Rv0205 Family assigned · medium auto-curated
H37Rv Rv0205 · MTBC0 mtbc0_000219 ·
367 aa · 243736–244839 (+) ·
RefSeq NP_214719.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | AI-2E family transporter |
| Revised (this work) | AI-2E family transporter. Pfam: AI-2E_transport (PF01594.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFM5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative transport protein Rv0205 |
UniProt still lists this protein as Putative transport protein Rv0205; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | AI-2E family transporter |
| Orthologous group | COG0628 |
| KEGG orthology |
K20469
|
| Gene Ontology (20) |
GO:0003674, GO:0005215, GO:0005575, GO:0005623, GO:0005886, GO:0005887, GO:0006810, GO:0008150, GO:0016020, GO:0016021, GO:0031224, GO:0031226 +8 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) pseudogene candidate
| pN/pS | 0.772 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 6 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 4.91% of strains (7135) · 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 |
|---|---|---|---|---|
AI-2E_transport | PF01594.23 | 1.2e-79 | 25–348 | AI-2E family transporter |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0204c (transmembrane protein), high confidence from genomic context alone (score 774 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0204c |
transmembrane protein | 972 | 774 ctx | neighborhood:767 textmining:883 |
Rv0206c mmpL3 |
transmembrane transport protein MmpL3 | 498 | 145 | textmining:437 |
Rv0202c mmpL11 |
transmembrane transport protein MmpL11 | 669 | 144 | textmining:630 |
Rv0207c hyp |
hypothetical protein | 493 | 67 | textmining:479 |
Rv0201c hyp |
hypothetical protein | 807 | 64 | textmining:803 |
Rv0200 |
transmembrane protein | 555 | 52 | textmining:550 |
Rv0208c trmB |
tRNA (guanine-N(7)-)-methyltransferase | 651 | 51 | textmining:648 |
Rv1972 |
Mce associated membrane protein | 657 | 41 | textmining:657 |
Rv0177 |
Mce associated protein | 550 | 41 | textmining:550 |
Rv3444c esxT |
ESAT-6 like protein EsxT | 510 | 41 | textmining:510 |
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: AI-2E family transporter
- Pfam (hmmscan --cut_ga): AI-2E_transport PF01594.23 (E=1e-79)
- (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_214719.1)
- Domains: Pfam-A via hmmscan --cut_ga — AI-2E_transport (PF01594.23)
- 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
COG0628 - Curated reference: UniProt P9WFM5 (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 —
10 functional partner(s); context anchor
Rv0204c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000219|Rv0205| MSASLDDASVAPLVRKTAAWAWRFLVILAAMVALLWVLNKFEVIVVPVLLALMLSALLVPPVDWLDSRGLPRAVAVTLVLLSGFAVLGGILTFVVSQFIAGLPHLVTEVERSIDSARRWLIEGPAHLRGEQIDNAGNAAIEALRNNQAKLTSGALSTAATITELVTAAVLVLFTLIFFLYGGRSIWQYVTKAFPASVRDRVRAAGRAGYASLIGYARATFLVALTDAAGVGAGLAVMGVPLALPLASLVFFGAFIPLIGAVVAGFLAVVVALLAKGIGYALITVGLLIAVNQLEAHLLQPLVMGRAVSIHPLAVVLAIAAGGVLAGVVGALLAVPTVAFFNNAVQVLLGGNPFADVADVSSDHLTEV