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= 041202
         (166 letters)

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

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



>pdb|1COL|A Chain A, Refined Structure Of The Pore-Forming Domain Of Colicin A
           At 2.4 Angstroms Resolution
 pdb|1COL|B Chain B, Refined Structure Of The Pore-Forming Domain Of Colicin A
           At 2.4 Angstroms Resolution
          Length = 204

 Score = 28.5 bits (62), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 4/53 (7%)

Query: 118 QKTGSVPEMADQAKKRVAGMAD----YVGQKTKEVGQDIQSKVHEAGGKTGRT 166
           +K     E+ ++  + +AGM D    ++G K K + +DI   +    GKT R+
Sbjct: 3   EKAKDERELLEKTSELIAGMGDKIGEHLGDKYKAIAKDIADNIKNFQGKTIRS 55


>pdb|3BLV|B Chain B, Yeast Isocitrate Dehydrogenase With Citrate Bound In The
           Regulatory Subunits
 pdb|3BLV|D Chain D, Yeast Isocitrate Dehydrogenase With Citrate Bound In The
           Regulatory Subunits
 pdb|3BLV|F Chain F, Yeast Isocitrate Dehydrogenase With Citrate Bound In The
           Regulatory Subunits
 pdb|3BLV|H Chain H, Yeast Isocitrate Dehydrogenase With Citrate Bound In The
           Regulatory Subunits
          Length = 354

 Score = 26.9 bits (58), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 13/36 (36%), Positives = 22/36 (61%)

Query: 96  LTSGAFGLTALSSLSWVLSILRQKTGSVPEMADQAK 131
           L++G+ GLT  +++   +SI     GS P++A Q K
Sbjct: 257 LSAGSLGLTPSANIGHKISIFEAVHGSAPDIAGQDK 292


>pdb|3BLW|B Chain B, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
           In The Regulatory Subunits
 pdb|3BLW|D Chain D, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
           In The Regulatory Subunits
 pdb|3BLW|F Chain F, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
           In The Regulatory Subunits
 pdb|3BLW|H Chain H, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
           In The Regulatory Subunits
 pdb|3BLW|J Chain J, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
           In The Regulatory Subunits
 pdb|3BLW|L Chain L, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
           In The Regulatory Subunits
 pdb|3BLW|N Chain N, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
           In The Regulatory Subunits
 pdb|3BLW|P Chain P, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
           In The Regulatory Subunits
 pdb|3BLX|B Chain B, Yeast Isocitrate Dehydrogenase (Apo Form)
 pdb|3BLX|D Chain D, Yeast Isocitrate Dehydrogenase (Apo Form)
 pdb|3BLX|F Chain F, Yeast Isocitrate Dehydrogenase (Apo Form)
 pdb|3BLX|H Chain H, Yeast Isocitrate Dehydrogenase (Apo Form)
 pdb|3BLX|J Chain J, Yeast Isocitrate Dehydrogenase (Apo Form)
 pdb|3BLX|L Chain L, Yeast Isocitrate Dehydrogenase (Apo Form)
 pdb|3BLX|N Chain N, Yeast Isocitrate Dehydrogenase (Apo Form)
 pdb|3BLX|P Chain P, Yeast Isocitrate Dehydrogenase (Apo Form)
          Length = 354

 Score = 26.9 bits (58), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 13/36 (36%), Positives = 22/36 (61%)

Query: 96  LTSGAFGLTALSSLSWVLSILRQKTGSVPEMADQAK 131
           L++G+ GLT  +++   +SI     GS P++A Q K
Sbjct: 257 LSAGSLGLTPSANIGHKISIFEAVHGSAPDIAGQDK 292


  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    0.134    0.377 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,768,643
Number of Sequences: 62578
Number of extensions: 117987
Number of successful extensions: 283
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 280
Number of HSP's gapped (non-prelim): 5
length of query: 166
length of database: 14,973,337
effective HSP length: 92
effective length of query: 74
effective length of database: 9,216,161
effective search space: 681995914
effective search space used: 681995914
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: 47 (22.7 bits)