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= psy7437
         (279 letters)

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

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



>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
           Pspc1NONO
          Length = 261

 Score =  120 bits (301), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 62/140 (44%), Positives = 82/140 (58%), Gaps = 1/140 (0%)

Query: 3   IERAVVLVDDRGNSKNEGIIEFTRKPAAAQALKRCQDGVFFLTQSLKPVIVEPLDLVDDE 62
           +ERAVV+VDDRG    +GI+EF+ KPAA +AL RC +G F LT   +PV VEP+D +DDE
Sbjct: 123 VERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCSEGSFLLTTFPRPVTVEPMDQLDDE 182

Query: 63  EGLSERTVSKKSSDYFKQRSIGPRFATIGSFEFEYGTRWKQLYXXXXXXXXXXXXXXXXX 122
           EGL E+ V  K+  + K+R   PRFA  GSFE+EY  RWK L                  
Sbjct: 183 EGLPEKLVI-KNQQFHKEREQPPRFAQPGSFEYEYAMRWKALIEMEKQQQDQVDRNIKEA 241

Query: 123 XXXXXXXMEFARYENETEIL 142
                  ME AR+E++  ++
Sbjct: 242 REKLEMEMEAARHEHQVMLM 261


>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
           Pspc1NONO
          Length = 261

 Score =  119 bits (297), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 54/102 (52%), Positives = 74/102 (72%), Gaps = 1/102 (0%)

Query: 3   IERAVVLVDDRGNSKNEGIIEFTRKPAAAQALKRCQDGVFFLTQSLKPVIVEPLDLVDDE 62
           +E+AVV+VDDRG +  +G +EF  KP A +AL+RC DG F LT + +PVIVEP++  DDE
Sbjct: 123 VEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDE 182

Query: 63  EGLSERTVSKKSSDYFKQRSIGPRFATIGSFEFEYGTRWKQL 104
           +GL E+ + +K+  Y K+R   PRFA  G+FEFEY +RWK L
Sbjct: 183 DGLPEK-LMQKTQQYHKEREQPPRFAQPGTFEFEYASRWKAL 223


>pdb|3ZV0|A Chain A, Structure Of The Shq1p-Cbf5p Complex
 pdb|3ZV0|B Chain B, Structure Of The Shq1p-Cbf5p Complex
          Length = 369

 Score = 28.5 bits (62), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 3/51 (5%)

Query: 47  SLKPVIVEPLDLVDDEEGLSERTVSKKSSDYFKQRSIGPRFATIGSFEFEY 97
           S  P +V P++  D+E+   +  + KKS   +    I P + TI S  F Y
Sbjct: 118 STNPNLVMPIEFTDEEQKQMQDNLPKKS---YLVEDIKPLYVTILSVLFSY 165


>pdb|3ZUZ|A Chain A, Structure Of Shq1p C-Terminal Domain
          Length = 365

 Score = 28.5 bits (62), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 3/51 (5%)

Query: 47  SLKPVIVEPLDLVDDEEGLSERTVSKKSSDYFKQRSIGPRFATIGSFEFEY 97
           S  P +V P++  D+E+   +  + KKS   +    I P + TI S  F Y
Sbjct: 120 STNPNLVMPIEFTDEEQKQMQDNLPKKS---YLVEDIKPLYVTILSVLFSY 167


>pdb|3UAH|A Chain A, Structure Of The Shq1 Specific Domain From Saccharomyces
           Cerevisiae
 pdb|3UAI|D Chain D, Structure Of The Shq1-Cbf5-Nop10-Gar1 Complex From
           Saccharomyces Cerevisiae
          Length = 366

 Score = 28.1 bits (61), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 3/51 (5%)

Query: 47  SLKPVIVEPLDLVDDEEGLSERTVSKKSSDYFKQRSIGPRFATIGSFEFEY 97
           S  P +V P++  D+E+   +  + KKS   +    I P + TI S  F Y
Sbjct: 121 STNPNLVMPIEFTDEEQKQMQDNLPKKS---YLVEDIKPLYVTILSVLFSY 168


  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    0.134    0.388 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,486,539
Number of Sequences: 62578
Number of extensions: 214492
Number of successful extensions: 606
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 537
Number of HSP's gapped (non-prelim): 67
length of query: 279
length of database: 14,973,337
effective HSP length: 98
effective length of query: 181
effective length of database: 8,840,693
effective search space: 1600165433
effective search space used: 1600165433
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: 51 (24.3 bits)