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= 019185
         (345 letters)

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

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



>pdb|3APZ|A Chain A, Apo Form Of Arabidopsis MediumLONG-Chain Length Prenyl
           Pyrophosphate Synthase
 pdb|3APZ|B Chain B, Apo Form Of Arabidopsis MediumLONG-Chain Length Prenyl
           Pyrophosphate Synthase
          Length = 348

 Score = 32.0 bits (71), Expect = 0.48,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 2/70 (2%)

Query: 271 VLSLLKDIPDVEGDKKSGIRTLPVILGKERVLSMSTGILLMAYASAALAGVFSPILLCKL 330
           V SLL D    + D + G+ +L V++G +  +S+  G  L++ A  ALA + +  ++  L
Sbjct: 101 VASLLHDDVLDDADTRRGVGSLNVVMGNK--MSVLAGDFLLSRACGALAALKNTEVVALL 158

Query: 331 VTMIGHSVLG 340
            T + H V G
Sbjct: 159 ATAVEHLVTG 168


>pdb|3AQ0|A Chain A, Ligand-Bound Form Of Arabidopsis MediumLONG-Chain Length
           Prenyl Pyrophosphate Synthase (Surface Polar Residue
           Mutant)
 pdb|3AQ0|B Chain B, Ligand-Bound Form Of Arabidopsis MediumLONG-Chain Length
           Prenyl Pyrophosphate Synthase (Surface Polar Residue
           Mutant)
 pdb|3AQ0|C Chain C, Ligand-Bound Form Of Arabidopsis MediumLONG-Chain Length
           Prenyl Pyrophosphate Synthase (Surface Polar Residue
           Mutant)
 pdb|3AQ0|D Chain D, Ligand-Bound Form Of Arabidopsis MediumLONG-Chain Length
           Prenyl Pyrophosphate Synthase (Surface Polar Residue
           Mutant)
 pdb|3AQ0|E Chain E, Ligand-Bound Form Of Arabidopsis MediumLONG-Chain Length
           Prenyl Pyrophosphate Synthase (Surface Polar Residue
           Mutant)
 pdb|3AQ0|F Chain F, Ligand-Bound Form Of Arabidopsis MediumLONG-Chain Length
           Prenyl Pyrophosphate Synthase (Surface Polar Residue
           Mutant)
 pdb|3AQ0|G Chain G, Ligand-Bound Form Of Arabidopsis MediumLONG-Chain Length
           Prenyl Pyrophosphate Synthase (Surface Polar Residue
           Mutant)
 pdb|3AQ0|H Chain H, Ligand-Bound Form Of Arabidopsis MediumLONG-Chain Length
           Prenyl Pyrophosphate Synthase (Surface Polar Residue
           Mutant)
          Length = 348

 Score = 32.0 bits (71), Expect = 0.50,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 2/70 (2%)

Query: 271 VLSLLKDIPDVEGDKKSGIRTLPVILGKERVLSMSTGILLMAYASAALAGVFSPILLCKL 330
           V SLL D    + D + G+ +L V++G +  +S+  G  L++ A  ALA + +  ++  L
Sbjct: 101 VASLLHDDVLDDADTRRGVGSLNVVMGNK--MSVLAGDFLLSRACGALAALKNTEVVALL 158

Query: 331 VTMIGHSVLG 340
            T + H V G
Sbjct: 159 ATAVEHLVTG 168


>pdb|2ZAY|A Chain A, Crystal Structure Of Response Regulator From
           Desulfuromonas Acetoxidans
 pdb|2ZAY|B Chain B, Crystal Structure Of Response Regulator From
           Desulfuromonas Acetoxidans
          Length = 147

 Score = 27.7 bits (60), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 14/52 (26%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 68  DMMNRYHKPLKKSTVPMALQDDSATKSQNENIVSTSFLDFLTKKLDAFYRLS 119
           D+ N   K  + +++P+      AT  +   ++   F+DF+ K ++A  RLS
Sbjct: 69  DLFNSLKKNPQTASIPVIALSGRATAKEEAQLLDMGFIDFIAKPVNAI-RLS 119


  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    0.138    0.399 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,404,645
Number of Sequences: 62578
Number of extensions: 298586
Number of successful extensions: 1029
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: 1028
Number of HSP's gapped (non-prelim): 3
length of query: 345
length of database: 14,973,337
effective HSP length: 100
effective length of query: 245
effective length of database: 8,715,537
effective search space: 2135306565
effective search space used: 2135306565
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)