gap Resolved · high auto-curated
H37Rv Rv1436 · MTBC0 mtbc0_001536 ·
339 aa · 1622672–1623691 (+) ·
RefSeq NP_215952.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glyceraldehyde 3-phosphate dehydrogenase |
|---|---|
| MTBC0 PGAP re-annotation | type I glyceraldehyde-3-phosphate dehydrogenase |
| Revised (this work) | Type I glyceraldehyde-3-phosphate dehydrogenase. Pfam: Gp_dh_N (PF00044.31), Gp_dh_C (PF02800.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WN83
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glyceraldehyde-3-phosphate dehydrogenase |
| EC (curated) |
EC 1.2.1.12
|
| Curated function | Catalyzes the oxidative phosphorylation of glyceraldehyde 3-phosphate (G3P) to 1,3-bisphosphoglycerate (BPG) using the cofactor NAD. The first reaction step involves the formation of a hemiacetal intermediate between G3P and a cysteine residue, and this hemiacetal intermediate is then oxidized to a thioester, with concomitant reduction of NAD to NADH. The reduced NADH is then exchanged with the second NAD, and the thioester is attacked by a nucleophilic inorganic phosphate to produce BPG. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | gap |
| eggNOG description | Belongs to the glyceraldehyde-3-phosphate dehydrogenase family |
| Orthologous group | COG0136 |
| EC number |
EC 1.2.1.12
|
| KEGG orthology |
K00134
|
| KEGG pathways |
map00010, map00710, map01100, map01110, map01120, map01130, map01200, map01230, map04066, map05010
|
| KEGG modules |
M00001, M00002, M00003, M00165, M00166, M00308, M00552
|
| Gene Ontology (34) |
GO:0000166, GO:0003674, GO:0003824, GO:0004365, GO:0005488, GO:0005575, GO:0005576, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829 +22 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 0 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 |
|---|---|---|---|---|
Gp_dh_N | PF00044.31 | 3.0e-31 | 3–109 | Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain |
Gp_dh_C | PF02800.26 | 5.2e-68 | 163–318 | Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pgk (phosphoglycerate kinase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1437 pgk |
phosphoglycerate kinase | 999 | 1000 ctx | neighborhood:882 cooccurence:731 coexpression:920 experimental:464 database:900 textmining:807 |
Rv1438 tpi |
triosephosphate isomerase | 999 | 1000 ctx | neighborhood:882 fusion:471 cooccurence:680 coexpression:879 experimental:526 database:900 textmining:715 |
Rv0363c fba |
fructose-bisphosphate aldolase | 992 | 982 | coexpression:793 database:900 textmining:573 |
Rv1023 eno |
enolase | 990 | 966 ctx | cooccurence:591 coexpression:842 experimental:474 textmining:745 |
Rv0946c pgi |
glucose-6-phosphate isomerase | 981 | 955 | coexpression:724 database:800 textmining:620 |
Rv1449c tkt |
transketolase | 960 | 934 | coexpression:564 database:800 textmining:429 |
Rv1617 pykA |
pyruvate kinase | 948 | 901 ctx | cooccurence:560 coexpression:735 textmining:497 |
Rv1121 zwf1 |
glucose-6-phosphate 1-dehydrogenase | 951 | 899 | coexpression:436 database:800 textmining:540 |
Rv1447c zwf2 |
glucose-6-phosphate 1-dehydrogenase | 953 | 898 | coexpression:428 database:800 textmining:560 |
Rv1448c tal |
transaldolase | 952 | 888 | coexpression:445 database:800 textmining:593 |
Rv0478 deoC |
2-deoxyribose-5-phosphate aldolase | 861 | 829 | database:800 |
Rv1240 mdh |
malate dehydrogenase | 833 | 783 | coexpression:740 |
Rv2606c snzP |
pyridoxine biosynthesis protein | 810 | 782 ctx | fusion:757 |
Rv3010c pfkA |
6-phosphofructokinase | 903 | 775 | coexpression:648 textmining:590 |
Rv3397c phyA |
phytoene synthase | 793 | 771 | coexpression:768 |
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: glyceraldehyde 3-phosphate dehydrogenase
- MTBC0 PGAP product: type I glyceraldehyde-3-phosphate dehydrogenase
- Pfam (hmmscan --cut_ga): Gp_dh_N PF00044.31 (E=3e-31), Gp_dh_C PF02800.26 (E=5e-68)
- (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_215952.1)
- Domains: Pfam-A via hmmscan --cut_ga — Gp_dh_N (PF00044.31), Gp_dh_C (PF02800.26)
- 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
COG0136 - Curated reference: UniProt P9WN83 (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 —
169 functional partner(s); context anchor
pgk - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001536|Rv1436|gap MTVRVGINGFGRIGRNFYRALLAQQEQGTADVEVVAANDITDNSTLAHLLKFDSILGRLPCDVGLEGDDTIVVGRAKIKALAVREGPAALPWGDLGVDVVVESTGLFTNAAKAKGHLDAGAKKVIISAPATDEDITIVLGVNDDKYDGSQNIISNASCTTNCLAPLAKVLDDEFGIVKGLMTTIHAYTQDQNLQDGPHKDLRRARAAALNIVPTSTGAAKAIGLVMPQLKGKLDGYALRVPIPTGSVTDLTVDLSTRASVDEINAAFKAAAEGRLKGILKYYDAPIVSSDIVTDPHSSIFDSGLTKVIDDQAKVVSWYDNEWGYSNRLVDLVTLVGKSL