVRQGKQVSYVRNSVKATVDAYDGTVTLFQFDRDDPVLRTWMRAFPGTVKSEDQIPDELRAHFRYPEDLFEVQRSLLAKYHVDEPREFFTTNAFWSVPSDPTNDANATQPPFYVLVGDQQSAQPSFRLASAMVGYNREFLSAYISAHSDPANYGKLTVLELPTDTLTQGPQQIQNSMISDTRVASERTLLERSNRIHYGNLLSLPIADGGVLYVEPLYTERISTSPSSSTFPQLSRVLVSVREPRTEGGVRVGYAPTLAESLDQVFGPGTGRVATAPGGDAASAPPPGAGGPAPPQAVPPPRTTQPPAAPPRGPDVPPATVAELRETLADLRAVLDRLEKAIDAAETPGG