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= 039786
         (210 letters)

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

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



>pdb|2P1M|B Chain B, Tir1-ask1 Complex Structure
 pdb|2P1N|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiqutin Ligase
 pdb|2P1N|E Chain E, Mechanism Of Auxin Perception By The Tir1 Ubiqutin Ligase
 pdb|2P1O|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
 pdb|2P1P|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
 pdb|2P1Q|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
 pdb|3C6N|B Chain B, Small Molecule Agonists And Antagonists Of F-Box Protein-
           Substrate Interactions In Auxin Perception And Signaling
 pdb|3C6O|B Chain B, Small Molecule Agonists And Antagonists Of F-Box
           Protein-Substrate Interactions In Auxin Perception And
           Signaling
 pdb|3C6P|B Chain B, Small Molecule Agonists And Antagonists Of F-Box Protein-
           Substrate Interactions In Auxin Perception And Signaling
          Length = 594

 Score = 30.8 bits (68), Expect = 0.56,   Method: Compositional matrix adjust.
 Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 1/41 (2%)

Query: 125 PKLQKLLLWDFIAVKSVIIEKGAVPDIRELRIGPC-PLLME 164
           PKLQ+L + D+I    + +      D+RELR+ P  P +ME
Sbjct: 314 PKLQRLWVLDYIEDAGLEVLASTCKDLRELRVFPSEPFVME 354


>pdb|3GZU|A Chain A, Vp7 Recoated Rotavirus Dlp
 pdb|3GZU|B Chain B, Vp7 Recoated Rotavirus Dlp
          Length = 800

 Score = 27.7 bits (60), Expect = 4.7,   Method: Composition-based stats.
 Identities = 10/23 (43%), Positives = 15/23 (65%)

Query: 132 LWDFIAVKSVIIEKGAVPDIREL 154
           LWD I   + I+ +  VPD++EL
Sbjct: 237 LWDTITTSNYILARSVVPDLKEL 259


>pdb|3N09|A Chain A, Atomic Model Of An Infectious Rotavirus Particle
 pdb|3N09|B Chain B, Atomic Model Of An Infectious Rotavirus Particle
          Length = 800

 Score = 27.7 bits (60), Expect = 5.0,   Method: Composition-based stats.
 Identities = 10/23 (43%), Positives = 15/23 (65%)

Query: 132 LWDFIAVKSVIIEKGAVPDIREL 154
           LWD I   + I+ +  VPD++EL
Sbjct: 237 LWDTITTSNYILARSVVPDLKEL 259


>pdb|3KZ4|A Chain A, Crystal Structure Of The Rotavirus Double Layered Particle
 pdb|3KZ4|B Chain B, Crystal Structure Of The Rotavirus Double Layered Particle
 pdb|4F5X|A Chain A, Location Of The Dsrna-dependent Polymerase, Vp1, In
           Rotavirus Particles
 pdb|4F5X|B Chain B, Location Of The Dsrna-dependent Polymerase, Vp1, In
           Rotavirus Particles
          Length = 880

 Score = 27.7 bits (60), Expect = 5.0,   Method: Composition-based stats.
 Identities = 10/23 (43%), Positives = 15/23 (65%)

Query: 132 LWDFIAVKSVIIEKGAVPDIREL 154
           LWD I   + I+ +  VPD++EL
Sbjct: 317 LWDTITTSNYILARSVVPDLKEL 339


>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
 pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
 pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
 pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
          Length = 727

 Score = 27.3 bits (59), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 25/82 (30%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 17  NGKDLCGLIANLKNLESLTVEMTSKEEILDXXXXXXPPQYLQRLYLTGNMKKLPDWIF-K 75
           NG  L  L A +KNL +L V   S   +            L+  Y   NM     W F  
Sbjct: 255 NGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMVTTLPWEFGN 314

Query: 76  LKNLIRLGLELSGLAEEPIRVL 97
           L NL  LG+E + L ++ +++L
Sbjct: 315 LCNLQFLGVEGNPLEKQFLKIL 336


  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    0.143    0.430 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,094,265
Number of Sequences: 62578
Number of extensions: 227870
Number of successful extensions: 449
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 444
Number of HSP's gapped (non-prelim): 9
length of query: 210
length of database: 14,973,337
effective HSP length: 95
effective length of query: 115
effective length of database: 9,028,427
effective search space: 1038269105
effective search space used: 1038269105
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: 49 (23.5 bits)