Rv0541c Family assigned · low auto-curated
H37Rv Rv0541c · MTBC0 mtbc0_000570 ·
449 aa · 636606–637955 (-) ·
RefSeq NP_215055.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | integral membrane protein |
| Revised (this work) | Integral membrane 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 |
O06407
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 28KB1 |
|---|
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 | 0.231 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: menE (2-succinylbenzoic acid--CoA ligase), high confidence from genomic context alone (score 935 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0542c menE |
2-succinylbenzoic acid--CoA ligase | 934 | 935 ctx | neighborhood:876 coexpression:494 |
Rv0540 hyp |
hypothetical protein | 974 | 811 ctx | cooccurence:771 textmining:870 |
Rv0536 galE3 |
UDP-glucose 4-epimerase GalE | 974 | 809 ctx | cooccurence:767 textmining:870 |
Rv1713 engA |
GTPase Der | 808 | 808 | coexpression:808 |
Rv0218 |
transmembrane protein | 802 | 802 ctx | cooccurence:767 |
Rv0543c hyp |
hypothetical protein | 797 | 797 ctx | neighborhood:792 |
Rv0539 |
dolichyl-phosphate sugar synthase | 971 | 793 ctx | cooccurence:741 textmining:870 |
Rv0219 |
transmembrane protein | 761 | 761 ctx | cooccurence:720 |
Rv1714 |
oxidoreductase | 759 | 759 | coexpression:759 |
Rv0545c pitA |
low-affinity inorganic phosphate transporter | 745 | 745 ctx | neighborhood:738 |
Rv0544c |
transmembrane protein | 743 | 743 ctx | neighborhood:738 |
Rv0547c |
oxidoreductase | 639 | 638 ctx | neighborhood:635 |
Rv1868 hyp |
hypothetical protein | 581 | 582 ctx | cooccurence:580 |
Rv1748 hyp |
hypothetical protein | 569 | 569 ctx | cooccurence:569 |
Rv1006 hyp |
hypothetical protein | 552 | 552 ctx | cooccurence:540 |
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: integral membrane protein
- (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_215055.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
28KB1 - Curated reference: UniProt O06407 (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 —
36 functional partner(s); context anchor
menE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000570|Rv0541c| MRIGRREGLAVAIGFVLVGAAFVLPRLNLGIKPRSDIGLERFATRAGAAPIFGYWDAHVGWGTAPAVLTAVAVVAWGPVVAHRLPWRVLTLSTWATAAAWAFSLAMIDGWQRGFAGRLTTRDEYLWQVPGIADIPATLRTFTSRILDFQPNSWVTHVSGHPPGALLTFVWLDRIGLRGGGWAGLVCLLVGSSAAAAVLIAVRVLASEQMARRTAPFVAVAPTAIWIAVSADGYFAGVAAWGIALLAVAVHGATRFPALVAAGAGLLLGWGVFLNYGLVLIVLPGMAVLAAADWRPVLRALGPAVLAALVVAVSFAVAGFSWFDGYTLVQQRYWQGIAKDRPFGYWSWANLACVVCAIGLGSVAGLSRVFDRAAISRRSGCHLLLLAVLAAIALADLSMLSKAETERIWLPFTIWLTAAPALLPPRSHRLWLAVNAAGALLLNSIIFTNW