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= 023065
         (288 letters)

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

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



>pdb|1SB7|A Chain A, Crystal Structure Of The E.Coli Pseudouridine Synthase
           Trud
 pdb|1SB7|B Chain B, Crystal Structure Of The E.Coli Pseudouridine Synthase
           Trud
          Length = 368

 Score = 29.6 bits (65), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 23/109 (21%), Positives = 44/109 (40%), Gaps = 13/109 (11%)

Query: 80  EVFGDLKKDLGKREIYARLCRMNSFDGGTKKVWLDKSTGGVCLSISAKGLAITGIDDRRY 139
           E   +L++ +  +E+        S + GT++  L      V      + L +        
Sbjct: 258 EELAELQRRVNDKELXITAALPGSGEWGTQREALAFEQAAVAAETELQALLV-------- 309

Query: 140 WNHIPTEESRFTSVAYLQQI---WWFEVDGEVEFPFPAGTYSIFIRLQL 185
                 E +R   + Y QQ+   WW +V  E+ F  PAG+++  +  +L
Sbjct: 310 --REKVEAARRAXLLYPQQLSWNWWDDVTVEIRFWLPAGSFATSVVREL 356


>pdb|1SI7|A Chain A, Structure Of E. Coli Trna Psi 13 Pseudouridine Synthase
           Trud
          Length = 369

 Score = 29.6 bits (65), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 23/109 (21%), Positives = 44/109 (40%), Gaps = 13/109 (11%)

Query: 80  EVFGDLKKDLGKREIYARLCRMNSFDGGTKKVWLDKSTGGVCLSISAKGLAITGIDDRRY 139
           E   +L++ +  +E+        S + GT++  L      V      + L +        
Sbjct: 259 EELAELQRRVNDKELMITAALPGSGEWGTQREALAFEQAAVAAETELQALLV-------- 310

Query: 140 WNHIPTEESRFTSVAYLQQI---WWFEVDGEVEFPFPAGTYSIFIRLQL 185
                 E +R   + Y QQ+   WW +V  E+ F  PAG+++  +  +L
Sbjct: 311 --REKVEAARRAMLLYPQQLSWNWWDDVTVEIRFWLPAGSFATSVVREL 357


>pdb|1SZW|A Chain A, Crystal Structure Of E. Coli Trna Pseudouridine Synthase
           Trud
 pdb|1SZW|B Chain B, Crystal Structure Of E. Coli Trna Pseudouridine Synthase
           Trud
          Length = 379

 Score = 29.6 bits (65), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 23/109 (21%), Positives = 44/109 (40%), Gaps = 13/109 (11%)

Query: 80  EVFGDLKKDLGKREIYARLCRMNSFDGGTKKVWLDKSTGGVCLSISAKGLAITGIDDRRY 139
           E   +L++ +  +E+        S + GT++  L      V      + L +        
Sbjct: 261 EELAELQRRVNDKELXITAALPGSGEWGTQREALAFEQAAVAAETELQALLV-------- 312

Query: 140 WNHIPTEESRFTSVAYLQQI---WWFEVDGEVEFPFPAGTYSIFIRLQL 185
                 E +R   + Y QQ+   WW +V  E+ F  PAG+++  +  +L
Sbjct: 313 --REKVEAARRAXLLYPQQLSWNWWDDVTVEIRFWLPAGSFATSVVREL 359


  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    0.139    0.452 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,510,424
Number of Sequences: 62578
Number of extensions: 403091
Number of successful extensions: 852
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 851
Number of HSP's gapped (non-prelim): 4
length of query: 288
length of database: 14,973,337
effective HSP length: 98
effective length of query: 190
effective length of database: 8,840,693
effective search space: 1679731670
effective search space used: 1679731670
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: 51 (24.3 bits)