deoC Resolved · high auto-curated
H37Rv Rv0478 · MTBC0 mtbc0_000503 ·
224 aa · 570587–571261 (+) ·
RefSeq NP_214992.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 2-deoxyribose-5-phosphate aldolase |
|---|---|
| MTBC0 PGAP re-annotation | deoxyribose-phosphate aldolase |
| Revised (this work) | Deoxyribose-phosphate aldolase. Pfam: DeoC (PF01791.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WP03
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Deoxyribose-phosphate aldolase |
| EC (curated) |
EC 4.1.2.4
|
| Curated function | Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | deoC |
| eggNOG description | Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy- D-ribose 5-phosphate |
| Orthologous group | COG0274 |
| EC number |
EC 4.1.2.4
|
| KEGG orthology |
K01619
|
| KEGG pathways |
map00030
|
| Gene Ontology (52) |
GO:0003674, GO:0003824, GO:0004139, GO:0005975, GO:0006139, GO:0006725, GO:0006753, GO:0006793, GO:0006796, GO:0006807, GO:0008150, GO:0008152 +40 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 | 0.193 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 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 |
|---|---|---|---|---|
DeoC | PF01791.16 | 8.1e-18 | 12–218 | DeoC/LacD family aldolase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rbsK (ribokinase RbsK), high confidence from genomic context alone (score 950 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2436 rbsK |
ribokinase RbsK | 955 | 950 ctx | fusion:493 database:900 |
Rv3314c deoA |
thymidine phosphorylase | 955 | 942 ctx | cooccurence:714 coexpression:728 |
Rv1449c tkt |
transketolase | 938 | 920 | database:900 |
Rv1448c tal |
transaldolase | 917 | 906 | database:900 |
Rv0363c fba |
fructose-bisphosphate aldolase | 915 | 902 | database:900 |
Rv0476 |
transmembrane protein | 884 | 884 ctx | neighborhood:882 |
Rv0477 hyp |
hypothetical protein | 883 | 883 ctx | neighborhood:882 |
Rv1438 tpi |
triosephosphate isomerase | 881 | 845 | database:800 |
Rv1436 gap |
glyceraldehyde 3-phosphate dehydrogenase | 861 | 829 | database:800 |
Rv0946c pgi |
glucose-6-phosphate isomerase | 843 | 820 | database:800 |
Rv1023 eno |
enolase | 820 | 811 | database:800 |
Rv1127c ppdK |
pyruvate, phosphate dikinase PpdK | 811 | 811 | database:800 |
Rv2454c korB |
2-oxoglutarate oxidoreductase subunit KorB | 808 | 808 | database:800 |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA | 808 | 808 | database:800 |
Rv0650 |
sugar kinase | 807 | 807 | 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
- Legacy H37Rv annotation: 2-deoxyribose-5-phosphate aldolase
- MTBC0 PGAP product: deoxyribose-phosphate aldolase
- Pfam (hmmscan --cut_ga): DeoC PF01791.16 (E=8e-18)
- (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_214992.1)
- Domains: Pfam-A via hmmscan --cut_ga — DeoC (PF01791.16)
- 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
COG0274 - Curated reference: UniProt P9WP03 (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 —
46 functional partner(s); context anchor
rbsK - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000503|Rv0478|deoC MLGQPTRAQLAALVDHTLLKPETTRADVAALVAEAAELGVYAVCVSPSMVPVAVQAGGVRVAAVTGFPSGKHVSSVKAHEAAAALASGASEIDMVIDIGAALCGDIDAVRSDIEAVRAAAAGAVLKVIVESAVLLGQSNAHTLVDACRAAEDAGADFVKTSTGCHPAGGATVRAVELMAETVGPRLGVKASGGIRTAADAVAMLNAGATRLGLSGTRAVLDGLS