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= 010461
(510 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 = 150/513 (29%), Positives = 236/513 (46%), Gaps = 61/513 (11%)
Query: 43 VEGEIPSWLNGTYLRNGPGVWHIGEFNFGHLFDGYAMLVKVHFEKNGRLIAGHRQIETEA 102
V G IP WL G+ LR GPG++ +G F HLFDG A+L K F K G + R I T+A
Sbjct: 30 VTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDF-KEGHVTYHRRFIRTDA 88
Query: 103 YKAAKKNKKLCYREFSVSPKPDNFLAYVGELAKLFSGASLTDNANNGIYKLGDGRIICLT 162
Y A K++ EF PD F G +TDNA IY +G+ C T
Sbjct: 89 YVRAMTEKRIVITEFGTCAFPDPCKNIFSRFFSYFRGVEVTDNALVNIYPVGEDYYAC-T 147
Query: 163 ETQKGSVIVDPDTLDTLGKFEYSDPLGGFIQSSHPIVTDDEFLTLLPDLLNP----GYLV 218
ET + V+P+TL+T+ + + + + ++HP + +D + + + Y +
Sbjct: 148 ETNFITK-VNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFGKNFSIAYNI 206
Query: 219 VRMEPGTNERK-------VIGRVNCRGGPAPGWVHSFTMTEHYVVVPEMPLQYSVQSLLK 271
V++ P +++ ++ + C P +VHSF +T +Y+V E P++ ++ L
Sbjct: 207 VKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLS 266
Query: 272 A----EPSALYQFEWRPERKAFLHVVCKASGK-IAASVEVPLYMVFHFINAYEEKDKDGR 326
+ + + FE +LH+ K K I + +FH IN YE+ +
Sbjct: 267 SWSLWGANYMDCFESNETMGVWLHIADKKRKKYINNKYRTSPFNLFHHINTYEDHE---- 322
Query: 327 VIAVIADCCEHNADTTIIETLSLKNLRSFHGQDVLPDAR------VGRFTIPF--DGSQF 378
+I D C + L L NLR + ++V +AR V R+ +P D +
Sbjct: 323 --FLIVDLCCWKGFEFVYNYLYLANLRE-NWEEVKKNARKAPQPEVRRYVLPLNIDKADT 379
Query: 379 GKL----------------ETV-MDPEEHGRG----VDMCSIN-PAYLGKKYRYAYAIGA 416
GK ET+ ++PE G + IN Y GK Y YAY +G
Sbjct: 380 GKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLGL 439
Query: 417 KRPCNFPNSLTKLDLVKQKAKNWCEEGIVPSEPLFVARPGATDEDDGVVISMISEKNGG- 475
P+ L KL++ ++ W E PSEP+FV+ P A +EDDGVV+S++ G
Sbjct: 440 NH--FVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQ 497
Query: 476 --AYVVLLDGSTFEEIARARFPFGLPYGFHGCW 506
AY+++L+ E+ARA +P FHG +
Sbjct: 498 KPAYLLILNAKDLSEVARAEVEINIPVTFHGLF 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 = 122 bits (306), Expect = 4e-28, Method: Compositional matrix adjust.
Identities = 135/517 (26%), Positives = 223/517 (43%), Gaps = 54/517 (10%)
Query: 11 PASVPERESCAEHRNHVAWTSVKQERWEGELV-VEGEIPSWLNGTYLRNGPGVWHIGEFN 69
P S P + S + + S QE W+ + VEG IP L GT RNGPG+ IG+
Sbjct: 6 PTSSPSQRSYSPQDWLRGYQSQPQE-WDYWVEDVEGSIPPDLQGTLYRNGPGLLEIGDRP 64
Query: 70 FGHLFDGYAMLVKVHFEKNGRLIAGHRQIETEAYKAAKKNKKLCYREFSVSPKPDNFLAY 129
H FDG M+ F +GR+ + + T+ Y +K K+ YR S +L
Sbjct: 65 LKHPFDGDGMVTAFKFPGDGRVHFQSKFVRTQGYVEEQKAGKMIYRGVFGSQPAGGWLKT 124
Query: 130 VGELAKLFSGASLTDNANNGIYKLGDGRIICLTETQKGSVIVDPDTLDTLGKFEYSDPLG 189
+ +L L + AN I GD R++ L E + + +P L T+G D LG
Sbjct: 125 IFDL-------RLKNIANTNITYWGD-RLLALWEGGQPHRL-EPSNLATIGL----DDLG 171
Query: 190 GFIQSSHPIVTD---DEFLTLLPDLLNPGYLVVRMEPGTNERKVIGRVNCRGG------- 239
G + P+ D T D P Y+ ++ + + ++ +G
Sbjct: 172 GILAEGQPLSAHPRIDPASTF--DGGQPCYVTFSIKSSLSSTLTLLELDPQGKLLRQKTE 229
Query: 240 --PAPGWVHSFTMTEHYVVVPEMPLQYSVQSLLKAEPSALYQFEWRPERKAFLHVVCKAS 297
P ++H F +T HY + + + + L A ++ P++ A + +V +
Sbjct: 230 TFPGFAFIHDFAITPHYAIFLQNNVTLNGLPYLFGLRGAGECVQFHPDKPAQIILVPRDG 289
Query: 298 GKIAASVEVPLYMVFHFINAYEEKDKDGRVIAVIADCCEHNADTTIIETLSLKNLRSFHG 357
G+I + V VFH NA+EE K +I D +N ++ + + + RS +
Sbjct: 290 GEI-KRIPVQAGFVFHHANAFEENGK------IILDSICYN---SLPQVDTDGDFRSTNF 339
Query: 358 QDVLPDARVGRFTIPFDGSQFGKLETVMDPEEHGRGVDMCSINPAYLGKKYRYAYAIGAK 417
++ P ++ RFTI + K V R + ++P +G+ YRY Y A
Sbjct: 340 DNLDP-GQLWRFTIDPAAATVEKQLMV------SRCCEFPVVHPQQVGRPYRYVYMGAAH 392
Query: 418 RPC-NFP-NSLTKLDLVK--QKAKNWCEEGIVPSEPLFVARPGATDEDDGVVISMISEKN 473
N P ++ K+DL + +++ G EP+FV RPG EDDG ++ +I + +
Sbjct: 393 HSTGNAPLQAILKVDLESGTETLRSFAPHGFA-GEPIFVPRPGGVAEDDGWLLCLIYKAD 451
Query: 474 -GGAYVVLLDGS--TFEEIARARFPFGLPYGFHGCWV 507
+ +V+LD T IA + +PY HG W
Sbjct: 452 LHRSELVILDAQDITAPAIATLKLKHHIPYPLHGSWA 488
>pdb|3NPE|A Chain A, Structure Of Vp14 In Complex With Oxygen
Length = 529
Score = 90.9 bits (224), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 130/498 (26%), Positives = 212/498 (42%), Gaps = 71/498 (14%)
Query: 40 ELVVEGEIPSWLNGTYLRNG------PGVWHIGEFNFGHLFDGYAMLVKVHFEKNGRLIA 93
EL V G IP +++G Y RNG P H HLFDG M+ +
Sbjct: 63 ELPVSGRIPPFIDGVYARNGANPCFDPVAGH-------HLFDGDGMVHALRIRNGAAESY 115
Query: 94 GHRQIETEAYKAAKKNKKLCYREFSVSPKPDNFL---AYVGELAKLFSGAS--LTD-NAN 147
R ET + + + V PK L + + LA ++ A+ L D +A
Sbjct: 116 ACRFTETARLRQERAIGR------PVFPKAIGELHGHSGIARLALFYARAACGLVDPSAG 169
Query: 148 NGIYKLG----DGRIICLTETQ--KGSVIVDPDTLDTLGKFEYSDPLGGFIQSSHPIV-- 199
G+ G +GR++ ++E + D L+T+G++++ LG + +HP +
Sbjct: 170 TGVANAGLVYFNGRLLAMSEDDLPYHVRVADDGDLETVGRYDFDGQLGCAM-IAHPKLDP 228
Query: 200 TDDEFLTLLPDLLNPGYL-VVRMEP-GTNERKVIGRVNCRGGPAPGWVHSFTMTEHYVVV 257
E L D++ YL P GT V + P +H F +TE+ VVV
Sbjct: 229 ATGELHALSYDVIKRPYLKYFYFRPDGTKSDDVEIPLE-----QPTMIHDFAITENLVVV 283
Query: 258 PEMPLQYSVQSLLKAEPSALYQFEWRPERKAFLHVVCK--ASGKIAASVEVPLYMVFHFI 315
P+ + + +Q +L+ + + + V+ K A A V+VP FH
Sbjct: 284 PDHQVVFKLQEMLRGGSPVVLD----AAKTSRFGVLPKHAADASEMAWVDVPDCFCFHLW 339
Query: 316 NAYEEKDKDGRVIAVIADCCEHNADTTIIETLSLKNLRSFHGQDVLPDARVGRFTIPFDG 375
NA+E+ + G V V+ C AD+ E S + L S + L DAR GR T
Sbjct: 340 NAWED-EATGEV--VVIGSCMTPADSIFNE--SDERLESVLTEIRL-DARTGRST----- 388
Query: 376 SQFGKLETVMDPEEHGRGVDMCSINPAYLGKKYRYAYAIGAKRPCNFPNSLTKLDL-VKQ 434
V+ P + +++ +N LG++ RYAY + P + K+DL +
Sbjct: 389 -----RRAVLPPSQQ-VNLEVGMVNRNLLGRETRYAY-LAVAEPWPKVSGFAKVDLSTGE 441
Query: 435 KAKNWCEEGIVPSEPLFV-ARPGATD---EDDGVVISMI-SEKNGGAYVVLLDGSTFEEI 489
K EG EP FV P A EDDG V++ + E+ G + +++++ +
Sbjct: 442 LTKFEYGEGRFGGEPCFVPMDPAAAHPRGEDDGYVLTFVHDERAGTSELLVVNAADMRLE 501
Query: 490 ARARFPFGLPYGFHGCWV 507
A + P +P+GFHG ++
Sbjct: 502 ATVQLPSRVPFGFHGTFI 519
>pdb|2AAF|A Chain A, Structure Of H278a Arginine Deiminase With L-Arginine
Forming A S- Alkylthiouronium Reaction Intermediate
pdb|2AAF|B Chain B, Structure Of H278a Arginine Deiminase With L-Arginine
Forming A S- Alkylthiouronium Reaction Intermediate
pdb|2AAF|C Chain C, Structure Of H278a Arginine Deiminase With L-Arginine
Forming A S- Alkylthiouronium Reaction Intermediate
pdb|2AAF|D Chain D, Structure Of H278a Arginine Deiminase With L-Arginine
Forming A S- Alkylthiouronium Reaction Intermediate
Length = 418
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 2/76 (2%)
Query: 224 GTNERKVI-GRVNCRGGPAPGWVHSFTMTEHYVVVPEMPLQYSVQSLLKAEPSALYQFEW 282
G ER ++ G R A V SF + V PE+ ++ V L+ +PS+ Y
Sbjct: 260 GAAERVIVAGLPKSRAAMALDTVFSFCDRDLVTVFPEV-VKEIVPFSLRPDPSSPYGMNI 318
Query: 283 RPERKAFLHVVCKASG 298
R E K FL VV ++ G
Sbjct: 319 RREEKTFLEVVAESLG 334
>pdb|3CMG|A Chain A, Crystal Structure Of Putative Beta-Galactosidase From
Bacteroides Fragilis
Length = 667
Score = 30.0 bits (66), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 39/85 (45%), Gaps = 10/85 (11%)
Query: 165 QKGSVIVDP------DTLDTLGKFEYSDPLGGFIQSSHPIVTDDEFLTLLPDLLNPGYLV 218
+K SV+V D + +G F + GG + H ++TD+ ++ L D +PG +
Sbjct: 110 EKNSVLVRANNGEQLDIMPLVGDFNF---YGGIYRDVHLLITDETCISPL-DYASPGVYL 165
Query: 219 VRMEPGTNERKVIGRVNCRGGPAPG 243
V+ E KV +VN A G
Sbjct: 166 VQEVVSPQEAKVCAKVNLSNRAADG 190
>pdb|2ABR|A Chain A, Structure Of D280a Arginine Deiminase With L-Arginine
Forming A S-Alkylthiouronium Reaction Intermediate
pdb|2ABR|B Chain B, Structure Of D280a Arginine Deiminase With L-Arginine
Forming A S-Alkylthiouronium Reaction Intermediate
pdb|2ABR|C Chain C, Structure Of D280a Arginine Deiminase With L-Arginine
Forming A S-Alkylthiouronium Reaction Intermediate
pdb|2ABR|D Chain D, Structure Of D280a Arginine Deiminase With L-Arginine
Forming A S-Alkylthiouronium Reaction Intermediate
Length = 418
Score = 29.6 bits (65), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 2/76 (2%)
Query: 224 GTNERKVI-GRVNCRGGPAPGWVHSFTMTEHYVVVPEMPLQYSVQSLLKAEPSALYQFEW 282
G ER ++ G R V SF + V PE+ ++ V L+ +PS+ Y
Sbjct: 260 GAAERVIVAGLPKSRAAMHLATVFSFCDRDLVTVFPEV-VKEIVPFSLRPDPSSPYGMNI 318
Query: 283 RPERKAFLHVVCKASG 298
R E K FL VV ++ G
Sbjct: 319 RREEKTFLEVVAESLG 334
>pdb|3H2I|A Chain A, Crystal Structure Of N228w Mutant Of The Rice Cell Wall
Degrading Esterase Lipa From Xanthomonas Oryzae
Length = 397
Score = 29.6 bits (65), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 27/60 (45%), Gaps = 2/60 (3%)
Query: 38 EGELVVEGEI--PSWLNGTYLRNGPGVWHIGEFNFGHLFDGYAMLVKVHFEKNGRLIAGH 95
E LV I P L T+L + G +GE+ FG L YA++ H KN L G
Sbjct: 196 EFHLVASAPISGPYALEQTFLDSWSGSNAVGEWTFGILLGSYAIVAMQHTYKNIYLEPGQ 255
>pdb|2A9G|A Chain A, Structure Of C406a Arginine Deiminase In Complex With
L-Arginine
pdb|2A9G|B Chain B, Structure Of C406a Arginine Deiminase In Complex With
L-Arginine
pdb|2A9G|C Chain C, Structure Of C406a Arginine Deiminase In Complex With
L-Arginine
pdb|2A9G|D Chain D, Structure Of C406a Arginine Deiminase In Complex With
L-Arginine
Length = 418
Score = 29.3 bits (64), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 2/76 (2%)
Query: 224 GTNERKVI-GRVNCRGGPAPGWVHSFTMTEHYVVVPEMPLQYSVQSLLKAEPSALYQFEW 282
G ER ++ G R V SF + V PE+ ++ V L+ +PS+ Y
Sbjct: 260 GAAERVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEV-VKEIVPFSLRPDPSSPYGMNI 318
Query: 283 RPERKAFLHVVCKASG 298
R E K FL VV ++ G
Sbjct: 319 RREEKTFLEVVAESLG 334
>pdb|2ACI|A Chain A, Structure Of D166a Arginine Deiminase
pdb|2ACI|B Chain B, Structure Of D166a Arginine Deiminase
pdb|2ACI|C Chain C, Structure Of D166a Arginine Deiminase
pdb|2ACI|D Chain D, Structure Of D166a Arginine Deiminase
Length = 418
Score = 28.9 bits (63), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 2/76 (2%)
Query: 224 GTNERKVI-GRVNCRGGPAPGWVHSFTMTEHYVVVPEMPLQYSVQSLLKAEPSALYQFEW 282
G ER ++ G R V SF + V PE+ ++ V L+ +PS+ Y
Sbjct: 260 GAAERVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEV-VKEIVPFSLRPDPSSPYGMNI 318
Query: 283 RPERKAFLHVVCKASG 298
R E K FL VV ++ G
Sbjct: 319 RREEKTFLEVVAESLG 334
>pdb|1RXX|A Chain A, Structure Of Arginine Deiminase
pdb|1RXX|B Chain B, Structure Of Arginine Deiminase
pdb|1RXX|C Chain C, Structure Of Arginine Deiminase
pdb|1RXX|D Chain D, Structure Of Arginine Deiminase
Length = 421
Score = 28.9 bits (63), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 2/76 (2%)
Query: 224 GTNERKVI-GRVNCRGGPAPGWVHSFTMTEHYVVVPEMPLQYSVQSLLKAEPSALYQFEW 282
G ER ++ G R V SF + V PE+ ++ V L+ +PS+ Y
Sbjct: 263 GAAERVIVAGLPKSRAAXHLDTVFSFCDRDLVTVFPEV-VKEIVPFSLRPDPSSPYGXNI 321
Query: 283 RPERKAFLHVVCKASG 298
R E K FL VV ++ G
Sbjct: 322 RREEKTFLEVVAESLG 337
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
0.319 0.138 0.428
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,239,935
Number of Sequences: 62578
Number of extensions: 793201
Number of successful extensions: 1442
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1423
Number of HSP's gapped (non-prelim): 11
length of query: 510
length of database: 14,973,337
effective HSP length: 103
effective length of query: 407
effective length of database: 8,527,803
effective search space: 3470815821
effective search space used: 3470815821
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)