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= 018312
         (358 letters)

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

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



>pdb|3ZF7|O Chain O, High-resolution Cryo-electron Microscopy Structure Of
          The Trypanosoma Brucei Ribosome
          Length = 222

 Score = 30.4 bits (67), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 18/40 (45%), Positives = 22/40 (55%), Gaps = 2/40 (5%)

Query: 11 KLTMAASLSATPYKQLVFRHITTRKISSPKLSPSPFTSPS 50
          KLT+A S      K L F  +  RK+S+PKL P    SPS
Sbjct: 58 KLTIAGSEIRNKIKYLQF--LRKRKLSNPKLGPFHHRSPS 95


>pdb|2X8A|A Chain A, Human Nuclear Valosin Containing Protein Like (Nvl), C-
           Terminal Aaa-Atpase Domain
          Length = 274

 Score = 30.4 bits (67), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 31/104 (29%), Positives = 44/104 (42%), Gaps = 9/104 (8%)

Query: 192 GRTATTSIFIAAAVT--DWLDGYIARKMRLGSTFGAFLDPVADKLMVAATLVLLCTKP-- 247
           G  A   +FI AA    D +D  I R  RL  T    L P AD+L +  T+    TKP  
Sbjct: 140 GLEARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITKNGTKPPL 199

Query: 248 -----LELPVFGQVPWLLTVPAIAIIGREITMSAVREWAASQNT 286
                LE           T   ++ + RE ++ A+R+  A Q +
Sbjct: 200 DADVNLEAIAGDLRCDCYTGADLSALVREASICALRQEMARQKS 243


  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
   0.322    0.134    0.413 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,041,041
Number of Sequences: 62578
Number of extensions: 325273
Number of successful extensions: 685
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 685
Number of HSP's gapped (non-prelim): 2
length of query: 358
length of database: 14,973,337
effective HSP length: 100
effective length of query: 258
effective length of database: 8,715,537
effective search space: 2248608546
effective search space used: 2248608546
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)