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= psy7337
         (233 letters)

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

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



>pdb|2LGV|A Chain A, Rbx1
          Length = 100

 Score = 30.0 bits (66), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 10/83 (12%)

Query: 55  DLKEDMSEATRSAEQVRNDIQACANRYHMIQNCDTCLLCEVQLVSNT-----FYIFPCGH 109
           ++K+  + A  + + V ++   C N  H++   D C+ C+    S T          C H
Sbjct: 15  EVKKSNASAQSAWDIVVDNCAICRN--HIM---DLCIECQANQASATSEECTVAWGVCNH 69

Query: 110 TFHSHCIVQDLDPEQKAKLDSEE 132
            FH HCI + L   Q   LD+ E
Sbjct: 70  AFHFHCISRWLKTRQVCPLDNRE 92


>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
           Site Containing Dna-Duplex
          Length = 117

 Score = 29.6 bits (65), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 21/50 (42%), Gaps = 5/50 (10%)

Query: 88  DTCLLCEVQLVSNT-----FYIFPCGHTFHSHCIVQDLDPEQKAKLDSEE 132
           D C+ C+    S T          C H FH HCI + L   Q   LD+ E
Sbjct: 60  DLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE 109


>pdb|4A0C|D Chain D, Structure Of The Cand1-Cul4b-Rbx1 Complex
 pdb|4A0C|F Chain F, Structure Of The Cand1-Cul4b-Rbx1 Complex
 pdb|4A0L|F Chain F, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
           Site Containing Dna-Duplex
 pdb|4A0L|I Chain I, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
           Site Containing Dna-Duplex
          Length = 98

 Score = 29.6 bits (65), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 21/50 (42%), Gaps = 5/50 (10%)

Query: 88  DTCLLCEVQLVSNT-----FYIFPCGHTFHSHCIVQDLDPEQKAKLDSEE 132
           D C+ C+    S T          C H FH HCI + L   Q   LD+ E
Sbjct: 41  DLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE 90


>pdb|1U6G|B Chain B, Crystal Structure Of The Cand1-Cul1-Roc1 Complex
 pdb|2HYE|D Chain D, Crystal Structure Of The Ddb1-cul4a-rbx1-sv5v Complex
          Length = 108

 Score = 29.6 bits (65), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 21/50 (42%), Gaps = 5/50 (10%)

Query: 88  DTCLLCEVQLVSNT-----FYIFPCGHTFHSHCIVQDLDPEQKAKLDSEE 132
           D C+ C+    S T          C H FH HCI + L   Q   LD+ E
Sbjct: 51  DLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE 100


>pdb|3DPL|R Chain R, Structural Insights Into Nedd8 Activation Of Cullin-Ring
           Ligases: Conformational Control Of Conjugation.
 pdb|3RTR|B Chain B, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
           Protein Transfer: Structural Insights Into Cullin-Ring
           Ligases
 pdb|3RTR|D Chain D, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
           Protein Transfer: Structural Insights Into Cullin-Ring
           Ligases
 pdb|3RTR|F Chain F, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
           Protein Transfer: Structural Insights Into Cullin-Ring
           Ligases
 pdb|3RTR|H Chain H, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
           Protein Transfer: Structural Insights Into Cullin-Ring
           Ligases
 pdb|4F52|B Chain B, Structure Of A Glomulin-Rbx1-Cul1 Complex
 pdb|4F52|D Chain D, Structure Of A Glomulin-Rbx1-Cul1 Complex
          Length = 106

 Score = 29.6 bits (65), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 19/58 (32%), Positives = 25/58 (43%), Gaps = 8/58 (13%)

Query: 80  RYHMIQNCDTCLLCEVQLVSNT-----FYIFPCGHTFHSHCIVQDLDPEQKAKLDSEE 132
           R H++   D C+ C+    S T          C H FH HCI + L   Q   LD+ E
Sbjct: 44  RNHIM---DLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE 98


>pdb|3DQV|R Chain R, Structural Insights Into Nedd8 Activation Of Cullin-Ring
           Ligases: Conformational Control Of Conjugation
 pdb|3DQV|Y Chain Y, Structural Insights Into Nedd8 Activation Of Cullin-Ring
           Ligases: Conformational Control Of Conjugation
          Length = 106

 Score = 29.3 bits (64), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 21/50 (42%), Gaps = 5/50 (10%)

Query: 88  DTCLLCEVQLVSNT-----FYIFPCGHTFHSHCIVQDLDPEQKAKLDSEE 132
           D C+ C+    S T          C H FH HCI + L   Q   LD+ E
Sbjct: 49  DLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE 98


>pdb|1LDJ|B Chain B, Structure Of The Cul1-rbx1-skp1-f Boxskp2 Scf Ubiquitin
           Ligase Complex
 pdb|1LDK|C Chain C, Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiquitin
           Ligase Complex
          Length = 90

 Score = 29.3 bits (64), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 21/50 (42%), Gaps = 5/50 (10%)

Query: 88  DTCLLCEVQLVSNT-----FYIFPCGHTFHSHCIVQDLDPEQKAKLDSEE 132
           D C+ C+    S T          C H FH HCI + L   Q   LD+ E
Sbjct: 33  DLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE 82


>pdb|2YRN|A Chain A, Solution Structure Of The Ch Domain From Human Neuron
          Navigator 2
          Length = 129

 Score = 27.7 bits (60), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 8/47 (17%)

Query: 53 IVDLKEDMSEATRSAEQVR-------NDIQACA-NRYHMIQNCDTCL 91
          I DL++D+++    A+ ++        DI  C  NR  MI+N D CL
Sbjct: 40 IRDLQQDVTDGVLLAQIIQVVANEKIEDINGCPKNRSQMIENIDACL 86


>pdb|3QUP|A Chain A, Inhibitor Bound Structure Of The Kinase Domain Of The
          Murine Receptor Tyrosine Kinase Tyro3 (Sky)
          Length = 323

 Score = 27.3 bits (59), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 1/40 (2%)

Query: 7  IKTALEFLDESDLISIEDILPFFSDFTCMDQFKHAICASL 46
          +K A++ L ++D+I+  DI  F  +  CM +F H   A L
Sbjct: 52 VKVAVKML-KADIIASSDIEEFLREAACMKEFDHPHVAKL 90


>pdb|3V4L|A Chain A, Mouse Malt1(Caspase-Ig3 Domains) In Complex With A
           Irreversible Peptidic Inhibitor
          Length = 396

 Score = 27.3 bits (59), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 13/30 (43%), Positives = 17/30 (56%)

Query: 119 DLDPEQKAKLDSEETGSEAVNNYLSRECPY 148
           D+DP+   K   EETGS  V+  L + C Y
Sbjct: 315 DIDPKHANKGTPEETGSYLVSKDLPKHCLY 344


  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    0.134    0.405 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,217,739
Number of Sequences: 62578
Number of extensions: 164733
Number of successful extensions: 401
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 390
Number of HSP's gapped (non-prelim): 19
length of query: 233
length of database: 14,973,337
effective HSP length: 96
effective length of query: 137
effective length of database: 8,965,849
effective search space: 1228321313
effective search space used: 1228321313
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)