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= 014893
         (416 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 =  105 bits (261), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 77/252 (30%), Positives = 121/252 (48%), Gaps = 19/252 (7%)

Query: 126 PPSFTWFTARYYAPALGFLMFAVGVNSSEKDFIEAFKRPAAIFAGYVGQFVVKPILGYIF 185
           P +F W    Y    LG +MF +G+     DF   FK P  +  G + QF + P   ++ 
Sbjct: 30  PDTFKW-AGPYIPWLLGIIMFGMGLTLKPSDFDILFKHPKVVIIGVIAQFAIMPATAWLL 88

Query: 186 GTISVSVFGLPTPIGAGIMLVSCVSGAQLSNYATFLTDPPLAPLSIVMTSLSTATAVFVT 245
             +      LP  I  G++LV C  G   SN  T+L    +A LS+ +TS+ST  +  +T
Sbjct: 89  SKL----LNLPAEIAVGVILVGCCPGGTASNVMTYLARGNVA-LSVAVTSVSTLISPLLT 143

Query: 246 PLLSLLLIGKRLPVDVKGMVSSILQIVVVPIAAGLLLNRFFPRICNAIRPFLPPLS---- 301
           P + L+L G+ L +   GM+ SI+++V++PI  GL++++        +   LP +S    
Sbjct: 144 PAIFLMLAGEMLEIQAAGMLMSIVKMVLLPIVLGLIVHKVLGSKTEKLTDALPLVSVAAI 203

Query: 302 VLVTACCVGAPLAINIESVMSPFGXXXXXXXXXFHLSAFVAGYVVTGLAFAEAHDVKALQ 361
           VL+    VGA     +ES +  F          + L  F A +  TGL +         Q
Sbjct: 204 VLIIGAVVGASKGKIMESGLLIFAVVVLHNGIGYLLGFFAAKW--TGLPYDA-------Q 254

Query: 362 RTLSYETGMQSS 373
           +TL+ E GMQ+S
Sbjct: 255 KTLTIEVGMQNS 266


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

 Score =  104 bits (259), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 77/252 (30%), Positives = 120/252 (47%), Gaps = 19/252 (7%)

Query: 126 PPSFTWFTARYYAPALGFLMFAVGVNSSEKDFIEAFKRPAAIFAGYVGQFVVKPILGYIF 185
           P +F W    Y    LG +MF +G+     DF   FK P  +  G + QF + P   +  
Sbjct: 35  PDTFKW-AGPYIPWLLGIIMFGMGLTLKPSDFDILFKHPKVVIIGVIAQFAIMPATAWCL 93

Query: 186 GTISVSVFGLPTPIGAGIMLVSCVSGAQLSNYATFLTDPPLAPLSIVMTSLSTATAVFVT 245
             +      LP  I  G++LV C  G   SN  T+L    +A LS+ +TS+ST T+  +T
Sbjct: 94  SKL----LNLPAEIAVGVILVGCCPGGTASNVMTYLARGNVA-LSVAVTSVSTLTSPLLT 148

Query: 246 PLLSLLLIGKRLPVDVKGMVSSILQIVVVPIAAGLLLNRFFPRICNAIRPFLPPLS---- 301
           P + L+L G+ L +   GM+ SI+++V++PI  GL++++        +   LP +S    
Sbjct: 149 PAIFLMLAGEMLEIQAAGMLMSIVKMVLLPIVLGLIVHKVLGSKTEKLTDALPLVSVAAI 208

Query: 302 VLVTACCVGAPLAINIESVMSPFGXXXXXXXXXFHLSAFVAGYVVTGLAFAEAHDVKALQ 361
           VL+    VGA     +ES +  F          + L  F A +  TGL +         Q
Sbjct: 209 VLIIGAVVGASKGKIMESGLLIFAVVVLHNGIGYLLGFFAAKW--TGLPYDA-------Q 259

Query: 362 RTLSYETGMQSS 373
           + L+ E GMQ+S
Sbjct: 260 KALTIEVGMQNS 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 = 28.5 bits (62), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 25/93 (26%), Positives = 38/93 (40%), Gaps = 10/93 (10%)

Query: 185 FGTISVSVFGLPTPIGAGIMLVSCVSGAQLS--NYATFLTDPPLAPLSIVMTSLSTATAV 242
           F  I  + F +P  + A   L+    G  +    Y  FL   P      +    ST+   
Sbjct: 75  FDEIGTNAFKIPAEVDA---LIGIGGGKAIDAVKYXAFLRKLPF-----ISVPTSTSNDG 126

Query: 243 FVTPLLSLLLIGKRLPVDVKGMVSSILQIVVVP 275
           F +P+ SLL+ GKR  V  K     ++ I V+ 
Sbjct: 127 FSSPVASLLINGKRTSVPAKTPDGIVVDIDVIK 159


  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
   0.325    0.137    0.404 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,300,870
Number of Sequences: 62578
Number of extensions: 374118
Number of successful extensions: 862
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: 852
Number of HSP's gapped (non-prelim): 4
length of query: 416
length of database: 14,973,337
effective HSP length: 101
effective length of query: 315
effective length of database: 8,652,959
effective search space: 2725682085
effective search space used: 2725682085
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 bits)