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= 025406
         (253 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 = 28.9 bits (63), Expect = 2.6,   Method: Composition-based stats.
 Identities = 9/13 (69%), Positives = 13/13 (100%)

Query: 80 KVVGWPPIRSFRK 92
          +VVGWPP+R++RK
Sbjct: 1  QVVGWPPVRNYRK 13


>pdb|2ZZV|A Chain A, Crystal Structure Of A Periplasmic Substrate Binding
           Protein In Complex With Calcium And Lactate
 pdb|2ZZV|B Chain B, Crystal Structure Of A Periplasmic Substrate Binding
           Protein In Complex With Calcium And Lactate
 pdb|2ZZW|A Chain A, Crystal Structure Of A Periplasmic Substrate Binding
           Protein In Complex With Zinc And Lactate
 pdb|2ZZW|B Chain B, Crystal Structure Of A Periplasmic Substrate Binding
           Protein In Complex With Zinc And Lactate
 pdb|2ZZX|A Chain A, Crystal Structure Of A Periplasmic Substrate Binding
           Protein In Complex With Lactate
 pdb|2ZZX|B Chain B, Crystal Structure Of A Periplasmic Substrate Binding
           Protein In Complex With Lactate
 pdb|2ZZX|C Chain C, Crystal Structure Of A Periplasmic Substrate Binding
           Protein In Complex With Lactate
 pdb|2ZZX|D Chain D, Crystal Structure Of A Periplasmic Substrate Binding
           Protein In Complex With Lactate
          Length = 361

 Score = 28.5 bits (62), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 2/56 (3%)

Query: 148 AYDSYEKLSAAVDELFRGLLAAQRDSSAGGIVNKQEEEKAI-TGVLDGSGEYTLVY 202
            Y  ++K +  V EL  G L  Q    AG +V   +   A+ TGVLDG   +TL +
Sbjct: 48  GYSLFQKFTERVKELTDGQLEVQ-PFPAGAVVGTFDMFDAVKTGVLDGMNPFTLYW 102


>pdb|3BU7|A Chain A, Crystal Structure And Biochemical Characterization Of
           Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter
           Pomeroyi
 pdb|3BU7|B Chain B, Crystal Structure And Biochemical Characterization Of
           Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter
           Pomeroyi
          Length = 394

 Score = 27.3 bits (59), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 7/82 (8%)

Query: 141 GRKVDLNAYDSYEKLSAAVDELFRGLLAAQRDSSAGGIVNKQEEEKAITGVLDGSGEYTL 200
           GR+V        + +SAA   LF G+   +    AG     +    A+  +++GSG YT+
Sbjct: 102 GRRVVYLRNPQRKDVSAACGWLFSGIQTMKAGERAGA---HRHAASALRFIMEGSGAYTI 158

Query: 201 V----YEDNEGDRMLVGDVPWH 218
           V     E    D +L  +  WH
Sbjct: 159 VDGHKVELGANDFVLTPNGTWH 180


  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
   0.320    0.136    0.398 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,045,281
Number of Sequences: 62578
Number of extensions: 280803
Number of successful extensions: 594
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 593
Number of HSP's gapped (non-prelim): 17
length of query: 253
length of database: 14,973,337
effective HSP length: 97
effective length of query: 156
effective length of database: 8,903,271
effective search space: 1388910276
effective search space used: 1388910276
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)