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= psy7008
         (101 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 = 34.3 bits (77), Expect = 0.020,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 18  SIVSMCIIKRIGKRPLSLISIGGTAFSALTCGILSYKGTVGSQILPFIMLLLLAFFTSIG 77
           +++++  + + G++PL +I   G A    + G   Y    G   L  ++  + AF  S G
Sbjct: 329 TVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWG 388

Query: 78  IAAIPWMLLSEVFP 91
              + W+LLSE+FP
Sbjct: 389 --PVCWVLLSEIFP 400


>pdb|1DMU|A Chain A, Crystal Structure Of The Restriction Endonuclease Bgli
           (E.C.3.1.21.4) Bound To Its Dna Recognition Sequence
          Length = 299

 Score = 29.3 bits (64), Expect = 0.58,   Method: Compositional matrix adjust.
 Identities = 31/108 (28%), Positives = 51/108 (47%), Gaps = 14/108 (12%)

Query: 2   LCSSPQIFVPTTGFIGSIVSMCIIKRIGKRP------LSLISIGGTA-FSALTCGILSYK 54
           L +SP I+  T GF  SI+    IK +G R       LS   + G   ++ L  GI + +
Sbjct: 120 LLTSPTIYSLTNGFTDSIMMFVDIKSVGPRDSDYDLVLSPNQVSGNGDWAQLEGGIQNNQ 179

Query: 55  GTV----GSQI-LPFIMLLLLAFFTSIGIAAIPWMLLSEVFPLRSVFR 97
            T+     SQI LP I  L +   +   IA +  + +  ++ +RS+ +
Sbjct: 180 QTIQGPRSSQIFLPTIPPLYI--LSDGTIAPVVHLFIKPIYAMRSLTK 225


>pdb|2JAD|A Chain A, Yellow Fluorescent Protein - Glutaredoxin Fusion Protein
          Length = 362

 Score = 26.9 bits (58), Expect = 2.5,   Method: Composition-based stats.
 Identities = 12/34 (35%), Positives = 16/34 (47%)

Query: 68  LLLAFFTSIGIAAIPWMLLSEVFPLRSVFRYHDY 101
           L L F  + G   +PW  L   F L+   RY D+
Sbjct: 42  LTLKFIVTTGKLPVPWPTLVTTFXLQCFARYPDH 75


  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
   0.332    0.146    0.450 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,600,687
Number of Sequences: 62578
Number of extensions: 79931
Number of successful extensions: 364
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 354
Number of HSP's gapped (non-prelim): 11
length of query: 101
length of database: 14,973,337
effective HSP length: 67
effective length of query: 34
effective length of database: 10,780,611
effective search space: 366540774
effective search space used: 366540774
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 45 (21.9 bits)