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# Program: MUSTANG-Lite v0.1: A  Multiple structural alignment algorithm
# Authors: A. S. Konagurthu, A. M. Lesk, J. C. Whisstock, and P. J. Stuckey
# Rundate: Fri Jul 22 19:28:33 2005
# Report_file: /mnt/EXTRA_STORAGE/MUSTANG_RESULTS/HOMSTRAD_Datasets/results/DNA_photolyase.html
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#====================================
# Aligned_structures: 2
#   1: 1dnpa.pdb
#   2: 1qnf.pdb
#
# Length:        497
# Identity:      171/497 ( 34.4%)  (Calculated as the percentage of conserved columns in the alignment.)
# Similarity:    171/497 ( 34.4%)  (Calculated as the percentage of semi-conserved columns in the alignment)
# Gaps:           50/497 ( 10.1%)  (Calculated as the percentage of columns with atleast one gap.)

#===========================================ALIGNMENT START=========================================


1dnpa.pdb               1  --TTHLVWFRQDLRLHDNLALAAACRNSSA-RVLALYIATPRQWATHNMSPRQAELINAQ   57
1qnf.pdb                1  MAAPILFWHRRDLRLSDNIGLAAARAQ--SAQLIGLFCLDPQILQSADMAPARVAYLQGC   58
                                L W R DLRL DN  LAAA           L    P       M P         

1dnpa.pdb              58  LNGLQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLFYNYQYEVNERARDVEVE  117
1qnf.pdb               59  LQELQQRYQQAGSRLLLLQG----DPQHLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVA  114
                           L  LQ      G  LL               Q            N   E   R RD  V 

1dnpa.pdb             118  RAL-R-NVVCEGFDDSVILPPGAVMTGNHEMYKVFTPFKNAWLKRLREGMPECVAAPKVR  175
1qnf.pdb              115  AALKTAGIRAVQLWDQLLHSPDQILSGSGNPYSVYGPFWKNWQAQ---PKPTPVATPTEL  171
                            AL           D     P     G    Y V  PF   W        P  VA P   

1dnpa.pdb             176  SSGS-----------IE-PSPSI--TLNYPRQSFDTAHFPVEEKAAIAQLRQFCQNGAGE  221
1qnf.pdb              172  VD--LSPEQLTAIAPLLLSELPTLKQLGF-DWDGGF-PVEPGETAAIARLQEFCDRAIAD  227
                                                     L               E AAIA L  FC      

1dnpa.pdb             222  YEQQRDFPAVEGTSRLSASLATGGLSPRQCLHRLLAEQP-----QALDGGAGSVWLNELI  276
1qnf.pdb              228  YDPQRNFPAEAGTSGLSPALKFGAIGIRQAWQAASAAHALSRSDEAR--NSIRVWQQELA  285
                           Y  QR FPA  GTS LS  L  G    RQ      A         A       VW  EL 

1dnpa.pdb             277  WREFYRHLITYHPSLCKHRPFIAWTDRVQWQSNPAHLQAWQEGKTGYPIVDAAMRQLNST  336
1qnf.pdb              286  WREFYQHALYHFPSLA-DGPYRSLWQQFPWENREALFTAWTQAQTGYPIVDAAMRQLTET  344
                           WREFY H     PSL    P         W    A   AW    TGYPIVDAAMRQL  T

1dnpa.pdb             337  GWMHNRLRMITASFLVKDLLIDWREGERYFMSQLIDGDLAANNGGWQWAASTGTDAAPY-  395
1qnf.pdb              345  GWMHNRCRMIVASFLTKDLIIDWRRGEQFFMQHLVDGDLAANNGGWQWSASSGMDPK--P  402
                           GWMHNR RMI ASFL KDL IDWR GE  FM  L DGDLAANNGGWQW AS G D     

1dnpa.pdb             396  FRIFNPTTQGEKFDHEGEFIRQWLPELRDVPGKVVHEPWK-WAQKAGVTLDYPQPIVEHK  454
1qnf.pdb              403  LRIFNPASQAKKFDATATYIKRWLPELRHVHPKDLISGE-ITPIER---RGYPAPIVNHN  458
                            RIFNP  Q  KFD     I  WLPELR V  K                  YP PIV H 

1dnpa.pdb             455  EARVQTLAAYEAARK--  469
1qnf.pdb              459  LRQKQFKALYNQLKAAI  475
                               Q  A Y       


#=========================================ALIGNMENT END=============================================
#LEGEND:
#
# Colours indicate the chemical nature of the amino acid;
# Red         = small hydrophobic including aromatic,{A,F,I,L,M,P,V,W}
# Blue        = Acidic,{D,E}
# Magenta     = Basic,{K,R} and
# Green       = Basic amino acids with hydroxyl groups and/or amine groups {C,G,H,N,Q,S,T,Y}.
#
# The "markup row" below each stretch of the multiple alignment is used to mark completely conserved
# residue (denoted in UPPERCASE) and semi-conserved reside ( denoted in lowercase) in a column of the alignment.
#
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