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= psy7369
         (265 letters)

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

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



>pdb|3NNE|A Chain A, Crystal Structure Of Choline Oxidase S101a Mutant
 pdb|3NNE|B Chain B, Crystal Structure Of Choline Oxidase S101a Mutant
 pdb|3NNE|C Chain C, Crystal Structure Of Choline Oxidase S101a Mutant
 pdb|3NNE|D Chain D, Crystal Structure Of Choline Oxidase S101a Mutant
 pdb|3NNE|E Chain E, Crystal Structure Of Choline Oxidase S101a Mutant
 pdb|3NNE|F Chain F, Crystal Structure Of Choline Oxidase S101a Mutant
 pdb|3NNE|G Chain G, Crystal Structure Of Choline Oxidase S101a Mutant
 pdb|3NNE|H Chain H, Crystal Structure Of Choline Oxidase S101a Mutant
          Length = 546

 Score = 32.0 bits (71), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 63  DTYISDRFYTLDPRSRPLYDLKYITFGFAYLQDMVEQSIIQEHTGRESTPGIVLQ 117
           D  + D  Y  DP     +D++ +  G    +++  Q  + E TGRE +PG+  Q
Sbjct: 397 DKPMVDPRYFTDPEG---HDMRVMVAGIRKAREIAAQPAMAEWTGRELSPGVEAQ 448


>pdb|3LJP|A Chain A, Crystal Structure Of Choline Oxidase V464a Mutant
 pdb|3LJP|B Chain B, Crystal Structure Of Choline Oxidase V464a Mutant
          Length = 546

 Score = 32.0 bits (71), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 63  DTYISDRFYTLDPRSRPLYDLKYITFGFAYLQDMVEQSIIQEHTGRESTPGIVLQ 117
           D  + D  Y  DP     +D++ +  G    +++  Q  + E TGRE +PG+  Q
Sbjct: 397 DKPMVDPRYFTDPEG---HDMRVMVAGIRKAREIAAQPAMAEWTGRELSPGVEAQ 448


>pdb|2JBV|A Chain A, Crystal Structure Of Choline Oxidase Reveals Insights Into
           The Catalytic Mechanism
 pdb|2JBV|B Chain B, Crystal Structure Of Choline Oxidase Reveals Insights Into
           The Catalytic Mechanism
          Length = 546

 Score = 32.0 bits (71), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 63  DTYISDRFYTLDPRSRPLYDLKYITFGFAYLQDMVEQSIIQEHTGRESTPGIVLQ 117
           D  + D  Y  DP     +D++ +  G    +++  Q  + E TGRE +PG+  Q
Sbjct: 397 DKPMVDPRYFTDPEG---HDMRVMVAGIRKAREIAAQPAMAEWTGRELSPGVEAQ 448


>pdb|4AKR|A Chain A, Crystal Structure Of The Cytoplasmic Actin Capping Protein
           Cap32_34 From Dictyostelium Discoideum
 pdb|4AKR|C Chain C, Crystal Structure Of The Cytoplasmic Actin Capping Protein
           Cap32_34 From Dictyostelium Discoideum
          Length = 281

 Score = 29.3 bits (64), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 31/107 (28%), Positives = 47/107 (43%), Gaps = 19/107 (17%)

Query: 35  NTSARHTLEEYKNSQMFGAKL-MSTALI-GDTYISDRFYTLDPRSRPLYDLKYITFGFAY 92
           N SA  T  EY  SQM   +    +ALI  +  IS+  Y LDP+++ +     IT+    
Sbjct: 41  NASAGSTFREYNTSQMVSVQTSKGSALITKEGEISNNEY-LDPKNKQV-----ITYDH-- 92

Query: 93  LQDMVEQSIIQEHTGRESTPGIVLQQFP-YPCYIEDQFIKAVSKTFP 138
                   I QE TG  S  G + Q    Y    +++  K  ++ +P
Sbjct: 93  --------IKQEVTGERSASGEIEQDIEQYRAAFDEEATKYCNEYYP 131


  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
   0.326    0.137    0.420 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,568,723
Number of Sequences: 62578
Number of extensions: 286926
Number of successful extensions: 645
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: 642
Number of HSP's gapped (non-prelim): 4
length of query: 265
length of database: 14,973,337
effective HSP length: 97
effective length of query: 168
effective length of database: 8,903,271
effective search space: 1495749528
effective search space used: 1495749528
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 bits)