Protein target profile

HT085_RS00170

tyrosine recombinase XerC

Genome: NZ_AP023069.1 Gene: WHOF_00392 NGO_0035 N776_09165 NCTC11421_02894 xerC ESCNG_30017 E8M63_03355 TUM19854C_00300 WHOF_00032 NGK_0043 3D evidence: AlphaFold DB model UniProt Q5FAI3 UniProt B4RNW5 UniProt A0AA44U8J9 UniProt A0A1D3FLG3
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Length 305
Functional annotation 0 EC 6 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 AlphaFold DB 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 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)
Y

Localization

Localization
Cytoplasmic

Binding-site evidence

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 Medium
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MVLDGFAAYFDAYLENIVREGKSEHTVAAYRRDLEELFALLAQMPSEDAGGVPQDLSRRDFTAALRRLSQRGLDGRTLARKLSAWRQYCAWLVKRGLMRADPTADIKPPKQPERVPKALPQEWLNRMLDLPVDGGDPLAVRDHALFELMYGSGLRVSEIHGLNADDVYLDEAWVHVTGKGRKQRQVPLTGKSVEALKNYLPLRQTASDGKALFTGRNGTRLSQRQIQKRLESWAAQYGDGRHVSPHMMRHSYAGHLLQASRDIRAVQELLGHSSLSTTQIYTKLDFDHIARLYDEAHPRAKRQDE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
  • GO:0007059 The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0009037 Catalysis of the formation of new phosphodiester bonds between a pair of short, unique DNA target sequences; occurs through a phosphotyrosyl intermediate in which the target sequence is first cleaved by the nucleophilic attack by a tyrosine in the active site.
  • GO:0006313 A type of transposition in which a transposable element (transposon) is moved to another part of a genome, either by a cut-and-paste mechanism or a replicative mechanism.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
11 96 Pfam PF02899 Phage integrase, N-terminal SAM-like domain
11 96 InterPro IPR004107 Integrase, SAM-like, N-terminal
13 302 NCBIfam TIGR02224 tyrosine recombinase XerC
13 302 InterPro IPR011931 Tyrosine recombinase XerC
114 294 ProSiteProfiles PS51898 Tyrosine recombinase domain profile.
114 294 InterPro IPR002104 Integrase, catalytic domain
120 285 Pfam PF00589 Phage integrase family
120 285 InterPro IPR002104 Integrase, catalytic domain
117 293 Gene3D G3DSA:1.10.443.10 Intergrase catalytic core
117 293 InterPro IPR013762 Integrase-like, catalytic domain superfamily
6 293 SUPERFAMILY SSF56349 DNA breaking-rejoining enzymes
6 293 InterPro IPR011010 DNA breaking-rejoining enzyme, catalytic core
7 105 Gene3D G3DSA:1.10.150.130 -
7 105 InterPro IPR010998 Integrase/recombinase, N-terminal
121 289 CDD cd00798 INT_XerDC_C
8 300 Hamap MF_01808 Tyrosine recombinase XerC [xerC].
8 300 InterPro IPR023009 Tyrosine recombinase XerC/XerD
6 284 PANTHER PTHR30629 PROPHAGE INTEGRASE
1 93 ProSiteProfiles PS51900 Core-binding (CB) domain profile.
1 93 InterPro IPR044068 Core-binding (CB) domain

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 · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #3
0.672
Likely same site as P2Rank 2 1.6 Å 12 shared residues 100% of smaller site
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Surrounding area
Site 2 FPocket #7
0.507
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Surrounding area
Site 3 FPocket #2
0.403
Likely same site as P2Rank 3 3.7 Å 9 shared residues 100% of smaller site
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.192
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Surrounding area
Site 2 P2Rank #2
0.072
Likely same site as FPocket 3 1.6 Å 12 shared residues 100% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.031
Likely same site as FPocket 2 3.7 Å 9 shared residues 100% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.03
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Surrounding area
Site 5 P2Rank #5
0.016
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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
AlphaFold DB HT085_RS00170
AlphaFold DB — — full sequence — Viewing