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= psy678
         (60 letters)

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

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



>pdb|3BJC|A Chain A, Crystal Structure Of The Pde5a Catalytic Domain In Complex
           With A Novel Inhibitor
          Length = 878

 Score = 28.9 bits (63), Expect = 0.79,   Method: Compositional matrix adjust.
 Identities = 17/55 (30%), Positives = 31/55 (56%)

Query: 6   SLLKCENAAKLLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLLIDESSS 60
           SLL+ +    LL++   +FEEQ S+E ++ KI     S ++ +   + ++DE  S
Sbjct: 326 SLLENKRNQVLLDLASLIFEEQQSLEVILKKIAATIISFMQVQKCTIFIVDEDCS 380


>pdb|3MF0|A Chain A, Crystal Structure Of Pde5a Gaf Domain (89-518)
 pdb|3MF0|B Chain B, Crystal Structure Of Pde5a Gaf Domain (89-518)
          Length = 432

 Score = 28.5 bits (62), Expect = 0.90,   Method: Compositional matrix adjust.
 Identities = 17/55 (30%), Positives = 31/55 (56%)

Query: 6   SLLKCENAAKLLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLLIDESSS 60
           SLL+ +    LL++   +FEEQ S+E ++ KI     S ++ +   + ++DE  S
Sbjct: 235 SLLENKRNQVLLDLASLIFEEQQSLEVILKKIAATIISFMQVQKCTIFIVDEDCS 289


>pdb|3LFV|A Chain A, Crystal Structure Of Unliganded Pde5a Gaf Domain
 pdb|3LFV|B Chain B, Crystal Structure Of Unliganded Pde5a Gaf Domain
          Length = 431

 Score = 28.5 bits (62), Expect = 0.93,   Method: Compositional matrix adjust.
 Identities = 17/55 (30%), Positives = 31/55 (56%)

Query: 6   SLLKCENAAKLLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLLIDESSS 60
           SLL+ +    LL++   +FEEQ S+E ++ KI     S ++ +   + ++DE  S
Sbjct: 234 SLLENKRNQVLLDLASLIFEEQQSLEVILKKIAATIISFMQVQKCTIFIVDEDCS 288


>pdb|3HCY|A Chain A, The Crystal Structure Of The Domain Of Putative
          Two-component Sensor Histidine Kinase Protein From
          Sinorhizobium Meliloti 1021
 pdb|3HCY|B Chain B, The Crystal Structure Of The Domain Of Putative
          Two-component Sensor Histidine Kinase Protein From
          Sinorhizobium Meliloti 1021
          Length = 151

 Score = 27.7 bits (60), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 11/33 (33%), Positives = 19/33 (57%)

Query: 28 TSIEQVVVKIMQRAQSLLKCENAAVLLIDESSS 60
           +IE+V    +   Q  L C+ A++LL DE+ +
Sbjct: 2  NAIEEVYEATLDAIQGALNCDRASILLFDEAGT 34


>pdb|3IBJ|A Chain A, X-Ray Structure Of Pde2a
 pdb|3IBJ|B Chain B, X-Ray Structure Of Pde2a
          Length = 691

 Score = 25.8 bits (55), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 17/51 (33%), Positives = 30/51 (58%), Gaps = 1/51 (1%)

Query: 8   LKCENAAKLLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLLIDES 58
           LKCE  A LL+V  +LF     +  ++ +I+  A++L   E  +V L+D++
Sbjct: 176 LKCECQA-LLQVAKNLFTHLDDVSVLLQEIITEARNLSNAEICSVFLLDQN 225


>pdb|1MC0|A Chain A, Regulatory Segment Of Mouse 3',5'-Cyclic Nucleotide
           Phosphodiesterase 2a, Containing The Gaf A And Gaf B
           Domains
          Length = 368

 Score = 25.4 bits (54), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 17/51 (33%), Positives = 30/51 (58%), Gaps = 1/51 (1%)

Query: 8   LKCENAAKLLEVVHDLFEEQTSIEQVVVKIMQRAQSLLKCENAAVLLIDES 58
           LKCE  A LL+V  +LF     +  ++ +I+  A++L   E  +V L+D++
Sbjct: 176 LKCECQA-LLQVAKNLFTHLDDVSVLLQEIITEARNLSNAEICSVFLLDQN 225


  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
   0.316    0.126    0.317 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,059,646
Number of Sequences: 62578
Number of extensions: 20920
Number of successful extensions: 112
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 104
Number of HSP's gapped (non-prelim): 9
length of query: 60
length of database: 14,973,337
effective HSP length: 31
effective length of query: 29
effective length of database: 13,033,419
effective search space: 377969151
effective search space used: 377969151
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)