aspB Resolved · high auto-curated
H37Rv Rv3565 · MTBC0 mtbc0_003782 ·
388 aa · 4029877–4031043 (+) ·
RefSeq NP_218082.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | aspartate aminotransferase AspB |
|---|---|
| MTBC0 PGAP re-annotation | pyridoxal phosphate-dependent aminotransferase |
| Revised (this work) | Pyridoxal phosphate-dependent aminotransferase. Pfam: Aminotran_1_2 (PF00155.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96847
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Valine--pyruvate aminotransferase |
| EC (curated) |
EC 2.6.1.66
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | aspB |
| eggNOG description | Aminotransferase |
| Orthologous group | COG0436 |
| EC number |
EC 2.6.1.1, EC 2.6.1.17, EC 2.6.1.2, EC 2.6.1.66
|
| KEGG orthology |
K00812, K14260, K14267
|
| KEGG pathways |
map00220, map00250, map00270, map00290, map00300, map00330, map00350, map00360, map00400, map00401, map00950, map00960, map01100, map01110, map01120, map01130, map01210, map01230
|
| KEGG modules |
M00016
|
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 | 1.257 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 7 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_1_2 | PF00155.28 | 9.4e-58 | 32–381 | Aminotransferase class I and II |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadE33 (acyl-CoA dehydrogenase FadE33), high confidence from genomic context alone (score 976 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3564 fadE33 |
acyl-CoA dehydrogenase FadE33 | 976 | 976 ctx | neighborhood:882 coexpression:804 |
Rv3563 fadE32 |
acyl-CoA dehydrogenase FadE32 | 967 | 968 ctx | neighborhood:881 coexpression:740 |
Rv3561 fadD3 |
fatty-acid--CoA ligase FadD3 | 945 | 944 ctx | neighborhood:801 coexpression:732 |
Rv3562 fadE31 |
acyl-CoA dehydrogenase FadE31 | 945 | 910 ctx | neighborhood:881 textmining:423 |
Rv3559c |
oxidoreductase | 883 | 786 ctx | neighborhood:610 coexpression:404 textmining:478 |
Rv3838c pheA |
prephenate dehydratase | 779 | 768 ctx | fusion:528 database:500 |
Rv3709c ask |
aspartokinase | 677 | 646 | database:500 |
Rv3560c fadE30 |
acyl-CoA dehydrogenase FadE30 | 692 | 644 ctx | neighborhood:612 |
Rv0393 hyp |
hypothetical protein | 443 | 444 | |
Rv1293 lysA |
diaminopimelate decarboxylase | 474 | 425 | coexpression:404 |
Rv3042c serB2 |
phosphoserine phosphatase SerB | 402 | 365 | |
Rv3859c gltB |
glutamate synthase large subunit | 599 | 287 | textmining:462 |
Rv2438c nadE |
glutamine-dependent NAD(+) synthetase | 420 | 248 | |
Rv2220 glnA1 |
glutamine synthetase | 402 | 207 | |
Rv1295 thrC |
threonine synthase | 518 | 205 | textmining:419 |
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: aspartate aminotransferase AspB
- MTBC0 PGAP product: pyridoxal phosphate-dependent aminotransferase
- Pfam (hmmscan --cut_ga): Aminotran_1_2 PF00155.28 (E=9e-58)
- (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_218082.1)
- Domains: Pfam-A via hmmscan --cut_ga — Aminotran_1_2 (PF00155.28)
- 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
COG0436 - Curated reference: UniProt P96847 (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 —
28 functional partner(s); context anchor
fadE33 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003782|Rv3565|aspB MTDRVALRAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIEEALRRIGSWLPSQ