Databases and Comparisons - CMB Education - Karolinska Institutet

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Example of PDB entry, cont.REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF HOLO 2HSD 20REMARK 1 TITL 2 3ALPHA,20BETA-HYDROXYSTEROID DEHYDROGENASE: 2HSD 21REMARK 1 TITL 3 A MEMBER OF A SHORT-CHAIN DEHYDROGENASE FAMILY 2HSD 22REMARK 1 REF PROC.NAT.ACAD.SCI.USA V. 88 10064 1991 2HSD 23REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 0040 2HSD 24REMARK 2 2HSD 25REMARK 2 RESOLUTION. 2.64 ANGSTROMS. 2HSD 26REMARK 3 2HSD 27REMARK 3 REFINEMENT. 2HSD 28REMARK 3 PROGRAM 1 PROLSQ 2HSD 29REMARK 3 AUTHORS 1 KONNERT,HENDRICKSON 2HSD 30REMARK 3 PROGRAM 2 X-PLOR 2HSD 31REMARK 3 AUTHORS 2 BRUNGER 2HSD 32REMARK 3 R VALUE 0.188 2HSD 33REMARK 3 RMSD BOND DISTANCES 0.012 ANGSTROMS 2HSD 34REMARK 3 RMSD BOND ANGLE DISTANCES 0.035 ANGSTROMS 2HSD 35REMARK 3 2HSD 36REMARK 3 NUMBER OF REFLECTIONS 28327 2HSD 37REMARK 3 RESOLUTION RANGE 8.0 - 2.64 ANGSTROMS 2HSD 38Linköping University & Karolinska Institutet 30
Example of PDB entry, cont.SEQRES 1 A 253 ASN ASP LEU SER GLY LYS THR VAL ILE ILE THR GLY GLY 2HSD 86SEQRES 2 A 253 ALA ARG GLY LEU GLY ALA GLU ALA ALA ARG GLN ALA VAL 2HSD 87SEQRES 3 A 253 ALA ALA GLY ALA ARG VAL VAL LEU ALA ASP VAL LEU ASP 2HSD 88SEQRES 4 A 253 GLU GLU GLY ALA ALA THR ALA ARG GLU LEU GLY ASP ALA 2HSD 89...HET NAD A 256 44 NICOTINAMIDE-ADENINE-DINUCLEOTIDE 2HSD 166HET NAD B 256 44 NICOTINAMIDE-ADENINE-DINUCLEOTIDE 2HSD 167HET NAD C 256 44 NICOTINAMIDE-ADENINE-DINUCLEOTIDE 2HSD 168HET NAD D 256 44 NICOTINAMIDE-ADENINE-DINUCLEOTIDE 2HSD 169FORMUL 5 NAD 4(C21 H28 N7 O14 P2) 2HSD 170HELIX 1 BA ARG A 16 ALA A 29 1 2HSD 171HELIX 2 CA ASP A 40 ALA A 54 1 2HSD 172HELIX 3 DA TRP A 67 GLU A 77 1 2HSD 173...SHEET 1 S1A 7 GLN A 57 THR A 62 0 2HSD 195SHEET 2 S1A 7 GLY A 30 VAL A 38 1 N LEU A 35 O LEU A 59 2HSD 196SHEET 3 S1A 7 GLY A 6 THR A 12 1 N ILE A 10 O VAL A 34 2HSD 197SHEET 4 S1A 7 ASP A 82 GLY A 93 1 N ASP A 82 O LYS A 7 2HSD 198Linköping University & Karolinska Institutet 31
Page 1 and 2: Introduction to BioinformaticsDatab
Page 3 and 4: Genome comparisons
Page 5 and 6: Completed genomesGenome sizeMb10000
Page 7 and 8: Genome comparisonsH. sapienscluster
Page 9 and 10: Protein foldingDNAProtein?Linköpin
Page 11 and 12: Molecular modellingHomology modelli
Page 13 and 14: Docking of bile acids into class I
Page 15 and 16: Predictions of important regionsCom
Page 17 and 18: Conserved amino acid residuesLinkö
Page 19 and 20: Databases with sequence information
Page 21 and 22: Example of Swissprot entryID 2BHD_S
Page 23 and 24: TrEMBLA computer-annotated suppleme
Page 25 and 26: Example of EMBL entryID HS3B5H5E st
Page 27 and 28: Example of EMBL entry, cont.FT CDS
Page 29: Example of PDB entryHEADER OXIDORED
Page 33 and 34: Pairwise sequence comparisons
Page 35 and 36: Why comparisons?Identification of p
Page 37 and 38: Results from diagonal plot analysis
Page 39 and 40: Improved comparisons 1Not just cons
Page 41 and 42: Selection of scoring matrixThe scor
Page 43 and 44: Using scoring matrixS 0 0 0 0 0=4C
Page 45 and 46: PAM, cont.The PAM series are based
Page 47 and 48: BLOSUMOne assumption inherent in th
Page 49 and 50: Improved comparisons 2Introduction
Page 51 and 52: Gap penaltyThe score from all pairs
Page 53 and 54: Lipman & PearsonFASTAIdentities / S
Page 55 and 56: Results from FASTA run, histogramop
Page 57 and 58: Results from FASTA run, alignment>>
Page 59 and 60: Caution with the interpretationsAn
Page 61 and 62: EBI home pageLinköping University
Page 63 and 64: http://www.ebi.ac.uk/fasta33/Linkö
Page 65 and 66: BLASTFast algorithmLocal installati
Page 67 and 68: NCBI home pageLinköping University
Page 69 and 70: Basic BLASTLinköping University &
Page 71 and 72: Basic BLAST, resultsLinköping Univ
Page 73 and 74: FASTA parametersScoring matrix- BLO
Page 75 and 76: Statistics, high penalties (48, 8)L
Page 77 and 78: Effect on alignment by gap penaltie
Page 79 and 80: Multiple sequence alignmentsCharact
Page 81 and 82:
Clustering + AligningClustalAll-aga
Page 83 and 84:
ClustalW main menu****************
Page 85 and 86:
Pairwise alignment parameters******
Page 87 and 88:
ClustalW at EBI, Submission formLin
Page 89 and 90:
waiting ...Linköping University &
Page 91 and 92:
ClustalW, Scores TableLinköping Un
Page 93 and 94:
ClustalW, Guide Tree & CladogramLin
Page 95 and 96:
JalViewA new experimental option ha
Page 97 and 98:
Sequence formats in ClustalW Pearso
Page 99 and 100:
Kalign, AlignmentLinköping Univers
Page 101 and 102:
PSI-BLASTQuery sequenceFound homolo
Page 103 and 104:
PSI-BLAST, resultsLinköping Univer
Page 105 and 106:
Expect valuesThe first of these (up
Page 107 and 108:
Advanced OptionsIn the "Advanced Op
Page 109 and 110:
Set the output formatting optionsBy
Page 111 and 112:
Output from initial BLAST searchThe
Page 113 and 114:
Examination, cont.Sequences produci
Page 115 and 116:
Examination, cont.sp|P42297|YXIE_BA
Page 117 and 118:
Performing PSI-BLAST iterationsThe
Page 119:
Assignment 1Sequence comparisons- F
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