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= 001353
(1093 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 = 249 bits (637), Expect = 5e-66, Method: Compositional matrix adjust.
Identities = 170/506 (33%), Positives = 261/506 (51%), Gaps = 38/506 (7%)
Query: 87 IQRGGLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLRSRSEDFELNGLIGIDARTLFTPP 146
I LIQP G ++ ++EP I S NC +L RS + L +G + P
Sbjct: 20 IHTAHLIQPHGLVVVLQEPDLTISQISANCTGIL---GRSPEDLLGRTLGEVFDSFQIDP 76
Query: 147 SGASLAKAAASREISLLNPILVHSNSRSIE-KPFYAILHRIDVGIVI-DLEPSKSGDPAL 204
+ L +IS LNP + + + F + HR G+++ +LEP+ + D L
Sbjct: 77 IQSRLTAG----QISSLNPSKLWARVMGDDFVIFDGVFHRNSDGLLVCELEPAYTSD-NL 131
Query: 205 SLAGAVQSQKLAVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEV 264
G +A +A++RL+ ++ D +VE+V+++TG+DRVMLY F +++HG+V
Sbjct: 132 PFLGFYH---MANAALNRLRQ--QANLRDFYDVIVEEVRRMTGFDRVMLYRFDENNHGDV 186
Query: 265 VSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCH--AIPVMVIQSKELKQPL 322
++E +R D+EPYLG+H+P +DIPQ AR LF N +R+I D + A+P+ + + +
Sbjct: 187 IAEDKRDDMEPYLGLHYPESDIPQPARRLFIHNPIRVIPDVYGVAVPLTPAVNPSTNRAV 246
Query: 323 CLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLR 382
L S LRS + CHL Y+ NMG ASL +++I KD LWGL+ CHH +P+ IPF LR
Sbjct: 247 DLTESILRSAYHCHLTYLKNMGVGASLTISLI---KDG-HLWGLIACHHQTPKVIPFELR 302
Query: 383 YACEF----LVQAFSLQLYME-LQVAMQLAEKNILRTQVLLCDMLLRDAPF--SIVTQSP 435
ACEF + S Q E +QLAE + +L D + A F +
Sbjct: 303 KACEFFGRVVFSNISAQEDTETFDYRVQLAEH-----EAVLLDKMTTAADFVEGLTNHPD 357
Query: 436 SIMDLVKCDGAALYYGGRCWLVGVTPTESQLKDIAWWLLNNHGDCTGLSTDSLAEAGYPG 495
++ L GAA+ +G + LVG TP E ++ + WL N T SL++ YP
Sbjct: 358 RLLGLTGSQGAAICFGEKLILVGETPDEKAVQYLLQWLENREVQDV-FFTSSLSQI-YPD 415
Query: 496 AALLGQAVCGMATARITSKDFLFWFRSHTAKEVKWGGAKHH---PEHKDNGGKMHPRSSF 552
A G+ I +FL WFR + V WGG +H +D ++HPR SF
Sbjct: 416 AVNFKSVASGLLAIPIARHNFLLWFRPEVLQTVNWGGDPNHAYEATQEDGKIELHPRQSF 475
Query: 553 KAFLEVVKNRSFPWEVSEINAIHSLQ 578
+ E+V+ +S PW+ EI + +L+
Sbjct: 476 DLWKEIVRLQSLPWQSVEIQSALALK 501
>pdb|3ZQ5|A Chain A, Structure Of The Y263f Mutant Of The Cyanobacterial
Phytochrome Cph1
Length = 520
Score = 248 bits (633), Expect = 1e-65, Method: Compositional matrix adjust.
Identities = 169/506 (33%), Positives = 261/506 (51%), Gaps = 38/506 (7%)
Query: 87 IQRGGLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLRSRSEDFELNGLIGIDARTLFTPP 146
I LIQP G ++ ++EP I S NC +L RS + L +G + P
Sbjct: 20 IHTAHLIQPHGLVVVLQEPDLTISQISANCTGIL---GRSPEDLLGRTLGEVFDSFQIDP 76
Query: 147 SGASLAKAAASREISLLNPILVHSNSRSIE-KPFYAILHRIDVGIVI-DLEPSKSGDPAL 204
+ L +IS LNP + + + F + HR G+++ +LEP+ + D L
Sbjct: 77 IQSRLTAG----QISSLNPSKLWARVMGDDFVIFDGVFHRNSDGLLVCELEPAYTSD-NL 131
Query: 205 SLAGAVQSQKLAVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEV 264
G +A +A++RL+ ++ D +VE+V+++TG+DRVMLY F +++HG+V
Sbjct: 132 PFLGFYH---MANAALNRLRQ--QANLRDFYDVIVEEVRRMTGFDRVMLYRFDENNHGDV 186
Query: 265 VSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCH--AIPVMVIQSKELKQPL 322
++E +R D+EPYLG+H+P +DIPQ AR LF N +R+I D + A+P+ + + +
Sbjct: 187 IAEDKRDDMEPYLGLHYPESDIPQPARRLFIHNPIRVIPDVYGVAVPLTPAVNPSTNRAV 246
Query: 323 CLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLR 382
L S LRS + CHL ++ NMG ASL +++I KD LWGL+ CHH +P+ IPF LR
Sbjct: 247 DLTESILRSAYHCHLTFLKNMGVGASLTISLI---KDG-HLWGLIACHHQTPKVIPFELR 302
Query: 383 YACEF----LVQAFSLQLYME-LQVAMQLAEKNILRTQVLLCDMLLRDAPF--SIVTQSP 435
ACEF + S Q E +QLAE + +L D + A F +
Sbjct: 303 KACEFFGRVVFSNISAQEDTETFDYRVQLAEH-----EAVLLDKMTTAADFVEGLTNHPD 357
Query: 436 SIMDLVKCDGAALYYGGRCWLVGVTPTESQLKDIAWWLLNNHGDCTGLSTDSLAEAGYPG 495
++ L GAA+ +G + LVG TP E ++ + WL N T SL++ YP
Sbjct: 358 RLLGLTGSQGAAICFGEKLILVGETPDEKAVQYLLQWLENREVQDV-FFTSSLSQI-YPD 415
Query: 496 AALLGQAVCGMATARITSKDFLFWFRSHTAKEVKWGGAKHH---PEHKDNGGKMHPRSSF 552
A G+ I +FL WFR + V WGG +H +D ++HPR SF
Sbjct: 416 AVNFKSVASGLLAIPIARHNFLLWFRPEVLQTVNWGGDPNHAYEATQEDGKIELHPRQSF 475
Query: 553 KAFLEVVKNRSFPWEVSEINAIHSLQ 578
+ E+V+ +S PW+ EI + +L+
Sbjct: 476 DLWKEIVRLQSLPWQSVEIQSALALK 501
>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 = 213 bits (541), Expect = 7e-55, Method: Compositional matrix adjust.
Identities = 162/522 (31%), Positives = 244/522 (46%), Gaps = 54/522 (10%)
Query: 81 TAYLSKIQR-----GGLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLRS--RSEDFELNG 133
TA LS +R G IQP G +L V EP RII S N E L+L S E++G
Sbjct: 34 TADLSNCEREEIHLAGSIQPHGALLVVSEPDHRIIQASANAAEFLNLGSVLGVPLAEIDG 93
Query: 134 LIGIDARTLFTPPSGASLAKAAASREISLLNPILVHSNSRSIEKPFYAILHRI-DVGIVI 192
+ I P + P+ V + + + HR + G++I
Sbjct: 94 DLLIKILPHLDPTAEGX--------------PVAVRCRIGNPSTEYDGLXHRPPEGGLII 139
Query: 193 DLEPSKSGDPALSLAGAVQSQKLAVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVM 252
+LE ++G P + L+G + A+ R++ G + LCD Q+ TGYDRV
Sbjct: 140 ELE--RAG-PPIDLSGTL------APALERIRT--AGSLRALCDDTALLFQQCTGYDRVX 188
Query: 253 LYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIPVMV 312
+Y F + HGEV SE LE Y G +P++DIPQ AR L+++ RVR++ D PV +
Sbjct: 189 VYRFDEQGHGEVFSERHVPGLESYFGNRYPSSDIPQXARRLYERQRVRVLVDVSYQPVPL 248
Query: 313 ------IQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGL 366
+ ++L C LRS HLQY+ N G A+LV+++++ KLWGL
Sbjct: 249 EPRLSPLTGRDLDXSGCF----LRSXSPIHLQYLKNXGVRATLVVSLVVGG----KLWGL 300
Query: 367 VVCHHTSPRYIPFPLRYACEFLVQAFSLQLYMELQVAMQLAEKNILRTQVLLCDMLLRDA 426
V CHH PR+I F LR CE L +A + ++ A +E + R + + + R+
Sbjct: 301 VACHHYLPRFIHFELRAICELLAEAIATRITALESFAQSQSELFVQRLEQRXIEAITREG 360
Query: 427 PF--SIVTQSPSIMDLVKCDGAALYYGGRCWLVGVTPTESQLKDIAWWLLNNHGDCTGLS 484
+ +I S SI+ + DG AL Y + +G P+ +++IA W L+ S
Sbjct: 361 DWRAAIFDTSQSILQPLHADGCALVYEDQIRTIGDVPSTQDVREIAGW-LDRQPRAAVTS 419
Query: 485 TDSLAEAGYPGAALLGQAVCGMATARITSK--DFLFWFRSHTAKEVKWGGAKHHP-EHKD 541
T SL P A L + G+ A I+ +FL WFR V WGG P D
Sbjct: 420 TASLG-LDVPELAHLTRXASGVVAAPISDHRGEFLXWFRPERVHTVTWGGDPKKPFTXGD 478
Query: 542 NGGKMHPRSSFKAFLEVVKNRSFPWEVSEINAIHSLQIVMRD 583
+ PR SF + +VV+ S PW +++ A ++ + D
Sbjct: 479 TPADLSPRRSFAKWHQVVEGTSDPWTAADLAAARTIGQTVAD 520
>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 = 177 bits (449), Expect = 3e-44, Method: Compositional matrix adjust.
Identities = 117/366 (31%), Positives = 180/366 (49%), Gaps = 33/366 (9%)
Query: 230 DIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQA 289
D L V ++++++TGYDRVM Y F DD GEVV+E RR DLE YLG+ +PA+DIP
Sbjct: 139 DTASLLSNVTDELRRMTGYDRVMAYRFRHDDSGEVVAESRREDLESYLGLRYPASDIPAQ 198
Query: 290 ARFLFKQNRVRMICDCHAIPVMVIQS--KELKQPLCLVNSTLRSPHGCHLQYMTNMGSIA 347
AR L+ QN +R+I D P+ V + E + L S LRS H +Y+TNMG A
Sbjct: 199 ARRLYIQNPIRLIADVAYTPMRVFPALNPETNESFDLSYSVLRSVSPIHCEYLTNMGVRA 258
Query: 348 SLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFS--LQLYMELQVAMQ 405
S+ +++++ KLWGL CHH SP+ IP+P+R + + Q S ++ + ++A
Sbjct: 259 SMSISIVVGG----KLWGLFSCHHMSPKLIPYPVRMSFQIFSQVCSAIVERLEQGRIAEL 314
Query: 406 LAEKNILRTQVLLCDMLLRDAPFSIVTQSPSIMDLVKCDGAALYYGGRCWLVGVTPTESQ 465
L R + D ++ I L+ CDGA + GGR L E Q
Sbjct: 315 LRVSTERRLALARRARDADDLFGALAHPDDGIAALIPCDGALVMLGGRT-LSIRGDFERQ 373
Query: 466 LKDIAWWLLNN------HGDCTGLSTDSLAEAGYPGAALLGQAVCGMATARITSKD--FL 517
++ L + H D ++ + G CG+ R ++ ++
Sbjct: 374 AGNVLQRLQRDPERDIYHTDNWPQPSEDSPDGG---------DCCGVLAIRFHRQESGWI 424
Query: 518 FWFRSHTAKEVKWGGAKHHPEH----KDNGGKMHPRSSFKAFLEVVKNRSFPWEVSEINA 573
FWFR ++WGG PE +G ++ PR SF+A+ EVV+ S PW +++
Sbjct: 425 FWFRHEEVHRIRWGGK---PEKLLTIGPSGPRLTPRGSFEAWEEVVRGHSTPWSETDLAI 481
Query: 574 IHSLQI 579
L++
Sbjct: 482 AEKLRL 487
>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 = 175 bits (444), Expect = 1e-43, Method: Compositional matrix adjust.
Identities = 117/366 (31%), Positives = 179/366 (48%), Gaps = 33/366 (9%)
Query: 230 DIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQA 289
D L V ++++++TGYDRVM Y F DD GEVV+E RR DLE YLG +PA+DIP
Sbjct: 139 DTASLLSNVTDELRRMTGYDRVMAYRFRHDDSGEVVAESRREDLESYLGQRYPASDIPAQ 198
Query: 290 ARFLFKQNRVRMICDCHAIPVMVIQS--KELKQPLCLVNSTLRSPHGCHLQYMTNMGSIA 347
AR L+ QN +R+I D P+ V + E + L S LRS H +Y+TNMG A
Sbjct: 199 ARRLYIQNPIRLIADVAYTPMRVFPALNPETNESFDLSYSVLRSVSPIHCEYLTNMGVRA 258
Query: 348 SLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFS--LQLYMELQVAMQ 405
S+ +++++ KLWGL CHH SP+ IP+P+R + + Q S ++ + ++A
Sbjct: 259 SMSISIVVGG----KLWGLFSCHHMSPKLIPYPVRMSFQIFSQVCSAIVERLEQGRIAEL 314
Query: 406 LAEKNILRTQVLLCDMLLRDAPFSIVTQSPSIMDLVKCDGAALYYGGRCWLVGVTPTESQ 465
L R + D ++ I L+ CDGA + GGR L E Q
Sbjct: 315 LRVSTERRLALARRARDADDLFGALAHPDDGIAALIPCDGALVMLGGRT-LSIRGDFERQ 373
Query: 466 LKDIAWWLLNN------HGDCTGLSTDSLAEAGYPGAALLGQAVCGMATARITSKD--FL 517
++ L + H D ++ + G CG+ R ++ ++
Sbjct: 374 AGNVLQRLQRDPERDIYHTDNWPQPSEDSPDGG---------DCCGVLAIRFHRQESGWI 424
Query: 518 FWFRSHTAKEVKWGGAKHHPEH----KDNGGKMHPRSSFKAFLEVVKNRSFPWEVSEINA 573
FWFR ++WGG PE +G ++ PR SF+A+ EVV+ S PW +++
Sbjct: 425 FWFRHEEVHRIRWGGK---PEKLLTIGPSGPRLTPRGSFEAWEEVVRGHSTPWSETDLAI 481
Query: 574 IHSLQI 579
L++
Sbjct: 482 AEKLRL 487
>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 = 170 bits (430), Expect = 5e-42, Method: Compositional matrix adjust.
Identities = 115/366 (31%), Positives = 175/366 (47%), Gaps = 33/366 (9%)
Query: 230 DIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQA 289
D L V +++++ TGYDRV Y F DD GEVV+E RR DLE YLG+ +PA+DIP
Sbjct: 139 DTASLLSNVTDELRRXTGYDRVXAYRFRHDDSGEVVAESRREDLESYLGLRYPASDIPAQ 198
Query: 290 ARFLFKQNRVRMICDCHAIPVMVIQS--KELKQPLCLVNSTLRSPHGCHLQYMTNMGSIA 347
AR L+ QN +R+I D P V + E + L S LRS H +Y+TN G A
Sbjct: 199 ARRLYIQNPIRLIADVAYTPXRVFPALNPETNESFDLSYSVLRSVSPIHCEYLTNXGVRA 258
Query: 348 SLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFS--LQLYMELQVAMQ 405
S +++++ KLWGL CHH SP+ IP+P+R + + Q S ++ + ++A
Sbjct: 259 SXSISIVVGG----KLWGLFSCHHXSPKLIPYPVRXSFQIFSQVCSAIVERLEQGRIAEL 314
Query: 406 LAEKNILRTQVLLCDMLLRDAPFSIVTQSPSIMDLVKCDGAALYYGGRCWLVGVTPTESQ 465
L R + D ++ I L+ CDGA + GGR L E Q
Sbjct: 315 LRVSTERRLALARRARDADDLFGALAHPDDGIAALIPCDGALVXLGGRT-LSIRGDFERQ 373
Query: 466 LKDIAWWLLNN------HGDCTGLSTDSLAEAGYPGAALLGQAVCGMATARITSKD--FL 517
++ L + H D ++ + G CG+ R ++ ++
Sbjct: 374 AGNVLQRLQRDPERDIYHTDNWPQPSEDSPDGG---------DCCGVLAIRFHRQESGWI 424
Query: 518 FWFRSHTAKEVKWGGAKHHPEH----KDNGGKMHPRSSFKAFLEVVKNRSFPWEVSEINA 573
FWFR ++WGG PE +G ++ PR SF+A+ EVV+ S PW +++
Sbjct: 425 FWFRHEEVHRIRWGGK---PEKLLTIGPSGPRLTPRGSFEAWEEVVRGHSTPWSETDLAI 481
Query: 574 IHSLQI 579
L++
Sbjct: 482 AEKLRL 487
>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 = 153 bits (387), Expect = 4e-37, Method: Composition-based stats.
Identities = 96/308 (31%), Positives = 155/308 (50%), Gaps = 21/308 (6%)
Query: 91 GLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLRSRSEDFELNGLIGIDARTLFTPPSGAS 150
G IQP G + V E RI S N ++L S L+ + T S A
Sbjct: 37 GAIQPHGYLFVVSETDLRIASVSANVEDLLRQPPAS-------LLNVPIAHYLTAASAAR 89
Query: 151 LAKAAASREISLLNPILVHSNSRSIEKPFYAILHRIDVGIVIDLEPSKSGDPALSLAGAV 210
L A + + +NPI + + E+ F ILHR D ++++LEP +V
Sbjct: 90 LTHALHGGDPAAINPIRLDVVTPDGERAFNGILHRHDSIVILELEPRDESRYTNEFFRSV 149
Query: 211 QSQKLAVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRR 270
+ AI RLQ D+ C +V+++TG+DR+ +Y F D G+V++E R
Sbjct: 150 RV------AIRRLQT--AADLPTACWIAASEVRRITGFDRIKVYQFAADWSGQVIAEDRD 201
Query: 271 SDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIPVMVIQ--SKELKQPLCLVNST 328
S + L HFP++DIP +R L+ N VR+I D P ++ + L P+ L S
Sbjct: 202 SGIPSLLDFHFPSSDIPAQSRALYTINPVRIIPDIGYRPSPLVPDINPRLGGPIDLSFSV 261
Query: 329 LRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFL 388
LRS HL+YM NMG A++ ++++ ++ +LWG++ CH+ +PR++ + +R ACE +
Sbjct: 262 LRSVSPTHLEYMVNMGMHAAMSISIVRDN----RLWGMISCHNLTPRFVSYEVRQACELI 317
Query: 389 VQAFSLQL 396
Q + Q+
Sbjct: 318 AQVLTWQI 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 = 153 bits (386), Expect = 5e-37, Method: Compositional matrix adjust.
Identities = 103/308 (33%), Positives = 156/308 (50%), Gaps = 21/308 (6%)
Query: 91 GLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLRSRSEDFELNGLIGIDARTLFTPPSGAS 150
G IQP G +LA+ I+ S+N E+ L + LIG A +F +
Sbjct: 24 GAIQPHGLLLALAA-DMTIVAGSDNLPELTGL-------AIGALIGRSAADVFDSETHNR 75
Query: 151 LAKAAASREISLLNPILVHSNSRSIEKPFYAILHRIDVGIVIDLEPSKSGDPALSLAGAV 210
L A A ++ PI V E+ F HR D + ++LEP P +
Sbjct: 76 LTIALAEPGAAVGAPIAVGFTMPDGERAFNGSWHRHDQLVFLELEP-----PQRDVRYPQ 130
Query: 211 QSQKLAVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRR 270
+ SAI RLQA + C ++V+++TG+DRVM+Y F D GEV++E R
Sbjct: 131 AFFRSVRSAIRRLQA--AETLESACAAAAQEVREITGFDRVMIYRFASDFSGEVIAEDRC 188
Query: 271 SDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIPVMVIQ--SKELKQPLCLVNST 328
+++E YLG+HFPA+DIP AR L+ N VR+I D + PV V + +P+ L +
Sbjct: 189 AEVESYLGLHFPASDIPAQARRLYTINPVRIIPDINYRPVPVTPDLNPRTGRPIDLSFAI 248
Query: 329 LRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFL 388
LRS HL+YM N+G ++ ++++ +LWGL+ CHH P Y+ +R ACE +
Sbjct: 249 LRSVSPVHLEYMRNIGMHGTMSISILRGE----RLWGLIACHHRKPNYVDLEVRQACELV 304
Query: 389 VQAFSLQL 396
Q + Q+
Sbjct: 305 AQVLAWQI 312
>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 = 119 bits (299), Expect = 6e-27, Method: Composition-based stats.
Identities = 72/219 (32%), Positives = 122/219 (55%), Gaps = 16/219 (7%)
Query: 183 LHRIDVGIVIDLEPSKSGDPALSLAGAVQSQKLAVSAISRLQALPGGDIGLLCDTVVEDV 242
+HR+ ++++ EP+++ D + A+++ A+ + L+AL + + V
Sbjct: 130 VHRVGELLILEFEPTEAWDS--TGPHALRNAMFALESAPNLRAL--------AEVATQTV 179
Query: 243 QKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMI 302
++LTG+DRVMLY F D GEV++E RR L +LG FPA+DIP AR L+ ++ +R+
Sbjct: 180 RELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLT 239
Query: 303 CDCH--AIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDS 360
D A+P+ + + + P L + LR+ H+QY+ NMG +SL ++
Sbjct: 240 ADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVS----VVVG 295
Query: 361 MKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFSLQLYME 399
+LWGL+ CHH +P +P LR E L + SLQ+ ++
Sbjct: 296 GQLWGLIACHHQTPYVLPPDLRTTLESLGRLLSLQVQVK 334
>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 (292), Expect = 5e-26, Method: Composition-based stats.
Identities = 71/219 (32%), Positives = 121/219 (55%), Gaps = 16/219 (7%)
Query: 183 LHRIDVGIVIDLEPSKSGDPALSLAGAVQSQKLAVSAISRLQALPGGDIGLLCDTVVEDV 242
+HR+ ++++ EP+++ D + A+++ A+ + L+AL + + V
Sbjct: 129 VHRVGELLILEFEPTEAWDS--TGPHALRNAMFALESAPNLRAL--------AEVATQTV 178
Query: 243 QKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMI 302
++LTG+DRVMLY F D GEV++E RR L +LG FPA+ IP AR L+ ++ +R+
Sbjct: 179 RELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASHIPAQARALYTRHLLRLT 238
Query: 303 CDCH--AIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDS 360
D A+P+ + + + P L + LR+ H+QY+ NMG +SL ++
Sbjct: 239 ADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVS----VVVG 294
Query: 361 MKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFSLQLYME 399
+LWGL+ CHH +P +P LR E L + SLQ+ ++
Sbjct: 295 GQLWGLIACHHQTPYVLPPDLRTTLESLGRLLSLQVQVK 333
>pdb|1ZTU|A Chain A, Structure Of The Chromophore Binding Domain Of Bacterial
Phytochrome
Length = 341
Score = 116 bits (290), Expect = 7e-26, Method: Composition-based stats.
Identities = 70/219 (31%), Positives = 120/219 (54%), Gaps = 16/219 (7%)
Query: 183 LHRIDVGIVIDLEPSKSGDPALSLAGAVQSQKLAVSAISRLQALPGGDIGLLCDTVVEDV 242
+HR+ ++++ EP+++ D + A+++ A+ + L+AL + + V
Sbjct: 129 VHRVGELLILEFEPTEAWDS--TGPHALRNAXFALESAPNLRAL--------AEVATQTV 178
Query: 243 QKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMI 302
++LTG+DRV LY F D GEV++E RR L +LG FPA+DIP AR L+ ++ +R+
Sbjct: 179 RELTGFDRVXLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLT 238
Query: 303 CDCH--AIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDS 360
D A+P+ + + + P L + LR+ H QY+ N G +SL ++
Sbjct: 239 ADTRAAAVPLDPVLNTQTNAPTPLGGAVLRATSPXHXQYLRNXGVGSSLSVS----VVVG 294
Query: 361 MKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFSLQLYME 399
+LWGL+ CHH +P +P LR E+L + SLQ+ ++
Sbjct: 295 GQLWGLIACHHQTPYVLPPDLRTTLEYLGRLLSLQVQVK 333
>pdb|3S7Q|A Chain A, Crystal Structure Of A Monomeric Infrared Fluorescent
Deinococcus Radiodurans Bacteriophytochrome Chromophore
Binding Domain
Length = 343
Score = 115 bits (288), Expect = 1e-25, Method: Composition-based stats.
Identities = 70/219 (31%), Positives = 121/219 (55%), Gaps = 16/219 (7%)
Query: 183 LHRIDVGIVIDLEPSKSGDPALSLAGAVQSQKLAVSAISRLQALPGGDIGLLCDTVVEDV 242
+HR+ ++++ EP+++ D A +A+S L++ P ++ L + + V
Sbjct: 129 VHRVGELLILEFEPTEAWDSTGPHA--------LRNAMSALESAP--NLRALAEVATQTV 178
Query: 243 QKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMI 302
++LTG+DRVMLY F D GEV++E RR L +LG FPA+ IP AR L+ ++ +R+
Sbjct: 179 RELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASHIPAQARALYTRHLLRLT 238
Query: 303 CDCH--AIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDS 360
D A+P+ + + + P L + LR+ H+Q++ NMG +SL ++
Sbjct: 239 ADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQFLRNMGVGSSLSVS----VVVG 294
Query: 361 MKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFSLQLYME 399
+LWGL+ CHH +P +P LR E+L + S Q+ ++
Sbjct: 295 GQLWGLIACHHQTPYVLPPDLRTTLEYLGRELSEQVQVK 333
>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 = 95.5 bits (236), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 58/152 (38%), Positives = 82/152 (53%), Gaps = 21/152 (13%)
Query: 234 LCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEP-YLGIHFPANDIPQAARF 292
+ VE+V+ G DRV +Y F + HG VV+E R + P LG+ FPA DIP+ AR
Sbjct: 34 ILRATVEEVRAFLGTDRVKVYRFDPEGHGTVVAEARGGERLPSLLGLTFPAGDIPEEARR 93
Query: 293 LFKQNRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHG---------CHLQYMTNM 343
LF+ +VR+I D A QS+ + QP S R P G CH+ Y+ +M
Sbjct: 94 LFRLAQVRVIVDVEA------QSRSISQPESWGLSA-RVPLGEPLQRPVDPCHVHYLKSM 146
Query: 344 GSIASLVMAVIINSKDSMKLWGLVVCHHTSPR 375
G +SLV+ ++ + +LWGL+V HH PR
Sbjct: 147 GVASSLVVPLMHHQ----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 = 95.5 bits (236), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 56/151 (37%), Positives = 81/151 (53%), Gaps = 19/151 (12%)
Query: 234 LCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEP-YLGIHFPANDIPQAARF 292
+ VE+V+ G DRV +Y F + HG VV+E R + P LG+ FPA DIP+ AR
Sbjct: 4 ILRATVEEVRAFLGTDRVKVYRFDPEGHGTVVAEARGGERLPSLLGLTFPAGDIPEEARR 63
Query: 293 LFKQNRVRMICDCHAIPVMVIQSKELKQP--------LCLVNSTLRSPHGCHLQYMTNMG 344
LF+ +VR+I D A QS+ + QP + L R CH+ Y+ +MG
Sbjct: 64 LFRLAQVRVIVDVEA------QSRSISQPESWGLSARVPLGEPLQRPVDPCHVHYLKSMG 117
Query: 345 SIASLVMAVIINSKDSMKLWGLVVCHHTSPR 375
+SLV+ ++ + +LWGL+V HH PR
Sbjct: 118 VASSLVVPLMHHQ----ELWGLLVSHHAEPR 144
>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 = 1.6, Method: Compositional matrix adjust.
Identities = 33/153 (21%), Positives = 72/153 (47%), Gaps = 11/153 (7%)
Query: 939 ILDAVVSQVMVLLRDKNLHLLHDIPEEIKALSLNGDRIRLQLVLSDFLHCVVRHAPSPDG 998
+ + VV+ V + L D N+ L+ D + L+ + D+I + VL + + ++ G
Sbjct: 13 VAERVVTLVSMELPD-NVRLIRDYDPSLPELAHDPDQI--EQVLLNIVRNALQALGPEGG 69
Query: 999 WVEIKVLPGLKLIKDADQF-VHVQFRLTHPGEGIPSHLIEDMY----NGRNQWTTPEGLG 1053
+ ++ +L +++ + + + G GIP HL + ++ +GR T GLG
Sbjct: 70 EIILRTRTAFQLTLHGERYRLAARIDVEDNGPGIPPHLQDTLFYPMVSGREGGT---GLG 126
Query: 1054 LKLSRKLLIMMNGRVRYVRENSKCYFVIDLELK 1086
L ++R L+ +G++ + F + L ++
Sbjct: 127 LSIARNLIDQHSGKIEFTSWPGHTEFSVYLPIR 159
>pdb|3W2Z|A Chain A, Crystal Structure Of The Cyanobacterial Protein
Length = 198
Score = 32.0 bits (71), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 38/160 (23%), Positives = 63/160 (39%), Gaps = 25/160 (15%)
Query: 215 LAVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLE 274
+AVS + + L +I + T +++++L DRV +Y F+ D GE V+E S
Sbjct: 21 MAVSKVME-KILRVSNIDKIFQTTTQEIRQLLKCDRVAVYRFNPDWSGEFVAESVGSGWV 79
Query: 275 PYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPH- 333
+G DI D H + Q +VN + H
Sbjct: 80 KLVG-----PDIKTVWE------------DTHLQETQ--GGRYRHQESFVVNDIYEAGHF 120
Query: 334 GCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTS 373
CHL+ + A +++ V + KLWGL+ + S
Sbjct: 121 SCHLEILEQFEIKAYIIVPVF----AAEKLWGLLAAYQNS 156
>pdb|3B1V|A Chain A, Crystal Structure Of An S. Thermophilus Nfeob E67a Mutant
Bound To Mgmppnp
pdb|3B1W|A Chain A, Crystal Structure Of An S. Thermophilus Nfeob E67a Mutant
Bound To Gdp
pdb|3B1W|B Chain B, Crystal Structure Of An S. Thermophilus Nfeob E67a Mutant
Bound To Gdp
pdb|3B1W|C Chain C, Crystal Structure Of An S. Thermophilus Nfeob E67a Mutant
Bound To Gdp
pdb|3B1W|D Chain D, Crystal Structure Of An S. Thermophilus Nfeob E67a Mutant
Bound To Gdp
Length = 272
Score = 30.4 bits (67), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 41/188 (21%), Positives = 81/188 (43%), Gaps = 34/188 (18%)
Query: 122 LRSRSEDFELNGLIGIDARTLFTPPSGASLAKAAASREISLLNPILVHSNSRSIEKPFYA 181
L +++D E+ L GI + + ++P + + + R S+LN + ++ ++E+ Y
Sbjct: 44 LVKKNKDLEIQDLPGIYSMSPYSPEAKVARDYLLSQRADSILNVV----DATNLERNLYL 99
Query: 182 ILHRIDVGIVIDLEPSKSGDPALSLAGAV--QSQKLAVSAISRLQALPGGDIGLLCDTVV 239
I+ GI + + AL++ + Q +K+ V +S +P L T V
Sbjct: 100 TTQLIETGIPVTI--------ALNMIDVLDGQGKKINVDKLSYHLGVPVVATSALKQTGV 151
Query: 240 EDVQKLTGYDRV-----MLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQ-AARF- 292
+ V K + + + +DD +S+I + N +PQ +ARF
Sbjct: 152 DQVVKKAAHTTTSTVGDLAFPIYDDRLEAAISQI----------LEVLGNSVPQRSARFY 201
Query: 293 ---LFKQN 297
LF+Q+
Sbjct: 202 AIKLFEQD 209
>pdb|1IRU|D Chain D, Crystal Structure Of The Mammalian 20s Proteasome At 2.75
A Resolution
pdb|1IRU|R Chain R, Crystal Structure Of The Mammalian 20s Proteasome At 2.75
A Resolution
Length = 248
Score = 30.4 bits (67), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 42/103 (40%), Gaps = 11/103 (10%)
Query: 597 QGNTQQNGSKMQGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPAS 656
Q TQ NG + G+ L +V T ++ D SGT + W A
Sbjct: 116 QRYTQSNGRRPFGISAL------IVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVR 169
Query: 657 EAMGKSLIDEVVHEESQGAVENLICRALL---GEEDKNVELKL 696
E + K+ DE + E+ L+ +ALL KN+EL +
Sbjct: 170 EFLEKNYTDEAI--ETDDLTIKLVIKALLEVVQSGGKNIELAV 210
>pdb|3B1X|A Chain A, Crystal Structure Of An S. Thermophilus Nfeob E66a Mutant
Bound To Gmppnp
pdb|3B1X|B Chain B, Crystal Structure Of An S. Thermophilus Nfeob E66a Mutant
Bound To Gmppnp
Length = 272
Score = 30.0 bits (66), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 41/188 (21%), Positives = 80/188 (42%), Gaps = 34/188 (18%)
Query: 122 LRSRSEDFELNGLIGIDARTLFTPPSGASLAKAAASREISLLNPILVHSNSRSIEKPFYA 181
L +++D E+ L GI + + ++P + + R S+LN + ++ ++E+ Y
Sbjct: 44 LVKKNKDLEIQDLPGIYSMSPYSPAEKVARDYLLSQRADSILNVV----DATNLERNLYL 99
Query: 182 ILHRIDVGIVIDLEPSKSGDPALSLAGAV--QSQKLAVSAISRLQALPGGDIGLLCDTVV 239
I+ GI + + AL++ + Q +K+ V +S +P L T V
Sbjct: 100 TTQLIETGIPVTI--------ALNMIDVLDGQGKKINVDKLSYHLGVPVVATSALKQTGV 151
Query: 240 EDVQKLTGYDRV-----MLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQ-AARF- 292
+ V K + + + +DD +S+I + N +PQ +ARF
Sbjct: 152 DQVVKKAAHTTTSTVGDLAFPIYDDRLEAAISQI----------LEVLGNSVPQRSARFY 201
Query: 293 ---LFKQN 297
LF+Q+
Sbjct: 202 AIKLFEQD 209
>pdb|3LX5|A Chain A, Crystal Structure Of Mgmppnp-Bound Nfeob From S.
Thermophilus
pdb|3LX8|A Chain A, Crystal Structure Of Gdp-Bound Nfeob From S. Thermophilus
pdb|3SS8|A Chain A, Crystal Structure Of Nfeob From S. Thermophilus Bound To
Gdp.Alf4- And K+
pdb|3SS8|B Chain B, Crystal Structure Of Nfeob From S. Thermophilus Bound To
Gdp.Alf4- And K+
Length = 272
Score = 30.0 bits (66), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 41/188 (21%), Positives = 80/188 (42%), Gaps = 34/188 (18%)
Query: 122 LRSRSEDFELNGLIGIDARTLFTPPSGASLAKAAASREISLLNPILVHSNSRSIEKPFYA 181
L +++D E+ L GI + + ++P + + R S+LN + ++ ++E+ Y
Sbjct: 44 LVKKNKDLEIQDLPGIYSMSPYSPEEKVARDYLLSQRADSILNVV----DATNLERNLYL 99
Query: 182 ILHRIDVGIVIDLEPSKSGDPALSLAGAV--QSQKLAVSAISRLQALPGGDIGLLCDTVV 239
I+ GI + + AL++ + Q +K+ V +S +P L T V
Sbjct: 100 TTQLIETGIPVTI--------ALNMIDVLDGQGKKINVDKLSYHLGVPVVATSALKQTGV 151
Query: 240 EDVQKLTGYDRV-----MLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQ-AARF- 292
+ V K + + + +DD +S+I + N +PQ +ARF
Sbjct: 152 DQVVKKAAHTTTSTVGDLAFPIYDDRLEAAISQI----------LEVLGNSVPQRSARFY 201
Query: 293 ---LFKQN 297
LF+Q+
Sbjct: 202 AIKLFEQD 209
>pdb|3B1Z|A Chain A, Crystal Structure Of An S. Thermophilus Nfeob T35s Mutant
Without Nucleotide
Length = 272
Score = 30.0 bits (66), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 41/188 (21%), Positives = 80/188 (42%), Gaps = 34/188 (18%)
Query: 122 LRSRSEDFELNGLIGIDARTLFTPPSGASLAKAAASREISLLNPILVHSNSRSIEKPFYA 181
L +++D E+ L GI + + ++P + + R S+LN + ++ ++E+ Y
Sbjct: 44 LVKKNKDLEIQDLPGIYSMSPYSPEEKVARDYLLSQRADSILNVV----DATNLERNLYL 99
Query: 182 ILHRIDVGIVIDLEPSKSGDPALSLAGAV--QSQKLAVSAISRLQALPGGDIGLLCDTVV 239
I+ GI + + AL++ + Q +K+ V +S +P L T V
Sbjct: 100 TTQLIETGIPVTI--------ALNMIDVLDGQGKKINVDKLSYHLGVPVVATSALKQTGV 151
Query: 240 EDVQKLTGYDRV-----MLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQ-AARF- 292
+ V K + + + +DD +S+I + N +PQ +ARF
Sbjct: 152 DQVVKKAAHTTTSTVGDLAFPIYDDRLEAAISQI----------LEVLGNSVPQRSARFY 201
Query: 293 ---LFKQN 297
LF+Q+
Sbjct: 202 AIKLFEQD 209
>pdb|3TAH|A Chain A, Crystal Structure Of An S. Thermophilus Nfeob N11a Mutant
Bound To Mgdp
pdb|3TAH|B Chain B, Crystal Structure Of An S. Thermophilus Nfeob N11a Mutant
Bound To Mgdp
Length = 272
Score = 30.0 bits (66), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 41/188 (21%), Positives = 80/188 (42%), Gaps = 34/188 (18%)
Query: 122 LRSRSEDFELNGLIGIDARTLFTPPSGASLAKAAASREISLLNPILVHSNSRSIEKPFYA 181
L +++D E+ L GI + + ++P + + R S+LN + ++ ++E+ Y
Sbjct: 44 LVKKNKDLEIQDLPGIYSMSPYSPEEKVARDYLLSQRADSILNVV----DATNLERNLYL 99
Query: 182 ILHRIDVGIVIDLEPSKSGDPALSLAGAV--QSQKLAVSAISRLQALPGGDIGLLCDTVV 239
I+ GI + + AL++ + Q +K+ V +S +P L T V
Sbjct: 100 TTQLIETGIPVTI--------ALNMIDVLDGQGKKINVDKLSYHLGVPVVATSALKQTGV 151
Query: 240 EDVQKLTGYDRV-----MLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQ-AARF- 292
+ V K + + + +DD +S+I + N +PQ +ARF
Sbjct: 152 DQVVKKAAHTTTSTVGDLAFPIYDDRLEAAISQI----------LEVLGNSVPQRSARFY 201
Query: 293 ---LFKQN 297
LF+Q+
Sbjct: 202 AIKLFEQD 209
>pdb|3B1Y|A Chain A, Crystal Structure Of An S. Thermophilus Nfeob T35a Mutant
Bound To Gdp
Length = 272
Score = 30.0 bits (66), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 41/188 (21%), Positives = 80/188 (42%), Gaps = 34/188 (18%)
Query: 122 LRSRSEDFELNGLIGIDARTLFTPPSGASLAKAAASREISLLNPILVHSNSRSIEKPFYA 181
L +++D E+ L GI + + ++P + + R S+LN + ++ ++E+ Y
Sbjct: 44 LVKKNKDLEIQDLPGIYSMSPYSPEEKVARDYLLSQRADSILNVV----DATNLERNLYL 99
Query: 182 ILHRIDVGIVIDLEPSKSGDPALSLAGAV--QSQKLAVSAISRLQALPGGDIGLLCDTVV 239
I+ GI + + AL++ + Q +K+ V +S +P L T V
Sbjct: 100 TTQLIETGIPVTI--------ALNMIDVLDGQGKKINVDKLSYHLGVPVVATSALKQTGV 151
Query: 240 EDVQKLTGYDRV-----MLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQ-AARF- 292
+ V K + + + +DD +S+I + N +PQ +ARF
Sbjct: 152 DQVVKKAAHTTTSTVGDLAFPIYDDRLEAAISQI----------LEVLGNSVPQRSARFY 201
Query: 293 ---LFKQN 297
LF+Q+
Sbjct: 202 AIKLFEQD 209
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
0.320 0.136 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 32,199,733
Number of Sequences: 62578
Number of extensions: 1360523
Number of successful extensions: 3055
Number of sequences better than 100.0: 44
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 2982
Number of HSP's gapped (non-prelim): 49
length of query: 1093
length of database: 14,973,337
effective HSP length: 109
effective length of query: 984
effective length of database: 8,152,335
effective search space: 8021897640
effective search space used: 8021897640
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)