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= 013020
         (451 letters)

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

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



>pdb|2YFH|A Chain A, Structure Of A Chimeric Glutamate Dehydrogenase
 pdb|2YFH|B Chain B, Structure Of A Chimeric Glutamate Dehydrogenase
 pdb|2YFH|C Chain C, Structure Of A Chimeric Glutamate Dehydrogenase
 pdb|2YFH|D Chain D, Structure Of A Chimeric Glutamate Dehydrogenase
 pdb|2YFH|E Chain E, Structure Of A Chimeric Glutamate Dehydrogenase
 pdb|2YFH|F Chain F, Structure Of A Chimeric Glutamate Dehydrogenase
          Length = 448

 Score = 31.6 bits (70), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 9/84 (10%)

Query: 171 KGSMRLMPSENLRFLNKACMAKHPEQDLT--PDGRAS-----NPNSLCTVEQVEELKALI 223
           KG +R  PS NL  +      +  +  LT  P G A      +PN     E +   +A +
Sbjct: 90  KGGLRFAPSVNLSIMKFLGFEQAFKDSLTTLPMGGAKGGSDFDPNGKSDREVMRFCQAFM 149

Query: 224 KASSMDRHVTPNFEIPSGSFNIFA 247
             + + RH+ P+ ++P+G   + A
Sbjct: 150 --TELYRHIGPDIDVPAGDLGVGA 171


>pdb|1HRD|A Chain A, Glutamate Dehydrogenase
 pdb|1HRD|B Chain B, Glutamate Dehydrogenase
 pdb|1HRD|C Chain C, Glutamate Dehydrogenase
 pdb|1BGV|A Chain A, Glutamate Dehydrogenase
          Length = 449

 Score = 31.2 bits (69), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 9/84 (10%)

Query: 171 KGSMRLMPSENLRFLNKACMAKHPEQDLT--PDGRAS-----NPNSLCTVEQVEELKALI 223
           KG +R  PS NL  +      +  +  LT  P G A      +PN     E +   +A +
Sbjct: 89  KGGLRFAPSVNLSIMKFLGFEQAFKDSLTTLPMGGAKGGSDFDPNGKSDREVMRFCQAFM 148

Query: 224 KASSMDRHVTPNFEIPSGSFNIFA 247
             + + RH+ P+ ++P+G   + A
Sbjct: 149 --TELYRHIGPDIDVPAGDLGVGA 170


>pdb|2XUT|A Chain A, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter.
 pdb|2XUT|B Chain B, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter.
 pdb|2XUT|C Chain C, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter
          Length = 524

 Score = 30.0 bits (66), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 4/61 (6%)

Query: 56  AFGAEQLDKGDGTKSKGALQSYFSWYYVFVSASSIVAVTCIVYIQDNLGWKVGFGVPAVI 115
           +F  +Q D+ +    K   Q  F  +Y  ++  S  A   +  +  N G  V FG+P V+
Sbjct: 132 SFMGDQFDQSN----KSLAQKAFDMFYFTINFGSFFASLSMPLLLKNFGAAVAFGIPGVL 187

Query: 116 M 116
           M
Sbjct: 188 M 188


  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    0.135    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,213,038
Number of Sequences: 62578
Number of extensions: 429529
Number of successful extensions: 799
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 797
Number of HSP's gapped (non-prelim): 4
length of query: 451
length of database: 14,973,337
effective HSP length: 102
effective length of query: 349
effective length of database: 8,590,381
effective search space: 2998042969
effective search space used: 2998042969
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)