Rv2573 Resolved · high auto-curated
H37Rv Rv2573 · MTBC0 - ·
246 aa · 2898043–2898783 (+) ·
RefSeq NP_217089.3
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 2-dehydropantoate 2-reductase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | 2-dehydropantoate 2-reductase. Pfam: ApbA (PF02558.23), ApbA_C (PF08546.18). |
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 |
P9WIL1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 2-dehydropantoate 2-reductase |
| EC (curated) |
EC 1.1.1.169
|
| Curated function | Catalyzes the NADPH-dependent reduction of ketopantoate into pantoic acid. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | apbA_1 |
| eggNOG description | Catalyzes the NADPH-dependent reduction of ketopantoate into pantoic acid |
| Orthologous group | COG1893 |
| EC number |
EC 1.1.1.169
|
| KEGG orthology |
K00077
|
| KEGG pathways |
map00770, map01100, map01110
|
| KEGG modules |
M00119
|
| Gene Ontology (57) |
GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006082, GO:0006520, GO:0006573, GO:0006575, GO:0006732 +45 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 | 0.094 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
ApbA | PF02558.23 | 5.1e-19 | 5–96 | Ketopantoate reductase PanE/ApbA |
ApbA_C | PF08546.18 | 3.1e-21 | 120–240 | Ketopantoate reductase PanE/ApbA C terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2575 (membrane protein), high confidence from genomic context alone (score 812 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3602c panC |
pantothenate synthetase | 933 | 913 | database:900 |
Rv2225 panB |
3-methyl-2-oxobutanoate hydroxymethyltransferase | 930 | 908 | database:900 |
Rv2575 |
membrane protein | 811 | 812 ctx | neighborhood:811 |
Rv2572c aspS |
aspartate--tRNA ligase | 745 | 746 ctx | neighborhood:745 |
Rv2574 hyp |
hypothetical protein | 742 | 742 ctx | neighborhood:703 |
Rv1000c hyp |
hypothetical protein | 682 | 682 | coexpression:682 |
Rv2687c |
antibiotic ABC transporter permease | 438 | 438 ctx | cooccurence:419 |
Rv0976c hyp |
hypothetical protein | 430 | 430 | coexpression:412 |
Rv1940 ribA1 |
riboflavin biosynthesis protein RibA | 544 | 413 | coexpression:413 |
Rv2686c |
antibiotic ABC transporter permease | 410 | 411 ctx | cooccurence:409 |
Rv1415 ribA2 |
bifunctional riboflavin biosynthesis GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase | 518 | 408 | coexpression:408 |
Rv2571c |
transmembrane protein | 404 | 404 ctx | neighborhood:400 |
Rv0630c recB |
exonuclease V subunit beta RecB | 527 | 232 | textmining:411 |
Rv2095c pafC |
proteasome accessory factor C | 554 | 74 | textmining:539 |
Rv1631 coaE |
dephospho-CoA kinase CoaE | 713 | 73 | textmining:703 |
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): 2-dehydropantoate 2-reductase
- Pfam (hmmscan --cut_ga): ApbA PF02558.23 (E=5e-19), ApbA_C PF08546.18 (E=3e-21)
- (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_217089.3)
- Domains: Pfam-A via hmmscan --cut_ga — ApbA (PF02558.23), ApbA_C (PF08546.18)
- 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
COG1893 - Curated reference: UniProt P9WIL1 (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 —
18 functional partner(s); context anchor
Rv2575 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2573| MVPGPVHTSPREVAGPVDVLILAVKATQNDAARPWLTRLCDERTVVAVLQNGVEQVEQVQPHCPSSAVVPAIVWCSAETQPQGWVRLRGEAALVVPTGPAAEQFAGLLRGAGATVDCDPDFTTAAWRKLLVNALAGFMVLSGRRSAMFRRDDVAALSRRYVAECLAVARAEGARLDDDVVDEVVRLVRSAPQDMGTSMLADRAAHRPLEWDLRNGVIVRKARAHGLATPISDVLVPLLAAASDGPG