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= 024476
         (267 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 =  171 bits (434), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 74/127 (58%), Positives = 100/127 (78%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLF+L N  ++R++HCGVLEF+A+EG+ Y+P+WMM+NLLL+EG +V+V++V L   TY K
Sbjct: 62  MLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSK 121

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
            QP + DFLDI+NPKA+LE  LRN++CLTTGD I + YN K Y + ++ETKP  A+SIIE
Sbjct: 122 FQPQSPDFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIE 181

Query: 121 TDCEVDF 127
            D  VDF
Sbjct: 182 CDMNVDF 188


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

 Score =  157 bits (397), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 74/140 (52%), Positives = 99/140 (70%), Gaps = 3/140 (2%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLF+L  N   RV+H GVLEFIAEEG +Y+P WMME L +Q G ++++ +  +P G +VK
Sbjct: 67  MLFKLTANETGRVTHGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVK 126

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKP---SNAIS 117
           L+P + DFLDIS+PKA+LE  LRN+S LT  D I ++YN K + I I+E KP   S +I 
Sbjct: 127 LEPQSVDFLDISDPKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILEVKPESSSKSIC 186

Query: 118 IIETDCEVDFAPPLDYKEPE 137
           +IETD   DFAPP+ Y EP+
Sbjct: 187 VIETDLVTDFAPPVGYVEPD 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 = 1.2,   Method: Compositional matrix adjust.
 Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 4/73 (5%)

Query: 28  IYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNP---KAILETTLRN 84
           ++  Y +M+NLL+Q     RV   +     Y+ L+    + L+I NP   K  L +  R 
Sbjct: 180 LWTHYDVMDNLLIQVTGKKRVVLFSPRDAQYLYLKGTKSEVLNIDNPDLAKYPLFSKARR 239

Query: 85  YSC-LTTGDSIMV 96
           Y C L  GD + +
Sbjct: 240 YECSLEAGDVLFI 252


>pdb|3IZA|A Chain A, Structure Of An Apoptosome-Procaspase-9 Card Complex
 pdb|3IZA|B Chain B, Structure Of An Apoptosome-Procaspase-9 Card Complex
 pdb|3IZA|C Chain C, Structure Of An Apoptosome-Procaspase-9 Card Complex
 pdb|3IZA|D Chain D, Structure Of An Apoptosome-Procaspase-9 Card Complex
 pdb|3IZA|E Chain E, Structure Of An Apoptosome-Procaspase-9 Card Complex
 pdb|3IZA|F Chain F, Structure Of An Apoptosome-Procaspase-9 Card Complex
 pdb|3IZA|G Chain G, Structure Of An Apoptosome-Procaspase-9 Card Complex
          Length = 1263

 Score = 28.9 bits (63), Expect = 3.2,   Method: Composition-based stats.
 Identities = 14/40 (35%), Positives = 22/40 (55%)

Query: 68  FLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDI 107
           FL++ +P+  +E  ++  S    G  IMVA  NK +  DI
Sbjct: 793 FLNLEDPQEDMEVIVKCCSWSADGARIMVAAKNKIFLFDI 832


  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
   0.312    0.130    0.375 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,583,208
Number of Sequences: 62578
Number of extensions: 310170
Number of successful extensions: 588
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 584
Number of HSP's gapped (non-prelim): 7
length of query: 267
length of database: 14,973,337
effective HSP length: 97
effective length of query: 170
effective length of database: 8,903,271
effective search space: 1513556070
effective search space used: 1513556070
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)