################################################################################################
# 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 Aug 12 23:11:57 2005
# Report_file: /mnt/EXTRA_STORAGE/MUSTANG_RESULTS/MUSTANG_HOMSTRAD/results/proteasome.html
################################################################################################
#====================================
# Aligned_structures: 17
#   1: 1neda.pdb
#   2: 1pma1.pdb
#   3: 1pmaa.pdb
#   4: 1ryp1.pdb
#   5: 1ryp2.pdb
#   6: 1rypa.pdb
#   7: 1rypb.pdb
#   8: 1rypc.pdb
#   9: 1rypd.pdb
#  10: 1rype.pdb
#  11: 1rypf.pdb
#  12: 1rypg.pdb
#  13: 1ryph.pdb
#  14: 1rypi.pdb
#  15: 1rypj.pdb
#  16: 1rypk.pdb
#  17: 1rypl.pdb
#
# Length:        399
# Identity:        4/399 (  1.0%)  (Calculated as the percentage of conserved columns in the alignment.)
# Similarity:      4/399 (  1.0%)  (Calculated as the percentage of semi-conserved columns in the alignment)
# Gaps:          247/399 ( 61.9%)  (Calculated as the percentage of columns with atleast one gap.)

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


1neda.pdb               1  -----------------------------------------------TTIVSVRRNGHVV   13
1pma1.pdb               1  -----------------------------------------------TTTVGITLKDAVI   13
1pmaa.pdb               1  -------------TVFSPDGRLFQVEYAR---------EAVK--K-GSTALGMKFANGVL   35
1ryp1.pdb               1  -------------------------------QFNPYG-----D-N-GGTILGIAGEDFAV   22
1ryp2.pdb               1  --------------------------------TQQP------IVT-GTSVISMKYDNGVI   21
1rypa.pdb               1  --A-GY--DR-HITIFSPEGRLYQVEYAF---------KATN--QTNINSLAVRGKDCTV   43
1rypb.pdb               1  ---MTDRYS-FSLTTFSPSGKLGQIDYAL---------TAVK--Q-GVTSLGIKATNGVV   44
1rypc.pdb               1  --G-SR-RYDSRTTIFSPEGRLYQVEYAL---------ESIS--H-AGTAIGIMASDGIV   44
1rypd.pdb               1  ------GYD-RALSIFSPDGHIFQVEYAL---------EAVK--R-GTCAVGVKGKNCVV   41
1rype.pdb               1  ---------DRGVSTFSPEGRLFQVEYSL---------EAIK--L-GSTAIGIATKEGVV   39
1rypf.pdb               1  FR--NN--YDGDTVTFSPTGRLFQVEYAL---------EAIK--Q-GSVTVGLRSNTHAV   44
1rypg.pdb               1  --G-TG--YDLSNSVFSPDGRNFQVEYAV---------KAVE--N-GTTSIGIKCNDGVV   43
1ryph.pdb               1  -----------------------------LKKGE--V-----S-L-GASIMAVTFKDGVI   22
1rypi.pdb               1  -----------------------------------------------TTIVGVKFNNGVV   13
1rypj.pdb               1  -------------------------------------SDPSSI-N-GGIVVAMTGKDCVA   21
1rypk.pdb               1  ----------------------------------------------MDIILGIRVQDSVI   14
1rypl.pdb               1  -----------------------------------------------TTTLAFRFQGGII   13
                                                                                       

1neda.pdb              14  IAGDGQATLGNT-VMKG--N-VKKVRRLYNDKVIAGFAGGTADAFTLFELFERKLEM-HQ   68
1pma1.pdb              14  MATERRVTMENF-IMHK--N-GKKLFQI-DTYTGMTIAGLVGDAQVLVRYMKAELEL-YR   67
1pmaa.pdb              36  LISDKKVR-SRLIE--QN-S-IEKIQLI-DDYVAAVTSGLVADARVLVDFARISAQQ-EK   88
1ryp1.pdb              23  LAGDTRNITDYS-INSR--Y-EPKVFDC-GDNIVMSANGFAADGDALVKRFKNSVKW-YH   76
1ryp2.pdb              22  IAADNLGSYGSL-LRFN--G-VERLIPV-GDNTVVGISGDISDMQHIERLLKDLVTE-NA   75
1rypa.pdb              44  VISQKKVP-DKLLD--PT-T-VSYIFCI-SRTIGMVVNGPIPDARNAALRAKAEAAE-FR   96
1rypb.pdb              45  IATEKKSS-SPLAM--SE-T-LSKVSLL-TPDIGAVYSGMGPDYRVLVDKSRKVAHTSYK   98
1rypc.pdb              45  LAAERKVT-STLLE--QD-TSTEKLYKL-NDKIAVAVAGLTADAEILINTARIHAQN-YL   98
1rypd.pdb              42  LGCERRST-LKLQD--TRIT-PSKVSKI-DSHVVLSFSGLNADSRILIEKARVEAQS-HR   95
1rype.pdb              40  LGVEKRAT-SPLLE--SD-S-IEKIVEI-DRHIGCAMSGLTADARSMIEHARTAAVT-HN   92
1rypf.pdb              45  LVALKRNA-DEL-S--S--Y-QKKIIKC-DEHMGLSLAGLAPDARVLSNYLRQQCNY-SS   95
1rypg.pdb              44  FAVEKLIT-SKLLV--PQ-K-NVKIQVV-DRHIGCVYSGLIPDGRHLVNRGREEAAS-FK   96
1ryph.pdb              23  LGADSRTTTGAY-IANR--V-TDKLTRV-HDKIWCCRSGSAADTQAIADIVQYHLEL-YT   76
1rypi.pdb              14  IAADTRSTQGPI-VADK--N-CAKLHRI-SPKIWCAGAGTAADTEAVTQLIGSNIEL-HS   67
1rypj.pdb              22  IACDLRLGSQSL-GVSN--K-FEKIFHY-G-HVFLGITGLATDVTTLNEMFRYKTNL-YK   74
1rypk.pdb              15  LASSKAVTRGIS-VLKD--S-DDKTRQL-SPHTLMSFAGEAGDTVQFAEYIQANIQL-YS   68
1rypl.pdb              14  VAVDSRATAGNW-VASQ--T-VKRVIEI-NPFLLGTMAGGAADCQFWETWLGSQCRL-HE   67
                                                                 G   D                 

1neda.pdb              69  -----------GHLVKAAVELAKDWRTDR----------M-LRKLEALLAVADE------  100
1pma1.pdb              68  LQRR-----VNMPIEAVATLLSNMLNQVK----------Y--MPYMVQLLVGGID---T-  106
1pmaa.pdb              89  VTYG-----SLVNIENLVKRVADQMQQYT----Q-Y--GG-VRPYGVSLIFAGIDQ--I-  132
1ryp1.pdb              77  FDHN----DKKLSINSAARNIQHLLYGKR----------F--FPYYVHTIIAGLDED-G-  118
1ryp2.pdb              76  YDNPLADAEEALEPSYIFEYLATVMYQRR----S-K---M--NPLWNAIIVAGVQSN-G-  123
1rypa.pdb              97  YKYG-----YDMPCDVLAKRMANLSQIYT----Q-R--AY-MRPLGVILTFVSVDE--EL  141
1rypb.pdb              99  RIYG-----EYPPTKLLVSEVAKIMQEAT----Q-S--GG-VRPFGVSLLIAGHDEF-N-  143
1rypc.pdb              99  KTYN-----EDIPVEILVRRLSDIKQGYT----Q-H--GG-LRPFGVSFIYAGYDD--RY  143
1rypd.pdb              96  LTLE-----DPVTVEYLTRYVAGVQQRYT----Q-S--GG-VRPFGVSTLIAGFDPR-DD  141
1rype.pdb              93  LYYD-----EDINVESLTQSVCDLALRFGEGASGEERL--MSRPFGVALLIAGHDAD-D-  143
1rypf.pdb              96  LVFN-----RKLAVERAGHLLCDKAQKNT----Q-S--YG-GRPYGVGLLIIGYDK--S-  139
1rypg.pdb              97  KLYK-----TPIPIPAFADRLGQYVQAHT----L-Y--NS-VRPFGVSTIFGGVDK--N-  140
1ryph.pdb              77  SQYG------TPSTETAASVFKELCYENK-------------DNLTAGIIVAGYDDK-N-  115
1rypi.pdb              68  LYTS-----REPRVVSALQMLKQHLFKYQ-------------GHIGAYLIVAGVDP--T-  106
1rypj.pdb              75  LKEE-----RAIEPETFTQLVSSSLYERR----------F--GPYFVGPVVAGINSK-SG  116
1rypk.pdb              69  IRED-----YELSPQAVSSFVRQELAKSI----------RSRRPYQVNVLIGGYDKKKN-  112
1rypl.pdb              68  LREK-----ERISVAAASKILSNLVYQYK----------G--AGLSMGTMICGYTRK-E-  108
                                                                                       

1neda.pdb             101  -TASLIITGNGDVVQPENDLIAIGSGGPYAQAAARALL-E-----N--------------  139
1pma1.pdb             107  APHVFSIDAAGGSVED--IYASTGSGSPFVYGVLESQY-S--------------------  143
1pmaa.pdb             133  GPRLFDCDPAGTINEY--KATAIGSGKDAVVSFLEREY-K--------------------  169
1ryp1.pdb             119  KGAVYSFDPVGSYERE--QCRAGGAAASLIMPFLDNQV-N-----FKNQYEPGTNGKVKK  170
1ryp2.pdb             124  DQFLRYVNLLGVTYSS--PTLATGFGAHMANPLLRKVVDRESDIP---------------  166
1rypa.pdb             142  GPSIYKTDPAGYYVGY--KATATGPKQQEITTNLENHF-K-----K--------------  179
1rypb.pdb             144  GFSLYQVDPSGSYFPW--KATAIGKGSVAAKTFLEKRW-N--------------------  180
1rypc.pdb             144  GYQLYTSNPSGNYTGW--KAISVGANTSAAQTLLQMDY-K--------------------  180
1rypd.pdb             142  EPKLYQTEPSGIYSSW--SAQTIGRNSKTVREFLEKNY-D--------------------  178
1rype.pdb             144  GYQLFHAEPSGTFYRY--NAKAIGSGSEGAQAELLNEW-H--------------------  180
1rypf.pdb             140  GAHLLEFQPSGNVTEL--YGTAIGARSQGAKTYLERTL-D--TF----------------  178
1rypg.pdb             141  GAHLYMLEPSGSYWGY--KGAATGKGRQSAKAELEKLV-D-----H--------------  178
1ryph.pdb             116  KGEVYTIPLGGSVHKL--PYAIAGSGSTFIYGYCDKNF-R--------------------  152
1rypi.pdb             107  GSHLFSIHAHGSTDVG--YYLSLGSGSLAAMAVLESHW-K--------------------  143
1rypj.pdb             117  KPFIAGFDLIGCIDEA-KDFIVSGTASDQLFGMCESLY-E--------------------  154
1rypk.pdb             113  KPELYQIDYLGTKVEL--PYGAHGYSGFYTFSLLDHHY-R--------------------  149
1rypl.pdb             109  GPTIYYVDSDGTRLKG--DIFCVGSGQTFAYGVLDSNY-K--------------------  145
                                     G            G                                    

1neda.pdb             140  ---T---E-L-------SAREIAEKALDIAGD-----ICIYT-NH----FHTIEELS---  172
1pma1.pdb             144  ---E---K-M---T-VDEGVDLVIRAISAAKQ-----RDSAS-GG----MIDVAVIT---  179
1pmaa.pdb             170  ---E---N-L---P-EKEAVTLGIKALKSSLE-----E--GEELK----APEIASIT---  204
1ryp1.pdb             171  P-LK---Y-L---S-VEEVIKLVRDSFTSATE-----RHIQV-GD----GLEILIVT---  208
1ryp2.pdb             167  -------K-T---T-VQVAEEAIVNAMRVLYY-----RDARS-SR----NFSLAIID---  201
1rypa.pdb             180  -SKIDHI-NE---ESWEKVVEFAITHMIDALG---------TEFSKN--DLEVGVAT---  220
1rypb.pdb             181  ---D---E-L---E-LEDAIHIALLTLKESVE---------G--EFNGDTIELAIIGDEN  218
1rypc.pdb             181  ---D---D-M---K-VDDAIELALKTLSKTT------D--SSALTYD--RLEFATIR---  216
1rypd.pdb             179  ---R-K-EPP---ATVEECVKLTVRSLLEVVQ---------T--GAK--NIEITVVK---  214
1rype.pdb             181  ---S---S-L---T-LKEAELLVLKILKQVMEEKLDE------N-----NAQLSCIT---  215
1rypf.pdb             179  ---I---K-IDG-N-PDELIKAGVEAISQSLRDESLT----V-D-----NLSIAIVG---  216
1rypg.pdb             179  -HPE--------GLSAREAVKQAAKIIYLAHE-----DN-KEKDF----ELEISWCS---  216
1ryph.pdb             153  ---E---N-M---S-KEETVDFIKHSLSQAIK-----WDGSS-GG----VIRMVVLT---  188
1rypi.pdb             144  ---Q---D-L---T-KEEAIKLASDAIQAGIW-----NDLGS-GS----NVDVCVME---  179
1rypj.pdb             155  ---P---N-L---E-PEDLFETISQALLNAAD-----RDALS-GW----GAVVYIIK---  190
1rypk.pdb             150  ---P---D-M---T-TEEGLDLLKLCVQELEK-----RMPMD-FK----GVIVKIVD---  185
1rypl.pdb             146  ---W---D-L---S-VEDALYLGKRSILAAAH-----RDAYS-GG----SVNLYHVT---  181
                                                                                       

1neda.pdb             173  -------------YK--------------------------------------A-EF---  177
1pma1.pdb             180  -------------RK--------DG-YVQLP-T-DQIESRIRKLG----L-IL-------  203
1pmaa.pdb             205  -------------VG--------NKYRIYDQ-E--EVKKFL-------------------  221
1ryp1.pdb             209  -------------KD--------GV-RKEFY-ELK----------------------RD-  222
1ryp2.pdb             202  -------------KN--------TGLTFKKNLQVE-----------------------NM  217
1rypa.pdb             221  -------------KD---------KFFTLSA-E--NIEERLVAIAEQ-D-----------  243
1rypb.pdb             219  PDLLGYTGIPTDK-G--------PRFRKLTS-Q--EINDRLEAL----------------  250
1rypc.pdb             217  -------------KGANDGE---VYQKIFKP-Q--EIKDILVKTG-IT------------  244
1rypd.pdb             215  -------------PD--------SDIVALSS-E--EINQYVTQIEQE-KQE---------  240
1rype.pdb             216  -------------KQ--------DGFKIYDN-E--KTAELIKELKEK-EAA---------  241
1rypf.pdb             217  -------------KD--------TPFTIYDGE---AVAK-YI------------------  233
1rypg.pdb             217  -------------LS-----ETNGLHKFVKG-D--LLQEAIDFAQKE-IN----------  244
1ryph.pdb             189  -------------AA--------GV-ERLIF-YPDEYEQL--------------------  205
1rypi.pdb             180  -------------IG--------KD-AEYLRN--Y-------------L----T-PNVR-  196
1rypj.pdb             191  -------------KD--------EV-VKRYL-KMR----------------------QD-  204
1rypk.pdb             186  -------------KD--------GI-RQVDD---F-------------Q----AQ-----  198
1rypl.pdb             182  -------------ED--------GW-IYHGNHDVGELFWK---VKEE-EG-SF----NN-  209
                                                                                       

1neda.pdb             178  -------HHH-----------------------------  180
1pma1.pdb                  ---------------------------------------     
1pmaa.pdb                  ---------------------------------------     
1ryp1.pdb                  ---------------------------------------     
1ryp2.pdb             218  KWDFAKD---IKGYGT--------------------QKI  233
1rypa.pdb                  ---------------------------------------     
1rypb.pdb                  ---------------------------------------     
1rypc.pdb                  ---------------------------------------     
1rypd.pdb             241  ----------Q----------------------------  241
1rype.pdb             242  ----------E----------------------------  242
1rypf.pdb                  ---------------------------------------     
1rypg.pdb                  ---------------------------------------     
1ryph.pdb                  ---------------------------------------     
1rypi.pdb             197  -------EEK--QKSYKFPRGTT-AVLKESIVNICD---  222
1rypj.pdb                  ---------------------------------------     
1rypk.pdb                  ---------------------------------------     
1rypl.pdb             210  ------V---------------IG---------------  212
                                                                  


#=========================================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.
#
################################################EOF#################################################