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= 041936
         (402 letters)

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

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



>pdb|4EX5|A Chain A, Crystal Structure Of Lysyl-Trna Synthetase Lysrs From
           Burkholderia Thailandensis Bound To Lysine
 pdb|4EX5|B Chain B, Crystal Structure Of Lysyl-Trna Synthetase Lysrs From
           Burkholderia Thailandensis Bound To Lysine
          Length = 529

 Score = 32.0 bits (71), Expect = 0.68,   Method: Compositional matrix adjust.
 Identities = 18/59 (30%), Positives = 25/59 (42%)

Query: 300 GNFEEAKKFYRIMSNSGLSPNSSVYFTMVYFMCKGGDYETALGFCKESIAKGWVPNFTT 358
           G FE   +  R   N G+SP  +  FTM+ F     DY   + F +  I +  V    T
Sbjct: 270 GGFERVFEINRNFRNEGVSPRHNPEFTMMEFYAAYTDYRWLMDFTERLIRQAAVDALGT 328


>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Mn
 pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Ca
          Length = 501

 Score = 30.8 bits (68), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 22/88 (25%), Positives = 36/88 (40%)

Query: 155 LTIAKDYKEVKRVFIEFPKTYGIKPDLDTYNRVIKAFCEXXXXXXXXXILAEMDRKSIKP 214
           L +AKD  E+    ++  K +GI+P L +Y   +  FC          + A M    + P
Sbjct: 114 LAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVP 173

Query: 215 NASSFGALVAGFYKEEKYEDVNKVLQMM 242
                 AL+      +  + V K LQ +
Sbjct: 174 EEPELAALLKVSMDTKNADKVYKTLQRL 201


>pdb|3D3F|A Chain A, Crystal Structure Of Yvgn And Cofactor Nadph From Bacillus
           Subtilis
 pdb|3D3F|B Chain B, Crystal Structure Of Yvgn And Cofactor Nadph From Bacillus
           Subtilis
          Length = 275

 Score = 29.6 bits (65), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 13/48 (27%), Positives = 29/48 (60%)

Query: 230 EKYEDVNKVLQMMERYGMKSGVSMYNVRIHSLCKLRKCAEAKALLDEM 277
           +KY+D  + L+ + + G    + + N ++H L +L K AE K +++++
Sbjct: 116 DKYKDTWRALEKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQV 163


>pdb|3F7J|A Chain A, B.Subtilis Yvgn
 pdb|3F7J|B Chain B, B.Subtilis Yvgn
          Length = 276

 Score = 29.6 bits (65), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 13/48 (27%), Positives = 29/48 (60%)

Query: 230 EKYEDVNKVLQMMERYGMKSGVSMYNVRIHSLCKLRKCAEAKALLDEM 277
           +KY+D  + L+ + + G    + + N ++H L +L K AE K +++++
Sbjct: 117 DKYKDTWRALEKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQV 164


>pdb|3B3D|A Chain A, B.Subtilis Ytbe
 pdb|3B3D|B Chain B, B.Subtilis Ytbe
 pdb|3B3D|C Chain C, B.Subtilis Ytbe
          Length = 314

 Score = 28.9 bits (63), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 13/49 (26%), Positives = 27/49 (55%)

Query: 229 EEKYEDVNKVLQMMERYGMKSGVSMYNVRIHSLCKLRKCAEAKALLDEM 277
           E KY++  + L+ + + G    + + N +IH L  L   AE K +++++
Sbjct: 154 EGKYKEAWRALETLYKEGRIKAIGVSNFQIHHLEDLMTAAEIKPMINQV 202


  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
   0.318    0.133    0.380 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,145,383
Number of Sequences: 62578
Number of extensions: 420539
Number of successful extensions: 1255
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1246
Number of HSP's gapped (non-prelim): 12
length of query: 402
length of database: 14,973,337
effective HSP length: 101
effective length of query: 301
effective length of database: 8,652,959
effective search space: 2604540659
effective search space used: 2604540659
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)