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= psy4021
         (65 letters)

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

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



>pdb|2ZDI|C Chain C, Crystal Structure Of Prefoldin From Pyrococcus
          Horikoshii Ot3
          Length = 151

 Score = 25.4 bits (54), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 4/64 (6%)

Query: 2  DIKVLQFQNKKLAQRLEQKNRAEAE---LRSRIEQLEKRQTQDDAVLNVVVNESVYFPNL 58
          + +VLQ Q + LAQ LE  N A+AE   +R  +E L+K + +   +L V +    +   +
Sbjct: 17 EYQVLQAQAQILAQNLELLNLAKAEVQTVRETLENLKKIEEEKPEIL-VPIGAGSFLKGV 75

Query: 59 IVTK 62
          IV K
Sbjct: 76 IVDK 79


>pdb|1ZL3|A Chain A, Coupling Of Active Site Motions And Rna Binding
          Length = 327

 Score = 25.4 bits (54), Expect = 8.9,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 24/47 (51%)

Query: 11  KKLAQRLEQKNRAEAELRSRIEQLEKRQTQDDAVLNVVVNESVYFPN 57
           ++L ++ EQ++   AEL   +         D  V+N+ +  SVYF N
Sbjct: 233 RELVEQAEQQDIPAAELLDPLLMPMDSPASDYPVVNLPLTSSVYFKN 279


>pdb|1K8W|A Chain A, Crystal Structure Of The E. Coli Pseudouridine Synthase
           Trub Bound To A T Stem-Loop Rna
          Length = 327

 Score = 25.4 bits (54), Expect = 8.9,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 24/47 (51%)

Query: 11  KKLAQRLEQKNRAEAELRSRIEQLEKRQTQDDAVLNVVVNESVYFPN 57
           ++L ++ EQ++   AEL   +         D  V+N+ +  SVYF N
Sbjct: 233 RELVEQAEQQDIPAAELLDPLLMPMDSPASDYPVVNLPLTSSVYFKN 279


>pdb|1R3F|A Chain A, Crystal Structure Of Trna Pseudouridine Synthase Trub And
           Its Rna Complex: Rna-Protein Recognition Through A
           Combination Of Rigid Docking And Induced Fit
          Length = 314

 Score = 25.4 bits (54), Expect = 9.3,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 24/47 (51%)

Query: 11  KKLAQRLEQKNRAEAELRSRIEQLEKRQTQDDAVLNVVVNESVYFPN 57
           ++L ++ EQ++   AEL   +         D  V+N+ +  SVYF N
Sbjct: 220 RELVEQAEQQDIPAAELLDPLLMPMDSPASDYPVVNLPLTSSVYFKN 266


  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    0.132    0.356 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,449,122
Number of Sequences: 62578
Number of extensions: 36101
Number of successful extensions: 176
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 169
Number of HSP's gapped (non-prelim): 8
length of query: 65
length of database: 14,973,337
effective HSP length: 36
effective length of query: 29
effective length of database: 12,720,529
effective search space: 368895341
effective search space used: 368895341
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: 45 (21.9 bits)