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= 022618
         (294 letters)

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

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



>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 = 33.1 bits (74), Expect = 0.17,   Method: Composition-based stats.
 Identities = 11/13 (84%), Positives = 13/13 (100%)

Query: 138 QVVGWPPIRSYRK 150
           QVVGWPP+R+YRK
Sbjct: 1   QVVGWPPVRNYRK 13


>pdb|1NLT|A Chain A, The Crystal Structure Of Hsp40 Ydj1
          Length = 248

 Score = 29.6 bits (65), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 7/57 (12%)

Query: 220 HNVPSRDG-----LSESRLMDLLHGSEYVLTYEDKDGDWMLVGDVPWEMFTDSCRRL 271
           H    RDG      +E  L+  + G E+ L  E   GDW+ VG VP E+     R++
Sbjct: 154 HKSFKRDGDDLVYEAEIDLLTAIAGGEFAL--EHVSGDWLKVGIVPGEVIAPGMRKV 208


>pdb|1XAO|A Chain A, Hsp40-Ydj1 Dimerization Domain
 pdb|1XAO|B Chain B, Hsp40-Ydj1 Dimerization Domain
          Length = 121

 Score = 29.6 bits (65), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 2/43 (4%)

Query: 229 SESRLMDLLHGSEYVLTYEDKDGDWMLVGDVPWEMFTDSCRRL 271
           +E  L+  + G E+ L  E   GDW+ VG VP E+     R++
Sbjct: 13  AEIDLLTAIAGGEFAL--EHVSGDWLKVGIVPGEVIAPGMRKV 53


>pdb|4DB1|A Chain A, Cardiac Human Myosin S1dc, Beta Isoform Complexed With
           Mn-Amppnp
 pdb|4DB1|B Chain B, Cardiac Human Myosin S1dc, Beta Isoform Complexed With
           Mn-Amppnp
          Length = 783

 Score = 28.9 bits (63), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 11/45 (24%), Positives = 20/45 (44%)

Query: 211 TIVSGQCSSHNVPSRDGLSESRLMDLLHGSEYVLTYEDKDGDWML 255
           T+   Q    N P  D + +  ++  LH    +   +D+ G WM+
Sbjct: 70  TVKEDQVMQQNPPKFDKIEDMAMLTFLHEPAVLYNLKDRYGSWMI 114


>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 = 27.3 bits (59), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 8/16 (50%), Positives = 13/16 (81%)

Query: 239 GSEYVLTYEDKDGDWM 254
           G  Y++TY+D DG+W+
Sbjct: 360 GQRYLVTYQDSDGNWL 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 = 27.3 bits (59), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 8/16 (50%), Positives = 13/16 (81%)

Query: 239 GSEYVLTYEDKDGDWM 254
           G  Y++TY+D DG+W+
Sbjct: 360 GQRYLVTYQDSDGNWL 375


  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    0.131    0.386 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,379,434
Number of Sequences: 62578
Number of extensions: 326036
Number of successful extensions: 573
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 568
Number of HSP's gapped (non-prelim): 10
length of query: 294
length of database: 14,973,337
effective HSP length: 98
effective length of query: 196
effective length of database: 8,840,693
effective search space: 1732775828
effective search space used: 1732775828
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 bits)