KpKP13 Protein target profile

HTH-type protein slmA

Accession: KP13_00182

Gene: AHE42097.1 slmA 3D evidence: Experimental + ColabFold model UniProt A6TFN2
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Length 198
Pocket druggability (FPocket · Experimental) 0.11
Functional annotation 0 EC 2 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

Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. 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 Experimental + ColabFold model

Risks to review

Microbiome similarity 125 of 4744 screened genomes (2.6%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.11.

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
2.6% 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.

Structure confidence

ColabFold pLDDT
95.02 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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)
Structure 5HSZ
Pocket No pockets
Druggability (FPocket) 0.11
Structure 5HSZ
Pocket Pocket 2
ColabFold model
P2Rank 0.038 · Pocket 1
FPocket 0.487 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 125 / 4744 genomes with a hit
Prevalence 2.6%

Sequence

Primary amino-acid sequence viewer.

MAEKQTAKRNRREEILQSLALMLESSDGSQRITTAKLAASVGVSEAALYRHFPSKTRMFDSLIEFIEDSLITRINLILKDEKDTTARLRLIVLLILGFGERNPGLTRILTGHALMFEQDRLQGRINQLFERIEAQLRQVMREKKMREGEGYTLDETLLASQLLAFCEGMLSRFVRSEFKYRPTDDFDARWPLVAAQLQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

2
  • GO:0010974 Any process that decreases the frequency, rate or extent of division septum formation. division septum formation is he assembly and arrangement of a septum that spans the plasma membrane interface between progeny cells following cytokinesis.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
20 61 Pfam PF00440 Bacterial regulatory proteins, tetR family
20 61 InterPro IPR001647 DNA-binding HTH domain, TetR-type
1 198 Hamap MF_01839 Nucleoid occlusion factor SlmA [slmA].
1 198 InterPro IPR023769 Nucleoid occlusion factor SlmA
3 193 PANTHER PTHR30055 HTH-TYPE TRANSCRIPTIONAL REGULATOR RUTR
9 198 FunFam G3DSA:1.10.357.10:FF:000002 Nucleoid occlusion factor SlmA
9 198 Gene3D G3DSA:1.10.357.10 Tetracycline Repressor, domain 2
84 192 SUPERFAMILY SSF48498 Tetracyclin repressor-like, C-terminal domain
84 192 InterPro IPR036271 Tetracyclin repressor-like, C-terminal domain superfamily
5 86 SUPERFAMILY SSF46689 Homeodomain-like
5 86 InterPro IPR009057 Homeobox-like domain superfamily
118 138 Coils Coil Coil
28 58 ProSitePatterns PS01081 TetR-type HTH domain signature.
28 58 InterPro IPR023772 DNA-binding HTH domain, TetR-type, conserved site
10 70 ProSiteProfiles PS50977 TetR-type HTH domain profile.
10 70 InterPro IPR001647 DNA-binding HTH domain, TetR-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.

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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
All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 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
PDB 5HSZ
X-ray — A —
PDBe RCSB PDBj File
Viewing
ColabFold KP13_00182
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A6TFN2

Structure

PDB 5HSZ