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= psy4496
         (228 letters)

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

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



>pdb|1MP1|A Chain A, Solution Structure Of The Pwi Motif From Srm160
          Length = 111

 Score = 66.2 bits (160), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 38/41 (92%)

Query: 16 QKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLE 56
          +KVDM+KV L+++KPWIT+++T++LG EDDVV+ F++NQLE
Sbjct: 13 KKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEFIFNQLE 53


>pdb|2FTC|E Chain E, Structural Model For The Large Subunit Of The Mammalian
           Mitochondrial Ribosome
 pdb|2FTC|F Chain F, Structural Model For The Large Subunit Of The Mammalian
           Mitochondrial Ribosome
          Length = 137

 Score = 50.4 bits (119), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 24/45 (53%), Positives = 30/45 (66%)

Query: 161 PKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQG 205
           PKI +L  DI+SLTLLE +DL+ LLKK L + D  +M MG    G
Sbjct: 1   PKIQQLVQDIASLTLLEISDLNELLKKTLKIQDVGLMPMGGMVPG 45


>pdb|1X4Q|A Chain A, Solution Structure Of Pwi Domain In U4U6 SMALL NUCLEAR
          Ribonucleoprotein Prp3(Hprp3)
          Length = 92

 Score = 31.2 bits (69), Expect = 0.49,   Method: Compositional matrix adjust.
 Identities = 13/34 (38%), Positives = 21/34 (61%)

Query: 20 MTKVKLDILKPWITQKITQLLGMEDDVVVAFVYN 53
          ++K +LD LKPWI + + ++LG  +  VV    N
Sbjct: 10 LSKRELDELKPWIEKTVKRVLGFSEPTVVTAALN 43


>pdb|3V53|A Chain A, Crystal Structure Of Human Rbm25
 pdb|3V53|B Chain B, Crystal Structure Of Human Rbm25
 pdb|3V53|C Chain C, Crystal Structure Of Human Rbm25
 pdb|3V53|D Chain D, Crystal Structure Of Human Rbm25
 pdb|3V53|E Chain E, Crystal Structure Of Human Rbm25
          Length = 119

 Score = 28.9 bits (63), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 11/31 (35%), Positives = 21/31 (67%)

Query: 28 LKPWITQKITQLLGMEDDVVVAFVYNQLEAE 58
          ++PWI +KI + +G E+  +V FV +++ A 
Sbjct: 47 IRPWINKKIIEYIGEEEATLVDFVCSKVMAH 77


  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
   0.319    0.133    0.378 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,922,380
Number of Sequences: 62578
Number of extensions: 208327
Number of successful extensions: 439
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 430
Number of HSP's gapped (non-prelim): 9
length of query: 228
length of database: 14,973,337
effective HSP length: 95
effective length of query: 133
effective length of database: 9,028,427
effective search space: 1200780791
effective search space used: 1200780791
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)