Protein target profile

VK055_2073

ftsX-like permease family protein

Genome: KpATCC43816 Gene: AIK80679.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GJC4
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Length 804
Pocket druggability 0.984
Functional annotation 0 EC 2 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

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. Second pocket predictor agrees P2Rank predicted binding-site probability 0.89. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 107 of 4744 screened genomes (2.3%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.98) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.98, but this pocket's geometry is unusually large/diffuse compared to this protein's other predicted pockets — may reflect a low-confidence or disordered model region rather than a real cavity.

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
2.3% 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.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
85.42 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 0.984
Structure A0A0H3GJC4
Pocket Pocket 65
P2Rank 0.893
Structure A0A0H3GJC4
Pocket Pocket 1
ColabFold model
FPocket 0.866 · Pocket 4
P2Rank 0.739 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 107 / 4744 genomes with a hit
Prevalence 2.3%

Cross-references

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

Sequence

UniProt A0A0H3GJC4

Sequence

Primary amino-acid sequence viewer.

MIARWFWREWRSPSLLIVWLALSLAVACVLALGSISDRMEKGLSQQSREFMAGDRTLRSSREVPAEWIAQARKSGLTVGEQLSFATMTFAGDTPQLADVKAVDDRYPLYGTLETQPPGLKPQAGSVLLAPRLMALLNLKTGDTIDVGDATLRIAGEVIQEPDAGFNPFQMAPRLMMNMADVAKTGAVQPGSRVAWRYKFAGDAEQLANYEQWLLPKLGPEHRWIGLDQDDSALGKSLERSQQFLLLSALLTLLLAVAAVAVAMSHYCRSRYDLVAILKTLGAGRSQLRKLIVGQWLLLLTLSVITGGVAGLALERLLLLVLKPVLPAALPAASGWPWLWAIGATGVISLLVGLRPYRLLLATLPLRVLRQDVVANVWPLKIWIPAVSVVVVGLLAWLLGGSPLLWSVLAGAVLLALLCGLVGWGLLWLLKRLTLKALPLRLAVNRLLRQPWSTLSQLAAFSLSFMLLALLLVLRGDLLDRWQQQLPPQSPNYFLINIAPEQIVPVKTFLAEHQTRAAEFYPIVRARLTQINGQSTDGNKDEALNRELNLTWSEQRPDHNPLVAGSWPPKPGEVSIEEGLAQRLGIKIGDTVTFTGDTQEFSAKVSSARKVDWESLRPNFFFIFPSGALDGQPQSWLTSFRWDNGPAMLTQLNREFPTVSLLDIGAILRQVGQVLSQVSRALEVMVGLVTACGVLLLLAQVQVGMRQRHQELVVWRTLGAGKSLLRATLWAEFALLGLVSGLVAAIGAEVALAMLQTKVFDFPWAPDWRLWVLLPLTGAVLLSLCGGGLGLRLLKGKALFRQFSQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

2
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

41 records
Show feature table
Start End DB Term Name
333 355 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
732 754 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 28 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile.
1 31 SignalP_EUK SignalP-TM SignalP-TM
13 35 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
769 791 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 14 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
404 429 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
376 398 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
408 430 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
377 398 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
767 793 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
474 682 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
430 449 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
318 336 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
32 242 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 31 Phobius SIGNAL_PEPTIDE Signal peptide region
264 294 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
748 766 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
684 794 Pfam PF02687 FtsX-like permease family
684 794 InterPro IPR003838 ABC3 transporter permease protein domain
248 359 Pfam PF02687 FtsX-like permease family
248 359 InterPro IPR003838 ABC3 transporter permease protein domain
683 702 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
723 747 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
2 799 PANTHER PTHR30287 MEMBRANE COMPONENT OF PREDICTED ABC SUPERFAMILY METABOLITE UPTAKE TRANSPORTER
2 799 InterPro IPR038766 Membrane component of ABC transporter, predicted
357 376 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
703 722 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
243 262 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
27 31 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
451 473 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
243 263 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
794 804 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
291 313 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
399 403 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
15 26 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
295 317 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
337 356 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
450 473 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
676 698 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 #65
0.984
Likely same site as P2Rank 1 3.3 Å 19 shared residues 66% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #64
0.943
Likely same site as P2Rank 4 0.9 Å 19 shared residues 100% of smaller site
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Surrounding area
Site 3 FPocket #66
0.695
Likely same site as P2Rank 3 5.3 Å 16 shared residues 73% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 4 FPocket #61
0.543
Likely same site as P2Rank 1 6.4 Å 14 shared residues 100% of smaller site
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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
0.893
Likely same site as FPocket 65 3.3 Å 19 shared residues 66% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.6
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Surrounding area
Site 3 P2Rank #3
0.583
Likely same site as FPocket 66 5.3 Å 16 shared residues 73% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.547
Likely same site as FPocket 64 0.9 Å 19 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.297
Show in viewer
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_A0A0H3GJC4
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_2073
ColabFold — — full sequence — Loaded