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= psy11609
         (83 letters)

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

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



>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
          Polyadenylation Binding Protein 3
          Length = 103

 Score = 28.5 bits (62), Expect = 0.97,   Method: Compositional matrix adjust.
 Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 2/41 (4%)

Query: 17 LYHEYKKHGKVSWVKIIGQGGDR--YGLVCFKKADDAEKAI 55
          L   +   G ++  K++ +GG    +G VCF   ++A KA+
Sbjct: 32 LRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV 72


>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
          Length = 104

 Score = 27.3 bits (59), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 5/56 (8%)

Query: 22  KKHGKVSWVKIIGQGGDRYG---LVCFKKADDAEKAILGSHEKHFFGCKI--DVSP 72
           +K+G+V  + +    GD       V F++ +DAEKA++  + + F G  I  ++SP
Sbjct: 49  EKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSP 104


>pdb|3MAH|A Chain A, A Putative C-Terminal Regulatory Domain Of Aspartate
           Kinase From Porphyromonas Gingivalis W83
          Length = 157

 Score = 26.6 bits (57), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 12/34 (35%), Positives = 18/34 (52%)

Query: 30  VKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHF 63
           V+ I  GG  Y +    KA+D +KA++    K F
Sbjct: 117 VRXISYGGSNYNVSVLVKAEDKKKALIALSNKLF 150


>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
          Motif Protein 9
          Length = 103

 Score = 25.8 bits (55), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 2/57 (3%)

Query: 17 LYHEYKKHGKVSWVKII--GQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVS 71
          L   + + GK+  V+II   +G   +G V F+ + DA++A    H     G KI+V+
Sbjct: 32 LRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN 88


>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
           Complex With Ugcaugu
          Length = 109

 Score = 25.8 bits (55), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 2/57 (3%)

Query: 17  LYHEYKKHGKVSWVKII--GQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVS 71
           L   + + GK+  V+II   +G   +G V F+ + DA++A    H     G KI+V+
Sbjct: 46  LRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN 102


>pdb|1OGY|A Chain A, Crystal Structure Of The Heterodimeric Nitrate Reductase
           From Rhodobacter Sphaeroides
 pdb|1OGY|C Chain C, Crystal Structure Of The Heterodimeric Nitrate Reductase
           From Rhodobacter Sphaeroides
 pdb|1OGY|E Chain E, Crystal Structure Of The Heterodimeric Nitrate Reductase
           From Rhodobacter Sphaeroides
 pdb|1OGY|G Chain G, Crystal Structure Of The Heterodimeric Nitrate Reductase
           From Rhodobacter Sphaeroides
 pdb|1OGY|I Chain I, Crystal Structure Of The Heterodimeric Nitrate Reductase
           From Rhodobacter Sphaeroides
 pdb|1OGY|K Chain K, Crystal Structure Of The Heterodimeric Nitrate Reductase
           From Rhodobacter Sphaeroides
 pdb|1OGY|M Chain M, Crystal Structure Of The Heterodimeric Nitrate Reductase
           From Rhodobacter Sphaeroides
 pdb|1OGY|O Chain O, Crystal Structure Of The Heterodimeric Nitrate Reductase
           From Rhodobacter Sphaeroides
          Length = 802

 Score = 25.4 bits (54), Expect = 9.4,   Method: Composition-based stats.
 Identities = 13/39 (33%), Positives = 21/39 (53%)

Query: 13  LKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDA 51
           +KDG+YH+  +   VSW +       +  LV  +KA +A
Sbjct: 77  MKDGVYHKEGEFAPVSWDEAFDVMAAQAKLVLKEKAPEA 115


  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
   0.324    0.143    0.451 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,921,728
Number of Sequences: 62578
Number of extensions: 112260
Number of successful extensions: 274
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 272
Number of HSP's gapped (non-prelim): 8
length of query: 83
length of database: 14,973,337
effective HSP length: 51
effective length of query: 32
effective length of database: 11,781,859
effective search space: 377019488
effective search space used: 377019488
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)