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= psy353
         (1363 letters)

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

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



>pdb|3NY1|A Chain A, Structure Of The Ubr-Box Of The Ubr1 Ubiquitin Ligase
 pdb|3NY1|B Chain B, Structure Of The Ubr-Box Of The Ubr1 Ubiquitin Ligase
          Length = 77

 Score =  115 bits (287), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 45/69 (65%), Positives = 54/69 (78%)

Query: 118 VCGRVFKMGEPTYNCRECGMDATCVLCVDCFKKSTHRNHKYKMGTSNAGGCCDCGDVEAW 177
           +CGRVFK GE TY+CR+C +D TCVLC+DCF+ S H+NH+YKM TS  GG CDCGD EAW
Sbjct: 7   LCGRVFKSGETTYSCRDCAIDPTCVLCMDCFQDSVHKNHRYKMHTSTGGGFCDCGDTEAW 66

Query: 178 KKEPYCDVH 186
           K  P+C  H
Sbjct: 67  KTGPFCVNH 75


>pdb|3NY2|A Chain A, Structure Of The Ubr-Box Of Ubr2 Ubiquitin Ligase
 pdb|3NY2|B Chain B, Structure Of The Ubr-Box Of Ubr2 Ubiquitin Ligase
 pdb|3NY2|C Chain C, Structure Of The Ubr-Box Of Ubr2 Ubiquitin Ligase
 pdb|3NY2|D Chain D, Structure Of The Ubr-Box Of Ubr2 Ubiquitin Ligase
 pdb|3NY2|E Chain E, Structure Of The Ubr-Box Of Ubr2 Ubiquitin Ligase
 pdb|3NY2|F Chain F, Structure Of The Ubr-Box Of Ubr2 Ubiquitin Ligase
 pdb|3NY2|G Chain G, Structure Of The Ubr-Box Of Ubr2 Ubiquitin Ligase
 pdb|3NY2|H Chain H, Structure Of The Ubr-Box Of Ubr2 Ubiquitin Ligase
 pdb|3NY3|A Chain A, Structure Of The Ubr-Box Of Ubr2 In Complex With N-Degron
          Length = 75

 Score = 96.3 bits (238), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 46/70 (65%), Positives = 57/70 (81%)

Query: 117 SVCGRVFKMGEPTYNCRECGMDATCVLCVDCFKKSTHRNHKYKMGTSNAGGCCDCGDVEA 176
           S+CGRVFK+GEPTY+CR+C +D TCVLC++CF  S HR+H+Y+M TS  GG CDCGD EA
Sbjct: 5   SLCGRVFKVGEPTYSCRDCAVDPTCVLCMECFLGSIHRDHRYRMTTSGGGGFCDCGDTEA 64

Query: 177 WKKEPYCDVH 186
           WK+ PYC  H
Sbjct: 65  WKEGPYCQKH 74


>pdb|3NIT|A Chain A, The Structure Of Ubr Box (Native1)
          Length = 90

 Score = 70.9 bits (172), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 39/67 (58%), Gaps = 2/67 (2%)

Query: 119 CGRVFKMGEPTYNCRECGMDATCVLCVDCFKKSTHRNHKY--KMGTSNAGGCCDCGDVEA 176
           CGR FK+GEP Y C ECG D TCVLC+ CF    H NH     + T    G CDCGD EA
Sbjct: 19  CGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEA 78

Query: 177 WKKEPYC 183
           W    +C
Sbjct: 79  WNSPLHC 85


>pdb|3NIH|A Chain A, The Structure Of Ubr Box (Riaaa)
 pdb|3NII|A Chain A, The Structure Of Ubr Box (Kiaa)
 pdb|3NIJ|A Chain A, The Structure Of Ubr Box (Hiaa)
 pdb|3NIK|A Chain A, The Structure Of Ubr Box (Reaa)
 pdb|3NIK|B Chain B, The Structure Of Ubr Box (Reaa)
 pdb|3NIK|D Chain D, The Structure Of Ubr Box (Reaa)
 pdb|3NIK|F Chain F, The Structure Of Ubr Box (Reaa)
 pdb|3NIL|A Chain A, The Structure Of Ubr Box (Rdaa)
 pdb|3NIL|B Chain B, The Structure Of Ubr Box (Rdaa)
 pdb|3NIL|D Chain D, The Structure Of Ubr Box (Rdaa)
 pdb|3NIL|F Chain F, The Structure Of Ubr Box (Rdaa)
 pdb|3NIM|A Chain A, The Structure Of Ubr Box (Rraa)
 pdb|3NIM|B Chain B, The Structure Of Ubr Box (Rraa)
 pdb|3NIM|D Chain D, The Structure Of Ubr Box (Rraa)
 pdb|3NIM|F Chain F, The Structure Of Ubr Box (Rraa)
 pdb|3NIN|A Chain A, The Structure Of Ubr Box (Rlges)
 pdb|3NIN|B Chain B, The Structure Of Ubr Box (Rlges)
 pdb|3NIS|A Chain A, The Structure Of Ubr Box (Native2)
 pdb|3NIS|B Chain B, The Structure Of Ubr Box (Native2)
 pdb|3NIS|D Chain D, The Structure Of Ubr Box (Native2)
 pdb|3NIS|F Chain F, The Structure Of Ubr Box (Native2)
          Length = 82

 Score = 70.1 bits (170), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 39/67 (58%), Gaps = 2/67 (2%)

Query: 119 CGRVFKMGEPTYNCRECGMDATCVLCVDCFKKSTHRNHKY--KMGTSNAGGCCDCGDVEA 176
           CGR FK+GEP Y C ECG D TCVLC+ CF    H NH     + T    G CDCGD EA
Sbjct: 11  CGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEA 70

Query: 177 WKKEPYC 183
           W    +C
Sbjct: 71  WNSPLHC 77


  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
   0.322    0.137    0.424 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 40,627,830
Number of Sequences: 62578
Number of extensions: 1713126
Number of successful extensions: 3816
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 3809
Number of HSP's gapped (non-prelim): 5
length of query: 1363
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1252
effective length of database: 8,027,179
effective search space: 10050028108
effective search space used: 10050028108
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (26.9 bits)