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= psy2089
         (216 letters)

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

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



>pdb|2YC3|A Chain A, Inhibitors Of The Herbicidal Target Ispd
 pdb|2YC5|A Chain A, Inhibitors Of The Herbicidal Target Ispd
          Length = 228

 Score = 32.0 bits (71), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 25/104 (24%), Positives = 51/104 (49%), Gaps = 20/104 (19%)

Query: 64  FLRRTREKFQSNKNVD------NNEQISLLYNEGLKELEVLKRQVLISQLFKPDKLVIET 117
           F R   E+++ + +VD        E+   +Y+ GL+E++V    V I    +P       
Sbjct: 58  FFRDIFEEYEESIDVDLSFAIPGKERQDSVYS-GLQEIDVNSELVCIHDSARP------- 109

Query: 118 QMQNSKDTEQ-----TALGCSLLGIPTKSYLSTMFSPRQISKSF 156
            + N++D E+     +A+G ++LG+P K+ +  + S   + K+ 
Sbjct: 110 -LVNTEDVEKVLKDGSAVGAAVLGVPAKATIKEVNSDSLVVKTL 152


>pdb|2YCM|A Chain A, Inhibitors Of Herbicidal Target Ispd
          Length = 227

 Score = 32.0 bits (71), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 25/104 (24%), Positives = 51/104 (49%), Gaps = 20/104 (19%)

Query: 64  FLRRTREKFQSNKNVD------NNEQISLLYNEGLKELEVLKRQVLISQLFKPDKLVIET 117
           F R   E+++ + +VD        E+   +Y+ GL+E++V    V I    +P       
Sbjct: 57  FFRDIFEEYEESIDVDLSFAIPGKERQDSVYS-GLQEIDVNSELVCIHDSARP------- 108

Query: 118 QMQNSKDTEQ-----TALGCSLLGIPTKSYLSTMFSPRQISKSF 156
            + N++D E+     +A+G ++LG+P K+ +  + S   + K+ 
Sbjct: 109 -LVNTEDVEKVLKDGSAVGAAVLGVPAKATIKEVNSDSLVVKTL 151


>pdb|1W77|A Chain A, 2c-methyl-d-erythritol 4-phosphate Cytidylyltransferase
           (ispd) From Arabidopsis Thaliana
          Length = 228

 Score = 32.0 bits (71), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 25/104 (24%), Positives = 51/104 (49%), Gaps = 20/104 (19%)

Query: 64  FLRRTREKFQSNKNVD------NNEQISLLYNEGLKELEVLKRQVLISQLFKPDKLVIET 117
           F R   E+++ + +VD        E+   +Y+ GL+E++V    V I    +P       
Sbjct: 58  FFRDIFEEYEESIDVDLRFAIPGKERQDSVYS-GLQEIDVNSELVCIHDSARP------- 109

Query: 118 QMQNSKDTEQ-----TALGCSLLGIPTKSYLSTMFSPRQISKSF 156
            + N++D E+     +A+G ++LG+P K+ +  + S   + K+ 
Sbjct: 110 -LVNTEDVEKVLKDGSAVGAAVLGVPAKATIKEVNSDSLVVKTL 152


>pdb|3BWG|A Chain A, The Crystal Structure Of Possible Transcriptional
          Regulator Yydk From Bacillus Subtilis Subsp. Subtilis
          Str. 168
 pdb|3BWG|B Chain B, The Crystal Structure Of Possible Transcriptional
          Regulator Yydk From Bacillus Subtilis Subsp. Subtilis
          Str. 168
 pdb|3BWG|C Chain C, The Crystal Structure Of Possible Transcriptional
          Regulator Yydk From Bacillus Subtilis Subsp. Subtilis
          Str. 168
          Length = 239

 Score = 27.3 bits (59), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 34/80 (42%), Gaps = 16/80 (20%)

Query: 14 QMGDKLPNVECLALSTPVTHMSVSKDMILKLYKALLRESSKFPAYNYRMYFLRRTREKFQ 73
          Q GDKLP +E L          VSK  I K  + L ++ + F      ++  +  R+ + 
Sbjct: 24 QQGDKLPVLETLX-----AQFEVSKSTITKSLELLEQKGAIFQVRGSGIFVRKHKRKGY- 77

Query: 74 SNKNVDNNEQISLLYNEGLK 93
                    ISLL N+G K
Sbjct: 78 ----------ISLLSNQGFK 87


  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
   0.323    0.136    0.390 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,153,982
Number of Sequences: 62578
Number of extensions: 175861
Number of successful extensions: 432
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 428
Number of HSP's gapped (non-prelim): 11
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 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)