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= 036667
(96 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3FY4|A Chain A, (6-4) Photolyase Crystal Structure
pdb|3FY4|B Chain B, (6-4) Photolyase Crystal Structure
pdb|3FY4|C Chain C, (6-4) Photolyase Crystal Structure
Length = 537
Score = 130 bits (327), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 56/89 (62%), Positives = 79/89 (88%)
Query: 1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQV 60
MPK+YIYEPWTAPL++QT+A CI+G+DYP P+V HDSASKECKRK+GEAYALN+K++G+V
Sbjct: 448 MPKQYIYEPWTAPLSVQTKANCIVGKDYPKPMVLHDSASKECKRKMGEAYALNKKMDGKV 507
Query: 61 SEDDLKNLRRKFEGEENQESGRRQKQKRL 89
E++L++LRRK + +E++ES R ++ +L
Sbjct: 508 DEENLRDLRRKLQKDEHEESKIRNQRPKL 536
>pdb|3CVU|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Ds Dna
With A T-T (6-4) Photolesion
pdb|3CVY|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Repaired
Ds Dna
pdb|2WB2|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Double
Stranded Dna Containing A T(6-4)c Photolesion
pdb|3CVV|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Ds Dna
With A T-T (6-4) Photolesion And F0 Cofactor
pdb|2WQ6|A Chain A, Structure Of The 6-4 Photolyase Of D. Melanogaster In
Complex With The Non-Natural N4-Methyl T(Dewar)c Lesion
pdb|2WQ7|A Chain A, Structure Of The 6-4 Photolyase Of D. Melanogaster In
Complex With The Non-Natural N4-Methyl T(6-4)c Lesion
Length = 543
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 33/55 (60%)
Query: 2 PKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKL 56
P IYEPW A L Q C++G DYP +V H+ KE +++G AY +N+++
Sbjct: 473 PAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKRMGAAYKVNREV 527
>pdb|3CVX|A Chain A, Drosophila Melanogaster (6-4) Photolyase H369m Mutant
Bound To Ds Dna With A T-T (6-4) Photolesion
Length = 543
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 33/55 (60%)
Query: 2 PKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKL 56
P IYEPW A L Q C++G DYP +V H+ KE +++G AY +N+++
Sbjct: 473 PAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKRMGAAYKVNREV 527
>pdb|3CVW|A Chain A, Drosophila Melanogaster (6-4) Photolyase H365n Mutant
Bound To Ds Dna With A T-T (6-4) Photolesion And
Cofactor F0
Length = 543
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 33/55 (60%)
Query: 2 PKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKL 56
P IYEPW A L Q C++G DYP +V H+ KE +++G AY +N+++
Sbjct: 473 PAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKRMGAAYKVNREV 527
>pdb|1U3C|A Chain A, Crystal Structure Of The Phr Domain Of Cryptochrome 1 From
Arabidopsis Thaliana
pdb|1U3D|A Chain A, Crystal Structure Of The Phr Domain Of Cryptochrome 1 From
Arabidopsis Thaliana With Amppnp Bound
Length = 509
Score = 39.7 bits (91), Expect = 5e-04, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 27/52 (51%)
Query: 1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYAL 52
+P ++I+ PW AP ++ A +G +YP P+V D A L + + L
Sbjct: 443 LPTDWIHHPWNAPESVLQAAGIELGSNYPLPIVGLDEAKARLHEALSQMWQL 494
>pdb|4GU5|A Chain A, Structure Of Full-Length Drosophila Cryptochrome
pdb|4GU5|B Chain B, Structure Of Full-Length Drosophila Cryptochrome
Length = 539
Score = 36.2 bits (82), Expect = 0.005, Method: Composition-based stats.
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASK 40
+PKE+++EPW Q + +C+IG YP ++ A K
Sbjct: 464 VPKEFVHEPWRMSAEQQEQYECLIGVHYPERIIDLSMAVK 503
>pdb|1NP7|A Chain A, Crystal Structure Analysis Of Synechocystis Sp. Pcc6803
Cryptochrome
pdb|1NP7|B Chain B, Crystal Structure Analysis Of Synechocystis Sp. Pcc6803
Cryptochrome
Length = 489
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKL 46
+P + I++PW T Q + +G DYP P V+ S E +RK+
Sbjct: 438 LPGDKIHQPWLLSATEQKQWGVQLGVDYPRPCVNFHQ-SVEARRKI 482
>pdb|2AUS|C Chain C, Crystal Structure Of The Archaeal Box HACA SRNP NOP10-Cbf5
Complex
pdb|2AUS|A Chain A, Crystal Structure Of The Archaeal Box HACA SRNP NOP10-Cbf5
Complex
Length = 334
Score = 28.5 bits (62), Expect = 0.89, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 22/42 (52%)
Query: 47 GEAYALNQKLNGQVSEDDLKNLRRKFEGEENQESGRRQKQKR 88
G+ Y L+G V ED ++ + ++FEGE Q R KR
Sbjct: 107 GKEYVALMHLHGDVPEDKIRAVMKEFEGEIIQRPPLRSAVKR 148
>pdb|3HJW|A Chain A, Structure Of A Functional Ribonucleoprotein Pseudouridine
Synthase Bound To A Substrate Rna
pdb|3HJY|A Chain A, Structure Of A Functional Ribonucleoprotein Pseudouridine
Synthase Bound To A Substrate Rna
Length = 327
Score = 27.3 bits (59), Expect = 2.0, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 21/42 (50%)
Query: 47 GEAYALNQKLNGQVSEDDLKNLRRKFEGEENQESGRRQKQKR 88
G+ Y L+G V ED + + ++FEGE Q R KR
Sbjct: 100 GKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKR 141
>pdb|2EY4|A Chain A, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex
pdb|2EY4|B Chain B, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex
Length = 333
Score = 27.3 bits (59), Expect = 2.2, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 21/42 (50%)
Query: 47 GEAYALNQKLNGQVSEDDLKNLRRKFEGEENQESGRRQKQKR 88
G+ Y L+G V ED + + ++FEGE Q R KR
Sbjct: 107 GKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKR 148
>pdb|3MQK|A Chain A, Cbf5-Nop10-Gar1 Complex Binding With 17mer Rna Containing
Aca Trinucleotide
Length = 328
Score = 27.3 bits (59), Expect = 2.2, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 21/42 (50%)
Query: 47 GEAYALNQKLNGQVSEDDLKNLRRKFEGEENQESGRRQKQKR 88
G+ Y L+G V ED + + ++FEGE Q R KR
Sbjct: 100 GKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKR 141
>pdb|2RFK|A Chain A, Substrate Rna Positioning In The Archaeal HACA
Ribonucleoprotein Complex
Length = 334
Score = 27.3 bits (59), Expect = 2.4, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 21/42 (50%)
Query: 47 GEAYALNQKLNGQVSEDDLKNLRRKFEGEENQESGRRQKQKR 88
G+ Y L+G V ED + + ++FEGE Q R KR
Sbjct: 103 GKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKR 144
>pdb|3LWO|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
5BRU
pdb|3LWP|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
5BRDU
pdb|3LWQ|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
3MU
pdb|3LWR|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
4SU
pdb|3LWV|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
2'- Deoxyuridine
Length = 340
Score = 26.9 bits (58), Expect = 2.6, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 21/42 (50%)
Query: 47 GEAYALNQKLNGQVSEDDLKNLRRKFEGEENQESGRRQKQKR 88
G+ Y L+G V ED + + ++FEGE Q R KR
Sbjct: 107 GKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKR 148
>pdb|2HVY|A Chain A, Crystal Structure Of An HACA BOX RNP FROM PYROCOCCUS
FURIOSUS
pdb|3HAX|A Chain A, Crystal Structure Of A Substrate-Bound Gar1-Minus HACA RNP
FROM Pyrococcus Furiosus
pdb|3HAY|A Chain A, Crystal Structure Of A Substrate-Bound Full HACA RNP FROM
Pyrococcus Furiosus
Length = 346
Score = 26.9 bits (58), Expect = 2.6, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 21/42 (50%)
Query: 47 GEAYALNQKLNGQVSEDDLKNLRRKFEGEENQESGRRQKQKR 88
G+ Y L+G V ED + + ++FEGE Q R KR
Sbjct: 107 GKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKR 148
>pdb|1IYG|A Chain A, Solution Structure Of Rsgi Ruh-001, A Fis1p-Like And
Cgi- 135 Homologous Domain From A Mouse Cdna
Length = 133
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 56 LNGQVSEDDLKNLRRKFEGEE 76
LN VS +DLKN RKF+ E+
Sbjct: 12 LNELVSVEDLKNFERKFQSEQ 32
>pdb|1DNP|A Chain A, Structure Of Deoxyribodipyrimidine Photolyase
pdb|1DNP|B Chain B, Structure Of Deoxyribodipyrimidine Photolyase
Length = 471
Score = 26.2 bits (56), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 6/38 (15%)
Query: 1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSA 38
+P + ++EPW + K + DYP P+V H A
Sbjct: 425 VPGKVVHEPW------KWAQKAGVTLDYPQPIVEHKEA 456
>pdb|4AMU|A Chain A, Structure Of Ornithine Carbamoyltransferase From
Mycoplasma Penetrans With A P321 Space Group
pdb|4AMU|B Chain B, Structure Of Ornithine Carbamoyltransferase From
Mycoplasma Penetrans With A P321 Space Group
pdb|4AMU|C Chain C, Structure Of Ornithine Carbamoyltransferase From
Mycoplasma Penetrans With A P321 Space Group
pdb|4AMU|D Chain D, Structure Of Ornithine Carbamoyltransferase From
Mycoplasma Penetrans With A P321 Space Group
pdb|4ANF|A Chain A, Structure Of The Ornithine Carbamoyltransferase From
Mycoplasma Penetrans With A P23 Space Group
pdb|4ANF|B Chain B, Structure Of The Ornithine Carbamoyltransferase From
Mycoplasma Penetrans With A P23 Space Group
pdb|4ANF|C Chain C, Structure Of The Ornithine Carbamoyltransferase From
Mycoplasma Penetrans With A P23 Space Group
pdb|4ANF|D Chain D, Structure Of The Ornithine Carbamoyltransferase From
Mycoplasma Penetrans With A P23 Space Group
Length = 365
Score = 26.2 bits (56), Expect = 5.7, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 29 PAPVVSHDSASKECKRKLGEAYALNQKLNGQVSEDDLKNLRRK-FEGEENQ 78
PA H S SKE LG Y + K +V+++ ++L K F+ EN+
Sbjct: 301 PAFHDDHTSFSKEVATTLGAKYPIVAKGEMEVTDEVFQSLHNKAFDQAENR 351
>pdb|1OWL|A Chain A, Structure Of Apophotolyase From Anacystis Nidulans
pdb|1OWM|A Chain A, Data1:dna Photolyase RECEIVED X-Rays Dose 1.2 Exp15
PhotonsMM2
pdb|1OWN|A Chain A, Data3:dna Photolyase RECEIVED X-Rays Dose 4.8 Exp15
PhotonsMM2
pdb|1OWO|A Chain A, Data4:photoreduced Dna Photolyase RECEIVED X-Rays Dose
1.2 Exp15 PhotonsMM2
pdb|1OWP|A Chain A, Data6:photoreduced Dna Pholyase RECEIVED X-Rays Dose 4.8
Exp15 PhotonsMM2
pdb|1QNF|A Chain A, Structure Of Photolyase
Length = 484
Score = 25.4 bits (54), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 7/37 (18%)
Query: 26 RDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQVSE 62
R YPAP+V+H+ K+ K AL +L ++E
Sbjct: 448 RGYPAPIVNHNLRQKQFK-------ALYNQLKAAIAE 477
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
0.313 0.131 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,947,959
Number of Sequences: 62578
Number of extensions: 105135
Number of successful extensions: 213
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 197
Number of HSP's gapped (non-prelim): 22
length of query: 96
length of database: 14,973,337
effective HSP length: 62
effective length of query: 34
effective length of database: 11,093,501
effective search space: 377179034
effective search space used: 377179034
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 45 (21.9 bits)