Rv0585c Family assigned · medium auto-curated
H37Rv Rv0585c · MTBC0 mtbc0_000615 ·
795 aa · 685436–687823 (-) ·
RefSeq NP_215099.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | lysylphosphatidylglycerol synthase transmembrane domain-containing protein |
| Revised (this work) | Lysylphosphatidylglycerol synthase transmembrane domain-containing 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 |
O53781
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| eggNOG description | integral membrane protein |
| Orthologous group | COG0392 |
| KEGG orthology |
K07027
|
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 | 0.32 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 13 synonymous, 11 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 1.08% of strains (1574) · 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 |
|---|---|---|---|---|
LPG_synthase_TM | PF03706.19 | 6.9e-27 | 498–782 | Lysylphosphatidylglycerol synthase TM region |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mce2C (Mce family protein Mce2C), medium confidence from genomic context alone (score 613 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0591 mce2C |
Mce family protein Mce2C | 613 | 613 ctx | neighborhood:545 |
Rv0594 mce2F |
Mce family protein Mce2F | 603 | 603 ctx | neighborhood:537 |
Rv0592 mce2D |
Mce family protein Mce2D | 600 | 600 ctx | neighborhood:537 |
Rv0479c |
membrane protein | 566 | 566 ctx | cooccurence:566 |
Rv0586 mce2R |
HTH-type transcriptional regulator Mce2R | 566 | 545 ctx | neighborhood:545 |
Rv0590 mce2B |
Mce-family protein Mce2B; Rv0590, (MTCY19H5.32c), len: 275 aa. Mce2B; belongs to 24-membered Mycobacterium tuberculosis Mce protein family ( | 545 | 545 ctx | neighborhood:544 |
Rv0587 yrbE2A hyp |
hypothetical protein | 545 | 545 ctx | neighborhood:545 |
Rv0589 mce2A |
Mce family protein Mce2A | 545 | 545 ctx | neighborhood:544 |
Rv0588 yrbE2B hyp |
hypothetical protein | 545 | 545 ctx | neighborhood:545 |
Rv0590A |
Mce-family related protein; Rv0590A, len: 84 aa. Probable continuation of mce2B|Rv0590. Can find no frameshift to account for this. Possible | 545 | 544 ctx | neighborhood:544 |
Rv0593 lprL |
Mce family lipoprotein LprL | 542 | 542 ctx | neighborhood:537 |
Rv1863c |
integral membrane protein | 535 | 535 ctx | cooccurence:525 |
Rv2876 |
transmembrane protein | 503 | 503 ctx | cooccurence:503 |
Rv2180c |
integral membrane protein | 492 | 492 ctx | cooccurence:489 |
Rv1203c hyp |
hypothetical protein | 470 | 470 ctx | cooccurence:467 |
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: integral membrane protein
- MTBC0 PGAP product: lysylphosphatidylglycerol synthase transmembrane domain-containing protein
- Pfam (hmmscan --cut_ga): LPG_synthase_TM PF03706.19 (E=7e-27)
- (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_215099.1)
- 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 O53781 (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 —
30 functional partner(s); context anchor
mce2C - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000615|Rv0585c| MRVDGRDIGVSGNLLQPLTRRTNDIIRAVLAAIYLVAVITSSLITRPQWVALEKSISEIVGVLSPSQSDLVYLGYGLAILALPFVILIGLIVSRQWKLLGAYAAAGLMAVLPLSISSSRIAAPRWHFDLSDRLATLLAQFLDDPRWIAMLAAVLTVSGPWLPARWRHWWWALLLAFVPIHLVVSAIVPARSLLGLAVGWLVGALVVLVVGTPALEVPLDGAIRALAKRGFAVSGLAVVRPAGPGPLVLSAACEQPNAGACSEALIELYGPHQSGGGALRQLWLKLTLRGTETAPLQASMRRAVEHRALMAIAFGDLGMANTTVIAVSPLDRGWTLYAHRPARGIGISECTKTTPTAHVWEALRTLHDQQISHGDLCSAEITVDNGAVLFGGFGEAEYGATDAQLQSDLAQLLVTTSALYDAEAAVTAAIDTFGKQAILAASRRLTKSAVPKRIRESITDPNAVIASTRAEVMRQTGADQIKAETITRFSRGQLIQLVLIGALVYVAYPFISTVPTFFSQLRTANWWWALLGLAVSALTYVGAAAALWACADGLVGFWKLSIMQVANTFAATTTPAGVGGLALSTRFLQKGGLTAVRATAAVALQQSVQVIVHLVLLILFSALAGTSTDLSHFVPNATVLYLIAGVALGIVGTFLFVPKLRRWLATAVRPKLREVTNDLIALAREPKRLALIVLGCAGTTLGAALALWASIEAFGGGTTFVTVTVVTMVGGTLASAAPTPGGVGAVEAALIGGLAAFGVPAALGVPSVLLYRLLTCWLPVFAGWQVMHWLTRHEMI