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= 040603
         (172 letters)

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

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



>pdb|1JRK|A Chain A, Crystal Structure Of A Nudix Protein From Pyrobaculum
          Aerophilum Reveals A Dimer With Intertwined Beta Sheets
 pdb|1JRK|B Chain B, Crystal Structure Of A Nudix Protein From Pyrobaculum
          Aerophilum Reveals A Dimer With Intertwined Beta Sheets
 pdb|1JRK|C Chain C, Crystal Structure Of A Nudix Protein From Pyrobaculum
          Aerophilum Reveals A Dimer With Intertwined Beta Sheets
 pdb|1JRK|D Chain D, Crystal Structure Of A Nudix Protein From Pyrobaculum
          Aerophilum Reveals A Dimer With Intertwined Beta Sheets
 pdb|1K26|A Chain A, Structure Of A Nudix Protein From Pyrobaculum Aerophilum
          Solved By The Single Wavelength Anomolous Scattering
          Method
 pdb|1K26|B Chain B, Structure Of A Nudix Protein From Pyrobaculum Aerophilum
          Solved By The Single Wavelength Anomolous Scattering
          Method
 pdb|1K2E|A Chain A, Crystal Structure Of A Nudix Protein From Pyrobaculum
          Aerophilum
 pdb|1K2E|B Chain B, Crystal Structure Of A Nudix Protein From Pyrobaculum
          Aerophilum
          Length = 156

 Score = 29.6 bits (65), Expect = 0.83,   Method: Compositional matrix adjust.
 Identities = 12/27 (44%), Positives = 16/27 (59%)

Query: 13 LGKHTRSAKVIFPGGEIRQIQTPIKAA 39
          L KH R    I+PGG +   +TPI+A 
Sbjct: 16 LVKHKRLGVYIYPGGHVEHNETPIEAV 42


>pdb|3LY5|A Chain A, Ddx18 Dead-Domain
 pdb|3LY5|B Chain B, Ddx18 Dead-Domain
          Length = 262

 Score = 28.5 bits (62), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 47/108 (43%), Gaps = 2/108 (1%)

Query: 1   MGNHISCTLSKPLGKHTRSAKVIFPGGEIRQI-QTPIKAAELMLEKPNFFLINSRSLKIG 59
           M +H+  T    +G   RSA+    G  I  I  TP +  + M   P F   N + L I 
Sbjct: 150 MTHHVH-TYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVID 208

Query: 60  QRFSPLNADEDLEPKNVYVMFPMKRATSKITATDMATLFVLANKAVKR 107
           +    L+   + E K +  + P +R T   +AT    +  LA  ++K+
Sbjct: 209 EADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKK 256


>pdb|3DM5|A Chain A, Structures Of Srp54 And Srp19, The Two Proteins Assembling
           The Ribonucleic Core Of The Signal Recognition Particle
           From The Archaeon Pyrococcus Furiosus.
 pdb|3DM5|B Chain B, Structures Of Srp54 And Srp19, The Two Proteins Assembling
           The Ribonucleic Core Of The Signal Recognition Particle
           From The Archaeon Pyrococcus Furiosus
          Length = 443

 Score = 28.1 bits (61), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 24/47 (51%), Gaps = 6/47 (12%)

Query: 126 VAACTAPMP------KLDDMEEFSQPEYVYRLSVSRSKKPLLETIEE 166
           VAA  AP+       K+DD+E F  P +V RL      + LLE  +E
Sbjct: 262 VAATGAPIKFIGTGEKIDDIEPFDPPRFVSRLLGLGDIQGLLEKFKE 308


  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    0.365 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,696,841
Number of Sequences: 62578
Number of extensions: 166319
Number of successful extensions: 273
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 269
Number of HSP's gapped (non-prelim): 10
length of query: 172
length of database: 14,973,337
effective HSP length: 92
effective length of query: 80
effective length of database: 9,216,161
effective search space: 737292880
effective search space used: 737292880
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: 48 (23.1 bits)