ribD Resolved · high auto-curated
H37Rv Rv2671 · MTBC0 mtbc0_002845 ·
258 aa · 3009042–3009818 (+) ·
RefSeq NP_217187.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase |
|---|---|
| MTBC0 PGAP re-annotation | bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase |
| Revised (this work) | Bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase. Pfam: RibD_C (PF01872.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71968
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Bacterial bifunctional deaminase-reductase C-terminal domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | ribD |
| eggNOG description | Riboflavin biosynthesis |
| Orthologous group | COG1985 |
| EC number |
EC 1.1.1.193
|
| KEGG orthology |
K00082
|
| KEGG pathways |
map00740, map01100, map01110
|
| KEGG modules |
M00125
|
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, 1 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 |
|---|---|---|---|---|
RibD_C | PF01872.23 | 7.7e-49 | 40–251 | RibD C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: aftC (alpha-(1->3)-arabinofuranosyltransferase), high confidence from genomic context alone (score 776 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1415 ribA2 |
bifunctional riboflavin biosynthesis GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase | 925 | 804 | coexpression:694 textmining:636 |
Rv1940 ribA1 |
riboflavin biosynthesis protein RibA | 901 | 804 | coexpression:694 textmining:517 |
Rv2670c zapE hyp |
hypothetical protein | 802 | 802 ctx | neighborhood:792 |
Rv2673 aftC |
alpha-(1->3)-arabinofuranosyltransferase | 844 | 776 ctx | neighborhood:773 |
Rv1412 ribC |
riboflavin synthase | 839 | 755 | coexpression:703 |
Rv2672 |
protease | 724 | 664 ctx | neighborhood:659 |
Rv1416 ribH |
6,7-dimethyl-8-ribityllumazine synthase | 856 | 531 | coexpression:435 textmining:706 |
Rv2674 msrB |
peptide methionine sulfoxide reductase MsrB | 525 | 526 ctx | neighborhood:523 |
Rv1722 |
carboxylase | 422 | 422 | |
Rv0199 |
membrane protein | 426 | 409 | |
Rv0200 |
transmembrane protein | 423 | 406 | |
Rv2629 hyp |
hypothetical protein | 406 | 406 | experimental:405 |
Rv2390c hyp |
hypothetical protein | 420 | 404 | |
Rv3492c |
Mce associated protein | 420 | 403 | |
Rv3859c gltB |
glutamate synthase large subunit | 402 | 403 |
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: bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase
- MTBC0 PGAP product: bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase
- Pfam (hmmscan --cut_ga): RibD_C PF01872.23 (E=8e-49)
- (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_217187.1)
- Domains: Pfam-A via hmmscan --cut_ga — RibD_C (PF01872.23)
- 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
COG1985 - Curated reference: UniProt P71968 (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 —
49 functional partner(s); context anchor
aftC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002845|Rv2671|ribD MPDSGQLGAADTPLRLLSSVHYLTDGELPQLYDYPDDGTWLRANFISSLDGGATVDGTSGAMAGPGDRFVFNLLRELADVIVVGVGTVRIEGYSGVRMGVVQRQHRQARGQSEVPQLAIVTRSGRLDRDMAVFTRTEMAPLVLTTTAVADDTRQRLAGLAEVIACSGDDPGTVDEAVLVSQLAARGLRRILTEGGPTLLGTFVERDVLDELCLTIAPYVVGGLARRIVTGPGQVLTRMRCAHVLTDDSGYLYTRYVKT