KpATCC43816 Protein target profile

type II secretion system (T2SS), F family protein

Accession: VK055_2463

Gene: AIK81060.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GI88
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Length 401
Pocket druggability (P2Rank · AlphaFold DB model) 0.084
Direct ligand evidence 0 51 total records
Functional annotation 0 EC 4 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. Strong predicted binding pocket FPocket selected-pocket score 0.89. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Microbiome similarity 62 of 4744 screened genomes (1.3%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.89) — check the ligand evidence before deprioritizing on off-target risk alone. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.08.

Evidence coverage

Core evidence streams are available for this target.
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
1.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
85.05 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) 0.084
Structure A0A0H3GI88
Pocket Pocket 1
Druggability (FPocket) 0.892
Structure A0A0H3GI88
Pocket Pocket 25
ColabFold model
P2Rank 0.178 · Pocket 1
FPocket 0.82 · Pocket 9
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 62 / 4744 genomes with a hit
Prevalence 1.3%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MATKRLWRWRGIDVQGAPCQGMLWQTKRLEVLQHLQQQRVIPLAVRRCAVKQSLWHPRYSCETIRQLATLLQAGLPLAEGLSLLAQQQSHAQWQALLEALGRELAQGVAFSAALAQWPQAFPPLYLAMISTGELTGKLDICCLQLANQQQEQQRLASKVKKALRYPLIVLSLALLVVLGMLYFVLPEFTAIYQTFSTPLPLLTRMVVAAGDMLSRGWPLLLASLLSPLLLNQLIRRRSDWLLRRQRLLNALPLIGSLIGGQQLSLIFTILALTQSAGISFLQGLQSVEESLSCPLWRQRLAQARALIVQGEPIWQALSRCGGFTPLCLQLIRTGESAGALDQMLENLAHHHRKQTYQRADSLAAHLEPMMLVITGSLVGILVVAMYLPVFHLGDAIGGAGG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

4
  • GO:0009306 The controlled release of proteins from a cell.
  • 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.
  • 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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

35 records
Show feature table
Start End DB Term Name
205 230 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
250 366 FunFam G3DSA:1.20.81.30:FF:000001 Type II secretion system protein F
48 165 FunFam G3DSA:1.20.81.30:FF:000001 Type II secretion system protein F
158 186 PRINTS PR00812 Bacterial general secretion pathway protein F signature
158 186 InterPro IPR003004 GspF/PilC family
361 375 PRINTS PR00812 Bacterial general secretion pathway protein F signature
361 375 InterPro IPR003004 GspF/PilC family
377 396 PRINTS PR00812 Bacterial general secretion pathway protein F signature
377 396 InterPro IPR003004 GspF/PilC family
59 71 PRINTS PR00812 Bacterial general secretion pathway protein F signature
59 71 InterPro IPR003004 GspF/PilC family
158 186 ProSitePatterns PS00874 Bacterial type II secretion system protein F signature.
158 186 InterPro IPR001992 T2SS_GspF/T4SS_PilC conserved site
186 204 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
273 368 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
231 249 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
162 185 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
369 387 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
212 234 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
60 165 Gene3D G3DSA:1.20.81.30 Type II secretion system (T2SS), domain F
60 165 InterPro IPR042094 Type II secretion system GspF domain superfamily
6 396 PANTHER PTHR30012 GENERAL SECRETION PATHWAY PROTEIN
6 396 InterPro IPR003004 GspF/PilC family
368 390 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
247 269 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
269 388 Pfam PF00482 Type II secretion system (T2SS), protein F
269 388 InterPro IPR018076 Type II secretion system protein GspF domain
64 186 Pfam PF00482 Type II secretion system (T2SS), protein F
64 186 InterPro IPR018076 Type II secretion system protein GspF domain
163 185 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 161 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
250 272 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
250 360 Gene3D G3DSA:1.20.81.30 Type II secretion system (T2SS), domain F
250 360 InterPro IPR042094 Type II secretion system GspF domain superfamily
388 401 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.

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
0.084
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Surrounding area
Pocket 2 P2Rank #2
0.057
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Surrounding area
Pocket 3 P2Rank #3
0.02
Likely same site as FPocket 12 3.8 Å 8 shared residues 100% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.016
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Surrounding area
Pocket 5 P2Rank #5
0.015
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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 #25
0.892
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Surrounding area
Pocket 2 FPocket #36
0.774
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Surrounding area
Pocket 3 FPocket #5
0.525
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Surrounding area
Pocket 4 FPocket #12
0.424
Likely same site as P2Rank 3 3.8 Å 8 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_A0A0H3GI88
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_2463
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
3C1Q
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.

Sequence

UniProt A0A0H3GI88