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= 040933
         (298 letters)

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

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



>pdb|3RG1|A Chain A, Crystal Structure Of The Rp105MD-1 Complex
 pdb|3RG1|E Chain E, Crystal Structure Of The Rp105MD-1 Complex
 pdb|3RG1|I Chain I, Crystal Structure Of The Rp105MD-1 Complex
 pdb|3RG1|M Chain M, Crystal Structure Of The Rp105MD-1 Complex
 pdb|3RG1|B Chain B, Crystal Structure Of The Rp105MD-1 Complex
 pdb|3RG1|F Chain F, Crystal Structure Of The Rp105MD-1 Complex
 pdb|3RG1|J Chain J, Crystal Structure Of The Rp105MD-1 Complex
 pdb|3RG1|N Chain N, Crystal Structure Of The Rp105MD-1 Complex
          Length = 612

 Score = 31.6 bits (70), Expect = 0.50,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 3/47 (6%)

Query: 197 LPDRVLPECPQLKLFSVRADHQESSSLTIPNNFFEKMIQVRVINLTY 243
           L D+   ECPQL+L  V   H     +  P++ F+ +  +RV+NL++
Sbjct: 390 LEDQAFKECPQLELLDVAFTHLH---VKAPHSPFQNLHLLRVLNLSH 433


>pdb|3K40|A Chain A, Crystal Structure Of Drosophila 3,4-Dihydroxyphenylalanine
           Decarboxylase
 pdb|3K40|B Chain B, Crystal Structure Of Drosophila 3,4-Dihydroxyphenylalanine
           Decarboxylase
          Length = 475

 Score = 31.6 bits (70), Expect = 0.56,   Method: Compositional matrix adjust.
 Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 3/57 (5%)

Query: 43  KWKDALKQLRR---PSSTNFKHIQPEAYKATALSYDKLEGEELKNLFLLIGYAYVES 96
           KW+D ++ + R   P  T++   +  AY  TA SY  +  + L      IG+ ++ S
Sbjct: 52  KWQDVMQDIERVIMPGVTHWHSPKFHAYFPTANSYPAIVADMLSGAIACIGFTWIAS 108


>pdb|2JE6|B Chain B, Structure Of A 9-Subunit Archaeal Exosome
 pdb|2JEA|B Chain B, Structure Of A 9-Subunit Archaeal Exosome Bound To Rna
 pdb|2JEB|B Chain B, Structure Of A 9-Subunit Archaeal Exosome Bound To Mn Ions
 pdb|4BA1|B Chain B, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
           Inorganic Phosphate
 pdb|4BA2|B Chain B, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
           Inorganic Phosphate
          Length = 250

 Score = 29.3 bits (64), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 15/33 (45%), Positives = 19/33 (57%)

Query: 121 DRVSTLVYKLKASCMLLDEGLPMHDVIRDVAIS 153
           D  S LV  + AS  L D G+PM D+I  VA+ 
Sbjct: 137 DAGSRLVSLMAASLALADAGIPMRDLIAGVAVG 169


>pdb|3L7Z|B Chain B, Crystal Structure Of The S. Solfataricus Archaeal Exosome
 pdb|3L7Z|E Chain E, Crystal Structure Of The S. Solfataricus Archaeal Exosome
 pdb|3L7Z|H Chain H, Crystal Structure Of The S. Solfataricus Archaeal Exosome
          Length = 245

 Score = 29.3 bits (64), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 15/33 (45%), Positives = 19/33 (57%)

Query: 121 DRVSTLVYKLKASCMLLDEGLPMHDVIRDVAIS 153
           D  S LV  + AS  L D G+PM D+I  VA+ 
Sbjct: 132 DAGSRLVSLMAASLALADAGIPMRDLIAGVAVG 164


>pdb|2BR2|B Chain B, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|D Chain D, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|F Chain F, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|H Chain H, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|J Chain J, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|L Chain L, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|N Chain N, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|P Chain P, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|R Chain R, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|T Chain T, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|V Chain V, Rnase Ph Core Of The Archaeal Exosome
 pdb|2BR2|X Chain X, Rnase Ph Core Of The Archaeal Exosome
 pdb|2C37|B Chain B, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|D Chain D, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|F Chain F, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|H Chain H, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|J Chain J, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|L Chain L, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|N Chain N, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|P Chain P, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|R Chain R, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|T Chain T, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|V Chain V, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C37|X Chain X, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
           Rna
 pdb|2C38|B Chain B, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|D Chain D, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|F Chain F, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|H Chain H, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|J Chain J, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|L Chain L, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|N Chain N, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|P Chain P, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|R Chain R, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|T Chain T, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|V Chain V, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C38|X Chain X, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
           Rna
 pdb|2C39|B Chain B, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|D Chain D, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|F Chain F, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|H Chain H, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|J Chain J, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|L Chain L, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|N Chain N, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|P Chain P, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|R Chain R, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|T Chain T, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|V Chain V, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
 pdb|2C39|X Chain X, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
          Length = 248

 Score = 29.3 bits (64), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 15/33 (45%), Positives = 19/33 (57%)

Query: 121 DRVSTLVYKLKASCMLLDEGLPMHDVIRDVAIS 153
           D  S LV  + AS  L D G+PM D+I  VA+ 
Sbjct: 135 DAGSRLVSLMAASLALADAGIPMRDLIAGVAVG 167


>pdb|1PMM|A Chain A, Crystal Structure Of Escherichia Coli Gadb (Low Ph)
 pdb|1PMM|B Chain B, Crystal Structure Of Escherichia Coli Gadb (Low Ph)
 pdb|1PMM|C Chain C, Crystal Structure Of Escherichia Coli Gadb (Low Ph)
 pdb|1PMM|D Chain D, Crystal Structure Of Escherichia Coli Gadb (Low Ph)
 pdb|1PMM|E Chain E, Crystal Structure Of Escherichia Coli Gadb (Low Ph)
 pdb|1PMM|F Chain F, Crystal Structure Of Escherichia Coli Gadb (Low Ph)
 pdb|1PMO|A Chain A, Crystal Structure Of Escherichia Coli Gadb (Neutral Ph)
 pdb|1PMO|B Chain B, Crystal Structure Of Escherichia Coli Gadb (Neutral Ph)
 pdb|1PMO|C Chain C, Crystal Structure Of Escherichia Coli Gadb (Neutral Ph)
 pdb|1PMO|D Chain D, Crystal Structure Of Escherichia Coli Gadb (Neutral Ph)
 pdb|1PMO|E Chain E, Crystal Structure Of Escherichia Coli Gadb (Neutral Ph)
 pdb|1PMO|F Chain F, Crystal Structure Of Escherichia Coli Gadb (Neutral Ph)
 pdb|2DGL|A Chain A, Crystal Structure Of Escherichia Coli Gadb In Complex With
           Bromide
 pdb|2DGL|B Chain B, Crystal Structure Of Escherichia Coli Gadb In Complex With
           Bromide
 pdb|2DGL|C Chain C, Crystal Structure Of Escherichia Coli Gadb In Complex With
           Bromide
 pdb|2DGL|D Chain D, Crystal Structure Of Escherichia Coli Gadb In Complex With
           Bromide
 pdb|2DGL|E Chain E, Crystal Structure Of Escherichia Coli Gadb In Complex With
           Bromide
 pdb|2DGL|F Chain F, Crystal Structure Of Escherichia Coli Gadb In Complex With
           Bromide
 pdb|2DGM|A Chain A, Crystal Structure Of Escherichia Coli Gadb In Complex With
           Iodide
 pdb|2DGM|B Chain B, Crystal Structure Of Escherichia Coli Gadb In Complex With
           Iodide
 pdb|2DGM|C Chain C, Crystal Structure Of Escherichia Coli Gadb In Complex With
           Iodide
 pdb|2DGM|D Chain D, Crystal Structure Of Escherichia Coli Gadb In Complex With
           Iodide
 pdb|2DGM|E Chain E, Crystal Structure Of Escherichia Coli Gadb In Complex With
           Iodide
 pdb|2DGM|F Chain F, Crystal Structure Of Escherichia Coli Gadb In Complex With
           Iodide
 pdb|3FZ6|A Chain A, Crystal Structure Of Glutamate Decarboxylase Beta From
           Escherichia Coli: Complex With Xenon
 pdb|3FZ6|B Chain B, Crystal Structure Of Glutamate Decarboxylase Beta From
           Escherichia Coli: Complex With Xenon
 pdb|3FZ6|C Chain C, Crystal Structure Of Glutamate Decarboxylase Beta From
           Escherichia Coli: Complex With Xenon
 pdb|3FZ6|D Chain D, Crystal Structure Of Glutamate Decarboxylase Beta From
           Escherichia Coli: Complex With Xenon
 pdb|3FZ6|E Chain E, Crystal Structure Of Glutamate Decarboxylase Beta From
           Escherichia Coli: Complex With Xenon
 pdb|3FZ6|F Chain F, Crystal Structure Of Glutamate Decarboxylase Beta From
           Escherichia Coli: Complex With Xenon
 pdb|3FZ7|A Chain A, Crystal Structure Of Apo Glutamate Decarboxylase Beta From
           Escherichia Coli
 pdb|3FZ7|B Chain B, Crystal Structure Of Apo Glutamate Decarboxylase Beta From
           Escherichia Coli
 pdb|3FZ7|C Chain C, Crystal Structure Of Apo Glutamate Decarboxylase Beta From
           Escherichia Coli
 pdb|3FZ7|D Chain D, Crystal Structure Of Apo Glutamate Decarboxylase Beta From
           Escherichia Coli
 pdb|3FZ7|E Chain E, Crystal Structure Of Apo Glutamate Decarboxylase Beta From
           Escherichia Coli
 pdb|3FZ7|F Chain F, Crystal Structure Of Apo Glutamate Decarboxylase Beta From
           Escherichia Coli
 pdb|3FZ8|A Chain A, Crystal Structure Of Glutamate Decarboxylase Beta From
           Escherichia Coli: Reduced Schiff Base With Plp
 pdb|3FZ8|B Chain B, Crystal Structure Of Glutamate Decarboxylase Beta From
           Escherichia Coli: Reduced Schiff Base With Plp
 pdb|3FZ8|C Chain C, Crystal Structure Of Glutamate Decarboxylase Beta From
           Escherichia Coli: Reduced Schiff Base With Plp
 pdb|3FZ8|D Chain D, Crystal Structure Of Glutamate Decarboxylase Beta From
           Escherichia Coli: Reduced Schiff Base With Plp
 pdb|3FZ8|E Chain E, Crystal Structure Of Glutamate Decarboxylase Beta From
           Escherichia Coli: Reduced Schiff Base With Plp
 pdb|3FZ8|F Chain F, Crystal Structure Of Glutamate Decarboxylase Beta From
           Escherichia Coli: Reduced Schiff Base With Plp
          Length = 466

 Score = 28.9 bits (63), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 1/44 (2%)

Query: 141 LPMHDVIRDVAISIVSAEKNV-FTATGELFDGCMEWSDENAVKL 183
            P+H++  DVA  I++ E  +   A   L   C  W DEN  KL
Sbjct: 32  FPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKL 75


>pdb|1XEY|A Chain A, Crystal Structure Of The Complex Of Escherichia Coli Gada
           With Glutarate At 2.05 A Resolution
 pdb|1XEY|B Chain B, Crystal Structure Of The Complex Of Escherichia Coli Gada
           With Glutarate At 2.05 A Resolution
          Length = 466

 Score = 28.9 bits (63), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 1/44 (2%)

Query: 141 LPMHDVIRDVAISIVSAEKNV-FTATGELFDGCMEWSDENAVKL 183
            P+H++  DVA  I++ E  +   A   L   C  W DEN  KL
Sbjct: 32  FPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKL 75


>pdb|2DGK|A Chain A, Crystal Structure Of An N-terminal Deletion Mutant Of
           Escherichia Coli Gadb In An Autoinhibited State
           (aldamine)
 pdb|2DGK|B Chain B, Crystal Structure Of An N-terminal Deletion Mutant Of
           Escherichia Coli Gadb In An Autoinhibited State
           (aldamine)
 pdb|2DGK|C Chain C, Crystal Structure Of An N-terminal Deletion Mutant Of
           Escherichia Coli Gadb In An Autoinhibited State
           (aldamine)
 pdb|2DGK|D Chain D, Crystal Structure Of An N-terminal Deletion Mutant Of
           Escherichia Coli Gadb In An Autoinhibited State
           (aldamine)
 pdb|2DGK|E Chain E, Crystal Structure Of An N-terminal Deletion Mutant Of
           Escherichia Coli Gadb In An Autoinhibited State
           (aldamine)
 pdb|2DGK|F Chain F, Crystal Structure Of An N-terminal Deletion Mutant Of
           Escherichia Coli Gadb In An Autoinhibited State
           (aldamine)
          Length = 452

 Score = 28.5 bits (62), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 1/44 (2%)

Query: 141 LPMHDVIRDVAISIVSAEKNV-FTATGELFDGCMEWSDENAVKL 183
            P+H++  DVA  I++ E  +   A   L   C  W DEN  KL
Sbjct: 18  FPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKL 61


>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1
           Bound To Adp
 pdb|1Z6T|B Chain B, Structure Of The Apoptotic Protease-activating Factor 1
           Bound To Adp
 pdb|1Z6T|C Chain C, Structure Of The Apoptotic Protease-activating Factor 1
           Bound To Adp
 pdb|1Z6T|D Chain D, Structure Of The Apoptotic Protease-activating Factor 1
           Bound To Adp
          Length = 591

 Score = 27.7 bits (60), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 8/64 (12%)

Query: 15  ARDVAKECVGLPVSIVAVARALRSASIFKWKDALKQLRRPSSTNFKHIQPEAYKATALSY 74
           A  + KEC G P+ +  +   LR     +W+  LKQL+   +  FK I+    K+++  Y
Sbjct: 310 AHSIIKECKGSPLVVSLIGALLRDFP-NRWEYYLKQLQ---NKQFKRIR----KSSSYDY 361

Query: 75  DKLE 78
           + L+
Sbjct: 362 EALD 365


  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
   0.321    0.137    0.395 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,607,121
Number of Sequences: 62578
Number of extensions: 272546
Number of successful extensions: 616
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 612
Number of HSP's gapped (non-prelim): 12
length of query: 298
length of database: 14,973,337
effective HSP length: 98
effective length of query: 200
effective length of database: 8,840,693
effective search space: 1768138600
effective search space used: 1768138600
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: 51 (24.3 bits)