KpATCC43816 Protein target profile

cobalamin biosynthesis protein CbiD

Accession: VK055_4329

Gene: cbiD AIK82874.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3H282
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Length 379
Pocket druggability (P2Rank · AlphaFold DB model) 0.835
Functional annotation 1 EC 5 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. Second pocket predictor agrees P2Rank predicted binding-site probability 0.83. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 52 of 4744 screened genomes (1.1%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.83) — check the ligand evidence before deprioritizing on off-target risk alone. Weak predicted binding pocket FPocket selected-pocket score 0.14.

Evidence gaps

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
1.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
31.046 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
92.9 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) 0.835
Structure A0A0H3H282
Pocket Pocket 1
Druggability (FPocket) 0.142
Structure A0A0H3H282
Pocket Pocket 28
ColabFold model
P2Rank 0.832 · Pocket 1
FPocket 0.265 · Pocket 5
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 52 / 4744 genomes with a hit
Prevalence 1.1%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSDQTFDAPVWHHGKALRKGYTTGSCATAAAKVAALMVMRQHLIHQVSIVTPSGVTLCLNVESPHVEGQQAVAAIRKDGGDDVDATHGMLIFARVTLNDSGEISLQGGEGIGTVTRKGIGLPTGSPAINRTPRHTIETAVREAIGPTRGAQVEIFAPEGALRAQKTYNARLGILGGISIIGTTGIVTPMSEESWKRSLSLELEIKRAAGLERVVLVPGNHGERFVREQMGIDPQMVVTMSNFVGYMIEEAVRLGFRQIVLIGHPGKLIKIAAGIFHTHSHIADARMETLVAHLALLGAPLPLLTLVSECDTTEAAMEHIDAWGYQRLYNHLAERICQRVLEMLRFTQQPPTCDAVLFSFDNQVLGSSRPLAAIARELTC

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
  • 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:0043780 Catalysis of the reaction: cobalt-precorrin 5B + S-adenosylmethionine = S-adenosylhomocysteine + cobalt-precorrin 6A.
  • GO:0019251 The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12) in the absence of oxygen.
  • GO:0032259 The process in which a methyl group is covalently attached to a molecule.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
10 368 PANTHER PTHR35863 COBALT-PRECORRIN-5B C(1)-METHYLTRANSFERASE
10 368 InterPro IPR002748 Cobalt-precorrin-5B C(1)-methyltransferase CbiD
13 374 PIRSF PIRSF026782 CbiD
13 374 InterPro IPR002748 Cobalt-precorrin-5B C(1)-methyltransferase CbiD
6 291 SUPERFAMILY SSF111342 CbiD-like
6 291 InterPro IPR036074 CbiD superfamily
17 273 Pfam PF01888 CbiD
17 273 InterPro IPR002748 Cobalt-precorrin-5B C(1)-methyltransferase CbiD
17 367 Hamap MF_00787 Cobalt-precorrin-5B C(1)-methyltransferase [cbiD].
17 367 InterPro IPR002748 Cobalt-precorrin-5B C(1)-methyltransferase CbiD
19 188 Gene3D G3DSA:3.30.2110.10 -
19 188 InterPro IPR036074 CbiD superfamily
17 365 NCBIfam TIGR00312 cobalt-precorrin-5B (C(1))-methyltransferase CbiD
17 365 InterPro IPR002748 Cobalt-precorrin-5B C(1)-methyltransferase CbiD

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
0.835
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Surrounding area
Pocket 2 P2Rank #2
0.28
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Surrounding area
Pocket 3 P2Rank #3
0.131
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Surrounding area
Pocket 4 P2Rank #4
0.013
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Surrounding area
Pocket 5 P2Rank #5
0.011
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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_A0A0H3H282
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4329
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3H282