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= 001215
(1122 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 = 1e-70, 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 = 264 bits (674), Expect = 3e-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 = 201 bits (511), Expect = 2e-51, Method: Compositional matrix adjust.
Identities = 183/673 (27%), Positives = 290/673 (43%), Gaps = 90/673 (13%)
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 ECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDC------LAPPVKVIQDKKLDQ 305
E P LE Y G YP++DIPQ +R L + +VR++ D L P + + + LD
Sbjct: 203 ERHVPGLESYFGNRYPSSDIPQXARRLYERQRVRVLVDVSYQPVPLEPRLSPLTGRDLDX 262
Query: 306 PLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHH 365
G LR+ H +Y++N G A+LV+S+ + G KLWGLV CHH
Sbjct: 263 ----SGCFLRSXSPIHLQYLKNXGVRATLVVSLVV-------------GGKLWGLVACHH 305
Query: 366 TSPRFVPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQTVLCDMLLR--DSPVG 423
PRF+ F LR CE L + ++ + E + R + + + R D
Sbjct: 306 YLPRFIHFELRAICELLAEAIATRITALESFAQSQSELFVQRLEQRXIEAITREGDWRAA 365
Query: 424 IVTQTPNVMDLVKCDGAALYYRGKLWLLGVTPTEEQIKDIAEWLLEYHRGSTGLSTDSLV 483
I + +++ + DG AL Y ++ +G P+ + +++IA WL R + ST SL
Sbjct: 366 IFDTSQSILQPLHADGCALVYEDQIRTIGDVPSTQDVREIAGWLDRQPRAAV-TSTASL- 423
Query: 484 EAGYPGALALGDAVCGIAAVKITSK--DFLFWFRSHTAKEIKWGG-AKHDSGGKDGGRKM 540
P L G+ A I+ +FL WFR + WGG K D +
Sbjct: 424 GLDVPELAHLTRXASGVVAAPISDHRGEFLXWFRPERVHTVTWGGDPKKPFTXGDTPADL 483
Query: 541 HPRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLILRGSLQDEVAEDSKMIVNVPSVDDRI 600
PR SF + +VV+ S PW ++ A ++ + + +++ +V I
Sbjct: 484 SPRRSFAKWHQVVEGTSDPWTAADLAAARTIGQTV-----------ADIVLQFRAVRTLI 532
Query: 601 EKIDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLV 660
R + + + P+L DA G + N + A+ +D +
Sbjct: 533 A-----REQYEQFSSQVHASXQPVLITDAEGRILLXNDSFRDXLPAGSPSAVH---LDDL 584
Query: 661 AG---DSVDVVKNMLSSAFLGIEERNVEIKLRAFGPRETSGPVILVVNACCTQDTKENVI 717
AG +S D ++N+ G R E+ LR G R P+ L V A T++ +
Sbjct: 585 AGFFVESNDFLRNVAELIDHGRGWRG-EVLLRGAGNR----PLPLAVRADPVTRTEDQSL 639
Query: 718 GVCFVGQDITGQK 730
G + D T ++
Sbjct: 640 GFVLIFSDATDRR 652
>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 = 3e-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 = 9e-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 (437), Expect = 7e-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 = 152 bits (385), Expect = 7e-37, Method: Composition-based stats.
Identities = 101/318 (31%), Positives = 159/318 (50%), Gaps = 35/318 (11%)
Query: 77 IQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAA 136
IQP G + V E + + S N ++L P A L + + T++ AA
Sbjct: 39 IQPHGYLFVVSETDLRIASVSANVEDLLRQPP----------ASLLNVPIAHYLTAASAA 88
Query: 137 ALQKAANFGEVNLLNPILIHCKTSG--KPFYAILHRIDVGLVIDLEPVNPDDVPVTAAGA 194
L A + G+ +NPI + T + F ILHR D ++++LEP D+ T
Sbjct: 89 RLTHALHGGDPAAINPIRLDVVTPDGERAFNGILHRHDSIVILELEP--RDESRYTN--- 143
Query: 195 LKSYKLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECR 254
+ ++ AI RLQ+ + ++ C + +EV +TG+DR+ VY+F D G+V+AE R
Sbjct: 144 -EFFRSVRVAIRRLQT--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 = 7e-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 = 120 bits (302), Expect = 3e-27, Method: Composition-based stats.
Identities = 100/316 (31%), Positives = 148/316 (46%), Gaps = 36/316 (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 N------AMFALESAP--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 G +LWGL+ CHH +P +P
Sbjct: 269 RATSPMHMQYLRNMGVGSSLSVSVV-------------VGGQLWGLIACHHQTPYVLPPD 315
Query: 375 LRYACEFLIQVFGVQV 390
LR E L ++ +QV
Sbjct: 316 LRTTLESLGRLLSLQV 331
>pdb|3S7Q|A Chain A, Crystal Structure Of A Monomeric Infrared Fluorescent
Deinococcus Radiodurans Bacteriophytochrome Chromophore
Binding Domain
Length = 343
Score = 119 bits (297), Expect = 1e-26, Method: Composition-based stats.
Identities = 99/326 (30%), Positives = 153/326 (46%), Gaps = 40/326 (12%)
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 +S G +LWGL+ CHH +P +P
Sbjct: 268 RATSPMHMQFLRNMGVGSSLSVS-------------VVVGGQLWGLIACHHQTPYVLPPD 314
Query: 375 LRYACEFLIQVFGVQVNKEVELSAQL 400
LR E+L G +++++V++ L
Sbjct: 315 LRTTLEYL----GRELSEQVQVKEAL 336
>pdb|1ZTU|A Chain A, Structure Of The Chromophore Binding Domain Of Bacterial
Phytochrome
Length = 341
Score = 118 bits (295), Expect = 2e-26, Method: Composition-based stats.
Identities = 98/316 (31%), Positives = 146/316 (46%), Gaps = 36/316 (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 G +LWGL+ CHH +P +P
Sbjct: 268 RATSPXHXQYLRNXGVGSSLSVSVV-------------VGGQLWGLIACHHQTPYVLPPD 314
Query: 375 LRYACEFLIQVFGVQV 390
LR E+L ++ +QV
Sbjct: 315 LRTTLEYLGRLLSLQV 330
>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 = 117 bits (294), Expect = 3e-26, Method: Composition-based stats.
Identities = 99/316 (31%), Positives = 147/316 (46%), Gaps = 36/316 (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 N------AMFALESAP--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 G +LWGL+ CHH +P +P
Sbjct: 268 RATSPMHMQYLRNMGVGSSLSVSVV-------------VGGQLWGLIACHHQTPYVLPPD 314
Query: 375 LRYACEFLIQVFGVQV 390
LR E L ++ +QV
Sbjct: 315 LRTTLESLGRLLSLQV 330
>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 = 88.2 bits (217), Expect = 3e-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 = 87.8 bits (216), Expect = 3e-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|3A0R|A Chain A, Crystal Structure Of Histidine Kinase Thka (Tm1359) In
Complex With Response Regulator Protein Trra (Tm1360)
Length = 349
Score = 48.5 bits (114), Expect = 2e-05, Method: Composition-based stats.
Identities = 85/368 (23%), Positives = 142/368 (38%), Gaps = 48/368 (13%)
Query: 757 IFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVM 816
I +DGR EWN E+L GLK+E + R R+K+ ++ V
Sbjct: 21 IITLSKDGRITEWNKKAEQLFGLKKENVLGR--------------RLKDLPDFEEIGSVA 66
Query: 817 NKVISGQDADKILFGFFDQQGKYVEALLSA--NKRTN-AEGKISGI--LCFLHVASPELQ 871
V ++ + + F+ +Y S N +T EG I I + L+ E +
Sbjct: 67 ESVF--ENKEPVFLNFYKFGERYFNIRFSPFRNAKTQLLEGVIITIDDVTELYKYEEERK 124
Query: 872 YALQVQRISEQAAANSLNKLEYIRREIRKPLNGI-AFMQNLMGTSDLSEEQKQLLKTSVL 930
++ + E A + EIR P+ I F+ + D E K+ +
Sbjct: 125 RRERLSILGEMTAR--------VAHEIRNPITIIGGFIMRMKKHLDDPETLKKYINIITN 176
Query: 931 CQEQLTNIVDDTDIESIEECYMVLKSGEFNLGEALDAVMTQVMIPSREHQVQFIRDLPAE 990
+L IV + S E VL+ EFNL E + V R+ + F + E
Sbjct: 177 ELSRLETIVKEILEYSKER--QVLEFTEFNLNELIREVYVLFEEKIRKMNIDFCFETDNE 234
Query: 991 VSTMNLHGDKLRLQQVLSDFLTNALIFTPAFEGSSIAFRVIPQKERIGKNIHIVHLEFRI 1050
+ + D+ R++QVL + + NA+ T I + K R+ +
Sbjct: 235 --DLRVEADRTRIKQVLINLVQNAIEATGENGKIKITSEDMYTKVRVS-----------V 281
Query: 1051 THPAPGIPEKLIHDMF--YHSQGASREGLGLYISQKLVKLMNGTVQYIREAERSSFLILI 1108
+ P IPE+L +F + + GLGL I +K+++ +G + E I
Sbjct: 282 WNSGPPIPEELKEKIFSPFFTTKTQGTGLGLSICRKIIEDEHGGKIWTENRENGVVFIF- 340
Query: 1109 EFPLAHQK 1116
E P +K
Sbjct: 341 EIPKTPEK 348
>pdb|3SL2|A Chain A, Atp Forms A Stable Complex With The Essential Histidine
Kinase Walk (yycg) Domain
Length = 177
Score = 47.0 bits (110), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 40/153 (26%), Positives = 71/153 (46%), Gaps = 22/153 (14%)
Query: 976 SREHQVQFIRDLPAEVSTMNLHGDKLRLQQVLSDFLTNALIFTPAFEGSSIAFRV-IPQK 1034
++E V+FIR+LP + + DK + QVL + ++NAL ++P EG + F + + ++
Sbjct: 19 TKEQHVEFIRNLPDRDLYVEIDQDK--ITQVLDNIISNALKYSP--EGGHVTFSIDVNEE 74
Query: 1035 ERIGKNIHIVHLEFRITHPAPGIPEK---LIHDMFYHSQGASRE-----GLGLYISQKLV 1086
E + L + GIP+K + D FY A GLGL I++++V
Sbjct: 75 EEL--------LYISVKDEGIGIPKKDVEKVFDRFYRVDKARTRKLGGTGLGLAIAKEMV 126
Query: 1087 KLMNGTVQYIREAERSSFLILIEFPLAHQKDAD 1119
+ G + + E I P +++ D
Sbjct: 127 QAHGGDI-WADSIEGKGTTITFTLPYKEEQEDD 158
>pdb|4EW8|A Chain A, Crystal Structure Of A C-Terminal Part Of Tyrosine Kinase
(Divl) From Caulobacter Crescentus Cb15 At 2.50 A
Resolution
pdb|4EW8|B Chain B, Crystal Structure Of A C-Terminal Part Of Tyrosine Kinase
(Divl) From Caulobacter Crescentus Cb15 At 2.50 A
Resolution
Length = 268
Score = 36.2 bits (82), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 56/230 (24%), Positives = 95/230 (41%), Gaps = 20/230 (8%)
Query: 870 LQYALQVQRISEQAAANSLNK--LEYIRREIRKPLNGIAFMQNLMGTSD-LSEEQKQLLK 926
LQ AL R + A A L + + + E+R PL I L+ +D +SE + +
Sbjct: 22 LQSAL-ADRSAALAEAERLKRDFVGNVSYELRTPLTTIIGYSELLERADGISERGRNHVA 80
Query: 927 TSVLCQEQLTNIVDDT-DIESIEECYMVLKSGEFNLGEALDAVMTQVMIPSREHQVQFIR 985
QL +DD D+ I+ M L+ + + + L + + ++ V
Sbjct: 81 AVRAAATQLARSIDDVLDMAQIDAGEMALEIEDIRVSDLLLNAQERALKDAQLGGVTLAV 140
Query: 986 DLPAEVSTMNLHGDKLRLQQVLSDFLTNALIFTPAFEGSSIAFRVIPQKERIGKNIHIVH 1045
+ +V + GD RL Q L + NAL TP +++ R + + V
Sbjct: 141 ECEEDVGL--IRGDGKRLAQTLDHLVENALRQTPPGGRVTLSAR---------RALGEVR 189
Query: 1046 LEFRITHPAPGIPEKLIHDMFYHSQGASR--EGLGLYISQKLVKLMNGTV 1093
L+ ++ G+P + +F G R GLGL + + LV+L G V
Sbjct: 190 LD--VSDTGRGVPFHVQAHIFDRFVGRDRGGPGLGLALVKALVELHGGWV 237
>pdb|3A0T|A Chain A, Catalytic Domain Of Histidine Kinase Thka (Tm1359) In
Complex With Adp And Mg Ion (Trigonal)
pdb|3A0W|A Chain A, Catalytic Domain Of Histidine Kinase Thka (Tm1359) For Mad
Phasing (Nucleotide Free Form 2, Orthorombic)
pdb|3A0W|B Chain B, Catalytic Domain Of Histidine Kinase Thka (Tm1359) For Mad
Phasing (Nucleotide Free Form 2, Orthorombic)
pdb|3A0X|A Chain A, Catalytic Domain Of Histidine Kinase Thka (Tm1359)
(Nucleotide Free Form 1: Ammomium Phosphate, Monoclinic)
pdb|3A0Y|A Chain A, Catalytic Domain Of Histidine Kinase Thka (Tm1359)
(Nucleotide Free Form 3: 1,2-Propanediol, Orthorombic)
pdb|3A0Y|B Chain B, Catalytic Domain Of Histidine Kinase Thka (Tm1359)
(Nucleotide Free Form 3: 1,2-Propanediol, Orthorombic)
pdb|3A0Z|A Chain A, Catalytic Domain Of Histidine Kinase Thka (Tm1359)
(Nucleotide Free Form 4: Isopropanol, Orthorombic)
pdb|3A0Z|B Chain B, Catalytic Domain Of Histidine Kinase Thka (Tm1359)
(Nucleotide Free Form 4: Isopropanol, Orthorombic)
Length = 152
Score = 35.0 bits (79), Expect = 0.25, Method: Composition-based stats.
Identities = 38/161 (23%), Positives = 65/161 (40%), Gaps = 16/161 (9%)
Query: 958 EFNLGEALDAVMTQVMIPSREHQVQFIRDLPAEVSTMNLHGDKLRLQQVLSDFLTNALIF 1017
EFNL E + V R+ + F + E + + D+ R++QVL + + NA+
Sbjct: 5 EFNLNELIREVYVLFEEKIRKMNIDFCFETDNE--DLRVEADRTRIKQVLINLVQNAIEA 62
Query: 1018 TPAFEGSSIAFRVIPQKERIGKNIHIVHLEFRITHPAPGIPEKLIHDMF--YHSQGASRE 1075
T I + K R+ + + P IPE+L +F + +
Sbjct: 63 TGENGKIKITSEDMYTKVRVS-----------VWNSGPPIPEELKEKIFSPFFTTKTQGT 111
Query: 1076 GLGLYISQKLVKLMNGTVQYIREAERSSFLILIEFPLAHQK 1116
GLGL I +K+++ +G + E I E P +K
Sbjct: 112 GLGLSICRKIIEDEHGGKIWTENRENGVVFIF-EIPKTPEK 151
>pdb|3A0S|A Chain A, Pas Domain Of Histidine Kinase Thka (Tm1359)
Length = 96
Score = 33.9 bits (76), Expect = 0.53, Method: Composition-based stats.
Identities = 15/33 (45%), Positives = 19/33 (57%)
Query: 757 IFMTDEDGRCLEWNDGMEKLSGLKREEAIERML 789
I +DGR EWN E+L GLK+E + R L
Sbjct: 5 IITLSKDGRITEWNKKAEQLFGLKKENVLGRRL 37
>pdb|3A0V|A Chain A, Pas Domain Of Histidine Kinase Thka (Tm1359) (Semet,
F486mF489M)
Length = 96
Score = 33.9 bits (76), Expect = 0.60, Method: Composition-based stats.
Identities = 15/33 (45%), Positives = 19/33 (57%)
Query: 757 IFMTDEDGRCLEWNDGMEKLSGLKREEAIERML 789
I +DGR EWN E+L GLK+E + R L
Sbjct: 5 IITLSKDGRITEWNKKAEQLFGLKKENVLGRRL 37
>pdb|3D36|A Chain A, How To Switch Off A Histidine Kinase: Crystal Structure Of
Geobacillus Stearothermophilus Kinb With The Inhibitor
Sda
pdb|3D36|B Chain B, How To Switch Off A Histidine Kinase: Crystal Structure Of
Geobacillus Stearothermophilus Kinb With The Inhibitor
Sda
Length = 244
Score = 32.7 bits (73), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 27/131 (20%), Positives = 62/131 (47%), Gaps = 15/131 (11%)
Query: 986 DLPAEVSTMNLHGDKLRLQQVLSDFLTNALIFTPAFEGSSIAFRVIPQKERIGKNIHIVH 1045
D+ A ++ ++ G++ + +Q L + + NA+ P G ++ V R+
Sbjct: 107 DIQATLAPFSVIGEREKFRQCLLNVMKNAIEAMP--NGGTLQVYVSIDNGRV-------- 156
Query: 1046 LEFRITHPAPGIPEKLIHDM---FYHSQGASREGLGLYISQKLVKLMNGTVQYIREAERS 1102
RI G+ ++ + + ++ ++G GLG+ + ++++ MNGT++ E +
Sbjct: 157 -LIRIADTGVGMTKEQLERLGEPYFTTKGVKGTGLGMMVVYRIIESMNGTIRIESEIHKG 215
Query: 1103 SFLILIEFPLA 1113
+ + I PLA
Sbjct: 216 T-TVSIYLPLA 225
>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 = 32.7 bits (73), Expect = 1.3, 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|1R62|A Chain A, Crystal Structure Of The C-terminal Domain Of The
Two-component System Transmitter Protein Nrii (ntrb)
Length = 160
Score = 32.3 bits (72), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 37/138 (26%), Positives = 62/138 (44%), Gaps = 20/138 (14%)
Query: 981 VQFIRDLPAEVSTMNLHGDKLRLQQVLSDFLTNAL-IFTPAFEGSSI------AFRVIPQ 1033
V+ IRD + S L D +++QVL + + NAL P EG I AF++
Sbjct: 29 VRLIRDY--DPSLPELAHDPDQIEQVLLNIVRNALQALGP--EGGEIILRTRTAFQLTLH 84
Query: 1034 KERIGKNIHIVHLEFRITHPAPGIPEKLIHDMFYHSQGASRE---GLGLYISQKLVKLMN 1090
ER + + + PGIP L D ++ + RE GLGL I++ L+ +
Sbjct: 85 GER-----YRLAARIDVEDNGPGIPPHL-QDTLFYPMVSGREGGTGLGLSIARNLIDQHS 138
Query: 1091 GTVQYIREAERSSFLILI 1108
G +++ + F + +
Sbjct: 139 GKIEFTSWPGHTEFSVYL 156
>pdb|3W2Z|A Chain A, Crystal Structure Of The Cyanobacterial Protein
Length = 198
Score = 32.3 bits (72), Expect = 1.6, 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|3DHT|A Chain A, The Crystal Structure Determination Of Rat (Rattus
Norvegicus) Hemoglobin
pdb|3HF4|A Chain A, Crystal Structure Of Rat Methemoglobin In R2 State
pdb|3HF4|E Chain E, Crystal Structure Of Rat Methemoglobin In R2 State
Length = 141
Score = 31.6 bits (70), Expect = 2.7, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 11/52 (21%)
Query: 984 IRDLPAEVSTM-NLHGDKLRLQQVLSDFLTNALI----------FTPAFEGS 1024
+ DLP +ST+ +LH KLR+ V FL++ L+ FTPA S
Sbjct: 73 VEDLPGALSTLSDLHAHKLRVDPVNFKFLSHCLLVTLACHHPGDFTPAMHAS 124
>pdb|3VG0|H Chain H, Antibody Fab Fragment
Length = 223
Score = 30.8 bits (68), Expect = 4.1, 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|3V6O|C Chain C, Leptin Receptor-Antibody Complex
pdb|3V6O|D Chain D, Leptin Receptor-Antibody Complex
Length = 221
Score = 30.8 bits (68), Expect = 4.1, 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|2VJY|A Chain A, Pyruvate Decarboxylase From Kluyveromyces Lactis In
Complex With The Substrate Analogue Methyl
Acetylphosphonate
pdb|2VJY|B Chain B, Pyruvate Decarboxylase From Kluyveromyces Lactis In
Complex With The Substrate Analogue Methyl
Acetylphosphonate
pdb|2VJY|C Chain C, Pyruvate Decarboxylase From Kluyveromyces Lactis In
Complex With The Substrate Analogue Methyl
Acetylphosphonate
pdb|2VJY|D Chain D, Pyruvate Decarboxylase From Kluyveromyces Lactis In
Complex With The Substrate Analogue Methyl
Acetylphosphonate
pdb|2VK4|A Chain A, Crystal Structure Of Pyruvate Decarboxylase From
Kluyveromyces Lactis
pdb|2VK4|B Chain B, Crystal Structure Of Pyruvate Decarboxylase From
Kluyveromyces Lactis
pdb|2VK4|C Chain C, Crystal Structure Of Pyruvate Decarboxylase From
Kluyveromyces Lactis
pdb|2VK4|D Chain D, Crystal Structure Of Pyruvate Decarboxylase From
Kluyveromyces Lactis
Length = 563
Score = 30.4 bits (67), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 7/64 (10%)
Query: 694 RETSGPVILVVNACCTQ-DTK---ENVIGVCFVGQDIT--GQKLVMDKYTRIQGDYVGIV 747
+E PVIL +ACC++ D K + +I + +T G+ + +K+ R G YVG +
Sbjct: 209 KEAKNPVILA-DACCSRHDAKAETKKLIDLTQFPAFVTPMGKGSIDEKHPRFGGVYVGTL 267
Query: 748 SSPS 751
SSP+
Sbjct: 268 SSPA 271
>pdb|3LYX|A Chain A, Crystal Structure Of The Pas Domain Of The Protein
Cps_1291 From Colwellia Psychrerythraea. Northeast
Structural Genomics Consortium Target Id Csr222b
pdb|3LYX|B Chain B, Crystal Structure Of The Pas Domain Of The Protein
Cps_1291 From Colwellia Psychrerythraea. Northeast
Structural Genomics Consortium Target Id Csr222b
Length = 124
Score = 30.4 bits (67), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 757 IFMTDEDGRCLEWNDGMEKLSGLKREEAI 785
I +TD G ++WN G E L G +E+AI
Sbjct: 20 IVVTDLQGFIIDWNKGSETLYGYSKEQAI 48
>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 = 30.0 bits (66), Expect = 7.2, 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|3EGV|B Chain B, Ribosomal Protein L11 Methyltransferase (Prma) In Complex
With Trimethylated Ribosomal Protein L11
Length = 146
Score = 30.0 bits (66), Expect = 7.2, 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: 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
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 0.136 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 31,227,465
Number of Sequences: 62578
Number of extensions: 1290494
Number of successful extensions: 3051
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 2979
Number of HSP's gapped (non-prelim): 38
length of query: 1122
length of database: 14,973,337
effective HSP length: 109
effective length of query: 1013
effective length of database: 8,152,335
effective search space: 8258315355
effective search space used: 8258315355
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: 57 (26.6 bits)