Protein profile

VK055_4338

cobalamin biosynthesis protein CbiM

Genome: KpATCC43816

Gene: AIK82883.1 cbiM Structure source: AlphaFold + ColabFold UniProt A0A0H3GSH6
Export view
Amino acids 245
Annotations 6
Features 33
PDB binders 0
Druggability 0.651

Overview

Basic information about this protein and its source genome.

Accession
VK055_4338
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK82883.1 cbiM
Status
annotated
Amino acids
245
Structure source
AlphaFold + ColabFold
GO
GO:0043190 A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0000041 The directed movement of transition metal ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver. GO:0009236 The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom. GO:0006824 The directed movement of cobalt (Co2+) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0015087 Enables the transfer of cobalt (Co2+) ions from one side of a membrane to the other.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
CytoplasmicMembrane
ColabFold pLDDT
85.44

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 0.651
Structure A0A0H3GSH6
Pocket Pocket 4
P2Rank 0.065
Structure A0A0H3GSH6
Pocket Pocket 1
ColabFold model
FPocket 0.837 · Pocket 3
P2Rank 0.043 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 340 / 4744 genomes with a hit
Normalized 0.072

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0043190 A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0000041 The directed movement of transition metal ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
  • GO:0009236 The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
  • GO:0006824 The directed movement of cobalt (Co2+) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • GO:0015087 Enables the transfer of cobalt (Co2+) ions from one side of a membrane to the other.

Sequence Features

Domain/signature hits from InterPro and related databases.

33 records
Show feature table
Start End DB Term Name
25 30 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
73 91 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
132 137 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
92 102 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
31 244 Hamap MF_01462 Cobalt transport protein CbiM [cbiM].
31 244 InterPro IPR018024 Cobalamin (vitamin B12) transport protein CbiM
40 61 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
208 230 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
232 245 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
195 205 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
31 240 Gene3D G3DSA:1.10.1760.20 -
138 157 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 30 Phobius SIGNAL_PEPTIDE Signal peptide region
31 240 FunFam G3DSA:1.10.1760.20:FF:000001 Cobalt transport protein CbiM
169 194 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
31 240 NCBIfam TIGR00123 cobalt ECF transporter S component CbiM
31 240 InterPro IPR018024 Cobalamin (vitamin B12) transport protein CbiM
13 24 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
12 34 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
44 61 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 12 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
206 231 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
105 127 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
103 131 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
73 95 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
62 72 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
9 238 PANTHER PTHR43627 -
9 238 InterPro IPR018024 Cobalamin (vitamin B12) transport protein CbiM
31 39 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
32 238 Pfam PF01891 Cobalt uptake substrate-specific transmembrane region
32 238 InterPro IPR002751 Metal transport protein CbiM/NikMN
158 168 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
171 193 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; predicted models typically cover the full protein.

3D visualization script Full viewer

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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_A0A0H3GSH6
AlphaFold — — full sequence — Viewing
ColabFold VK055_4338
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
3 0.346
6 0.121
9 0.002
14 0.0

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 Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 2.69 0.065
2 2.5 0.056
3 1.39 0.014
4 0.92 0.004