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= 020791
         (321 letters)

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

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



>pdb|2YUJ|A Chain A, Solution Structure Of Human Ubiquitin Fusion Degradation
           Protein 1 Homolog Ufd1
          Length = 190

 Score =  216 bits (551), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 97/173 (56%), Positives = 129/173 (74%), Gaps = 4/173 (2%)

Query: 13  FEQSYRCYPASFIEKPQ----IESGDKIIMPPSALDRLASLHIDYPMLFELRNNAAERVS 68
           F   YRC+  S +  P     +E G KIIMPPSALD+L+ L+I YPMLF+L N  ++R++
Sbjct: 16  FSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLTNKNSDRMT 75

Query: 69  HCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNP 128
           HCGVLEF+A+EG+ Y+P+WMM+NLLL+EG +V+V++V L   TY K QP + DFLDI+NP
Sbjct: 76  HCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSPDFLDITNP 135

Query: 129 KAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDF 181
           KA+LE  LRN++CLTTGD I + YN K Y + ++ETKP  A+SIIE D  VDF
Sbjct: 136 KAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVDF 188


>pdb|1ZC1|A Chain A, Ufd1 Exhibits The Aaa-Atpase Fold With Two Distinct
           Ubiquitin Interaction Sites
          Length = 208

 Score =  197 bits (500), Expect = 9e-51,   Method: Compositional matrix adjust.
 Identities = 95/187 (50%), Positives = 128/187 (68%), Gaps = 7/187 (3%)

Query: 12  SFEQSYRCYPASF----IEKPQIESGDKIIMPPSALDRLASLHIDYPMLFELRNNAAERV 67
           +FE+ +RCYP +     I K     G KI +PPSAL +L+ L+I YPMLF+L  N   RV
Sbjct: 20  TFEEFFRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKLSMLNIRYPMLFKLTANETGRV 79

Query: 68  SHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISN 127
           +H GVLEFIAEEG +Y+P WMME L +Q G ++++ +  +P G +VKL+P + DFLDIS+
Sbjct: 80  THGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVKLEPQSVDFLDISD 139

Query: 128 PKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKP---SNAISIIETDCEVDFAPP 184
           PKA+LE  LRN+S LT  D I ++YN K + I I+E KP   S +I +IETD   DFAPP
Sbjct: 140 PKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILEVKPESSSKSICVIETDLVTDFAPP 199

Query: 185 LDYKEPE 191
           + Y EP+
Sbjct: 200 VGYVEPD 206


>pdb|3AL5|A Chain A, Crystal Structure Of Human Tyw5
 pdb|3AL5|B Chain B, Crystal Structure Of Human Tyw5
 pdb|3AL5|C Chain C, Crystal Structure Of Human Tyw5
 pdb|3AL5|D Chain D, Crystal Structure Of Human Tyw5
 pdb|3AL6|A Chain A, Crystal Structure Of Human Tyw5
 pdb|3AL6|B Chain B, Crystal Structure Of Human Tyw5
 pdb|3AL6|C Chain C, Crystal Structure Of Human Tyw5
 pdb|3AL6|D Chain D, Crystal Structure Of Human Tyw5
          Length = 338

 Score = 30.4 bits (67), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 4/73 (5%)

Query: 82  IYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNP---KAILETTLRN 138
           ++  Y +M+NLL+Q     RV   +     Y+ L+    + L+I NP   K  L +  R 
Sbjct: 180 LWTHYDVMDNLLIQVTGKKRVVLFSPRDAQYLYLKGTKSEVLNIDNPDLAKYPLFSKARR 239

Query: 139 YSC-LTTGDSIMV 150
           Y C L  GD + +
Sbjct: 240 YECSLEAGDVLFI 252


  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
   0.314    0.132    0.387 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,545,166
Number of Sequences: 62578
Number of extensions: 391189
Number of successful extensions: 687
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 683
Number of HSP's gapped (non-prelim): 7
length of query: 321
length of database: 14,973,337
effective HSP length: 99
effective length of query: 222
effective length of database: 8,778,115
effective search space: 1948741530
effective search space used: 1948741530
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 bits)