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= 035240
         (69 letters)

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

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



>pdb|2WWB|B Chain B, Cryo-Em Structure Of The Mammalian Sec61 Complex Bound
          To The Actively Translating Wheat Germ 80s Ribosome
          Length = 68

 Score = 73.6 bits (179), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 38/68 (55%), Positives = 42/68 (61%)

Query: 1  MDAIDNVFDPLRDFAKDSLRLVKRCHKPDRKEFTKVAFRTAIXXXXXXXXXXXXKLIFIP 60
          MD +    +P R F KDS+RLVKRC KPDRKEF K+A  TAI            KLI IP
Sbjct: 1  MDQVMQFVEPSRQFVKDSIRLVKRCTKPDRKEFQKIAMATAIGFAIMGFIGFFVKLIHIP 60

Query: 61 INNIIVGS 68
          INNIIVG 
Sbjct: 61 INNIIVGG 68


>pdb|2WW9|B Chain B, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound
          To The Yeast 80s Ribosome
 pdb|2WWA|B Chain B, Cryo-Em Structure Of Idle Yeast Ssh1 Complex Bound To
          The Yeast 80s Ribosome
          Length = 80

 Score = 38.5 bits (88), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 18/65 (27%), Positives = 32/65 (49%)

Query: 2  DAIDNVFDPLRDFAKDSLRLVKRCHKPDRKEFTKVAFRTAIXXXXXXXXXXXXKLIFIPI 61
          + ++ + +   +F ++  + + +C KPD KE+TK+     I            KLI IPI
Sbjct: 16 NQVEKLVEAPVEFVREGTQFLAKCKKPDLKEYTKIVKAVGIGFIAVGIIGYAIKLIHIPI 75

Query: 62 NNIIV 66
            +IV
Sbjct: 76 RYVIV 80


>pdb|3AIB|A Chain A, Crystal Structure Of Glucansucrase
 pdb|3AIB|B Chain B, Crystal Structure Of Glucansucrase
 pdb|3AIB|C Chain C, Crystal Structure Of Glucansucrase
 pdb|3AIB|D Chain D, Crystal Structure Of Glucansucrase
 pdb|3AIB|G Chain G, Crystal Structure Of Glucansucrase
 pdb|3AIB|E Chain E, Crystal Structure Of Glucansucrase
 pdb|3AIB|F Chain F, Crystal Structure Of Glucansucrase
 pdb|3AIB|H Chain H, Crystal Structure Of Glucansucrase
 pdb|3AIC|A Chain A, Crystal Structure Of Glucansucrase From Streptococcus
           Mutans
 pdb|3AIC|B Chain B, Crystal Structure Of Glucansucrase From Streptococcus
           Mutans
 pdb|3AIC|C Chain C, Crystal Structure Of Glucansucrase From Streptococcus
           Mutans
 pdb|3AIC|D Chain D, Crystal Structure Of Glucansucrase From Streptococcus
           Mutans
 pdb|3AIC|E Chain E, Crystal Structure Of Glucansucrase From Streptococcus
           Mutans
 pdb|3AIC|F Chain F, Crystal Structure Of Glucansucrase From Streptococcus
           Mutans
 pdb|3AIC|G Chain G, Crystal Structure Of Glucansucrase From Streptococcus
           Mutans
 pdb|3AIC|H Chain H, Crystal Structure Of Glucansucrase From Streptococcus
           Mutans
 pdb|3AIE|A Chain A, Crystal Structure Of Glucansucrase From Streptococcus
           Mutans
 pdb|3AIE|B Chain B, Crystal Structure Of Glucansucrase From Streptococcus
           Mutans
 pdb|3AIE|C Chain C, Crystal Structure Of Glucansucrase From Streptococcus
           Mutans
 pdb|3AIE|D Chain D, Crystal Structure Of Glucansucrase From Streptococcus
           Mutans
 pdb|3AIE|E Chain E, Crystal Structure Of Glucansucrase From Streptococcus
           Mutans
 pdb|3AIE|F Chain F, Crystal Structure Of Glucansucrase From Streptococcus
           Mutans
 pdb|3AIE|G Chain G, Crystal Structure Of Glucansucrase From Streptococcus
           Mutans
 pdb|3AIE|H Chain H, Crystal Structure Of Glucansucrase From Streptococcus
           Mutans
          Length = 844

 Score = 26.6 bits (57), Expect = 3.7,   Method: Composition-based stats.
 Identities = 13/30 (43%), Positives = 17/30 (56%)

Query: 1   MDAIDNVFDPLRDFAKDSLRLVKRCHKPDR 30
           +DA+DNV   L   A D L+  K  HK D+
Sbjct: 233 VDAVDNVDADLLQIAGDYLKAAKGIHKNDK 262


  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
   0.329    0.146    0.432 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,471,597
Number of Sequences: 62578
Number of extensions: 30933
Number of successful extensions: 64
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 61
Number of HSP's gapped (non-prelim): 3
length of query: 69
length of database: 14,973,337
effective HSP length: 39
effective length of query: 30
effective length of database: 12,532,795
effective search space: 375983850
effective search space used: 375983850
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 45 (21.9 bits)