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= 015524
         (405 letters)

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

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



>pdb|1V9F|A Chain A, Crystal Structure Of Catalytic Domain Of Pseudouridine
           Synthase Rlud From Escherichia Coli
 pdb|2IST|A Chain A, Crystal Structure Of Rlud From E. Coli
          Length = 325

 Score = 29.3 bits (64), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 31/145 (21%), Positives = 56/145 (38%), Gaps = 16/145 (11%)

Query: 173 PDGTTPVTCRVSIYDGSAD-KKVGVGSLFDK------AIAPSLPVGSLYIEEVHAKLGEE 225
           PDGT  +   +  Y   AD  + G+    DK       +A ++P  +  +E +  +    
Sbjct: 110 PDGTV-LNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITR 168

Query: 226 LHFTVGSQHIPFGASPQDVWTELGRPCGIHQKQVDQMVIHSASDPRPRSTLCGDYFYNYY 285
            +  V   H+  G +       +  P   H  +   M +H    P        ++F   +
Sbjct: 169 EYEAVAIGHMTAGGT-------VDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHF-RVH 220

Query: 286 TRGLDILFDGQTHKIKKFIMHTNYP 310
           TR    L  G+TH+I+  + H  +P
Sbjct: 221 TRLRLRLETGRTHQIRVHMAHITHP 245


  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
   0.323    0.141    0.441 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,522,030
Number of Sequences: 62578
Number of extensions: 618260
Number of successful extensions: 982
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 982
Number of HSP's gapped (non-prelim): 2
length of query: 405
length of database: 14,973,337
effective HSP length: 101
effective length of query: 304
effective length of database: 8,652,959
effective search space: 2630499536
effective search space used: 2630499536
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)