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= psy14454
         (117 letters)

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

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



>pdb|2DHZ|A Chain A, Solution Structure Of The Ra Domain In The Human Link
           Guanine Nucleotide Exchange Factor Ii (Link-Gefii)
          Length = 120

 Score = 28.5 bits (62), Expect = 0.99,   Method: Compositional matrix adjust.
 Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 49  KQRLDRADADLLHSRKENIRLTEQIANIEKELQMAKLSADDREDLLQDPKKDKELTSL 106
           + RL  +  D+L S  E ++ +E+ A  E  L +  +S+   + LLQ P +D   T+L
Sbjct: 25  RSRLSASVQDILGSVTEKLQYSEEPAGREDSLILVAVSSSGEKVLLQ-PTEDCVFTAL 81


>pdb|1XUU|A Chain A, Crystal Structure Of Sialic Acid Synthase (Neub) In
           Complex With Mn2+ And Malate From Neisseria Meningitidis
 pdb|1XUZ|A Chain A, Crystal Structure Analysis Of Sialic Acid Synthase
           (Neub)from Neisseria Meningitidis, Bound To Mn2+,
           Phosphoenolpyruvate, And N- Acetyl Mannosaminitol
 pdb|2ZDR|A Chain A, Crystal Structure Of Sialic Acid Synthase (Neub) From
           Neisseria Meningitidis In Complex With Mg2+ And (4s)-2-
           Methyl-2,4-Pentanediol
 pdb|3CM4|A Chain A, Crystal Structure Of Metal-Free Sialic Acid Synthase
           (Neub) From Neisseria Meningitidis In Complex With
           Malate
          Length = 349

 Score = 26.2 bits (56), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 2/70 (2%)

Query: 48  YKQRLDRADADLLHSRKENIRLTEQIANIEKELQMAKLSADDREDLLQDPKKDKELTSLI 107
           +  R+DR   D++ S   N    +++      L++A+    D     + P KD    S++
Sbjct: 237 FTDRMDRPGPDIVCSM--NPDTFKELKQGAHALKLARGGKKDTIIAGEKPTKDFAFASVV 294

Query: 108 MDMDAKHGRL 117
            D D K G L
Sbjct: 295 ADKDIKKGEL 304


>pdb|3CO4|A Chain A, Crystal Structure Of A Chitinase From Bacteroides
           Thetaiotaomicron
 pdb|3FND|A Chain A, Crystal Structure Of A Chitinase From Bacteroides
           Thetaiotaomicron
          Length = 312

 Score = 25.4 bits (54), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 15/46 (32%), Positives = 24/46 (52%)

Query: 63  RKENIRLTEQIANIEKELQMAKLSADDREDLLQDPKKDKELTSLIM 108
           R E++R T    N++  + +AK S  +    + DPK  KEL   I+
Sbjct: 53  RIESVRETAHKHNVKILISLAKNSPGEFTTAINDPKARKELIQQII 98


  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
   0.308    0.125    0.312 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,721,497
Number of Sequences: 62578
Number of extensions: 84176
Number of successful extensions: 275
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 251
Number of HSP's gapped (non-prelim): 39
length of query: 117
length of database: 14,973,337
effective HSP length: 80
effective length of query: 37
effective length of database: 9,967,097
effective search space: 368782589
effective search space used: 368782589
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 45 (21.9 bits)