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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: Sat Jul 23 07:43:23 2005
# Report_file: /mnt/EXTRA_STORAGE/MUSTANG_RESULTS/HOMSTRAD_Datasets/results/MHC_II_alpha_NC.html
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#====================================
# Aligned_structures: 4
#   1: 1fnga.pdb
#   2: 1fv1a.pdb
#   3: 1hdma.pdb
#   4: 1iaka.pdb
#
# Length:        195
# Identity:       33/195 ( 16.9%)  (Calculated as the percentage of conserved columns in the alignment.)
# Similarity:     94/195 ( 48.2%)  (Calculated as the percentage of semi-conserved columns in the alignment)
# Gaps:           24/195 ( 12.3%)  (Calculated as the percentage of columns with atleast one gap.)

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


1fnga.pdb               1  I--KEEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFA-----S   53
1fv1a.pdb               1  ----EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFA-----S   51
1hdma.pdb               1  ---LQNHTFLHTVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADWAQEQGD-   56
1iaka.pdb               1  -IEADHVGSYGITVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFAQLR-----R   54
                                 h       y  p   g   f fDgDe F vD  k etvwrL EFa  a      

1fnga.pdb              54  FEAQGALANIAVDKANLDVMK-ERSNNTPDANVAPEVTVLSRSPVNLGEPNILICFIDKF  112
1fv1a.pdb              52  FEAQGALANIAVDKANLEIMT-KRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKF  110
1hdma.pdb              57  ----AILFDKEFCEWMIQQIPKLDGK-IPVSRGFPIAEVFTLKPLEFGKPNTLVCFVSNL  111
1iaka.pdb              55  FEPQGGLQNIATGKHNLEILT-KRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNI  113
                               g L nia  k nl      rsn tP  n  P  tV   sPv lg PN LiCF d  

1fnga.pdb             113  SPPVVNVTWLRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDHWG-LE  171
1fv1a.pdb             111  TPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWG-LD  169
1hdma.pdb             112  FPPMLTVNWHDHSVPVE-GFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVTHEPD-R  169
1iaka.pdb             114  FPPVINITWLRNSKSVTDGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWG-LE  172
                            PPv nvtWlrn  pVt Gv eT f    d  F kf YL F Ps  D ydC V Hwg   

1fnga.pdb             172  EPLRKHWEFEE----  182
1fv1a.pdb             170  EPLLKHWEFD-----  179
1hdma.pdb             170  YTAIAYWVPRNALPS  184
1iaka.pdb             173  EPVLKHWEPE-----  182
                           ep  khWe       


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