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= psy12536
         (205 letters)

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

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



>pdb|1KSF|X Chain X, Crystal Structure Of Clpa, An Hsp100 Chaperone And
           Regulator Of Clpap Protease: Structural Basis Of
           Differences In Function Of The Two Aaa+ Atpase Domains
 pdb|1R6B|X Chain X, High Resolution Crystal Structure Of Clpa
          Length = 758

 Score = 33.5 bits (75), Expect = 0.075,   Method: Compositional matrix adjust.
 Identities = 28/103 (27%), Positives = 46/103 (44%), Gaps = 6/103 (5%)

Query: 27  DLAVQALGMELRVAGCSLIYRKALRLSKTALGDTTVG------QVVNLLSNDVNRFDTAC 80
           D A++AL   +++A   L +      S    G T VG      Q+   L  ++ RFD + 
Sbjct: 464 DKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSE 523

Query: 81  IFLHHLINRLLGAKKMYLGKKTSELRLKTALRTDERVRLMNEI 123
               H ++RL+GA   Y+G     L     ++    V L++EI
Sbjct: 524 YMERHTVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEI 566


>pdb|1E8C|A Chain A, Structure Of Mure The Udp-N-Acetylmuramyl Tripeptide
           Synthetase From E. Coli
 pdb|1E8C|B Chain B, Structure Of Mure The Udp-N-Acetylmuramyl Tripeptide
           Synthetase From E. Coli
          Length = 498

 Score = 27.3 bits (59), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 10/27 (37%), Positives = 17/27 (62%)

Query: 177 IKNIKAKWLPDQPDYTLNDITLDVKNA 203
           ++++ A W+PD P   L + TLD + A
Sbjct: 5   LRDLLAPWVPDAPSRALREXTLDSRVA 31


  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    0.136    0.398 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,845,442
Number of Sequences: 62578
Number of extensions: 156116
Number of successful extensions: 489
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 487
Number of HSP's gapped (non-prelim): 9
length of query: 205
length of database: 14,973,337
effective HSP length: 94
effective length of query: 111
effective length of database: 9,091,005
effective search space: 1009101555
effective search space used: 1009101555
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: 49 (23.5 bits)