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= psy6455
         (249 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 = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 60/249 (24%), Positives = 107/249 (42%), Gaps = 34/249 (13%)

Query: 28  ILVIFGGLLYAY--AAISITVLS----FVLPSAQCDFGMTSSDKGWLNAAPMLGMVFGSY 81
           ++   GGLL+ Y  A IS TV S    FV P    +    +S  G+  A+ ++G + G  
Sbjct: 15  LVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSE-SAANSLLGFCVASALIGCIIGGA 73

Query: 82  FWGCLADTQGRKITLIGALLVDGLCGIASS------------------VAQYYGVFLALR 123
             G  ++  GR+ +L  A ++  + G+ S+                  +A Y   F+  R
Sbjct: 74  LGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPEFVIYR 133

Query: 124 FINGFAVTGTLGICFP-YLGEFQPTAYREKVLCWLEMFWTGGIIVLPAVAWLLIPLNLRI 182
            I G  V G   +  P Y+ E  P   R K++ + +     G +++  V + +       
Sbjct: 134 IIGGIGV-GLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSG--- 189

Query: 183 ETPYFLYSSWNLFVTLVSVPSILLALWLTRFPESPKFLFECGEYDQALDILRQM----FS 238
           +  +     W        +P++L  + L   PESP++L   G+ +QA  ILR++     +
Sbjct: 190 DASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGNTLA 249

Query: 239 ANTGKEIEH 247
               +EI+H
Sbjct: 250 TQAVQEIKH 258


>pdb|3ECS|A Chain A, Crystal Structure Of Human Eif2b Alpha
 pdb|3ECS|B Chain B, Crystal Structure Of Human Eif2b Alpha
 pdb|3ECS|C Chain C, Crystal Structure Of Human Eif2b Alpha
 pdb|3ECS|D Chain D, Crystal Structure Of Human Eif2b Alpha
 pdb|3ECS|E Chain E, Crystal Structure Of Human Eif2b Alpha
 pdb|3ECS|F Chain F, Crystal Structure Of Human Eif2b Alpha
 pdb|3ECS|G Chain G, Crystal Structure Of Human Eif2b Alpha
 pdb|3ECS|H Chain H, Crystal Structure Of Human Eif2b Alpha
          Length = 315

 Score = 27.7 bits (60), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 17/37 (45%), Positives = 22/37 (59%), Gaps = 2/37 (5%)

Query: 90  QGRKITLIGALLVDGLCGIASSVAQYYGVFLALRFIN 126
           QG +  L  A  ++ LCG+ SSVA   G  L LRFI+
Sbjct: 43  QGLRANLTSA--IETLCGVDSSVAVSSGGELFLRFIS 77


  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    0.144    0.468 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,679,750
Number of Sequences: 62578
Number of extensions: 310971
Number of successful extensions: 593
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 590
Number of HSP's gapped (non-prelim): 4
length of query: 249
length of database: 14,973,337
effective HSP length: 96
effective length of query: 153
effective length of database: 8,965,849
effective search space: 1371774897
effective search space used: 1371774897
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 bits)