KpKP13 Protein target profile

Protein cbiM

Accession: KP13_02336

Gene: cbiM AHE42906.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GSH6
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Length 245
Pocket druggability (P2Rank · AlphaFold DB model) 0.065
Functional annotation 0 EC 6 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. Moderate predicted binding pocket FPocket selected-pocket score 0.65. This supports review but is not experimental validation. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 338 of 4744 screened genomes (7.1%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.65) — check the ligand evidence before deprioritizing on off-target risk alone. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.07.

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
7.1% 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.

Structure confidence

ColabFold pLDDT
86.46 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.065
Structure A0A0H3GSH6
Pocket Pocket 1
Druggability (FPocket) 0.651
Structure A0A0H3GSH6
Pocket Pocket 4
ColabFold model
P2Rank 0.047 · Pocket 1
FPocket 0.958 · Pocket 6
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 338 / 4744 genomes with a hit
Prevalence 7.1%

Sequence

Primary amino-acid sequence viewer.

MNQVKSLKQLSYGGLAAAVLLIIVPQEAFAMHIMEGFLPPMWALAWWLLFLPCLWYGLVRLRRIVQEESNQKVLLALCGAFIFVLSALKIPSVTGSCSHPTGVGLAVILFGPGVVAVLGAIVLLFQALLLAHGGLTTLGANGMSMAVIGPMVGYLVWKLACRAGIRRDVGVFLCAMLADLMTYFVTSVQLGVAFPDPATGAGGSIAKFMGIFCLTQIPIAIAEGLLTVMIYDQLTKRRLIAAEAH

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

6
  • 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:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • 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: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: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:0015087 Enables the transfer of cobalt (Co2+) ions from one side of a membrane to the other.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
31 243 Hamap MF_01462 Cobalt transport protein CbiM [cbiM].
31 243 InterPro IPR018024 Cobalamin (vitamin B12) transport protein CbiM
31 240 NCBIfam TIGR00123 cobalt ECF transporter S component CbiM
31 240 InterPro IPR018024 Cobalamin (vitamin B12) transport protein CbiM
42 61 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
169 188 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
130 134 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
189 207 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
232 245 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
169 188 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
12 30 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
32 238 Pfam PF01891 Cobalt uptake substrate-specific transmembrane region
32 238 InterPro IPR002751 Metal transport protein CbiM/NikMN
36 58 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
31 41 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
134 156 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
103 129 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
9 238 PANTHER PTHR43627 -
9 238 InterPro IPR018024 Cobalamin (vitamin B12) transport protein CbiM
73 95 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
62 72 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
31 240 FunFam G3DSA:1.10.1760.20:FF:000001 Cobalt transport protein CbiM
92 102 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
208 231 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
135 157 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
10 29 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
73 91 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
102 124 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
31 240 Gene3D G3DSA:1.10.1760.20 -
208 230 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
158 168 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.

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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.065
Likely same site as FPocket 2 5.2 Å 4 shared residues 50% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.056
Likely same site as FPocket 4 1.3 Å 8 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.014
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Surrounding area
Pocket 4 P2Rank #4
0.004
Likely same site as FPocket 2 2.8 Å 6 shared residues 100% of smaller site
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #4
0.651
Likely same site as P2Rank 2 1.3 Å 8 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #3
0.346
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Surrounding area
Pocket 3 FPocket #2
0.321
Likely same site as P2Rank 4 2.8 Å 6 shared residues 100% of smaller site
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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_A0A0H3GSH6
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_02336
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GSH6