Rv3402c Family assigned · medium auto-curated
H37Rv Rv3402c · MTBC0 mtbc0_001626 ·
50 aa · 1720659–1720811 (+) ·
RefSeq NP_217919.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DegT/DnrJ/EryC1/StrS family aminotransferase |
| Revised (this work) | DegT/DnrJ/EryC1/StrS family aminotransferase. Pfam: DegT_DnrJ_EryC1 (PF01041.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGJ7
SwissProt · reviewed
· Evidence at transcript level
|
|---|---|
| UniProt name | Protein Rv3402c |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | vioA |
| eggNOG description | UDP-4-amino-4-deoxy-L-arabinose aminotransferase |
| Orthologous group | COG0399 |
| EC number |
EC 2.6.1.33
|
| KEGG orthology |
K13308, K20429
|
| KEGG pathways |
map00523, map01130
|
| KEGG modules |
M00797
|
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 | 0.292 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 5 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 11.98% of strains (17403) · 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 |
|---|---|---|---|---|
DegT_DnrJ_EryC1 | PF01041.24 | 4.1e-101 | 50–405 | DegT/DnrJ/EryC1/StrS aminotransferase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1503c (Rv1503c, (MTCY277.25c), len: 182 aa. Conserved hypothetical protein, similar to C-terminal region of P27833|RFFA_ECOLI lipopolysaccharide bi), high confidence from genomic context alone (score 717 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2386c mbtI |
salicylate synthase | 913 | 831 | coexpression:831 textmining:510 |
Rv2383c mbtB |
phenyloxazoline synthase | 853 | 823 | coexpression:788 |
Rv1347c mbtK |
lysine N-acetyltransferase MbtK | 863 | 816 | coexpression:810 |
Rv1349 irtB |
iron ABC transporter ATP-binding protein/permease IrtB | 848 | 808 | coexpression:802 |
Rv1348 irtA |
iron ABC transporter ATP-binding protein/permease IrtA | 831 | 787 | coexpression:780 |
Rv2385 mbtJ |
acetyl hydrolase | 785 | 785 | coexpression:785 |
Rv2384 mbtA |
2,3-dihydroxybenzoate-AMP ligase | 869 | 779 | coexpression:778 textmining:436 |
Rv2380c mbtE |
peptide synthetase | 777 | 777 | coexpression:735 |
Rv2379c mbtF |
peptide synthetase | 764 | 765 | coexpression:732 |
Rv1505c hyp |
hypothetical protein | 756 | 741 ctx | cooccurence:570 |
Rv1503c |
Rv1503c, (MTCY277.25c), len: 182 aa. Conserved hypothetical protein, similar to C-terminal region of P27833|RFFA_ECOLI lipopolysaccharide bi | 716 | 717 ctx | cooccurence:715 |
Rv3404c hyp |
hypothetical protein | 676 | 657 | |
Rv3784 |
dTDP-glucose 4,6-dehydratase | 605 | 581 | coexpression:478 |
Rv1500 pimF |
glycosyltransferase | 554 | 537 | |
Rv1752 hyp |
hypothetical protein | 573 | 533 | coexpression:506 |
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: hypothetical protein
- MTBC0 PGAP product: DegT/DnrJ/EryC1/StrS family aminotransferase
- Pfam (hmmscan --cut_ga): DegT_DnrJ_EryC1 PF01041.24 (E=4e-101)
- (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_217919.1)
- Domains: Pfam-A via hmmscan --cut_ga — DegT_DnrJ_EryC1 (PF01041.24)
- 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
COG0399 - Curated reference: UniProt P9WGJ7 (SwissProt, reviewed; Evidence at transcript 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 —
33 functional partner(s); context anchor
Rv1503c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001626|Rv3402c| MNAELVESADLTVTEDICSRIVSLPVHDHMAIADVARVVAPFGEGLARGG