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= psy8637
         (216 letters)

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

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



>pdb|3E0J|A Chain A, X-Ray Structure Of The Complex Of Regulatory Subunits Of
           Human Dna Polymerase Delta
 pdb|3E0J|C Chain C, X-Ray Structure Of The Complex Of Regulatory Subunits Of
           Human Dna Polymerase Delta
 pdb|3E0J|E Chain E, X-Ray Structure Of The Complex Of Regulatory Subunits Of
           Human Dna Polymerase Delta
 pdb|3E0J|G Chain G, X-Ray Structure Of The Complex Of Regulatory Subunits Of
           Human Dna Polymerase Delta
          Length = 476

 Score =  157 bits (398), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 77/154 (50%), Positives = 101/154 (65%), Gaps = 2/154 (1%)

Query: 12  PTADYKNLSQCFRLASKDYSKQFAHIYAVRLNKMRECLLARVSQKWGKSVSVLKLSDLNE 71
           P A Y N SQ FRL  + +S+Q+AHIYA RL +MR  L  R  Q WG  V V KL +L  
Sbjct: 35  PVATYTNSSQPFRLGERSFSRQYAHIYATRLIQMRPFLENRAQQHWGSGVGVKKLCELQP 94

Query: 72  TDTEECVIIGTLFKHQQLKPNILKEISEELKLVPQPQHTHFVSDSDELILEDELQRIPLH 131
              E+C ++GTLFK   L+P+IL+E+SEE  L+PQP  + ++   DEL+LEDELQRI L 
Sbjct: 95  E--EKCCVVGTLFKAMPLQPSILREVSEEHNLLPQPPRSKYIHPDDELVLEDELQRIKLK 152

Query: 132 GNIDIHNQVTGVVVAIKGTPVGNGKFKVSDVCYA 165
           G ID+   VTG V+A+ G+   +GKF V D C+A
Sbjct: 153 GTIDVSKLVTGTVLAVFGSVRDDGKFLVEDYCFA 186


>pdb|3HNP|A Chain A, Crystal Structure Of An Oxidoreductase From Bacillus
           Cereus. Northeast Structural Genomics Consortium Target
           Id Bcr251
 pdb|3HNP|B Chain B, Crystal Structure Of An Oxidoreductase From Bacillus
           Cereus. Northeast Structural Genomics Consortium Target
           Id Bcr251
 pdb|3HNP|C Chain C, Crystal Structure Of An Oxidoreductase From Bacillus
           Cereus. Northeast Structural Genomics Consortium Target
           Id Bcr251
 pdb|3HNP|D Chain D, Crystal Structure Of An Oxidoreductase From Bacillus
           Cereus. Northeast Structural Genomics Consortium Target
           Id Bcr251
 pdb|3HNP|E Chain E, Crystal Structure Of An Oxidoreductase From Bacillus
           Cereus. Northeast Structural Genomics Consortium Target
           Id Bcr251
 pdb|3HNP|F Chain F, Crystal Structure Of An Oxidoreductase From Bacillus
           Cereus. Northeast Structural Genomics Consortium Target
           Id Bcr251
          Length = 353

 Score = 27.3 bits (59), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 15/57 (26%), Positives = 33/57 (57%), Gaps = 4/57 (7%)

Query: 88  QLKPNILKEISEELKLVPQPQHTHFVSDSDELILEDELQRI----PLHGNIDIHNQV 140
           ++K   +++I+EEL    + +  +F +D DEL+ + E+Q +    P H + ++  +V
Sbjct: 29  KVKTIFVRQINEELAAPYEERGVYFTTDLDELLNDKEIQVVTICTPAHTHYELAKKV 85


>pdb|1DST|A Chain A, Mutant Of Factor D With Enhanced Catalytic Activity
          Length = 228

 Score = 26.9 bits (58), Expect = 9.4,   Method: Compositional matrix adjust.
 Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 6/87 (6%)

Query: 36  HIYAVRLNKMRECLLARVSQKWGKSVSVLKLSDLNETDTEECVIIGTLFKHQQLKPNILK 95
           ++ +V+LN    C    V+++W     VL  +   E D  +  +   L  H   +P   K
Sbjct: 14  YMASVQLNGAHLCGGVLVAEQW-----VLSAAHCLE-DAADGKVQVLLGAHSLSQPEPSK 67

Query: 96  EISEELKLVPQPQHTHFVSDSDELILE 122
            + + L+ VP P +     D D L+L+
Sbjct: 68  RLYDVLRAVPHPDYQPDTIDHDLLLLQ 94


  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
   0.319    0.135    0.405 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,579,015
Number of Sequences: 62578
Number of extensions: 269406
Number of successful extensions: 617
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 613
Number of HSP's gapped (non-prelim): 6
length of query: 216
length of database: 14,973,337
effective HSP length: 95
effective length of query: 121
effective length of database: 9,028,427
effective search space: 1092439667
effective search space used: 1092439667
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: 49 (23.5 bits)