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= psy5252
         (285 letters)

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

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



>pdb|3OPB|A Chain A, Crystal Structure Of She4p
 pdb|3OPB|B Chain B, Crystal Structure Of She4p
          Length = 778

 Score = 32.0 bits (71), Expect = 0.42,   Method: Compositional matrix adjust.
 Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 7/60 (11%)

Query: 97  TSFGEDIRALCKNHRETWIFLNLNWSIVADMTLYVVLPLRRSTAEAFQILISHAFGDAGS 156
           TS GE++   CK+   T ++    WS + ++ L   +PL+RST E    ++SH    A  
Sbjct: 591 TSDGEEV---CKHIVSTKVY----WSTIENLMLDENVPLQRSTLELISNMMSHPLTIAAK 643


>pdb|3FBS|A Chain A, The Crystal Structure Of The Oxidoreductase From
           Agrobacterium Tumefaciens
 pdb|3FBS|B Chain B, The Crystal Structure Of The Oxidoreductase From
           Agrobacterium Tumefaciens
          Length = 297

 Score = 28.9 bits (63), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 29/99 (29%), Positives = 41/99 (41%), Gaps = 5/99 (5%)

Query: 89  EGRVTEERTSFGEDIRALCKNHRETWIFLNLNWSIVADMTLYVVLPLRRSTAEAFQILIS 148
           EGRVT+ + SFGE I  +    RET   L L   +  ++     L  R  +A  F     
Sbjct: 76  EGRVTDAKGSFGEFIVEIDGGRRETAGRLILAMGVTDELPEIAGLRERWGSA-VFHCPYC 134

Query: 149 HAFG-DAGSPYLIGLLSEMFRHSLQL---GASTLVANAM 183
           H +  D G   +I        H+L L   G +T   N +
Sbjct: 135 HGYELDQGKIGVIAASPMAIHHALMLPDWGETTFFTNGI 173


>pdb|2W11|A Chain A, Structure Of The L-2-Haloacid Dehalogenase From Sulfolobus
           Tokodaii
 pdb|2W11|B Chain B, Structure Of The L-2-Haloacid Dehalogenase From Sulfolobus
           Tokodaii
          Length = 206

 Score = 28.1 bits (61), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 10/64 (15%)

Query: 22  VKDLRSQMLAFFYFAIPIGSGLGYIVGSTAFSVMGAWPWSLR----------VTPVLGAC 71
           VK+ +     + YF   IG+   ++V S AF V+GA    +R          V P+ G  
Sbjct: 129 VKEYKPSPKVYKYFLDSIGAKEAFLVSSNAFDVIGAKNAGMRSIFVNRKNTIVDPIGGKP 188

Query: 72  AVLL 75
            V++
Sbjct: 189 DVIV 192


>pdb|2W43|A Chain A, Structure Of L-Haloacid Dehalogenase From S. Tokodaii
 pdb|2W43|B Chain B, Structure Of L-Haloacid Dehalogenase From S. Tokodaii
          Length = 201

 Score = 27.7 bits (60), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 10/64 (15%)

Query: 22  VKDLRSQMLAFFYFAIPIGSGLGYIVGSTAFSVMGAWPWSLR----------VTPVLGAC 71
           VK+ +     + YF   IG+   ++V S AF V+GA    +R          V P+ G  
Sbjct: 124 VKEYKPSPKVYKYFLDSIGAKEAFLVSSNAFDVIGAKNAGMRSIFVNRKNTIVDPIGGKP 183

Query: 72  AVLL 75
            V++
Sbjct: 184 DVIV 187


>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 = 27.7 bits (60), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 16/45 (35%), Positives = 25/45 (55%)

Query: 3   GIGEASYSTIAPTIISDLFVKDLRSQMLAFFYFAIPIGSGLGYIV 47
           GIG    S ++P  I++L    +R ++++F  FAI  G  L Y V
Sbjct: 137 GIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCV 181


  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
   0.324    0.138    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,108,111
Number of Sequences: 62578
Number of extensions: 253895
Number of successful extensions: 591
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 588
Number of HSP's gapped (non-prelim): 13
length of query: 285
length of database: 14,973,337
effective HSP length: 98
effective length of query: 187
effective length of database: 8,840,693
effective search space: 1653209591
effective search space used: 1653209591
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: 51 (24.3 bits)