Protein target profile

KP13_03687

Protoheme IX farnesyltransferase

Genome: KpKP13 Gene: cyoE AHE46025.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GKG4
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Length 295
Pocket druggability 0.857
Functional annotation 1 EC 6 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: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.86, P2Rank 0.98). Use the 3D pocket comparison to verify whether they identify the same site. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.86. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.98. Review the complete evidence below

Risks to review

Human similarity Top human hit identity: 37.5%. This target also has a predicted binding pocket (FPocket 0.86) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 125 of 4744 screened genomes (2.6%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.86) — 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
Hit
Human identity (%)
37.5 Lower values reduce human off-target concern.
Human E-value
3.73e-27
Gut microbiome similarity
2.6% 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.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
95.07 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.857
Structure A0A0H3GKG4
Pocket Pocket 1
P2Rank 0.984
Structure A0A0H3GKG4
Pocket Pocket 1
ColabFold model
FPocket 0.762 · Pocket 1
P2Rank 0.985 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 125 / 4744 genomes with a hit
Prevalence 2.6%

Cross-references

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

Sequence

UniProt A0A0H3GKG4

Sequence

Primary amino-acid sequence viewer.

MFKQYLQVTKPGIIFGNLISVIGGFLLASKGHIDYPLFVWTLLGVSLVVASGCVFNNYIDRDIDRKMERTKNRVLVKGLISPEASLVYATLLGIAGFMLLWFGANPLACWLGVMGFVVYVGVYSLYMKRHSVYGTLIGSLSGAAPPVIGYCAVTGDFDSGAAILLAIFSLWQMPHSYAIAIFRFKDYQAANIPVLPVVKGISVAKNHITLYIVAFAVATLMLSLGGYAGYKYLVVAAAVSVWWLGMALRGYKVADDKVWARKLFVFSIVAITALSVMMSVDFMVPDSHSLLAYVR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0016765 Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0008495 Catalysis of the reaction: protoheme IX + (2E,6E)-farnesyl diphosphate + H2O = heme O + diphosphate.
  • GO:0006783 The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0048034 The chemical reactions and pathways resulting in the formation of heme O, a derivative of heme containing a 17-carbon hydroxyethylfarnesyl side chain at position 8 of the tetrapyrrole macrocycle.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

42 records
Show feature table
Start End DB Term Name
5 27 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
32 36 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
37 59 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
234 251 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
3 281 NCBIfam TIGR01473 heme o synthase
3 281 InterPro IPR006369 Protohaem IX farnesyltransferase
133 155 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 283 Hamap MF_00154 Protoheme IX farnesyltransferase [cyoE].
1 283 InterPro IPR006369 Protohaem IX farnesyltransferase
127 132 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
107 126 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
3 281 PANTHER PTHR43448 PROTOHEME IX FARNESYLTRANSFERASE, MITOCHONDRIAL
6 277 CDD cd13957 PT_UbiA_Cox10
6 277 InterPro IPR006369 Protohaem IX farnesyltransferase
12 31 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
37 59 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
80 101 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
263 285 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
133 155 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
156 160 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
232 251 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
107 126 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
18 267 Pfam PF01040 UbiA prenyltransferase family
18 267 InterPro IPR000537 UbiA prenyltransferase family
60 79 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
252 262 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
208 226 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
183 207 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
13 181 Gene3D G3DSA:1.10.357.140 UbiA prenyltransferase
13 181 InterPro IPR044878 UbiA prenyltransferase superfamily
161 182 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
160 182 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
56 78 ProSitePatterns PS00943 UbiA prenyltransferase family signature.
56 78 InterPro IPR030470 UbiA prenyltransferase conserved site
227 231 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
208 230 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
285 295 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
102 106 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
263 284 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
9 163 FunFam G3DSA:1.10.357.140:FF:000001 Protoheme IX farnesyltransferase
80 102 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.

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 · FPocket

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

Site 1 FPocket #1
0.857
Likely same site as P2Rank 1 1.4 Å 46 shared residues 96% of smaller site
Unusual size
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.984
Likely same site as FPocket 1 1.4 Å 46 shared residues 96% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.148
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Surrounding area
Site 3 P2Rank #3
0.098
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Surrounding area
Site 4 P2Rank #4
0.032
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Surrounding area
Site 5 P2Rank #5
0.026
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Surrounding area
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_A0A0H3GKG4
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_03687
ColabFold — — full sequence — Loaded