KpATCC43816 Protein target profile

preprotein translocase, SecY subunit

Accession: VK055_3775

Gene: secY AIK82330.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GZ91
Length 443
Pocket druggability (P2Rank · AlphaFold DB model) 0.884
Direct ligand evidence 0 53 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
6.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
78.27 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) 0.884
Structure A0A0H3GZ91
Pocket Pocket 1
Druggability (FPocket) 0.924
Structure A0A0H3GZ91
Pocket Pocket 44
ColabFold model
P2Rank 0.879 · Pocket 1
FPocket 0.931 · Pocket 3
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 313 / 4744 genomes with a hit
Prevalence 6.6%

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.

MAKQPGLDFQSAKGGLGELKRRLLFVVGALIVFRIGSFIPIPGIDAAVLAKLLEQQRGTIIEMFNMFSGGALSRASIFALGIMPYISASIIVQLLTVVYQPLAELKKEGESGRRKISQYTRYGTLVLAIFQSIGIATGLPNMPGMQGLVINPGFAFYFTAVVSLVTGTMFLMWLGEQITERGIGNGISIIIFAGIVAGLPPAIAHTIEQARQGDLHFLLLLLVAVLVFAVTFFVVFVERGQRRIVVNYAKRQQGRRVYAAQSTHLPLKVNMAGVIPAIFASSIILFPATITSWFGGGTGWNWLTTISLYLQPGQPLYVLLYASAIIFFCFFYTALVFNPRETADNLKKSGAFVPGIRPGEQTAKYIDKVMTRLTLVGALYITFICLIPEFMRDAMKVPFYFGGTSLLIVVVVIMDFMAQVQTLMMSSQYESALKKANLKGYGR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

6
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0015031 The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • 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: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: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.

59 records
Show feature table
Start End DB Term Name
10 433 Hamap MF_01465 Protein translocase subunit SecY [secY].
10 433 InterPro IPR026593 Protein translocase subunit SecY
75 99 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
238 273 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
119 138 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
18 422 PANTHER PTHR10906 SECY/SEC61-ALPHA FAMILY MEMBER
18 422 InterPro IPR002208 SecY/SEC61-alpha family
16 424 SUPERFAMILY SSF103491 Preprotein translocase SecY subunit
16 424 InterPro IPR023201 SecY domain superfamily
154 174 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 22 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
204 214 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
77 99 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
297 315 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
419 443 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
45 74 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
119 139 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
215 237 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
274 296 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
316 337 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
392 396 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
397 414 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
76 417 Pfam PF00344 SecY
76 417 InterPro IPR002208 SecY/SEC61-alpha family
11 441 PIRSF PIRSF004557 SecY_Sec61alpha
11 441 InterPro IPR002208 SecY/SEC61-alpha family
373 392 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
76 95 ProSitePatterns PS00755 Protein secY signature 1.
76 95 InterPro IPR030659 SecY conserved site
316 338 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
100 118 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
153 175 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
370 388 PRINTS PR00303 Preprotein translocase SecY subunit signature
180 203 PRINTS PR00303 Preprotein translocase SecY subunit signature
272 291 PRINTS PR00303 Preprotein translocase SecY subunit signature
315 337 PRINTS PR00303 Preprotein translocase SecY subunit signature
402 420 PRINTS PR00303 Preprotein translocase SecY subunit signature
154 179 PRINTS PR00303 Preprotein translocase SecY subunit signature
23 41 PRINTS PR00303 Preprotein translocase SecY subunit signature
75 95 PRINTS PR00303 Preprotein translocase SecY subunit signature
116 139 PRINTS PR00303 Preprotein translocase SecY subunit signature
373 391 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
173 190 ProSitePatterns PS00756 Protein secY signature 2.
173 190 InterPro IPR030659 SecY conserved site
140 153 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
20 429 NCBIfam TIGR00967 preprotein translocase subunit SecY
20 429 InterPro IPR002208 SecY/SEC61-alpha family
186 203 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
397 418 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
23 44 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
175 185 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
22 44 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
215 237 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
15 429 Gene3D G3DSA:1.10.3370.10 SecY subunit domain
15 429 InterPro IPR023201 SecY domain superfamily
338 372 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
274 296 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
182 204 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
9 429 FunFam G3DSA:1.10.3370.10:FF:000001 Preprotein translocase subunit SecY

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
0.884
Likely same site as FPocket 25 3.8 Å 15 shared residues 79% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.569
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Surrounding area
Pocket 3 P2Rank #3
0.557
Likely same site as FPocket 44 1.6 Å 19 shared residues 100% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.532
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Surrounding area
Pocket 5 P2Rank #5
0.525
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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 #44
0.924 Unusual size
Likely same site as P2Rank 3 1.6 Å 19 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #25
0.484 Unusual size
Likely same site as P2Rank 1 3.8 Å 15 shared residues 79% of smaller site
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Surrounding area
Pocket 3 FPocket #3
0.204
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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_A0A0H3GZ91
AlphaFold DB full sequence Viewing
ColabFold VK055_3775
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
BEF PDB via homolog 66.0 Da · LogP 0.88 · TPSA 0.0 Open detail RCSB PDB
OLC PDB via homolog Detail RCSB PDB
PGV PDB via homolog Detail RCSB PDB
ZINC32840902 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC32840903 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
BEF RCSB PDB A4IJK8 66.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean [Be-](F)(F)F
OLC RCSB PDB Q5SHQ8 356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H](CO)O
PGV RCSB PDB A4IJK8 749.0 Da LogP 10.45 TPSA 148.8 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@](=O)(O)OC[C@H…

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.