tpi Resolved · high auto-curated
H37Rv Rv1438 · MTBC0 mtbc0_001538 ·
261 aa · 1624929–1625714 (+) ·
RefSeq NP_215954.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | triosephosphate isomerase |
|---|---|
| MTBC0 PGAP re-annotation | triose-phosphate isomerase |
| Revised (this work) | Triose-phosphate isomerase. Pfam: TIM (PF00121.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WG43
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Triosephosphate isomerase |
| EC (curated) |
EC 5.3.1.1
|
| Curated function | Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | tpiA |
| eggNOG description | Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P) |
| Orthologous group | COG0149 |
| EC number |
EC 5.3.1.1
|
| KEGG orthology |
K01803
|
| KEGG pathways |
map00010, map00051, map00562, map00710, map01100, map01110, map01120, map01130, map01200, map01230
|
| KEGG modules |
M00001, M00002, M00003
|
| Gene Ontology (152) |
GO:0003674, GO:0003824, GO:0004807, GO:0005575, GO:0005576, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0005975, GO:0005996 +140 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 | 0.226 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
TIM | PF00121.25 | 1.1e-89 | 5–253 | Triosephosphate isomerase |
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 fusion:900 cooccurence:656 coexpression:963 textmining:832 |
Rv1436 gap |
glyceraldehyde 3-phosphate dehydrogenase | 999 | 1000 ctx | neighborhood:882 fusion:471 cooccurence:680 coexpression:879 experimental:526 database:900 textmining:715 |
Rv0946c pgi |
glucose-6-phosphate isomerase | 995 | 979 | coexpression:851 database:800 textmining:804 |
Rv0363c fba |
fructose-bisphosphate aldolase | 995 | 977 | coexpression:763 database:900 textmining:831 |
Rv1023 eno |
enolase | 985 | 941 | coexpression:858 experimental:476 textmining:762 |
Rv0727c fucA |
L-fuculose phosphate aldolase FucA | 941 | 923 | database:900 |
Rv1448c tal |
transaldolase | 969 | 908 | coexpression:440 database:800 textmining:680 |
Rv1449c tkt |
transketolase | 977 | 907 | coexpression:447 database:800 textmining:769 |
Rv1617 pykA |
pyruvate kinase | 958 | 905 ctx | cooccurence:561 coexpression:781 textmining:576 |
Rv0478 deoC |
2-deoxyribose-5-phosphate aldolase | 881 | 845 | database:800 |
Rv0489 gpm1 |
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | 948 | 824 | coexpression:787 textmining:720 |
Rv1121 zwf1 |
glucose-6-phosphate 1-dehydrogenase | 871 | 818 | database:800 |
Rv1447c zwf2 |
glucose-6-phosphate 1-dehydrogenase | 891 | 814 | database:800 textmining:440 |
Rv3010c pfkA |
6-phosphofructokinase | 945 | 811 | coexpression:707 textmining:725 |
Rv2881c cdsA |
phosphatidate cytidylyltransferase | 811 | 774 | coexpression: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
- Legacy H37Rv annotation: triosephosphate isomerase
- MTBC0 PGAP product: triose-phosphate isomerase
- Pfam (hmmscan --cut_ga): TIM PF00121.25 (E=1e-89)
- (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_215954.1)
- Domains: Pfam-A via hmmscan --cut_ga — TIM (PF00121.25)
- 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
COG0149 - Curated reference: UniProt P9WG43 (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 —
173 functional partner(s); context anchor
pgk - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001538|Rv1438|tpi MSRKPLIAGNWKMNLNHYEAIALVQKIAFSLPDKYYDRVDVAVIPPFTDLRSVQTLVDGDKLRLTYGAQDLSPHDSGAYTGDVSGAFLAKLGCSYVVVGHSERRTYHNEDDALVAAKAATALKHGLTPIVCIGEHLDVREAGNHVAHNIEQLRGSLAGLLAEQIGSVVIAYEPVWAIGTGRVASAADAQEVCAAIRKELASLASPRIADTVRVLYGGSVNAKNVGDIVAQDDVDGGLVGGASLDGEHFATLAAIAAGGPLP