Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antibiotic-resistance protein |
|---|
| MTBC0 PGAP re-annotation | amidohydrolase family protein |
|---|
| Revised (this work) | Amidohydrolase family protein. Pfam: Amidohydro_2 (PF04909.21). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
Q50662
TrEMBL · unreviewed
· Evidence at protein level
|
|---|
| UniProt name | Probable antibiotic-resistance protein |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|
| eggNOG description | Amidohydrolase |
|---|
| Orthologous group | COG2159 |
|---|
| KEGG orthology |
K07045
|
|---|
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 |
0.395 · purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
5 synonymous, 6 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 |
|---|
Amidohydro_2 | PF04909.21 |
4.8e-54 | 11–305 |
Amidohydrolase |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv2304c hyp |
hypothetical protein |
888 |
888 ctx |
neighborhood:882 |
Rv0187 |
O-methyltransferase |
656 |
111 |
textmining:630 |
Rv1862 adhA |
alcohol dehydrogenase A |
688 |
97 |
textmining:669 |
Rv2923c hyp |
hypothetical protein |
810 |
78 |
textmining:803 |
Rv3095 |
HTH-type transcriptional regulator |
670 |
71 |
textmining:660 |
Rv2593c ruvA |
Holliday junction ATP-dependent DNA helicase RuvA |
444 |
62 |
textmining:432 |
Rv1594 nadA |
quinolinate synthetase A |
436 |
50 |
textmining:431 |
Rv1053c |
Hypothetical protein; Rv1053c, (MTV017.06c), len: 91 aa. Hypothetical unknown protein. This region is a possible MT-complex-specific genomic |
804 |
47 |
textmining:803 |
Rv3724B cut5b |
Rv3724B, (MTV025.072), len: 187 aa. Probable cut5b,truncated cutinase, similar to C-terminal end of others e.g. Q9XB09|RVD2-RV1758 protein ( |
661 |
47 |
textmining:659 |
Rv1907c hyp |
hypothetical protein |
655 |
46 |
textmining:654 |
Rv1147 hyp |
hypothetical protein |
803 |
45 |
textmining:803 |
Rv0421c hyp |
hypothetical protein |
803 |
44 |
textmining:803 |
Rv1706c PPE23 |
PPE family protein PPE23 |
631 |
44 |
textmining:630 |
Rv1705c PPE22 |
PPE family protein PPE22 |
619 |
44 |
textmining:618 |
Rv1877 |
MFS-type transporter |
533 |
44 |
textmining:532 |
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: antibiotic-resistance protein
- MTBC0 PGAP product: amidohydrolase family protein
- Pfam (hmmscan --cut_ga): Amidohydro_2 PF04909.21 (E=5e-54)
- (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_216819.1)
- Domains: Pfam-A via hmmscan --cut_ga — Amidohydro_2 (PF04909.21)
- 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
COG2159
- Curated reference: UniProt
Q50662
(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 —
24 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002443|Rv2303c|
MTAPEPRVPVIDMWAPFVPSAEVIDDLREGFPVELLSYFEVFTKTTISAEQFGAYAESLRRTDDQILDSLDDAGITRSLITGFDERSTCGVTFVHNASVAAVAARYPDRFLPFAGADILAGDSAVDEFERWVVEHGFRGLSLRPFMIGRPASDPAYFPCYAKCVELGVPVSIHTSADWTRTRLSDLGHPRHIDDVACRFPELTILMSHGGYPWVLQACLIAWKHPNVYLELAAHRPKYFASPGAGWEPLMRFGQTTIRNKIVYGTGGFLINRPYLQLCDEMRALPVPREVLEDWLWRNATRVLRLDT
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