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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 Aug 12 23:11:57 2005
# Report_file: /mnt/EXTRA_STORAGE/MUSTANG_RESULTS/MUSTANG_HOMSTRAD/results/proteasome.html
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#====================================
# 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.
#
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