rimP Resolved · high auto-curated
H37Rv Rv2842c · MTBC0 mtbc0_003021 ·
183 aa · 3170091–3170642 (-) ·
RefSeq NP_217358.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribosome maturation factor RimP |
|---|---|
| MTBC0 PGAP re-annotation | ribosome maturation factor RimP |
| Revised (this work) | Ribosome maturation factor RimP. Pfam: RimP_N (PF02576.23), DUF150_C (PF17384.9). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WH17
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribosome maturation factor RimP |
| Curated function | Required for maturation of 30S ribosomal subunits. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | rimP |
| eggNOG description | Required for maturation of 30S ribosomal subunits |
| Orthologous group | COG0779 |
| KEGG orthology |
K09748
|
| Gene Ontology (53) |
GO:0000028, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006412, GO:0006518, GO:0006807, GO:0006996, GO:0008150 +41 more
|
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, 2 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 |
|---|---|---|---|---|
RimP_N | PF02576.23 | 1.1e-11 | 22–89 | RimP N-terminal domain |
DUF150_C | PF17384.9 | 2.6e-09 | 92–157 | RimP C-terminal SH3 domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nusA (transcription termination/antitermination protein NusA), high confidence from genomic context alone (score 994 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2841c nusA |
transcription termination/antitermination protein NusA | 994 | 994 ctx | neighborhood:881 coexpression:953 |
Rv0682 rpsL |
30S ribosomal protein S12 | 969 | 968 | coexpression:667 experimental:909 |
Rv2840c hyp |
hypothetical protein | 957 | 951 ctx | neighborhood:760 coexpression:805 |
Rv2839c infB |
translation initiation factor IF-2 | 911 | 853 ctx | neighborhood:492 coexpression:722 textmining:420 |
Rv2838c rbfA |
ribosome-binding factor RbfA | 892 | 830 ctx | neighborhood:492 coexpression:416 experimental:474 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 851 | 822 | coexpression:676 experimental:474 |
Rv2909c rpsP |
30S ribosomal protein S16 | 793 | 793 | coexpression:622 experimental:474 |
Rv3443c rplM |
50S ribosomal protein L13 | 788 | 774 | coexpression:774 |
Rv2890c rpsB |
30S ribosomal protein S2 | 766 | 764 | coexpression:534 experimental:474 |
Rv2844 hyp |
hypothetical protein | 761 | 762 ctx | neighborhood:760 |
Rv2843 hyp |
hypothetical protein | 761 | 761 ctx | neighborhood:760 |
Rv0053 rpsF |
30S ribosomal protein S6 | 768 | 731 | coexpression:440 experimental:474 |
Rv0639 nusG |
transcription termination/antitermination protein NusG | 724 | 725 | coexpression:716 |
Rv2907c rimM |
16S rRNA processing protein RimM | 833 | 723 | coexpression:723 textmining:421 |
Rv0683 rpsG |
30S ribosomal protein S7 | 750 | 718 | coexpression:462 experimental:498 |
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: ribosome maturation factor RimP
- MTBC0 PGAP product: ribosome maturation factor RimP
- Pfam (hmmscan --cut_ga): RimP_N PF02576.23 (E=1e-11), DUF150_C PF17384.9 (E=3e-09)
- (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_217358.1)
- Domains: Pfam-A via hmmscan --cut_ga — RimP_N (PF02576.23), DUF150_C (PF17384.9)
- 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
COG0779 - Curated reference: UniProt P9WH17 (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 —
91 functional partner(s); context anchor
nusA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003021|Rv2842c|rimP MTTGLPSQRQVIELLGADFACAGYEIEDVVIDARARPPRIAVIADGDAPLDLDTIAALSRRASALLDGLDGANKIRGRYLLEVSSPGVERPLTSEKHFRRARGRKVELVLSDGSRLTGRVGEMRAGTVALVIREDRGWAVREIPLAEIVKAVVQVEFSPPAPAELELAQSSEMGLARGTEAGA