rbsK Resolved · high auto-curated
H37Rv Rv2436 · MTBC0 mtbc0_002594 ·
304 aa · 2757478–2758392 (+) ·
RefSeq NP_216952.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribokinase RbsK |
|---|---|
| MTBC0 PGAP re-annotation | ribokinase RbsK |
| Revised (this work) | Ribokinase RbsK. Pfam: PfkB (PF00294.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71913
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribokinase |
| EC (curated) |
EC 2.7.1.15
|
| Curated function | Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5-phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | rbsK |
| eggNOG description | Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5- phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway |
| Orthologous group | COG0524 |
| EC number |
EC 2.7.1.15
|
| KEGG orthology |
K00852
|
| KEGG pathways |
map00030
|
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 | 0.769 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 10 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 |
|---|---|---|---|---|
PfkB | PF00294.30 | 7.4e-56 | 15–288 | pfkB family carbohydrate kinase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: deoC (2-deoxyribose-5-phosphate aldolase), high confidence from genomic context alone (score 950 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0478 deoC |
2-deoxyribose-5-phosphate aldolase | 955 | 950 ctx | fusion:493 database:900 |
Rv1449c tkt |
transketolase | 937 | 929 | database:900 |
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 934 | 925 | database:900 |
Rv3068c pgmA |
phosphoglucomutase PgmA | 940 | 912 | database:900 |
Rv2465c rpiB |
ribose-5-phosphate isomerase B | 918 | 908 | database:900 |
Rv2606c snzP |
pyridoxine biosynthesis protein | 819 | 800 | database:800 |
Rv2604c snoP |
glutamine amidotransferase SnoP | 819 | 800 | database:800 |
Rv3393 iunH |
nucleoside hydrolase | 887 | 794 ctx | cooccurence:726 textmining:478 |
Rv2437 |
transmembrane protein | 742 | 741 ctx | neighborhood:728 |
Rv1603 hisA |
1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase | 710 | 693 | coexpression:682 |
Rv0498 hyp |
hypothetical protein | 614 | 562 | coexpression:537 |
Rv2584c apt |
adenine phosphoribosyltransferase | 613 | 562 | |
Rv1416 ribH |
6,7-dimethyl-8-ribityllumazine synthase | 575 | 518 | coexpression:502 |
Rv0792c |
transcriptional regulator | 534 | 488 ctx | cooccurence:408 |
Rv0729 xylB |
D-xylulose kinase XylB | 537 | 475 |
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: ribokinase RbsK
- MTBC0 PGAP product: ribokinase RbsK
- Pfam (hmmscan --cut_ga): PfkB PF00294.30 (E=7e-56)
- (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_216952.1)
- Domains: Pfam-A via hmmscan --cut_ga — PfkB (PF00294.30)
- 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
COG0524 - Curated reference: UniProt P71913 (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 —
48 functional partner(s); context anchor
deoC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002594|Rv2436|rbsK MANASETNVGPMAPRVCVVGSVNMDLTFVVDALPRPGETVLAASLTRTPGGKGANQAVAAARAGAQVQFSGAFGDDPAAAQLRAHLRANAVGLDRTVTVPGPSGTAIIVVDASAENTVLVAPGANAHLTPVPSAVANCDVLLTQLEIPVATALAAARAAQSADAVVMVNASPAGQDRSSLQDLAAIADVVIANEHEANDWPSPPTHFVITLGVRGARYVGADGVFEVPAPTVTPVDTAGAGDVFAGVLAANWPRNPGSPAERLRALRRACAAGALATLVSGAGDCAPAAAAIDAALRANRHNGS