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= psy6305
         (52 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>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 = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 27/41 (65%), Positives = 29/41 (70%), Gaps = 4/41 (9%)

Query: 14 VHWFRHGLRLHDNPALFEASLNS----VLYPVFIFDGETAG 50
          V WFRHGLRLHDNPAL  A  +      L PVFIFDGE+AG
Sbjct: 8  VIWFRHGLRLHDNPALLAALADKDQGIALIPVFIFDGESAG 48


>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 = 43.9 bits (102), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 20/31 (64%), Positives = 23/31 (74%), Gaps = 1/31 (3%)

Query: 16 WFRHGLRLHDNPALFEASLNS-VLYPVFIFD 45
          WFR GLR+HDNPAL  AS  S  +YPVF+ D
Sbjct: 10 WFRKGLRVHDNPALEYASKGSEFMYPVFVID 40


>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 = 41.2 bits (95), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/45 (46%), Positives = 27/45 (60%), Gaps = 7/45 (15%)

Query: 8  NNKEVAVHWFRHGLRLHDNPAL---FEASLNS----VLYPVFIFD 45
          + +   VHWFR GLRLHDNPAL   F A+  +     + P+FI D
Sbjct: 26 SQRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILD 70


>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 = 41.2 bits (95), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/45 (46%), Positives = 27/45 (60%), Gaps = 7/45 (15%)

Query: 8  NNKEVAVHWFRHGLRLHDNPAL---FEASLNS----VLYPVFIFD 45
          + +   VHWFR GLRLHDNPAL   F A+  +     + P+FI D
Sbjct: 26 SQRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILD 70


>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 = 41.2 bits (95), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/45 (46%), Positives = 27/45 (60%), Gaps = 7/45 (15%)

Query: 8  NNKEVAVHWFRHGLRLHDNPAL---FEASLNS----VLYPVFIFD 45
          + +   VHWFR GLRLHDNPAL   F A+  +     + P+FI D
Sbjct: 26 SQRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILD 70


>pdb|2VTB|B Chain B, Structure Of Cryptochrome 3 - Dna Complex
          Length = 525

 Score = 33.9 bits (76), Expect = 0.025,   Method: Compositional matrix adjust.
 Identities = 16/39 (41%), Positives = 24/39 (61%), Gaps = 1/39 (2%)

Query: 8  NNKEVAVHWFRHGLRLHDNPALFEA-SLNSVLYPVFIFD 45
            K V + WFR+ LR+ DN AL++A S +  + PV+  D
Sbjct: 38 KGKGVTILWFRNDLRVLDNDALYKAWSSSDTILPVYCLD 76


>pdb|2IJG|X Chain X, Crystal Structure Of Cryptochrome 3 From Arabidopsis
          Thaliana
 pdb|2VTB|A Chain A, Structure Of Cryptochrome 3 - Dna Complex
 pdb|2VTB|C Chain C, Structure Of Cryptochrome 3 - Dna Complex
 pdb|2VTB|D Chain D, Structure Of Cryptochrome 3 - Dna Complex
 pdb|2VTB|E Chain E, Structure Of Cryptochrome 3 - Dna Complex
 pdb|2VTB|F Chain F, Structure Of Cryptochrome 3 - Dna Complex
          Length = 526

 Score = 33.1 bits (74), Expect = 0.041,   Method: Composition-based stats.
 Identities = 16/37 (43%), Positives = 24/37 (64%), Gaps = 1/37 (2%)

Query: 10 KEVAVHWFRHGLRLHDNPALFEA-SLNSVLYPVFIFD 45
          K V + WFR+ LR+ DN AL++A S +  + PV+  D
Sbjct: 40 KGVTILWFRNDLRVLDNDALYKAWSSSDTILPVYCLD 76


>pdb|2J4D|A Chain A, Cryptochrome 3 From Arabidopsis Thaliana
 pdb|2J4D|B Chain B, Cryptochrome 3 From Arabidopsis Thaliana
          Length = 525

 Score = 33.1 bits (74), Expect = 0.042,   Method: Composition-based stats.
 Identities = 16/37 (43%), Positives = 24/37 (64%), Gaps = 1/37 (2%)

Query: 10 KEVAVHWFRHGLRLHDNPALFEA-SLNSVLYPVFIFD 45
          K V + WFR+ LR+ DN AL++A S +  + PV+  D
Sbjct: 39 KGVTILWFRNDLRVLDNDALYKAWSSSDTILPVYCLD 75


>pdb|1DNP|A Chain A, Structure Of Deoxyribodipyrimidine Photolyase
 pdb|1DNP|B Chain B, Structure Of Deoxyribodipyrimidine Photolyase
          Length = 471

 Score = 31.2 bits (69), Expect = 0.14,   Method: Composition-based stats.
 Identities = 14/21 (66%), Positives = 14/21 (66%)

Query: 16 WFRHGLRLHDNPALFEASLNS 36
          WFR  LRLHDN AL  A  NS
Sbjct: 6  WFRQDLRLHDNLALAAACRNS 26


>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 = 30.4 bits (67), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 14/37 (37%), Positives = 20/37 (54%)

Query: 14 VHWFRHGLRLHDNPALFEASLNSVLYPVFIFDGETAG 50
          + WFR  LR+ DNPAL  A     +  +F++  E  G
Sbjct: 15 IVWFRRDLRVEDNPALAAAVRAGPVIALFVWAPEEEG 51


>pdb|1IQR|A Chain A, Crystal Structure Of Dna Photolyase From Thermus
          Thermophilus
 pdb|1IQU|A Chain A, Crystal Structure Of Photolyase-Thymine Complex
 pdb|2J07|A Chain A, Thermus Dna Photolyase With 8-Hdf Antenna Chromophore
 pdb|2J08|A Chain A, Thermus Dna Photolyase With 8-Iod-Riboflavin Antenna
          Chromophore
 pdb|2J09|A Chain A, Thermus Dna Photolyase With Fmn Antenna Chromophore
          Length = 420

 Score = 28.9 bits (63), Expect = 0.75,   Method: Compositional matrix adjust.
 Identities = 13/30 (43%), Positives = 17/30 (56%)

Query: 16 WFRHGLRLHDNPALFEASLNSVLYPVFIFD 45
          W R  LRLHD+PAL EA     +  + + D
Sbjct: 7  WHRGDLRLHDHPALLEALARGPVVGLVVLD 36


>pdb|1Z01|A Chain A, 2-Oxoquinoline 8-Monooxygenase Component: Active Site
           Modulation By Rieske-[2fe-2s] Center OxidationREDUCTION
 pdb|1Z01|B Chain B, 2-Oxoquinoline 8-Monooxygenase Component: Active Site
           Modulation By Rieske-[2fe-2s] Center OxidationREDUCTION
 pdb|1Z01|C Chain C, 2-Oxoquinoline 8-Monooxygenase Component: Active Site
           Modulation By Rieske-[2fe-2s] Center OxidationREDUCTION
 pdb|1Z01|D Chain D, 2-Oxoquinoline 8-Monooxygenase Component: Active Site
           Modulation By Rieske-[2fe-2s] Center OxidationREDUCTION
 pdb|1Z01|E Chain E, 2-Oxoquinoline 8-Monooxygenase Component: Active Site
           Modulation By Rieske-[2fe-2s] Center OxidationREDUCTION
 pdb|1Z01|F Chain F, 2-Oxoquinoline 8-Monooxygenase Component: Active Site
           Modulation By Rieske-[2fe-2s] Center OxidationREDUCTION
 pdb|1Z02|A Chain A, 2-Oxoquinoline 8-Monooxygenase Component: Active Site
           Modulation By Rieske-[2fe-2s] Center OxidationREDUCTION
 pdb|1Z02|B Chain B, 2-Oxoquinoline 8-Monooxygenase Component: Active Site
           Modulation By Rieske-[2fe-2s] Center OxidationREDUCTION
 pdb|1Z02|C Chain C, 2-Oxoquinoline 8-Monooxygenase Component: Active Site
           Modulation By Rieske-[2fe-2s] Center OxidationREDUCTION
 pdb|1Z02|D Chain D, 2-Oxoquinoline 8-Monooxygenase Component: Active Site
           Modulation By Rieske-[2fe-2s] Center OxidationREDUCTION
 pdb|1Z02|E Chain E, 2-Oxoquinoline 8-Monooxygenase Component: Active Site
           Modulation By Rieske-[2fe-2s] Center OxidationREDUCTION
 pdb|1Z02|F Chain F, 2-Oxoquinoline 8-Monooxygenase Component: Active Site
           Modulation By Rieske-[2fe-2s] Center OxidationREDUCTION
 pdb|1Z03|A Chain A, 2-Oxoquinoline 8-Monooxygenase Component: Active Site
           Modulation By Rieske-[2fe-2s] Center OxidationREDUCTION
 pdb|1Z03|B Chain B, 2-Oxoquinoline 8-Monooxygenase Component: Active Site
           Modulation By Rieske-[2fe-2s] Center OxidationREDUCTION
 pdb|1Z03|C Chain C, 2-Oxoquinoline 8-Monooxygenase Component: Active Site
           Modulation By Rieske-[2fe-2s] Center OxidationREDUCTION
 pdb|1Z03|D Chain D, 2-Oxoquinoline 8-Monooxygenase Component: Active Site
           Modulation By Rieske-[2fe-2s] Center OxidationREDUCTION
 pdb|1Z03|E Chain E, 2-Oxoquinoline 8-Monooxygenase Component: Active Site
           Modulation By Rieske-[2fe-2s] Center OxidationREDUCTION
 pdb|1Z03|F Chain F, 2-Oxoquinoline 8-Monooxygenase Component: Active Site
           Modulation By Rieske-[2fe-2s] Center OxidationREDUCTION
          Length = 446

 Score = 26.6 bits (57), Expect = 4.0,   Method: Composition-based stats.
 Identities = 14/32 (43%), Positives = 16/32 (50%)

Query: 20  GLRLHDNPALFEASLNSVLYPVFIFDGETAGL 51
           G+RL + P  F  S  S  Y  F FD ET  L
Sbjct: 88  GVRLSEKPTCFTKSTISCWYHGFTFDLETGKL 119


>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 = 25.8 bits (55), Expect = 6.2,   Method: Composition-based stats.
 Identities = 10/17 (58%), Positives = 12/17 (70%)

Query: 16 WFRHGLRLHDNPALFEA 32
          WFR+ LRLHD+  L  A
Sbjct: 11 WFRNDLRLHDHEPLHRA 27


  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
   0.322    0.139    0.447 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,682,541
Number of Sequences: 62578
Number of extensions: 47047
Number of successful extensions: 95
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 81
Number of HSP's gapped (non-prelim): 13
length of query: 52
length of database: 14,973,337
effective HSP length: 24
effective length of query: 28
effective length of database: 13,471,465
effective search space: 377201020
effective search space used: 377201020
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)