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= psy5244
         (90 letters)

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

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



>pdb|1RZ4|A Chain A, Crystal Structure Of Human Eif3k
          Length = 226

 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 23/48 (47%), Positives = 36/48 (75%)

Query: 42  LRLWVKKYGWKELDNGYIFIANQDENIKTKNITEKIEFENAATIMTSN 89
           L++W  KYGW   ++G IFI +Q+E+IK KNI EKI+F++ ++I  S+
Sbjct: 170 LKVWXSKYGWSADESGQIFICSQEESIKPKNIVEKIDFDSVSSIXASS 217


>pdb|3R2T|A Chain A, 2.2 Angstrom Resolution Crystal Structure Of
           Superantigen-Like Protein From Staphylococcus Aureus
           Subsp. Aureus Nctc 8325.
 pdb|3R2T|B Chain B, 2.2 Angstrom Resolution Crystal Structure Of
           Superantigen-Like Protein From Staphylococcus Aureus
           Subsp. Aureus Nctc 8325
          Length = 249

 Score = 30.0 bits (66), Expect = 0.35,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 2/48 (4%)

Query: 43  RLWVKKYGWKE--LDNGYIFIANQDENIKTKNITEKIEFENAATIMTS 88
           +L +KKY   E   D G I I  +DEN    ++++K++FE  A ++ S
Sbjct: 191 KLLIKKYKLYEGSADKGRIVINMKDENKYEIDLSDKLDFERMADVINS 238


>pdb|1Y56|B Chain B, Crystal Structure Of L-Proline Dehydrogenase From
           P.Horikoshii
          Length = 382

 Score = 26.9 bits (58), Expect = 3.1,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 5/49 (10%)

Query: 42  LRLWVK---KYGWKELDNGYIFIANQDENIKTKNITEKIEFENAATIMT 87
           + LW K   +YG+     GY+F+   DE +KT      IE +N   + T
Sbjct: 68  VELWKKYSEEYGFSFKQTGYLFLLYDDEEVKT--FKRNIEIQNKFGVPT 114


>pdb|3Q73|B Chain B, Cryptococcus Neoformans Protein Farnesyltransferase, Apo
           Enzyme
 pdb|3Q75|B Chain B, Cryptococcus Neoformans Protein Farnesyltransferase In
           Complex With Fpt-Ii And Tkcvvm Peptide
 pdb|3Q78|B Chain B, Cryptococcus Neoformans Protein Farnesyltransferase In
           Complex With Fspp And Ddptasacniq Peptide
 pdb|3Q79|B Chain B, Cryptococcus Neoformans Protein Farnesyltransferase In
           Complex With Farnesyl-Ddptasacniq Product
 pdb|3Q7A|B Chain B, Cryptococcus Neoformans Protein Farnesyltransferase In
           Complex With Fpp And L-778,123
 pdb|3Q7F|B Chain B, Cryptococcus Neoformans Protein Farnesyltransferase In
           Complex With Fpp And Ethylenediamine Inhibitor 1
 pdb|3SFX|B Chain B, Cryptococcus Neoformans Protein Farnesyltransferase In
           Complex With Fpt-Ii And Tipifarnib
 pdb|3SFY|B Chain B, Cryptococcus Neoformans Protein Farnesyltransferase In
           Complex With Fpt-Ii And Ethylenediamine Inhibitor 2
          Length = 520

 Score = 25.8 bits (55), Expect = 5.8,   Method: Composition-based stats.
 Identities = 9/27 (33%), Positives = 13/27 (48%)

Query: 44  LWVKKYGWKELDNGYIFIANQDENIKT 70
           +W    GW E + G I +  +D  I T
Sbjct: 470 IWANALGWIEEEGGEIIVGGKDNRINT 496


  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
   0.315    0.130    0.377 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,943,160
Number of Sequences: 62578
Number of extensions: 49580
Number of successful extensions: 176
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 172
Number of HSP's gapped (non-prelim): 6
length of query: 90
length of database: 14,973,337
effective HSP length: 57
effective length of query: 33
effective length of database: 11,406,391
effective search space: 376410903
effective search space used: 376410903
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)