KpKP13 Protein target profile

Spermidine/putrescine transport system permease protein potC

Accession: KP13_04875

Gene: AHE45235.1 potC 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GLJ9
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Length 261
Pocket druggability (P2Rank · AlphaFold DB model) 0.115
Functional annotation 0 EC 3 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 0.48. This supports review but is not experimental validation. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 127 of 4744 screened genomes (2.7%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.48) — check the ligand evidence before deprioritizing on off-target risk alone. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.12.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. 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
2.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
89.23 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) 0.115
Structure A0A0H3GLJ9
Pocket Pocket 1
Druggability (FPocket) 0.482
Structure A0A0H3GLJ9
Pocket Pocket 5
ColabFold model
P2Rank 0.153 · Pocket 1
FPocket 0.92 · Pocket 17
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 127 / 4744 genomes with a hit
Prevalence 2.7%

Sequence

Primary amino-acid sequence viewer.

MIGRLLRGGFMTAIYAYLYIPIIILIVNSFNRSRFGINWQGFTTDWYSLLMNNDSLLQAAQHSLTMAVLSATFATLIGSLTAVALYRYRFRGKPFVSGMLFVVMMSPDIVMAISLLVLFMLIGVQLGFWSLLFSHITFCLPFVVVTVYSRLKGFDVRMLEAAKDLGASEMTILRKIILPLALPAVAAGWLLSFTLSMDDVVVSSFVTGPGYEILPLKIYSMVKVGVSPEVNALATILLVLSLVMVIASQLIARDKTQGTLK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

3
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • 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.

31 records
Show feature table
Start End DB Term Name
64 86 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
75 253 Pfam PF00528 Binding-protein-dependent transport system inner membrane component
75 253 InterPro IPR000515 ABC transporter type 1, transmembrane domain MetI-like
5 27 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
152 171 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
60 245 CDD cd06261 TM_PBP2
60 245 InterPro IPR000515 ABC transporter type 1, transmembrane domain MetI-like
98 122 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
192 229 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
87 97 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
60 248 ProSiteProfiles PS50928 ABC transporter integral membrane type-1 domain profile.
60 248 InterPro IPR000515 ABC transporter type 1, transmembrane domain MetI-like
8 258 Gene3D G3DSA:1.10.3720.10 -
8 258 InterPro IPR035906 MetI-like superfamily
176 195 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
12 30 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
172 191 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
126 148 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
230 252 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
230 252 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
253 261 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
6 257 PANTHER PTHR43848 PUTRESCINE TRANSPORT SYSTEM PERMEASE PROTEIN POTI
31 63 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
128 151 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
8 258 FunFam G3DSA:1.10.3720.10:FF:000013 Spermidine/putrescine ABC transporter permease PotC
3 254 SUPERFAMILY SSF161098 MetI-like
3 254 InterPro IPR035906 MetI-like superfamily
99 121 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
123 127 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
64 86 TMHMM TMhelix 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

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.115
Likely same site as FPocket 7 1.0 Å 7 shared residues 100% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.001
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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 #5
0.482
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Surrounding area
Pocket 2 FPocket #2
0.477
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Surrounding area
Pocket 3 FPocket #7
0.456
Likely same site as P2Rank 1 1.0 Å 7 shared residues 100% of smaller site
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Surrounding area
Pocket 4 FPocket #13
0.214
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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_A0A0H3GLJ9
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_04875
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GLJ9