KpATCC43816 Protein target profile

mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase

Accession: VK055_5027

Gene: AIK83553.1 manC 3D evidence: AlphaFold DB model + ColabFold model Metabolism 3 reactions UniProt Q48462
Length 471
Pocket druggability (P2Rank · AlphaFold DB model) 0.923
Metabolic reactions 3
Chokepoint Yes
Direct ligand evidence 0 51 total records
Functional annotation 1 EC 8 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

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
2.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
58.298 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
94.84 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) 0.923
Structure Q48462
Pocket Pocket 1
Druggability (FPocket) 0.103
Structure Q48462
Pocket Pocket 1
ColabFold model
P2Rank 0.931 · Pocket 1
FPocket 0.097 · Pocket 6
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 108 / 4744 genomes with a hit
Prevalence 2.3%

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a consuming chokepoint reaction in Amino sugar and nucleotide sugar metabolism, no human homolog detected.

Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Chokepoint gene
Catalyzed reactions

3 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MLLPVIMAGGTGSRLWPMSRELYPKQFLRLFGQNSMLQETITRLSGLEIHEPMVICNEEHRFLVAEQLRQLNKLSNNIILEPVGRNTAPAIALAALQATRHGDDPLMLVLAADHIINNQPVFHDAIRVAEQYADEGHLVTFGIVPNAPETGYGYIQRGVALTDSAHTPYQVARFVEKPDRERAEAYLASGEYYWNSGMFMFRAKKYLSELAKFRPDILEACQAAVNAADNGSDFISIPHDIFCECPDESVDYAVMEKTADAVVVGLDADWSDVGSWSALWEVSPKDEQGNVLSGDAWVHNSENCYINSDEKLVAAIGVENLVIVSTKDAVLVMNRERSQDVKKAVEFLKQNQRSEYKRHREIYRPWGRCDVVVQTPRFNVNRITVKPGGAFSMQMHHHRAEHWVILAGTGQVTVNGKQFLLTENQSTFIPIGAEHSLENPGRIPLEVLEIQSGSYLGEDDIIRIKDQYGRC

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
  • GO:0005976 The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
  • GO:0016779 Catalysis of the transfer of a nucleotidyl group from one compound (donor) to another (acceptor).
  • GO:0000271 The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
  • GO:0005525 Binding to GTP, guanosine triphosphate.
  • GO:0004475 Catalysis of the reaction: alpha-D-mannose 1-phosphate + GTP = diphosphate + GDP-alpha-D-mannose.
  • GO:0009298 The chemical reactions and pathways resulting in the formation of GDP-mannose, a substance composed of mannose in glycosidic linkage with guanosine diphosphate.
  • GO:0009103 The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
2 282 SUPERFAMILY SSF53448 Nucleotide-diphospho-sugar transferases
2 282 InterPro IPR029044 Nucleotide-diphospho-sugar transferases
349 470 Gene3D G3DSA:2.60.120.10 Jelly Rolls
349 470 InterPro IPR014710 RmlC-like jelly roll fold
2 351 FunFam G3DSA:3.90.550.10:FF:000046 Mannose-1-phosphate guanylyltransferase (GDP)
2 464 PANTHER PTHR46390 MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE
316 466 Pfam PF01050 Mannose-6-phosphate isomerase
316 466 InterPro IPR001538 Mannose-6-phosphate isomerase, type II, C-terminal
2 348 Gene3D G3DSA:3.90.550.10 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
2 348 InterPro IPR029044 Nucleotide-diphospho-sugar transferases
2 470 NCBIfam TIGR01479 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
2 470 InterPro IPR006375 Mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
348 465 FunFam G3DSA:2.60.120.10:FF:000032 Mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
337 464 CDD cd02213 cupin_PMI_typeII_C
186 470 SUPERFAMILY SSF51182 RmlC-like cupins
186 470 InterPro IPR011051 RmlC-like cupin domain superfamily
4 279 CDD cd02509 GDP-M1P_Guanylyltransferase
4 288 Pfam PF00483 Nucleotidyl transferase
4 288 InterPro IPR005835 Nucleotidyl transferase domain

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
0.923
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Surrounding area
Pocket 2 P2Rank #2
0.854
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Surrounding area
Pocket 3 P2Rank #3
0.549
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Surrounding area
Pocket 4 P2Rank #4
0.175
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Surrounding area
Pocket 5 P2Rank #5
0.162
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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_Q48462
AlphaFold DB full sequence Viewing
ColabFold VK055_5027
ColabFold full sequence Loaded

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

51 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 1 records from similar proteins
Structural ligands 1 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
GDD PDB via homolog 605.3 Da · LogP -4.63 · TPSA 331.7 Open detail RCSB PDB
ZINC104869865 ZINC proposed compound · Tanimoto 0.761 Detail ZINC
ZINC12504289 ZINC proposed compound · Tanimoto 0.761 Detail ZINC
ZINC34541308 ZINC proposed compound · Tanimoto 0.761 Detail ZINC
ZINC35000839 ZINC proposed compound · Tanimoto 0.761 Detail ZINC

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
GDD RCSB PDB Q9X0C3 605.3 Da LogP -4.63 TPSA 331.7 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.

Cross-references

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