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= psy11409
         (320 letters)

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

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



>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
           Polyadenylation Element Binding Protein 3
          Length = 114

 Score =  161 bits (408), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 75/92 (81%), Positives = 84/92 (91%)

Query: 63  PHYDHEEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDACIVDED 122
           P  D +EITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ+ESSVQ LIDAC+ ++ 
Sbjct: 18  PDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDG 77

Query: 123 KCYLCVSSPTIKDKPVQIRPWKLTDADFVLDA 154
           K YLCVSSPTIKDKPVQIRPW L+D+DFV+D+
Sbjct: 78  KLYLCVSSPTIKDKPVQIRPWNLSDSDFVMDS 109


>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
           Daz- Associated Protein 1
          Length = 99

 Score = 32.7 bits (73), Expect = 0.25,   Method: Composition-based stats.
 Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 5/57 (8%)

Query: 61  GTPHYDHE-EITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLID 115
           G PH   E E+   F++FG +  V   + AE +    P+G+ F+ F+DE SV Q ++
Sbjct: 17  GIPHNCGETELREYFKKFGVVTEVVMIYDAEKQR---PRGFGFITFEDEQSVDQAVN 70


>pdb|1N8Y|C Chain C, Crystal Structure Of The Extracellular Region Of Rat Her2
          Length = 608

 Score = 29.6 bits (65), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 24/91 (26%), Positives = 42/91 (46%), Gaps = 10/91 (10%)

Query: 119 VDEDKCYLCVSSPTIKDKPVQ----IRPWKLTDADFVLDASMPLDPRKTVFV---GGVPR 171
           + E + Y+ ++   +K  P+Q    +R  +L +  + L      DP+  V     G  P 
Sbjct: 55  IQEVQGYMLIAHNQVKRVPLQRLRIVRGTQLFEDKYALAVLDNRDPQDNVAASTPGRTPE 114

Query: 172 PLKALELAMIMDRLYGGVCYAGIDTDPELKY 202
            L+ L+L  + + L GGV   G   +P+L Y
Sbjct: 115 GLRELQLRSLTEILKGGVLIRG---NPQLCY 142


>pdb|1MHZ|B Chain B, Methane Monooxygenase Hydroxylase
 pdb|1MHY|B Chain B, Methane Monooxygenase Hydroxylase
          Length = 395

 Score = 28.1 bits (61), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 12/34 (35%), Positives = 20/34 (58%)

Query: 284 HSKPGREFHKPLVKEGAYDSLQTRTRVSQTSSEG 317
           H  P R +H P VK+ + ++  T+  ++  SSEG
Sbjct: 101 HRDPARRWHHPYVKDKSEEARYTQRFLAAYSSEG 134


  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    0.141    0.453 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,059,161
Number of Sequences: 62578
Number of extensions: 359346
Number of successful extensions: 556
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 553
Number of HSP's gapped (non-prelim): 5
length of query: 320
length of database: 14,973,337
effective HSP length: 99
effective length of query: 221
effective length of database: 8,778,115
effective search space: 1939963415
effective search space used: 1939963415
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: 51 (24.3 bits)