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= 023183
         (286 letters)

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

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



>pdb|2AX5|A Chain A, Solution Structure Of Urm1 From Saccharomyces Cerevisiae
          Length = 107

 Score = 28.5 bits (62), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 21/77 (27%), Positives = 42/77 (54%), Gaps = 4/77 (5%)

Query: 122 IGALVSIRGVGRVKIVKFFQADPFLKGEVIP-MQDTTSASPSDVSSKV--LSVKEAVYSL 178
           +G L +I G  RV  +K  + DP   G++I  +  T   +P+DVS  +   S++  + +L
Sbjct: 9   LGGLDAIFGKQRVHKIKMDKEDPVTVGDLIDHIVSTMINNPNDVSIFIEDDSIRPGIITL 68

Query: 179 -NSLEIKLKAPKEAVMQ 194
            N  + +L+  K+ +++
Sbjct: 69  INDTDWELEGEKDYILE 85


>pdb|2QJL|A Chain A, Crystal Structure Of Urm1
 pdb|2PKO|A Chain A, Crystal Structure Of Yeast Urm1 At 1.8 A Resolution
          Length = 99

 Score = 28.1 bits (61), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 21/77 (27%), Positives = 42/77 (54%), Gaps = 4/77 (5%)

Query: 122 IGALVSIRGVGRVKIVKFFQADPFLKGEVIP-MQDTTSASPSDVSSKV--LSVKEAVYSL 178
           +G L +I G  RV  +K  + DP   G++I  +  T   +P+DVS  +   S++  + +L
Sbjct: 9   LGGLDAIFGKQRVHKIKMDKEDPVTVGDLIDHIVSTMINNPNDVSIFIEDDSIRPGIITL 68

Query: 179 -NSLEIKLKAPKEAVMQ 194
            N  + +L+  K+ +++
Sbjct: 69  INDTDWELEGEKDYILE 85


  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
   0.319    0.131    0.362 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,497,720
Number of Sequences: 62578
Number of extensions: 215899
Number of successful extensions: 420
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 420
Number of HSP's gapped (non-prelim): 8
length of query: 286
length of database: 14,973,337
effective HSP length: 98
effective length of query: 188
effective length of database: 8,840,693
effective search space: 1662050284
effective search space used: 1662050284
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)