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= psy11608
         (99 letters)

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

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



>pdb|2KHC|A Chain A, Bruno Rrm3+
          Length = 118

 Score = 28.5 bits (62), Expect = 0.92,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 6   VDIKKQSSASA-FAFVQYTDIASVVRAMRAMDGEYVGHNRVNLGYGK 51
           V I KQ+S S  F FV + +  S   A++AM+G  VG  R+ +   K
Sbjct: 72  VFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118


>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
           Repeat Rna-Binding Protein 1
 pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
           Rna-Binding Protein 1
 pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
           Complex With Rna (Ug)3
          Length = 115

 Score = 26.9 bits (58), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 6   VDIKKQSSASA-FAFVQYTDIASVVRAMRAMDGEYVGHNRVNLGYGKS 52
           V I KQ++ S  F FV Y +  S   A+++M+G  +G  R+ +   +S
Sbjct: 57  VFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRS 104


>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
          9g8
          Length = 101

 Score = 26.9 bits (58), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 11/35 (31%), Positives = 20/35 (57%)

Query: 13 SASAFAFVQYTDIASVVRAMRAMDGEYVGHNRVNL 47
          +   FAFV++ D      A+R +DG+ +  +RV +
Sbjct: 35 NPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRV 69


>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
 pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
          Length = 97

 Score = 26.6 bits (57), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 10/36 (27%), Positives = 21/36 (58%)

Query: 14 ASAFAFVQYTDIASVVRAMRAMDGEYVGHNRVNLGY 49
          +  +AF+++ D+ S   A+R ++G  +G   +  GY
Sbjct: 44 SKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGY 79


>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
          Length = 96

 Score = 26.6 bits (57), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 10/36 (27%), Positives = 21/36 (58%)

Query: 14 ASAFAFVQYTDIASVVRAMRAMDGEYVGHNRVNLGY 49
          +  +AF+++ D+ S   A+R ++G  +G   +  GY
Sbjct: 43 SKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGY 78


>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition
          In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
          Complex
          Length = 84

 Score = 26.6 bits (57), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 10/36 (27%), Positives = 21/36 (58%)

Query: 14 ASAFAFVQYTDIASVVRAMRAMDGEYVGHNRVNLGY 49
          +  +AF+++ D+ S   A+R ++G  +G   +  GY
Sbjct: 45 SKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGY 80


  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
   0.321    0.134    0.422 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,919,753
Number of Sequences: 62578
Number of extensions: 104009
Number of successful extensions: 311
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 284
Number of HSP's gapped (non-prelim): 34
length of query: 99
length of database: 14,973,337
effective HSP length: 65
effective length of query: 34
effective length of database: 10,905,767
effective search space: 370796078
effective search space used: 370796078
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)