Protein target profile

VK055_0401

cytochrome c biogenesis protein CcmH

Genome: KpATCC43816 Gene: AIK79027.1 ccmH2 3D evidence: AlphaFold DB model + ColabFold model UniProt A0AAX3FF54

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Length 280

Pocket druggability 0.997

Functional annotation 0 EC 5 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. Structure available AlphaFold DB model + ColabFold model

Risks to review

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: 0.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 0.0 Higher values support similarity to known essential genes.

Localization

Localization: CytoplasmicMembrane

Structure confidence

ColabFold pLDDT: 82.78 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 0.997

Structure A0AAX3FF54

Pocket Pocket 18

P2Rank 0.066

Structure A0AAX3FF54

Pocket Pocket 1

ColabFold model

FPocket 0.191 · Pocket 7

P2Rank 0.018 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 7 / 4744 genomes with a hit

Prevalence 0.1%

Cross-references

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

Sequence

UniProt A0AAX3FF54

Sequence

Primary amino-acid sequence viewer.

MSLLVVIVALLLAGALGLLYFPWSGKGAVDRDALNRALYQSRLQELAQERGEDNPALVVELQRTLLTDIPPQAQSGERPLRRWALFPGALLLVVLSLGLYLKTSDIGQVLLWQQAERHFPALLQQVKDPTAAPLRMDELAELRLGLRSHLQDTPNDLAGWQLLGRLGLLLNDGETAIGAFGRAHALAADDPAAAFDYASALVRAGDRGQVRMGELLLRDLHQRQPNSLPVLEMLALSAVRNEDYPEAVAALQALLARLPEGDARREAIVRQLAQAQQQAQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

GO:0005515 Binding to a protein.
GO:0030313 An envelope that surrounds a bacterial cell and includes the cytoplasmic membrane and everything external, encompassing the periplasmic space, cell wall, and outer membrane if present.
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:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

17 records

Show feature table

Start	End	DB	Term	Name
14	17	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
144	280	Gene3D	G3DSA:1.25.40.10	Tetratricopeptide repeat domain
144	280	InterPro	IPR011990	Tetratricopeptide-like helical domain superfamily
1	17	SignalP_EUK	SignalP-TM	SignalP-TM
1	2	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
1	17	Phobius	SIGNAL_PEPTIDE	Signal peptide region
3	13	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
83	101	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
83	101	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
2	24	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
18	82	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
80	279	PANTHER	PTHR47870	CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCMH
102	280	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
4	103	NCBIfam	TIGR03142	c-type cytochrome biogenesis protein CcmI
4	103	InterPro	IPR017560	Cytochrome c-type biogenesis protein CcmI
154	260	SUPERFAMILY	SSF48452	TPR-like
154	260	InterPro	IPR011990	Tetratricopeptide-like helical domain 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 · FPocket

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

Site 1 FPocket #18

0.997

Unusual size

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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

0.066

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Surrounding area

Site 2 P2Rank #2

0.01

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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_A0AAX3FF54	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_0401	ColabFold	—	—	full sequence	—	Loaded