ribG Resolved · high auto-curated
H37Rv Rv1409 · MTBC0 mtbc0_001510 ·
339 aa · 1594538–1595557 (+) ·
RefSeq NP_215925.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | bifunctional riboflavin biosynthesis diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino) uracil reductase |
|---|---|
| MTBC0 PGAP re-annotation | bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD |
| Revised (this work) | Bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD. Pfam: dCMP_cyt_deam_1 (PF00383.30), MafB19-deam (PF14437.13), 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 |
P9WPH1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Riboflavin biosynthesis protein RibD [Includes: Diaminohydroxyphosphoribosylaminopyrimidine deaminase |
| EC (curated) |
EC 1.1.1.193, EC 3.5.4.26
|
| Curated function | Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)-pyrimidinedione 5'-phosphate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | ribD |
| eggNOG description | Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate |
| Orthologous group | COG0117 |
| EC number |
EC 1.1.1.193, EC 3.5.4.26
|
| KEGG orthology |
K11752
|
| KEGG pathways |
map00740, map01100, map01110, map02024
|
| KEGG modules |
M00125
|
| Gene Ontology (29) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006139, GO:0006725, GO:0006807, GO:0008150, GO:0008152, GO:0009451 +17 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 | 1.827 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 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 |
|---|---|---|---|---|
dCMP_cyt_deam_1 | PF00383.30 | 2.7e-17 | 10–106 | Cytidine and deoxycytidylate deaminase zinc-binding region |
MafB19-deam | PF14437.13 | 2.1e-07 | 30–113 | MafB19-like deaminase |
RibD_C | PF01872.23 | 1.7e-52 | 154–334 | RibD C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ribA1 (riboflavin biosynthesis protein RibA), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1940 ribA1 |
riboflavin biosynthesis protein RibA | 999 | 1000 ctx | neighborhood:544 cooccurence:772 coexpression:980 experimental:759 database:900 textmining:805 |
Rv1415 ribA2 |
bifunctional riboflavin biosynthesis GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase | 999 | 1000 ctx | neighborhood:544 fusion:519 cooccurence:772 coexpression:980 experimental:759 database:900 textmining:812 |
Rv1412 ribC |
riboflavin synthase | 999 | 999 ctx | fusion:662 cooccurence:772 coexpression:987 textmining:627 |
Rv1416 ribH |
6,7-dimethyl-8-ribityllumazine synthase | 995 | 978 ctx | cooccurence:772 coexpression:824 textmining:796 |
Rv1722 |
carboxylase | 897 | 898 | experimental:883 |
Rv1408 rpe |
ribulose-phosphate 3-epimerase | 896 | 887 ctx | neighborhood:881 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 957 | 884 ctx | neighborhood:854 textmining:648 |
Rv1406 fmt |
methionyl-tRNA formyltransferase | 866 | 846 ctx | neighborhood:846 |
Rv3859c gltB |
glutamate synthase large subunit | 604 | 605 ctx | neighborhood:544 |
Rv2047c hyp |
hypothetical protein | 621 | 602 ctx | neighborhood:544 |
Rv2228c |
multifunctional RNASE H/alpha-ribazole phosphatase/acid phosphatase | 597 | 598 ctx | neighborhood:479 |
Rv2840c hyp |
hypothetical protein | 590 | 590 | |
Rv2438c nadE |
glutamine-dependent NAD(+) synthetase | 853 | 587 ctx | neighborhood:544 textmining:659 |
Rv2524c fas |
fatty acid synthase | 751 | 580 ctx | neighborhood:544 textmining:433 |
Rv2727c miaA |
tRNA delta(2)-isopentenylpyrophosphate transferase | 579 | 579 | coexpression:421 |
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 riboflavin biosynthesis diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino) uracil reductase
- MTBC0 PGAP product: bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD
- Pfam (hmmscan --cut_ga): dCMP_cyt_deam_1 PF00383.30 (E=3e-17), MafB19-deam PF14437.13 (E=2e-07), RibD_C PF01872.23 (E=2e-52)
- (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_215925.1)
- Domains: Pfam-A via hmmscan --cut_ga — dCMP_cyt_deam_1 (PF00383.30), MafB19-deam (PF14437.13), 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
COG0117 - Curated reference: UniProt P9WPH1 (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 —
172 functional partner(s); context anchor
ribA1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001510|Rv1409|ribG MNVEQVKSIDEAMGLAIEHSYQVKGTTYPNPPVGAVIVDPNGRIVGAGGTEPAGGDHAEVVALRRAGGLATGAIVVVTMEPCNHYGKTPPCVNALIEARVGTVVYAVADPNGIAGGGAGRLSAAGLQVRSGVLAEQVAAGPLREWLHKQRTGLPHVTWKYATSIDGRSAAADGSSQWISSEAARLDLHRRRAIADAILVGTGTVLADDPALTARLADGSLAPQQPLRVVVGKRDIPPEARVLNDEARTMMIRTHEPMEVLRALSDRTDVLLEGGPTLAGAFLRAGAINRILAYVAPILLGGPVTAVDDVGVSNITNALRWQFDSVEKVGPDLLLSLVAR