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= 047302
         (188 letters)

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

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



>pdb|2CW3|A Chain A, X-Ray Structure Of Pmsod2, Superoxide Dismutase From
           Perkinsus Marinus
 pdb|2CW3|B Chain B, X-Ray Structure Of Pmsod2, Superoxide Dismutase From
           Perkinsus Marinus
          Length = 280

 Score = 32.3 bits (72), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 19/51 (37%), Positives = 25/51 (49%), Gaps = 8/51 (15%)

Query: 114 SPISENLGKV-----DSLEE---LDISGTAIRQLSRLCSLTKWDLSDCNLP 156
           SP+SE+ GK+     D  E    LD        L+R  SL  W+ +D NLP
Sbjct: 226 SPLSEDAGKIPLFTCDVWEHAYYLDYQHDRAAYLTRWWSLINWEFADSNLP 276


>pdb|1NF3|C Chain C, Structure Of Cdc42 In A Complex With The Gtpase-Binding
           Domain Of The Cell Polarity Protein, Par6
 pdb|1NF3|D Chain D, Structure Of Cdc42 In A Complex With The Gtpase-Binding
           Domain Of The Cell Polarity Protein, Par6
          Length = 128

 Score = 29.3 bits (64), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 11/32 (34%), Positives = 20/32 (62%)

Query: 69  WGSMKSLTMLILDGTAIRELPLSVEYLTGLFV 100
           +G+ K L   I DG+++R  P  +E + G+F+
Sbjct: 38  YGTEKPLGFYIRDGSSVRVTPHGLEKVPGIFI 69


>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
 pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
 pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
 pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
          Length = 727

 Score = 27.7 bits (60), Expect = 4.5,   Method: Composition-based stats.
 Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 75  LTMLILDGTAIRELPLSVEYLTGLFVLNFKDWQNLECLPSPI 116
           LT L L+G ++ ELP  ++ L+ L VL+      L  LP+ +
Sbjct: 249 LTRLYLNGNSLTELPAEIKNLSNLRVLDLSH-NRLTSLPAEL 289


>pdb|1RY4|A Chain A, Nmr Structure Of The Crib-Pdz Module Of Par-6
          Length = 128

 Score = 26.9 bits (58), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 2/47 (4%)

Query: 54  IVGNCYKRIANLERFWGSMKSLTMLILDGTAIRELPLSVEYLTGLFV 100
           IV   ++R+  L+   GS K L   I DGT++R     +E   G+F+
Sbjct: 26  IVPETHRRVRLLK--HGSDKPLGFYIRDGTSVRVTASGLEKQPGIFI 70


  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
   0.320    0.139    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,740,672
Number of Sequences: 62578
Number of extensions: 226361
Number of successful extensions: 435
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 426
Number of HSP's gapped (non-prelim): 21
length of query: 188
length of database: 14,973,337
effective HSP length: 93
effective length of query: 95
effective length of database: 9,153,583
effective search space: 869590385
effective search space used: 869590385
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: 48 (23.1 bits)