Protein target profile

VK055_0398

cytochrome c-type biogenesis protein CcmF

Genome: KpATCC43816 Gene: ccmF AIK79024.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GR06
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Length 650
Pocket druggability 1
Functional annotation 0 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

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 1.00. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 166 of 4744 screened genomes (3.5%) 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
3.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
92.34 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 1
Structure A0A0H3GR06
Pocket Pocket 2
P2Rank 0.998
Structure A0A0H3GR06
Pocket Pocket 1
ColabFold model
FPocket 0.995 · Pocket 5
P2Rank 0.998 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 166 / 4744 genomes with a hit
Prevalence 3.5%

Cross-references

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

Sequence

UniProt A0A0H3GR06

Sequence

Primary amino-acid sequence viewer.

MMPELGNFLLCLAAGLALLLSVYPLWGAARQDRRLMALARPLACGLFACIGGAFLLLVHAFVVNDFTVRYVAENSNSALPVWYRVAATWGAHEGSLLLWVLLLSVWTFAVAIFSRRMPLDAVARVLAVMGMIAFGFLLFILFTSNPFSRGLPQYPIDGRDLNPLLQDIGMIFHPPILYMGYVGFSVAFAFAIASLLAGRLDTAWARWSRPWTQAAWMFLTLGIVLGSAWAYYELGWGGWWFWDPVENASFMPWLVGTALLHSLAVTEKRGSFRAWTVLLAIAAFSLCLLGTFLVRSGVLVSVHAFASDPSRGLFILVLLIVAIGGSLLLYALKGGRVRARVEHTLWSRESFLLGNNILLMAAMLVVLLGTLLPLVHKELGLGSISIGEPFFNTMFTALMAPFALLLGLGPLIRWRRDDVARQIKRLIIALLVTLSLSLALPWLLQDRITAMAVIGLMMALWVLIFALMEVHERATHRHGFWRGLRTLTRSQWGMVLGHVGVAVTVIGITFSQNYSVERDVRMRPGDSIDIHRYHFVFNGVRNIVGPNWTGGEGIIAVTRNGRPEATLYAEKRFYTASRMMMTEAAISGGLTRDLYAALGEELSDGSWAVRLYYKPFVRWIWYGGVLMALGGLCCMLDPRYRMRKKLQEAS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

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: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:0020037 Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring.
  • 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: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.

84 records
Show feature table
Start End DB Term Name
176 198 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
38 62 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
206 574 PANTHER PTHR43653 CYTOCHROME C ASSEMBLY PROTEIN-RELATED
206 574 InterPro IPR003567 Cytochrome c-type biogenesis protein
210 230 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
250 266 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
267 277 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
132 149 PRINTS PR01410 Cytochrome c-type biogenesis protein signature
132 149 InterPro IPR003567 Cytochrome c-type biogenesis protein
80 106 PRINTS PR01410 Cytochrome c-type biogenesis protein signature
80 106 InterPro IPR003567 Cytochrome c-type biogenesis protein
160 182 PRINTS PR01410 Cytochrome c-type biogenesis protein signature
160 182 InterPro IPR003567 Cytochrome c-type biogenesis protein
295 311 PRINTS PR01410 Cytochrome c-type biogenesis protein signature
295 311 InterPro IPR003567 Cytochrome c-type biogenesis protein
211 237 PRINTS PR01410 Cytochrome c-type biogenesis protein signature
211 237 InterPro IPR003567 Cytochrome c-type biogenesis protein
245 265 PRINTS PR01410 Cytochrome c-type biogenesis protein signature
245 265 InterPro IPR003567 Cytochrome c-type biogenesis protein
311 330 PRINTS PR01410 Cytochrome c-type biogenesis protein signature
311 330 InterPro IPR003567 Cytochrome c-type biogenesis protein
275 295 PRINTS PR01410 Cytochrome c-type biogenesis protein signature
275 295 InterPro IPR003567 Cytochrome c-type biogenesis protein
307 311 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
53 641 NCBIfam TIGR00353 heme lyase CcmF/NrfE family subunit
53 641 InterPro IPR003568 Cytochrome c-type biogenesis protein CcmF
450 470 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
176 198 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
445 449 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
353 375 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
619 636 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
333 352 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
115 120 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
376 394 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
471 490 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.
415 425 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
449 471 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
277 299 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
353 375 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
425 444 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
40 62 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
314 332 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
619 636 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
95 114 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
395 414 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
314 329 PRINTS PR01411 Cytochrome c-type biogenesis protein CcmF signature
314 329 InterPro IPR003568 Cytochrome c-type biogenesis protein CcmF
395 414 PRINTS PR01411 Cytochrome c-type biogenesis protein CcmF signature
395 414 InterPro IPR003568 Cytochrome c-type biogenesis protein CcmF
631 644 PRINTS PR01411 Cytochrome c-type biogenesis protein CcmF signature
631 644 InterPro IPR003568 Cytochrome c-type biogenesis protein CcmF
4 28 PRINTS PR01411 Cytochrome c-type biogenesis protein CcmF signature
4 28 InterPro IPR003568 Cytochrome c-type biogenesis protein CcmF
352 369 PRINTS PR01411 Cytochrome c-type biogenesis protein CcmF signature
352 369 InterPro IPR003568 Cytochrome c-type biogenesis protein CcmF
113 136 PRINTS PR01411 Cytochrome c-type biogenesis protein CcmF signature
113 136 InterPro IPR003568 Cytochrome c-type biogenesis protein CcmF
190 205 PRINTS PR01411 Cytochrome c-type biogenesis protein CcmF signature
190 205 InterPro IPR003568 Cytochrome c-type biogenesis protein CcmF
5 27 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
278 306 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
248 265 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
6 26 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
491 510 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
96 114 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
121 142 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
89 296 Pfam PF01578 Cytochrome C assembly protein
89 296 InterPro IPR002541 Cytochrome c assembly protein
390 412 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
426 444 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
316 637 Pfam PF16327 Cytochrome c-type biogenesis protein CcmF C-terminal
316 637 InterPro IPR032523 Cytochrome c-type biogenesis protein CcmF, C-terminal
637 650 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
121 143 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
27 37 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
143 175 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
492 514 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
312 332 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
211 233 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
511 618 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
199 209 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
63 95 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
231 249 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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 #2
1.0
Likely same site as P2Rank 1 1.1 Å 53 shared residues 96% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #7
0.769
Likely same site as P2Rank 2 1.0 Å 27 shared residues 93% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.998
Likely same site as FPocket 2 1.1 Å 53 shared residues 96% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.969
Likely same site as FPocket 7 1.0 Å 27 shared residues 93% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.584
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.263
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Surrounding area
Site 5 P2Rank #5
0.217
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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_A0A0H3GR06
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_0398
ColabFold — — full sequence — Loaded