KpATCC43816 Protein target profile

preprotein translocase, SecE subunit

Accession: VK055_3116

Gene: secE AIK81697.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GH93
Export view
Length 127
Pocket druggability (FPocket · AlphaFold DB model) 0.696
Functional annotation 0 EC 8 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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. Moderate predicted binding pocket FPocket selected-pocket score 0.70. This supports review but is not experimental validation. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 117 of 4744 screened genomes (2.5%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.70) — check the ligand evidence before deprioritizing on off-target risk alone.

Evidence gaps

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
2.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
95.276 Higher values support similarity to known essential genes.
DEG E-value
1.3999999999999998e-82 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
82.53 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)
Structure A0A0H3GH93
Pocket No pockets
Druggability (FPocket) 0.696
Structure A0A0H3GH93
Pocket Pocket 3
ColabFold model
FPocket 0.69 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 117 / 4744 genomes with a hit
Prevalence 2.5%

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.

MSANTEAQGSGRGLEAMKWIIVAVLLIVAIVGNFLYRDIMLAVRALAVVILIAAAGGVALLTTKGKATVAFAREARTEVRKVIWPTRQETLHTTLIVAAVTAVMSLILWGLDGILVRLVSFITGLRF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

8
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0009306 The controlled release of proteins from a cell.
  • GO:0008320 Enables the transfer of a protein from one side of a membrane to the other.
  • GO:0006886 The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
  • GO:0006605 The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif.
  • 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:0065002 The directed movement of proteins in a cell, from one side of a membrane to another by means of some agent such as a transporter or pore.
  • GO:0043952 The process in which unfolded proteins are transported across the cytoplasmic membrane in Gram-positive and Gram-negative bacteria by the Sec complex, in a process involving proteolytic cleavage of an N-terminal signal peptide.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

31 records
Show feature table
Start End DB Term Name
16 36 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
65 85 PRINTS PR01650 Bacterial translocase SecE signature
65 85 InterPro IPR005807 SecE subunit of protein translocation complex, bacterial-like
109 125 PRINTS PR01650 Bacterial translocase SecE signature
109 125 InterPro IPR005807 SecE subunit of protein translocation complex, bacterial-like
89 109 PRINTS PR01650 Bacterial translocase SecE signature
89 109 InterPro IPR005807 SecE subunit of protein translocation complex, bacterial-like
44 65 PRINTS PR01650 Bacterial translocase SecE signature
44 65 InterPro IPR005807 SecE subunit of protein translocation complex, bacterial-like
95 119 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
66 122 Gene3D G3DSA:1.20.5.1030 Preprotein translocase secy subunit
66 122 InterPro IPR038379 SecE superfamily
70 122 Pfam PF00584 SecE/Sec61-gamma subunits of protein translocation complex
70 122 InterPro IPR001901 Protein translocase complex, SecE/Sec61-gamma subunit
71 99 ProSitePatterns PS01067 Protein secE/sec61-gamma signature.
71 99 InterPro IPR001901 Protein translocase complex, SecE/Sec61-gamma subunit
41 63 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
43 61 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
69 123 NCBIfam TIGR00964 preprotein translocase subunit SecE
69 123 InterPro IPR005807 SecE subunit of protein translocation complex, bacterial-like
66 122 FunFam G3DSA:1.20.5.1030:FF:000001 Preprotein translocase subunit SecE
94 116 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 15 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
24 125 PANTHER PTHR33910 PROTEIN TRANSLOCASE SUBUNIT SECE
24 125 InterPro IPR005807 SecE subunit of protein translocation complex, bacterial-like
62 94 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
120 127 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
19 36 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
67 121 Hamap MF_00422 Protein translocase subunit SecE [secE].
67 121 InterPro IPR001901 Protein translocase complex, SecE/Sec61-gamma subunit
37 42 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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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

Pocket 1 FPocket #3
0.696
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_A0A0H3GH93
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_3116
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GH93