KpATCC43816 Protein target profile

RIP metalloprotease RseP

Accession: VK055_2376

Gene: rseP AIK80973.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GMW3
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Length 450
Pocket druggability (P2Rank · AlphaFold DB model) 0.94
Functional annotation 1 EC 6 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

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.94, FPocket 0.91). Use the 3D pocket comparison to verify whether they identify the same site. 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. Strong predicted binding pocket FPocket selected-pocket score 0.91. This is a computational pocket signal, not binding validation. Review the complete evidence below

Risks to review

Microbiome similarity 141 of 4744 screened genomes (3.0%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.94) — check the ligand evidence before deprioritizing on off-target risk alone.

Evidence gaps

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
3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
88.444 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
94.01 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) 0.94
Structure A0A0H3GMW3
Pocket Pocket 1
Druggability (FPocket) 0.911
Structure A0A0H3GMW3
Pocket Pocket 28
ColabFold model
P2Rank 0.969 · Pocket 1
FPocket 0.72 · Pocket 32
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 141 / 4744 genomes with a hit
Prevalence 3.0%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MLSVLWNLAAFIIALGVLITVHEFGHFWVARRCGIRVERFSIGFGKALWRRMDKQGTEFVIALIPLGGYVKMLDERVEAVAPEMRHYAFNNKTVGQRAAVIAAGPIANFIFAIFAYWLVFIIGVPGVRPVVDEITPNSVAAQAQIAKGTELKAIDGIETPDWDAVRLQLVAKIGNPQTIVTVAPFGTNQRQDKIVDLRHWSFEPDKQDPVTSLGIQPRSAQIDTVLAEVQAGSAAQKAGLQAGDRIVKVDGQPLTQWMTFVNLVRDNPGKALALEIERQGSALPLTLTPDAKTVKGKAEGFAGVVPKVIPLPEEYKTVRQYGPFAAIAEATDKTWQLMSLTVRMLGKLITGDVKLNNLSGPISIAQGAGMSAEFGLIYYLMFLALISVNLGIINLFPLPVLDGGHLLFLAIEKLKGGPVSERVQDFSYRIGSILLVLLMGLALFNDFSRL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization
CytoplasmicMembrane

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0004222 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
  • GO:0005515 Binding to a protein.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

43 records
Show feature table
Start End DB Term Name
98 119 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
115 185 SMART SM00228 pdz_new
115 185 InterPro IPR001478 PDZ domain
211 280 SMART SM00228 pdz_new
211 280 InterPro IPR001478 PDZ domain
216 450 PANTHER PTHR42837 REGULATOR OF SIGMA-E PROTEASE RSEP
216 450 InterPro IPR004387 Peptidase M50, putative membrane-associated zinc metallopeptidase
87 181 SUPERFAMILY SSF50156 PDZ domain-like
87 181 InterPro IPR036034 PDZ superfamily
74 97 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
98 120 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
120 375 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
376 398 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
227 278 Pfam PF17820 PDZ domain
227 278 InterPro IPR041489 PDZ domain 6
56 73 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
3 450 NCBIfam TIGR00054 RIP metalloprotease RseP
3 450 InterPro IPR004387 Peptidase M50, putative membrane-associated zinc metallopeptidase
212 289 CDD cd00989 PDZ_metalloprotease
10 182 Pfam PF02163 Peptidase family M50
10 182 InterPro IPR008915 Peptidase M50
224 438 Pfam PF02163 Peptidase family M50
224 438 InterPro IPR008915 Peptidase M50
8 120 CDD cd06163 S2P-M50_PDZ_RseP-like
426 444 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
196 290 SUPERFAMILY SSF50156 PDZ domain-like
196 290 InterPro IPR036034 PDZ superfamily
445 450 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
116 189 CDD cd00989 PDZ_metalloprotease
426 445 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
397 425 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
220 309 Gene3D G3DSA:2.30.42.10 -
220 309 InterPro IPR036034 PDZ superfamily
376 396 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
30 55 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
199 291 ProSiteProfiles PS50106 PDZ domain profile.
199 291 InterPro IPR001478 PDZ domain
6 29 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
221 309 FunFam G3DSA:2.30.42.10:FF:000095 Zinc metalloprotease
2 21 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
126 219 Gene3D G3DSA:2.30.42.10 -
126 219 InterPro IPR036034 PDZ superfamily

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
0.94
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Surrounding area
Pocket 2 P2Rank #2
0.211
Likely same site as FPocket 28 1.4 Å 12 shared residues 80% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.073
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Surrounding area
Pocket 4 P2Rank #4
0.06
Likely same site as FPocket 11 1.1 Å 9 shared residues 100% of smaller site
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Surrounding area
Pocket 5 P2Rank #5
0.026
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #28
0.911
Likely same site as P2Rank 2 1.4 Å 12 shared residues 80% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #11
0.9
Likely same site as P2Rank 4 1.1 Å 9 shared residues 100% of smaller site
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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_A0A0H3GMW3
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_2376
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GMW3