Rv3779 Family assigned · low auto-curated
H37Rv Rv3779 · MTBC0 mtbc0_004007 ·
666 aa · 4249106–4251106 (+) ·
RefSeq NP_218296.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF6541 family protein |
| Revised (this work) | DUF6541 family 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 |
P72045
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved transmembrane protein alanine and leucine rich |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Psort location CytoplasmicMembrane, score |
| Orthologous group | COG5617 |
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 | 0.513 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 10 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 |
|---|---|---|---|---|
DUF6541 | PF20176.4 | 3.0e-80 | 12–656 | Family of unknown function (DUF6541) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rfbE (O-antigen/lipopolysaccharide ABC transporter ATP-binding protein RfbE), high confidence from genomic context alone (score 882 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3781 rfbE |
O-antigen/lipopolysaccharide ABC transporter ATP-binding protein RfbE | 930 | 882 ctx | neighborhood:881 textmining:434 |
Rv3780 bpa hyp |
hypothetical protein | 897 | 882 ctx | neighborhood:881 |
Rv3783 rfbD |
O-antigen/lipopolysaccharide ABC transporter permease RfbD | 930 | 881 ctx | neighborhood:881 textmining:434 |
Rv3782 glfT1 |
galactofuranosyl transferase GlfT | 908 | 881 ctx | neighborhood:881 |
Rv3632 |
membrane protein | 893 | 787 ctx | cooccurence:768 textmining:519 |
Rv0048c |
membrane protein | 773 | 773 ctx | cooccurence:767 |
Rv0875c hyp |
hypothetical protein | 745 | 745 ctx | cooccurence:743 |
Rv0517 |
acyltransferase | 737 | 738 ctx | cooccurence:734 |
Rv3630 |
integral membrane protein | 734 | 735 ctx | cooccurence:718 |
Rv1510 hyp |
hypothetical protein | 704 | 705 ctx | cooccurence:686 |
Rv3773c hyp |
hypothetical protein | 703 | 703 ctx | cooccurence:703 |
Rv1182 papA3 |
acyltransferase papA3 | 670 | 670 ctx | cooccurence:670 |
Rv3446c hyp |
hypothetical protein | 667 | 667 ctx | cooccurence:667 |
Rv2079 hyp |
hypothetical protein | 661 | 661 ctx | cooccurence:660 |
Rv3824c papA1 |
acyltransferase | 662 | 653 ctx | cooccurence:653 |
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: DUF6541 family protein
- Pfam (hmmscan --cut_ga): DUF6541 PF20176.4 (E=3e-80)
- (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_218296.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF6541 (PF20176.4)
- 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
COG5617 - Curated reference: UniProt P72045 (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 —
88 functional partner(s); context anchor
rfbE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004007|Rv3779| MGLWFGTLIALILLIAPGAMVARIAQLRWPVAIAVGPALTYGVVALAIIPYGALGIPWNGWTALAALAVTCAVATGLQLLLARFRDLDAEALAVSRWPAVTVAAGVLLGALLIGWAAYRGIPHWQSIPSTWDAVWHANTVRFILDTGQASSTHMGELRNVETHAPLYYPSVFHGLVAVFCQLTGAAPTTGYTLSSLAASVWLFPVSAAVLTWRAVRSHPGALWSASCASAEWRAAGAAGTAAALSASFTAVPYVEFDTAAMPNLAAYGIAVPTMVLITSTLRHRDRIPVAVLALVGVFSLHITGGIVVALLVSAWWLFEALRHPVRSRLADLLTLAGVAAMAGLVMLPQFLSVRQQEDIIAGHAFPTYLSKKRGLFDAVFQHSRHLNDFPVQYALIVLAAIGGLILLVKKIWWPLAVWLLLIVMNVDAGTPLGGPIGGVAGALGEFFYHDPRRIAAATTLLLMLMAGVALFATVMLLVAAAKRLTDRFRPQPVSVWASATATLLIGATLVSAWHYFPRHRFLFGDKYDSVMIDQKDLDAMAYLASLPGARDTLIGNANTDGTAWMYAVAGLHPLWTHYDYPLQQGPGYHRFIFWAYGRNGESDPRVLEAIQVLRIRYILTSTPTVRGFAVPDGLVSLETSRSWAKIYDNGEARIYEWRGTAAATHS