KpKP13 Protein target profile

tRNA sulfurtransferase

Accession: KP13_03703

Gene: AHE46040.1 thiI 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GKE9
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Length 482
Pocket druggability (P2Rank · AlphaFold DB model) 0.918
Functional annotation 1 EC 12 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.92, FPocket 0.96). Use the 3D pocket comparison to verify whether they identify the same site. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.96. This is a computational pocket signal, not binding validation. Review the complete evidence below

Risks to review

Microbiome similarity 156 of 4744 screened genomes (3.3%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.92) — check the ligand evidence before deprioritizing on off-target risk alone.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. No ligand evidence No experimental PDB ligands, measured ChEMBL bioactivity, or proposed ZINC compound records are available.
Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
No hit
Gut microbiome similarity
3.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
91.14 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.918
Structure A0A0H3GKE9
Pocket Pocket 1
Druggability (FPocket) 0.958
Structure A0A0H3GKE9
Pocket Pocket 1
ColabFold model
P2Rank 0.904 · Pocket 1
FPocket 0.874 · Pocket 28
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 156 / 4744 genomes with a hit
Prevalence 3.3%

Sequence

Primary amino-acid sequence viewer.

MKFIIKLFPEITIKSQSVRLRFIKILTGNIRNVLKNYDETLAVVRHWDHIEVRAKDENQRPAIRDALTRIPGIHHILEVEDVPFTSLHDIFEQTLPLWREALEGKTFCVRVKRRGKHEFTSIEVERYVGGGLNQHIETARVKLTDPDVTVNLEIENDRLLLVKGRYEGIGGFPIGTQEDVLSLISGGFDSGVSSYMLMRRGCRVHYCFFNLGGAAHEIGVRQVAHYLWNRFGSSHRVRFVAINFEPVVGEILEKVDDGQMGVVLKRMMVRAASKVAERYGVQALVTGEALGQVSSQTLTNLRLIDNVSDTLILRPLISHDKEHIIDLAREIGTEDFARTMPEYCGVISKSPTVKAVKAKIEAEEEHFDFSILDKVVEEASNIDIREIAQQTEETVVEVETVTGFGANDAILDIRSIDEQEDKPLKVEGVEVVSLPFYKLSTKFGDLDQSKTWLLWCERGVMSRLQALYLREQGFNNVKVYRP

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 12 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

12
  • GO:0003723 Binding to an RNA molecule or a portion thereof.
  • GO:0052837 The chemical reactions and pathways resulting in the formation of a thiazole, a five-membered heterocyclic ring structure containing a sulfur in the 1-position and a nitrogen in the 3-position.
  • GO:0004810 Catalysis of the reaction: a tRNA precursor + ATP + 2 CTP = a tRNA with a 3' CCA end + 3 diphosphate.
  • GO:0034227 The addition a sulfur atom to a nucleotide in a tRNA molecule.
  • GO:0016783 Catalysis of the transfer of sulfur atoms from one compound (donor) to another (acceptor).
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0000049 Binding to a transfer RNA.
  • GO:0140741 Catalyzes the reaction: ATP + [ThiI sulfur-carrier protein]-S-sulfanyl-L-cysteine + uracil in tRNA + 2 reduced ferredoxin [iron-sulfur] cluster = AMP + diphosphate + 4-thiouracil in tRNA + [ThiI sulfur-carrier protein]-L-cysteine + 2 oxidized ferredoxin [iron-sulfur] cluster.
  • GO:0009228 The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
  • GO:0009229 The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.
  • GO:0002937 The processes whereby a uridine residue in a tRNA is converted to 4-thiouridine. Typically 4-thiouridine is found at position 8, in many transfer RNAs.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
75 165 SMART SM00981 THUMP_a_2
75 165 InterPro IPR004114 THUMP domain
1 174 FunFam G3DSA:3.30.2130.30:FF:000002 tRNA sulfurtransferase
1 174 Gene3D G3DSA:3.30.2130.30 -
397 482 FunFam G3DSA:3.40.250.10:FF:000003 tRNA sulfurtransferase
175 369 Pfam PF02568 Thiamine biosynthesis protein (ThiI)
175 369 InterPro IPR020536 Thil, AANH domain
1 482 Hamap MF_00021 tRNA sulfurtransferase [thiI].
1 482 InterPro IPR003720 tRNA sulfurtransferase ThiI
4 377 NCBIfam TIGR00342 tRNA 4-thiouridine(8) synthase ThiI
4 377 InterPro IPR003720 tRNA sulfurtransferase ThiI
174 372 SUPERFAMILY SSF52402 Adenine nucleotide alpha hydrolases-like
175 396 FunFam G3DSA:3.40.50.620:FF:000029 tRNA sulfurtransferase
61 165 ProSiteProfiles PS51165 THUMP domain profile.
61 165 InterPro IPR004114 THUMP domain
1 399 PANTHER PTHR43209 TRNA SULFURTRANSFERASE
175 395 Gene3D G3DSA:3.40.50.620 HUPs
175 395 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
432 480 ProSiteProfiles PS50206 Rhodanese domain profile.
432 480 InterPro IPR001763 Rhodanese-like domain
396 482 Gene3D G3DSA:3.40.250.10 -
396 482 InterPro IPR036873 Rhodanese-like domain superfamily
28 161 Pfam PF02926 THUMP domain
28 161 InterPro IPR004114 THUMP domain
1 173 SUPERFAMILY SSF143437 THUMP domain-like
2 170 CDD cd11716 THUMP_ThiI
407 481 SUPERFAMILY SSF52821 Rhodanese/Cell cycle control phosphatase
407 481 InterPro IPR036873 Rhodanese-like domain superfamily
180 353 CDD cd01712 ThiI
180 353 InterPro IPR020536 Thil, AANH domain
382 482 NCBIfam TIGR04271 thiazole biosynthesis domain
382 482 InterPro IPR026340 Thiazole biosynthesis domain

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.918
Likely same site as FPocket 10 1.3 Å 29 shared residues 94% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.235
Likely same site as FPocket 1 4.4 Å 13 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.159
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Surrounding area
Pocket 4 P2Rank #4
0.039
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Surrounding area
Pocket 5 P2Rank #5
0.017
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Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #1
0.958 Unusual size
Likely same site as P2Rank 2 4.4 Å 13 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #10
0.704 Unusual size
Likely same site as P2Rank 1 1.3 Å 29 shared residues 94% of smaller site
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Surrounding area
Residue sets
UniProt: Active site:456-456 Cysteine persulfide intermediate
UniProt: Binding site:183-184
UniProt: Binding site:265-265
UniProt: Binding site:287-287
UniProt: Binding site:296-296
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GKE9
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_03703
ColabFold — — full sequence — Loaded

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GKE9