Protein target profile

HT085_RS00060

helix-turn-helix domain-containing protein

Genome: NZ_AP023069.1 Gene: TUM19854C_00100 3D evidence: ColabFold model
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Length 103
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

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Structure available ColabFold model

Risks to review

No major risk signal surfaced in the loaded evidence.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. No FPocket pocket score No selected computational pocket-druggability value is available. No P2Rank pocket score No second computational pocket-prediction value is available. 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 off-target
Hit

Essentiality

Essential (DEG)
N

Localization

Localization
Unknown

Sequence

Primary amino-acid sequence viewer.

MKYKSGIFAAIHETMQGLHDIGAIDKKTMRGFDKSCLTEIKPLSGGDIKAIREKEALSQAAFAIYLNVGKNHVSAWERGVKKPGGAAFKLLTIVKNKGIEAIA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

1
  • 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.

13 records
Show feature table
Start End DB Term Name
48 83 ProSiteProfiles PS50943 Cro/C1-type HTH domain profile.
48 83 InterPro IPR001387 Cro/C1-type helix-turn-helix domain
45 91 CDD cd00093 HTH_XRE
45 91 InterPro IPR001387 Cro/C1-type helix-turn-helix domain
48 87 Pfam PF01381 Helix-turn-helix
48 87 InterPro IPR001387 Cro/C1-type helix-turn-helix domain
38 99 Gene3D G3DSA:1.10.260.40 -
38 99 InterPro IPR010982 Lambda repressor-like, DNA-binding domain superfamily
45 100 SUPERFAMILY SSF47413 lambda repressor-like DNA-binding domains
45 100 InterPro IPR010982 Lambda repressor-like, DNA-binding domain superfamily
47 102 SMART SM00530 mbf_short4
47 102 InterPro IPR001387 Cro/C1-type helix-turn-helix domain
2 102 PANTHER PTHR36511 MERR FAMILY BACTERIAL REGULATORY PROTEIN

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

No pockets are loaded yet for the displayed ColabFold model HT085_RS00060 structure. Run experimental pocket backfill to show FPocket/P2Rank overlays on this structure.

Loading 3D structure...

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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'.
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 HT085_RS00060
ColabFold — — full sequence — Viewing