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= psy2555
         (90 letters)

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

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



>pdb|1WMW|A Chain A, Crystal Structure Of Geranulgeranyl Diphosphate Synthase
          From Thermus Thermophilus
 pdb|1WMW|B Chain B, Crystal Structure Of Geranulgeranyl Diphosphate Synthase
          From Thermus Thermophilus
 pdb|1WMW|C Chain C, Crystal Structure Of Geranulgeranyl Diphosphate Synthase
          From Thermus Thermophilus
 pdb|1WMW|D Chain D, Crystal Structure Of Geranulgeranyl Diphosphate Synthase
          From Thermus Thermophilus
          Length = 330

 Score = 25.8 bits (55), Expect = 6.9,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 26/54 (48%), Gaps = 3/54 (5%)

Query: 29 SMQEAVKFQIDHRKGNFKKGSVILSNHPKAGGSHLPDLTVITPVFIDSQPVEEG 82
          ++QE +  ++DH    ++    +L ++P+ GG  L  L  +        P+E G
Sbjct: 11 ALQERLLARLDHPDPLYRD---LLQDYPRRGGKMLRGLLTVYSALAHGAPLEAG 61


>pdb|3AK0|A Chain A, Crystal Structure Of Ancestral Congerin Con-Anc'-N28k
 pdb|3AK0|B Chain B, Crystal Structure Of Ancestral Congerin Con-Anc'-N28k
          Length = 135

 Score = 25.4 bits (54), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 1/29 (3%)

Query: 14 GGLV-SNAPHIPVHLGSMQEAVKFQIDHR 41
          GG+V SNA    +++G   +++   IDHR
Sbjct: 21 GGVVNSNAKRFSINVGESTDSIALHIDHR 49


>pdb|2RAD|A Chain A, Crystal Structure Of The Succinoglycan Biosynthesis
           Protein. Northeast Structural Genomics Consortium Target
           Bcr135
 pdb|2RAD|B Chain B, Crystal Structure Of The Succinoglycan Biosynthesis
           Protein. Northeast Structural Genomics Consortium Target
           Bcr135
 pdb|3B55|A Chain A, Crystal Structure Of The Q81bn2_baccr Protein From
           Bacillus Cereus. Nesg Target Bcr135
          Length = 451

 Score = 25.4 bits (54), Expect = 9.4,   Method: Composition-based stats.
 Identities = 17/55 (30%), Positives = 25/55 (45%)

Query: 6   SKESFGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPKAGG 60
           S   FGP G L S+ P+   ++    +  +F ID RK N    + +   HP   G
Sbjct: 353 SDGEFGPYGTLKSDDPNSYNYIFGQVKKDQFFIDLRKANGVTKTWLNEQHPIFAG 407


  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    0.138    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,900,072
Number of Sequences: 62578
Number of extensions: 105064
Number of successful extensions: 190
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: 189
Number of HSP's gapped (non-prelim): 3
length of query: 90
length of database: 14,973,337
effective HSP length: 57
effective length of query: 33
effective length of database: 11,406,391
effective search space: 376410903
effective search space used: 376410903
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)