Rv3329 Resolved · high auto-curated
H37Rv Rv3329 · MTBC0 - ·
438 aa · 3714392–3715708 (+) ·
RefSeq NP_217846.3
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | aminotransferase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Aminotransferase. Pfam: Aminotran_3 (PF00202.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O53379
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable aminotransferase Rv3329 |
| EC (curated) |
EC 2.6.1.-
|
| Curated function | Probable aminotransferase. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | tpa |
| eggNOG description | Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family |
| Orthologous group | COG0161 |
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 | 0.88 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 12 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.19% of strains (280) · 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 |
|---|---|---|---|---|
Aminotran_3 | PF00202.28 | 3.1e-89 | 12–426 | Aminotransferase class-III |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sigJ (ECF RNA polymerase sigma factor SigJ), high confidence from genomic context alone (score 788 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3328c sigJ |
ECF RNA polymerase sigma factor SigJ | 788 | 788 ctx | neighborhood:787 |
Rv1589 bioB |
biotin synthetase | 764 | 733 | coexpression:693 |
Rv1570 bioD |
ATP-dependent dethiobiotin synthetase BioD | 743 | 710 | coexpression:693 |
Rv3330 dacB1 |
penicillin-binding protein DacB | 909 | 654 ctx | neighborhood:628 textmining:750 |
Rv3332 nagA |
N-acetylglucosamine-6-phosphate deacetylase NagA | 929 | 480 ctx | neighborhood:477 textmining:870 |
Rv1569 bioF1 |
8-amino-7-oxononanoate synthase | 519 | 474 | coexpression:454 |
Rv0032 bioF2 |
8-amino-7-oxononanoate synthase | 518 | 472 | coexpression:454 |
Rv3331 sugI |
sugar-transport integral membrane protein SugI | 887 | 448 ctx | neighborhood:445 textmining:804 |
Rv2322c rocD1 |
Rv2322c, (MTCY3G12.12), len: 221 aa. Probable rocD1,ornithine aminotransferase, highly similar to N-terminal region of other ornithine amino | 404 | 403 | |
Rv2859c |
glutamine amidotransferase | 411 | 389 | |
Rv2860c glnA4 |
glutamine synthetase | 404 | 274 | |
Rv2438c nadE |
glutamine-dependent NAD(+) synthetase | 445 | 194 | |
Rv2294 |
cystathionine beta-lyase | 890 | 192 | textmining:870 |
Rv0075 |
aminotransferase | 888 | 175 | textmining:870 |
Rv1178 dapC |
aminotransferase | 839 | 165 | textmining:816 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): aminotransferase
- Pfam (hmmscan --cut_ga): Aminotran_3 PF00202.28 (E=3e-89)
- (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_217846.3)
- Domains: Pfam-A via hmmscan --cut_ga — Aminotran_3 (PF00202.28)
- 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
COG0161 - Curated reference: UniProt O53379 (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 —
18 functional partner(s); context anchor
sigJ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3329| MHFARHGAGIQHPVIVRGDGVTIFDDRGKSYLDALSGLFVVQVGYGRAELAEAAARQAGTLGYFPLWGYATPPAIELAERLARYAPGDLNRVFFTSGGTEAVETAWKVAKQYFKLTGKPGKQKVISRSIAYHGTTQGALAITGLPLFKAPFEPLTPGGFRVPNTNFYRAPLHTDLKEFGRWAADRIAEAIEFEGPDTVAAVFLEPVQNAGGCIPAPPGYFERVREICDRYDVLLVSDEVICAFGRIGSMFACEDLGYVPDMITCAKGLTSGYSPLGAMIASDRLFEPFNDGETMFAHGYTFGGHPVSAAVGLANLDIFEREGLSDHVKRNSPALRATLEKLYDLPIVGDIRGEGYFFGIELVKDQATKQTFTDDERARLLGQVSAALFEAGLYCRTDDRGDPVVQVAPPLISGQPEFDTIETILRSVLTDTGRKYLHL