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= psy2968
         (173 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 = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 3/71 (4%)

Query: 23  NWQYLCVITSLPLLVAVITPWIVPESARWLVSQGRVDEAVVIMKRFEKINNKKVDPKLYQ 82
            W+Y+     +P L+ ++  + VPES RWL+S+G+ ++A  I++   KI    +  +  Q
Sbjct: 198 GWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILR---KIMGNTLATQAVQ 254

Query: 83  QLKETCQRQAK 93
           ++K +     K
Sbjct: 255 EIKHSLDHGRK 265


>pdb|2HYE|C Chain C, Crystal Structure Of The Ddb1-cul4a-rbx1-sv5v Complex
          Length = 759

 Score = 28.9 bits (63), Expect = 1.5,   Method: Composition-based stats.
 Identities = 10/28 (35%), Positives = 18/28 (64%)

Query: 69  EKINNKKVDPKLYQQLKETCQRQAKQEI 96
           E + + KV P LY+QL++ C+   + +I
Sbjct: 91  ENLCSHKVSPMLYKQLRQACEDHVQAQI 118


>pdb|4A0K|A Chain A, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
           Site Containing Dna-Duplex
          Length = 742

 Score = 28.9 bits (63), Expect = 1.5,   Method: Composition-based stats.
 Identities = 10/28 (35%), Positives = 18/28 (64%)

Query: 69  EKINNKKVDPKLYQQLKETCQRQAKQEI 96
           E + + KV P LY+QL++ C+   + +I
Sbjct: 74  ENLCSHKVSPMLYKQLRQACEDHVQAQI 101


  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    0.434 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,633,617
Number of Sequences: 62578
Number of extensions: 154906
Number of successful extensions: 864
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 860
Number of HSP's gapped (non-prelim): 4
length of query: 173
length of database: 14,973,337
effective HSP length: 92
effective length of query: 81
effective length of database: 9,216,161
effective search space: 746509041
effective search space used: 746509041
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 48 (23.1 bits)