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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: Sun Jul 24 01:31:12 2005
# Report_file: /mnt/EXTRA_STORAGE/MUSTANG_RESULTS/HOMSTRAD_Datasets/results/MHC_II_N.html
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#====================================
# Aligned_structures: 13
#   1: 1a6ab.pdb
#   2: 1d5zb.pdb
#   3: 1es0b.pdb
#   4: 1fnga.pdb
#   5: 1fngb.pdb
#   6: 1fv1a.pdb
#   7: 1fv1b.pdb
#   8: 1hdma.pdb
#   9: 1hdmb.pdb
#  10: 1iaka.pdb
#  11: 1iakb.pdb
#  12: 2iada.pdb
#  13: 2iadb.pdb
#
# Length:        121
# Identity:        1/121 (  0.8%)  (Calculated as the percentage of conserved columns in the alignment.)
# Similarity:      1/121 (  0.8%)  (Calculated as the percentage of semi-conserved columns in the alignment)
# Gaps:           78/121 ( 64.5%)  (Calculated as the percentage of columns with atleast one gap.)

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


1a6ab.pdb               1  -------PRFLE-YSTSECHFFNGTE-RVRYLDRYFHNQEENVRFDSDVGEFRAVTE-LG   50
1d5zb.pdb               1  GDT---RPRFLE-QVKHECHFFNGTE-RVRFLDRYFYHQEEYVRFDSDVGEYRAVTE-LG   54
1es0b.pdb               1  -------RHFVH-QFKGECYFTNGTQ-RIRLVTRYIYNREEYLRFDSDVGEYRAVTE-LG   50
1fnga.pdb               1  -----IKEEHTI-IQAEFYLLP-----DKRGEFMFDFDGDEIFHVDIEKSETIWRLEEFA   49
1fngb.pdb               1  --------WFLE-YCKSECHFYNGTQ-RVRLLVRYFYNLEENLRFDSDVGEFRAVTE-LG   49
1fv1a.pdb               1  -------EEHVI-IQAEFYLNP-----DQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFG   47
1fv1b.pdb               1  GDT---RPRFLQ-QDKYECHFFNGTE-RVRFLHRDIYNQEEDLRFDSDVGEYRAVTE-LG   54
1hdma.pdb               1  ------LQNHTF-LHTVYCQDG-----SPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFA   48
1hdmb.pdb               1  ---------FVA-HVESTCLLDDAGTP-KDFTYCISFNKDLLTCWDPEENKMAPCN-SLA   48
1iaka.pdb               1  ---IE-A-DHVGSYGITVYQSP-----GDIGQYTFEFDGDELFYVDLDKKETVWMLPEFA   50
1iakb.pdb               1  -------GSFVH-QFQPFCYFTNGTQ-RIRLVIRYIYNREEYVRFDSDVGEYRAVTE-LG   50
2iada.pdb               1  -------------------------------------DGDELFYVDLDKKKTVWRLPEFG   23
2iadb.pdb               1  -------RHFVV-QFKGECYYTNGTQ-RIRLVTRYIYNREEYVRYDSDVGEYRAVTE-LG   50
                                                                        D              

1a6ab.pdb              51  RPDAEYW---NSQKDLL-E---QKR---GRVDNYCRHNYGVVESFTV-------Q-----   88
1d5zb.pdb              55  RPDAEYW---NSQKDLL-E---QKR---AAVDTYCRHNYGVGESFTV-------Q-----   92
1es0b.pdb              51  RHSAEYY---NKQ--YL-E---RTR---AELDTACRHNYEETEVPTS-------L-----   86
1fnga.pdb              50  KFA-------SF----EAQ---GAL---ANI-AVDKANLDVMKERS-NNTPD--------   82
1fngb.pdb              50  RPDAENW---NSQP-EFLE---QKR---AEV-DTVCRHNYEIFDN---------------   83
1fv1a.pdb              48  RFA-------SF----EAQ---GAL---ANI-AVDKANLEIMTKRS-NYTP---------   79
1fv1b.pdb              55  RPDAEYW---NSQKDFL-E---DRR---AAVDTYCRHNYGVGESFTV-------Q-----   92
1hdma.pdb              49  DWA-QE-QGD------------AIL---FDK-EFCEWMIQQIPKLD-G----KIPV----   81
1hdmb.pdb              49  NVLSQHL---NQ-----KD---TLMQRLNGL-QNCATHTQPFWGSLTN----R-------   85
1iaka.pdb              51  QLR-------RF----EPQ---GGL---QNI-ATGKHNLEILTKRS-NSTP---------   82
1iakb.pdb              51  RPDAEYW---NKQ--YL-E---RTR---AELDTVCRHNYEKTETPTS-------L-----   86
2iada.pdb              24  QLI-------LF-------EPQGGL---QNI-AAEKHNLGILTKRS-N--------FTPA   56
2iadb.pdb              51  RPDAEYW---NSQP-EILE---RTR---AEVDTACRHNYEGPETSTS-------L-----   88
                                                                                       

1a6ab.pdb                  -     
1d5zb.pdb                  -     
1es0b.pdb              87  R   87
1fnga.pdb                  -     
1fngb.pdb                  -     
1fv1a.pdb                  -     
1fv1b.pdb                  -     
1hdma.pdb                  -     
1hdmb.pdb                  -     
1iaka.pdb                  -     
1iakb.pdb              87  R   87
2iada.pdb                  -     
2iadb.pdb              89  R   89
                            


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