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= psy11137
         (831 letters)

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

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



>pdb|4DM4|A Chain A, The Conserved Domain Of Yeast Cdc73
 pdb|4DM4|B Chain B, The Conserved Domain Of Yeast Cdc73
          Length = 167

 Score = 43.5 bits (101), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 32/104 (30%), Positives = 56/104 (53%), Gaps = 13/104 (12%)

Query: 19  RTPIIIIPAANTSLITMF----VTTEAK----RAAGSKRENEILIQRSKGDGTTVPYR-- 68
           + PII+IP+A +S++T+        E+K    R   S     + I+++  +  + P R  
Sbjct: 2   KDPIILIPSAASSILTVANIKQFLLESKYVNPRNLPSVPNGLVNIEKN-FERISRPIRFI 60

Query: 69  VIDNPLKLARTD-WDRVVAVFVMGPAWQFKGWPWDANPVEIFSK 111
           ++DN     + + WDRVVA+F  G  WQF  + W++ P E+F +
Sbjct: 61  IVDNTRMFTKPEYWDRVVAIFTTGHTWQFNNYQWNS-PQELFQR 103


>pdb|3V46|A Chain A, Crystal Structure Of Yeast Cdc73 C-Terminal Domain
          Length = 170

 Score = 43.1 bits (100), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 32/104 (30%), Positives = 56/104 (53%), Gaps = 13/104 (12%)

Query: 19  RTPIIIIPAANTSLITMF----VTTEAK----RAAGSKRENEILIQRSKGDGTTVPYR-- 68
           + PII+IP+A +S++T+        E+K    R   S     + I+++  +  + P R  
Sbjct: 13  KDPIILIPSAASSILTVANIKQFLLESKYVNPRNLPSVPNGLVNIEKN-FERISRPIRFI 71

Query: 69  VIDNPLKLARTD-WDRVVAVFVMGPAWQFKGWPWDANPVEIFSK 111
           ++DN     + + WDRVVA+F  G  WQF  + W++ P E+F +
Sbjct: 72  IVDNTRMFTKPEYWDRVVAIFTTGHTWQFNNYQWNS-PQELFQR 114


>pdb|1XKU|A Chain A, Crystal Structure Of The Dimeric Protein Core Of Decorin,
           The Archetypal Small Leucine-Rich Repeat Proteoglycan
          Length = 330

 Score = 35.0 bits (79), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 16/35 (45%), Positives = 20/35 (57%), Gaps = 1/35 (2%)

Query: 798 PQCPFRCICFRTTVRCMFQHLEYVPR-VSNDTTIL 831
           P CPFRC C    V+C    LE VP+ +  DT +L
Sbjct: 23  PVCPFRCQCHLRVVQCSDLGLEKVPKDLPPDTALL 57


>pdb|1XCD|A Chain A, Dimeric Bovine Tissue-Extracted Decorin, Crystal Form 1
 pdb|1XEC|A Chain A, Dimeric Bovine Tissue-Extracted Decorin, Crystal Form 2
 pdb|1XEC|B Chain B, Dimeric Bovine Tissue-Extracted Decorin, Crystal Form 2
          Length = 329

 Score = 35.0 bits (79), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 16/35 (45%), Positives = 20/35 (57%), Gaps = 1/35 (2%)

Query: 798 PQCPFRCICFRTTVRCMFQHLEYVPR-VSNDTTIL 831
           P CPFRC C    V+C    LE VP+ +  DT +L
Sbjct: 23  PVCPFRCQCHLRVVQCSDLGLEKVPKDLPPDTALL 57


>pdb|2FT3|A Chain A, Crystal Structure Of The Biglycan Dimer Core Protein
 pdb|2FT3|B Chain B, Crystal Structure Of The Biglycan Dimer Core Protein
 pdb|2FT3|C Chain C, Crystal Structure Of The Biglycan Dimer Core Protein
 pdb|2FT3|D Chain D, Crystal Structure Of The Biglycan Dimer Core Protein
 pdb|2FT3|E Chain E, Crystal Structure Of The Biglycan Dimer Core Protein
 pdb|2FT3|F Chain F, Crystal Structure Of The Biglycan Dimer Core Protein
          Length = 332

 Score = 32.3 bits (72), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 1/34 (2%)

Query: 799 QCPFRCICFRTTVRCMFQHLEYVPR-VSNDTTIL 831
            CPF C C    V+C    L+ VP+ +S DTT+L
Sbjct: 26  MCPFGCHCHLRVVQCSDLGLKAVPKEISPDTTLL 59


>pdb|2WFH|A Chain A, The Human Slit 2 Dimerization Domain D4
 pdb|2WFH|B Chain B, The Human Slit 2 Dimerization Domain D4
          Length = 193

 Score = 30.4 bits (67), Expect = 3.8,   Method: Composition-based stats.
 Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 1/34 (2%)

Query: 799 QCPFRCICFRTTVRCMFQHLEYVPR-VSNDTTIL 831
           +CP  C C  T VRC  + L+ +P+ +  D T L
Sbjct: 3   RCPTECTCLDTVVRCSNKGLKVLPKGIPRDVTEL 36


  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
   0.317    0.132    0.384 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,518,430
Number of Sequences: 62578
Number of extensions: 752596
Number of successful extensions: 1362
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1356
Number of HSP's gapped (non-prelim): 6
length of query: 831
length of database: 14,973,337
effective HSP length: 107
effective length of query: 724
effective length of database: 8,277,491
effective search space: 5992903484
effective search space used: 5992903484
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)