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= 044992
(597 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 = 303 bits (775), Expect = 2e-82, Method: Compositional matrix adjust.
Identities = 179/507 (35%), Positives = 269/507 (53%), Gaps = 25/507 (4%)
Query: 91 NKLIKPKLQAQPLSLDPSRAFSNNLAPVDELHPTQCQVTQGSLPSCLEGAYIRNGPNPQY 150
N L +P P + DP+ + N APV E P G +P ++G Y RNG NP +
Sbjct: 30 NVLERP--HGLPSTADPAVQIAGNFAPVGERPPVHELPVSGRIPPFIDGVYARNGANPCF 87
Query: 151 PPRSEPYSPFDGDGMLHCIKISQGQA-TFCSRYVKTYKYTIENTXXXXXXXXXXXXXXXX 209
P + + FDGDGM+H ++I G A ++ R+ +T + E
Sbjct: 88 DPVAG-HHLFDGDGMVHALRIRNGAAESYACRFTETARLRQERAIGRPVFPKAIGELHGH 146
Query: 210 LAFLTRAGVLAARVLTGQLSINSGFGLANTSLAFLGNRLLALYEGDLPYAVRLTSNGDIE 269
+ + R + AR G + ++G G+AN L + RLLA+ E DLPY VR+ +GD+E
Sbjct: 147 -SGIARLALFYARAACGLVDPSAGTGVANAGLVYFNGRLLAMSEDDLPYHVRVADDGDLE 205
Query: 270 TLGRCDLDGKLVMNMTAHPKKDPETGEMFAFRYSPMP-PFVTYFWFDANGEKQPDVHIKM 328
T+GR D DG+L M AHPK DP TGE+ A Y + P++ YF+F +G K DV I
Sbjct: 206 TVGRYDFDGQLGCAMIAHPKLDPATGELHALSYDVIKRPYLKYFYFRPDGTKSDDVEIP- 264
Query: 329 PGQWLRHPPLMHDFAITKRYAIFVDTQVQAYGMEMILRREPLLHSDPTKVSRIGVMPRYA 388
L P ++HDFAIT+ + D QV EM+ P++ D K SR GV+P++A
Sbjct: 265 ----LEQPTMIHDFAITENLVVVPDHQVVFKLQEMLRGGSPVV-LDAAKTSRFGVLPKHA 319
Query: 389 KNSSQMRWFDAPGLNNIHAVNAWDEEDGNVIVMVAPNILSVEQVF-ERMELIHCLMEKVR 447
++S+M W D P H NAW++E +V++ + + +F E E + ++ ++R
Sbjct: 320 ADASEMAWVDVPDCFCFHLWNAWEDEATGEVVVIGSCMTPADSIFNESDERLESVLTEIR 379
Query: 448 IDLRTGVVSRH----PISARNLDMAVINPGYVAKKNRYVYAAVGDPMPKMTGLVKLDLTK 503
+D RTG +R P NL++ ++N + ++ RY Y AV +P PK++G K+DL+
Sbjct: 380 LDARTGRSTRRAVLPPSQQVNLEVGMVNRNLLGRETRYAYLAVAEPWPKVSGFAKVDLST 439
Query: 504 GERQECTVATRIYGPDCYGGEP-FFXXXXXXXXXXXXXXGYILSYVHDEKAGESKFLVMD 562
GE + YG +GGEP F GY+L++VHDE+AG S+ LV++
Sbjct: 440 GELTKFE-----YGEGRFGGEPCFVPMDPAAAHPRGEDDGYVLTFVHDERAGTSELLVVN 494
Query: 563 AKSPHLDIVAEVKLPQRVPAGFHGLFV 589
A L+ A V+LP RVP GFHG F+
Sbjct: 495 AADMRLE--ATVQLPSRVPFGFHGTFI 519
>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 = 110 bits (276), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 116/487 (23%), Positives = 197/487 (40%), Gaps = 60/487 (12%)
Query: 129 TQGSLPSCLEGAYIRNGPNPQYPPRSEPYSPFDGDGMLHCIKI-SQGQATFCSRYVKTYK 187
+GS+P L+G RNGP PFDGDGM+ K G+ F S++V+T
Sbjct: 38 VEGSIPPDLQGTLYRNGPGLLEIGDRPLKHPFDGDGMVTAFKFPGDGRVHFQSKFVRTQG 97
Query: 188 YTIENTXXXXXXXXXXXXXXXXLAFLTRAGVLAARVLTGQLSINSGFGL---ANTSLAFL 244
Y E + GV ++ G L L ANT++ +
Sbjct: 98 YVEEQKAGK----------------MIYRGVFGSQPAGGWLKTIFDLRLKNIANTNITYW 141
Query: 245 GNRLLALYEGDLPYAVRLTSNGDIETLGRCDLDGKLVMN--MTAHPKKDPETGEMFAFRY 302
G+RLLAL+EG P+ + + ++ T+G DL G L ++AHP+ DP + F
Sbjct: 142 GDRLLALWEGGQPHRLEPS---NLATIGLDDLGGILAEGQPLSAHPRIDPAS----TFD- 193
Query: 303 SPMPPFVTYFWFDANGEKQPDVHIKMPGQWLRHP-------PLMHDFAITKRYAIFVDTQ 355
P +VT+ + + + G+ LR +HDFAIT YAIF+
Sbjct: 194 GGQPCYVTFSIKSSLSSTLTLLELDPQGKLLRQKTETFPGFAFIHDFAITPHYAIFLQNN 253
Query: 356 VQAYGMEMILRRE---PLLHSDPTKVSRIGVMPRYAKNSSQMRWFDAPGLNNIHAVNAWD 412
V G+ + + P K ++I ++PR + +++ H NA++
Sbjct: 254 VTLNGLPYLFGLRGAGECVQFHPDKPAQIILVPR---DGGEIKRIPVQAGFVFHHANAFE 310
Query: 413 EEDGNVIVMVAPNIL---SVEQVFERMELIHC---LMEKVRIDLRTGVVSRHPISARNLD 466
E ++ + N L + F + + + ID V + + +R +
Sbjct: 311 ENGKIILDSICYNSLPQVDTDGDFRSTNFDNLDPGQLWRFTIDPAAATVEKQLMVSRCCE 370
Query: 467 MAVINPGYVAKKNRYVYAAVGDPMPK---MTGLVKLDLTKGERQECTVATRIYGPDCYGG 523
V++P V + RYVY + ++K+DL G T R + P + G
Sbjct: 371 FPVVHPQQVGRPYRYVYMGAAHHSTGNAPLQAILKVDLESG-----TETLRSFAPHGFAG 425
Query: 524 EPFFXXXXXXXXXXXXXXGYILSYVHDEKAGESKFLVMDAKSPHLDIVAEVKLPQRVPAG 583
EP F G++L ++ S+ +++DA+ +A +KL +P
Sbjct: 426 EPIF---VPRPGGVAEDDGWLLCLIYKADLHRSELVILDAQDITAPAIATLKLKHHIPYP 482
Query: 584 FHGLFVR 590
HG + +
Sbjct: 483 LHGSWAQ 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 = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 65/276 (23%), Positives = 109/276 (39%), Gaps = 50/276 (18%)
Query: 107 PSRAFSNNLAPVDELH-PTQCQVTQGSLPSCLEGAYIRNGPNPQYPPRSEP-YSPFDGDG 164
P+ + V+EL P VT G +P L G+ +R GP + SEP Y FDG
Sbjct: 8 PAGGYKKLFETVEELSSPLTAHVT-GRIPLWLTGSLLRCGPG-LFEVGSEPFYHLFDGQA 65
Query: 165 MLHCIKISQGQATFCSRYVKTYKYTIENTXXXXXXXXXXXXXXXXLAFLTRAGVLA---- 220
+LH +G T+ R+++T Y T +T G A
Sbjct: 66 LLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIV--------------ITEFGTCAFPDP 111
Query: 221 -ARVLTGQLSINSGFGLANTSLAFL---GNRLLALYEGDLPYAVRLTSNGDIETLGRCDL 276
+ + S G + + +L + G A E + V + +ET+ + DL
Sbjct: 112 CKNIFSRFFSYFRGVEVTDNALVNIYPVGEDYYACTETNFITKVNPET---LETIKQVDL 168
Query: 277 DGKLVMN-MTAHPKKDPET---------GEMFAFRYS--PMPPFVTYFWFDANGE---KQ 321
+ +N TAHP + + G+ F+ Y+ +PP A+ E +
Sbjct: 169 CNYVSVNGATAHPHIENDGTVYNIGNCFGKNFSIAYNIVKIPP------LQADKEDPISK 222
Query: 322 PDVHIKMPGQWLRHPPLMHDFAITKRYAIFVDTQVQ 357
++ ++ P P +H F +T Y +FV+T V+
Sbjct: 223 SEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVK 258
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 34/75 (45%), Gaps = 7/75 (9%)
Query: 518 PDCYGGEPFFXXXXXXXXXXXXXXGYILSYVHDEKAGE--SKFLVMDAKSPHLDIVAEVK 575
PD Y EP F G +LS V AG+ + L+++AK L VA +
Sbjct: 463 PDSYPSEPIFVSHPDALEEDD---GVVLSVVVSPGAGQKPAYLLILNAKD--LSEVARAE 517
Query: 576 LPQRVPAGFHGLFVR 590
+ +P FHGLF +
Sbjct: 518 VEINIPVTFHGLFKK 532
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
0.321 0.137 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,917,084
Number of Sequences: 62578
Number of extensions: 631644
Number of successful extensions: 1052
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1031
Number of HSP's gapped (non-prelim): 7
length of query: 597
length of database: 14,973,337
effective HSP length: 104
effective length of query: 493
effective length of database: 8,465,225
effective search space: 4173355925
effective search space used: 4173355925
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: 54 (25.4 bits)