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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 19:33:31 2005
# Report_file: /mnt/EXTRA_STORAGE/MUSTANG_RESULTS/HOMSTRAD_Datasets/results/DNA_topoisoIV.html
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#====================================
# Aligned_structures: 2
#   1: 1ab4.pdb
#   2: 1bjt.pdb
#
# Length:        552
# Identity:       81/552 ( 14.7%)  (Calculated as the percentage of conserved columns in the alignment.)
# Similarity:     81/552 ( 14.7%)  (Calculated as the percentage of semi-conserved columns in the alignment)
# Gaps:          158/552 ( 28.6%)  (Calculated as the percentage of columns with atleast one gap.)

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


1ab4.pdb                1  -------------VGRALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVIGK   47
1bjt.pdb                1  FINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNL---KSELKVAQLAPYVSEC   57
                                          R  P V DG KP  R VLY          K   K A     V   

1ab4.pdb               48  YHPHGDS------AVYDTIVRMAQPF--SLRYMLVDGQGNFGSIDGD---SAAAMRYTEI   96
1bjt.pdb               58  TA-----YHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTRAT-GGKDAAAARYIYT  111
                                            TI   AQ F  S    L    G FG         AAA RY   

1ab4.pdb               97  RLAKIAHELMAD-LEKETVDFVDNYDGTE-KIPDVMPTKIPNLLVNGSSGIAVGMATNIP  154
1bjt.pdb              112  ELNKLTRKIFHPAD-DPLYKYIQE--DEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIP  168
                            L K                            P       P  LVNG  GI  G  T IP

1ab4.pdb              155  PHNLTEVINGCLAYIDDEDISIEGLME----HIPGPDFPTAAII-NGRRGIEEAYRTGR-  208
1bjt.pdb              169  PFNPLEIIKNIRHLMND----------EELEQ-MHPWFRGWTGTIEE------------I  205
                           P N  E I        D                  P F                      

1ab4.pdb              209  --GKVYIRARAEV-EVETIIVHEIPYQVNKARLIEKIAELVKEKRVE-----GISALRDE  260
1bjt.pdb              206  EPLRYRMYGRIEQIGDNVLEITELPARTWTSTIKEYLLLGLSG-N--DKIKPWIKDMEEQ  262
                                    R E          E P         E                  I      

1ab4.pdb              261  SDKDGMRIVIE-G---EVVLN--NLYSQTQLQVSFGI-NMVALHHGQ-PKIM-----NLK  307
1bjt.pdb              263  HD-DNIKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSVNEILS  321
                            D D     I               Y    L       NMVA       K        L 

1ab4.pdb              308  DIIAAFVRHRREVVTRRTIFELRKARDRAHILEALAVALANIDPIIE--LIRHAPTPAEA  365
1bjt.pdb              322  EFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEK------ELTVTN-KPRNAI  374
                                                                                       

1ab4.pdb              366  KTALVANPWQLGN-VAAMLEDAARPEWLEPEFGVR--------DGLYYLTEQQAQAILDL  416
1bjt.pdb              375  IQELENLGFPRFNKEG-------------------KPYYGSPEELYG-----TYEYLLGM  410
                              L        N                                            L  

1ab4.pdb              417  RLQKLTGLEHEKLLDEYKELLDQIAELLRILGSADRL-MEVIREELELVREQFGDKRRTE  475
1bjt.pdb              411  RIWSLTKERYQKLLKQKQEKETELENLLKL------SAKDIWNTDLKAFEVGYQE-----  459
                           R   LT     KLL    E       LL                 L              

1ab4.pdb              476  IT----------  477
1bjt.pdb              460  --FLQRDAEARG  469
                                       


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