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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: Fri Jul 22 23:05:28 2005
# Report_file: /mnt/EXTRA_STORAGE/MUSTANG_RESULTS/HOMSTRAD_Datasets/results/RNA_dep_RNA_pol.html
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#====================================
# Aligned_structures: 2
#   1: 1khva.pdb
#   2: 1rdr.pdb
#
# Length:        516
# Identity:       59/516 ( 11.4%)  (Calculated as the percentage of conserved columns in the alignment.)
# Similarity:     59/516 ( 11.4%)  (Calculated as the percentage of semi-conserved columns in the alignment)
# Gaps:          223/516 ( 43.2%)  (Calculated as the percentage of columns with atleast one gap.)

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


1khva.pdb               1  -----FCGEPIDYRGITAHRLVGAEPRPPVSGTRYAKVPGVPDEYKTGYRPANLGRSDPD   55
1rdr.pdb                1  VGYPIINAPSK---------------------TKLEPSAF--------------------   19
                                                           T                           

1khva.pdb              56  SDKSLMNIAV--KNLQVYQQEPK--LDKVDEFIERAAADVLGYLRFLTKGERQANLNFKA  111
1rdr.pdb               20  ----------HYVFE--------GVITEVDEYMKEAVDHYAGQLMSLD-I----------   50
                                                       VDE    A     G L  L             

1khva.pdb             112  AFNTLDLSTSCGPFVPGKKIDHVKDGVMDQVLAKHLYKCWSVANSGKALHHIYACGLKDE  171
1rdr.pdb               51  --------------------------------------------------NTEQMCL---   57
                                                                                   L   

1khva.pdb             172  LRPLDGKKRLLWGCDVGV--AVCAAAVFHNICYKLKMVARF-GPIAVGVDMTSRDVDVII  228
1rdr.pdb               58  ------------------NDSVAMRMAFGNLYAAFHKNPGVITGSAVGCDP-DLFWSKIP   98
                                                V     F N               AVG D        I 

1khva.pdb             229  NNLTSKASDFLCLDYSKWDSTMSPCVVRLAIDILADCCEQTEL--TKSVVLTLKSHPMTI  286
1rdr.pdb               99  VLM---EEKLFAFDYTGYDASLSPAWFEALKMVLEKIG-F---GDRVDYIDYLN------  145
                                        DY   D   SP         L                  L       

1khva.pdb             287  LDAMIVQTKRGLPSGMPFTSVINSICHWLLWSAAVYKSCAEIGLHC-SNLYEDAPFYTYG  345
1rdr.pdb              146  ----------------SGTSIFNSMINNLIIRTLLLKTYK------GIDL-DHLKMIAYG  182
                                             TS  NS    L       K            L        YG

1khva.pdb             346  DDGVYAMTPMMVSLLP-AIIENLRDYGLSPTAADKTEFIDVCPLNKISFLKRTFELT-DI  403
1rdr.pdb              183  DDVIASY-PHE-V-DASLLAQSGKDYGLTMTPADKSATFETVTWENVTFLKRFFRADEK-  238
                           DD      P               DYGL  T ADK             FLKR F      

1khva.pdb             404  ---GWVSKLDKSSILRQLEWSKTTSRHMVIEETYDLA-KEERGVQLEELQVAAAAHGQEF  459
1rdr.pdb              239  YPFLIHPVMPMKEIHESIRWTKD--------------PR-NTQDHVRSLCLLAWHNGEEE  283
                                        I     W K                          L   A   G E 

1khva.pdb             460  FNFVCRELERQQ--AYTQFSVYSYDAARKILADRKR  493
1rdr.pdb              284  YNKFLAKIRSVPIGRA-L-LLPEYSTLYRRWLDSF-  316
                            N                     Y        D   


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