Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | aminotransferase |
|---|
| MTBC0 PGAP re-annotation | MalY/PatB family protein |
|---|
| Revised (this work) | MalY/PatB family protein. 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 |
O53620
TrEMBL · unreviewed
· Evidence at protein level
|
|---|
| UniProt name | cysteine-S-conjugate beta-lyase |
|---|
| EC (curated) |
EC 4.4.1.13
|
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
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 |
0.807 · relaxed/neutral
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
3 synonymous, 6 missense, 1 nonsense, 2 frameshift
|
|---|
| Disruption |
3 distinct premature-stop/frameshift site(s); most common in
2.24% of strains
(3256) · 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_1_2 | PF00155.28 |
2.5e-35 | 97–381 |
Aminotransferase class I and II |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv0074 hyp |
hypothetical protein |
934 |
934 ctx |
neighborhood:777 coexpression:716 |
Rv1079 metB |
cystathionine gamma-synthase |
951 |
931 |
database:900 |
Rv0391 metZ |
O-succinylhomoserine sulfhydrylase |
934 |
924 |
database:900 |
Rv2294 |
cystathionine beta-lyase |
932 |
917 |
database:900 |
Rv3340 metC |
O-acetylhomoserine sulfhydrylase |
918 |
906 |
database:900 |
Rv2334 cysK1 |
O-acetylserine sulfhydrylase |
913 |
905 |
database:900 |
Rv3684 |
lyase |
909 |
905 |
database:900 |
Rv1077 cbs |
cystathionine beta-synthase |
912 |
904 |
database:900 |
Rv1133c metE |
5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase |
907 |
904 |
database:900 |
Rv2291 sseB |
thiosulfate sulfurtransferase SseB |
903 |
903 |
database:900 |
Rv2124c metH |
methionine synthase |
913 |
901 |
database:900 |
Rv3283 sseA |
thiosulfate sulfurtransferase SseA |
900 |
901 |
database:900 |
Rv3248c sahH |
adenosylhomocysteinase |
900 |
901 |
database:900 |
Rv2458 mmuM |
homocysteine S-methyltransferase MmuM |
903 |
900 |
database:900 |
Rv0815c cysA2 |
thiosulfate sulfurtransferase CysA |
900 |
900 |
database:900 |
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: aminotransferase
- MTBC0 PGAP product: MalY/PatB family protein
- Pfam (hmmscan --cut_ga): Aminotran_1_2 PF00155.28 (E=2e-35)
- (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_214589.1)
- 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
COG1168
- Curated reference: UniProt
O53620
(TrEMBL, unreviewed; 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 —
36 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000083|Rv0075|
MQDSIFNLLTEEQLRGRNTLKWNYFGPDVVPLWLAEMDFPTAPAVLDGVRACVDNEEFGYPPLGEDSLPRATADWCRQRYGWCPRPDWVRVVPDVLKGMEVVVEFLTRPESPVALPVPAYMPFFDVLHVTGRQRVEVPMVQQDSGRYLLDLDALQAAFVRGAGSVIICNPNNPLGTAFTEAELRAIVDIAARHGARVIADEIWAPVVYGSRHVAAASVSEAAAEVVVTLVSASKGWNLPGLMCAQVILSNRRDAHDWDRINMLHRMGASTVGIRANIAAYHHGESWLDELLPYLRANRDHLARALPELAPGVEVNAPDGTYLSWVDFRALALPSEPAEYLLSKAKVALSPGIPFGAAVGSGFARLNFATTRAILDRAIEAIAAALRDIID
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