ribF Resolved · high auto-curated
H37Rv Rv2786c · MTBC0 - ·
331 aa · 3093905–3094900 (-) ·
RefSeq NP_217302.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | bifunctional riboflavin kinase /FMN adenylyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Bifunctional riboflavin kinase /FMN adenylyltransferase. Pfam: FAD_syn (PF06574.19), CTP_transf_like (PF01467.33), Flavokinase (PF01687.24). |
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 |
I6X5C9
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Riboflavin biosynthesis protein [Includes: Riboflavin kinase |
| EC (curated) |
EC 2.7.1.26, EC 2.7.7.2
|
| Curated function | Catalyzes the phosphorylation of riboflavin to FMN followed by the adenylation of FMN to FAD. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | ribF |
| eggNOG description | Belongs to the ribF family |
| Orthologous group | COG0196 |
| EC number |
EC 2.7.1.26, EC 2.7.7.2
|
| KEGG orthology |
K11753
|
| KEGG pathways |
map00740, map01100, map01110
|
| KEGG modules |
M00125
|
| Gene Ontology (95) |
GO:0003674, GO:0003824, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005739, GO:0005740, GO:0005743, GO:0006139, GO:0006725 +83 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 | 0.232 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 4 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 |
|---|---|---|---|---|
FAD_syn | PF06574.19 | 8.2e-52 | 19–167 | FAD synthetase |
CTP_transf_like | PF01467.33 | 3.9e-04 | 26–180 | Cytidylyltransferase-like |
Flavokinase | PF01687.24 | 4.8e-39 | 195–328 | Riboflavin kinase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: truB (tRNA pseudouridine synthase B), high confidence from genomic context alone (score 810 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1412 ribC |
riboflavin synthase | 933 | 913 | database:900 |
Rv1416 ribH |
6,7-dimethyl-8-ribityllumazine synthase | 974 | 883 | coexpression:762 database:500 textmining:787 |
Rv2793c truB |
tRNA pseudouridine synthase B | 944 | 810 ctx | fusion:614 coexpression:412 textmining:720 |
Rv2785c rpsO |
30S ribosomal protein S15 | 935 | 759 ctx | neighborhood:749 textmining:745 |
Rv2784c lppU |
lipoprotein LppU | 744 | 745 ctx | neighborhood:745 |
Rv1712 cmk |
cytidylate kinase | 741 | 725 ctx | fusion:545 |
Rv2788 sirR |
transcriptional repressor SirR | 699 | 699 ctx | neighborhood:696 |
Rv2783c gpsI |
bifunctional guanosine pentaphosphate synthetase/polyribonucleotide nucleotidyltransferase | 654 | 653 ctx | neighborhood:651 |
Rv2782c pepR |
zinc protease | 652 | 652 ctx | neighborhood:651 |
Rv2965c kdtB |
phosphopantetheine adenylyltransferase | 840 | 611 ctx | cooccurence:594 textmining:608 |
Rv1409 ribG |
bifunctional riboflavin biosynthesis diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino) uracil reductas | 930 | 555 | coexpression:412 textmining:851 |
Rv2787 hyp |
hypothetical protein | 488 | 488 ctx | neighborhood:488 |
Rv2883c pyrH |
uridylate kinase | 459 | 459 ctx | cooccurence:411 |
Rv1710 scpB |
segregation and condensation protein ScpB | 459 | 459 | coexpression:442 |
Rv1631 coaE |
dephospho-CoA kinase CoaE | 769 | 440 | textmining:606 |
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): bifunctional riboflavin kinase /FMN adenylyltransferase
- Pfam (hmmscan --cut_ga): FAD_syn PF06574.19 (E=8e-52), CTP_transf_like PF01467.33 (E=4e-04), Flavokinase PF01687.24 (E=5e-39)
- (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_217302.1)
- Domains: Pfam-A via hmmscan --cut_ga — FAD_syn (PF06574.19), CTP_transf_like (PF01467.33), Flavokinase (PF01687.24)
- 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
COG0196 - Curated reference: UniProt I6X5C9 (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 —
51 functional partner(s); context anchor
truB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2786c|ribF MRRRLAIVQRWRGQDEIPTDWGRCVLTIGVFDGVHRGHAELIAHAVKAGRARGVPAVLMTFDPHPMEVVYPGSHPAQLTTLTRRAELVQDLGIEVFLVMPFTTDFMKLTPDRFIHELLVEHLHVVEVVVGENFTFGKKAAGNVDTLRRAGERFGFAVESMSLVSEHHSNETVTFSSTYIRSCVDAGDMVAAMEALGRPHRVEGVVVRGEGRGAELGFPTANVAPPMYSAIPADGVYAAWFTVLGHGPVTGTVVPGERYQAAVSVGTNPTFSGRTRTVEAFVLDTTADLYGQHVALDFVGRIRGQKKFESVRQLVAAMGADTERARDLLSTG