KpATCC43816 Protein target profile

type II secretion system protein E

Accession: VK055_2409

Gene: gspE AIK81006.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GRZ5
Length 487
Pocket druggability (P2Rank · AlphaFold DB model) 0.702
Direct ligand evidence 0 53 total records
Functional annotation 0 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.

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
2.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
60.656 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
87.66 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) 0.702
Structure A0A0H3GRZ5
Pocket Pocket 1
Druggability (FPocket) 0.522
Structure A0A0H3GRZ5
Pocket Pocket 1
ColabFold model
P2Rank 0.749 · Pocket 1
FPocket 0.916 · Pocket 31
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 124 / 4744 genomes with a hit
Prevalence 2.6%

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.

MPFAWARAHHLVLLSDGERCEALCRPDTAARALLEARRLADGPMRVSRLAPDAFEKVLVLSYQRDSAEAHRMMADIGNELDLYTLAEELPDTDDLLDSEDDAPIIRLINAMLTEAIKEKASDIHIETYERHLQIRFRVDGVLREILRPQRRLAALLISRIKVMASLDIAEKRVPQDGRMALRIGGRAIDVRVSTLPSSHGERVVLRLLDKNSVNLDLLTLGMPPALLDRVDALIARPHGIILVTGPTGSGKSTTLYAALSRLDARERNIMTIEDPVEYELEGIGQTQVNAKVEMTFARGLRAILRQDPDVVLVGEIRDGETAQIAVQASLTGHLVLSTLHTNSALGAISRLQDMGVEPFLLSTSLLAVMSQRLVRQLCPHCRQPWQADANTARQMAVPVGARLWQPKGCPECNFIGYRGRTGIHELLLVDDRVRAAIHRGENEITLIQQLGPAWQTLRHAGRDKALAGITSWEEVMRVTEQQTTESV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

7
  • 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:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
  • 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.
  • GO:0008564 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + protein+(in) = ADP + phosphate + protein+(out); drives the concomitant secretion of proteins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
110 376 Pfam PF00437 Type II/IV secretion system protein
110 376 InterPro IPR001482 Type II/IV secretion system domain
1 63 SUPERFAMILY SSF160246 EspE N-terminal domain-like
1 63 InterPro IPR037257 Type II secretion system protein GspE, N-terminal superfamily
304 318 ProSitePatterns PS00662 Bacterial type II secretion system protein E signature.
304 318 InterPro IPR001482 Type II/IV secretion system domain
1 76 Gene3D G3DSA:3.30.300.160 -
1 76 InterPro IPR037257 Type II secretion system protein GspE, N-terminal superfamily
237 360 SMART SM00382 AAA_5
237 360 InterPro IPR003593 AAA+ ATPase domain
210 486 Gene3D G3DSA:3.40.50.300 -
210 486 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
209 481 FunFam G3DSA:3.40.50.300:FF:000398 Type IV pilus assembly ATPase PilB
93 479 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
93 479 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
228 376 CDD cd01129 PulE-GspE-like
77 208 FunFam G3DSA:3.30.450.90:FF:000001 Type II secretion system ATPase GspE
76 486 PANTHER PTHR30258 TYPE II SECRETION SYSTEM PROTEIN GSPE-RELATED
1 479 NCBIfam TIGR02533 type II secretion system ATPase GspE
1 479 InterPro IPR013369 Type II secretion system protein GspE
77 209 Gene3D G3DSA:3.30.450.90 -

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
0.702
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Surrounding area
Pocket 2 P2Rank #2
0.244
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.053
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.049
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.039
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.522 Unusual size
Show in viewer
Surrounding area
Pocket 2 FPocket #19
0.304 Unusual size
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_A0A0H3GRZ5
AlphaFold DB full sequence Viewing
ColabFold VK055_2409
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.

53 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ACP PDB via homolog 505.2 Da · LogP -1.52 · TPSA 269.9 Open detail RCSB PDB
AGS PDB via homolog Detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
ZINC3873854 ZINC proposed compound · Tanimoto 0.873 Detail ZINC
ZINC12360002 ZINC proposed compound · Tanimoto 0.810 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
ACP RCSB PDB P24559 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AGS RCSB PDB Q5SLC9 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP RCSB PDB P37093 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.