pgk Resolved · high auto-curated
H37Rv Rv1437 · MTBC0 mtbc0_001537 ·
412 aa · 1623694–1624932 (+) ·
RefSeq NP_215953.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphoglycerate kinase |
|---|---|
| MTBC0 PGAP re-annotation | phosphoglycerate kinase |
| Revised (this work) | Phosphoglycerate kinase. Pfam: PGK (PF00162.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WID1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphoglycerate kinase |
| EC (curated) |
EC 2.7.2.3
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | pgk |
| eggNOG description | Belongs to the phosphoglycerate kinase family |
| Orthologous group | COG0126 |
| EC number |
EC 2.7.2.3, EC 5.3.1.1
|
| KEGG orthology |
K00927, K01803
|
| KEGG pathways |
map00010, map00051, map00562, map00710, map01100, map01110, map01120, map01130, map01200, map01230
|
| KEGG modules |
M00001, M00002, M00003, M00165, M00166, M00308, M00552
|
| Gene Ontology (12) |
GO:0005575, GO:0005576, GO:0005622, GO:0005623, GO:0005737, GO:0005886, GO:0008150, GO:0016020, GO:0040007, GO:0044424, GO:0044464, GO:0071944
|
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 | 0.727 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
PGK | PF00162.25 | 1.0e-134 | 14–394 | Phosphoglycerate kinase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: tpi (triosephosphate isomerase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1438 tpi |
triosephosphate isomerase | 999 | 1000 ctx | neighborhood:882 fusion:900 cooccurence:656 coexpression:963 textmining:832 |
Rv1436 gap |
glyceraldehyde 3-phosphate dehydrogenase | 999 | 1000 ctx | neighborhood:882 cooccurence:731 coexpression:920 experimental:464 database:900 textmining:807 |
Rv1023 eno |
enolase | 995 | 985 ctx | cooccurence:685 coexpression:858 experimental:665 textmining:733 |
Rv0489 gpm1 |
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | 990 | 975 | coexpression:727 database:900 textmining:648 |
Rv1617 pykA |
pyruvate kinase | 962 | 902 ctx | cooccurence:561 coexpression:738 textmining:630 |
Rv0946c pgi |
glucose-6-phosphate isomerase | 975 | 888 | coexpression:853 textmining:793 |
Rv0363c fba |
fructose-bisphosphate aldolase | 958 | 884 | coexpression:827 textmining:653 |
Rv1408 rpe |
ribulose-phosphate 3-epimerase | 925 | 798 ctx | cooccurence:676 textmining:649 |
Rv1449c tkt |
transketolase | 913 | 762 | coexpression:653 textmining:652 |
Rv3010c pfkA |
6-phosphofructokinase | 880 | 748 | coexpression:652 textmining:545 |
Rv1392 metK |
S-adenosylmethionine synthetase | 787 | 722 ctx | cooccurence:566 |
Rv2614c thrS |
threonine--tRNA ligase | 737 | 712 ctx | cooccurence:625 |
Rv1732c hyp |
hypothetical protein | 661 | 661 ctx | fusion:641 |
Rv1389 gmk |
guanylate kinase | 675 | 623 ctx | cooccurence:574 |
Rv0684 fusA1 |
elongation factor G | 710 | 622 | coexpression:434 |
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: phosphoglycerate kinase
- MTBC0 PGAP product: phosphoglycerate kinase
- Pfam (hmmscan --cut_ga): PGK PF00162.25 (E=1e-134)
- (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_215953.1)
- Domains: Pfam-A via hmmscan --cut_ga — PGK (PF00162.25)
- 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
COG0126 - Curated reference: UniProt P9WID1 (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 —
158 functional partner(s); context anchor
tpi - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001537|Rv1437|pgk MSVANLKDLLAEGVSGRGVLVRSDLNVPLDEDGTITDAGRIIASAPTLKALLDADAKVVVAAHLGRPKDGPDPTLSLAPVAVALGEQLGRHVQLAGDVVGADALARAEGLTGGDILLLENIRFDKRETSKNDDDRRALAKQLVELVGTGGVFVSDGFGVVHRKQASVYDIATLLPHYAGTLVADEMRVLEQLTSSTQRPYAVVLGGSKVSDKLGVIESLATKADSIVIGGGMCFTFLAAQGFSVGTSLLEDDMIEVCRGLLETYHDVLRLPVDLVVTEKFAADSPPQTVDVGAVPNGLMGLDIGPGSIKRFSTLLSNAGTIFWNGPMGVFEFPAYAAGTRGVAEAIVAATGKGAFSVVGGGDSAAAVRAMNIPEGAFSHISTGGGASLEYLEGKTLPGIEVLSREQPTGGVL