rpiB Resolved · high auto-curated
H37Rv Rv2465c · MTBC0 - ·
162 aa · 2767671–2768159 (-) ·
RefSeq YP_177884.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribose-5-phosphate isomerase B |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Ribose-5-phosphate isomerase B. Pfam: LacAB_rpiB (PF02502.24). |
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 |
P9WKD7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribose-5-phosphate isomerase B |
| EC (curated) |
EC 5.3.1.6
|
| Curated function | Catalyzes the interconversion of ribulose-5-P and ribose-5-P. It has not isomerase activity towards D-allose 6-phosphate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | rpiB |
| eggNOG description | Ribose 5-phosphate isomerase |
| Orthologous group | COG0698 |
| EC number |
EC 5.3.1.6
|
| KEGG orthology |
K01808
|
| KEGG pathways |
map00030, map00051, map00710, map01100, map01110, map01120, map01130, map01200, map01230
|
| KEGG modules |
M00004, M00007, M00165, M00167
|
| Gene Ontology (42) |
GO:0003674, GO:0003824, GO:0004751, GO:0005575, GO:0005576, GO:0006081, GO:0006098, GO:0006139, GO:0006725, GO:0006732, GO:0006733, GO:0006739 +30 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 | 0.11 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 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 |
|---|---|---|---|---|
LacAB_rpiB | PF02502.24 | 2.7e-45 | 6–143 | Ribose/Galactose Isomerase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: upp (uracil phosphoribosyltransferase), high confidence from genomic context alone (score 916 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1408 rpe |
ribulose-phosphate 3-epimerase | 941 | 924 | database:900 |
Rv3309c upp |
uracil phosphoribosyltransferase | 920 | 916 ctx | fusion:899 |
Rv1449c tkt |
transketolase | 959 | 913 | database:900 textmining:549 |
Rv1844c gnd1 |
6-phosphogluconate dehydrogenase | 919 | 908 | database:900 |
Rv2436 rbsK |
ribokinase RbsK | 918 | 908 | database:900 |
Rv1122 gnd2 |
6-phosphogluconate dehydrogenase (decarboxylating) | 914 | 908 | database:900 |
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 928 | 906 | database:900 |
Rv3068c pgmA |
phosphoglucomutase PgmA | 900 | 900 | database:900 |
Rv2464c nei1 |
DNA glycosylase | 884 | 884 ctx | neighborhood:882 |
Rv2466c hyp |
hypothetical protein | 817 | 818 ctx | neighborhood:773 |
Rv2606c snzP |
pyridoxine biosynthesis protein | 804 | 804 | database:800 |
Rv2604c snoP |
glutamine amidotransferase SnoP | 800 | 800 | database:800 |
Rv2029c pfkB |
6-phosphofructokinase PfkB | 828 | 775 | coexpression:757 |
Rv2467 pepN |
aminopeptidase PepN | 740 | 712 ctx | neighborhood:708 |
Rv1093 glyA1 |
serine hydroxymethyltransferase | 629 | 629 | coexpression:401 |
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): ribose-5-phosphate isomerase B
- Pfam (hmmscan --cut_ga): LacAB_rpiB PF02502.24 (E=3e-45)
- (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_177884.1)
- Domains: Pfam-A via hmmscan --cut_ga — LacAB_rpiB (PF02502.24)
- 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
COG0698 - Curated reference: UniProt P9WKD7 (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 —
34 functional partner(s); context anchor
upp - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2465c|rpiB MSGMRVYLGADHAGYELKQRIIEHLKQTGHEPIDCGALRYDADDDYPAFCIAAATRTVADPGSLGIVLGGSGNGEQIAANKVPGARCALAWSVQTAALAREHNNAQLIGIGGRMHTVAEALAIVDAFVTTPWSKAQRHQRRIDILAEYERTHEAPPVPGAPA