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= 042559
         (547 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 = 31.6 bits (70), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 28/103 (27%), Positives = 47/103 (45%), Gaps = 16/103 (15%)

Query: 263 HLYNIERMDNASLSMALSACPSLLDLEI-------VGLHVEL-RQTLMSVSMSCPLLERL 314
            L+ ++ +++A L +  S C  L +L +       +  +V L  Q L+SVSM CP LE +
Sbjct: 318 RLWVLDYIEDAGLEVLASTCKDLRELRVFPSEPFVMEPNVALTEQGLVSVSMGCPKLESV 377

Query: 315 FFESSKTGRDDSLKSPTCVDFVNNCPNLTSMALRGF--KLPDY 355
            +   +      + +   +    N PN+T   L     K PDY
Sbjct: 378 LYFCRQ------MTNAALITIARNRPNMTRFRLCIIEPKAPDY 414


>pdb|3N6X|A Chain A, Crystal Structure Of A Putative Glutathionylspermidine
           Synth (Mfla_0391) From Methylobacillus Flagellatus Kt At
           2.35 A R
          Length = 474

 Score = 30.0 bits (66), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 13/31 (41%), Positives = 21/31 (67%)

Query: 273 ASLSMALSACPSLLDLEIVGLHVELRQTLMS 303
           A  ++ALS CP+L++  I   HV+LR  ++S
Sbjct: 405 AQPTLALSTCPTLVETGIAPRHVDLRPFVLS 435


>pdb|4AEH|H Chain H, Crystal Structure Of The Anti-Aahi Fab9c2 Antibody
          Length = 231

 Score = 29.6 bits (65), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 16/34 (47%), Positives = 22/34 (64%), Gaps = 2/34 (5%)

Query: 497 QLSSRTSDDSLLMSCSESSYNSDHGSGNEEGQDS 530
           QLSS TSDDS +  C+   Y+ D+GS +  GQ +
Sbjct: 82  QLSSLTSDDSAVYYCAR--YDGDYGSFDYWGQGT 113


>pdb|2J3W|B Chain B, The Crystal Structure Of The Bet3-Trs31-Sedlin Complex.
 pdb|2J3W|F Chain F, The Crystal Structure Of The Bet3-Trs31-Sedlin Complex
          Length = 188

 Score = 28.9 bits (63), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 373 STSYSIT--GAFLRNLGSGTGGNLLEVLILRDCMHLKEVEVARFLTAVLTGDFKFL 426
           S  YS++   A L ++G G G +LL+VL++R+    +E +V   L  +    +K L
Sbjct: 42  SRVYSVSELQARLADMGQGVGASLLDVLVMREKNGKRETKVLNILLFIKVNVWKAL 97


>pdb|2J3R|B Chain B, The Crystal Structure Of The Bet3-Trs31 Heterodimer
          Length = 157

 Score = 28.9 bits (63), Expect = 7.2,   Method: Composition-based stats.
 Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 373 STSYSIT--GAFLRNLGSGTGGNLLEVLILRDCMHLKEVEVARFLTAVLTGDFKFL 426
           S  YS++   A L ++G G G +LL+VL++R+    +E +V   L  +    +K L
Sbjct: 23  SRVYSVSELQARLADMGQGVGASLLDVLVMREKNGKRETKVLNILLFIKVNVWKAL 78


>pdb|4F9P|D Chain D, Crystal Structure Of The Human Btn3a1 Ectodomain In
           Complex With The 103.2 Single Chain Antibody
 pdb|4F9P|C Chain C, Crystal Structure Of The Human Btn3a1 Ectodomain In
           Complex With The 103.2 Single Chain Antibody
          Length = 254

 Score = 28.5 bits (62), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 14/28 (50%), Positives = 17/28 (60%)

Query: 497 QLSSRTSDDSLLMSCSESSYNSDHGSGN 524
           QLSS TSDDS +  C+ S Y +  G G 
Sbjct: 82  QLSSLTSDDSAVYFCARSDYGAYWGQGT 109


  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
   0.318    0.133    0.384 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,608,154
Number of Sequences: 62578
Number of extensions: 561394
Number of successful extensions: 1500
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1495
Number of HSP's gapped (non-prelim): 12
length of query: 547
length of database: 14,973,337
effective HSP length: 104
effective length of query: 443
effective length of database: 8,465,225
effective search space: 3750094675
effective search space used: 3750094675
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)