Genome KpATCC43816

Protein target profile

signal peptidase II

Accession: VK055_2553

Gene: lspA AIK81150.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GI12
Length 166
Pocket druggability (P2Rank) 0.621
Direct ligand evidence 0 53 total records
Functional annotation 1 EC 4 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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
3.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
92.169 Higher values support similarity to known essential genes.
DEG E-value
1.3999999999999999e-112 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
91.24 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) 0.621
Structure A0A0H3GI12
Pocket Pocket 1
Druggability (FPocket) 0.979
Structure A0A0H3GI12
Pocket Pocket 1
ColabFold model
P2Rank 0.624 · Pocket 1
FPocket 0.887 · Pocket 7
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 146 / 4744 genomes with a hit
Prevalence 3.1%

Cross-references

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

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.

MSKSICSTGLRWLWVVVAVLIIDLGSKFLILQNFALGETVPLFPSLNLHYARNYGAAFSFLADSGGWQRWFFSGIAIGICVVLTVLMYRSKATQKLNNIAYALIIGGALGNLFDRLWHGFVVDMIDFYVGDWHFATFNLADSAICIGAALIVLEGFLPKPTVKEQA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization
CytoplasmicMembrane

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0004190 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
  • 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.

29 records
Show feature table
Start End DB Term Name
121 131 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
67 86 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
136 158 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
104 116 ProSitePatterns PS00855 Signal peptidases II signature.
104 116 InterPro IPR001872 Peptidase A8, signal peptidase II
12 35 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
70 88 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 162 PANTHER PTHR33695 LIPOPROTEIN SIGNAL PEPTIDASE
1 162 InterPro IPR001872 Peptidase A8, signal peptidase II
101 116 PRINTS PR00781 Lipoprotein signal peptidase family (A8) signature
101 116 InterPro IPR001872 Peptidase A8, signal peptidase II
53 61 PRINTS PR00781 Lipoprotein signal peptidase family (A8) signature
53 61 InterPro IPR001872 Peptidase A8, signal peptidase II
137 153 PRINTS PR00781 Lipoprotein signal peptidase family (A8) signature
137 153 InterPro IPR001872 Peptidase A8, signal peptidase II
13 35 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 163 NCBIfam TIGR00077 signal peptidase II
1 163 InterPro IPR001872 Peptidase A8, signal peptidase II
132 153 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
154 166 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
36 69 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
99 121 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
89 99 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
8 162 Hamap MF_00161 Lipoprotein signal peptidase [lspA].
8 162 InterPro IPR001872 Peptidase A8, signal peptidase II
1 11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
16 154 Pfam PF01252 Signal peptidase (SPase) II
16 154 InterPro IPR001872 Peptidase A8, signal peptidase II
100 120 Phobius TRANSMEMBRANE 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 · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.621
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Surrounding area
Pocket 2 P2Rank #2
0.026
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Surrounding area
Pocket 3 P2Rank #3
0.02
Likely same site as FPocket 8 2.1 Å 5 shared residues 100% of smaller site
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.979
Show in viewer
Surrounding area
Pocket 2 FPocket #8
0.261
Likely same site as P2Rank 3 2.1 Å 5 shared residues 100% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:123-123
UniProt: Active site:141-141
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_A0A0H3GI12
AlphaFold DB full sequence Viewing
ColabFold VK055_2553
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
7PE PDB via homolog 310.4 Da · LogP 0.10 · TPSA 75.6 Open detail RCSB PDB
KNH PDB via homolog Detail RCSB PDB
OLC PDB via homolog Detail RCSB PDB
ZINC1501016272 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC1501016273 ZINC proposed compound · Tanimoto 1.000 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
7PE RCSB PDB Q6GHN9 310.4 Da LogP 0.10 TPSA 75.6 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCO
KNH RCSB PDB Q6GHN9 623.9 Da LogP 5.20 TPSA 142.4 2 viol. ✓ Clean CCC[C@H]1C(=O)NC[C@H](C[C@@H]([C@@H](CC/C(=C/C=…
OLC RCSB PDB Q6GHN9 356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H](CO)O

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.