pykA Resolved · high auto-curated
H37Rv Rv1617 · MTBC0 mtbc0_001724 ·
472 aa · 1828153–1829571 (+) ·
RefSeq NP_216133.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | pyruvate kinase |
|---|---|
| MTBC0 PGAP re-annotation | pyruvate kinase |
| Revised (this work) | Pyruvate kinase. Pfam: PK (PF00224.28), PK_C (PF02887.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKE5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Pyruvate kinase |
| EC (curated) |
EC 2.7.1.40
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | pyk |
| eggNOG description | Belongs to the pyruvate kinase family |
| Orthologous group | COG0469 |
| EC number |
EC 2.7.1.40
|
| KEGG orthology |
K00873
|
| KEGG pathways |
map00010, map00230, map00620, map01100, map01110, map01120, map01130, map01200, map01230, map04922, map04930, map05165, map05203, map05230
|
| KEGG modules |
M00001, M00002, M00049, M00050
|
| Gene Ontology (127) |
GO:0003674, GO:0003824, GO:0004743, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0005975, GO:0006082, GO:0006090 +115 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 | 0.532 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 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 |
|---|---|---|---|---|
PK | PF00224.28 | 1.0e-113 | 3–323 | Pyruvate kinase, barrel domain |
PK_C | PF02887.22 | 1.4e-25 | 354–465 | Pyruvate kinase, alpha/beta domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1023 eno |
enolase | 998 | 987 | coexpression:819 database:900 textmining:857 |
Rv0651 rplJ |
50S ribosomal protein L10 | 975 | 975 | coexpression:651 experimental:928 |
Rv0715 rplX |
50S ribosomal protein L24 | 974 | 974 | coexpression:663 experimental:920 |
Rv0704 rplB |
50S ribosomal protein L2 | 976 | 973 | coexpression:672 experimental:914 |
Rv0716 rplE |
50S ribosomal protein L5 | 975 | 973 | coexpression:658 experimental:917 |
Rv0719 rplF |
50S ribosomal protein L6 | 973 | 973 | coexpression:690 experimental:911 |
Rv0720 rplR |
50S ribosomal protein L18 | 975 | 972 | coexpression:671 experimental:911 |
Rv0703 rplW |
50S ribosomal protein L23 | 974 | 972 | coexpression:658 experimental:915 |
Rv0706 rplV |
50S ribosomal protein L22 | 972 | 971 | coexpression:659 experimental:911 |
Rv0714 rplN |
50S ribosomal protein L14 | 971 | 971 | coexpression:658 experimental:913 |
Rv0946c pgi |
glucose-6-phosphate isomerase | 991 | 970 | coexpression:822 database:800 textmining:719 |
Rv0709 rpmC |
50S ribosomal protein L29 | 969 | 970 | coexpression:648 experimental:911 |
Rv0707 rpsC |
30S ribosomal protein S3 | 966 | 965 | coexpression:705 experimental:878 |
Rv2890c rpsB |
30S ribosomal protein S2 | 967 | 963 | coexpression:703 experimental:877 |
Rv0705 rpsS |
30S ribosomal protein S19 | 963 | 961 | coexpression:650 experimental:885 |
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: pyruvate kinase
- MTBC0 PGAP product: pyruvate kinase
- Pfam (hmmscan --cut_ga): PK PF00224.28 (E=1e-113), PK_C PF02887.22 (E=1e-25)
- (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_216133.1)
- Domains: Pfam-A via hmmscan --cut_ga — PK (PF00224.28), PK_C (PF02887.22)
- 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
COG0469 - Curated reference: UniProt P9WKE5 (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 — 181 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001724|Rv1617|pykA MTRRGKIVCTLGPATQRDDLVRALVEAGMDVARMNFSHGDYDDHKVAYERVRVASDATGRAVGVLADLQGPKIRLGRFASGATHWAEGETVRITVGACEGSHDRVSTTYKRLAQDAVAGDRVLVDDGKVALVVDAVEGDDVVCTVVEGGPVSDNKGISLPGMNVTAPALSEKDIEDLTFALNLGVDMVALSFVRSPADVELVHEVMDRIGRRVPVIAKLEKPEAIDNLEAIVLAFDAVMVARGDLGVELPLEEVPLVQKRAIQMARENAKPVIVATQMLDSMIENSRPTRAEASDVANAVLDGADALMLSGETSVGKYPLAAVRTMSRIICAVEENSTAAPPLTHIPRTKRGVISYAARDIGERLDAKALVAFTQSGDTVRRLARLHTPLPLLAFTAWPEVRSQLAMTWGTETFIVPKMQSTDGMIRQVDKSLLELARYKRGDLVVIVAGAPPGTVGSTNLIHVHRIGEDDV