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= psy4340
         (218 letters)

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

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



>pdb|3LM4|A Chain A, Crystal Structure Of 2,3-Dihydroxy Biphenyl Dioxygenase
          From Rhodococcus Sp. (Strain Rha1)
 pdb|3LM4|B Chain B, Crystal Structure Of 2,3-Dihydroxy Biphenyl Dioxygenase
          From Rhodococcus Sp. (Strain Rha1)
 pdb|3LM4|C Chain C, Crystal Structure Of 2,3-Dihydroxy Biphenyl Dioxygenase
          From Rhodococcus Sp. (Strain Rha1)
 pdb|3LM4|D Chain D, Crystal Structure Of 2,3-Dihydroxy Biphenyl Dioxygenase
          From Rhodococcus Sp. (Strain Rha1)
          Length = 339

 Score = 29.3 bits (64), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 3/40 (7%)

Query: 52 VAHMGITGLFMGPPQH---FFYKYLDKYLPKRSGKSIALK 88
          +AH+    LF   PQ    FF K+L  Y+  R G+S+ L+
Sbjct: 9  IAHLARAELFSPKPQETLDFFTKFLGXYVTHREGQSVYLR 48


>pdb|2LJ1|A Chain A, The Third Sh3 Domain Of R85fl With Ataxin-7 Prr
          Length = 64

 Score = 28.5 bits (62), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 15/30 (50%), Positives = 17/30 (56%)

Query: 163 FVYDILLSYIKYNDDVFGLRGEEIVHHVEK 192
           F Y  L SYI  NDD   LR  +IV  +EK
Sbjct: 7   FSYQALYSYIPQNDDELELRDGDIVDVMEK 36


>pdb|2LJ0|A Chain A, The Third Sh3 Domain Of R85fl
          Length = 65

 Score = 28.5 bits (62), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 15/30 (50%), Positives = 17/30 (56%)

Query: 163 FVYDILLSYIKYNDDVFGLRGEEIVHHVEK 192
           F Y  L SYI  NDD   LR  +IV  +EK
Sbjct: 7   FSYQALYSYIPQNDDELELRDGDIVDVMEK 36


>pdb|3BBO|I Chain I, Homology Model For The Spinach Chloroplast 50s Subunit
           Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome
          Length = 223

 Score = 27.7 bits (60), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 3/64 (4%)

Query: 24  VLMCLGDTIQQTIELYTKADKTGYDLKRVAHMGITGLFMGPPQHF---FYKYLDKYLPKR 80
           V M + D+++  +E  T+   +GYD   +     T     PP+ +     KY D+ + ++
Sbjct: 156 VKMQIPDSLKVKVEENTRITVSGYDKSEIGQFAATVRKWRPPEPYKGKGVKYSDEIVRRK 215

Query: 81  SGKS 84
            GK+
Sbjct: 216 EGKA 219


>pdb|2R01|A Chain A, Crystal Structure Of A Putative Fmn-Dependent
           Nitroreductase (Ct0345) From Chlorobium Tepidum Tls At
           1.15 A Resolution
          Length = 210

 Score = 26.9 bits (58), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 12/36 (33%), Positives = 21/36 (58%)

Query: 167 ILLSYIKYNDDVFGLRGEEIVHHVEKDKIEESLANA 202
           +++  IK  DD+   R +  +HHV K +++E L  A
Sbjct: 168 VVIDQIKPGDDIRYWRDKHGIHHVPKRQVDELLVTA 203


  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
   0.324    0.143    0.430 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,637,122
Number of Sequences: 62578
Number of extensions: 276320
Number of successful extensions: 516
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 513
Number of HSP's gapped (non-prelim): 5
length of query: 218
length of database: 14,973,337
effective HSP length: 95
effective length of query: 123
effective length of database: 9,028,427
effective search space: 1110496521
effective search space used: 1110496521
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)