rimJ Resolved · high auto-curated
H37Rv Rv0995 · MTBC0 - ·
203 aa · 1111612–1112223 (+) ·
RefSeq NP_215510.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribosomal-protein-alanine acetyltransferase RimJ |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Ribosomal-protein-alanine acetyltransferase RimJ. Pfam: Acetyltransf_3 (PF13302.14), Acetyltransf_1 (PF00583.32). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O05578
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribosomal-protein-alanine acetyltransferase RimJ |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rimJ |
| eggNOG description | acetyltransferase |
| Orthologous group | COG1670 |
| EC number |
EC 2.3.1.128
|
| KEGG orthology |
K03790
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 8 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.11% of strains (165) · 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 |
|---|---|---|---|---|
Acetyltransf_3 | PF13302.14 | 4.3e-14 | 14–158 | Acetyltransferase (GNAT) domain |
Acetyltransf_1 | PF00583.32 | 3.1e-08 | 68–157 | Acetyltransferase (GNAT) family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: moeA1 (molybdopterin molybdenumtransferase 1), high confidence from genomic context alone (score 842 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0994 moeA1 |
molybdopterin molybdenumtransferase 1 | 841 | 842 ctx | neighborhood:799 |
Rv0993 galU |
UTP--glucose-1-phosphate uridylyltransferase | 772 | 762 ctx | neighborhood:731 |
Rv0996 |
transmembrane protein | 750 | 751 ctx | neighborhood:747 |
Rv0992c |
5-formyltetrahydrofolate cyclo-ligase | 696 | 696 ctx | neighborhood:680 |
Rv0991c hyp |
hypothetical protein | 643 | 643 ctx | neighborhood:638 |
Rv2925c rnc |
ribonuclease III | 544 | 544 | coexpression:542 |
Rv2378c mbtG |
L-lysine N6-monooxygenase | 563 | 523 | coexpression:507 |
Rv1210 tagA |
DNA-3-methyladenine glycosylase I TagA | 446 | 446 ctx | cooccurence:417 |
Rv0990c hyp |
hypothetical protein | 412 | 412 ctx | neighborhood:412 |
Rv3623 lpqG |
lipoprotein LpqG | 411 | 411 | |
Rv3420c rimI |
ribosomal-protein-alanine acetyltransferase RimI | 920 | 305 | textmining:890 |
Rv3417c groEL1 |
chaperonin GroEL | 417 | 211 | |
Rv0408 pta |
phosphate acetyltransferase | 403 | 182 | |
Rv1299 prfA |
peptide chain release factor PrfA | 434 | 108 | |
Rv2005c |
universal stress protein | 816 | 69 | textmining:811 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): ribosomal-protein-alanine acetyltransferase RimJ
- Pfam (hmmscan --cut_ga): Acetyltransf_3 PF13302.14 (E=4e-14), Acetyltransf_1 PF00583.32 (E=3e-08)
- (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_215510.1)
- Domains: Pfam-A via hmmscan --cut_ga — Acetyltransf_3 (PF13302.14), Acetyltransf_1 (PF00583.32)
- 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
COG1670 - Curated reference: UniProt O05578 (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 —
22 functional partner(s); context anchor
moeA1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0995|rimJ MAVGPLRVSAGVIRLRPVRMRDGVHWSRIRLADRAHLEPWEPSADGEWTVRHTVAAWPAVCSGLRSEARNGRMLPYVIELDGQFCGQLTIGNVTHGALRSAWIGYWVPSAATGGGVATGALALGLDHCFGPVMLHRVEATVRPENAASRAVLAKVGFREEGLLRRYLEVDRAWRDHLLMAITVEEVYGSVASTLVRAGHASWP