Rv0204c Family assigned · medium auto-curated
H37Rv Rv0204c · MTBC0 mtbc0_000218 ·
412 aa · 242328–243566 (-) ·
RefSeq NP_214718.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | TIGR00374 family protein |
| Revised (this work) | TIGR00374 family protein. Pfam: LPG_synthase_TM (PF03706.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y748
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 | integral membrane protein |
| Orthologous group | COG0392 |
| KEGG orthology |
K20468
|
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 | 0.542 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 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 |
|---|---|---|---|---|
LPG_synthase_TM | PF03706.19 | 4.5e-40 | 44–346 | Lysylphosphatidylglycerol synthase TM region |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0205 (transmembrane protein), high confidence from genomic context alone (score 774 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0205 |
transmembrane protein | 972 | 774 ctx | neighborhood:767 textmining:883 |
Rv0128 |
transmembrane protein | 716 | 717 ctx | cooccurence:706 |
Rv0955 |
integral membrane protein | 680 | 680 ctx | cooccurence:671 |
Rv0236c aftD |
alpha-(1->3)-arabinofuranosyltransferase | 739 | 666 ctx | cooccurence:616 |
Rv1978 hyp |
hypothetical protein | 643 | 643 ctx | cooccurence:631 |
Rv3912 rsmA |
anti-sigma-M factor RsmA | 616 | 617 ctx | cooccurence:604 |
Rv0048c |
membrane protein | 582 | 583 ctx | cooccurence:580 |
Rv2248 hyp |
hypothetical protein | 582 | 583 ctx | cooccurence:581 |
Rv2181 |
alpha-(1-2)-phosphatidylinositol mannoside mannosyltransferase | 575 | 575 ctx | cooccurence:567 |
Rv0256c PPE2 |
PPE family protein PPE2 | 567 | 567 ctx | cooccurence:562 |
Rv3604c |
transmembrane protein | 567 | 567 ctx | cooccurence:561 |
Rv1863c |
integral membrane protein | 566 | 567 ctx | cooccurence:543 |
Rv2942 mmpL7 |
transmembrane transport protein MmpL7 | 563 | 563 ctx | cooccurence:546 |
Rv3779 |
transmembrane protein | 561 | 561 ctx | cooccurence:551 |
Rv2687c |
antibiotic ABC transporter permease | 535 | 535 ctx | cooccurence:530 |
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: TIGR00374 family protein
- Pfam (hmmscan --cut_ga): LPG_synthase_TM PF03706.19 (E=5e-40)
- (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_214718.2)
- Domains: Pfam-A via hmmscan --cut_ga — LPG_synthase_TM (PF03706.19)
- 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
COG0392 - Curated reference: UniProt I6Y748 (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 —
50 functional partner(s); context anchor
Rv0205 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000218|Rv0204c| MSHDAPARNLRQRVGALPRTRVGAPPAEGVPPRGKYWWLRWAVLAIVAIVLAIEVALGWDQLAKAWVSLYRAKWWWLLAAVAAAGASMHSFAQIQRTLLKSAGVHVKQWRSEAAFYAANSLSTTLPGGPVLSATFLLRQQRIWGASTVVASWQLVMSGVLQAVGLALLGLGGAFFLGAKNNPFSLLFTLGGFVTLLLLAQAVASRPELIEGIGRRVLSWANSVRGRPADAGLPKWRETLMQLESVSLGRRDLGVAFGWSLFNWIADVACLGFAAYAAGDHASVGGLAVAYAAARAVGTIPLMPGGLLVVEAVLVPGLVSSGMPLPSAISAMLIYRLISWLLIAAIGWVVFFFMFRTESTADSDNDRDPPTDPNLRLVIQPQGTPCDDPVETTPQGPAPTPDLRPEGGETPPR