lat Resolved · high auto-curated
H37Rv Rv3290c · MTBC0 mtbc0_003498 ·
449 aa · 3692525–3693874 (-) ·
RefSeq NP_217807.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | L-lysine-epsilon aminotransferase |
|---|---|
| MTBC0 PGAP re-annotation | L-lysine 6-transaminase |
| Revised (this work) | L-lysine 6-transaminase. 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.
Curated reference (UniProt)
| UniProt |
P9WQ77
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | L-lysine-epsilon aminotransferase |
| EC (curated) |
EC 2.6.1.36
|
| Curated function | Catalyzes the transfer of the terminal amino group of L-lysine to alpha-ketoglutarate to yield L-glutamate and 2-aminoadipate 6-semialdehyde ((S)-2-amino-6-oxohexanoate), which is spontaneously converted to the dehydrated form 1-piperideine 6-carboxylate. Probably plays a role in persistence (Probable). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | lat |
| eggNOG description | Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family |
| Orthologous group | COG0160 |
| EC number |
EC 2.6.1.36
|
| KEGG orthology |
K03918
|
| KEGG pathways |
map01100
|
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 | 0.345 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Aminotran_3 | PF00202.28 | 5.9e-76 | 35–444 | Aminotransferase class-III |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3289c (transmembrane protein), high confidence from genomic context alone (score 976 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3289c |
transmembrane protein | 975 | 976 ctx | neighborhood:835 coexpression:860 |
Rv3288c usfY hyp |
hypothetical protein | 945 | 946 ctx | neighborhood:657 coexpression:848 |
Rv3291c lrpA |
transcriptional regulator LrpA | 982 | 852 ctx | neighborhood:813 textmining:884 |
Rv3293 pcd |
piperideine-6-carboxylic acid dehydrogenase | 853 | 840 ctx | neighborhood:722 |
Rv3292 hyp |
hypothetical protein | 648 | 635 ctx | neighborhood:526 |
Rv2378c mbtG |
L-lysine N6-monooxygenase | 600 | 571 | coexpression:405 |
Rv1187 rocA |
pyrroline-5-carboxylate dehydrogenase RocA | 539 | 501 | |
Rv2377c mbtH hyp |
hypothetical protein | 487 | 436 | coexpression:404 |
Rv3287c rsbW |
anti-sigma factor RsbW | 426 | 387 | |
Rv2438c nadE |
glutamine-dependent NAD(+) synthetase | 463 | 382 | |
Rv2852c mqo |
malate:quinone oxidoreductase | 441 | 379 | |
Rv0480c |
amidohydrolase | 512 | 361 | |
Rv0753c mmsA |
methylmalonate-semialdehyde dehydrogenase | 403 | 353 | |
Rv0147 |
aldehyde dehydrogenase | 402 | 352 | |
Rv0458 |
aldehyde dehydrogenase | 402 | 351 |
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: L-lysine-epsilon aminotransferase
- MTBC0 PGAP product: L-lysine 6-transaminase
- Pfam (hmmscan --cut_ga): Aminotran_3 PF00202.28 (E=6e-76)
- (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_217807.1)
- 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
COG0160 - Curated reference: UniProt P9WQ77 (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 —
37 functional partner(s); context anchor
Rv3289c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003498|Rv3290c|lat MAAVVKSVALAGRPTTPDRVHEVLGRSMLVDGLDIVLDLTRSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNSDVYSVAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPALGTQVLHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEAEALRQARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTGCGLTGTAWAYQQLDVAPDIVAFGKKTQVCGVMAGRRVDEVADNVFAVPSRLNSTWGGNLTDMVRARRILEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCAFSLPTTADRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAVRSALPVVT