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= psy15011
         (334 letters)

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

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



>pdb|2E3U|A Chain A, Crystal Structure Analysis Of Dim2p From Pyrococcus
           Horikoshii Ot3
 pdb|3AEV|B Chain B, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From
           Pyrococcus Horikoshii Ot3
          Length = 219

 Score = 54.7 bits (130), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 33/108 (30%), Positives = 59/108 (54%), Gaps = 2/108 (1%)

Query: 104 KAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVPYEQAVRVLQDDISCDIIKIG 163
           K  +D   G + + +T++T DP  + KARD++  + R    E+A R+L +    +II + 
Sbjct: 66  KITIDSETGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPERAFRLLNEGEYLEIINLT 125

Query: 164 NLV--QNKQRFVKRRQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALG 209
           +++    K    + R R+IG  G T + IE ++   + V G+TVA +G
Sbjct: 126 DIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYGKTVAIIG 173


>pdb|2BL5|A Chain A, Solution Structure Of The Kh-Qua2 Region Of The Xenopus
           Star-Gsg Quaking Protein
          Length = 140

 Score = 30.8 bits (68), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 11/26 (42%), Positives = 18/26 (69%)

Query: 178 RLIGPNGCTLKSIELLTNCYMLVQGQ 203
           R++GP G T K +E  T C ++V+G+
Sbjct: 21  RILGPRGLTAKQLEAETGCKIMVRGK 46


>pdb|1K1G|A Chain A, Structural Basis For Recognition Of The Intron Branch Site
           Rna By Splicing Factor 1
          Length = 131

 Score = 28.9 bits (63), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 13/31 (41%), Positives = 19/31 (61%)

Query: 179 LIGPNGCTLKSIELLTNCYMLVQGQTVAALG 209
           LIGP G TLK+IE   N  ++++G+     G
Sbjct: 27  LIGPRGNTLKNIEKECNAKIMIRGKGSVKEG 57


>pdb|3ETL|A Chain A, Rada Recombinase From Methanococcus Maripaludis In Complex
           With Amppnp
 pdb|3EW9|A Chain A, Rada Recombinase From Methanococcus Maripaludis In Complex
           With Amppnp And Potassium Ions
 pdb|3EWA|A Chain A, Rada Recombinase From Methanococcus Maripaludis In Complex
           With Amppnp And Ammonium Ions
          Length = 322

 Score = 27.7 bits (60), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 164 NLVQNKQRFVKRRQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPHKGLLQSNIGPN 222
           N    + +  +R+Q+L G +  TL  +  L NC +LV  Q  A    + G+ +  IG +
Sbjct: 219 NEFTGRGKLAERQQKL-GRHMATLNKLADLYNCIVLVTNQVAAKPDAYFGVAEQAIGGH 276


  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
   0.320    0.137    0.417 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,285,809
Number of Sequences: 62578
Number of extensions: 347013
Number of successful extensions: 874
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 24
Number of HSP's that attempted gapping in prelim test: 843
Number of HSP's gapped (non-prelim): 54
length of query: 334
length of database: 14,973,337
effective HSP length: 99
effective length of query: 235
effective length of database: 8,778,115
effective search space: 2062857025
effective search space used: 2062857025
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)