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= 035839
         (238 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 =  187 bits (476), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 93/174 (53%), Positives = 118/174 (67%), Gaps = 5/174 (2%)

Query: 13  FEKHYHCYSLSHVAKPQH----EPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTT 68
           F   Y C+S+S +A P      E G KIIMP SA D+L+   + YPM+F+L N +S + T
Sbjct: 16  FSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLTNKNSDRMT 75

Query: 69  HCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSN 128
           HCGV+EF ADEG  YLP+WMM N+ L+E  LV+V +V+L  ATY K QP +  FLD ++N
Sbjct: 76  HCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSPDFLD-ITN 134

Query: 129 PRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDF 182
           P+AVLE  LR F+CLTTGD I I +NE  Y + V+ETKP  AVSI E D  VDF
Sbjct: 135 PKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVDF 188


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

 Score =  156 bits (395), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 76/189 (40%), Positives = 116/189 (61%), Gaps = 8/189 (4%)

Query: 13  FEKHYHCYSLS----HVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTT 68
           FE+ + CY ++     + K     G KI +P SA  +L+   + YPM+F+L    +G+ T
Sbjct: 21  FEEFFRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKLSMLNIRYPMLFKLTANETGRVT 80

Query: 69  HCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSN 128
           H GV+EF A+EG +YLP WMM+ + +Q   L+++++  +    ++KL+P +  FLD +S+
Sbjct: 81  HGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVKLEPQSVDFLD-ISD 139

Query: 129 PRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKP---SNAVSITETDCEVDFAPP 185
           P+AVLE +LR FS LT  D I I +N   + I +LE KP   S ++ + ETD   DFAPP
Sbjct: 140 PKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILEVKPESSSKSICVIETDLVTDFAPP 199

Query: 186 LDYKEPDEK 194
           + Y EPD K
Sbjct: 200 VGYVEPDYK 208


>pdb|1NAM|B Chain B, Murine Alloreactive Scfv Tcr-Peptide-Mhc Class I
          Molecule Complex
 pdb|2OL3|B Chain B, Crystal Structure Of Bm3.3 Scfv Tcr In Complex With
          Pbm8-h-2kbm8 Mhc Class I Molecule
          Length = 113

 Score = 27.7 bits (60), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 12/41 (29%), Positives = 19/41 (46%)

Query: 30 HEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHC 70
            PGDK +      D LA       +  ++ N+S G+T +C
Sbjct: 51 RSPGDKEVKSLPGADYLATRVTDTELRLQVANMSQGRTLYC 91


>pdb|1FO0|B Chain B, Murine Alloreactive Scfv Tcr-Peptide-Mhc Class I
          Molecule Complex
          Length = 112

 Score = 27.7 bits (60), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 12/41 (29%), Positives = 19/41 (46%)

Query: 30 HEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHC 70
            PGDK +      D LA       +  ++ N+S G+T +C
Sbjct: 51 RSPGDKEVKSLPGADYLATRVTDTELRLQVANMSQGRTLYC 91


>pdb|1KB5|B Chain B, Murine T-Cell Receptor Variable DomainFAB COMPLEX
 pdb|1KJ2|B Chain B, Murine Alloreactive Scfv Tcr-peptide-mhc Class I
          Molecule Complex
 pdb|1KJ2|E Chain E, Murine Alloreactive Scfv Tcr-peptide-mhc Class I
          Molecule Complex
          Length = 117

 Score = 27.7 bits (60), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 12/41 (29%), Positives = 19/41 (46%)

Query: 30 HEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHC 70
            PGDK +      D LA       +  ++ N+S G+T +C
Sbjct: 51 RSPGDKEVKSLPGADYLATRVTDTELRLQVANMSQGRTLYC 91


>pdb|3TO4|D Chain D, Structure Of Mouse
          Valpha14vbeta2-Mousecd1d-Alpha-Galactosylceramide
          Length = 253

 Score = 27.7 bits (60), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 12/39 (30%), Positives = 19/39 (48%)

Query: 32 PGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHC 70
          PGDK +      D LA       +  ++ N+S G+T +C
Sbjct: 53 PGDKEVKSLPGADYLATRVTDTELRLQVANMSQGRTLYC 91


  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
   0.317    0.133    0.394 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,297,740
Number of Sequences: 62578
Number of extensions: 286611
Number of successful extensions: 569
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 559
Number of HSP's gapped (non-prelim): 12
length of query: 238
length of database: 14,973,337
effective HSP length: 96
effective length of query: 142
effective length of database: 8,965,849
effective search space: 1273150558
effective search space used: 1273150558
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)