KpKP13 Protein target profile

Multiple antibiotic resistance protein marA

Accession: KP13_05276

Gene: marA AHE44683.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GN41
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Length 125
Pocket druggability (P2Rank · AlphaFold DB model) 0.085
Functional annotation 0 EC 4 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. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 92 of 4744 screened genomes (1.9%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.13. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.09.

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
1.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
92.742 Higher values support similarity to known essential genes.
DEG E-value
5.26e-85 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
92.41 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) 0.085
Structure A0A0H3GN41
Pocket Pocket 1
Druggability (FPocket) 0.132
Structure A0A0H3GN41
Pocket Pocket 1
ColabFold model
P2Rank 0.06 · Pocket 1
FPocket 0.358 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 92 / 4744 genomes with a hit
Prevalence 1.9%

Sequence

Primary amino-acid sequence viewer.

MMSRRNNDAITIHSILSWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKLTEIAQKLKQSNEPILYLAERYGFESQQTLTRTFKNYFDVPPHKYRITNVPGESRYLHPLNN

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

4
  • GO:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
  • GO:0046677 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
1 63 Gene3D G3DSA:1.10.10.60 -
33 109 Pfam PF12833 Helix-turn-helix domain
33 109 InterPro IPR018060 DNA binding HTH domain, AraC-type
11 60 SUPERFAMILY SSF46689 Homeodomain-like
11 60 InterPro IPR009057 Homeobox-like domain superfamily
8 60 FunFam G3DSA:1.10.10.60:FF:000013 DNA-binding transcriptional activator MarA
13 111 ProSiteProfiles PS01124 Bacterial regulatory proteins, araC family DNA-binding domain profile.
13 111 InterPro IPR018060 DNA binding HTH domain, AraC-type
63 105 ProSitePatterns PS00041 Bacterial regulatory proteins, araC family signature.
63 105 InterPro IPR018062 HTH domain AraC-type, conserved site
64 125 Gene3D G3DSA:1.10.10.60 -
63 110 SUPERFAMILY SSF46689 Homeodomain-like
63 110 InterPro IPR009057 Homeobox-like domain superfamily
2 119 PANTHER PTHR47504 RIGHT ORIGIN-BINDING PROTEIN
26 109 SMART SM00342 aracneu4
26 109 InterPro IPR018060 DNA binding HTH domain, AraC-type

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

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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
0.085
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_A0A0H3GN41
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_05276
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GN41