Rv3789 Resolved · high auto-curated
H37Rv Rv3789 · MTBC0 mtbc0_004017 ·
121 aa · 4259495–4259860 (+) ·
RefSeq NP_218306.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | GtrA family protein |
|---|---|
| MTBC0 PGAP re-annotation | arabinogalactan biosynthesis protein |
| Revised (this work) | Arabinogalactan biosynthesis protein. Pfam: GtrA_DPMS_TM (PF04138.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMS9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Arabinogalactan biosynthesis recruiting protein Rv3789 |
| Curated function | Required for arabinosylation of arabinogalactan (AG), an essential component of the mycobacterial cell wall. Probably acts as an anchor protein recruiting AftA, the first arabinosyl transferase involved in AG biosynthesis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | capsule polysaccharide biosynthetic process |
| Orthologous group | COG2246 |
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 | 0.175 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 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 |
|---|---|---|---|---|
GtrA_DPMS_TM | PF04138.21 | 2.3e-20 | 2–118 | GtrA/DPMS, transmembrane domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dprE1 (decaprenylphosphoryl-beta-D-ribose oxidase), high confidence from genomic context alone (score 958 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3790 dprE1 |
decaprenylphosphoryl-beta-D-ribose oxidase | 965 | 958 ctx | neighborhood:823 cooccurence:762 |
Rv3791 dprE2 |
decaprenylphosphoryl-D-2-keto erythropentose reductase | 966 | 957 ctx | neighborhood:823 cooccurence:764 |
Rv3793 embC |
arabinosyltransferase C | 964 | 949 ctx | neighborhood:823 cooccurence:720 |
Rv3792 aftA |
arabinofuranosyltransferase | 911 | 886 ctx | neighborhood:823 |
Rv3794 embA |
arabinosyltransferase A | 882 | 862 ctx | neighborhood:527 cooccurence:711 |
Rv3795 embB |
arabinosyltransferase B | 874 | 860 ctx | neighborhood:503 cooccurence:726 |
Rv3788 hyp |
hypothetical protein | 776 | 777 ctx | neighborhood:768 |
Rv3806c ubiA |
decaprenyl-phosphate phosphoribosyltransferase | 798 | 756 ctx | cooccurence:742 |
Rv2073c |
oxidoreductase | 735 | 736 ctx | cooccurence:726 |
Rv0531 |
membrane protein | 613 | 599 ctx | cooccurence:596 |
Rv3438 hyp |
hypothetical protein | 590 | 590 ctx | cooccurence:579 |
Rv2673 aftC |
alpha-(1->3)-arabinofuranosyltransferase | 635 | 562 ctx | cooccurence:554 |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 567 | 527 ctx | cooccurence:503 |
Rv3311 hyp |
hypothetical protein | 525 | 526 ctx | cooccurence:522 |
Rv3802c |
membrane protein | 513 | 514 ctx | cooccurence:511 |
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: GtrA family protein
- MTBC0 PGAP product: arabinogalactan biosynthesis protein
- Pfam (hmmscan --cut_ga): GtrA_DPMS_TM PF04138.21 (E=2e-20)
- (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_218306.1)
- Domains: Pfam-A via hmmscan --cut_ga — GtrA_DPMS_TM (PF04138.21)
- 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
COG2246 - Curated reference: UniProt P9WMS9 (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 —
40 functional partner(s); context anchor
dprE1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004017|Rv3789| MRFVVTGGLAGIVDFGLYVVLYKVAGLQVDLSKAISFIVGTITAYLINRRWTFQAEPSTARFVAVMLLYGITFAVQVGLNHLCLALLHYRAWAIPVAFVIAQGTATVINFIVQRAVIFRIR