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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 12:25:53 2005
# Report_file: /mnt/EXTRA_STORAGE/MUSTANG_RESULTS/HOMSTRAD_Datasets/results/TNF.html
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#====================================
# Aligned_structures: 5
#   1: 1aly.pdb
#   2: 1d4vb.pdb
#   3: 1tnra.pdb
#   4: 2tnfa.pdb
#   5: 4tsva.pdb
#
# Length:        188
# Identity:       13/188 (  6.9%)  (Calculated as the percentage of conserved columns in the alignment.)
# Similarity:     28/188 ( 14.9%)  (Calculated as the percentage of semi-conserved columns in the alignment)
# Gaps:           63/188 ( 33.5%)  (Calculated as the percentage of columns with atleast one gap.)

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


1aly.pdb                1  GDQN-PQIAAHVISEA------------SS-KTTSVL-Q-WAE-KGYYTMSNNLVTLENG   43
1d4vb.pdb               1  ----PQRVAAHITGTRGRSNTLSSPNSKNEKALGRKINSWESSRSGHSFLSN--LH-LRN   53
1tnra.pdb               1  ------KPAAHLIGDPSKQ---------------NSL-L-WRANTDRAFLQDG-FS-LSN   35
2tnfa.pdb               1  ---S-DKPVAHVVANHQVE---------------EQL-E-WLSQRANALLANG-MD-LKD   37
4tsva.pdb               1  -----DKPVAHVVANPQAE---------------GQL-Q-WSNRRANALLANG-VE-LRD   36
                                    AH                         l   w        l n     l  

1aly.pdb               44  KQLTVKRQGLYYIYAQVTFCSNRE-----ASSQ-------APFIASLCLKSP-G-RFERI   89
1d4vb.pdb              54  GELVIHEKGFYYIYSQTYFRFQE-E----I---KENTKNDKQMVQYIYKYTS-Y-PDPIL  103
1tnra.pdb              36  NSLLVPTSGIYFVYSQVVFSGKA-YSPKAT-------SSPLYLAHEVQLFSSQY-PFHVP   86
2tnfa.pdb              38  NQLVVPADGLYLVYSQVLFKGQG------C-------PDYVLLTHTVSRFAISY-QEKVN   83
4tsva.pdb              37  NQLVVPIEGLFLIYSQVLFKGQG------C---P---STHVLLTHTISRIAV-SYQTKVN   83
                             L v   G y  YsQv F                                         

1aly.pdb               90  LLRAANTHSSA---K------PCGQQSIHLGGVFELQPGASVFVNVTDPSQVSHGTGFT-  139
1d4vb.pdb             104  LMKSARNSCWS-KDA------EYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEAS-  155
1tnra.pdb              87  LLSSQKMVYPG--------LQEPWLHSMYHGAAFQLTQGDQLSTHTDGIPHLVLSPSTV-  137
2tnfa.pdb              84  LLSAVKSPC--PKDTPEGAELKPWYEPIYLGGVFQLEKGDQLSAEVNLPKYLDFAESGQV  141
4tsva.pdb              84  LLSAIKSPC--QRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQV  141
                           Ll                         iy Gg F L  gd                    

1aly.pdb              140  SFGLLKL-  146
1d4vb.pdb             156  FFGAFLVG  163
1tnra.pdb             138  FFGAFAL-  144
2tnfa.pdb             142  YFGVIAL-  148
4tsva.pdb             142  YFGIIA--  147
                            FG     


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