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= 016442
         (389 letters)

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

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



>pdb|1PW4|A Chain A, Crystal Structure Of The Glycerol-3-Phosphate Transporter
           From E.Coli
          Length = 451

 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 47/194 (24%), Positives = 75/194 (38%), Gaps = 21/194 (10%)

Query: 48  LTPWAADTSLLALLAMRAVVGLAEGVALPAMNNMVARWFPQTERARAVAIAMGGFTSGNA 107
             PWA  +S+  +  +  + G  +G+  P     +  W+ Q ER   V++       G  
Sbjct: 111 FVPWAT-SSIAVMFVLLFLCGWFQGMGWPPCGRTMVHWWSQKERGGIVSVWNCAHNVGGG 169

Query: 108 IGLVLSPILMS-----QAGIFGPFVIFGLSGFLWVLVWLSATSSTPDRH--PQISKYELE 160
           I  +L  + M+      A ++ P         L  L   +    TP     P I +Y+ +
Sbjct: 170 IPPLLFLLGMAWFNDWHAALYMP----AFCAILVALFAFAMMRDTPQSCGLPPIEEYKND 225

Query: 161 Y--ILREKQKPLLMGNKHKPATVIPPFRRLLSKMPTWSIIVANAMHSWGFFVILSWMPIY 218
           Y     EK +  L   +     V+P   +LL     W I +AN       + IL W P Y
Sbjct: 226 YPDDYNEKAEQELTAKQIFMQYVLP--NKLL-----WYIAIANVFVYLLRYGILDWSPTY 278

Query: 219 FNFVYHIDLRQASW 232
              V H  L ++SW
Sbjct: 279 LKEVKHFALDKSSW 292


>pdb|1KNM|A Chain A, Streptomyces Lividans Xylan Binding Domain Cbm13 In
           Complex With Lactose
          Length = 130

 Score = 31.2 bits (69), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 17/56 (30%), Positives = 25/56 (44%)

Query: 29  YGGKIIMAWGVALWSLATFLTPWAADTSLLALLAMRAVVGLAEGVALPAMNNMVAR 84
           YG K + A G +  S     + W  D     L +  +VVG+  G+ L A+ N  A 
Sbjct: 55  YGDKCLDAAGTSNGSKVQIYSCWGGDNQKWRLNSDGSVVGVQSGLCLDAVGNGTAN 110


>pdb|1KNL|A Chain A, Streptomyces Lividans Xylan Binding Domain Cbm13
 pdb|1MC9|A Chain A, Strepromyces Lividans Xylan Binding Domain Cbm13 In
           Complex With Xylopentaose
          Length = 130

 Score = 31.2 bits (69), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 17/56 (30%), Positives = 25/56 (44%)

Query: 29  YGGKIIMAWGVALWSLATFLTPWAADTSLLALLAMRAVVGLAEGVALPAMNNMVAR 84
           YG K + A G +  S     + W  D     L +  +VVG+  G+ L A+ N  A 
Sbjct: 55  YGDKCLDAAGTSNGSKVQIYSCWGGDNQKWRLNSDGSVVGVQSGLCLDAVGNGTAN 110


  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    0.138    0.433 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,853,784
Number of Sequences: 62578
Number of extensions: 422591
Number of successful extensions: 1220
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1216
Number of HSP's gapped (non-prelim): 13
length of query: 389
length of database: 14,973,337
effective HSP length: 101
effective length of query: 288
effective length of database: 8,652,959
effective search space: 2492052192
effective search space used: 2492052192
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: 52 (24.6 bits)