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= 017170
         (376 letters)

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

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



>pdb|3VB9|A Chain A, Crystal Structure Of Vpa0735 From Vibrio Parahaemolyticus
           In Monoclinic Form, Northeast Structural Genomics Target
           Vpr109
 pdb|3VB9|B Chain B, Crystal Structure Of Vpa0735 From Vibrio Parahaemolyticus
           In Monoclinic Form, Northeast Structural Genomics Target
           Vpr109
 pdb|3VB9|C Chain C, Crystal Structure Of Vpa0735 From Vibrio Parahaemolyticus
           In Monoclinic Form, Northeast Structural Genomics Target
           Vpr109
 pdb|3VB9|D Chain D, Crystal Structure Of Vpa0735 From Vibrio Parahaemolyticus
           In Monoclinic Form, Northeast Structural Genomics Target
           Vpr109
          Length = 483

 Score = 32.0 bits (71), Expect = 0.62,   Method: Compositional matrix adjust.
 Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 13/58 (22%)

Query: 279 NYGELSSALEKMFSCFTIGQCGSHEAPGREMLSESKLKDLLHGSEYVLTYEDKDGDWM 336
           NY EL       +   T+ +      PG              G  Y++TY+D DG+W+
Sbjct: 331 NYDELDERAAWFYEAITVSRGXKSTIPG-------------FGQRYLVTYQDSDGNWL 375


>pdb|2P3Y|A Chain A, Crystal Structure Of Vpa0735 From Vibrio Parahaemolyticus.
           Northeast Structural Genomics Target Vpr109
 pdb|2P3Y|B Chain B, Crystal Structure Of Vpa0735 From Vibrio Parahaemolyticus.
           Northeast Structural Genomics Target Vpr109
          Length = 491

 Score = 32.0 bits (71), Expect = 0.62,   Method: Compositional matrix adjust.
 Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 13/58 (22%)

Query: 279 NYGELSSALEKMFSCFTIGQCGSHEAPGREMLSESKLKDLLHGSEYVLTYEDKDGDWM 336
           NY EL       +   T+ +      PG              G  Y++TY+D DG+W+
Sbjct: 331 NYDELDERAAWFYEAITVSRGXKSTIPG-------------FGQRYLVTYQDSDGNWL 375


>pdb|2P1N|C Chain C, Mechanism Of Auxin Perception By The Tir1 Ubiqutin Ligase
 pdb|2P1N|F Chain F, Mechanism Of Auxin Perception By The Tir1 Ubiqutin Ligase
 pdb|2P1O|C Chain C, Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
 pdb|2P1Q|C Chain C, Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
          Length = 13

 Score = 30.0 bits (66), Expect = 2.0,   Method: Composition-based stats.
 Identities = 10/13 (76%), Positives = 13/13 (100%)

Query: 223 QVVGWPPIRSFRK 235
           QVVGWPP+R++RK
Sbjct: 1   QVVGWPPVRNYRK 13


  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
   0.312    0.132    0.386 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,795,603
Number of Sequences: 62578
Number of extensions: 426590
Number of successful extensions: 648
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 645
Number of HSP's gapped (non-prelim): 6
length of query: 376
length of database: 14,973,337
effective HSP length: 100
effective length of query: 276
effective length of database: 8,715,537
effective search space: 2405488212
effective search space used: 2405488212
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 bits)