Rv0428c Family assigned · medium auto-curated
H37Rv Rv0428c · MTBC0 mtbc0_000450 ·
302 aa · 520260–521168 (-) ·
RefSeq NP_214942.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | GCN5-like N-acetyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | GNAT family N-acetyltransferase |
| Revised (this work) | GNAT family N-acetyltransferase. Pfam: SH3_Rv0428c (PF24551.2), Rv0428c_C (PF24553.3). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96274
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable histone acetyltransferase Rv0428c |
| EC (curated) |
EC 2.3.1.48
|
| Curated function | Shows histone acetyl transferase (HAT) activity with recombinant eukaryotic H3 histone expressed in bacteria as substrate and acetyl-CoA as donor. May be involved in survival under stress conditions. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | acetyltransferase |
| Orthologous group | COG0454 |
| EC number |
EC 2.3.1.1
|
| KEGG orthology |
K22476
|
| KEGG pathways |
map00220, map01210, map01230
|
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 | 0.51 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.13% of strains (187) · 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 |
|---|---|---|---|---|
SH3_Rv0428c | PF24551.2 | 9.0e-22 | 6–60 | Probable histone acetyltransferase Rv0428c SH3 domain |
Rv0428c_C | PF24553.3 | 7.0e-97 | 69–292 | Probable histone acetyltransferase Rv0428c C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: def (polypeptide deformylase), high confidence from genomic context alone (score 887 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1653 argJ |
bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase | 940 | 905 | database:900 |
Rv1654 argB |
acetylglutamate kinase | 914 | 905 | database:900 |
Rv2747 argA |
L-glutamate alpha-N-acetyltranferase | 907 | 903 | database:900 |
Rv0337c aspC |
aspartate aminotransferase | 905 | 901 | database:900 |
Rv2476c gdh |
NAD-dependent glutamate dehydrogenase | 900 | 901 | database:900 |
Rv0429c def |
polypeptide deformylase | 961 | 887 ctx | neighborhood:882 textmining:669 |
Rv0427c xthA |
exodeoxyribonuclease III protein XthA | 946 | 883 ctx | neighborhood:881 textmining:562 |
Rv0495c hyp |
hypothetical protein | 737 | 738 ctx | cooccurence:737 |
Rv0430 hyp |
hypothetical protein | 699 | 700 ctx | neighborhood:698 |
Rv0432 sodC |
superoxide dismutase | 669 | 669 ctx | neighborhood:664 |
Rv0433 |
carboxylate-amine ligase | 665 | 666 ctx | neighborhood:664 |
Rv0434 hyp |
hypothetical protein | 665 | 665 ctx | neighborhood:609 |
Rv1125 hyp |
hypothetical protein | 653 | 654 ctx | cooccurence:645 |
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 ( | 586 | 586 ctx | cooccurence:586 |
Rv2326c |
ABC transporter ATP-binding protein | 565 | 566 ctx | cooccurence:552 |
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: GCN5-like N-acetyltransferase
- MTBC0 PGAP product: GNAT family N-acetyltransferase
- Pfam (hmmscan --cut_ga): SH3_Rv0428c PF24551.2 (E=9e-22), Rv0428c_C PF24553.3 (E=7e-97)
- (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_214942.1)
- Domains: Pfam-A via hmmscan --cut_ga — SH3_Rv0428c (PF24551.2), Rv0428c_C (PF24553.3)
- 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
COG0454 - Curated reference: UniProt P96274 (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 —
54 functional partner(s); context anchor
def - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000450|Rv0428c| MVSWPGLGTRVTVRYRRPAGSMPPLTDAVGRLLAVDPTVRVQTKTGTIVEFSPVDVVALRVLTDAPVRTAAIRALEHAAAAAWPGVERTWLDGWLLRAGHGAVLAANSAVPLDISAHTNTITEISAWYASRDLQPWLAVPDRLLPLPAGLAGERREQVLVRDVSTGEPDRSVTLLDHPDDTWLRLYHQRLPLDMATPVIDGELAFGSYLGVAVARAAVTDAPDGTRWVGLSAMRAADEQSATGSAGRQLWEALLGWGAGRGATRGYVRVHDTATSVLAESLGFRLHHHCRYLPAQSVGWDTF