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= 022453
         (297 letters)

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

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



>pdb|3ZUY|A Chain A, Crystal Structure Of A Bacterial Homologue Of The Bile
           Acid Sodium Symporter Asbt
          Length = 323

 Score =  103 bits (258), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 79/253 (31%), Positives = 123/253 (48%), Gaps = 21/253 (8%)

Query: 7   PPSFTWFTARYYAPAL-GFLMFAVGVNSSEKDFIEAFKRPAAIFAGYVGQFVVKPILGYI 65
           P +F W  A  Y P L G +MF +G+     DF   FK P  +  G + QF + P   ++
Sbjct: 30  PDTFKW--AGPYIPWLLGIIMFGMGLTLKPSDFDILFKHPKVVIIGVIAQFAIMPATAWL 87

Query: 66  FGTISVSVFGLPTPIGAGIMLVSCVSGAQLSNYATFLTDPPLAPLSIVMTSLSTATAVFV 125
              +      LP  I  G++LV C  G   SN  T+L    +A LS+ +TS+ST  +  +
Sbjct: 88  LSKL----LNLPAEIAVGVILVGCCPGGTASNVMTYLARGNVA-LSVAVTSVSTLISPLL 142

Query: 126 TPLLSLLLIGKRLPVDVKGMVSSILQIVVVPIAAGLLLNRFFPRICNAIRPFLPPLS--- 182
           TP + L+L G+ L +   GM+ SI+++V++PI  GL++++        +   LP +S   
Sbjct: 143 TPAIFLMLAGEMLEIQAAGMLMSIVKMVLLPIVLGLIVHKVLGSKTEKLTDALPLVSVAA 202

Query: 183 -VLVTACCVGAPLAINIESVMSPFGXXXXXXXXXFHLSAFVAGYVVTGLAFAEAHDVKAL 241
            VL+    VGA     +ES +  F          + L  F A +  TGL +         
Sbjct: 203 IVLIIGAVVGASKGKIMESGLLIFAVVVLHNGIGYLLGFFAAKW--TGLPYDA------- 253

Query: 242 QRTLSYETGMQSS 254
           Q+TL+ E GMQ+S
Sbjct: 254 QKTLTIEVGMQNS 266


>pdb|3ZUX|A Chain A, Crystal Structure Of A Bacterial Homologue Of The Bile
           Acid Sodium Symporter Asbt
          Length = 332

 Score =  103 bits (256), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 79/253 (31%), Positives = 122/253 (48%), Gaps = 21/253 (8%)

Query: 7   PPSFTWFTARYYAPAL-GFLMFAVGVNSSEKDFIEAFKRPAAIFAGYVGQFVVKPILGYI 65
           P +F W  A  Y P L G +MF +G+     DF   FK P  +  G + QF + P   + 
Sbjct: 35  PDTFKW--AGPYIPWLLGIIMFGMGLTLKPSDFDILFKHPKVVIIGVIAQFAIMPATAWC 92

Query: 66  FGTISVSVFGLPTPIGAGIMLVSCVSGAQLSNYATFLTDPPLAPLSIVMTSLSTATAVFV 125
              +      LP  I  G++LV C  G   SN  T+L    +A LS+ +TS+ST T+  +
Sbjct: 93  LSKL----LNLPAEIAVGVILVGCCPGGTASNVMTYLARGNVA-LSVAVTSVSTLTSPLL 147

Query: 126 TPLLSLLLIGKRLPVDVKGMVSSILQIVVVPIAAGLLLNRFFPRICNAIRPFLPPLS--- 182
           TP + L+L G+ L +   GM+ SI+++V++PI  GL++++        +   LP +S   
Sbjct: 148 TPAIFLMLAGEMLEIQAAGMLMSIVKMVLLPIVLGLIVHKVLGSKTEKLTDALPLVSVAA 207

Query: 183 -VLVTACCVGAPLAINIESVMSPFGXXXXXXXXXFHLSAFVAGYVVTGLAFAEAHDVKAL 241
            VL+    VGA     +ES +  F          + L  F A +  TGL +         
Sbjct: 208 IVLIIGAVVGASKGKIMESGLLIFAVVVLHNGIGYLLGFFAAKW--TGLPYDA------- 258

Query: 242 QRTLSYETGMQSS 254
           Q+ L+ E GMQ+S
Sbjct: 259 QKALTIEVGMQNS 271


>pdb|3CE9|A Chain A, Crystal Structure Of Glycerol Dehydrogenase (Np_348253.1)
           From Clostridium Acetobutylicum At 2.37 A Resolution
 pdb|3CE9|B Chain B, Crystal Structure Of Glycerol Dehydrogenase (Np_348253.1)
           From Clostridium Acetobutylicum At 2.37 A Resolution
 pdb|3CE9|C Chain C, Crystal Structure Of Glycerol Dehydrogenase (Np_348253.1)
           From Clostridium Acetobutylicum At 2.37 A Resolution
 pdb|3CE9|D Chain D, Crystal Structure Of Glycerol Dehydrogenase (Np_348253.1)
           From Clostridium Acetobutylicum At 2.37 A Resolution
          Length = 354

 Score = 28.1 bits (61), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 23/85 (27%), Positives = 35/85 (41%), Gaps = 10/85 (11%)

Query: 58  VKPILGYIFGTISVSVFGLPTPIGAGIMLVSCVSGAQLS--NYATFLTDPPLAPLSIVMT 115
           V+ +    F  I  + F +P  + A   L+    G  +    Y  FL   P      +  
Sbjct: 67  VETVKNIDFDEIGTNAFKIPAEVDA---LIGIGGGKAIDAVKYXAFLRKLPF-----ISV 118

Query: 116 SLSTATAVFVTPLLSLLLIGKRLPV 140
             ST+   F +P+ SLL+ GKR  V
Sbjct: 119 PTSTSNDGFSSPVASLLINGKRTSV 143


  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
   0.328    0.141    0.419 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,141,516
Number of Sequences: 62578
Number of extensions: 245925
Number of successful extensions: 502
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: 492
Number of HSP's gapped (non-prelim): 6
length of query: 297
length of database: 14,973,337
effective HSP length: 98
effective length of query: 199
effective length of database: 8,840,693
effective search space: 1759297907
effective search space used: 1759297907
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 bits)