BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 005722
(681 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2VEA|A Chain A, The Complete Sensory Module Of The Cyanobacterial
Phytochrome Cph1 In The Pr-State
Length = 520
Score = 265 bits (677), Expect = 6e-71, Method: Compositional matrix adjust.
Identities = 166/523 (31%), Positives = 267/523 (51%), Gaps = 49/523 (9%)
Query: 71 VQRGRLIQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLF 130
+ LIQP G ++ + E + T+ S N +L +P + LG + +F
Sbjct: 20 IHTAHLIQPHGLVVVLQEPDLTISQISANCTGILGRSPEDL----------LGRTLGEVF 69
Query: 131 TSSGAAALQKAANFGEVNLLNPILIHCKTSGKPFY---AILHRIDVGLVI-DLEPV-NPD 185
S +Q G+++ LNP + + G F + HR GL++ +LEP D
Sbjct: 70 DSFQIDPIQSRLTAGQISSLNPSKLWARVMGDDFVIFDGVFHRNSDGLLVCELEPAYTSD 129
Query: 186 DVPVTAAGALKSYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDE 245
++P L Y +A A++RL+ N+ DV+V EV +TG+DRVM+Y+F E+
Sbjct: 130 NLPF-----LGFYHMANAALNRLRQ--QANLRDFYDVIVEEVRRMTGFDRVMLYRFDENN 182
Query: 246 HGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDC--LAPPVKVIQDKKL 303
HG+V+AE +R D+EPYLG HYP +DIPQ +R L + N +R+I D +A P+ +
Sbjct: 183 HGDVIAEDKRDDMEPYLGLHYPESDIPQPARRLFIHNPIRVIPDVYGVAVPLTPAVNPST 242
Query: 304 DQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVC 363
++ + L S LR+ + CH Y++NMG ASL +S+ + LWGL+ C
Sbjct: 243 NRAVDLTESILRSAYHCHLTYLKNMGVGASLTISLI-------------KDGHLWGLIAC 289
Query: 364 HHTSPRFVPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQTVLCDMLLR--DSP 421
HH +P+ +PF LR ACEF +V ++ + + + + VL D + D
Sbjct: 290 HHQTPKVIPFELRKACEFFGRVVFSNISAQEDTETFDYRVQLAEHEAVLLDKMTTAADFV 349
Query: 422 VGIVTQTPNVMDLVKCDGAALYYRGKLWLLGVTPTEEQIKDIAEWLLEYHRGSTGLSTDS 481
G+ ++ L GAA+ + KL L+G TP E+ ++ + +W LE T S
Sbjct: 350 EGLTNHPDRLLGLTGSQGAAICFGEKLILVGETPDEKAVQYLLQW-LENREVQDVFFTSS 408
Query: 482 LVEAGYPGALALGDAVCGIAAVKITSKDFLFWFRSHTAKEIKWGG---AKHDSGGKDGGR 538
L + YP A+ G+ A+ I +FL WFR + + WGG +++ +DG
Sbjct: 409 LSQI-YPDAVNFKSVASGLLAIPIARHNFLLWFRPEVLQTVNWGGDPNHAYEATQEDGKI 467
Query: 539 KMHPRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQ-----LILR 576
++HPR SF + E+V+ +SLPW+ VE+ + +L+ LILR
Sbjct: 468 ELHPRQSFDLWKEIVRLQSLPWQSVEIQSALALKKAIVNLILR 510
>pdb|3ZQ5|A Chain A, Structure Of The Y263f Mutant Of The Cyanobacterial
Phytochrome Cph1
Length = 520
Score = 263 bits (673), Expect = 2e-70, Method: Compositional matrix adjust.
Identities = 165/523 (31%), Positives = 267/523 (51%), Gaps = 49/523 (9%)
Query: 71 VQRGRLIQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLF 130
+ LIQP G ++ + E + T+ S N +L +P + LG + +F
Sbjct: 20 IHTAHLIQPHGLVVVLQEPDLTISQISANCTGILGRSPEDL----------LGRTLGEVF 69
Query: 131 TSSGAAALQKAANFGEVNLLNPILIHCKTSGKPFY---AILHRIDVGLVI-DLEPV-NPD 185
S +Q G+++ LNP + + G F + HR GL++ +LEP D
Sbjct: 70 DSFQIDPIQSRLTAGQISSLNPSKLWARVMGDDFVIFDGVFHRNSDGLLVCELEPAYTSD 129
Query: 186 DVPVTAAGALKSYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDE 245
++P L Y +A A++RL+ N+ DV+V EV +TG+DRVM+Y+F E+
Sbjct: 130 NLPF-----LGFYHMANAALNRLRQ--QANLRDFYDVIVEEVRRMTGFDRVMLYRFDENN 182
Query: 246 HGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDC--LAPPVKVIQDKKL 303
HG+V+AE +R D+EPYLG HYP +DIPQ +R L + N +R+I D +A P+ +
Sbjct: 183 HGDVIAEDKRDDMEPYLGLHYPESDIPQPARRLFIHNPIRVIPDVYGVAVPLTPAVNPST 242
Query: 304 DQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVC 363
++ + L S LR+ + CH +++NMG ASL +S+ + LWGL+ C
Sbjct: 243 NRAVDLTESILRSAYHCHLTFLKNMGVGASLTISLI-------------KDGHLWGLIAC 289
Query: 364 HHTSPRFVPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQTVLCDMLLR--DSP 421
HH +P+ +PF LR ACEF +V ++ + + + + VL D + D
Sbjct: 290 HHQTPKVIPFELRKACEFFGRVVFSNISAQEDTETFDYRVQLAEHEAVLLDKMTTAADFV 349
Query: 422 VGIVTQTPNVMDLVKCDGAALYYRGKLWLLGVTPTEEQIKDIAEWLLEYHRGSTGLSTDS 481
G+ ++ L GAA+ + KL L+G TP E+ ++ + +W LE T S
Sbjct: 350 EGLTNHPDRLLGLTGSQGAAICFGEKLILVGETPDEKAVQYLLQW-LENREVQDVFFTSS 408
Query: 482 LVEAGYPGALALGDAVCGIAAVKITSKDFLFWFRSHTAKEIKWGG---AKHDSGGKDGGR 538
L + YP A+ G+ A+ I +FL WFR + + WGG +++ +DG
Sbjct: 409 LSQI-YPDAVNFKSVASGLLAIPIARHNFLLWFRPEVLQTVNWGGDPNHAYEATQEDGKI 467
Query: 539 KMHPRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQ-----LILR 576
++HPR SF + E+V+ +SLPW+ VE+ + +L+ LILR
Sbjct: 468 ELHPRQSFDLWKEIVRLQSLPWQSVEIQSALALKKAIVNLILR 510
>pdb|4GW9|A Chain A, Structure Of A Bacteriophytochrome And Light-Stimulated
Protomer Swapping With A Gene Repressor
pdb|4GW9|B Chain B, Structure Of A Bacteriophytochrome And Light-Stimulated
Protomer Swapping With A Gene Repressor
pdb|4GW9|C Chain C, Structure Of A Bacteriophytochrome And Light-Stimulated
Protomer Swapping With A Gene Repressor
pdb|4GW9|D Chain D, Structure Of A Bacteriophytochrome And Light-Stimulated
Protomer Swapping With A Gene Repressor
Length = 655
Score = 199 bits (507), Expect = 3e-51, Method: Compositional matrix adjust.
Identities = 152/509 (29%), Positives = 233/509 (45%), Gaps = 59/509 (11%)
Query: 77 IQPFGCMIAVDEQNFTVLGYSENAPEMLDLAP-HAVPNIEQQDALTLGIDVRTLFTSSGA 135
IQP G ++ V E + ++ S NA E L+L VP E L + I T+ G
Sbjct: 51 IQPHGALLVVSEPDHRIIQASANAAEFLNLGSVLGVPLAEIDGDLLIKILPHLDPTAEGX 110
Query: 136 AALQKAANFGEVNLLNPILIHCKTSGKP---FYAILHRI-DVGLVIDLEPVNPDDVPVTA 191
P+ + C+ G P + + HR + GL+I+LE P P+
Sbjct: 111 ----------------PVAVRCRI-GNPSTEYDGLXHRPPEGGLIIELERAGP---PIDL 150
Query: 192 AGALKSYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVA 251
+G L A A+ R+++ +G++ LCD TGYDRV VY+F E HGEV +
Sbjct: 151 SGTL------APALERIRT--AGSLRALCDDTALLFQQCTGYDRVXVYRFDEQGHGEVFS 202
Query: 252 ECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQDKKLD----QPL 307
E P LE Y G YP++DIPQ +R L + +VR++ D PV + + +L + L
Sbjct: 203 ERHVPGLESYFGNRYPSSDIPQXARRLYERQRVRVLVDVSYQPVPL--EPRLSPLTGRDL 260
Query: 308 SLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTS 367
G LR+ H +Y++N G A+LV+S+ + G KLWGLV CHH
Sbjct: 261 DXSGCFLRSXSPIHLQYLKNXGVRATLVVSLVV-------------GGKLWGLVACHHYL 307
Query: 368 PRFVPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQTVLCDMLLR--DSPVGIV 425
PRF+ F LR CE L + ++ + E + R + + + R D I
Sbjct: 308 PRFIHFELRAICELLAEAIATRITALESFAQSQSELFVQRLEQRXIEAITREGDWRAAIF 367
Query: 426 TQTPNVMDLVKCDGAALYYRGKLWLLGVTPTEEQIKDIAEWLLEYHRGSTGLSTDSLVEA 485
+ +++ + DG AL Y ++ +G P+ + +++IA WL R + ST SL
Sbjct: 368 DTSQSILQPLHADGCALVYEDQIRTIGDVPSTQDVREIAGWLDRQPRAAV-TSTASL-GL 425
Query: 486 GYPGALALGDAVCGIAAVKITSK--DFLFWFRSHTAKEIKWGG-AKHDSGGKDGGRKMHP 542
P L G+ A I+ +FL WFR + WGG K D + P
Sbjct: 426 DVPELAHLTRXASGVVAAPISDHRGEFLXWFRPERVHTVTWGGDPKKPFTXGDTPADLSP 485
Query: 543 RSSFKAFLEVVKQRSLPWEDVEMDAIHSL 571
R SF + +VV+ S PW ++ A ++
Sbjct: 486 RRSFAKWHQVVEGTSDPWTAADLAAARTI 514
>pdb|3G6O|A Chain A, Crystal Structure Of P. Aeruginosa Bacteriophytochrome
Pabphp Photosensory Core Domain Mutant Q188l
pdb|3G6O|B Chain B, Crystal Structure Of P. Aeruginosa Bacteriophytochrome
Pabphp Photosensory Core Domain Mutant Q188l
Length = 505
Score = 180 bits (457), Expect = 2e-45, Method: Compositional matrix adjust.
Identities = 127/401 (31%), Positives = 196/401 (48%), Gaps = 49/401 (12%)
Query: 194 ALKSYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAEC 253
++ S+ L A+ I L + SLL +V +E+ +TGYDRVM Y+F D+ GEVVAE
Sbjct: 119 SITSFTLNAQRIIAQVQLHNDTASLLSNV-TDELRRMTGYDRVMAYRFRHDDSGEVVAES 177
Query: 254 RRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQ--DKKLDQPLSLCG 311
RR DLE YLG YPA+DIP +R L ++N +R+I D P++V + + ++ L
Sbjct: 178 RREDLESYLGLRYPASDIPAQARRLYIQNPIRLIADVAYTPMRVFPALNPETNESFDLSY 237
Query: 312 STLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFV 371
S LR+ H Y+ NMG AS+ +S+ + G KLWGL CHH SP+ +
Sbjct: 238 SVLRSVSPIHCEYLTNMGVRASMSISIVV-------------GGKLWGLFSCHHMSPKLI 284
Query: 372 PFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQT-----VLCDMLLRDSPVGIVT 426
P+P+R + Q+F + VE Q R +LR T + D G +
Sbjct: 285 PYPVRMS----FQIFSQVCSAIVERLEQGRIAELLRVSTERRLALARRARDADDLFGALA 340
Query: 427 QTPN-VMDLVKCDGAALYYRGK-LWLLGVTPTEEQIKDIAEWLLE------YHRGSTGLS 478
+ + L+ CDGA + G+ L + G E Q ++ + L YH +
Sbjct: 341 HPDDGIAALIPCDGALVMLGGRTLSIRG--DFERQAGNVLQRLQRDPERDIYHTDNWPQP 398
Query: 479 TDSLVEAGYPGALALGDAVCGIAAVKITSKD--FLFWFRSHTAKEIKWGGAKHD--SGGK 534
++ + G CG+ A++ ++ ++FWFR I+WGG + G
Sbjct: 399 SEDSPDGG---------DCCGVLAIRFHRQESGWIFWFRHEEVHRIRWGGKPEKLLTIGP 449
Query: 535 DGGRKMHPRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLIL 575
G R + PR SF+A+ EVV+ S PW + ++ L+L L
Sbjct: 450 SGPR-LTPRGSFEAWEEVVRGHSTPWSETDLAIAEKLRLDL 489
>pdb|3C2W|A Chain A, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|B Chain B, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|C Chain C, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|D Chain D, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|E Chain E, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|F Chain F, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|G Chain G, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|H Chain H, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3NHQ|A Chain A, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|B Chain B, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|C Chain C, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|D Chain D, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|E Chain E, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|F Chain F, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|G Chain G, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|H Chain H, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NOP|C Chain C, Light-Induced Intermediate Structure L1 Of Pseudomonas
Aeruginosa Bacteriophytochrome
pdb|3NOT|C Chain C, Light-Induced Intermediate Structure L2 Of P. Aeruginosa
Bacteriophytochrome
pdb|3NOU|C Chain C, Light-Induced Intermediate Structure L3 Of P. Aeruginosa
Bacteriophytochrome
Length = 505
Score = 179 bits (454), Expect = 5e-45, Method: Compositional matrix adjust.
Identities = 127/401 (31%), Positives = 196/401 (48%), Gaps = 49/401 (12%)
Query: 194 ALKSYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAEC 253
++ S+ L A+ I L + SLL +V +E+ +TGYDRVM Y+F D+ GEVVAE
Sbjct: 119 SITSFTLNAQRIIAQVQLHNDTASLLSNV-TDELRRMTGYDRVMAYRFRHDDSGEVVAES 177
Query: 254 RRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQ--DKKLDQPLSLCG 311
RR DLE YLG YPA+DIP +R L ++N +R+I D P++V + + ++ L
Sbjct: 178 RREDLESYLGQRYPASDIPAQARRLYIQNPIRLIADVAYTPMRVFPALNPETNESFDLSY 237
Query: 312 STLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFV 371
S LR+ H Y+ NMG AS+ +S+ + G KLWGL CHH SP+ +
Sbjct: 238 SVLRSVSPIHCEYLTNMGVRASMSISIVV-------------GGKLWGLFSCHHMSPKLI 284
Query: 372 PFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQT-----VLCDMLLRDSPVGIVT 426
P+P+R + Q+F + VE Q R +LR T + D G +
Sbjct: 285 PYPVRMS----FQIFSQVCSAIVERLEQGRIAELLRVSTERRLALARRARDADDLFGALA 340
Query: 427 QTPN-VMDLVKCDGAALYYRGK-LWLLGVTPTEEQIKDIAEWLLE------YHRGSTGLS 478
+ + L+ CDGA + G+ L + G E Q ++ + L YH +
Sbjct: 341 HPDDGIAALIPCDGALVMLGGRTLSIRG--DFERQAGNVLQRLQRDPERDIYHTDNWPQP 398
Query: 479 TDSLVEAGYPGALALGDAVCGIAAVKITSKD--FLFWFRSHTAKEIKWGGAKHD--SGGK 534
++ + G CG+ A++ ++ ++FWFR I+WGG + G
Sbjct: 399 SEDSPDGG---------DCCGVLAIRFHRQESGWIFWFRHEEVHRIRWGGKPEKLLTIGP 449
Query: 535 DGGRKMHPRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLIL 575
G R + PR SF+A+ EVV+ S PW + ++ L+L L
Sbjct: 450 SGPR-LTPRGSFEAWEEVVRGHSTPWSETDLAIAEKLRLDL 489
>pdb|3IBR|A Chain A, Crystal Structure Of P. Aeruginosa Bacteriophytochrome
Photosensory Core Module Mutant Q188l In The Mixed PrPFR
STATE
pdb|3IBR|B Chain B, Crystal Structure Of P. Aeruginosa Bacteriophytochrome
Photosensory Core Module Mutant Q188l In The Mixed PrPFR
STATE
Length = 505
Score = 172 bits (436), Expect = 5e-43, Method: Compositional matrix adjust.
Identities = 125/401 (31%), Positives = 191/401 (47%), Gaps = 49/401 (12%)
Query: 194 ALKSYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAEC 253
++ S+ L A+ I L + SLL +V +E+ TGYDRV Y+F D+ GEVVAE
Sbjct: 119 SITSFTLNAQRIIAQVQLHNDTASLLSNV-TDELRRXTGYDRVXAYRFRHDDSGEVVAES 177
Query: 254 RRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQ--DKKLDQPLSLCG 311
RR DLE YLG YPA+DIP +R L ++N +R+I D P +V + + ++ L
Sbjct: 178 RREDLESYLGLRYPASDIPAQARRLYIQNPIRLIADVAYTPXRVFPALNPETNESFDLSY 237
Query: 312 STLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFV 371
S LR+ H Y+ N G AS +S+ + G KLWGL CHH SP+ +
Sbjct: 238 SVLRSVSPIHCEYLTNXGVRASXSISIVV-------------GGKLWGLFSCHHXSPKLI 284
Query: 372 PFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQT-----VLCDMLLRDSPVGIVT 426
P+P+R + Q+F + VE Q R +LR T + D G +
Sbjct: 285 PYPVRXS----FQIFSQVCSAIVERLEQGRIAELLRVSTERRLALARRARDADDLFGALA 340
Query: 427 QTPN-VMDLVKCDGAALYYRGK-LWLLGVTPTEEQIKDIAEWLLE------YHRGSTGLS 478
+ + L+ CDGA + G+ L + G E Q ++ + L YH +
Sbjct: 341 HPDDGIAALIPCDGALVXLGGRTLSIRG--DFERQAGNVLQRLQRDPERDIYHTDNWPQP 398
Query: 479 TDSLVEAGYPGALALGDAVCGIAAVKITSKD--FLFWFRSHTAKEIKWGGAKHD--SGGK 534
++ + G CG+ A++ ++ ++FWFR I+WGG + G
Sbjct: 399 SEDSPDGG---------DCCGVLAIRFHRQESGWIFWFRHEEVHRIRWGGKPEKLLTIGP 449
Query: 535 DGGRKMHPRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLIL 575
G R + PR SF+A+ EVV+ S PW + ++ L+L L
Sbjct: 450 SGPR-LTPRGSFEAWEEVVRGHSTPWSETDLAIAEKLRLDL 489
>pdb|2OOL|A Chain A, Crystal Structure Of The Chromophore-Binding Domain Of An
Unusual Bacteriophytochrome Rpbphp3 From R. Palustris
pdb|2OOL|B Chain B, Crystal Structure Of The Chromophore-Binding Domain Of An
Unusual Bacteriophytochrome Rpbphp3 From R. Palustris
Length = 337
Score = 154 bits (388), Expect = 2e-37, Method: Compositional matrix adjust.
Identities = 99/318 (31%), Positives = 158/318 (49%), Gaps = 35/318 (11%)
Query: 77 IQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAA 136
IQP G + V E + + S N ++L Q A L + + T++ AA
Sbjct: 39 IQPHGYLFVVSETDLRIASVSANVEDLL----------RQPPASLLNVPIAHYLTAASAA 88
Query: 137 ALQKAANFGEVNLLNPILIHCKTSG--KPFYAILHRIDVGLVIDLEPVNPDDVPVTAAGA 194
L A + G+ +NPI + T + F ILHR D ++++LEP + +
Sbjct: 89 RLTHALHGGDPAAINPIRLDVVTPDGERAFNGILHRHDSIVILELEPRD------ESRYT 142
Query: 195 LKSYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECR 254
+ ++ AI RLQ+ + ++ C + +EV +TG+DR+ VY+F D G+V+AE R
Sbjct: 143 NEFFRSVRVAIRRLQT--AADLPTACWIAASEVRRITGFDRIKVYQFAADWSGQVIAEDR 200
Query: 255 RPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQD--KKLDQPLSLCGS 312
+ L FH+P++DIP SR L N VR+I D P ++ D +L P+ L S
Sbjct: 201 DSGIPSLLDFHFPSSDIPAQSRALYTINPVRIIPDIGYRPSPLVPDINPRLGGPIDLSFS 260
Query: 313 TLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVP 372
LR+ H YM NMG A++ +S+ + +LWG++ CH+ +PRFV
Sbjct: 261 VLRSVSPTHLEYMVNMGMHAAMSISIV-------------RDNRLWGMISCHNLTPRFVS 307
Query: 373 FPLRYACEFLIQVFGVQV 390
+ +R ACE + QV Q+
Sbjct: 308 YEVRQACELIAQVLTWQI 325
>pdb|4E04|A Chain A, Rpbphp2 Chromophore-binding Domain Crystallized By
Homologue-directed Mutagenesis.
pdb|4E04|B Chain B, Rpbphp2 Chromophore-binding Domain Crystallized By
Homologue-directed Mutagenesis
Length = 327
Score = 143 bits (360), Expect = 4e-34, Method: Compositional matrix adjust.
Identities = 101/319 (31%), Positives = 152/319 (47%), Gaps = 35/319 (10%)
Query: 77 IQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAA 136
IQP G ++A+ + T++ S+N PE+ LA A+ +G +F S
Sbjct: 26 IQPHGLLLAL-AADMTIVAGSDNLPELTGLAIGAL----------IGRSAADVFDSETHN 74
Query: 137 ALQKAANFGEVNLLNPILIHCKTSG--KPFYAILHRIDVGLVIDLEPVNPDDVPVTAAGA 194
L A + PI + + F HR D + ++LEP D V A
Sbjct: 75 RLTIALAEPGAAVGAPIAVGFTMPDGERAFNGSWHRHDQLVFLELEPPQRD---VRYPQA 131
Query: 195 LKSYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECR 254
++ AI RLQ+ + + C EV ++TG+DRVM+Y+F D GEV+AE R
Sbjct: 132 F--FRSVRSAIRRLQA--AETLESACAAAAQEVREITGFDRVMIYRFASDFSGEVIAEDR 187
Query: 255 RPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQD--KKLDQPLSLCGS 312
++E YLG H+PA+DIP +R L N VR+I D PV V D + +P+ L +
Sbjct: 188 CAEVESYLGLHFPASDIPAQARRLYTINPVRIIPDINYRPVPVTPDLNPRTGRPIDLSFA 247
Query: 313 TLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVP 372
LR+ H YM N+G ++ +S+ +G +LWGL+ CHH P +V
Sbjct: 248 ILRSVSPVHLEYMRNIGMHGTMSISIL-------------RGERLWGLIACHHRKPNYVD 294
Query: 373 FPLRYACEFLIQVFGVQVN 391
+R ACE + QV Q+
Sbjct: 295 LEVRQACELVAQVLAWQIG 313
>pdb|2O9B|A Chain A, Crystal Structure Of Bacteriophytochrome Chromophore
Binding Domain
pdb|2O9C|A Chain A, Crystal Structure Of Bacteriophytochrome Chromophore
Binding Domain At 1.45 Angstrom Resolution
Length = 342
Score = 121 bits (304), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 99/317 (31%), Positives = 147/317 (46%), Gaps = 36/317 (11%)
Query: 77 IQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAA 136
IQP G ++ D + VL S NA L Q+ + G + L A
Sbjct: 50 IQPHGALLTADGHSGEVLQMSLNAATFLG----------QEPTVLRGQTLAALLPEQWPA 99
Query: 137 ALQKAANFGEVNLLNPILIHCKTSGKPFYAILHRIDVGLVIDLEPVNPDDVPVTAAGALK 196
LQ A G + L + +HR+ L+++ EP D T AL+
Sbjct: 100 -LQAALPPGCPDALQYRATLDWPAAGHLSLTVHRVGELLILEFEPTEAWDS--TGPHALR 156
Query: 197 SYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRP 256
+ A L+S P N+ L +V V +LTG+DRVM+YKF D GEV+AE RR
Sbjct: 157 NAMFA------LESAP--NLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARRE 208
Query: 257 DLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAP--PVKVIQDKKLDQPLSLCGSTL 314
L +LG +PA+DIP +R L ++ +R+ D A P+ + + + + P L G+ L
Sbjct: 209 GLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVL 268
Query: 315 RAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVPFP 374
RA H +Y+ NMG +SL +SV + +LWGL+ CHH +P +P
Sbjct: 269 RATSPMHMQYLRNMGVGSSLSVSVVVGG-------------QLWGLIACHHQTPYVLPPD 315
Query: 375 LRYACEFLIQVFGVQVN 391
LR E L ++ +QV
Sbjct: 316 LRTTLESLGRLLSLQVQ 332
>pdb|3S7Q|A Chain A, Crystal Structure Of A Monomeric Infrared Fluorescent
Deinococcus Radiodurans Bacteriophytochrome Chromophore
Binding Domain
Length = 343
Score = 120 bits (300), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 98/317 (30%), Positives = 147/317 (46%), Gaps = 36/317 (11%)
Query: 77 IQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAA 136
IQP G ++ D + VL S NA L Q+ + G + L A
Sbjct: 49 IQPHGALLTADGHSGEVLQMSLNAATFLG----------QEPTVLRGQTLAALLPEQWPA 98
Query: 137 ALQKAANFGEVNLLNPILIHCKTSGKPFYAILHRIDVGLVIDLEPVNPDDVPVTAAGALK 196
LQ A G + L + +HR+ L+++ EP D T AL+
Sbjct: 99 -LQAALPPGCPDALQYRATLDWPAAGHLSLTVHRVGELLILEFEPTEAWDS--TGPHALR 155
Query: 197 SYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRP 256
+ A+S L+S P N+ L +V V +LTG+DRVM+YKF D GEV+AE RR
Sbjct: 156 N------AMSALESAP--NLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARRE 207
Query: 257 DLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAP--PVKVIQDKKLDQPLSLCGSTL 314
L +LG +PA+ IP +R L ++ +R+ D A P+ + + + + P L G+ L
Sbjct: 208 GLHAFLGHRFPASHIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVL 267
Query: 315 RAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVPFP 374
RA H +++ NMG +SL +SV + +LWGL+ CHH +P +P
Sbjct: 268 RATSPMHMQFLRNMGVGSSLSVSVVVGG-------------QLWGLIACHHQTPYVLPPD 314
Query: 375 LRYACEFLIQVFGVQVN 391
LR E+L + QV
Sbjct: 315 LRTTLEYLGRELSEQVQ 331
>pdb|3S7N|A Chain A, Crystal Structure Of The Alternate His 207 Conformation Of
The Infrared Fluorescent D207h Variant Of Deinococcus
Bacteriophytochrome Chromophore Binding Domain At 2.45
Angstrom Resolution
pdb|3S7O|A Chain A, Crystal Structure Of The Infrared Fluorescent D207h
Variant Of Deinococcus Bacteriophytochrome Chromophore
Binding Domain At 1.24 Angstrom Resolution
pdb|3S7P|A Chain A, Crystal Structure Of The Infrared Fluorescent D207h
Variant Of Deinococcus Bacteriophytochrome Chromophore
Binding Domain At 1.72 Angstrom Resolution
Length = 343
Score = 119 bits (297), Expect = 7e-27, Method: Compositional matrix adjust.
Identities = 98/317 (30%), Positives = 146/317 (46%), Gaps = 36/317 (11%)
Query: 77 IQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAA 136
IQP G ++ D + VL S NA L Q+ + G + L A
Sbjct: 49 IQPHGALLTADGHSGEVLQMSLNAATFLG----------QEPTVLRGQTLAALLPEQWPA 98
Query: 137 ALQKAANFGEVNLLNPILIHCKTSGKPFYAILHRIDVGLVIDLEPVNPDDVPVTAAGALK 196
LQ A G + L + +HR+ L+++ EP D T AL+
Sbjct: 99 -LQAALPPGCPDALQYRATLDWPAAGHLSLTVHRVGELLILEFEPTEAWDS--TGPHALR 155
Query: 197 SYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRP 256
+ A L+S P N+ L +V V +LTG+DRVM+YKF D GEV+AE RR
Sbjct: 156 NAMFA------LESAP--NLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARRE 207
Query: 257 DLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAP--PVKVIQDKKLDQPLSLCGSTL 314
L +LG +PA+ IP +R L ++ +R+ D A P+ + + + + P L G+ L
Sbjct: 208 GLHAFLGHRFPASHIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVL 267
Query: 315 RAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVPFP 374
RA H +Y+ NMG +SL +SV + +LWGL+ CHH +P +P
Sbjct: 268 RATSPMHMQYLRNMGVGSSLSVSVVVGG-------------QLWGLIACHHQTPYVLPPD 314
Query: 375 LRYACEFLIQVFGVQVN 391
LR E L ++ +QV
Sbjct: 315 LRTTLESLGRLLSLQVQ 331
>pdb|1ZTU|A Chain A, Structure Of The Chromophore Binding Domain Of Bacterial
Phytochrome
Length = 341
Score = 118 bits (296), Expect = 8e-27, Method: Compositional matrix adjust.
Identities = 97/317 (30%), Positives = 146/317 (46%), Gaps = 36/317 (11%)
Query: 77 IQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAA 136
IQP G ++ D + VL S NA L Q+ + G + L A
Sbjct: 49 IQPHGALLTADGHSGEVLQMSLNAATFLG----------QEPTVLRGQTLAALLPEQWPA 98
Query: 137 ALQKAANFGEVNLLNPILIHCKTSGKPFYAILHRIDVGLVIDLEPVNPDDVPVTAAGALK 196
LQ A G + L + +HR+ L+++ EP D T AL+
Sbjct: 99 -LQAALPPGCPDALQYRATLDWPAAGHLSLTVHRVGELLILEFEPTEAWDS--TGPHALR 155
Query: 197 SYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRP 256
+ A L+S P N+ L +V V +LTG+DRV +YKF D GEV+AE RR
Sbjct: 156 NAXFA------LESAP--NLRALAEVATQTVRELTGFDRVXLYKFAPDATGEVIAEARRE 207
Query: 257 DLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAP--PVKVIQDKKLDQPLSLCGSTL 314
L +LG +PA+DIP +R L ++ +R+ D A P+ + + + + P L G+ L
Sbjct: 208 GLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNTQTNAPTPLGGAVL 267
Query: 315 RAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVPFP 374
RA H +Y+ N G +SL +SV + +LWGL+ CHH +P +P
Sbjct: 268 RATSPXHXQYLRNXGVGSSLSVSVVVGG-------------QLWGLIACHHQTPYVLPPD 314
Query: 375 LRYACEFLIQVFGVQVN 391
LR E+L ++ +QV
Sbjct: 315 LRTTLEYLGRLLSLQVQ 331
>pdb|2LB5|A Chain A, Refined Structural Basis For The Photoconversion Of A
Phytochrome To The Activated Far-Red Light-Absorbing
Form
pdb|2LB9|A Chain A, Refined Solution Structure Of A Cyanobacterial Phytochrome
Gaf Domain In The Red Light-Absorbing Ground State
(Corrected Pyrrole Ring Planarity)
Length = 208
Score = 87.8 bits (216), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 57/156 (36%), Positives = 78/156 (50%), Gaps = 30/156 (19%)
Query: 224 VNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEP-YLGFHYPATDIPQASRFLIMKN 282
V EV G DRV VY+F + HG VVAE R + P LG +PA DIP+ +R L
Sbjct: 39 VEEVRAFLGTDRVKVYRFDPEGHGTVVAEARGGERLPSLLGLTFPAGDIPEEARRLFRLA 98
Query: 283 KVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHG---------CHARYMENMGSIAS 333
+VR+I D A Q + + QP S G + R P G CH Y+++MG +S
Sbjct: 99 QVRVIVDVEA------QSRSISQPES-WGLSARVPLGEPLQRPVDPCHVHYLKSMGVASS 151
Query: 334 LVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPR 369
LV+ + ++ +LWGL+V HH PR
Sbjct: 152 LVVPLMHHQ-------------ELWGLLVSHHAEPR 174
>pdb|2K2N|A Chain A, Solution Structure Of A Cyanobacterial Phytochrome Gaf
Domain In The Red Light-Absorbing Ground State
pdb|2KLI|A Chain A, Structural Basis For The Photoconversion Of A Phytochrome
To The Activated Far-Red Light-Absorbing Form
pdb|2KOI|A Chain A, Refined Solution Structure Of A Cyanobacterial Phytochrome
Gaf Domain In The Red Light-Absorbing Ground State
Length = 172
Score = 87.4 bits (215), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 57/156 (36%), Positives = 78/156 (50%), Gaps = 30/156 (19%)
Query: 224 VNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEP-YLGFHYPATDIPQASRFLIMKN 282
V EV G DRV VY+F + HG VVAE R + P LG +PA DIP+ +R L
Sbjct: 9 VEEVRAFLGTDRVKVYRFDPEGHGTVVAEARGGERLPSLLGLTFPAGDIPEEARRLFRLA 68
Query: 283 KVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHG---------CHARYMENMGSIAS 333
+VR+I D A Q + + QP S G + R P G CH Y+++MG +S
Sbjct: 69 QVRVIVDVEA------QSRSISQPES-WGLSARVPLGEPLQRPVDPCHVHYLKSMGVASS 121
Query: 334 LVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPR 369
LV+ + ++ +LWGL+V HH PR
Sbjct: 122 LVVPLMHHQ-------------ELWGLLVSHHAEPR 144
>pdb|3W2Z|A Chain A, Crystal Structure Of The Cyanobacterial Protein
Length = 198
Score = 32.3 bits (72), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 197 SYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAE 252
S+ +K + ++ L NI + E+ L DRV VY+F+ D GE VAE
Sbjct: 19 SHMAVSKVMEKI--LRVSNIDKIFQTTTQEIRQLLKCDRVAVYRFNPDWSGEFVAE 72
>pdb|3GEE|A Chain A, Crystal Structure Of Mnme From Chlorobium Tepidum In
Complex With Gdp And Folinic Acid
pdb|3GEI|A Chain A, Crystal Structure Of Mnme From Chlorobium Tepidum In
Complex With Gcp
pdb|3GEI|B Chain B, Crystal Structure Of Mnme From Chlorobium Tepidum In
Complex With Gcp
pdb|3GEI|C Chain C, Crystal Structure Of Mnme From Chlorobium Tepidum In
Complex With Gcp
Length = 476
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 30/131 (22%), Positives = 57/131 (43%), Gaps = 19/131 (14%)
Query: 274 ASRFLIMKNKVRMICDCLAPPVKVIQDKKLDQPLSLCG------STLRAPHGCHARYMEN 327
A++FL + NK+ + A ++ I D + + + TL+ G + ++
Sbjct: 343 AAKFLTVANKLDRAANADAL-IRAIADGTGTEVIGISALNGDGIDTLKQHMGDLVKNLDK 401
Query: 328 MGSIASLVMSV----TINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVPFPLRYACEFLI 383
+ + LV S+ + A D L N E ++ H + + F LR A +++
Sbjct: 402 LHEASVLVTSLRHYEALRNASDALQNALE--------LIAHESETELIAFELRAALDYVG 453
Query: 384 QVFGVQVNKEV 394
Q+ G VN+EV
Sbjct: 454 QITGKVVNEEV 464
>pdb|1TG6|A Chain A, Crystallography And Mutagenesis Point To An Essential Role
For The N- Terminus Of Human Mitochondrial Clpp
pdb|1TG6|B Chain B, Crystallography And Mutagenesis Point To An Essential Role
For The N- Terminus Of Human Mitochondrial Clpp
pdb|1TG6|C Chain C, Crystallography And Mutagenesis Point To An Essential Role
For The N- Terminus Of Human Mitochondrial Clpp
pdb|1TG6|D Chain D, Crystallography And Mutagenesis Point To An Essential Role
For The N- Terminus Of Human Mitochondrial Clpp
pdb|1TG6|E Chain E, Crystallography And Mutagenesis Point To An Essential Role
For The N- Terminus Of Human Mitochondrial Clpp
pdb|1TG6|F Chain F, Crystallography And Mutagenesis Point To An Essential Role
For The N- Terminus Of Human Mitochondrial Clpp
pdb|1TG6|G Chain G, Crystallography And Mutagenesis Point To An Essential Role
For The N- Terminus Of Human Mitochondrial Clpp
Length = 277
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 15/27 (55%)
Query: 247 GEVVAECRRPDLEPYLGFHYPATDIPQ 273
G VA CR P L P L H+PA PQ
Sbjct: 9 GARVASCRYPALGPRLAAHFPAQRPPQ 35
>pdb|3V6O|C Chain C, Leptin Receptor-Antibody Complex
pdb|3V6O|D Chain D, Leptin Receptor-Antibody Complex
Length = 221
Score = 30.4 bits (67), Expect = 3.8, Method: Composition-based stats.
Identities = 25/92 (27%), Positives = 44/92 (47%), Gaps = 11/92 (11%)
Query: 482 LVEAGYPGALALGDAV---CGIAAVKITSKDFLFWFRSHTAKEIKWGGAKHDSGGKDGGR 538
L+E+G PG +A +++ C I+ +T D + W R K ++W G GG
Sbjct: 5 LLESG-PGLVAPSESLSITCTISGFSLTD-DGVSWIRQPPGKGLEWLGVIW------GGG 56
Query: 539 KMHPRSSFKAFLEVVKQRSLPWEDVEMDAIHS 570
+ S FK+ L + + S +EMD++ +
Sbjct: 57 STYFNSLFKSRLSITRDNSKSQVFLEMDSLQT 88
>pdb|3VG0|H Chain H, Antibody Fab Fragment
Length = 223
Score = 30.0 bits (66), Expect = 4.2, Method: Composition-based stats.
Identities = 25/92 (27%), Positives = 44/92 (47%), Gaps = 11/92 (11%)
Query: 482 LVEAGYPGALALGDAV---CGIAAVKITSKDFLFWFRSHTAKEIKWGGAKHDSGGKDGGR 538
L+E+G PG +A +++ C I+ +T D + W R K ++W G GG
Sbjct: 6 LLESG-PGLVAPSESLSITCTISGFSLTD-DGVSWIRQPPGKGLEWLGVIW------GGG 57
Query: 539 KMHPRSSFKAFLEVVKQRSLPWEDVEMDAIHS 570
+ S FK+ L + + S +EMD++ +
Sbjct: 58 STYFNSLFKSRLSITRDNSKSQVFLEMDSLQT 89
>pdb|3LD8|C Chain C, Structure Of Jmjd6 And Fab Fragments
pdb|3LDB|C Chain C, Structure Of Jmjd6 Complexd With Alpha-Ketoglutarate And
Fab Fragment
Length = 221
Score = 30.0 bits (66), Expect = 4.7, Method: Composition-based stats.
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 5/67 (7%)
Query: 482 LVEAGYPGALALGDAV---CGIAAVKITSKDFLFWFRSHTAKEIKWGGAKHDSGGKDGGR 538
L E+G PG + ++ C + ITS + W R K+++W G ++SGG D
Sbjct: 4 LQESG-PGLVTPSQSLTLTCSVTGDSITSYHW-SWIRQFPGKKLEWMGYIYNSGGTDYNP 61
Query: 539 KMHPRSS 545
+ R S
Sbjct: 62 SLKSRVS 68
>pdb|1I7K|A Chain A, Crystal Structure Of Human Mitotic-Specific Ubiquitin-
Conjugating Enzyme, Ubch10
pdb|1I7K|B Chain B, Crystal Structure Of Human Mitotic-Specific Ubiquitin-
Conjugating Enzyme, Ubch10
Length = 179
Score = 30.0 bits (66), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 32/72 (44%), Gaps = 16/72 (22%)
Query: 95 GYSENAPEMLDLAPHAVPNIEQQDALTLGI---------DVRTLFTSSGAAALQKAANFG 145
GY NAP + L P PN++ Q ++L I DVRT+ L + G
Sbjct: 88 GYPYNAPTVKFLTPCYHPNVDTQGNISLDILKEKWSALYDVRTIL-------LSIQSLLG 140
Query: 146 EVNLLNPILIHC 157
E N+ +P+ H
Sbjct: 141 EPNIDSPLNTHA 152
>pdb|3EGV|B Chain B, Ribosomal Protein L11 Methyltransferase (Prma) In Complex
With Trimethylated Ribosomal Protein L11
Length = 146
Score = 30.0 bits (66), Expect = 5.0, Method: Composition-based stats.
Identities = 28/126 (22%), Positives = 52/126 (41%), Gaps = 7/126 (5%)
Query: 473 GSTGLSTDSLVEAGYPGALALGDAVCGIAAVKITSKDFLFWFRSHTAKEIKWGGAKHDSG 532
G G + V+A +GDA+ + + F F ++ A + A + G
Sbjct: 27 GQHGANIMEFVKAFNAATANMGDAIVPVEITIYADRSFTFVTKTPPASYLIRKAAGLEKG 86
Query: 533 GKDGGRKMHPRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLILRGSLQDEVAEDSKMIVN 592
GR+ R +++ LE+ KQ+ +P D+ + + ++ GS + E +V
Sbjct: 87 AHKPGREKVGRITWEQVLEIAKQK-MP--DLNTTDLEAAARMIAGSARSMGVE----VVG 139
Query: 593 VPSVDD 598
P V D
Sbjct: 140 APEVKD 145
>pdb|2J01|K Chain K, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 2 Of 4).
This File Contains The 50s Subunit From Molecule I.
pdb|2J03|K Chain K, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 4 Of 4).
This File Contains The 50s Subunit From Molecule Ii.
pdb|2HGJ|L Chain L, Crystal Structure Of The 70s Thermus Thermophilus Ribosome
Showing How The 16s 3'-End Mimicks Mrna E And P Codons.
This Entry 2hgj Contains 50s Ribosomal Subunit. The 30s
Ribosomal Subunit Can Be Found In Pdb Entry 2hgi.
pdb|2HGQ|L Chain L, Crystal Structure Of The 70s Thermus Thermophilus Ribosome
With Translocated And Rotated Shine-Dalgarno Duplex.
This Entry 2hgq Contains 50s Ribosomal Subunit. The 30s
Ribosomal Subunit Can Be Found In Pdb Entry 2hgp.
pdb|2HGU|L Chain L, 70s T.Th. Ribosome Functional Complex With Mrna And E- And
P-Site Trnas At 4.5a. This Entry 2hgu Contains 50s
Ribosomal Subunit. The 30s Ribosomal Subunit Can Be
Found In Pdb Entry 2hgr.
pdb|2NXN|B Chain B, T. Thermophilus Ribosomal Protein L11 Methyltransferase
(Prma) In Complex With Ribosomal Protein L11
pdb|2H8W|A Chain A, Solution Structure Of Ribosomal Protein L11
pdb|2E34|A Chain A, L11 Structure With Rdc And Rg Refinement
pdb|2E35|A Chain A, The Minimized Average Structure Of L11 With Rg Refinement
pdb|2E36|A Chain A, L11 With Sans Refinement
pdb|3CJT|B Chain B, Ribosomal Protein L11 Methyltransferase (prma) In Complex
With Dimethylated Ribosomal Protein L11
pdb|3CJT|D Chain D, Ribosomal Protein L11 Methyltransferase (prma) In Complex
With Dimethylated Ribosomal Protein L11
pdb|3CJT|F Chain F, Ribosomal Protein L11 Methyltransferase (prma) In Complex
With Dimethylated Ribosomal Protein L11
pdb|3CJT|H Chain H, Ribosomal Protein L11 Methyltransferase (prma) In Complex
With Dimethylated Ribosomal Protein L11
pdb|3CJT|J Chain J, Ribosomal Protein L11 Methyltransferase (prma) In Complex
With Dimethylated Ribosomal Protein L11
pdb|3CJT|L Chain L, Ribosomal Protein L11 Methyltransferase (prma) In Complex
With Dimethylated Ribosomal Protein L11
pdb|3CJT|N Chain N, Ribosomal Protein L11 Methyltransferase (prma) In Complex
With Dimethylated Ribosomal Protein L11
pdb|3CJT|P Chain P, Ribosomal Protein L11 Methyltransferase (prma) In Complex
With Dimethylated Ribosomal Protein L11
pdb|3F1F|K Chain K, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes As Described In
Remark 400.
pdb|3F1H|K Chain K, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
50s Subunit Of The Second 70s Ribosome. The Entire
Crystal Structure Contains Two 70s Ribosomes As
Described In Remark 400.
pdb|2WH2|K Chain K, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome
pdb|2WH4|K Chain K, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome
pdb|2KLM|A Chain A, Solution Structure Of L11 With Saxs And Rdc
pdb|2WRJ|K Chain K, The Structure Of The Ribosome With Elongation Factor G
Trapped In The Post-Translocational State (Part 2 Of 4).
pdb|2WRL|K Chain K, The Structure Of The Ribosome With Elongation Factor G
Trapped In The Post-Translocational State. (Part 4 Of
4).
pdb|3I8I|L Chain L, Elongation Complex Of The 70s Ribosome With Three Trnas
And Entry 3i8i Contains 50s Ribosomal Subnit. The 30s
Ribosomal Can Be Found In Pdb Entry 3i8h. Molecule A In
The Same Asym Unit Is Deposited As 3i8f (50s) And 3i8g
(30s).
pdb|2X9S|K Chain K, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2X9U|K Chain K, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2XTG|K Chain K, Trna Tranlocation On The 70s Ribosome: The Pre-
Translocational Translocation Intermediate Ti(Pre)
pdb|2XUX|K Chain K, Trna Translocation On The 70s Ribosome: The Post-
Translocational Translocation Intermediate Ti(Post)
Length = 147
Score = 29.6 bits (65), Expect = 5.2, Method: Composition-based stats.
Identities = 28/126 (22%), Positives = 52/126 (41%), Gaps = 7/126 (5%)
Query: 473 GSTGLSTDSLVEAGYPGALALGDAVCGIAAVKITSKDFLFWFRSHTAKEIKWGGAKHDSG 532
G G + V+A +GDA+ + + F F ++ A + A + G
Sbjct: 28 GQHGANIMEFVKAFNAATANMGDAIVPVEITIYADRSFTFVTKTPPASYLIRKAAGLEKG 87
Query: 533 GKDGGRKMHPRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLILRGSLQDEVAEDSKMIVN 592
GR+ R +++ LE+ KQ+ +P D+ + + ++ GS + E +V
Sbjct: 88 AHKPGREKVGRITWEQVLEIAKQK-MP--DLNTTDLEAAARMIAGSARSMGVE----VVG 140
Query: 593 VPSVDD 598
P V D
Sbjct: 141 APEVKD 146
>pdb|2PFM|A Chain A, Crystal Structure Of Adenylosuccinate Lyase (Purb) From
Bacillus Anthracis
pdb|2PFM|B Chain B, Crystal Structure Of Adenylosuccinate Lyase (Purb) From
Bacillus Anthracis
Length = 444
Score = 28.9 bits (63), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 31/131 (23%), Positives = 55/131 (41%), Gaps = 20/131 (15%)
Query: 200 LAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLE 259
LA +A + L +P + V ++ + +D +Y+ ++ +VVA R
Sbjct: 38 LACEAWAELGDIPKED--------VKKIREHASFDIDRIYEIEKETRHDVVAFTRAVSET 89
Query: 260 PYLG-----FHY--PATDIPQASRFLIMKNKVRMICDCLAPPVKVIQDKKLDQPLS-LCG 311
P LG HY +TD+ + I+K +I L V ++ +K + + + G
Sbjct: 90 PALGEERKWVHYGLTSTDVVDTALSYILKQANEIILKDLENFVSILANKAKEHKYTIMMG 149
Query: 312 STLRAPHGCHA 322
T HG HA
Sbjct: 150 RT----HGVHA 156
>pdb|3CJR|B Chain B, Ribosomal Protein L11 Methyltransferase (prma) In Complex
With Ribosomal Protein L11 (k39a) And Inhibitor
Sinefungin
Length = 147
Score = 28.9 bits (63), Expect = 9.0, Method: Composition-based stats.
Identities = 28/126 (22%), Positives = 51/126 (40%), Gaps = 7/126 (5%)
Query: 473 GSTGLSTDSLVEAGYPGALALGDAVCGIAAVKITSKDFLFWFRSHTAKEIKWGGAKHDSG 532
G G + V A +GDA+ + + F F ++ A + A + G
Sbjct: 28 GQHGANIMEFVAAFNAATANMGDAIVPVEITIYADRSFTFVTKTPPASYLIRKAAGLEKG 87
Query: 533 GKDGGRKMHPRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLILRGSLQDEVAEDSKMIVN 592
GR+ R +++ LE+ KQ+ +P D+ + + ++ GS + E +V
Sbjct: 88 AHKPGREKVGRITWEQVLEIAKQK-MP--DLNTTDLEAAARMIAGSARSMGVE----VVG 140
Query: 593 VPSVDD 598
P V D
Sbjct: 141 APEVKD 146
>pdb|3CJQ|B Chain B, Ribosomal Protein L11 Methyltransferase (Prma) In Complex
With Dimethylated Ribosomal Protein L11 In Space Group
P212121
pdb|3CJQ|E Chain E, Ribosomal Protein L11 Methyltransferase (Prma) In Complex
With Dimethylated Ribosomal Protein L11 In Space Group
P212121
pdb|3CJQ|H Chain H, Ribosomal Protein L11 Methyltransferase (Prma) In Complex
With Dimethylated Ribosomal Protein L11 In Space Group
P212121
Length = 146
Score = 28.9 bits (63), Expect = 9.1, Method: Composition-based stats.
Identities = 28/126 (22%), Positives = 51/126 (40%), Gaps = 7/126 (5%)
Query: 473 GSTGLSTDSLVEAGYPGALALGDAVCGIAAVKITSKDFLFWFRSHTAKEIKWGGAKHDSG 532
G G + V A +GDA+ + + F F ++ A + A + G
Sbjct: 27 GQHGANIMEFVAAFNAATANMGDAIVPVEITIYADRSFTFVTKTPPASYLIRKAAGLEKG 86
Query: 533 GKDGGRKMHPRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLILRGSLQDEVAEDSKMIVN 592
GR+ R +++ LE+ KQ+ +P D+ + + ++ GS + E +V
Sbjct: 87 AHKPGREKVGRITWEQVLEIAKQK-MP--DLNTTDLEAAARMIAGSARSMGVE----VVG 139
Query: 593 VPSVDD 598
P V D
Sbjct: 140 APEVKD 145
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.135 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,133,264
Number of Sequences: 62578
Number of extensions: 781245
Number of successful extensions: 1930
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1863
Number of HSP's gapped (non-prelim): 30
length of query: 681
length of database: 14,973,337
effective HSP length: 105
effective length of query: 576
effective length of database: 8,402,647
effective search space: 4839924672
effective search space used: 4839924672
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)