Rv0007 Still unknown · low auto-curated
H37Rv Rv0007 · MTBC0 mtbc0_000007 ·
304 aa · 9914–10828 (+) ·
RefSeq NP_214521.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF3566 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF3566. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMA7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0007 |
UniProt still lists this protein as Uncharacterized protein Rv0007; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Transmembrane domain of unknown function (DUF3566) |
| Orthologous group | COG3266 |
| Gene Ontology (14) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0005887, GO:0016020, GO:0016021, GO:0030312, GO:0031224, GO:0031226, GO:0044425, GO:0044459 +2 more
|
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 | 0.305 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 11 synonymous, 9 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 |
|---|---|---|---|---|
DUF3566 | PF12089.14 | 1.7e-41 | 187–302 | Transmembrane domain of unknown function (DUF3566) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gyrA (DNA gyrase subunit A), high confidence from genomic context alone (score 943 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0006 gyrA |
DNA gyrase subunit A | 946 | 943 ctx | neighborhood:775 coexpression:757 |
Rv1024 |
membrane protein | 771 | 771 ctx | cooccurence:768 |
Rv0005 gyrB |
DNA gyrase subunit B | 772 | 759 ctx | neighborhood:743 |
Rv3909 hyp |
hypothetical protein | 743 | 744 ctx | cooccurence:740 |
Rv2164c hyp |
hypothetical protein | 729 | 729 ctx | cooccurence:723 |
Rv0538 |
membrane protein | 722 | 723 ctx | cooccurence:720 |
Rv3835 hyp |
hypothetical protein | 722 | 722 ctx | cooccurence:719 |
Rv2843 hyp |
hypothetical protein | 719 | 720 ctx | cooccurence:719 |
Rv3258c hyp |
hypothetical protein | 707 | 707 ctx | cooccurence:703 |
Rv3658c |
transmembrane protein | 715 | 705 ctx | cooccurence:702 |
Rv0004 hyp |
hypothetical protein | 704 | 704 ctx | neighborhood:635 |
Rv2709 |
transmembrane protein | 682 | 682 ctx | cooccurence:680 |
Rv3903c cpnT hyp |
hypothetical protein | 686 | 673 ctx | cooccurence:671 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 677 | 655 ctx | neighborhood:652 |
Rv2771c hyp |
hypothetical protein | 660 | 648 | coexpression:648 |
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: membrane protein
- MTBC0 PGAP product: DUF3566 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF3566 PF12089.14 (E=2e-41)
- (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_214521.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF3566 (PF12089.14)
- 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
COG3266 - Curated reference: UniProt P9WMA7 (SwissProt, reviewed; 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 —
58 functional partner(s); context anchor
gyrA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000007|Rv0007| MTAPNEPGALSKGDGPNADGLVDRGGAHRAATGPGRIPDAGDPPPWQRAATRQSQAGHRQPPPVSHPEGRPTNPPAAADARLNRFISGASAPVTGPAAAVRTPQPDPDASLGCGDGSPAEAYASELPDLSGPTPRAPQRNPAPARPAEGGAGSRGDSAAGSSGGRSITAESRDARVQLSARRSRGPVRASMQIRRIDPWSTLKVSLLLSVALFFVWMITVAFLYLVLGGMGVWAKLNSNVGDLLNNASGSSAELVSSGTIFGGAFLIGLVNIVLMTALATIGAFVYNLITDLIGGIEVTLADRD