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= psy4372
         (50 letters)

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

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



>pdb|1C4Z|A Chain A, Structure Of E6ap: Insights Into Ubiquitination Pathway
 pdb|1C4Z|B Chain B, Structure Of E6ap: Insights Into Ubiquitination Pathway
 pdb|1C4Z|C Chain C, Structure Of E6ap: Insights Into Ubiquitination Pathway
 pdb|1D5F|A Chain A, Structure Of An E6ap-Ubch7 Complex: Insights Into The
           Ubiquitination Pathway
 pdb|1D5F|B Chain B, Structure Of An E6ap-Ubch7 Complex: Insights Into The
           Ubiquitination Pathway
 pdb|1D5F|C Chain C, Structure Of An E6ap-Ubch7 Complex: Insights Into The
           Ubiquitination Pathway
          Length = 358

 Score = 29.6 bits (65), Expect = 0.38,   Method: Composition-based stats.
 Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 4/44 (9%)

Query: 2   ESFREGFECVFPLAQLS-MFYPEELEYVFCGS---DFTSCPQET 41
           ++FR GF  V   + L  +F PEE+E + CGS   DF +  + T
Sbjct: 214 KAFRRGFHMVTNESPLKYLFRPEEIELLICGSRNLDFQALEETT 257


>pdb|1ND7|A Chain A, Conformational Flexibility Underlies Ubiquitin Ligation
           Mediated By The Wwp1 Hect Domain E3 Ligase
          Length = 374

 Score = 29.3 bits (64), Expect = 0.58,   Method: Compositional matrix adjust.
 Identities = 15/47 (31%), Positives = 21/47 (44%)

Query: 2   ESFREGFECVFPLAQLSMFYPEELEYVFCGSDFTSCPQETACTFFIH 48
           ++F +GF  V PL  L  F  +ELE + CG            T + H
Sbjct: 231 KAFLDGFNEVVPLQWLQYFDEKELEVMLCGMQEVDLADWQRNTVYRH 277


>pdb|3JVZ|C Chain C, E2~ubiquitin-Hect
 pdb|3JVZ|D Chain D, E2~ubiquitin-Hect
          Length = 385

 Score = 28.9 bits (63), Expect = 0.79,   Method: Composition-based stats.
 Identities = 12/31 (38%), Positives = 18/31 (58%)

Query: 1   MESFREGFECVFPLAQLSMFYPEELEYVFCG 31
           M +F EGF  + P+  + +F   ELE + CG
Sbjct: 234 MNAFLEGFTELLPIDLIKIFDENELELLMCG 264


>pdb|3JW0|C Chain C, E2~ubiquitin-Hect
 pdb|3JW0|D Chain D, E2~ubiquitin-Hect
          Length = 385

 Score = 28.9 bits (63), Expect = 0.80,   Method: Composition-based stats.
 Identities = 12/31 (38%), Positives = 18/31 (58%)

Query: 1   MESFREGFECVFPLAQLSMFYPEELEYVFCG 31
           M +F EGF  + P+  + +F   ELE + CG
Sbjct: 234 MNAFLEGFTELLPIDLIKIFDENELELLMCG 264


>pdb|2XBB|A Chain A, Nedd4 Hect:ub Complex
 pdb|2XBB|B Chain B, Nedd4 Hect:ub Complex
 pdb|2XBF|A Chain A, Nedd4 Hect Structure
          Length = 386

 Score = 28.1 bits (61), Expect = 1.2,   Method: Composition-based stats.
 Identities = 12/31 (38%), Positives = 18/31 (58%)

Query: 1   MESFREGFECVFPLAQLSMFYPEELEYVFCG 31
           M +F+EGF  + P   + +F   ELE + CG
Sbjct: 235 MAAFKEGFFELIPQDLIKIFDENELELLMCG 265


>pdb|2ONI|A Chain A, Catalytic Domain Of The Human Nedd4-Like E3 Ligase
          Length = 392

 Score = 26.2 bits (56), Expect = 4.7,   Method: Composition-based stats.
 Identities = 11/29 (37%), Positives = 17/29 (58%)

Query: 3   SFREGFECVFPLAQLSMFYPEELEYVFCG 31
           +F EGF  + P+  + +F   ELE + CG
Sbjct: 251 AFLEGFTELLPIDLIKIFDENELELLXCG 279


>pdb|3TUG|A Chain A, Crystal Structure Of The Hect Domain Of Itch E3 Ubiquitin
           Ligase
          Length = 398

 Score = 25.4 bits (54), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 12/30 (40%), Positives = 17/30 (56%)

Query: 2   ESFREGFECVFPLAQLSMFYPEELEYVFCG 31
           ++F EGF  + P   L  F  +ELE + CG
Sbjct: 250 QAFFEGFNEILPQQYLQYFDAKELEVLLCG 279


  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
   0.331    0.142    0.486 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,509,261
Number of Sequences: 62578
Number of extensions: 38804
Number of successful extensions: 134
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 128
Number of HSP's gapped (non-prelim): 7
length of query: 50
length of database: 14,973,337
effective HSP length: 23
effective length of query: 27
effective length of database: 13,534,043
effective search space: 365419161
effective search space used: 365419161
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 45 (21.9 bits)