Protein profile

KP13_00320

Nickel transport system permease protein nikB

Genome: KpKP13

Gene: nikB AHE42229.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H488
Export view
Amino acids 314
Annotations 4
Features 36
PDB binders 0
Druggability 0.566

Overview

Basic information about this protein and its source genome.

Accession
KP13_00320
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
nikB AHE42229.1
Status
annotated
Amino acids
314
Structure source
AlphaFold + ColabFold
GO
GO:0015099 Enables the transfer of nickel (Ni) cations from one side of a membrane to the other. GO:0035444 The directed movement of nickel (Ni) cations across a membrane by means of some agent such as a transporter or pore. GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.

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
91.8

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 0.566
Structure A0A0H3H488
Pocket Pocket 10
P2Rank 0.478
Structure A0A0H3H488
Pocket Pocket 1
ColabFold model
FPocket 0.546 · Pocket 23
P2Rank 0.416 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 40 / 4744 genomes with a hit
Normalized 0.008

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • GO:0015099 Enables the transfer of nickel (Ni) cations from one side of a membrane to the other.
  • GO:0035444 The directed movement of nickel (Ni) cations across a membrane by means of some agent such as a transporter or pore.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.

Sequence Features

Domain/signature hits from InterPro and related databases.

36 records
Show feature table
Start End DB Term Name
9 27 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
256 274 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
101 123 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
133 156 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 8 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
173 195 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 309 PANTHER PTHR43163 DIPEPTIDE TRANSPORT SYSTEM PERMEASE PROTEIN DPPB-RELATED
196 231 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
114 290 CDD cd06261 TM_PBP2
114 290 InterPro IPR000515 ABC transporter type 1, transmembrane domain MetI-like
157 175 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
97 121 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 104 Pfam PF19300 Binding-prot-dependent transport system membrane comp, N-term
1 104 InterPro IPR045621 ABC transporter type 1, GsiC-like, N-terminal domain
122 132 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
90 303 Gene3D G3DSA:1.10.3720.10 -
90 303 InterPro IPR035906 MetI-like superfamily
275 298 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
9 31 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
230 252 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
28 32 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
299 314 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
98 295 ProSiteProfiles PS50928 ABC transporter integral membrane type-1 domain profile.
98 295 InterPro IPR000515 ABC transporter type 1, transmembrane domain MetI-like
33 96 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
232 255 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
136 158 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
117 308 Pfam PF00528 Binding-protein-dependent transport system inner membrane component
117 308 InterPro IPR000515 ABC transporter type 1, transmembrane domain MetI-like
93 308 SUPERFAMILY SSF161098 MetI-like
93 308 InterPro IPR035906 MetI-like superfamily
280 302 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
176 195 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 312 NCBIfam TIGR02789 nickel ABC transporter permease subunit NikB
1 312 InterPro IPR014156 Nickel ABC transporter, permease subunit NikB
1 32 Phobius SIGNAL_PEPTIDE Signal peptide region

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_A0A0H3H488
AlphaFold — — full sequence — Viewing
ColabFold KP13_00320
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
10 0.566
15 0.031
18 0.001
9 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 10.33 0.478
2 5.39 0.211
3 5.06 0.19
4 1.16 0.008
5 1.02 0.005