rpe Resolved · high auto-curated
H37Rv Rv1408 · MTBC0 mtbc0_001509 ·
232 aa · 1593843–1594541 (+) ·
RefSeq NP_215924.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribulose-phosphate 3-epimerase |
|---|---|
| MTBC0 PGAP re-annotation | ribulose-phosphate 3-epimerase |
| Revised (this work) | Ribulose-phosphate 3-epimerase. Pfam: Ribul_P_3_epim (PF00834.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WI51
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribulose-phosphate 3-epimerase |
| EC (curated) |
EC 5.1.3.1
|
| Curated function | Catalyzes the reversible epimerization of D-ribulose 5-phosphate to D-xylulose 5-phosphate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | rpe |
| eggNOG description | Belongs to the ribulose-phosphate 3-epimerase family |
| Orthologous group | COG0036 |
| EC number |
EC 5.1.3.1
|
| KEGG orthology |
K01783
|
| KEGG pathways |
map00030, map00040, map00710, map01100, map01110, map01120, map01130, map01200, map01230
|
| KEGG modules |
M00004, M00007
|
| Gene Ontology (62) |
GO:0003674, GO:0003824, GO:0004750, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005975, GO:0005996, GO:0006081 +50 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) pseudogene candidate
| pN/pS | 0.35 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 3.44% of strains (5001) · clonal |
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 |
|---|---|---|---|---|
Ribul_P_3_epim | PF00834.26 | 2.6e-83 | 13–207 | Ribulose-phosphate 3 epimerase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fmu (16S rRNA m5C967 methyltransferase), high confidence from genomic context alone (score 892 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1449c tkt |
transketolase | 991 | 973 | coexpression:408 database:900 textmining:719 |
Rv1844c gnd1 |
6-phosphogluconate dehydrogenase | 951 | 928 | database:900 |
Rv2465c rpiB |
ribose-5-phosphate isomerase B | 941 | 924 | database:900 |
Rv0729 xylB |
D-xylulose kinase XylB | 938 | 920 | database:900 |
Rv1122 gnd2 |
6-phosphogluconate dehydrogenase (decarboxylating) | 909 | 902 | database:900 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 896 | 892 ctx | neighborhood:846 |
Rv1406 fmt |
methionyl-tRNA formyltransferase | 898 | 888 ctx | neighborhood:846 |
Rv1409 ribG |
bifunctional riboflavin biosynthesis diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino) uracil reductas | 896 | 887 ctx | neighborhood:881 |
Rv1437 pgk |
phosphoglycerate kinase | 925 | 798 ctx | cooccurence:676 textmining:649 |
Rv1392 metK |
S-adenosylmethionine synthetase | 797 | 776 ctx | cooccurence:683 |
Rv2555c alaS |
alanine--tRNA ligase | 697 | 698 ctx | cooccurence:501 coexpression:400 |
Rv1389 gmk |
guanylate kinase | 723 | 683 ctx | cooccurence:540 |
Rv1438 tpi |
triosephosphate isomerase | 876 | 664 ctx | cooccurence:564 textmining:648 |
Rv1405c |
methyltransferase | 612 | 612 ctx | neighborhood:602 |
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 821 | 606 | coexpression:411 textmining:566 |
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: ribulose-phosphate 3-epimerase
- MTBC0 PGAP product: ribulose-phosphate 3-epimerase
- Pfam (hmmscan --cut_ga): Ribul_P_3_epim PF00834.26 (E=3e-83)
- (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_215924.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribul_P_3_epim (PF00834.26)
- 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
COG0036 - Curated reference: UniProt P9WI51 (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 —
61 functional partner(s); context anchor
fmu - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001509|Rv1408|rpe MSLMAGSTGGPLIAPSILAADFARLADEAAAVNGADWLHVDVMDGHFVPNLTIGLPVVESLLAVTDIPMDCHLMIDNPDRWAPPYAEAGAYNVTFHAEATDNPVGVARDIRAAGAKAGISVKPGTPLEPYLDILPHFDTLLVMSVEPGFGGQRFIPEVLSKVRAVRKMVDAGELTILVEIDGGINDDTIEQAAEAGVDCFVAGSAVYGADDPAAAVAALRRQAGAASLHLSL