KpATCC43816 Protein target profile

sugar (Glycoside-Pentoside-Hexuronide) transporter domain protein

Accession: VK055_2723

Gene: gph3 AIK81313.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GIH6
Length 484
Pocket druggability (P2Rank · AlphaFold DB model) 0.995
Direct ligand evidence 0 52 total records
Functional annotation 0 EC 5 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.

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
0.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
29.114 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
89.0 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) 0.995
Structure A0A0H3GIH6
Pocket Pocket 1
Druggability (FPocket) 0.142
Structure A0A0H3GIH6
Pocket Pocket 7
ColabFold model
P2Rank 0.996 · Pocket 1
FPocket 0.803 · Pocket 28
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 36 / 4744 genomes with a hit
Prevalence 0.8%

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.

MSKNIMHSRHDEYHKLTRGERIGYGMGDFAQNLVFGTIGGFLALHMLTVNTISTATAGFIFLFVRIINVFWDPMVGTYVDKRTSKAGKYRPWLLRAGVPLVILSALLFAPIPGVKGSVAFAFIIYLALDLVYSLVNIPYGSLNASLTRDPESIDKLTSTRMMLANSANLLVYTLFPMFVQMAAPKDRSLKDTGFFGLELNLGNYTDPSANYAWFGVYAIYMIIGAVALFICYKCTKERVVATAEQTANVKTTDLFHELRHNRPLVILGMFFMLAFTFMFFMNTVNGFFNQFVVGHSEWMGAVGLVASIPGIAFPVFWPKLKKIFGKKGFFHLFLAMFIVGELLTYAWSREGMHDALWLAYIATFIKQWGLTSATGFMWALVPEVIAYGELKSGKRNAAIINAIMGLFFKIGFTIGGAIPLWLLAVYGFNESGAVQSASAIDGIIMTAVWIPIALAAISMVIMQVYPISDKHVTDINRQLDEIRV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

5
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0008643 The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are a group of organic compounds based of the general formula Cx(H2O)y.
  • GO:0015293 Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported together in the same direction in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy.
  • GO:0006814 The directed movement of sodium ions (Na+) 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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

49 records
Show feature table
Start End DB Term Name
368 387 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
47 51 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
117 142 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
233 263 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
423 441 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
21 469 CDD cd17332 MFS_MelB_like
318 328 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
442 461 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
21 480 NCBIfam TIGR00792 glycoside-pentoside-hexuronide (GPH):cation symporter
21 480 InterPro IPR001927 Sodium:galactoside symporter
52 71 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
368 390 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
14 480 PANTHER PTHR11328 MAJOR FACILITATOR SUPERFAMILY DOMAIN-CONTAINING PROTEIN
14 480 InterPro IPR039672 Lactose permease-like
298 317 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
72 91 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
210 232 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
329 348 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
445 467 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
264 283 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
92 114 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
22 469 SUPERFAMILY SSF103473 MFS general substrate transporter
22 469 InterPro IPR036259 MFS transporter superfamily
112 116 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
287 297 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
161 183 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
211 232 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
264 286 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
92 111 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
403 425 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
49 71 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
118 140 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
23 469 Pfam PF13347 MFS/sugar transport protein
349 367 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
163 183 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
22 44 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
388 398 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 20 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
298 317 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
259 472 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains
259 472 InterPro IPR036259 MFS transporter superfamily
22 239 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains
22 239 InterPro IPR036259 MFS transporter superfamily
21 46 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
184 210 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
399 422 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
462 484 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
329 348 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
143 162 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 · P2Rank

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

Pocket 1 P2Rank #1
0.995
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.112
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.051
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_A0A0H3GIH6
AlphaFold DB full sequence Viewing
ColabFold VK055_2723
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.

52 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 2 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
9PG PDB via homolog 301.3 Da · LogP -1.23 · TPSA 142.5 Open detail RCSB PDB
LMO PDB via homolog Detail RCSB PDB
ZINC1070097 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC12359987 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC12359988 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
9PG RCSB PDB P30878 301.3 Da LogP -1.23 TPSA 142.5 ✓ Ro5 ✓ Clean c1cc(ccc1[N+](=O)[O-])O[C@@H]2[C@@H]([C@H]([C@H…
LMO RCSB PDB P30878 510.6 Da LogP -0.45 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1…

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.