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= 008235
         (573 letters)

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

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



>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein
           Drosophila Vasa
 pdb|2DB3|B Chain B, Structural Basis For Rna Unwinding By The Dead-Box Protein
           Drosophila Vasa
 pdb|2DB3|C Chain C, Structural Basis For Rna Unwinding By The Dead-Box Protein
           Drosophila Vasa
 pdb|2DB3|D Chain D, Structural Basis For Rna Unwinding By The Dead-Box Protein
           Drosophila Vasa
          Length = 434

 Score = 34.7 bits (78), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 1/61 (1%)

Query: 504 VIVPDFIISMKNYVEILTSMARHTVSGILHSFFTKD-DAAHAGQMIEILEQCGQVVPDAL 562
           VI  D    + +YV  +    R   +G   SFF  + D A A  +++ILE  GQ VPD L
Sbjct: 372 VINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKILEGSGQTVPDFL 431

Query: 563 R 563
           R
Sbjct: 432 R 432


>pdb|4GND|A Chain A, Crystal Structure Of Nsd3 Tandem Phd5-C5hch Domains
 pdb|4GND|C Chain C, Crystal Structure Of Nsd3 Tandem Phd5-C5hch Domains
 pdb|4GNE|A Chain A, Crystal Structure Of Nsd3 Tandem Phd5-C5hch Domains
           Complexed With H3 Peptide 1-7
 pdb|4GNF|A Chain A, Crystal Structure Of Nsd3 Tandem Phd5-C5hch Domains
           Complexed With H3 Peptide 1-15
 pdb|4GNG|A Chain A, Crystal Structure Of Nsd3 Tandem Phd5-C5hch Domains
           Complexed With H3k9me3 Peptide
 pdb|4GNG|D Chain D, Crystal Structure Of Nsd3 Tandem Phd5-C5hch Domains
           Complexed With H3k9me3 Peptide
          Length = 107

 Score = 30.0 bits (66), Expect = 3.8,   Method: Composition-based stats.
 Identities = 11/25 (44%), Positives = 15/25 (60%)

Query: 160 CANGHHGQACEKLDCPSKFLILCLN 184
           C +G     C+K DCP  + +LCLN
Sbjct: 21  CGDGGELVMCDKKDCPKAYHLLCLN 45


>pdb|1YAV|A Chain A, Crystal Structure Of Cbs Domain-Containing Protein Ykul
           From Bacillus Subtilis
 pdb|1YAV|B Chain B, Crystal Structure Of Cbs Domain-Containing Protein Ykul
           From Bacillus Subtilis
          Length = 159

 Score = 28.9 bits (63), Expect = 9.2,   Method: Composition-based stats.
 Identities = 12/43 (27%), Positives = 24/43 (55%)

Query: 376 VQNLLLGSINRLSLNQSVASQSACIIQSVNVCASDEEKILKGI 418
           V+ ++L  I RL +N  +      +I +  VC  ++E++ +GI
Sbjct: 88  VEEVMLTDIPRLHINDPIMKGFGMVINNGFVCVENDEQVFEGI 130


  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: 14,453,199
Number of Sequences: 62578
Number of extensions: 530012
Number of successful extensions: 1214
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1210
Number of HSP's gapped (non-prelim): 5
length of query: 573
length of database: 14,973,337
effective HSP length: 104
effective length of query: 469
effective length of database: 8,465,225
effective search space: 3970190525
effective search space used: 3970190525
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: 54 (25.4 bits)