Protein target profile

KP13_04307

Inner membrane transporter rhtA

Genome: KpKP13 Gene: AHE45541.1 rhtA 3D evidence: ColabFold model

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Length 259

Pocket druggability 0.072

Functional annotation 0 EC 1 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

Risks to review

Microbiome similarity 133 of 4744 screened genomes (2.8%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.07.

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: 2.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 0.0 Higher values support similarity to known essential genes.

Localization

Localization: CytoplasmicMembrane

Structure confidence

ColabFold pLDDT: 74.51 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

ColabFold / curated model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.072

Structure CB_KP13_04307

Pocket Pocket 18

P2Rank 0.658

Structure CB_KP13_04307

Pocket Pocket 1

ColabFold model

FPocket 0.072 · Pocket 18

P2Rank 0.658 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 133 / 4744 genomes with a hit

Prevalence 2.8%

Sequence

Primary amino-acid sequence viewer.

MVGAPGVTALRLALGTLILVVVFKPWRLRFSPAQRVPLLLYGLALGAMNYLFYLSLQRIPLGVAVALEFTGPLAVALFGSRRPLDFVWVALAILGLWYLLPLGQNVAQVDLTGALFALGAGACWAVYILTGQRAGEEHGPATVAMGSLIASLVFVPLGMAQATDTLWQWSLLPLGLGIAILSTALPYSLEMMALTRLPTRTFGTLMSLEPALAALSGMIFLGETLKLSQTLALGAIIIASMGATLTMQRQSKVEQVDIN

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

33 records

Show feature table

Start	End	DB	Term	Name
24	34	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
246	259	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
104	108	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
141	163	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
80	85	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
201	220	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
10	100	SUPERFAMILY	SSF103481	Multidrug resistance efflux transporter EmrE
112	241	Pfam	PF00892	EamA-like transporter family
112	241	InterPro	IPR000620	EamA domain
1	5	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
59	79	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
148	244	SUPERFAMILY	SSF103481	Multidrug resistance efflux transporter EmrE
167	189	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
130	140	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
201	221	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
36	53	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
109	129	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
166	189	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
227	245	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
230	247	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
57	79	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
161	165	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
6	251	PANTHER	PTHR22911	ACYL-MALONYL CONDENSING ENZYME-RELATED
86	103	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
86	103	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
6	23	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
54	58	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
141	160	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
107	129	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
190	200	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
222	226	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
4	23	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
35	53	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

Site 1 P2Rank #1

0.658

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Surrounding area

Site 2 P2Rank #2

0.54

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Surrounding area

Site 3 P2Rank #3

0.007

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Surrounding area

All structural evidence 0 experimental · 1 predicted

Structural evidence

0 + 1

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
ColabFold KP13_04307	ColabFold	—	—	full sequence	—	Viewing