ribC Resolved · high auto-curated
H37Rv Rv1412 · MTBC0 mtbc0_001513 ·
201 aa · 1597911–1598516 (+) ·
RefSeq NP_215928.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | riboflavin synthase |
|---|---|
| MTBC0 PGAP re-annotation | riboflavin synthase |
| Revised (this work) | Riboflavin synthase. Pfam: Lum_binding (PF00677.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WK35
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Riboflavin synthase |
| EC (curated) |
EC 2.5.1.9
|
| Curated function | Catalyzes the dismutation of two molecules of 6,7-dimethyl-8-ribityllumazine, resulting in the formation of riboflavin and 5-amino-6-(D-ribitylamino)uracil. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | ribE |
| eggNOG description | riboflavin synthase alpha |
| Orthologous group | COG0307 |
| EC number |
EC 2.5.1.9
|
| KEGG orthology |
K00793
|
| KEGG pathways |
map00740, map01100, map01110
|
| KEGG modules |
M00125
|
| Gene Ontology (41) |
GO:0003674, GO:0003824, GO:0004746, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006766, GO:0006767, GO:0006771, GO:0006807 +29 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 | 0.742 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
Lum_binding | PF00677.24 | 3.1e-26 | 100–187 | Lumazine binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ribA2 (bifunctional riboflavin biosynthesis GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase), high confidence from genomic context alone (score 1000 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 | 999 | 1000 ctx | neighborhood:505 fusion:896 cooccurence:774 coexpression:985 textmining:418 |
Rv1416 ribH |
6,7-dimethyl-8-ribityllumazine synthase | 999 | 999 ctx | neighborhood:675 cooccurence:774 coexpression:853 database:900 textmining:638 |
Rv1409 ribG |
bifunctional riboflavin biosynthesis diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino) uracil reductas | 999 | 999 ctx | fusion:662 cooccurence:772 coexpression:987 textmining:627 |
Rv1940 ribA1 |
riboflavin biosynthesis protein RibA | 999 | 998 ctx | fusion:436 cooccurence:774 coexpression:985 textmining:418 |
Rv2786c ribF |
bifunctional riboflavin kinase /FMN adenylyltransferase | 933 | 913 | database:900 |
Rv1410c |
aminoglycosides/tetracycline-transport integral membrane protein | 893 | 805 ctx | neighborhood:783 textmining:474 |
Rv1411c lprG |
lipoprotein LprG | 786 | 786 ctx | neighborhood:783 |
Rv2671 ribD |
bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase | 839 | 755 | coexpression:703 |
Rv1298 rpmE |
50S ribosomal protein L31 | 685 | 686 | coexpression:686 |
Rv0331 |
dehydrogenase/reductase | 684 | 684 | coexpression:684 |
Rv1417 |
membrane protein | 678 | 677 ctx | neighborhood:675 |
Rv2122c hisE |
phosphoribosyl-ATP pyrophosphatase | 495 | 496 | coexpression:411 |
Rv1392 metK |
S-adenosylmethionine synthetase | 504 | 473 | |
Rv1414 hyp |
hypothetical protein | 471 | 471 ctx | neighborhood:468 |
Rv1413 hyp |
hypothetical protein | 469 | 470 ctx | neighborhood:468 |
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: riboflavin synthase
- MTBC0 PGAP product: riboflavin synthase
- Pfam (hmmscan --cut_ga): Lum_binding PF00677.24 (E=3e-26)
- (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_215928.1)
- Domains: Pfam-A via hmmscan --cut_ga — Lum_binding (PF00677.24)
- 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
COG0307 - Curated reference: UniProt P9WK35 (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 —
30 functional partner(s); context anchor
ribA2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001513|Rv1412|ribC MFTGIVEERGEVTGREALVDAARLTIRGPMVTADAGHGDSIAVNGVCLTVVDVLPDGQFTADVMAETLNRSNLGELRPGSRVNLERAAALGSRLGGHIVQGHVDATGEIVARCPSEHWEVVRIEMPASVARYVVEKGSITVDGISLTVSGLGAEQRDWFEVSLIPTTRELTTLGSAAVGTRVNLEVDVVAKYVERLMRSAG