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= 007197
         (613 letters)

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

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



>pdb|1JSW|A Chain A, Native L-Aspartate Ammonia Lyase
 pdb|1JSW|B Chain B, Native L-Aspartate Ammonia Lyase
 pdb|1JSW|C Chain C, Native L-Aspartate Ammonia Lyase
 pdb|1JSW|D Chain D, Native L-Aspartate Ammonia Lyase
          Length = 478

 Score = 32.7 bits (73), Expect = 0.61,   Method: Compositional matrix adjust.
 Identities = 20/50 (40%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 155 EVKSFPFMKALETIENKSDPCGGRYIYVHDLPSRFNEDMLKDCKSLSLWT 204
           EV  FP + A + IE  SD CG  Y+ VH    R    M K C  L L +
Sbjct: 255 EVTGFPCVPAEDLIEATSD-CGA-YVMVHGALKRLAVKMSKICNDLRLLS 302


>pdb|4E2K|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
 pdb|4EDG|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
           Bound To Atp And Manganese
 pdb|4EDK|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
           Bound To Gtp And Manganese
 pdb|4EDR|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
           Bound To Utp And Manganese
 pdb|4EDT|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
           Bound To Ppgpp And Manganese
 pdb|4EDV|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
           Bound To Pppgpp And Manganese
 pdb|4EE1|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
           Bound To Ctp And Manganese
          Length = 329

 Score = 28.9 bits (63), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 15/52 (28%), Positives = 32/52 (61%), Gaps = 1/52 (1%)

Query: 478 AYTQYTWHLPKNYSSYSVFIPEDDIRKRNVSIEERLKQISPEQIKEMRETVI 529
           A+T +  +  K+++ Y V I +D+I   ++S E  LK++S + I  M+ +++
Sbjct: 248 AFTTFVKNDKKSFAHYKVSILKDEIAHNDLSYERYLKELSHD-ISLMKSSIL 298


  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
   0.319    0.134    0.421 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,919,433
Number of Sequences: 62578
Number of extensions: 794422
Number of successful extensions: 1558
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1558
Number of HSP's gapped (non-prelim): 2
length of query: 613
length of database: 14,973,337
effective HSP length: 105
effective length of query: 508
effective length of database: 8,402,647
effective search space: 4268544676
effective search space used: 4268544676
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)