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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 07:44:32 2005
# Report_file: /mnt/EXTRA_STORAGE/MUSTANG_RESULTS/HOMSTRAD_Datasets/results/MHC_II_beta_NC.html
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#====================================
# Aligned_structures: 4
#   1: 1fngb.pdb
#   2: 1fv1b.pdb
#   3: 1hdmb.pdb
#   4: 1iakb.pdb
#
# Length:        235
# Identity:       35/235 ( 14.9%)  (Calculated as the percentage of conserved columns in the alignment.)
# Similarity:     96/235 ( 40.9%)  (Calculated as the percentage of semi-conserved columns in the alignment)
# Gaps:           73/235 ( 31.1%)  (Calculated as the percentage of columns with atleast one gap.)

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


1fngb.pdb               1  KKVITAFNEGLKGGGGSLVGGGSGGGG--SRPWFLEYCKSECHFYNGTQRVRLLVRYFYN   58
1fv1b.pdb               1  ---------------------------GDTRPRFLQQDKYECHFFNGTERVRFLHRDIYN   33
1hdmb.pdb               1  ---------------------------------FVAHVESTCLLDDAGTPKDFTYCISFN   27
1iakb.pdb               1  -------------------------------GSFVHQFQPFCYFTNGTQRIRLVIRYIYN   29
                                                            F       C f ngt r r   r  yN

1fngb.pdb              59  LEENLRFDSDVGEFRAVTELGRPDAENWNSQPEFLEQKR---------AEVDTVCRHNY-  108
1fv1b.pdb              34  QEEDLRFDSDVGEYRAVTELGRPDAEYWNSQKDFLEDRR---------AAVDTYCRHNY-   83
1hdmb.pdb              28  KDLLTCWDPEENKMAPCNSLANVLSQHLNQKDTLMQRLNGLQNCATHT------------   75
1iakb.pdb              30  REEYVRFDSDVGEYRAVTELGRPDAEYWNKQ--YLERTR---------AELDTVCRHNYE   78
                            ee  rfDsdvge ravteLgrpdae wN q   le  r                     

1fngb.pdb             109  EIFDNFLVPRRVEPTVTVYPTKTQP--LEH---HNLLVCSVSDFYPGNIEVRWFRNGKEE  163
1fv1b.pdb              84  GVGESFTVQRRVEPKVTVYPARTQT--LQH---HNLLVCSVNGFYPGSIEVRWFRNSQEE  138
1hdmb.pdb              76  QPFWGSLTNRTRPPSVQVAKTT--PFN---TREPVMLACYVWGFYPAEVTITWRKNGKLV  130
1iakb.pdb              79  KTETPTSLRRLEQPSVVISLSR-TEAL--NH--HNTLVCSVTDFYPAKIKVRWFRNGQEE  133
                                    R   P V v               hn LvCsV  FYP  i vrWfrNg ee

1fngb.pdb             164  K--TGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEW---  213
1fv1b.pdb             139  K--AGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA-  190
1hdmb.pdb             131  MHSSAHK--TAQPNGDWTYQTLSHLALTPSYGDTYTCVVEHIGAPEPILRDWTPG  183
1iakb.pdb             134  T--VGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLTSPITVEWRA-  185
                               g     l  NGDWTfQtLvmLe  P  GevYTC VEHps t P tveW   


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