Protein profile

VK055_0398

cytochrome c-type biogenesis protein CcmF

Genome: KpATCC43816

Gene: AIK79024.1 ccmF Structure source: AlphaFold + ColabFold UniProt A0A0H3GR06

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Amino acids 650

Annotations 6

Features 84

PDB binders 0

Druggability 1

Overview

Basic information about this protein and its source genome.

Accession: VK055_0398
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK79024.1 ccmF
Status: annotated
Amino acids: 650
Structure source: AlphaFold + ColabFold

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.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 65.432
DEG E-value: 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 92.34

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its 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

Normalized 0.035

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GR06	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_0398	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
2				1.0
7				0.769

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	100.14	0.996
2	33.91	0.948
3	11.41	0.61
4	7.73	0.409
5	5.1	0.234

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
5				0.995
1				0.76
26				0.594
19				0.245

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	102.46	0.996
2	32.19	0.942
3	13.94	0.705
4	11.27	0.603
5	3.65	0.137