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= 008275
(571 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NPE|A Chain A, Structure Of Vp14 In Complex With Oxygen
Length = 529
Score = 155 bits (391), Expect = 8e-38, Method: Compositional matrix adjust.
Identities = 142/533 (26%), Positives = 230/533 (43%), Gaps = 85/533 (15%)
Query: 48 NFAPVDALREAVLVTNIDGEIPEDFPEGVYIRNGPNPLFGGLKSTKSMFGSSNHIWVEGE 107
NFAPV R V + G IP F +GVY RNG NP F + + H +G+
Sbjct: 51 NFAPVGE-RPPVHELPVSGRIPP-FIDGVYARNGANPCFDPV---------AGHHLFDGD 99
Query: 108 GMLHALYFKKETDGSWNVVYMNRHVESETFKQEKQRNRSSFLPAI---EGDXXXXXXXXX 164
GM+HAL + S Y R E+ +QE+ R F AI G
Sbjct: 100 GMVHALRIRNGAAES----YACRFTETARLRQERAIGRPVFPKAIGELHGHSGIARLALF 155
Query: 165 XXXXRFGKINKY----ISNTNIFEHAGKFYSVAENHMPQEIDIFT---LETLGNWDVNGA 217
G ++ ++N + G+ +++E+ +P + + LET+G +D +G
Sbjct: 156 YARAACGLVDPSAGTGVANAGLVYFNGRLLAMSEDDLPYHVRVADDGDLETVGRYDFDGQ 215
Query: 218 WNRPFTSHPKKASGTGELVIMGVDATK-PFVEIGVISADGDKLVHKVDLKLSRCSLCHEI 276
+HPK TGEL + D K P+++ DG K V++ L + ++ H+
Sbjct: 216 LGCAMIAHPKLDPATGELHALSYDVIKRPYLKYFYFRPDGTK-SDDVEIPLEQPTMIHDF 274
Query: 277 GITQRYNVFLDYPLSIDLTRLAFGGPLIKYEHEGYAKIGIMPRY-GDADSVKWFDVEPNC 335
IT+ V D+ + L + GG + + ++ G++P++ DA + W DV P+C
Sbjct: 275 AITENLVVVPDHQVVFKLQEMLRGGSPVVLDAAKTSRFGVLPKHAADASEMAWVDV-PDC 333
Query: 336 -TFHIINCFED---GDEVIVWGCRALESIIPGPDLGLNKFEWFSKKFRHAELADESVDTS 391
FH+ N +ED G+ V++ C + P AD + S
Sbjct: 334 FCFHLWNAWEDEATGEVVVIGSC-----MTP---------------------ADSIFNES 367
Query: 392 PDDVPLFSRVYEWRLNMQNGDVKETNL--SGTKVSMDFPMINGGYTGIKNKYGYTQIVDS 449
D L S + E RL+ + G + +V+++ M+N G + +Y Y +
Sbjct: 368 --DERLESVLTEIRLDARTGRSTRRAVLPPSQQVNLEVGMVNRNLLGRETRYAYLAV--- 422
Query: 450 IASSASGMPKYGGLAKLSFEEPDNTESEELIKVEYHKFEENIFCTGGAFVPKGRGVE--- 506
A PK G AK+ + + EL K EY E F FVP
Sbjct: 423 ----AEPWPKVSGFAKV------DLSTGELTKFEYG---EGRFGGEPCFVPMDPAAAHPR 469
Query: 507 -EDDGWIITFLHNEDTNISQVYIIDTKKFTDEPVAKITLSHRVPYGFHGAFMS 558
EDDG+++TF+H+E S++ +++ E A + L RVP+GFHG F++
Sbjct: 470 GEDDGYVLTFVHDERAGTSELLVVNAADMRLE--ATVQLPSRVPFGFHGTFIT 520
>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 = 109 bits (273), Expect = 4e-24, Method: Compositional matrix adjust.
Identities = 120/533 (22%), Positives = 210/533 (39%), Gaps = 75/533 (14%)
Query: 44 PSQRNFAPVDALREA--------VLVTNIDGEIPEDFPEGVYIRNGPNPLFGGLKSTKSM 95
PSQR+++P D LR V +++G IP D +G RNGP L G + K
Sbjct: 10 PSQRSYSPQDWLRGYQSQPQEWDYWVEDVEGSIPPDL-QGTLYRNGPGLLEIGDRPLKHP 68
Query: 96 FGSSNHIWVEGEGMLHALYFKKETDGSWNVVYMNRHVESETFKQEKQRNRSSFLPAIEGD 155
F +G+GM+ A F G V + ++ V ++ + +E++ + + + G
Sbjct: 69 F--------DGDGMVTAFKFP----GDGRVHFQSKFVRTQGYVEEQKAGKMIYR-GVFGS 115
Query: 156 XXXXXXXXXXXXXRFGKINKYISNTNIFEHAGKFYSVAENHMPQEIDIFTLETLGNWDVN 215
R K I+NTNI + ++ E P ++ L T+G D+
Sbjct: 116 QPAGGWLKTIFDLRL----KNIANTNITYWGDRLLALWEGGQPHRLEPSNLATIGLDDLG 171
Query: 216 G--AWNRPFTSHPK--KAS----GTGELVIMGVDATKPFVEIGVISADGDKLVHKVDLKL 267
G A +P ++HP+ AS G V + ++ + KL+ +
Sbjct: 172 GILAEGQPLSAHPRIDPASTFDGGQPCYVTFSIKSSLSSTLTLLELDPQGKLLRQKTETF 231
Query: 268 SRCSLCHEIGITQRYNVFLDYPLSIDLTRLAFG----GPLIKYEHEGYAKIGIMPRYGDA 323
+ H+ IT Y +FL ++++ FG G +++ + A+I ++PR D
Sbjct: 232 PGFAFIHDFAITPHYAIFLQNNVTLNGLPYLFGLRGAGECVQFHPDKPAQIILVPR--DG 289
Query: 324 DSVKWFDVEPNCTFHIINCFEDGDEVIVWGCRALESIIPGPDLGLNKFEWFSKKFRHAEL 383
+K V+ FH N FE+ ++I L+SI +
Sbjct: 290 GEIKRIPVQAGFVFHHANAFEENGKII------LDSIC----------------YNSLPQ 327
Query: 384 ADESVDTSPDDVPLFSRVYEWRLNMQNGDVKETNLSGTKVSMDFPMINGGYTGIKNKYGY 443
D D + WR + +FP+++ G +Y Y
Sbjct: 328 VDTDGDFRSTNFDNLDPGQLWRFTIDPAAATVEKQLMVSRCCEFPVVHPQQVGRPYRYVY 387
Query: 444 TQIVDSIASSASGMPKYGGLAKLSFEEPDNTESEELIKVEYHKFEENIFCTGGAFVPKGR 503
A ++G + K+ E TE+ F + F FVP+
Sbjct: 388 M----GAAHHSTGNAPLQAILKVDLES--GTET-------LRSFAPHGFAGEPIFVPRPG 434
Query: 504 GVEEDDGWIITFLHNEDTNISQVYIIDTKKFTDEPVAKITLSHRVPYGFHGAF 556
GV EDDGW++ ++ D + S++ I+D + T +A + L H +PY HG++
Sbjct: 435 GVAEDDGWLLCLIYKADLHRSELVILDAQDITAPAIATLKLKHHIPYPLHGSW 487
>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 = 56.2 bits (134), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 116/574 (20%), Positives = 195/574 (33%), Gaps = 103/574 (17%)
Query: 38 VDQPLLPSQRNFAPVDALREAVLVTNIDGEIPEDFPEGVYIRNGPNPLFGGLKSTKSMFG 97
V+ P ++ F V+ L + L ++ G IP + G +R GP G + +F
Sbjct: 5 VEHPAGGYKKLFETVEEL-SSPLTAHVTGRIPL-WLTGSLLRCGPGLFEVGSEPFYHLF- 61
Query: 98 SSNHIWVEGEGMLHALYFKKETDGSWNVVYMNRHVESETFKQEKQRNRSSFLPAIEGDXX 157
+G+ +LH FK+ +V Y R + ++ + + R + E
Sbjct: 62 -------DGQALLHKFDFKEG-----HVTYHRRFIRTDAYVRAMTEKR---IVITEFGTC 106
Query: 158 XXXXXXXXXXXRFGKINKYISNT-----NIFEHAGKFYSVAENHMPQEIDIFTLETLGNW 212
RF + + T NI+ +Y+ E + +++ TLET+
Sbjct: 107 AFPDPCKNIFSRFFSYFRGVEVTDNALVNIYPVGEDYYACTETNFITKVNPETLETIKQV 166
Query: 213 D------VNGAWNRPFTSHPKKASGTGELVIMGVDATKPFVEIGVISADGDKLVHKVDLK 266
D VNGA P + G V+I + AD + + K ++
Sbjct: 167 DLCNYVSVNGATAHPHIENDGTVYNIGNCFGKNFSIAYNIVKIPPLQADKEDPISKSEIV 226
Query: 267 LS-------RCSLCHEIGITQRYNVFLDYPLSIDLTRLAFGGPLIKYEH----EGYAKIG 315
+ + S H G+T Y VF++ P+ I+L + L + E +G
Sbjct: 227 VQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSSWSLWGANYMDCFESNETMG 286
Query: 316 IMPRYGDADSVKW----FDVEPNCTFHIINCFEDGDEVIVWGCRALESIIPGPDLGLNKF 371
+ D K+ + P FH IN +ED + +IV C F
Sbjct: 287 VWLHIADKKRKKYINNKYRTSPFNLFHHINTYEDHEFLIVDLC------------CWKGF 334
Query: 372 EWFSKKFRHAELAD--ESVDTSPDDVPLFS-RVYEWRLNMQNGDV--------------- 413
E+ A L + E V + P R Y LN+ D
Sbjct: 335 EFVYNYLYLANLRENWEEVKKNARKAPQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAI 394
Query: 414 ----------KETNLSGTKVSMDFPMIN-GGYTGIKNKYGYTQIVDSIASSASGMPKYGG 462
E SG + + +FP IN Y G Y Y ++
Sbjct: 395 LCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLGLNHFVPDRLCKLNVKT 454
Query: 463 LAKLSFEEPDNTESEELIKVEYHKFEENIFCTGGAFVPKGRGVEEDDGWIITFLHNEDTN 522
++EPD+ SE + FV +EEDDG +++ + +
Sbjct: 455 KETWVWQEPDSYPSEPI------------------FVSHPDALEEDDGVVLSVVVSPGAG 496
Query: 523 ISQVYIIDTKKFTDEPVAKITLSHRVPYGFHGAF 556
Y++ VA+ + +P FHG F
Sbjct: 497 QKPAYLLILNAKDLSEVARAEVEINIPVTFHGLF 530
>pdb|2OHF|A Chain A, Crystal Structure Of Human Ola1 In Complex With Amppcp
Length = 396
Score = 30.0 bits (66), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 31/128 (24%), Positives = 52/128 (40%), Gaps = 9/128 (7%)
Query: 398 FSRVYEWRLNMQNGDVKETNLSGTKVSMDFP-MINGGYTGIKNKYGYTQIVDSIAS---- 452
FS E +L + + ++ L P +I G+ ++ +Y +T D + +
Sbjct: 263 FSGALELKLQELSAEERQKYLEANMTQSALPKIIKAGFAALQLEYFFTAGPDEVRAWTIR 322
Query: 453 SASGMPKYGGLAKLSFEEPDNTESEELIKVEYHKFE--ENIFCTGGAFVPKGRGVEEDDG 510
+ P+ G FE+ E++K E K E EN G + +GR +DG
Sbjct: 323 KGTKAPQAAGKIHTDFEK--GFIMAEVMKYEDFKEEGSENAVKAAGKYRQQGRNYIVEDG 380
Query: 511 WIITFLHN 518
II F N
Sbjct: 381 DIIFFKFN 388
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
0.318 0.138 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,411,299
Number of Sequences: 62578
Number of extensions: 852633
Number of successful extensions: 1630
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1616
Number of HSP's gapped (non-prelim): 7
length of query: 571
length of database: 14,973,337
effective HSP length: 104
effective length of query: 467
effective length of database: 8,465,225
effective search space: 3953260075
effective search space used: 3953260075
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)