KpKP13 Protein target profile

General secretion pathway protein F

Accession: KP13_01839

Gene: pulF AHE46279.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GJJ6
Length 404
Pocket druggability (P2Rank · AlphaFold DB model) 0.091
Direct ligand evidence 0 51 total records
Functional annotation 0 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.

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
0.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
52.84 Higher values support similarity to known essential genes.
DEG E-value
1.04e-151 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
86.26 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) 0.091
Structure A0A0H3GJJ6
Pocket Pocket 1
Druggability (FPocket) 0.906
Structure A0A0H3GJJ6
Pocket Pocket 21
ColabFold model
P2Rank 0.135 · Pocket 1
FPocket 0.408 · Pocket 5
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 30 / 4744 genomes with a hit
Prevalence 0.6%

Sequence

Primary amino-acid sequence viewer.

MALFRYQALDAQGKTRRGLQQADSARHARQLLRDKGWLALEVTTADPARRLWAGGSLTRRTSAGDLALLTRQLATLVAAGIPLEKALDAVAQQCEKPSLRTLMAGVRSKVLEGHSLAEAMRGYPACFDGLFCAMVAAGETSGHLDGVLNRLADYTEQRQQLRARLLQAMIYPIVLTLVAISVIAILLSTVVPKVVEQFVHLKQALPFSTRLLMSLSDIVRSAGPWLALLSLLALLALRYLLRQPARRLAWDRALLRLPVIGRVARSVNSARYARTLSILNASAVPLLLSMRISADVLSNAWARSQLAAASESVREGVSLHRALESTALFPPMMRYMIASGEQSGELTAMLERAAENQDRELSAQIQMALSLFEPLLVVTMAGMVLFIVLAILQPILQLNTLMSM

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

6
  • GO:0009306 The controlled release of proteins from a cell.
  • GO:0015627 A large protein complex, containing 12-15 subunits, that spans the cell envelope of Gram-negative bacteria and mediates the movement of proteins into the extracellular environment. The complex includes a component in the cytoplasm, an inner membrane subcomplex that reaches into the periplasmic compartment and a secretion pore in the outer membrane. Proteins using the Type II pathway are transported across the cytoplasmic membrane by the Sec or Tat complex.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0015628 The process in which proteins are secreted across the outer membrane of Gram-negative bacteria by the type II secretion system. Proteins using this pathway are first translocated across the cytoplasmic membrane via the Sec or Tat pathways.
  • 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:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

35 records
Show feature table
Start End DB Term Name
222 241 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
255 368 Gene3D G3DSA:1.20.81.30 Type II secretion system (T2SS), domain F
255 368 InterPro IPR042094 Type II secretion system GspF domain superfamily
144 164 Coils Coil Coil
383 402 PRINTS PR00812 Bacterial general secretion pathway protein F signature
383 402 InterPro IPR003004 GspF/PilC family
65 77 PRINTS PR00812 Bacterial general secretion pathway protein F signature
65 77 InterPro IPR003004 GspF/PilC family
164 192 PRINTS PR00812 Bacterial general secretion pathway protein F signature
164 192 InterPro IPR003004 GspF/PilC family
367 381 PRINTS PR00812 Bacterial general secretion pathway protein F signature
367 381 InterPro IPR003004 GspF/PilC family
4 401 NCBIfam TIGR02120 type II secretion system inner membrane protein GspF
4 401 InterPro IPR011850 Type II secretion system protein GspF
164 192 ProSitePatterns PS00874 Bacterial type II secretion system protein F signature.
164 192 InterPro IPR001992 T2SS_GspF/T4SS_PilC conserved site
242 374 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
222 241 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
55 171 Gene3D G3DSA:1.20.81.30 Type II secretion system (T2SS), domain F
55 171 InterPro IPR042094 Type II secretion system GspF domain superfamily
168 191 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
168 190 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
255 371 FunFam G3DSA:1.20.81.30:FF:000001 Type II secretion system protein F
70 192 Pfam PF00482 Type II secretion system (T2SS), protein F
70 192 InterPro IPR018076 Type II secretion system protein GspF domain
273 393 Pfam PF00482 Type II secretion system (T2SS), protein F
273 393 InterPro IPR018076 Type II secretion system protein GspF domain
397 404 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
375 396 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
192 221 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 167 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
374 396 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 402 PANTHER PTHR30012 GENERAL SECRETION PATHWAY PROTEIN
1 402 InterPro IPR003004 GspF/PilC family
55 171 FunFam G3DSA:1.20.81.30:FF:000001 Type II secretion system protein F

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
0.091
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Surrounding area
Pocket 2 P2Rank #2
0.089
Likely same site as FPocket 29 7.9 Å 11 shared residues 92% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.083
Likely same site as FPocket 29 3.3 Å 10 shared residues 100% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.005
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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 #21
0.906
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Surrounding area
Pocket 2 FPocket #30
0.372
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Surrounding area
Pocket 3 FPocket #29
0.297 Unusual size
Likely same site as P2Rank 3 3.3 Å 10 shared residues 100% of smaller site
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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_A0A0H3GJJ6
AlphaFold DB full sequence Viewing
ColabFold KP13_01839
ColabFold full sequence Loaded

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

51 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 1 records from similar proteins
Structural ligands 1 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
PE5 PDB via homolog 398.5 Da · LogP 0.13 · TPSA 94.1 Open detail RCSB PDB
ZINC5650743 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC6403917 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC12501520 ZINC proposed compound · Tanimoto 0.688 Detail ZINC
ZINC3874716 ZINC proposed compound · Tanimoto 0.688 Detail ZINC

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
PE5 RCSB PDB P45780 398.5 Da LogP 0.13 TPSA 94.1 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCOCCOCCO

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.

Cross-references

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