Protein target profile

VK055_1544

DNA internalization-related competence protein ComEC/Rec2

Genome: KpATCC43816 Gene: AIK80164.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GMB1
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Length 750
Pocket druggability 0.999
Functional annotation 0 EC 3 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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 0.92. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 58 of 4744 screened genomes (1.2%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 1.00) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 1.00, but this pocket's geometry is unusually large/diffuse compared to this protein's other predicted pockets — may reflect a low-confidence or disordered model region rather than a real cavity.

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
1.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
32.644 Higher values support similarity to known essential genes.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
89.23 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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 0.999
Structure A0A0H3GMB1
Pocket Pocket 65
P2Rank 0.919
Structure A0A0H3GMB1
Pocket Pocket 1
ColabFold model
FPocket 0.987 · Pocket 35
P2Rank 0.908 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 58 / 4744 genomes with a hit
Prevalence 1.2%

Cross-references

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

Sequence

UniProt A0A0H3GMB1

Sequence

Primary amino-acid sequence viewer.

MLPLLWLPVLPGPCSLAGAGALALALIRLHGRAVAGVAMTLLLVVWGVLSAHQALWPTRHLTGAIRQAEVILSETDGQTLHRGQMVRLRGRYLFPPVGVTLYGELAPAPACAGQHWLMTLRLRPVHGQLNDGGFDSQRYALAQHRPLSGGIVAASALDARCSLRARYLTSLTRRLQTYPWRAVMLGLGMGERLSLPTEIKVLMQNTGTSHLMAISGLHIALAASLIMLLLRGVQYILPGRWIGWRLPLLAGLAGAVGYAWLTGMQPPALRTCLGLAVCCALRLSGQRWTAWQVWLCCLGAILVVDPLAVLSQSLWLSAFAVAGLIFWFQWLPLPAGRWRWPWKTIIALVHLQAGVTLLLLLLLLLLLLLPLQLLLFHGVSLTSMAANLLAVPLVTLLAVPLILTAMLVHLSGPEIVESLLWLAADRVLALLFWGLRRLPDGWLTLDTRWLWISILPWLLVMGWRFQSWRHSPALCLSVLFLLTRPFSRQPPADEWRVTMLDVGQGLAMVIERHGKALLYDTGPAWPQGDSGQQVIIPWLRWHHLQLQGIMLSHEHLDHRGGLDSVLQAWPQAWVRSPLGWAHHLPCHRGERWQWQGLNFQALWPLPGSTAKGNNHSCVVRIDDGRSSILLTGDIERQAEQAMISRYWRHLTSTLIQVPHHGSNTSSSALLIRRVDGAAALASASRYNAWRMPSYKVVQRYRQRGYRWFATPQQGQITVVFSAEGWQIHSLRDQVLPRWYHQWFGAPADNG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0030420 The process in which a naturally transformable bacterium acquires the ability to take up exogenous DNA. This term should be applied only to naturally transformable bacteria, and should not be used in the context of artificially induced bacterial transformation.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

48 records
Show feature table
Start End DB Term Name
57 210 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
211 230 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
188 461 Pfam PF03772 Competence protein
188 461 InterPro IPR004477 ComEC/Rec2-related protein
334 344 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
501 674 Pfam PF00753 Metallo-beta-lactamase superfamily
501 674 InterPro IPR001279 Metallo-beta-lactamase
28 33 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
288 310 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
34 56 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
466 750 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
5 27 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
208 230 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
496 660 CDD cd07731 ComA-like_MBL-fold
496 660 InterPro IPR035681 ComA-like, MBL domain
419 436 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
291 308 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
34 56 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
53 714 NCBIfam TIGR00361 DNA internalization-related competence protein ComEC/Rec2
53 714 InterPro IPR004797 Competence protein ComEC/Rec2
408 418 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
267 284 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
314 333 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
242 261 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
437 447 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
242 264 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
6 27 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
285 290 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
353 375 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
309 313 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
504 685 SMART SM00849 Lactamase_B_5a
504 685 InterPro IPR001279 Metallo-beta-lactamase
389 407 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
231 241 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
262 266 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
208 400 NCBIfam TIGR00360 ComEC/Rec2-related protein
208 400 InterPro IPR004477 ComEC/Rec2-related protein
492 731 Gene3D G3DSA:3.60.15.10 -
492 731 InterPro IPR036866 Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
1 5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
388 410 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
6 743 PANTHER PTHR30619 DNA INTERNALIZATION/COMPETENCE PROTEIN COMEC/REC2
448 465 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
370 388 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
315 333 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
491 737 SUPERFAMILY SSF56281 Metallo-hydrolase/oxidoreductase
491 737 InterPro IPR036866 Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
345 369 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.

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 #65
0.999
Likely same site as P2Rank 1 4.8 Å 22 shared residues 81% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #35
0.956
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Surrounding area
Site 3 FPocket #69
0.392
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Surrounding area
Site 4 FPocket #66
0.267
Likely same site as P2Rank 3 7.0 Å 11 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
0.919
Likely same site as FPocket 65 4.8 Å 22 shared residues 81% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.809
Likely same site as FPocket 65 7.3 Å 24 shared residues 100% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.69
Likely same site as FPocket 66 7.0 Å 11 shared residues 100% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.407
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Surrounding area
Site 5 P2Rank #5
0.37
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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_A0A0H3GMB1
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_1544
ColabFold — — full sequence — Loaded