KpATCC43816 Protein target profile

heme exporter protein CcmB

Accession: VK055_0394

Gene: AIK79020.1 ccmB 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GU00
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Length 219
Pocket druggability (P2Rank · AlphaFold DB model) 0.183
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. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Moderate predicted binding pocket FPocket selected-pocket score 0.69. This supports review but is not experimental validation. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 116 of 4744 screened genomes (2.4%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.69) — check the ligand evidence before deprioritizing on off-target risk alone. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.18.

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
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
43.192 Higher values support similarity to known essential genes.
DEG E-value
5.91e-42 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
94.07 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) 0.183
Structure A0A0H3GU00
Pocket Pocket 1
Druggability (FPocket) 0.69
Structure A0A0H3GU00
Pocket Pocket 3
ColabFold model
P2Rank 0.233 · Pocket 1
FPocket 0.726 · Pocket 3
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 116 / 4744 genomes with a hit
Prevalence 2.4%

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.

MMRALLARELRLAWRSGAEILNPLWFFLIVITLFPFGVGAAPQLLAQIAPGVVWVAALLAALLVMDRLFRDDWQDGSLEQLMLLPTPLVAVVLVKVVAHWMMSGLPLLIVSPLAALLLGMSLHDAGVLALTLLLGTPTLSFLGAVGVGLTVGLKRGGVLLSLLVLPLAVPLLIFATAACQAAAAELPVGGYLAMLAAFLTASATLCPFATAAALRLTVR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Subcellular localization

Localization
CytoplasmicMembrane

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:0015886 The directed movement of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • GO:0017004 The aggregation, arrangement and bonding together of a cytochrome complex. A cytochrome complex is a protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions.
  • GO:0015232 Enables the transfer of heme from one side of a membrane to the other.
  • 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:1903607 The chemical reactions and pathways resulting in the formation of cytochrome c.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

33 records
Show feature table
Start End DB Term Name
96 118 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
215 219 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
127 151 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
44 69 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
128 150 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
39 43 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
189 214 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
184 188 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
52 69 PRINTS PR01414 Cytochrome c-type biogenesis protein CcmB signature
131 154 PRINTS PR01414 Cytochrome c-type biogenesis protein CcmB signature
100 118 PRINTS PR01414 Cytochrome c-type biogenesis protein CcmB signature
26 47 PRINTS PR01414 Cytochrome c-type biogenesis protein CcmB signature
75 98 PRINTS PR01414 Cytochrome c-type biogenesis protein CcmB signature
192 215 PRINTS PR01414 Cytochrome c-type biogenesis protein CcmB signature
2 215 Pfam PF03379 CcmB protein
2 215 InterPro IPR003544 Cytochrome c-type biogenesis protein CcmB
1 19 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
20 38 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
158 183 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
20 39 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
157 179 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 219 PIRSF PIRSF002764 CcmB
1 219 InterPro IPR026031 Cytochrome c-type biogenesis protein CcmB, bacteria
70 80 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
2 205 PANTHER PTHR30070 HEME EXPORTER PROTEIN B
2 205 InterPro IPR003544 Cytochrome c-type biogenesis protein CcmB
103 126 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
5 215 NCBIfam TIGR01190 heme exporter protein CcmB
5 215 InterPro IPR026031 Cytochrome c-type biogenesis protein CcmB, bacteria
81 102 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
194 216 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
152 157 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
43 65 TMHMM TMhelix 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 · P2Rank

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

Pocket 1 P2Rank #1
0.183
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Surrounding area
Pocket 2 P2Rank #2
0.089
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Surrounding area
Pocket 3 P2Rank #3
0.068
Likely same site as FPocket 3 1.8 Å 8 shared residues 100% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.002
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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 #3
0.69
Likely same site as P2Rank 3 1.8 Å 8 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_A0A0H3GU00
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_0394
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GU00