KpKP13 Protein target profile

7-carboxy-7-deazaguanine synthase-like protein

Accession: KP13_02392

Gene: AHE42963.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GSC0
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Length 223
Pocket druggability (P2Rank · AlphaFold DB model) 0.961
Functional annotation 1 EC 7 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. Second pocket predictor agrees P2Rank predicted binding-site probability 0.96. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 119 of 4744 screened genomes (2.5%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.96) — check the ligand evidence before deprioritizing on off-target risk alone. Weak predicted binding pocket FPocket selected-pocket score 0.20.

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
2.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
91.928 Higher values support similarity to known essential genes.
DEG E-value
3.22e-159 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
95.96 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) 0.961
Structure A0A0H3GSC0
Pocket Pocket 1
Druggability (FPocket) 0.201
Structure A0A0H3GSC0
Pocket Pocket 4
ColabFold model
P2Rank 0.96 · Pocket 1
FPocket 0.14 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 119 / 4744 genomes with a hit
Prevalence 2.5%

Sequence

Primary amino-acid sequence viewer.

MQYPINEMFQTLQGEGYFTGVPAIFIRLQGCPVGCAWCDTKHTWDKLADREVSLFSILAKTKESDKWGPASSEDLLAIIGRQGWTARHVVITGGEPCIHDLTPLTSLLEQNGFSCQIETSGTHEVRCSPNTWVTVSPKVNMRGGYDVLSQALQRADEIKHPVGRVRDIEALDELLETLSDDKPRIIALQPISQKEDATRLCIDTCIARNWRLSMQTHKYLNIA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0016840 Catalysis of the release of ammonia or one of its derivatives, with the formation of a double bond or ring. Enzymes with this activity may catalyze the actual elimination of the ammonia, amine or amide, e.g. CH-CH(-NH-R) = C=CH- + NH2-R. Others, however, catalyze elimination of another component, e.g. water, which is followed by spontaneous reactions that lead to breakage of the C-N bond, e.g. L-serine ammonia-lyase (EC:4.3.1.17), so that the overall reaction is C(-OH)-CH(-NH2) = CH2-CO- + NH4+, i.e. an elimination with rearrangement. The sub-subclasses of EC:4.3 are the ammonia-lyases (EC:4.3.1), lyases acting on amides, amidines, etc. (EC:4.3.2), the amine-lyases (EC:4.3.3), and other carbon-nitrogen lyases (EC:4.3.99).
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:1904047 Binding to S-adenosyl-L-methionine.
  • GO:0008616 The chemical reactions and pathways resulting in the formation of queuosines, a series of nucleosides found in position 34 of tRNA and having an additional pentenyl ring added via an NH group to the methyl group of 7-methylguanosine. The pentenyl ring may carry other substituents. The wobble nucleoside of the tRNA sequence (position 34) corresponds to the first position of the anticodon.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
24 119 SUPERFAMILY SSF102114 Radical SAM enzymes
1 223 PIRSF PIRSF000370 QueE
1 223 InterPro IPR024924 7-carboxy-7-deazaguanine synthase-like
2 223 FunFam G3DSA:3.20.20.70:FF:000085 7-carboxy-7-deazaguanine synthase
2 223 Gene3D G3DSA:3.20.20.70 Aldolase class I
2 223 InterPro IPR013785 Aldolase-type TIM barrel
1 222 PANTHER PTHR42836 7-CARBOXY-7-DEAZAGUANINE SYNTHASE
27 183 Pfam PF04055 Radical SAM superfamily
27 183 InterPro IPR007197 Radical SAM
3 223 Hamap MF_00917 7-carboxy-7-deazaguanine synthase [queE].
3 223 InterPro IPR024924 7-carboxy-7-deazaguanine synthase-like
18 223 ProSiteProfiles PS51918 Radical SAM core domain profile.
18 223 InterPro IPR007197 Radical SAM
9 223 NCBIfam TIGR04322 7-carboxy-7-deazaguanine synthase QueE
9 223 InterPro IPR027609 7-carboxy-7-deazaguanine synthase, proteobacteria
26 183 SFLD SFLDS00029 Radical SAM
26 183 InterPro IPR007197 Radical SAM
24 127 Pfam PF13394 4Fe-4S single cluster 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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.961
Likely same site as FPocket 4 1.6 Å 30 shared residues 91% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.054
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #4
0.201 Unusual size
Likely same site as P2Rank 1 1.6 Å 30 shared residues 91% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:12-14
UniProt: Binding site:136-138
UniProt: Binding site:27-27
UniProt: Binding site:31-31
UniProt: Binding site:35-35
UniProt: Binding site:37-39
UniProt: Binding site:38-38
UniProt: Binding site:40-40
UniProt: Binding site:92-92
UniProt: Binding site:94-94
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_A0A0H3GSC0
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_02392
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GSC0