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= 033555
         (117 letters)

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

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



>pdb|1SE9|A Chain A, Structure Of At3g01050, A Ubiquitin-Fold Protein From
           Arabidopsis Thaliana
          Length = 126

 Score =  171 bits (433), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 77/116 (66%), Positives = 99/116 (85%)

Query: 2   ASVQDQLEIKFRLTDGSDIGPKSFPAATSVATLKESVLSQWPKEKENGPRTVKDVKLISA 61
           A V +QLEIKFRLTDGSDIGPK+FP AT+V+ LKE+V+S+WP+EKENGP+TVK+VKLISA
Sbjct: 11  AEVHNQLEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISA 70

Query: 62  GKILENNRTLGECRSPLCDIPGGVTTMHVVVQPPSTEKEKKAASQPKQNKCVCVIL 117
           GK+LEN++T+ + RSP+ ++ G VTTMHV++Q P TEKEKK    PK NKCVC ++
Sbjct: 71  GKVLENSKTVKDYRSPVSNLAGAVTTMHVIIQAPVTEKEKKPKGDPKMNKCVCSVM 126


>pdb|3M62|B Chain B, Crystal Structure Of Ufd2 In Complex With The
          Ubiquitin-Like (Ubl) Domain Of Rad23
          Length = 106

 Score = 28.1 bits (61), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 14/42 (33%), Positives = 25/42 (59%), Gaps = 5/42 (11%)

Query: 56 VKLISAGKILENNRTLGECRSPLCDIPGGVTTMHVVVQPPST 97
          +KLI +GK+L++++T+ E     C +  G   + +V Q  ST
Sbjct: 42 IKLIYSGKVLQDSKTVSE-----CGLKDGDQVVFMVSQKKST 78


  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    0.129    0.373 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,297,559
Number of Sequences: 62578
Number of extensions: 117901
Number of successful extensions: 268
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 266
Number of HSP's gapped (non-prelim): 4
length of query: 117
length of database: 14,973,337
effective HSP length: 80
effective length of query: 37
effective length of database: 9,967,097
effective search space: 368782589
effective search space used: 368782589
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: 45 (21.9 bits)