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= 034970
         (77 letters)

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

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



>pdb|2NUD|C Chain C, The Structure Of The Type Iii Effector Avrb Complexed
          With A High-Affinity Rin4 Peptide
 pdb|2NUD|D Chain D, The Structure Of The Type Iii Effector Avrb Complexed
          With A High-Affinity Rin4 Peptide
          Length = 35

 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 19/34 (55%), Positives = 28/34 (82%)

Query: 3  DKGRPLPKFGEWDVNDPASAEGFTVIFNKARDEK 36
          +K   +PKFG+WD N+P+SA+G+T IFNK R+E+
Sbjct: 2  EKVTVVPKFGDWDENNPSSADGYTHIFNKVREER 35


>pdb|1L5J|A Chain A, Crystal Structure Of E. Coli Aconitase B.
 pdb|1L5J|B Chain B, Crystal Structure Of E. Coli Aconitase B
          Length = 865

 Score = 28.5 bits (62), Expect = 0.91,   Method: Composition-based stats.
 Identities = 20/62 (32%), Positives = 27/62 (43%), Gaps = 12/62 (19%)

Query: 12  GEWDVNDPASAEGFTVIFNKARDEKKT---GGKPDSPGKVDPPI---------RHGVDPA 59
            EW +N PA AE  TV   K   E  T      PD+  + D P+         R G++P 
Sbjct: 153 AEWFLNRPALAEKLTVTVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKNAREGIEPD 212

Query: 60  KP 61
           +P
Sbjct: 213 QP 214


>pdb|2ZKR|FF Chain f, Structure Of A Mammalian Ribosomal 60s Subunit Within An
           80s Complex Obtained By Docking Homology Models Of The
           Rna And Proteins Into An 8.7 A Cryo-Em Map
          Length = 266

 Score = 28.1 bits (61), Expect = 1.4,   Method: Composition-based stats.
 Identities = 14/26 (53%), Positives = 16/26 (61%)

Query: 32  ARDEKKTGGKPDSPGKVDPPIRHGVD 57
           AR EKK  GK D P K  P +R GV+
Sbjct: 116 ARAEKKAAGKGDVPTKRPPVLRAGVN 141


  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
   0.314    0.136    0.445 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,997,497
Number of Sequences: 62578
Number of extensions: 116948
Number of successful extensions: 87
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 83
Number of HSP's gapped (non-prelim): 5
length of query: 77
length of database: 14,973,337
effective HSP length: 46
effective length of query: 31
effective length of database: 12,094,749
effective search space: 374937219
effective search space used: 374937219
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 45 (21.9 bits)