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= 003353
         (827 letters)

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

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



>pdb|2HQB|A Chain A, Crystal Structure Of A Transcriptional Activator Of Comk
           Gene From Bacillus Halodurans
          Length = 296

 Score = 31.6 bits (70), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 18/78 (23%), Positives = 39/78 (50%), Gaps = 3/78 (3%)

Query: 139 VEVVNRWKWGPELETQLDKLQFVPKMVHITQALKVINDSDTSLSLFRWAKRQS---WYVP 195
           V V+  + W PE+E  +D  ++  +     + +    D+D +L LF+  +++    +Y  
Sbjct: 129 VGVIAAFPWQPEVEGFVDGAKYXNESEAFVRYVGEWTDADKALELFQELQKEQVDVFYPA 188

Query: 196 GDECYVMLFDVLNESRDF 213
           GD  +V + + + +  DF
Sbjct: 189 GDGYHVPVVEAIKDQGDF 206


>pdb|2VE3|A Chain A, Retinoic Acid Bound Cyanobacterial Cyp120a1
 pdb|2VE3|B Chain B, Retinoic Acid Bound Cyanobacterial Cyp120a1
 pdb|2VE4|A Chain A, Substrate Free Cyanobacterial Cyp120a1
 pdb|2VE4|B Chain B, Substrate Free Cyanobacterial Cyp120a1
          Length = 444

 Score = 31.6 bits (70), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 14/39 (35%), Positives = 20/39 (51%)

Query: 699 AWSLDVRNLSVGAALIAVMHTLHRFRKRMLYYGVVPRRI 737
            W L  R L    AL   M  +HR R+++LY   +PR +
Sbjct: 79  TWPLSTRILLGPNALATQMGEIHRSRRKILYQAFLPRTL 117


>pdb|1TFF|A Chain A, Structure Of Otubain-2
          Length = 234

 Score = 30.4 bits (67), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 3/44 (6%)

Query: 328 FQEMKERNFRPSFNIFASLVDSMGKAGRLDTSMKVYMEMQGCGH 371
           F+E K RNF   FN F S+V+ + K G + + +KV+ +     H
Sbjct: 90  FEEHKFRNF---FNAFYSVVELVEKDGSVSSLLKVFNDQSASDH 130


  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
   0.322    0.136    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,260,252
Number of Sequences: 62578
Number of extensions: 929121
Number of successful extensions: 1787
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1783
Number of HSP's gapped (non-prelim): 6
length of query: 827
length of database: 14,973,337
effective HSP length: 107
effective length of query: 720
effective length of database: 8,277,491
effective search space: 5959793520
effective search space used: 5959793520
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 56 (26.2 bits)