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= 008934
         (548 letters)

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

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



>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 = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 45/203 (22%), Positives = 76/203 (37%), Gaps = 32/203 (15%)

Query: 17  RTLPFIIANEAFERMATVG----FTPNMI--LYLCREYNMETTAATNIIFIWTAATNFLP 70
           R +P+IIA+EA ER +  G     TP ++  L L     +    A ++   +     F P
Sbjct: 12  RQIPYIIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFP 71

Query: 71  IVGALLADSYVGRYRMIGFGCFTCLLGMVLLWSTTILPGAKPPACDQLRNGCESATWSQL 130
           ++G  +AD + G+Y  I             LW + I        C  + +   +     +
Sbjct: 72  LLGGWIADRFFGKYNTI-------------LWLSLIY-------C--VGHAFLAIFEHSV 109

Query: 131 MPLYFAFXXXXXXXXXXXXXXXAFGAEQLDKGDGTKSKGALQSYFSWYYVFVSASSIVAV 190
              Y                  +F  +Q D+ +    K   Q  F  +Y  ++  S  A 
Sbjct: 110 QGFYTGLFLIALGSGGIKPLVSSFMGDQFDQSN----KSLAQKAFDMFYFTINFGSFFAS 165

Query: 191 TCIVYIQDNLGWKVGFGVPAVIM 213
             +  +  N G  V FG+P V+M
Sbjct: 166 LSMPLLLKNFGAAVAFGIPGVLM 188


>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 = 31.2 bits (69), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 9/84 (10%)

Query: 268 KGSMRLMPSENLRFLNKACMAKHPEQDLT--PDGRAS-----NPNSLCTVEQVEELKALI 320
           KG +R  PS NL  +      +  +  LT  P G A      +PN     E +   +A +
Sbjct: 90  KGGLRFAPSVNLSIMKFLGFEQAFKDSLTTLPMGGAKGGSDFDPNGKSDREVMRFCQAFM 149

Query: 321 KASSMDRHVTPNFEIPSGSFNIFA 344
             + + 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 = 30.8 bits (68), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 9/84 (10%)

Query: 268 KGSMRLMPSENLRFLNKACMAKHPEQDLT--PDGRAS-----NPNSLCTVEQVEELKALI 320
           KG +R  PS NL  +      +  +  LT  P G A      +PN     E +   +A +
Sbjct: 89  KGGLRFAPSVNLSIMKFLGFEQAFKDSLTTLPMGGAKGGSDFDPNGKSDREVMRFCQAFM 148

Query: 321 KASSMDRHVTPNFEIPSGSFNIFA 344
             + + RH+ P+ ++P+G   + A
Sbjct: 149 --TELYRHIGPDIDVPAGDLGVGA 170


  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
   0.323    0.137    0.424 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,922,973
Number of Sequences: 62578
Number of extensions: 539274
Number of successful extensions: 921
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: 917
Number of HSP's gapped (non-prelim): 6
length of query: 548
length of database: 14,973,337
effective HSP length: 104
effective length of query: 444
effective length of database: 8,465,225
effective search space: 3758559900
effective search space used: 3758559900
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)