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= psy14865
         (98 letters)

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

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



>pdb|3RIT|A Chain A, Crystal Structure Of Dipeptide Epimerase From
           Methylococcus Capsulatus Complexed With Mg And Dipeptide
           L-Arg-D-Lys
 pdb|3RIT|B Chain B, Crystal Structure Of Dipeptide Epimerase From
           Methylococcus Capsulatus Complexed With Mg And Dipeptide
           L-Arg-D-Lys
 pdb|3RIT|C Chain C, Crystal Structure Of Dipeptide Epimerase From
           Methylococcus Capsulatus Complexed With Mg And Dipeptide
           L-Arg-D-Lys
 pdb|3RIT|D Chain D, Crystal Structure Of Dipeptide Epimerase From
           Methylococcus Capsulatus Complexed With Mg And Dipeptide
           L-Arg-D-Lys
 pdb|3RIT|E Chain E, Crystal Structure Of Dipeptide Epimerase From
           Methylococcus Capsulatus Complexed With Mg And Dipeptide
           L-Arg-D-Lys
 pdb|3RO6|B Chain B, Crystal Structure Of Dipeptide Epimerase From
           Methylococcus Capsulatus Complexed With Mg Ion
 pdb|3RO6|A Chain A, Crystal Structure Of Dipeptide Epimerase From
           Methylococcus Capsulatus Complexed With Mg Ion
 pdb|3RO6|C Chain C, Crystal Structure Of Dipeptide Epimerase From
           Methylococcus Capsulatus Complexed With Mg Ion
 pdb|3RO6|D Chain D, Crystal Structure Of Dipeptide Epimerase From
           Methylococcus Capsulatus Complexed With Mg Ion
 pdb|3RO6|E Chain E, Crystal Structure Of Dipeptide Epimerase From
           Methylococcus Capsulatus Complexed With Mg Ion
 pdb|3RO6|F Chain F, Crystal Structure Of Dipeptide Epimerase From
           Methylococcus Capsulatus Complexed With Mg Ion
          Length = 356

 Score = 28.5 bits (62), Expect = 0.89,   Method: Composition-based stats.
 Identities = 16/42 (38%), Positives = 21/42 (50%)

Query: 25  FALPKFYLLFGVSLCIPANNTIFIKSISETLAKNEPHLTLEF 66
             LP   +L      +P + TI IK + ETLA+   HL L F
Sbjct: 115 LGLPLVEILGRAHDSLPTSVTIGIKPVEETLAEAREHLALGF 156


>pdb|4GWP|B Chain B, Structure Of The Mediator Head Module From S. Cerevisiae
 pdb|4GWQ|B Chain B, Structure Of The Mediator Head Module From S. Cerevisiae
           In Complex With The Carboxy-Terminal Domain (Ctd) Of Rna
           Polymerase Ii Rpb1 Subunit
          Length = 687

 Score = 27.7 bits (60), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 6/45 (13%)

Query: 54  TLAKNEPHLTLEFLEECISGFKQSTIVLKHLCLEYMTPWLPNLVK 98
            LA NE  L LEF+   +S  K+ST       +  M+P+L  +VK
Sbjct: 212 NLAMNESSLALEFVSLLLSSVKEST------GMSSMSPFLRKVVK 250


  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
   0.325    0.139    0.426 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,640,157
Number of Sequences: 62578
Number of extensions: 83773
Number of successful extensions: 250
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: 248
Number of HSP's gapped (non-prelim): 4
length of query: 98
length of database: 14,973,337
effective HSP length: 64
effective length of query: 34
effective length of database: 10,968,345
effective search space: 372923730
effective search space used: 372923730
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: 45 (21.9 bits)