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= psy10040
         (93 letters)

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

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



>pdb|2Q5H|A Chain A, Crystal Structure Of Apo-Wildtype Glycyl-Trna Synthetase
          Length = 691

 Score = 25.4 bits (54), Expect = 7.4,   Method: Composition-based stats.
 Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 2/33 (6%)

Query: 62  KMMKRKKCLDVVKKAQKVSLMARM-NFGQDNTA 93
           K+M  KKC  V KK++  S++A++ N+GQ   A
Sbjct: 170 KLMSDKKC-SVEKKSEMESVLAQLDNYGQQELA 201


>pdb|2Q5I|A Chain A, Crystal Structure Of Apo S581l Glycyl-Trna Synthetase
           Mutant
          Length = 691

 Score = 25.4 bits (54), Expect = 7.4,   Method: Composition-based stats.
 Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 2/33 (6%)

Query: 62  KMMKRKKCLDVVKKAQKVSLMARM-NFGQDNTA 93
           K+M  KKC  V KK++  S++A++ N+GQ   A
Sbjct: 170 KLMSDKKC-SVEKKSEMESVLAQLDNYGQQELA 201


>pdb|2PMF|A Chain A, The Crystal Structure Of A Human Glycyl-trna Synthetase
           Mutant
          Length = 693

 Score = 25.4 bits (54), Expect = 7.4,   Method: Composition-based stats.
 Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 2/33 (6%)

Query: 62  KMMKRKKCLDVVKKAQKVSLMARM-NFGQDNTA 93
           K+M  KKC  V KK++  S++A++ N+GQ   A
Sbjct: 170 KLMSDKKC-SVEKKSEMESVLAQLDNYGQQELA 201


>pdb|2PME|A Chain A, The Apo Crystal Structure Of The Glycyl-Trna Synthetase
 pdb|2ZT5|A Chain A, Crystal Structure Of Human Glycyl-Trna Synthetase (Glyrs)
           In Complex With Ap4a (Cocrystallized With Atp)
 pdb|2ZT6|A Chain A, Crystal Structure Of Human Glycyl-Trna Synthetase (Glyrs)
           In Complex With Ampcpp
 pdb|2ZT7|A Chain A, Crystal Structure Of Human Glycyl-Trna Synthetase (Glyrs)
           In Complex With Glycine And Atp
 pdb|2ZT8|A Chain A, Crystal Structure Of Human Glycyl-Trna Synthetase (Glyrs)
           In Complex With Gly-Amp Analog
 pdb|2ZXF|A Chain A, Crystal Structure Of Human Glycyl-Trna Synthetase (Glyrs)
           In Complex With Ap4a (Cocrystallized With Ap4a)
          Length = 693

 Score = 25.4 bits (54), Expect = 7.4,   Method: Composition-based stats.
 Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 2/33 (6%)

Query: 62  KMMKRKKCLDVVKKAQKVSLMARM-NFGQDNTA 93
           K+M  KKC  V KK++  S++A++ N+GQ   A
Sbjct: 170 KLMSDKKC-SVEKKSEMESVLAQLDNYGQQELA 201


>pdb|2EKL|A Chain A, Structure Of St1218 Protein From Sulfolobus Tokodaii
          Length = 313

 Score = 25.4 bits (54), Expect = 9.0,   Method: Composition-based stats.
 Identities = 9/21 (42%), Positives = 15/21 (71%)

Query: 71 DVVKKAQKVSLMARMNFGQDN 91
          DV++K +K+ ++AR   G DN
Sbjct: 61 DVIEKGKKLKIIARAGIGLDN 81


  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
   0.324    0.141    0.472 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,376,298
Number of Sequences: 62578
Number of extensions: 138585
Number of successful extensions: 197
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 196
Number of HSP's gapped (non-prelim): 7
length of query: 93
length of database: 14,973,337
effective HSP length: 60
effective length of query: 33
effective length of database: 11,218,657
effective search space: 370215681
effective search space used: 370215681
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 45 (21.9 bits)