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= psy2962
         (690 letters)

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

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



>pdb|4GBY|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To D-Xylose
 pdb|4GBZ|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To D-Glucose
 pdb|4GC0|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To
           6-Bromo-6-Deoxy-D-Glucose
          Length = 491

 Score = 55.5 bits (132), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 77/382 (20%), Positives = 154/382 (40%), Gaps = 66/382 (17%)

Query: 196 MMGVLLGSLIFGDISDRFGRKPTFMISILIMDVFGT---------------------LAA 234
           ++G ++G  + G  S+RFGR+ +  I+ ++  + G                      LA 
Sbjct: 65  LIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAG 124

Query: 235 FAPDFWTFTACRLI--VGASTSGVFLVAYVLALEMVGPSKRIIAGTVIHMFFSIGFLLIA 292
           + P+F  +   R+I  +G   + +    Y+  L       ++++     + F  G LL+ 
Sbjct: 125 YVPEFVIY---RIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIF--GQLLVY 179

Query: 293 GLAYFV-----------HDWRHLDILVTLPGLIYLAYWWFIPESARWLISKGRNEEAKLI 341
            + YF+             WR++     +P L++L   + +PES RWL+S+G+ E+A+ I
Sbjct: 180 CVNYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGI 239

Query: 342 IQAVAEENKVILEGFVLDGLLAPSPEEEEKLKAQNDGPKPSIFELFRHPNLFKKSVIIFF 401
           ++             ++   LA    +E K    +         +F    +    ++  F
Sbjct: 240 LRK------------IMGNTLATQAVQEIKHSLDHGRKTGGRLLMFGVGVIVIGVMLSIF 287

Query: 402 LWFV---CSLTYYGLSWNTANLGGNI-YLNFIISGMVEIPAYLSSMLTLDRYGRKNFLCP 457
             FV     L Y    + T     +I  L  II G++ +   + +++T+D++GRK    P
Sbjct: 288 QQFVGINVVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRK----P 343

Query: 458 CLILSGLCLIVS--ALLPLDLNTVSIVLAMMGKFFITGAYG-----AVYIFSAEQFPTVI 510
             I+  L + +   +L          ++A++   F   A+        ++  +E FP  I
Sbjct: 344 LQIIGALGMAIGMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAI 403

Query: 511 RNIGIGAGSTFARVGGIFASYT 532
           R   +        +   F S+T
Sbjct: 404 RGKALAIAVAAQWLANYFVSWT 425


>pdb|3IVZ|A Chain A, Crystal Structure Of Hyperthermophilic Nitrilase
 pdb|3IVZ|B Chain B, Crystal Structure Of Hyperthermophilic Nitrilase
 pdb|3IW3|A Chain A, Crystal Structure Of Hyperthermophilic Nitrilase
 pdb|3IW3|B Chain B, Crystal Structure Of Hyperthermophilic Nitrilase
 pdb|3KI8|A Chain A, Crystal Structure Of Hyperthermophilic Nitrilase
 pdb|3KI8|B Chain B, Crystal Structure Of Hyperthermophilic Nitrilase
 pdb|3KLC|A Chain A, Crystal Structure Of Hyperthermophilic Nitrilase
 pdb|3KLC|B Chain B, Crystal Structure Of Hyperthermophilic Nitrilase
          Length = 262

 Score = 32.7 bits (73), Expect = 0.67,   Method: Compositional matrix adjust.
 Identities = 28/95 (29%), Positives = 41/95 (43%), Gaps = 16/95 (16%)

Query: 251 ASTSGVFLVAYVLALE---------MVGPSKRIIAGTVIHMFFSIGFLLIAG-LAYFVHD 300
           A  +GV++VA     +         +VGP   I     IH+F+   F    G L + V D
Sbjct: 76  ARDTGVYIVAGTAEKDGDVLYNSAVVVGPRGFIGKYRKIHLFYREKFFFEPGDLGFRVFD 135

Query: 301 WRHLDILVTLPGLIYLAYWWFIPESARWLISKGRN 335
              + + V +       + WF PESAR L  KG +
Sbjct: 136 LGFMKVGVMI------XFDWFFPESARTLALKGAD 164


  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
   0.326    0.141    0.439 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,935,754
Number of Sequences: 62578
Number of extensions: 835625
Number of successful extensions: 1954
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: 1948
Number of HSP's gapped (non-prelim): 7
length of query: 690
length of database: 14,973,337
effective HSP length: 106
effective length of query: 584
effective length of database: 8,340,069
effective search space: 4870600296
effective search space used: 4870600296
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (25.8 bits)