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= psy5322
(476 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3FSN|A Chain A, Crystal Structure Of Rpe65 At 2.14 Angstrom Resolution
pdb|3FSN|B Chain B, Crystal Structure Of Rpe65 At 2.14 Angstrom Resolution
pdb|3KVC|A Chain A, Crystal Structure Of Bovine Rpe65 At 1.9 Angstrom
Resolution
pdb|3KVC|B Chain B, Crystal Structure Of Bovine Rpe65 At 1.9 Angstrom
Resolution
pdb|4F2Z|A Chain A, Crystal Structure Of Rpe65 In A Lipid Environment
pdb|4F2Z|E Chain E, Crystal Structure Of Rpe65 In A Lipid Environment
pdb|4F30|A Chain A, Structure Of Rpe65: P6522 Crystal Form Grown In Ammonium
Phosphate Solution
pdb|4F3A|A Chain A, Structure Of Rpe65: P6522 Crystal Form, Iridium Derivative
pdb|4F3D|A Chain A, Structure Of Rpe65: P65 Crystal Form Grown In
Fos-Choline-10
pdb|4F3D|B Chain B, Structure Of Rpe65: P65 Crystal Form Grown In
Fos-Choline-10
Length = 533
Score = 179 bits (453), Expect = 4e-45, Method: Compositional matrix adjust.
Identities = 88/247 (35%), Positives = 148/247 (59%), Gaps = 9/247 (3%)
Query: 53 EVDQPVQGTVEGVIPSWIDGVLIRNGPGSWNVGEESFDHLFDCSGLLHRFKISSGLVTYQ 112
E+ P+ V G IP W+ G L+R GPG + VG E F HLFD LLH+F G VTY
Sbjct: 21 ELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEGHVTYH 80
Query: 113 CKFIKSESYIKNHAARRIVVTGFGTRFVPDPCASIFQRIATLFK--PGSDNTLVSVYPIQ 170
+FI++++Y++ +RIV+T FGT PDPC +IF R + F+ +DN LV++YP+
Sbjct: 81 RRFIRTDAYVRAMTEKRIVITEFGTCAFPDPCKNIFSRFFSYFRGVEVTDNALVNIYPVG 140
Query: 171 DQVYALGDSNYMHRIDPATLDTLEKMDLARDVTILHQTSHPLTTSDGETFNLGVTL-RPT 229
+ YA ++N++ +++P TL+T++++DL V++ T+HP +DG +N+G +
Sbjct: 141 EDYYACTETNFITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFGKNF 200
Query: 230 GPRYCILQL----NDVAD--HRVKLVTSVPVRWKFHPGYMHTFAMTPHYFIIVEQPLSIS 283
Y I+++ D D + ++V P +F P Y+H+F +TP+Y + VE P+ I+
Sbjct: 201 SIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKIN 260
Query: 284 VPRLIKN 290
+ + + +
Sbjct: 261 LFKFLSS 267
Score = 77.0 bits (188), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 44/118 (37%), Positives = 69/118 (58%), Gaps = 6/118 (5%)
Query: 353 ETPRMNGQ-HQGRPYTYFYAISADIDRDNPGTLIKVNVQNNTCKSWSQKDVYPSEPVFVA 411
E P++N Q + G+PYTY Y + ++ P L K+NV+ W + D YPSEP+FV+
Sbjct: 417 EFPQINYQKYGGKPYTYAYGLG--LNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVS 474
Query: 412 TPNAVKEDEGVLLSVLLWSHHPTR-VSLLVLNARTMQELGRVNFTTPTPVPKCLHGWY 468
P+A++ED+GV+LSV++ + LL+LNA+ + E+ R PV HG +
Sbjct: 475 HPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPV--TFHGLF 530
>pdb|2BIW|A Chain A, Crystal Structure Of Apocarotenoid Cleavage Oxygenase From
Synechocystis, Native Enzyme
pdb|2BIW|B Chain B, Crystal Structure Of Apocarotenoid Cleavage Oxygenase From
Synechocystis, Native Enzyme
pdb|2BIW|C Chain C, Crystal Structure Of Apocarotenoid Cleavage Oxygenase From
Synechocystis, Native Enzyme
pdb|2BIW|D Chain D, Crystal Structure Of Apocarotenoid Cleavage Oxygenase From
Synechocystis, Native Enzyme
pdb|2BIX|A Chain A, Crystal Structure Of Apocarotenoid Cleavage Oxygenase From
Synechocystis, Fe-Free Apoenzyme
pdb|2BIX|B Chain B, Crystal Structure Of Apocarotenoid Cleavage Oxygenase From
Synechocystis, Fe-Free Apoenzyme
Length = 490
Score = 104 bits (259), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 114/475 (24%), Positives = 192/475 (40%), Gaps = 97/475 (20%)
Query: 62 VEGVIPSWIDGVLIRNGPGSWNVGEESFDHLFDCSGLLHRFKI-SSGLVTYQCKFIKSES 120
VEG IP + G L RNGPG +G+ H FD G++ FK G V +Q KF++++
Sbjct: 38 VEGSIPPDLQGTLYRNGPGLLEIGDRPLKHPFDGDGMVTAFKFPGDGRVHFQSKFVRTQG 97
Query: 121 YIKNHAARRIVVTG-FGTRFVPDPCASIFQRIATLFKPGSDNTLVSVYPIQDQVYALGDS 179
Y++ A +++ G FG++ P + I L NT ++ + D++ AL +
Sbjct: 98 YVEEQKAGKMIYRGVFGSQ----PAGGWLKTIFDLRLKNIANTNITYW--GDRLLALWEG 151
Query: 180 NYMHRIDPATLDTLEKMDLARDVTILHQTSHPLTTSDGETFNLGVTLRPTGPRYCILQLN 239
HR++P+ L T+ DL + S TF+ G P Y +
Sbjct: 152 GQPHRLEPSNLATIGLDDLGGILAEGQPLSAHPRIDPASTFDGGQ------PCYVTFSIK 205
Query: 240 DVA---------DHRVKLVTSVPVRWKFHPG--YMHTFAMTPHYFIIVEQPLSIS-VPRL 287
D + KL+ + + PG ++H FA+TPHY I ++ ++++ +P L
Sbjct: 206 SSLSSTLTLLELDPQGKLLRQ---KTETFPGFAFIHDFAITPHYAIFLQNNVTLNGLPYL 262
Query: 288 IKNSVTNRPLATCLKFF-EKQSNIHSTPRYAQMFRARPL--------------------- 325
R C++F +K + I PR + P+
Sbjct: 263 FG----LRGAGECVQFHPDKPAQIILVPRDGGEIKRIPVQAGFVFHHANAFEENGKIILD 318
Query: 326 ------------------------------RFRLDLASPRTAPTGKVRPSVICDVGCETP 355
RF +D A+ V ++ CE P
Sbjct: 319 SICYNSLPQVDTDGDFRSTNFDNLDPGQLWRFTIDPAA------ATVEKQLMVSRCCEFP 372
Query: 356 RMNGQHQGRPYTYFYAISADIDRDNP--GTLIKVNVQNN--TCKSWSQKDVYPSEPVFVA 411
++ Q GRPY Y Y +A N ++KV++++ T +S++ + EP+FV
Sbjct: 373 VVHPQQVGRPYRYVYMGAAHHSTGNAPLQAILKVDLESGTETLRSFAPHG-FAGEPIFVP 431
Query: 412 TPNAVKEDEGVLLSVLLWSHHPTRVSLLVLNARTMQELGRVNFTTPTPVPKCLHG 466
P V ED+G LL L++ R L++L+A+ + +P LHG
Sbjct: 432 RPGGVAEDDGWLL-CLIYKADLHRSELVILDAQDITAPAIATLKLKHHIPYPLHG 485
>pdb|3NPE|A Chain A, Structure Of Vp14 In Complex With Oxygen
Length = 529
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 37/76 (48%), Gaps = 12/76 (15%)
Query: 62 VEGVIPSWIDGVLIRNGPGSWNVGEESFD-----HLFDCSGLLHRFKISSGLV-TYQCKF 115
V G IP +IDGV RNG FD HLFD G++H +I +G +Y C+F
Sbjct: 66 VSGRIPPFIDGVYARNG------ANPCFDPVAGHHLFDGDGMVHALRIRNGAAESYACRF 119
Query: 116 IKSESYIKNHAARRIV 131
++ + A R V
Sbjct: 120 TETARLRQERAIGRPV 135
>pdb|2P1M|B Chain B, Tir1-ask1 Complex Structure
pdb|2P1N|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiqutin Ligase
pdb|2P1N|E Chain E, Mechanism Of Auxin Perception By The Tir1 Ubiqutin Ligase
pdb|2P1O|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
pdb|2P1P|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
pdb|2P1Q|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
pdb|3C6N|B Chain B, Small Molecule Agonists And Antagonists Of F-Box Protein-
Substrate Interactions In Auxin Perception And Signaling
pdb|3C6O|B Chain B, Small Molecule Agonists And Antagonists Of F-Box
Protein-Substrate Interactions In Auxin Perception And
Signaling
pdb|3C6P|B Chain B, Small Molecule Agonists And Antagonists Of F-Box Protein-
Substrate Interactions In Auxin Perception And Signaling
Length = 594
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 36/82 (43%), Gaps = 11/82 (13%)
Query: 387 VNVQNNTCKSWSQKDVYPSEPVFVATPNAVKEDEGV---------LLSVLLWSHHPTRVS 437
+ V +TCK + V+PSEP FV PN ++G+ L SVL + T +
Sbjct: 330 LEVLASTCKDLRELRVFPSEP-FVMEPNVALTEQGLVSVSMGCPKLESVLYFCRQMTNAA 388
Query: 438 LLVLNARTMQELGRVNFTTPTP 459
L+ + AR + R P
Sbjct: 389 LITI-ARNRPNMTRFRLCIIEP 409
>pdb|1I3J|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Intron
Endonuclease I-Tevi With Its Substrate
pdb|1T2T|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Intron
Endonuclease I-Tevi With Operator Site
Length = 116
Score = 30.4 bits (67), Expect = 2.1, Method: Composition-based stats.
Identities = 15/24 (62%), Positives = 18/24 (75%), Gaps = 1/24 (4%)
Query: 92 LFDCSGLLHR-FKISSGLVTYQCK 114
+FDC+ R FKISSGLVTY+ K
Sbjct: 82 IFDCAADAARHFKISSGLVTYRVK 105
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
0.322 0.137 0.433
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,516,042
Number of Sequences: 62578
Number of extensions: 664339
Number of successful extensions: 1199
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1186
Number of HSP's gapped (non-prelim): 8
length of query: 476
length of database: 14,973,337
effective HSP length: 102
effective length of query: 374
effective length of database: 8,590,381
effective search space: 3212802494
effective search space used: 3212802494
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)