Protein profile

KP13_02325

Cobalamin biosynthesis protein cobD

Genome: KpKP13

Gene: AHE42895.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GXL8
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Amino acids 319
Annotations 5
Features 29
PDB binders 0
Druggability 0.865

Overview

Basic information about this protein and its source genome.

Accession
KP13_02325
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE42895.1
Status
annotated
Amino acids
319
Structure source
AlphaFold + ColabFold
GO
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 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:0048472 Catalysis of the reaction: O-phospho-L-threonine + H+ = (R)-1-aminopropan-2-yl phosphate + CO2. 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:0015420 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: vitamin B12(out) + ATP + H2O = ADP + an vitamin B12(in) + H+ + phosphate. Vitamin B12 is alkylcob(III)alamin.

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
94.35

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 0.865
Structure A0A0H3GXL8
Pocket Pocket 3
P2Rank 0.94
Structure A0A0H3GXL8
Pocket Pocket 1
ColabFold model
FPocket 0.874 · Pocket 3
P2Rank 0.936 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 68 / 4744 genomes with a hit
Normalized 0.014

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • 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:0048472 Catalysis of the reaction: O-phospho-L-threonine + H+ = (R)-1-aminopropan-2-yl phosphate + CO2.
  • 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:0015420 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: vitamin B12(out) + ATP + H2O = ADP + an vitamin B12(in) + H+ + phosphate. Vitamin B12 is alkylcob(III)alamin.

Sequence Features

Domain/signature hits from InterPro and related databases.

29 records
Show feature table
Start End DB Term Name
178 203 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
13 17 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
27 44 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
77 81 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
45 55 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 17 SignalP_EUK SignalP-TM SignalP-TM
225 295 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
204 224 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
8 307 NCBIfam TIGR00380 adenosylcobinamide-phosphate synthase CbiB
8 307 InterPro IPR004485 Cobalamin biosynthesis CobD/CbiB
1 1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 318 Hamap MF_00024 Cobalamin biosynthesis protein CbiB [cbiB].
1 318 InterPro IPR004485 Cobalamin biosynthesis CobD/CbiB
52 74 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
7 297 Pfam PF03186 CobD/Cbib protein
7 297 InterPro IPR004485 Cobalamin biosynthesis CobD/CbiB
18 26 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
296 315 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
294 316 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
56 76 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
2 12 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
156 177 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
155 177 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 17 Phobius SIGNAL_PEPTIDE Signal peptide region
316 319 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
103 155 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
2 316 PANTHER PTHR34308 COBALAMIN BIOSYNTHESIS PROTEIN CBIB
2 316 InterPro IPR004485 Cobalamin biosynthesis CobD/CbiB
82 102 Phobius TRANSMEMBRANE 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.

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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_A0A0H3GXL8
AlphaFold — — full sequence — Viewing
ColabFold KP13_02325
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 0.865

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 27.67 0.922
2 6.18 0.308
3 4.68 0.205
4 4.03 0.161
5 1.75 0.032