The University of Texas Medical Branch
Department of Biochemistry and Molecular Biology Sealy Center for Structural Biology Computational Biology



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                SDAP - Structural Database of Allergenic Proteins
Go to: SDAP All allergens       Go to: SDAP Food allergens
Send a comment to Werner Braun      Submit new allergen information to SDAP
  
Alphabetical listing of allergens: A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
Access to SDAP is available free of charge for Academic and non-profit use.
Licenses for commercial use can be obtained by contacting W. Braun (webraun@utmb.edu).
Secure access to SDAP is available from https://fermi.utmb.edu/SDAP
Allergen Info Description
Allergen ID 1
Allergen Scientific Name Amb a 1
Allergen Species - Systematic Name Ambrosia artemisiifolia
Allergen Species - Common Name short ragweed
Allergen Common source weed
Allergen Common name Asterales
Allergen Keywords antigen E; AgE
Allergen IUIS (Yes=1, No=0) 1
ID Allergen Name
Amb a 1 - References
ID Reference
Pubmed ID: 1809687
Griffith IJ, Pollock J, Klapper DG, Rogers BL, Nault AK, Sequence polymorphism of Amb a I and Amb a II, the major allergens in Ambrosia artemisiifolia (short ragweed). Int Arch Allergy Appl Immunol. 1991;96(4):296-304.
Pubmed ID: 1702434
Rafnar T, Griffith IJ, Kuo MC, Bond JF, Rogers BL, Klapper DG. Cloning of Amb a I (antigen E), the major allergen family of short ragweed pollen. J Biol Chem. 1991 Jan 15;266(2):1229-36.
Pubmed ID: 15208597
Simons FE, Shikishima Y, Van Nest G, Eiden JJ, HayGlass KT, Selective immune redirection in humans with ragweed allergy by injecting Amb a 1 linked to immunostimulatory DNA. J Allergy Clin Immunol. 2004 Jun;113(6):1144-51.
Amb a 1 - Protein Sequences
Source Link to source
SwissProt P27759
SwissProt P27760
SwissProt P27761
SwissProt P28744
GenBank 166443
Amb a 1 - Theoretical Model Structure
Model ID PDB file PDB Snapshot PDB Snapshot 90 PDB Snapshot 180 PDB Snapshot 270 3D PDB View
15 GetModel Model Pic Model Pic Model Pic Model Pic Click here
16 GetModel Model Pic Model Pic Model Pic Model Pic Click here
17 GetModel Model Pic Model Pic Model Pic Model Pic Click here
797 GetModel Model Pic Model Pic Model Pic Model Pic Click here
Amb a 1 - Sequence Search
Sequence Header Sequence
Amb a 1
SDAP Sequence ID: 15
SDAP Allergen ID: 1
MGIKHCCYILYFTLALVTLLQPVRSAEDLQEILPVNETRRLTTSGAYNIIDGCWRGKADWAENRKALADCAQGFGKGTVGGKDGDIYTVTSELDDDVANPKEGTLRFGAAQNRPLWIIFERDMVIRLDKEMVVNSDKTIDGRGAKVEIINAGFTLNGVKNVIIHNINMHDVKVNPGGLIKSNDGPAAPRAGSDGDAISISGSSQIWIDHCSLSKSVDGLVDAKLGTTRLTVSNSLFTQHQFVLLFGAGDENIEDRGMLATVAFNTFTDNVDQRMPRCRHGFFQVVNNNYDKWGSYAIGGSASPTILSQGNRFCAPDERSKKNVLGRHGEAAAESMKWNWRTNKDVLENGAIFVASGVDPVLTPEQSAGMIPAEPGESALSLTSSAGVLSCQPGAPC
View 3D Structure Click here to view 3D model structure of allergen
Fasta Search in SDAP
Blast Swissprot database search at NCBI
Blast PDB database search at NCBI
Blast NR database search at NCBI
Expasy Blast Search
Amb a 1
SDAP Sequence ID: 16
SDAP Allergen ID: 1
MGIKHCCYILYFTLALVTLLQPVRSAEDVEEFLPSANETRRSLKACEAHNIIDKCWRCKADWANNRQALADCAQGFAKGTYGGKHGDVYTVTSDKDDDVANPKEGTLRFAAAQNRPLWIIFKRNMVIHLNQELVVNSDKTIDGRGVKVNIVNAGLTLMNVKNIIIHNINIHDIKVCPGGMIKSNDGPPILRQQSDGDAINVAGSSQIWIDHCSLSKASDGLLDITLGSSHVTVSNCKFTQHQFVLLLGADDTHYQDKGMLATVAFNMFTDHVDQRMPRCRFGFFQVVNNNYDRWGTYAIGGSSAPTILSQGNRFFAPDDIIKKNVLARTGTGNAESMSWNWRTDRDLLENGAIFLPSGSDPVLTPEQKAGMIPAEPGEAVLRLTSSAGVLSCHQGAPC
View 3D Structure Click here to view 3D model structure of allergen
Fasta Search in SDAP
Blast Swissprot database search at NCBI
Blast PDB database search at NCBI
Blast NR database search at NCBI
Expasy Blast Search
Amb a 1
SDAP Sequence ID: 17
SDAP Allergen ID: 1
MGIKQCCYILYFTLALVALLQPVRSAEGVGEILPSVNETRSLQACEALNIIDKCWRGKADWENNRQALADCAQGFAKGTYGGKWGDVYTVTSNLDDDVANPKEGTLRFAAAQNRPLWIIFKNDMVINLNQELVVNSDKTIDGRGVKVEIINGGLTLMNVKNIIIHNINIHDVKVLPGGMIKSNDGPPILRQASDGDTINVAGSSQIWIDHCSLSKSFDGLVDVTLGSTHVTISNCKFTQQSKAILLGADDTHVQDKGMLATVAFNMFTDNVDQRMPRCRFGFFQVVNNNYDRWGTYAIGGSSAPTILCQGNRFLAPDDQIKKNVLARTGTGAAESMAWNWRSDKDLLENGAIFVTSGSDPVLTPVQSAGMIPAEPGEAAIKLTSSAGVFSCHPGAPC
View 3D Structure Click here to view 3D model structure of allergen
Fasta Search in SDAP
Blast Swissprot database search at NCBI
Blast PDB database search at NCBI
Blast NR database search at NCBI
Expasy Blast Search
Amb a 1
SDAP Sequence ID: 18
SDAP Allergen ID: 1
MGIKHCCYILYFTLALVTLLQPVRSAEDLQQILPSANETRSLTTCGTYNIIDGCWRGKADWAENRKALADCAQGFAKGTIGGKDGDIYTVTSELDDDVANPKEGTLRFGAAQNRPLWIIFARDMVIRLDRELAINNDKTIDGRGAKVEIINAGFAIYNVKNIIIHNIIMHDIVVNPGGLIKSHDGPPVPRKGSDGDAIGISGGSQIWIDHCSLSKAVDGLIDAKHGSTHFTVSNCLFTQHQYLLLFWDFDERGMLCTVAFNKFTDNVDQRMPNLRHGFVQVVNNNYERWGSYALGGSAGPTILSQGNRFLASDIKKEVVGRYGESAMSESINWNWRSYMDVFENGAIFVPSGVDPVLTPEQNAGMIPAEPGEAVLRLTSSAGVLSCQPGAPC
View 3D Structure Click here to view 3D model structure of allergen
Fasta Search in SDAP
Blast Swissprot database search at NCBI
Blast PDB database search at NCBI
Blast NR database search at NCBI
Expasy Blast Search
Amb a 1
SDAP Sequence ID: 797
SDAP Allergen ID: 1
MGIKQCCYILYFTLALVALLQPVRSAEGVGEILPSVNETRSLQACEALNIIDKCWRGKADWENNRQALADCAQGFAKGTYGGKWGDVYTVTSNLDDDVANPKEGTLRFAAAQNRPLWIIFKNDMVINLNQELVVNSDKTIDGRGVKVEIINGGLTLMNVKNIIIHNINIHDVKVLPGGMIKSNDGPPILRQASDGDTINVAGSSQIWIDHCSLSKSFDGLVDVTLGSTHVTISNCKFTQQSKAILLGADDTHVQDKGMLATVAFNMFTDNVDQRMPRCRFGFFQVVNNNYDRWGTYAIGGSSAPTILCQGNRFLAPDDQIKKNVLARTGTGAAESMAWNWRSDKDLLENGAIFVTSGSDPVLTPVQSAGMIPAEPGEAAIKLTSSAGVFSCRPGAPC
View 3D Structure Click here to view 3D model structure of allergen
Fasta Search in SDAP
Blast Swissprot database search at NCBI
Blast PDB database search at NCBI
Blast NR database search at NCBI
Expasy Blast Search
Amb a 1 - Statistics from Alphafold ( SI is sequence id, Best template format: PDB_ChainID)
Allergen Name pLDDT Score pTM Score Best PDB template %Seq ID Align length Seq length Query Range Sequence Range E-Value Bit Score Download Model
Amb a 1 91 0.8 1PXZ_A 46.532 346 396 48 - 389 2 - 346 0 300 Download (SI: 15)
Amb a 1 91.2 0.83 1PXZ_A 46.974 347 398 50 - 391 2 - 346 0 296 Download (SI: 16)
Amb a 1 90.95 0.82 1PXZ_A 48.851 348 397 49 - 390 2 - 346 0 307 Download (SI: 797)
Amb a 1 89.95 0.8 1PXZ_A 45.665 346 392 49 - 385 2 - 346 0 273 Download (SI: 18)
Amb a 1 90.9 0.82 1PXZ_A 48.851 348 397 49 - 390 2 - 346 0 307 Download (SI: 17)
Amb a 1 - Alphafold Theoretical Model Structure
Model Structure
797_relaxed_rank_1_model_3.pdb


Coverage Plddt
Amb a 1 - Protein Sequence Properties!
Protein Sequence Protease cleavage sites PeptideCutter at ExPASy
P27759 Click here to process the data
P27760 Click here to process the data
P27761 Click here to process the data
P28744 Click here to process the data
166443 Click here to process the data
Amb a 1 - PFAM Information
SeqID Aller ID AlnS AlnE EnvS EnvE PFAM ID Family Type Clan Description
15 1 130 312 126 312 PF00544 Pectate_lyase_4 Repeat CL0268 Pectate lyase
16 1 132 314 127 314 PF00544 Pectate_lyase_4 Repeat CL0268 Pectate lyase
17 1 131 313 125 313 PF00544 Pectate_lyase_4 Repeat CL0268 Pectate lyase
18 1 132 309 126 309 PF00544 Pectate_lyase_4 Repeat CL0268 Pectate lyase
797 1 131 313 125 313 PF00544 Pectate_lyase_4 Repeat CL0268 Pectate lyase
Where: AlnS= Alignment start position, AlnE= Alignment end position, EnvS= Envelope start position, EnvE= Envelope end position.

Welcome

Predicted B-Cell epitope using BCEP method for Amb a 1

Probe radius : 1.400

POLAR area/energy = 7147.85

APOLAR area/energy = 12235.20

Total area/energy = 19383.05

Number of surface atoms = 1559

Number of buried atoms = 1453

Residues Predicted with high probability (in top five patches) are: 66,80,83,84,85,115,78,137 , and medium probability (next top five patches) are : 137,77,73,2,86,114,135,136 . Predicted residues are shown in red and green color stick representation.

Original PDB file 3872.test.pdb
Original PDB file with surface residue only. All amino acid residue are replaced by their CB atom, in case of GLY CA atom is used. Solvent accessible surface area of each residue is stored in last column of the PDB file. 13872.test.txt
Patch drawn around the residues by patch analysis are stored in this file
How to read: Col 1: Patch No. Col 2: Center Res Name. Col 3: Sum(Pint*Area), Col 4: Sum(Psur*Area), Col 5: Total Residue, Col 6: Interface score, Col 7: Surface Score, Col 8: Max Interface Score, Col 9: Minimum Interface Score
3872.test.tmppat
Residues predicted by patch analysis are stored in this file.
How to read: Col 1: Patch No. Col 2: Center Res Name. Col 3: Res Number Col 4: Neigbouring Res Name, Col 5: Sum(Pint*Area). Col 6: Sum(PSur*Area), Col 7: Sum(Area), Col 8: Similar no of residue in patch (e.g CYS, CYS = 2)
3872.test.res
All residues scored by patch analysis are stored in this file.
How to read: Col 1: Patch No. Col 2: Center Res Name. Col 3: Sum(Pint*Area)/sum(Area), Col 4: Sum(Psur*Area)/sum(Area), Col 5: Total Residue
3872.test.resALL

[For BCEP predicted results, please cite our websites http://fermi.utmb.edu/ http://curie.utmb.edu/ for your future publications (Negi et al., Bioinformatics, 23, 3397-3399, 2007 , Negi et al., J. Mol. Model., 13, 1157-1167, 2007; Negi et al., J. Mol. Model., 12, 921-929, 2006)]



List of B-cell epitopes predicted by BepiPred method using a window size of 9 amino acids
Peptides predicted from BepiPred method can be used to search related peptides in SDAP using PD search and Cross-React method.
Please note: BepiPred Epitopes are predicted using BepiPred webserver implemented in IEDB Analysis Resource at http://tools.iedb.org/main/bcell/
Cleck here for epitopes predicted by BepiPred method

Amb a 1 - Epitope Information from published data
No. Position Epitope Sequence Epitope Type View epitope Search epitope in SDAP PD search in SDAP Cross-React search
No epitope information found!
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