ribA1 Resolved · high auto-curated
H37Rv Rv1940 · MTBC0 - ·
353 aa · 2192606–2193667 (+) ·
RefSeq YP_177851.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | riboflavin biosynthesis protein RibA |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Riboflavin biosynthesis protein RibA. Pfam: DHBP_synthase (PF00926.25), GTP_cyclohydro2 (PF00925.26). |
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 |
L7N669
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | 3,4-dihydroxy-2-butanone-4-phosphate synthase |
| EC (curated) |
EC 4.1.99.12
|
| Curated function | Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | ribA1 |
| eggNOG description | belongs to the DHBP synthase family |
| Orthologous group | COG0108 |
| EC number |
EC 3.5.4.25, EC 4.1.99.12
|
| KEGG orthology |
K14652
|
| KEGG pathways |
map00740, map00790, map01100, map01110
|
| KEGG modules |
M00125, M00840
|
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 | 1.505 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
DHBP_synthase | PF00926.25 | 5.3e-57 | 10–194 | 3,4-dihydroxy-2-butanone 4-phosphate synthase |
GTP_cyclohydro2 | PF00925.26 | 1.4e-20 | 207–289 | GTP cyclohydrolase II |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ribG (bifunctional riboflavin biosynthesis diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino) uracil reductas), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1409 ribG |
bifunctional riboflavin biosynthesis diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino) uracil reductas | 999 | 1000 ctx | neighborhood:544 cooccurence:772 coexpression:980 experimental:759 database:900 textmining:805 |
Rv1416 ribH |
6,7-dimethyl-8-ribityllumazine synthase | 999 | 1000 ctx | cooccurence:774 coexpression:985 database:900 textmining:418 |
Rv1412 ribC |
riboflavin synthase | 999 | 998 ctx | fusion:436 cooccurence:774 coexpression:985 textmining:418 |
Rv1937 |
oxygenase | 983 | 981 ctx | neighborhood:882 coexpression:845 |
Rv1939 |
oxidoreductase | 971 | 970 ctx | neighborhood:807 coexpression:852 |
Rv1938 ephB |
epoxide hydrolase EphB | 967 | 966 ctx | neighborhood:787 coexpression:846 |
Rv1415 ribA2 |
bifunctional riboflavin biosynthesis GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase | 943 | 921 | database:900 |
Rv3609c folE |
GTP cyclohydrolase I | 972 | 908 | database:900 textmining:715 |
Rv3109 moaA1 |
cyclic pyranopterin monophosphate synthase | 909 | 906 | database:900 |
Rv0869c moaA2 |
molybdenum cofactor biosynthesis protein MoaA | 906 | 903 | database:900 |
Rv2445c ndkA |
nucleoside diphosphate kinase | 903 | 898 | database:800 |
Rv1941 |
short-chain type dehydrogenase/reductase | 887 | 882 ctx | neighborhood:881 |
Rv1936 |
monooxygenase | 854 | 849 ctx | neighborhood:760 |
Rv2583c relA |
bifunctional (p)ppGpp synthase/hydrolase RelA | 840 | 834 | database:800 |
Rv3645 |
transmembrane protein | 812 | 812 | database:800 |
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): riboflavin biosynthesis protein RibA
- Pfam (hmmscan --cut_ga): DHBP_synthase PF00926.25 (E=5e-57), GTP_cyclohydro2 PF00925.26 (E=1e-20)
- (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 YP_177851.1)
- Domains: Pfam-A via hmmscan --cut_ga — DHBP_synthase (PF00926.25), GTP_cyclohydro2 (PF00925.26)
- 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
COG0108 - Curated reference: UniProt L7N669 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
134 functional partner(s); context anchor
ribG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1940|ribA1 MKTTDVRVRRAITAMAGGHAVVLTGDPNGDGYLVFAAQAATPRLVAFAVRHTSGYLRVALPGAECERLHLPPMCDRDTTHCVSVDVRGTGTGISASDRAWTIAALASATSVAADFQRPGHVVPVQAQADGVLGRRGPAEAAVDLARLAERRPAAALCEIVSPDNPVQMAHHAESVEFAVEHGLAMVSIGELVAYRRRIEPQVVRFTAATLPTWAGASRVIGFRDVYDLGEHLAVIVGAVGAGVPVPLHVHIECLTGDVFGSTACRCGEELNGALARMSAQGSGVVLYLRPPGPAQACGLFARGDAATDVMPETVTWILRDLGVYAIRLSDDVPGFGLVMFGAIREASTLAAAG