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= 039955
(420 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 = 120 bits (302), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 92/335 (27%), Positives = 140/335 (41%), Gaps = 82/335 (24%)
Query: 77 YKLQPSLDPKRALSNNFAPVDELPPTQCQVIQGSLPSCLDEPY---------------HL 121
+ L + DP ++ NFAPV E PP + G +P +D Y HL
Sbjct: 36 HGLPSTADPAVQIAGNFAPVGERPPVHELPVSGRIPPFIDGVYARNGANPCFDPVAGHHL 95
Query: 122 FDGDAMLHCIRISQGQA-TFCSRCVKTYKYTIENT----------------HELLSLQLV 164
FDGD M+H +RI G A ++ R +T + E + L L
Sbjct: 96 FDGDGMVHALRIRNGAAESYACRFTETARLRQERAIGRPVFPKAIGELHGHSGIARLALF 155
Query: 165 FSQA--NLISINNGFGLANASLSFLGDHLFAICEGDLPYAVRLTSNGDTDTKTLGRHDFD 222
+++A L+ + G G+ANA L + L A+ E DLPY VR+ +GD + T+GR+DFD
Sbjct: 156 YARAACGLVDPSAGTGVANAGLVYFNGRLLAMSEDDLPYHVRVADDGDLE--TVGRYDFD 213
Query: 223 VKSGMNMTAHPK----------------KRP-----------CNRRNVCFPLWSNTSVCD 255
+ G M AHPK KRP +V PL T + D
Sbjct: 214 GQLGCAMIAHPKLDPATGELHALSYDVIKRPYLKYFYFRPDGTKSDDVEIPLEQPTMIHD 273
Query: 256 -------------TLLLRCKRLF-----AAFGSTKASRIGVIPRCAKDSLQMRWFDVPGF 297
++ + + + + K SR GV+P+ A D+ +M W DVP
Sbjct: 274 FAITENLVVVPDHQVVFKLQEMLRGGSPVVLDAAKTSRFGVLPKHAADASEMAWVDVPDC 333
Query: 298 NNIHAINEW-DEEDGNVIILAPNILSIEQAFGKTE 331
H N W DE G V+++ + + F +++
Sbjct: 334 FCFHLWNAWEDEATGEVVVIGSCMTPADSIFNESD 368
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 30/91 (32%), Positives = 45/91 (49%), Gaps = 7/91 (7%)
Query: 319 NILSIEQAFGKTELVPCLMEKNTRSGGVAANTEADEDNGYVVSYVHDAKTGESKFLVTDA 378
+ E G+ PC + + AA ED+GYV+++VHD + G S+ LV +A
Sbjct: 441 ELTKFEYGEGRFGGEPCFVPMDP-----AAAHPRGEDDGYVLTFVHDERAGTSELLVVNA 495
Query: 379 KSPHLDIEAVVKSTQSVPTGSHGLFVREIEL 409
+ +EA V+ VP G HG F+ EL
Sbjct: 496 AD--MRLEATVQLPSRVPFGFHGTFITGQEL 524
>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 = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 38/143 (26%), Positives = 64/143 (44%), Gaps = 14/143 (9%)
Query: 120 HLFDGDAMLHCIRI-SQGQATFCSRCVKTYKYTIENTHELLSLQLVF-SQANLISINNGF 177
H FDGD M+ + G+ F S+ V+T Y E + + VF SQ + F
Sbjct: 67 HPFDGDGMVTAFKFPGDGRVHFQSKFVRTQGYVEEQKAGKMIYRGVFGSQPAGGWLKTIF 126
Query: 178 GL-----ANASLSFLGDHLFAICEGDLPYAVRLTSNGDTDTKTLGRHDFD--VKSGMNMT 230
L AN ++++ GD L A+ EG P+ + ++ T+G D + G ++
Sbjct: 127 DLRLKNIANTNITYWGDRLLALWEGGQPHRLE-----PSNLATIGLDDLGGILAEGQPLS 181
Query: 231 AHPKKRPCNRRNVCFPLWSNTSV 253
AHP+ P + + P + S+
Sbjct: 182 AHPRIDPASTFDGGQPCYVTFSI 204
Score = 28.9 bits (63), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 6/64 (9%)
Query: 342 RSGGVAANTEADEDNGYVVSYVHDAKTGESKFLVTDAKSPHLDIEAVVKSTQSVPTGSHG 401
R GGVA ED+G+++ ++ A S+ ++ DA+ A +K +P HG
Sbjct: 432 RPGGVA------EDDGWLLCLIYKADLHRSELVILDAQDITAPAIATLKLKHHIPYPLHG 485
Query: 402 LFVR 405
+ +
Sbjct: 486 SWAQ 489
>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 = 36.2 bits (82), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 32/83 (38%), Gaps = 16/83 (19%)
Query: 85 PKRALSNNFAPVDELPPTQCQVIQGSLPSCL---------------DEP-YHLFDGDAML 128
P F V+EL + G +P L EP YHLFDG A+L
Sbjct: 8 PAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALL 67
Query: 129 HCIRISQGQATFCSRCVKTYKYT 151
H +G T+ R ++T Y
Sbjct: 68 HKFDFKEGHVTYHRRFIRTDAYV 90
>pdb|1XDW|A Chain A, Nad+-Dependent (R)-2-Hydroxyglutarate Dehydrogenase From
Acidaminococcus Fermentans
Length = 331
Score = 28.9 bits (63), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 9/68 (13%)
Query: 354 EDNGYVVSYVHDAKTGESKFLVTDAKSPHLDIEAVVKSTQSVPTGSHG---------LFV 404
++NG VV+ K + LV A+ +D EAV+++ +S G +G +F
Sbjct: 210 KENGAVVTRDFLKKMKDGAILVNCARGQLVDTEAVIEAVESGKLGGYGCDVLDGEASVFG 269
Query: 405 REIELRKL 412
+++E +KL
Sbjct: 270 KDLEGQKL 277
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 0.135 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,512,269
Number of Sequences: 62578
Number of extensions: 446220
Number of successful extensions: 818
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 806
Number of HSP's gapped (non-prelim): 11
length of query: 420
length of database: 14,973,337
effective HSP length: 101
effective length of query: 319
effective length of database: 8,652,959
effective search space: 2760293921
effective search space used: 2760293921
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: 53 (25.0 bits)