KpATCC43816 Protein target profile

4-amino-4-deoxy-L-arabinose (L-Ara4N) transferase

Accession: VK055_3627

Gene: arnT AIK82182.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GZQ8
Length 551
Pocket druggability (P2Rank · AlphaFold DB model) 0.933
Direct ligand evidence 0 55 total records
Functional annotation 1 EC 9 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
1.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
92.78 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) 0.933
Structure A0A0H3GZQ8
Pocket Pocket 1
Druggability (FPocket) 0.915
Structure A0A0H3GZQ8
Pocket Pocket 1
ColabFold model
P2Rank 0.904 · Pocket 1
FPocket 0.925 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 73 / 4744 genomes with a hit
Prevalence 1.5%

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.

MKSIRYGVSLIALFALYYLLPLNFRLLWQPDETRYAEISREMLATGDWVVPHFLGLRYFEKPIAGYWINSIGQWLFGHNNFGVRFGSVFAITMTALLVAWLAWRIFRDKRVAILSPIIFLTAMLVYAIGTYAVLDPMITLWLALAMCSFWGAAQAHSRSGKILGYVLLGVACGMGVMTKGFLALAVPVVGVLPWVIARKRWREVLTYGWLAVIVCTLVVLPWGLAIAQREPDFWRYFFWVEHIQRFAEKDAQHKAPFWYYIPFLIAGSLPWLALLPGALKRGWLERDEARGALYLLGWVAMPFLFFSIAKGKLPTYILPCFAPLSILMARYALEAAKTGAKALRINGMINLGVGLLGLIAVLVVSPWGFMHKPVWTKIELYKCLLAAIAFAVWALMGWLAMKDSGRRWSLAALCPLGLALLVGFAIPDRVIDSKQPQFLVDIVSESLQPSRYVLTNNVGIAGGLAWELKRSDIIMFDKQGELKYGLDWPDAQGSFVSQAGFADWLAAHRQQGPVSLVLLMDKGESMLDLPLPKPDNAYELGRVVFLQYLPQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Subcellular localization

Localization
CytoplasmicMembrane

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0016763 Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0000030 Catalysis of the transfer of a mannosyl group to an acceptor molecule, typically another carbohydrate or a lipid.
  • GO:0006493 A glycoprotein biosynthetic process starting with the covalent linkage of carbohydrate or carbohydrate derivative unit via a glycosidic bond to the oxygen atom of a serine, threonine, hydroxylysine, hydroxyproline or tyrosine side chain in a protein, which can be further elongated with the sequential addition of sugar units resulting in the formation of a protein O-linked glycan.
  • 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:0103015 Catalysis of the reaction: (Kdo)2-lipid A + 2 4-amino-4-deoxy-alpha-L-arabinopyranosyl di-trans,poly-cis-undecaprenyl phosphate = (beta-L-Ara4N)2-(KDO)2-lipid A + 2 ditrans,polycis-undecaprenyl phosphate.
  • GO:0009245 The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
  • 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.
  • GO:0010041 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an iron(III) ion stimulus.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

41 records
Show feature table
Start End DB Term Name
112 134 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
132 137 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
334 344 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
257 279 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
112 131 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
310 314 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
207 227 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
10 542 PANTHER PTHR33908 MANNOSYLTRANSFERASE YKCB-RELATED
1 551 Hamap MF_01165 Undecaprenyl phosphate-alpha-4-amino-4-deoxy-L-arabinose arabinosyl transferase [arnT].
1 551 InterPro IPR022839 Undecaprenyl phosphate-alpha-4-amino-4-deoxy-L-arabinose arabinosyl transferase
384 401 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
408 426 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
315 333 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
280 290 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
291 309 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
175 197 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
157 161 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
7 29 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
313 335 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
162 195 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
402 407 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
257 279 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
384 401 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
292 309 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
138 156 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
204 226 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
107 111 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
81 103 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
347 369 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
6 24 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
365 383 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
4 237 Pfam PF02366 Dolichyl-phosphate-mannose-protein mannosyltransferase
4 237 InterPro IPR003342 Glycosyl transferase family 39/83
345 364 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
228 256 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
427 551 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
408 427 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
85 106 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
25 84 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
196 206 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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.933
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.753
Likely same site as FPocket 4 1.8 Å 15 shared residues 94% of smaller site
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.289
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.177
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.128
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.915 Unusual size
Show in viewer
Surrounding area
Pocket 2 FPocket #4
0.854
Likely same site as P2Rank 2 1.8 Å 15 shared residues 94% of smaller site
Show in viewer
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_A0A0H3GZQ8
AlphaFold DB full sequence Viewing
ColabFold VK055_3627
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.

55 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
5TR PDB via homolog 847.3 Da · LogP 18.33 · TPSA 66.8 Open detail RCSB PDB
DSL PDB via homolog Detail RCSB PDB
MPG PDB via homolog Detail RCSB PDB
PC PDB via homolog Detail RCSB PDB
CHEMBL255766 ChEMBL via homolog Detail ChEMBL

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
5TR RCSB PDB Q1LDT6 847.3 Da LogP 18.33 TPSA 66.8 2 viol. ✓ Clean CC(=CCC/C(=C/CC/C(=C/CC/C(=C/CC/C(=C\CC/C(=C/CC…
DSL RCSB PDB Q1LDT6 779.2 Da LogP 16.60 TPSA 66.8 2 viol. ✓ Clean CC(=CCC/C(=C/CC/C(=C\CC/C(=C\CC/C(=C\CC/C(=C\CC…
MPG RCSB PDB Q1LDT6 356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC/C=C\CCCCCCCCOC(=O)[C@@H](CO)O
PC RCSB PDB Q1LDT6 184.2 Da LogP -0.20 TPSA 66.8 ✓ Ro5 ✓ Clean C[N+](C)(C)CCOP(=O)(O)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.