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= psy8220
         (161 letters)

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

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



>pdb|1PUJ|A Chain A, Structure Of B. Subtilis Ylqf Gtpase
          Length = 282

 Score = 33.9 bits (76), Expect = 0.036,   Method: Compositional matrix adjust.
 Identities = 16/41 (39%), Positives = 27/41 (65%), Gaps = 3/41 (7%)

Query: 26 DVILEVVDARDPMGTRCKVAEDLVVGTPGKKLVIVINKAGK 66
          D++ E+VDAR PM +R  + ED++   P    ++++NKA K
Sbjct: 25 DIVYELVDARIPMSSRNPMIEDILKNKP---RIMLLNKADK 62


>pdb|1TJ7|A Chain A, Structure Determination And Refinement At 2.44 A
           Resolution Of Argininosuccinate Lyase From E. Coli
 pdb|1TJ7|B Chain B, Structure Determination And Refinement At 2.44 A
           Resolution Of Argininosuccinate Lyase From E. Coli
          Length = 457

 Score = 27.7 bits (60), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 11  GVVVQEIERSVVEAADVILEVVDARDPMGTRCKVAEDLVVGTPGKKLVIVINKAGKPSTK 70
           GV+  E +  + EA +V+LE V AR P       AED+     GK    +I+K G+   K
Sbjct: 48  GVLTAEEQAQLEEALNVLLEDVRAR-PQQILESDAEDIHSWVEGK----LIDKVGQLGKK 102

Query: 71  IQSG 74
           + +G
Sbjct: 103 LHTG 106


>pdb|3R9W|A Chain A, Crystal Structure Of Era In Complex With Mggdpnp And
           Nucleotides 1506- 1542 Of 16s Ribosomal Rna
 pdb|3R9X|A Chain A, Crystal Structure Of Era In Complex With Mggdpnp,
           Nucleotides 1506- 1542 Of 16s Ribosomal Rna, And Ksga
          Length = 307

 Score = 26.2 bits (56), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 17/51 (33%), Positives = 27/51 (52%)

Query: 16  EIERSVVEAADVILEVVDARDPMGTRCKVAEDLVVGTPGKKLVIVINKAGK 66
           EI +  +E ADVIL ++DA +    R +      +    K +++VINK  K
Sbjct: 83  EIAKQSLEEADVILFMIDATEGWRPRDEEIYQNFIKPLNKPVIVVINKIDK 133


>pdb|3IEV|A Chain A, Crystal Structure Of Era In Complex With Mggnp And The 3'
           End Of 16s Rrna
          Length = 308

 Score = 26.2 bits (56), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 17/51 (33%), Positives = 27/51 (52%)

Query: 16  EIERSVVEAADVILEVVDARDPMGTRCKVAEDLVVGTPGKKLVIVINKAGK 66
           EI +  +E ADVIL ++DA +    R +      +    K +++VINK  K
Sbjct: 84  EIAKQSLEEADVILFMIDATEGWRPRDEEIYQNFIKPLNKPVIVVINKIDK 134


  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
   0.317    0.133    0.370 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,673,439
Number of Sequences: 62578
Number of extensions: 114314
Number of successful extensions: 236
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 232
Number of HSP's gapped (non-prelim): 6
length of query: 161
length of database: 14,973,337
effective HSP length: 91
effective length of query: 70
effective length of database: 9,278,739
effective search space: 649511730
effective search space used: 649511730
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 bits)