Bacterial thiamine diphosphate biosynthesis

Species-neutral bacterial pathway for de novo synthesis of thiamine diphosphate (ThDP), the active thiamine cofactor. The pathway has two converging branches: a hydroxymethylpyrimidine branch in which ThiC converts an AIR-derived precursor to HMP phosphate and ThiD phosphorylates it to the diphosphate, and a thiazole branch in which Dxs, alternative ThiO or ThiH routes, sulfur-relay proteins, and ThiG form the thiazole phosphate moiety. ThiE couples the pyrimidine and thiazole moieties to thiamine phosphate, and ThiL phosphorylates thiamine phosphate to ThDP. The thiazole branch includes the ThiS sulfur-carrier activation/thiocarboxylation relay rather than treating sulfur delivery as a single enzyme reaction.

MODULE:thiamine_diphosphate_biosynthesisDRAFTMetabolic Pathwaymodules/thiamine_diphosphate_biosynthesis.yaml

thiamine biosynthetic processGO:0009228 thiamine diphosphate biosynthetic processGO:0009229

GO:0009228

thiamine biosynthetic process

GO biological-process term for thiamine biosynthesis; used as the parent process grounding for the module.

GO:0009229

thiamine diphosphate biosynthetic process

GO biological-process term for synthesis of active thiamine diphosphate; used as the specific process grounding for the module.

KEGG:map00730

Thiamine metabolism

KEGG thiamine-metabolism pathway context. The PSEPK map includes de novo thiamine genes plus nucleotide-metabolism and ribosome-biogenesis spillover that require curator filtering.

UniPathway:UPA00060

Thiamine diphosphate biosynthesis

UniPathway pathway context for bacterial thiamine diphosphate biosynthesis used by UniProt metadata for several PSEPK candidate genes.

file:projects/P_PUTIDA/data/psepk_gene_list.tsv

PSEPK UniProt metadata inventory

Local UniProt-derived inventory provides the Pseudomonas putida KT2440 exemplar accessions, GO terms, EC numbers, and PANTHER families used to ground representative members in this module.

file:PSEPK/thiO/thiO-ai-review.yaml

PSEPK thiO gene review

Existing review supports ThiO glycine oxidase activity and its role in supplying glyoxyl imine for thiazole/thiamine biosynthesis.

file:PSEPK/thiI/thiI-ai-review.yaml

PSEPK thiI gene review

Existing review supports ThiI tRNA sulfurtransferase activity and the family-inferred ThiS sulfur-carrier transfer role in thiazole/thiamine biosynthesis, while noting that GO lacks a precise ThiS-transfer MF term.

file:modules/thiamine_diphosphate_biosynthesis-deep-research-openscientist.md

OpenScientist module review for bacterial thiamine diphosphate biosynthesis

Generic module-level retrieval supports the de novo ThDP boundary, separates salvage/transport from the core pathway, and highlights the IscS/ThiF/ThiI/ThiS sulfur-relay order for thiazole synthesis.

file:projects/P_PUTIDA/deep-research/PSEPK__thiamine_diphosphate_biosynthesis__ppu00730-deep-research-openscientist.md

OpenScientist PSEPK ppu00730 thiamine diphosphate biosynthesis review

Species/pathway satisfiability review finds the KT2440 de novo ThDP pathway largely covered, adds PP_5105/ThiS as a missing module member, excludes KEGG overview artifacts such as adk and rsgA, and flags the ThiF-type ThiS adenylylation step as candidate_uncertain because KT2440 lacks a dedicated thiF gene.

This module is narrower than KEGG ppu00730 "Thiamine metabolism": it models de novo ThDP biosynthesis. Adenylate kinase (adk), RsgA, thiamine triphosphatase, aminopyrimidine aminohydrolases, and transport/salvage proteins are pathway neighbors or salvage context rather than required core biosynthetic steps. In P. putida KT2440, PP_5105 encodes the ThiS sulfur carrier and is a likely module member even though it is assigned to KEGG sulfur-relay map ppu04122 rather than ppu00730. The KT2440 ThiF-type ThiS adenylylation enzyme is unresolved: OpenScientist found no dedicated thiF and nominated MoeB/PP_0735 as the only plausible but unconfirmed E1-like substitute, so the module keeps a species-neutral ThiF-family step and records the PSEPK assignment as a curation gap.

13Nodes

10Parts

1Variant Sets

2Variants

12Annotons

10Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

thiamine_diphosphate_biosynthesis-deep-research-openscientist.md (openscientist)

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

thiC_step → thiD_step [NOT_CHECKED]
thiE_coupling_step → thiL_activation_step [NOT_CHECKED]

Function consistency and core coverage

4 gene-function check(s) reflected in core functions · 0 conflict(s) · 19 evidence or coverage gap(s) (23 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

Annoton	Participant	Function	Assessment
phosphomethylpyrimidine_synthase_activity	thiC (Pseudomonas putida KT2440) UniProtKB:Q88DA5 Family Representative	phosphomethylpyrimidine synthase activity GO:0070284	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
phosphomethylpyrimidine_kinase_activity	thiD (Pseudomonas putida KT2440) UniProtKB:Q88DP2 Family Representative	phosphomethylpyrimidine kinase activity GO:0008972	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
dxp_synthase_activity	dxs (Pseudomonas putida KT2440) UniProtKB:Q88QG7 Family Representative	1-deoxy-D-xylulose-5-phosphate synthase activity GO:0008661	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
glycine_oxidase_activity	thiO (Pseudomonas putida KT2440) UniProtKB:Q88Q83 Family Representative	glycine oxidase activity GO:0043799	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
glycine_oxidase_activity	thiO (Bacillus subtilis 168) UniProtKB:O31616 Family Representative	glycine oxidase activity GO:0043799	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
iminoacetate_synthase_activity	thiH (Escherichia coli K-12) UniProtKB:P30140 Family Representative	2-iminoacetate synthase activity GO:0036355	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cysteine_desulfurase_activity	iscS (Pseudomonas putida KT2440) UniProtKB:Q88PK8 Family Representative	cysteine desulfurase activity GO:0031071	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cysteine_desulfurase_activity	iscS-II (Pseudomonas putida KT2440) UniProtKB:Q88K56 Family Representative	cysteine desulfurase activity GO:0031071	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
thiF_this_adenylylation_activity	thiF (Escherichia coli K-12) UniProtKB:P30138 Family Representative	ThiS ubiquitin-like sulfur-carrier activating enzyme activity GO:0008641	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
thiS_sulfur_carrier_role	ThiS sulfur carrier protein (Pseudomonas putida KT2440) UniProtKB:Q88CS5 Gene	sulfur carrier activity GO:0097163	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
thiazole_synthase_activity	thiG (Pseudomonas putida KT2440) UniProtKB:Q88CS6 Family Representative	thiazole synthase activity GO:1990107	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
thiamine_phosphate_diphosphorylase_activity	thiE (Pseudomonas putida KT2440) UniProtKB:Q88DP1 Family Representative	thiamine-phosphate diphosphorylase activity GO:0004789	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
thiamine_phosphate_kinase_activity	thiL (Pseudomonas putida KT2440) UniProtKB:Q88QH4 Family Representative	thiamine-phosphate kinase activity GO:0009030	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
phosphomethylpyrimidine_synthase_activity	ThiC phosphomethylpyrimidine synthase family PANTHER:PTHR30557 Family	phosphomethylpyrimidine synthase activity GO:0070284	Family Review Missing No supported structured family review is available for PANTHER:PTHR30557.
phosphomethylpyrimidine_kinase_activity	ThiD hydroxymethylpyrimidine/phosphomethylpyrimidine kinase family PANTHER:PTHR20858 Family	phosphomethylpyrimidine kinase activity GO:0008972	Family Scope Restricted GO:0008972 is SUBFAMILY_ONLY; this family grounding does not establish the allowed subfamily scope. ThiD/THI20 subfamilies, as both thiamine modules assert on the base family. THI22 is a member exception.
dxp_synthase_activity	Dxs 1-deoxy-D-xylulose-5-phosphate synthase family PANTHER:PTHR43322 Family	1-deoxy-D-xylulose-5-phosphate synthase activity GO:0008661	Family Review Missing No supported structured family review is available for PANTHER:PTHR43322.
glycine_oxidase_activity	ThiO glycine oxidase family PANTHER:PTHR13847:SF289 Family	glycine oxidase activity GO:0043799	Family Function Unreviewed The family review has no applicable adjudication supporting or excluding GO:0043799.
iminoacetate_synthase_activity	ThiH 2-iminoacetate synthase family PANTHER:PTHR43583:SF1 Family	2-iminoacetate synthase activity GO:0036355	Family Review Missing No supported structured family review is available for PANTHER:PTHR43583:SF1.
cysteine_desulfurase_activity	IscS cysteine desulfurase family PANTHER:PTHR11601 Family	cysteine desulfurase activity GO:0031071	Family Scope Restricted GO:0031071 is SUBFAMILY_ONLY; this family grounding does not establish the allowed subfamily scope. Cysteine desulfurase activity is experimentally established for SF34 members in bacteria (E. coli IscS) and eukaryotes (NFS1) and is the shared chemistry of the small bacterial SF36 and SF50 groups. It is excluded from the selenocysteine lyase subfamily SF62, which is specific for L-selenocysteine.
thiF_this_adenylylation_activity	ThiF sulfur carrier protein ThiS adenylyltransferase subfamily PANTHER:PTHR10953:SF240 Family	ThiS ubiquitin-like sulfur-carrier activating enzyme activity GO:0008641	Family Function Unreviewed Family review leaves GO:0008641 UNRESOLVED. GO defines this activity as activation of a ubiquitin-like protein through formation of an ATP-dependent high-energy thiolester bond. The eukaryotic E1 and ATG7 subfamilies meet that definition. The bacterial ThiF (SF240) and MoeB (SF194) enzymes adenylate their ubiquitin-fold carriers (ThiS, MoaD), but for MoeB no E1-like thioester intermediate was observed. Whether ThiF forms a thioester with ThiS was not adjudicated here, so the term is not granted to SF240 or SF194.
thiazole_synthase_activity	ThiG thiazole synthase family PANTHER:PTHR34266 Family	thiazole synthase activity GO:1990107	Family Review Missing No supported structured family review is available for PANTHER:PTHR34266.
thiamine_phosphate_diphosphorylase_activity	ThiE thiamine-phosphate synthase family PANTHER:PTHR20857 Family	thiamine-phosphate diphosphorylase activity GO:0004789	Family Scope Restricted GO:0004789 is SUBFAMILY_ONLY; this family grounding does not establish the allowed subfamily scope. ThiE (SF15) and bifunctional THI6 (SF23). eukaryotic_thiamine_biosynthesis selects SF23; thiamine_diphosphate_biosynthesis selects the base family, which also takes in TenI.
thiamine_phosphate_kinase_activity	ThiL thiamine-phosphate kinase family PANTHER:PTHR30270 Family	thiamine-phosphate kinase activity GO:0009030	Family Review Missing No supported structured family review is available for PANTHER:PTHR30270.

Gene-review completeness (5/14 grounded genes reviewed)

4 complete review(s) · 4 with deep research · 9 missing review · 1 reviewed but lacking deep research

Gene	Review	Complete	Deep research
dxs Q88QG7	✓	✓	✓
iscS Q88PK8	✓	5/6	✓
thiO (Bacillus subtilis 168) O31616	✗	—	—
thiF (Escherichia coli K-12) P30138	✗	—	—
ThiS sulfur carrier protein (Pseudomonas putida KT2440) Q88CS5	✗	—	—
thiG (Pseudomonas putida KT2440) Q88CS6	✗	—	—
thiC (Pseudomonas putida KT2440) Q88DA5	✗	—	—
thiE (Pseudomonas putida KT2440) Q88DP1	✗	—	—
thiD (Pseudomonas putida KT2440) Q88DP2	✗	—	—
iscS-II (Pseudomonas putida KT2440) Q88K56	✗	—	—
thiL (Pseudomonas putida KT2440) Q88QH4	✗	—	—
thiH P30140	✓	✓	✗
thiI Q88CY4	✓	✓	✓
thiO Q88Q83	✓	✓	✓

Tree

Thiamine diphosphate biosynthesisMetabolic Pathwaythiamine_diphosphate_biosynthesis

Parts
1. 1. hydroxymethylpyrimidine branch
2. Hydroxymethylpyrimidine diphosphate branchMetabolic Pathwayhmp_branch
  
  Parts
  1. 1. HMP phosphate formation
  2. AIR-derived precursor to HMP phosphateReactionthiC_step
    
    Annotons
    
    ThiC: phosphomethylpyrimidine synthase Family: ThiC phosphomethylpyrimidine synthase family
  3. 2. HMP phosphate activation
  4. HMP phosphate to HMP diphosphateReactionthiD_step
    
    Annotons
    
    ThiD: phosphomethylpyrimidine kinase Family: ThiD hydroxymethylpyrimidine/phosphomethylpyrimidine kinase family
3. 2. thiazole branch
4. Thiazole phosphate branchMetabolic Pathwaythiazole_branch
  
  Parts
  1. 1. DXP precursor supply
  2. DXP formationReactiondxs_step
    
    Annotons
    
    Dxs: 1-deoxy-D-xylulose-5-phosphate synthase Family: Dxs 1-deoxy-D-xylulose-5-phosphate synthase family
  3. 2. dehydroglycine supply
  4. Alternative dehydroglycine supply routesReactiondehydroglycine_supply
    
    Variants
    
    Dehydroglycine-generating enzyme route by lineage and oxygen-dependent enzyme route (One Or More)
    
    Glycine oxidation to 2-iminoacetateReactionthiO_step
    
    Annotons
    
    ThiO: glycine oxidase Family: ThiO glycine oxidase family
    
    Tyrosine cleavage to 2-iminoacetateReactionthiH_step
    
    Annotons
    
    ThiH: 2-iminoacetate synthase Family: ThiH 2-iminoacetate synthase family
  5. 3. sulfur mobilization and ThiS thiocarboxylation
  6. ThiS sulfur-carrier thiocarboxylationMetabolic Pathwaythis_sulfur_relay
    
    Annotons
    
    IscS: cysteine desulfurase sulfur donor Family: IscS cysteine desulfurase family
    
    ThiF: ThiS sulfur-carrier activation Family: ThiF sulfur carrier protein ThiS adenylyltransferase subfamily
    
    ThiI: sulfur transfer to ThiS Family: ThiI tRNA/ThiS sulfurtransferase family
    
    ThiS: sulfur carrier protein Gene Product: ThiS sulfur carrier protein (Pseudomonas putida KT2440)
  7. 4. thiazole phosphate formation
  8. Thiazole phosphate synthesisReactionthiG_step
    
    Annotons
    
    ThiG: thiazole synthase Family: ThiG thiazole synthase family
5. 3. pyrimidine-thiazole coupling
6. HMP diphosphate plus thiazole phosphate to thiamine phosphateReactionthiE_coupling_step
  
  Annotons
  - ThiE: thiamine-phosphate diphosphorylase Family: ThiE thiamine-phosphate synthase family
7. 4. thiamine diphosphate activation
8. Thiamine phosphate to thiamine diphosphateReactionthiL_activation_step
  
  Annotons
  - ThiL: thiamine-phosphate kinase Family: ThiL thiamine-phosphate kinase family

Details

Thiamine diphosphate biosynthesisMetabolic Pathwaythiamine_diphosphate_biosynthesis

thiamine biosynthetic processGO:0009228 thiamine diphosphate biosynthetic processGO:0009229

Connections

thiC_step -> thiD_step Precedes

dxs_step -> thiG_step Provides Input For

dehydroglycine_supply -> thiG_step Provides Input For

cysteine_desulfurase_activity -> thiI_this_sulfurtransfer_role Provides Input For

thiF_this_adenylylation_activity -> thiI_this_sulfurtransfer_role Provides Input For

thiI_this_sulfurtransfer_role -> thiS_sulfur_carrier_role Provides Input For

thiS_sulfur_carrier_role -> thiG_step Provides Input For

thiD_step -> thiE_coupling_step Provides Input For

thiG_step -> thiE_coupling_step Provides Input For

thiE_coupling_step -> thiL_activation_step Precedes

Part 1: hydroxymethylpyrimidine branch

Hydroxymethylpyrimidine diphosphate branchMetabolic Pathwayhmp_branch

Produces the activated pyrimidine moiety, HMP diphosphate, for coupling to thiazole phosphate.

Part 1: HMP phosphate formation

AIR-derived precursor to HMP phosphateReactionthiC_step

Annotons

ThiC: phosphomethylpyrimidine synthase

phosphomethylpyrimidine_synthase_activity

Participant: Family: ThiC phosphomethylpyrimidine synthase family

Family:

ThiC phosphomethylpyrimidine synthase familyPANTHER:PTHR30557

Representative Members: thiC (Pseudomonas putida KT2440)UniProtKB:Q88DA5

Function

phosphomethylpyrimidine synthase activityGO:0070284

Substrates: 5-aminoimidazole ribonucleotide-derived precursor

Products: 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate

Cofactors: iron-sulfur cluster

Forms the phosphorylated HMP pyrimidine moiety.

Part 2: HMP phosphate activation

HMP phosphate to HMP diphosphateReactionthiD_step

Annotons

ThiD: phosphomethylpyrimidine kinase

phosphomethylpyrimidine_kinase_activity

Participant: Family: ThiD hydroxymethylpyrimidine/phosphomethylpyrimidine kinase family

Family:

ThiD hydroxymethylpyrimidine/phosphomethylpyrimidine kinase familyPANTHER:PTHR20858

Representative Members: thiD (Pseudomonas putida KT2440)UniProtKB:Q88DP2

Function

phosphomethylpyrimidine kinase activityGO:0008972

Substrates: 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate ATP

Products: 4-amino-5-hydroxymethyl-2-methylpyrimidine diphosphate ADP

Activates HMP phosphate to the diphosphate used by ThiE.

ThiD-family enzymes may also support HMP salvage via hydroxymethylpyrimidine kinase activity; this annoton represents the de novo HMP-P to HMP-PP step.

Part 2: thiazole branch

Thiazole phosphate branchMetabolic Pathwaythiazole_branch

Produces the thiazole phosphate moiety from DXP, ThiO- or ThiH-derived 2-iminoacetate, and sulfur carried through IscS/ThiI/ThiS.

Part 1: DXP precursor supply

DXP formationReactiondxs_step

Annotons

Dxs: 1-deoxy-D-xylulose-5-phosphate synthase

dxp_synthase_activity

Participant: Family: Dxs 1-deoxy-D-xylulose-5-phosphate synthase family

Family:

Dxs 1-deoxy-D-xylulose-5-phosphate synthase familyPANTHER:PTHR43322

Representative Members: dxs (Pseudomonas putida KT2440)UniProtKB:Q88QG7

Function

1-deoxy-D-xylulose-5-phosphate synthase activityGO:0008661

Substrates: pyruvate D-glyceraldehyde 3-phosphate

Products: 1-deoxy-D-xylulose 5-phosphate carbon dioxide

Supplies DXP, the carbon precursor for the thiazole moiety.

DXP is also used in non-mevalonate isoprenoid biosynthesis; the Dxs step is substrate supply for this module rather than a thiamine-specific commitment step.

Part 2: dehydroglycine supply

Alternative dehydroglycine supply routesReactiondehydroglycine_supply

Supplies the 2-iminoacetate (dehydroglycine) input to ThiG through oxygen-dependent ThiO or radical-SAM ThiH chemistry.

Variant set: Dehydroglycine-generating enzyme route by lineage and oxygen-dependent enzyme route (One Or More)

Glycine oxidation to 2-iminoacetateReactionthiO_step

Annotons

ThiO: glycine oxidase

glycine_oxidase_activity

Participant: Family: ThiO glycine oxidase family

Family:

ThiO glycine oxidase familyPANTHER:PTHR13847:SF289

Representative Members: thiO (Pseudomonas putida KT2440)UniProtKB:Q88Q83 thiO (Bacillus subtilis 168)UniProtKB:O31616

Function

glycine oxidase activityGO:0043799

Substrates: glycine oxygen

Products: 2-iminoacetate (dehydroglycine) hydrogen peroxide

Cofactors: FAD

Supplies 2-iminoacetate from glycine under oxic conditions. PTHR13847:SF289 also contains proteins annotated with other functions, so the exact MF and reviewed exemplars constrain this role; no glycine-oxidase PAINT node is asserted.

Tyrosine cleavage to 2-iminoacetateReactionthiH_step

Annotons

ThiH: 2-iminoacetate synthase

iminoacetate_synthase_activity

Participant: Family: ThiH 2-iminoacetate synthase family

Family:

ThiH 2-iminoacetate synthase familyPANTHER:PTHR43583:SF1

Representative Members: thiH (Escherichia coli K-12)UniProtKB:P30140

Function

2-iminoacetate synthase activityGO:0036355

Substrates: L-tyrosine S-adenosyl-L-methionine

Products: 2-iminoacetate (dehydroglycine) 4-methylphenol (p-cresol)

Cofactors: 4Fe-4S cluster

Supplies 2-iminoacetate from tyrosine through oxygen-sensitive radical-SAM chemistry.

Part 3: sulfur mobilization and ThiS thiocarboxylation

ThiS sulfur-carrier thiocarboxylationMetabolic Pathwaythis_sulfur_relay

Annotons

IscS: cysteine desulfurase sulfur donor

cysteine_desulfurase_activity

Participant: Family: IscS cysteine desulfurase family

Family:

IscS cysteine desulfurase familyPANTHER:PTHR11601

Representative Members: iscS (Pseudomonas putida KT2440)UniProtKB:Q88PK8 iscS-II (Pseudomonas putida KT2440)UniProtKB:Q88K56

Function

cysteine desulfurase activityGO:0031071

Substrates: L-cysteine

Products: enzyme-bound persulfide sulfur L-alanine

Mobilizes sulfur as persulfide for ThiI-mediated ThiS thiocarboxylation.

P. putida KT2440 encodes iscS and iscS-II candidates; the exact thiamine-branch contributor should be checked in full gene reviews.

ThiF: ThiS sulfur-carrier activation

thiF_this_adenylylation_activity

Participant: Family: ThiF sulfur carrier protein ThiS adenylyltransferase subfamily

Family:

ThiF sulfur carrier protein ThiS adenylyltransferase subfamilyPANTHER:PTHR10953:SF240

Representative Members: thiF (Escherichia coli K-12)UniProtKB:P30138

Function

ThiS ubiquitin-like sulfur-carrier activating enzyme activityGO:0008641

Substrates: ThiS C-terminal glycine ATP

Products: adenylylated ThiS diphosphate

Activates the ThiS C-terminus by ATP-dependent adenylylation before sulfur transfer and thiocarboxylate formation.

P. putida KT2440 lacks a dedicated thiF gene. MoeB/PP_0735 is an E1-like PTHR10953 paralog and the only plausible local substitute identified by OpenScientist, but it remains a candidate_uncertain member until full gene review or experiment resolves whether it activates ThiS in vivo.

ThiI: sulfur transfer to ThiS

thiI_this_sulfurtransfer_role

Participant: Family: ThiI tRNA/ThiS sulfurtransferase family

Family:

ThiI tRNA/ThiS sulfurtransferase familyPANTHER:PTHR43209

Representative Members: thiI (Pseudomonas putida KT2440)UniProtKB:Q88CY4

Processes

thiazole biosynthetic processGO:0052837

Transfers sulfur to the ThiS sulfur carrier to form ThiS thiocarboxylate for thiazole biosynthesis.

file:PSEPK/thiI/thiI-ai-review.yaml

Existing PSEPK review accepts the family-inferred ThiI role in thiazole biosynthesis and notes the missing precise ThiS-transfer MF term.

GO currently lacks the precise ThiS sulfur-carrier protein sulfurtransferase MF proposed in the PSEPK thiI review, so this role is represented by the specific thiazole process and curator notes rather than a broad sulfurtransferase MF.

ThiS: sulfur carrier protein

thiS_sulfur_carrier_role

Participant: Gene Product: ThiS sulfur carrier protein (Pseudomonas putida KT2440)

Gene Product:

ThiS sulfur carrier protein (Pseudomonas putida KT2440)UniProtKB:Q88CS5

Function

sulfur carrier activityGO:0097163

Targets: thiazole synthase reaction

Cargo: sulfur

Processes

thiazole biosynthetic processGO:0052837

Carries activated sulfur for ThiG-mediated thiazole phosphate formation.

PP_5105 is assigned to KEGG sulfur-relay map ppu04122 in the local partition but is a likely missing ppu00730 member for the thiazole branch.

Part 4: thiazole phosphate formation

Thiazole phosphate synthesisReactionthiG_step

Annotons

ThiG: thiazole synthase

thiazole_synthase_activity

Participant: Family: ThiG thiazole synthase family

Family:

ThiG thiazole synthase familyPANTHER:PTHR34266

Representative Members: thiG (Pseudomonas putida KT2440)UniProtKB:Q88CS6

Function

thiazole synthase activityGO:1990107

Substrates: 1-deoxy-D-xylulose 5-phosphate glyoxyl imine ThiS-thiocarboxylate

Products: 4-methyl-5-(2-phosphooxyethyl)thiazole

Forms the activated thiazole phosphate moiety.

Part 3: pyrimidine-thiazole coupling

HMP diphosphate plus thiazole phosphate to thiamine phosphateReactionthiE_coupling_step

Annotons

ThiE: thiamine-phosphate diphosphorylase

thiamine_phosphate_diphosphorylase_activity

Participant: Family: ThiE thiamine-phosphate synthase family

Family:

ThiE thiamine-phosphate synthase familyPANTHER:PTHR20857

Representative Members: thiE (Pseudomonas putida KT2440)UniProtKB:Q88DP1

Function

thiamine-phosphate diphosphorylase activityGO:0004789

Substrates: HMP diphosphate thiazole phosphate

Products: thiamine phosphate diphosphate

Couples the pyrimidine and thiazole moieties to form thiamine phosphate.

Part 4: thiamine diphosphate activation

Thiamine phosphate to thiamine diphosphateReactionthiL_activation_step

Annotons

ThiL: thiamine-phosphate kinase

thiamine_phosphate_kinase_activity

Participant: Family: ThiL thiamine-phosphate kinase family

Family:

ThiL thiamine-phosphate kinase familyPANTHER:PTHR30270

Representative Members: thiL (Pseudomonas putida KT2440)UniProtKB:Q88QH4

Function

thiamine-phosphate kinase activityGO:0009030

Substrates: thiamine phosphate ATP

Products: thiamine diphosphate ADP

Cofactors: magnesium ion

Produces the active cofactor thiamine diphosphate.