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= 047222
         (342 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 =  214 bits (546), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 96/173 (55%), Positives = 133/173 (76%), Gaps = 4/173 (2%)

Query: 10  FERKYRCYPISFI----DKPHLENGDKIVMPPSALDRLAYLHIEYPMLFELSNTSAGRVT 65
           F  +YRC+ +S +    D+  +E G KI+MPPSALD+L+ L+I YPMLF+L+N ++ R+T
Sbjct: 16  FSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLTNKNSDRMT 75

Query: 66  YCGVMEFIADEGLIYLPYWMMENMLLQEGDIVEVKNASLAKGSYVKLQPHTKDFLDISNP 125
           +CGV+EF+ADEG+ YLP+WMM+N+LL+EG +V+V++ +L   +Y K QP + DFLDI+NP
Sbjct: 76  HCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSPDFLDITNP 135

Query: 126 KAVLETTLRSYSCLTTGDTIMVPYNNKKYYINVVETKPSTAVSIIETDCEVDF 178
           KAVLE  LR+++CLTTGD I + YN K Y + V+ETKP  AVSIIE 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 =  185 bits (469), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 89/187 (47%), Positives = 125/187 (66%), Gaps = 7/187 (3%)

Query: 9   AFERKYRCYPISF----IDKPHLENGDKIVMPPSALDRLAYLHIEYPMLFELSNTSAGRV 64
            FE  +RCYPI+     I K     G KI +PPSAL +L+ L+I YPMLF+L+    GRV
Sbjct: 20  TFEEFFRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKLSMLNIRYPMLFKLTANETGRV 79

Query: 65  TYCGVMEFIADEGLIYLPYWMMENMLLQEGDIVEVKNASLAKGSYVKLQPHTKDFLDISN 124
           T+ GV+EFIA+EG +YLP WMME + +Q G ++++ +  +  G +VKL+P + DFLDIS+
Sbjct: 80  THGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVKLEPQSVDFLDISD 139

Query: 125 PKAVLETTLRSYSCLTTGDTIMVPYNNKKYYINVVETKP---STAVSIIETDCEVDFIPP 181
           PKAVLE  LR++S LT  D I + YN K + I ++E KP   S ++ +IETD   DF PP
Sbjct: 140 PKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILEVKPESSSKSICVIETDLVTDFAPP 199

Query: 182 LDFKEPE 188
           + + 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 = 33.5 bits (75), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 29/103 (28%), Positives = 48/103 (46%), Gaps = 8/103 (7%)

Query: 73  IADEGL-IYLPYWMMENMLLQEGDIVEVKNASLAKGSYVKLQPHTKDFLDISNP---KAV 128
           I+  GL ++  Y +M+N+L+Q      V   S     Y+ L+    + L+I NP   K  
Sbjct: 173 ISSPGLQLWTHYDVMDNLLIQVTGKKRVVLFSPRDAQYLYLKGTKSEVLNIDNPDLAKYP 232

Query: 129 LETTLRSYSC-LTTGDTIMVPYNNKKYYINVVETKPSTAVSII 170
           L +  R Y C L  GD + +P     ++ NV+  +    V+I 
Sbjct: 233 LFSKARRYECSLEAGDVLFIP---ALWFHNVISEEFGVGVNIF 272


>pdb|3CB4|D Chain D, The Crystal Structure Of Lepa
 pdb|3CB4|A Chain A, The Crystal Structure Of Lepa
 pdb|3CB4|B Chain B, The Crystal Structure Of Lepa
 pdb|3CB4|C Chain C, The Crystal Structure Of Lepa
 pdb|3CB4|E Chain E, The Crystal Structure Of Lepa
 pdb|3CB4|F Chain F, The Crystal Structure Of Lepa
          Length = 599

 Score = 28.1 bits (61), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 4/43 (9%)

Query: 96  IVEVKNASLAKGSYVKL----QPHTKDFLDISNPKAVLETTLR 134
           ++ +KN +L KG  VK+    Q +  D L I  PK V  T L+
Sbjct: 209 LIRIKNGTLRKGDKVKVMSTGQTYNADRLGIFTPKQVDRTELK 251


>pdb|3DEG|C Chain C, Complex Of Elongating Escherichia Coli 70s Ribosome And
           Ef4(Lepa)- Gmppnp
          Length = 545

 Score = 28.1 bits (61), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 4/43 (9%)

Query: 96  IVEVKNASLAKGSYVKL----QPHTKDFLDISNPKAVLETTLR 134
           ++ +KN +L KG  VK+    Q +  D L I  PK V  T L+
Sbjct: 209 LIRIKNGTLRKGDKVKVMSTGQTYNADRLGIFTPKQVDRTELK 251


  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    0.134    0.396 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,172,428
Number of Sequences: 62578
Number of extensions: 331803
Number of successful extensions: 427
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 422
Number of HSP's gapped (non-prelim): 6
length of query: 342
length of database: 14,973,337
effective HSP length: 100
effective length of query: 242
effective length of database: 8,715,537
effective search space: 2109159954
effective search space used: 2109159954
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: 52 (24.6 bits)