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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: Mon Jul 25 15:10:09 2005
# Report_file: /mnt/EXTRA_STORAGE/MUSTANG_RESULTS/HOMSTRAD_Datasets/results/CODH.html
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#====================================
# Aligned_structures: 2
#   1: 1jjya.pdb
#   2: 1jqka.pdb
#
# Length:        637
# Identity:      348/637 ( 54.6%)  (Calculated as the percentage of conserved columns in the alignment.)
# Similarity:    348/637 ( 54.6%)  (Calculated as the percentage of semi-conserved columns in the alignment)
# Gaps:           31/637 (  4.9%)  (Calculated as the percentage of columns with atleast one gap.)

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


1jjya.pdb               1  QNLKSTDRAVQQMLDKAKREGIQTVWDRYEAMKPQCGFGETGLCCRHCLQGPCRINPFGD   60
1jqka.pdb               1  ----------------------ETAWHRYEKQQPQCGFGSAGLCCRICLKGPCRIDPFGE   38
                                                  T W RYE   PQCGFG  GLCCR CL GPCRI PFG 

1jjya.pdb              61  EPKVGICGATAEVIVARGLDRSIAAGAAGHSGHAKHLAHTLKKAVQGKAASYMIKDRTKL  120
1jqka.pdb              39  GPKYGVCGADRDTIVARHLVRMIAAGTAAHSEHGRHIALAMQHISQGELHDYSIRDEAKL   98
                            PK G CGA    IVAR L R IAAG A HS H  H A       QG    Y I D  KL

1jjya.pdb             121  HSIAKRLGIPTEGQKDEDIALEVAKAALADFHEK---DTPVLWVTTVLPPSRVKVLSAHG  177
1jqka.pdb              99  YAIAKTLGVATEGRGLLAIVGDLAAITLGDFQN-QDYDKPCAWLAASLTPRRVKRLGDLG  157
                             IAK LG  TEG     I    A   L DF      D P  W    L P RVK L   G

1jjya.pdb             178  LIPAGIDHEIAEIMHRTSMGCDADAQNLLLGGLRCSLADLAGCYMGTDLADILFGTPAPV  237
1jqka.pdb             158  LLPHNIDASVAQTMSRTHVGCDADPTNLILGGLRVAMADLDGSMLATELSDALFGTPQPV  217
                           L P  ID   A  M RT  GCDAD  NL LGGLR   ADL G    T L D LFGTP PV

1jjya.pdb             238  VTESNLGVLKADAVNVAVHGHNPVLSDIIVSVSKEMENEARAAGAT-GINVVGICCTGNE  296
1jqka.pdb             218  VSAANLGVMKRGAVNIAVNGHNPMLSDIICDVAADLRDEAIAAGAAEGINIIGICCTGHE  277
                           V   NLGV K  AVN AV GHNP LSDII  V      EA AAGA  GIN  GICCTG E

1jjya.pdb             297  VLMRHGIPACTHSVSQEMAMITGALDAMILDYQCIQPSVATIAECTGTTVITTMEMSKIT  356
1jqka.pdb             278  VMMRHGVPLATNYLSQELPILTGALEAMVVDVQCIMPSLPRIAECFHTQIITTDKHNKIS  337
                           V MRHG P  T   SQE    TGAL AM  D QCI PS   IAEC  T  ITT    KI 

1jjya.pdb             357  GATHVNFAEEAAVENAKQILRLAIDTFKRRKGKPVEIPNIKTKVVAGFSTEAIINALSKL  416
1jqka.pdb             338  GATHVPFDEHKAVETAKTIIRMAIAAFGRRDPNRVAIPAFKQKSIVGFSAEAVVAALAKV  397
                           GATHV F E  AVE AK I R AI  F RR    V IP  K K   GFS EA   AL K 

1jjya.pdb             417  NANDPLKPLIDNVVNGNIRGVCLFAGCNNVKVPQDQNFTTIARKLLKQNVLVVATGCGAG  476
1jqka.pdb             398  NADDPLKPLVDNVVNGNIQGIVLFVGCNTTKVQQDSAYVDLAKSLAKRNVLVLATGCAAG  457
                           NA DPLKPL DNVVNGNI G  LF GCN  KV QD      A  L K NVLV ATGC AG

1jjya.pdb             477  ALMRHGFMDPANVDELCGDGLKAVLTAIGEANGLGGPLPPVLHMGSCVDNSRSVALVAAL  536
1jqka.pdb             458  AFAKAGLMTSEATTQYAGEGLKGVLSAIGTAAGLGGPLPLVMHMGSCVDNSRAVALATAL  517
                           A    G M         G GLK VL AIG A GLGGPLP V HMGSCVDNSR VAL  AL

1jjya.pdb             537  ANRLGVDMDRLPVVASAAQAMHEKAVAIGTWAVTIGLPTHIGVFPPITGSLPVTQILTSS  596
1jqka.pdb             518  ANKLGVDLSDLPLVASAPECMSEKALAIGSWAVTIGLPTHVGSVPPVIGSQIVTKLVTET  577
                           AN LGVD   LP VASA   M EKA AIG WAVTIGLPTH G  PP  GS  VT   T  

1jjya.pdb             597  VKDITGGYFIVELDPQVAADKLLAAINERRAGLGLPR  633
1jqka.pdb             578  AKDLVGGYFIVDTDPKSAGDKLYAAIQERRAGL----  610
                            KD  GGYFIV  DP  A DKL AAI ERRAGL    


#=========================================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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