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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 15:46:03 2005
# Report_file: /mnt/EXTRA_STORAGE/MUSTANG_RESULTS/HOMSTRAD_Datasets/results/Cys-protease-3C.html
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#====================================
# Aligned_structures: 3
#   1: 1cqqa.pdb
#   2: 1l1na.pdb
#   3: 1qa7a.pdb
#
# Length:        229
# Identity:       26/229 ( 11.4%)  (Calculated as the percentage of conserved columns in the alignment.)
# Similarity:     89/229 ( 38.9%)  (Calculated as the percentage of semi-conserved columns in the alignment)
# Gaps:           63/229 ( 27.5%)  (Calculated as the percentage of columns with atleast one gap.)

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


1cqqa.pdb               1  --S---TLEIAGLVRKNLVQFGVGEKNGSVRWVMNALGVKDDWLLVPSHAYKFEKDYEMM   55
1l1na.pdb               1  ---GPGFDYAVAMAKRNIVTATT-----SKG-EFTMLGVHDNVAILPTHAS---------   42
1qa7a.pdb               1  GPE---EEFGMSLIKHNSCVITT-----ENG-KFTGLGVYDRFVVVPTHAD---------   42
                                       l k N v  tt     s g  ft LGV D    vPtHA          

1cqqa.pdb              56  E--FYFNRGGTYYSISAGNVVIQSLD--V-GAQDVVLMKVPTIPKFRDITQHFIKKGDVP  110
1l1na.pdb              43  -PGESIVIDGKEVEIL----DAKALEDQAGTNLEITIITLKRNEKFRDIRPHIPTQ----   93
1qa7a.pdb              43  -PGKEIQVDGITTKVI----DSYDLYNKNGIKLEITVLKLDRNEKFRDIRRYIPNN----   93
                                i  dG    i     d   L       leit  kl rneKFRDIr hip      

1cqqa.pdb             111  RA---LNRLATLVTTVN-GTPMLISEGPLKMEEKATYVHKKNDGTTVD--LTVDQAWRGK  164
1l1na.pdb              94  --ITET-NDGVLIVNTSKYPNMYVPVGAVTEQGYLNL-----------GGRQTARTLMYN  139
1qa7a.pdb              94  --EDDY-PNCNLALLANQPEPTIINVGDVVSYGNILL-----------SGNQTARMLKYS  139
                                      L    n   pm i vG v   g   l              qtar l y 

1cqqa.pdb             165  GEGLPGMCGGALVSSNQSIQNAILGIHVAGGNSILVAKLVTQEMFQNID  213
1l1na.pdb             140  FPTRAGQCGGVITC-T----GKVIGMHVGGNGSHGFAAALKRSYFT---  180
1qa7a.pdb             140  YPTKSGYCGGVLYK-I----GQVLGIHVGGNGRDGFSAMLLRSYFT---  180
                            pt  G CGGvl        g vlGiHVgGngs gfaa l rsyFt   


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