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= psy14636
(447 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 = 204 bits (519), Expect = 9e-53, Method: Compositional matrix adjust.
Identities = 144/517 (27%), Positives = 241/517 (46%), Gaps = 87/517 (16%)
Query: 4 SEVDQPVQGTVEGVIPSWIDGVLIRNGPGSWNVGEESFDHLFDCSGLLHRFKISSGLVTY 63
E+ P+ V G IP W+ G L+R GPG + VG E F HLFD LLH+F G VTY
Sbjct: 20 EELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEGHVTY 79
Query: 64 QCKFIKSESYIKNHAARRIVVTGFGTRFVPDPCASIFQRIATLFK--PGSDNTLVSVYPI 121
+FI++++Y++ +RIV+T FGT PDPC +IF R + F+ +DN LV++YP+
Sbjct: 80 HRRFIRTDAYVRAMTEKRIVITEFGTCAFPDPCKNIFSRFFSYFRGVEVTDNALVNIYPV 139
Query: 122 QDQVYALGDSNYMHRIDPATLDTLGKIDLAGDVTILHQTSHPLTTSD----------GET 171
+ YA ++N++ +++P TL+T+ ++DL V++ T+HP +D G+
Sbjct: 140 GEDYYACTETNFITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFGKN 199
Query: 172 FNLGVTL-----------RPTGPRYCILQL--NDAFSYPDLSHXXXXXXSL--------- 209
F++ + P ++Q +D F P H +
Sbjct: 200 FSIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFK-PSYVHSFGLTPNYIVFVETPVK 258
Query: 210 ---------------RFRDDIDMTSTI---FHVLDKTNGSVVH-RFQADSFFYLHIINAY 250
+ D + T+ H+ DK ++ +++ F H IN Y
Sbjct: 259 INLFKFLSSWSLWGANYMDCFESNETMGVWLHIADKKRKKYINNKYRTSPFNLFHHINTY 318
Query: 251 EDTNDGIVVDICCYRNPAML-DCMY----REALKNIHSTPRYAQMFRARPLRFRLDLASP 305
ED ++ ++VD+CC++ + + +Y RE + + R A R L++
Sbjct: 319 ED-HEFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQPEVRRYVLPLNIDKA 377
Query: 306 RTAPTGKVRP-----SVICD----------------VGCETPRMNGQ-HQGRSYTYFYAI 343
T P +++C E P++N Q + G+ YTY Y +
Sbjct: 378 DTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGL 437
Query: 344 SADIDRDNPGTLIKVNVQNNTCKSWSQKDVYPSEPVFVATPNARKEDEGVLLSVLLWSHH 403
++ P L K+NV+ W + D YPSEP+FV+ P+A +ED+GV+LSV++
Sbjct: 438 G--LNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGA 495
Query: 404 PTRVS-LLVLNARTMQELGRVNFTTPTPVPKCLHGWY 439
+ + LL+LNA+ + E+ R PV HG +
Sbjct: 496 GQKPAYLLILNAKDLSEVARAEVEINIPV--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 = 113 bits (283), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 119/473 (25%), Positives = 196/473 (41%), Gaps = 74/473 (15%)
Query: 14 VEGVIPSWIDGVLIRNGPGSWNVGEESFDHLFDCSGLLHRFKI-SSGLVTYQCKFIKSES 72
VEG IP + G L RNGPG +G+ H FD G++ FK G V +Q KF++++
Sbjct: 38 VEGSIPPDLQGTLYRNGPGLLEIGDRPLKHPFDGDGMVTAFKFPGDGRVHFQSKFVRTQG 97
Query: 73 YIKNHAARRIVVTG-FGTRFVPDPCASIFQRIATLFKPGSDNTLVSVYPIQDQVYALGDS 131
Y++ A +++ G FG++ P + I L NT ++ + D++ AL +
Sbjct: 98 YVEEQKAGKMIYRGVFGSQ----PAGGWLKTIFDLRLKNIANTNITYW--GDRLLALWEG 151
Query: 132 NYMHRIDPATLDTLGKIDLAGDVT-----ILHQTSHPLTTSDGE-----TFNLGVT---- 177
HR++P+ L T+G DL G + H P +T DG TF++ +
Sbjct: 152 GQPHRLEPSNLATIGLDDLGGILAEGQPLSAHPRIDPASTFDGGQPCYVTFSIKSSLSST 211
Query: 178 -----LRPTG----------------------PRYCILQLNDAF--SYPDLSHXXXXXXS 208
L P G P Y I N+ P L
Sbjct: 212 LTLLELDPQGKLLRQKTETFPGFAFIHDFAITPHYAIFLQNNVTLNGLPYLFGLRGAGEC 271
Query: 209 LRFRDDIDMTSTIFHVLDKTNGSVVHRFQADSFFYLHIINAYEDTNDGIVVDICCYRNPA 268
++F D +L +G + R + F H NA+E+ N I++D CY +
Sbjct: 272 VQFHPDKPAQI----ILVPRDGGEIKRIPVQAGFVFHHANAFEE-NGKIILDSICYNSLP 326
Query: 269 MLDCMYREALKNIHSTPRYAQMFRARPLRFRLDLASPRTAPTGKVRPSVICDVGCETPRM 328
+D + ST + + + RF +D A+ V ++ CE P +
Sbjct: 327 QVDTD-----GDFRST-NFDNLDPGQLWRFTIDPAA------ATVEKQLMVSRCCEFPVV 374
Query: 329 NGQHQGRSYTYFYAISADIDRDNP--GTLIKVNVQNN--TCKSWSQKDVYPSEPVFVATP 384
+ Q GR Y Y Y +A N ++KV++++ T +S++ + EP+FV P
Sbjct: 375 HPQQVGRPYRYVYMGAAHHSTGNAPLQAILKVDLESGTETLRSFAPHG-FAGEPIFVPRP 433
Query: 385 NARKEDEGVLLSVLLWSHHPTRVSLLVLNARTMQELGRVNFTTPTPVPKCLHG 437
ED+G LL L++ R L++L+A+ + +P LHG
Sbjct: 434 GGVAEDDGWLL-CLIYKADLHRSELVILDAQDITAPAIATLKLKHHIPYPLHG 485
>pdb|3NPE|A Chain A, Structure Of Vp14 In Complex With Oxygen
Length = 529
Score = 60.8 bits (146), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 115/488 (23%), Positives = 181/488 (37%), Gaps = 81/488 (16%)
Query: 14 VEGVIPSWIDGVLIRNGPGSWNVGEESFD-----HLFDCSGLLHRFKISSGLV-TYQCKF 67
V G IP +IDGV RNG FD HLFD G++H +I +G +Y C+F
Sbjct: 66 VSGRIPPFIDGVYARNG------ANPCFDPVAGHHLFDGDGMVHALRIRNGAAESYACRF 119
Query: 68 IKSESYIKNHA-ARRIVVTGFGTRFVPDPCASI---FQRIATLFKPGSDNTLVS----VY 119
++ + A R + G A + + R A S T V+ VY
Sbjct: 120 TETARLRQERAIGRPVFPKAIGELHGHSGIARLALFYARAACGLVDPSAGTGVANAGLVY 179
Query: 120 PIQDQVYALGDSNYMHRI---DPATLDTLGKIDLAGDVTILHQTSHPLTTSDGETFNLGV 176
++ A+ + + + + D L+T+G+ D G + L + GE L
Sbjct: 180 -FNGRLLAMSEDDLPYHVRVADDGDLETVGRYDFDGQLGCAMIAHPKLDPATGELHALSY 238
Query: 177 TL-----------RPTGPRYCILQLNDAFSYPDLSHXXXXXXSLRFRDDIDMTSTIFH-- 223
+ RP G + +++ P + H +L D + +
Sbjct: 239 DVIKRPYLKYFYFRPDGTKSDDVEI--PLEQPTMIHDFAITENLVVVPDHQVVFKLQEML 296
Query: 224 ------VLDKTNGS---VVHRFQADSF----------FYLHIINAYEDTNDGIVVDICCY 264
VLD S V+ + AD+ F H+ NA+ED G VV I
Sbjct: 297 RGGSPVVLDAAKTSRFGVLPKHAADASEMAWVDVPDCFCFHLWNAWEDEATGEVVVIGSC 356
Query: 265 RNPAMLDCMYREALKNIHSTPRYAQMFRARPLRFRLDLASPRTAPTGKVRPSVICDVGCE 324
PA D ++ E+ + + S RLD + R+ + PS V E
Sbjct: 357 MTPA--DSIFNESDERLESV----------LTEIRLDARTGRSTRRAVLPPSQ--QVNLE 402
Query: 325 TPRMNGQHQGRSYTYFYAISADIDRDNPGTLIKVNVQNNTCKSWSQKD-VYPSEPVFV-- 381
+N GR Y Y A+ G KV++ + + + EP FV
Sbjct: 403 VGMVNRNLLGRETRYAYLAVAEPWPKVSG-FAKVDLSTGELTKFEYGEGRFGGEPCFVPM 461
Query: 382 --ATPNARKEDEGVLLSVLLWSHHPTRVSLLVLNARTMQELGRVNFTTPTPVPKCLHGWY 439
A + R ED+G +L+ + LLV+NA M+ V P+ VP HG +
Sbjct: 462 DPAAAHPRGEDDGYVLT-FVHDERAGTSELLVVNAADMRLEATVQL--PSRVPFGFHGTF 518
Query: 440 FPHERKDA 447
+ +A
Sbjct: 519 ITGQELEA 526
>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 = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 36/82 (43%), Gaps = 11/82 (13%)
Query: 358 VNVQNNTCKSWSQKDVYPSEPVFVATPNARKEDEGV---------LLSVLLWSHHPTRVS 408
+ V +TCK + V+PSEP FV PN ++G+ L SVL + T +
Sbjct: 330 LEVLASTCKDLRELRVFPSEP-FVMEPNVALTEQGLVSVSMGCPKLESVLYFCRQMTNAA 388
Query: 409 LLVLNARTMQELGRVNFTTPTP 430
L+ + AR + R P
Sbjct: 389 LITI-ARNRPNMTRFRLCIIEP 409
>pdb|2ORD|A Chain A, Crystal Structure Of Acetylornithine Aminotransferase (Ec
2.6.1.11) (Acoat) (Tm1785) From Thermotoga Maritima At
1.40 A Resolution
pdb|2ORD|B Chain B, Crystal Structure Of Acetylornithine Aminotransferase (Ec
2.6.1.11) (Acoat) (Tm1785) From Thermotoga Maritima At
1.40 A Resolution
Length = 397
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 4/72 (5%)
Query: 236 FQADSFFYLHIINAYEDTNDGIVVDICCYRNPAMLDCMYREALKNIHSTPRYAQMFRARP 295
+ S+ Y NAY D GI V++ + +P +++ + +A K IH + +F RP
Sbjct: 28 YGKGSWIYDEKGNAYLDFTSGIAVNVLGHSHPRLVEAIKDQAEKLIHCS----NLFWNRP 83
Query: 296 LRFRLDLASPRT 307
+L S T
Sbjct: 84 QXELAELLSKNT 95
>pdb|2E54|A Chain A, Crystal Structure Of Acetylornithine Aminotransferase From
Thermotoga Maritima
Length = 385
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 4/72 (5%)
Query: 236 FQADSFFYLHIINAYEDTNDGIVVDICCYRNPAMLDCMYREALKNIHSTPRYAQMFRARP 295
+ S+ Y NAY D GI V++ + +P +++ + +A K IH + +F RP
Sbjct: 16 YGKGSWIYDEKGNAYLDFTSGIAVNVLGHSHPRLVEAIKDQAEKLIHCS----NLFWNRP 71
Query: 296 LRFRLDLASPRT 307
+L S T
Sbjct: 72 QMELAELLSKNT 83
>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 = 2.0, Method: Composition-based stats.
Identities = 15/24 (62%), Positives = 18/24 (75%), Gaps = 1/24 (4%)
Query: 44 LFDCSGLLHR-FKISSGLVTYQCK 66
+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 0.138 0.431
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,364,365
Number of Sequences: 62578
Number of extensions: 609213
Number of successful extensions: 1048
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1036
Number of HSP's gapped (non-prelim): 12
length of query: 447
length of database: 14,973,337
effective HSP length: 102
effective length of query: 345
effective length of database: 8,590,381
effective search space: 2963681445
effective search space used: 2963681445
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)