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= 003170
         (842 letters)

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

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



>pdb|1YGA|A Chain A, Crystal Structure Of Saccharomyces Cerevisiae Yn9a
           Protein, New York Structural Genomics Consortium
 pdb|1YGA|B Chain B, Crystal Structure Of Saccharomyces Cerevisiae Yn9a
           Protein, New York Structural Genomics Consortium
          Length = 342

 Score = 33.5 bits (75), Expect = 0.54,   Method: Compositional matrix adjust.
 Identities = 43/185 (23%), Positives = 64/185 (34%), Gaps = 41/185 (22%)

Query: 165 PGD------FSCGRSSMPRDLPNPQMLSPAARTPLHFRNNSFEGRNHFPGRSSSEGA--- 215
           PGD      ++   + M  D+     L     TP++  N+S+   N      S  G    
Sbjct: 137 PGDLEVTVKYTLNVAEMTLDMEYQAQLVRGDATPINMTNHSYFNLNKVKSEKSIRGTEVK 196

Query: 216 --SNALLSPNHHLPVPYASTTSQIVWYFD--------EDPAAMD---IFSASKQL----- 257
             SN  L       +P      + +  FD        ED    D   I  A+K L     
Sbjct: 197 VCSNKSLEVTEGALLPTGKIIERNIATFDSTKPTVLHEDTPVFDCTFIIDANKDLKTTDS 256

Query: 258 -----WLGSFGPEASEAHIRFQIDRFGPLEHFF--------FFPIKGFALVEYINIIDAI 304
                 +  F     E+HI+F++    P  H +        F P  GFA V+    +DAI
Sbjct: 257 VSVNKLVPVFKAYHPESHIKFEVSTTEPTVHLYTGDNLCGKFVPRSGFA-VQQGRYVDAI 315

Query: 305 RAREY 309
              E+
Sbjct: 316 NRDEW 320


>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
           Hypothetical Rna Binding Protein Bc052180
          Length = 97

 Score = 32.3 bits (72), Expect = 1.2,   Method: Composition-based stats.
 Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 1/53 (1%)

Query: 254 SKQLWLGSFGPEASEAHIRFQIDRFGPLEHFFFFPIKGFALVEYINIIDAIRA 306
           + +LW+G  GP  S A +  + DRFG +          FA ++Y + +DA +A
Sbjct: 17  TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYES-LDAAQA 68


  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
   0.318    0.132    0.410 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,989,043
Number of Sequences: 62578
Number of extensions: 954118
Number of successful extensions: 1730
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1729
Number of HSP's gapped (non-prelim): 4
length of query: 842
length of database: 14,973,337
effective HSP length: 107
effective length of query: 735
effective length of database: 8,277,491
effective search space: 6083955885
effective search space used: 6083955885
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)