Protein target profile

KP13_00579

1,4-dihydroxy-2-naphthoate octaprenyltransferase

Genome: KpKP13 Gene: AHE47054.1 menA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GGB8
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Length 306
Pocket druggability 0.995
Functional annotation 1 EC 7 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 0.99, P2Rank 0.99). 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 0.99. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.99. Review the complete evidence below

Risks to review

Low human similarity A human hit was flagged, but identity is only 28.947% - a weak match, lower risk than a close homolog. This target also has a predicted binding pocket (FPocket 0.99) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 128 of 4744 screened genomes (2.7%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.99) — 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 (%)
28.947 Lower values reduce human off-target concern.
Human E-value
2.74e-20
Gut microbiome similarity
2.7% 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
93.19 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 0.995
Structure A0A0H3GGB8
Pocket Pocket 1
P2Rank 0.992
Structure A0A0H3GGB8
Pocket Pocket 1
ColabFold model
FPocket 0.998 · Pocket 1
P2Rank 0.992 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 128 / 4744 genomes with a hit
Prevalence 2.7%

Cross-references

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

Sequence

UniProt A0A0H3GGB8

Sequence

Primary amino-acid sequence viewer.

MTDISRSQAWLESLRPKTLPLAFAAIIVGTVLAWEQGHFDPWVALLALITAGLLQILSNLANDYGDAVKGSDKPDRIGPLRGMQKGVITPQQMKRALIVTVVLICLFGLALLCAAWQSVGDFIGFLALGGLSIVAAITYTVGTRPYGYIGLGDISVLVFFGWLSVLGSWYLQAHNVEAAIFLPATACGLLATAVLNINNLRDIDSDRQNGKNTLAVRLGPVNARRYHACLLLGALLCLALFNLLALHSAWGWLFILATPLLVKQARYVLRESDPLAMRPMLEKTVKGALLTNLLFVIGIIASKLMA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0004659 Catalysis of the transfer of a prenyl group from one compound (donor) to another (acceptor).
  • GO:0009234 The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.
  • GO:0046428 Catalysis of the reaction: 1,4-dihydroxy-2-naphthoate + an all-trans-polyprenyl diphosphate + H+ = a 2-demethylmenaquinol + CO2 + diphosphate.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0016765 Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
  • 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:0042371 The chemical reactions and pathways resulting in the formation of any of the forms of vitamin K, quinone-derived vitamins which are involved in the synthesis of blood-clotting factors in mammals.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

43 records
Show feature table
Start End DB Term Name
154 172 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
182 305 Gene3D G3DSA:1.20.120.1780 UbiA prenyltransferase
62 95 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
146 168 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
178 200 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
306 306 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
245 249 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 17 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
3 303 PANTHER PTHR13929 1,4-DIHYDROXY-2-NAPHTHOATE OCTAPRENYLTRANSFERASE
3 303 InterPro IPR026046 UbiA prenyltransferase domain containing protein 1
173 177 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
15 176 Gene3D G3DSA:1.10.357.140 UbiA prenyltransferase
15 176 InterPro IPR044878 UbiA prenyltransferase superfamily
178 197 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
29 33 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
11 298 CDD cd13962 PT_UbiA_UBIAD1
11 298 InterPro IPR026046 UbiA prenyltransferase domain containing protein 1
250 269 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
143 153 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
289 305 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
24 267 Pfam PF01040 UbiA prenyltransferase family
24 267 InterPro IPR000537 UbiA prenyltransferase family
5 299 Hamap MF_01937 1,4-dihydroxy-2-naphthoate octaprenyltransferase [menA].
5 299 InterPro IPR004657 1,4-dihydroxy-2-naphthoate octaprenyltransferase
198 225 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
270 288 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
96 117 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
226 244 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
231 253 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
287 304 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
34 42 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
123 142 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
13 32 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
2 304 PIRSF PIRSF005355 UBIAD1
2 304 InterPro IPR026046 UbiA prenyltransferase domain containing protein 1
122 141 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
42 61 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 33 Phobius SIGNAL_PEPTIDE Signal peptide region
118 122 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
18 28 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
15 298 NCBIfam TIGR00751 1,4-dihydroxy-2-naphthoate octaprenyltransferase
43 61 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
96 118 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
0.995
Likely same site as P2Rank 1 2.0 Å 58 shared residues 95% 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
0.992
Likely same site as FPocket 1 2.0 Å 58 shared residues 95% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.041
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Surrounding area
Site 3 P2Rank #3
0.041
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Surrounding area
Site 4 P2Rank #4
0.034
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Surrounding area
Site 5 P2Rank #5
0.013
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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_A0A0H3GGB8
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_00579
ColabFold — — full sequence — Loaded