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= 025397
         (253 letters)

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

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



>pdb|3GFB|A Chain A, L-Threonine Dehydrogenase (Tktdh) From The
           Hyperthermophilic Archaeon Thermococcus Kodakaraensis
 pdb|3GFB|B Chain B, L-Threonine Dehydrogenase (Tktdh) From The
           Hyperthermophilic Archaeon Thermococcus Kodakaraensis
 pdb|3GFB|C Chain C, L-Threonine Dehydrogenase (Tktdh) From The
           Hyperthermophilic Archaeon Thermococcus Kodakaraensis
 pdb|3GFB|D Chain D, L-Threonine Dehydrogenase (Tktdh) From The
           Hyperthermophilic Archaeon Thermococcus Kodakaraensis
          Length = 350

 Score = 32.0 bits (71), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 5/75 (6%)

Query: 46  SSLFGLSLPQNLKSTALKHISGSDDDVTFRIKEFDRDHASKLASDYITAIADELKDDPL- 104
           S+L   + P  L   A+   SG+   +     EF R  A K+ +DY+    +  ++DP+ 
Sbjct: 170 STLITGAGPLGLLGIAVAKASGAYPVIVSEPSEFRRKLAKKVGADYVV---NPFEEDPVK 226

Query: 105 -VVCVLDGNMLKLFL 118
            V+ + DG  +++FL
Sbjct: 227 FVMDITDGAGVEVFL 241


>pdb|3KD3|A Chain A, Crystal Structure Of A Phosphoserine Phosphohydrolase-Like
           Protein From Francisella Tularensis Subsp. Tularensis
           Schu S4
 pdb|3KD3|B Chain B, Crystal Structure Of A Phosphoserine Phosphohydrolase-Like
           Protein From Francisella Tularensis Subsp. Tularensis
           Schu S4
          Length = 219

 Score = 27.7 bits (60), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 22/96 (22%), Positives = 35/96 (36%), Gaps = 16/96 (16%)

Query: 54  PQNLKSTALKHISGSDDDVTFR----------------IKEFDRDHASKLASDYITAIAD 97
           P  LK        G   D++FR                IKEF   +   L +D I  +  
Sbjct: 33  PAKLKEIEYITNLGXQGDISFRDSLQKRLAIASPTKQSIKEFSNKYCPNLLTDGIKELVQ 92

Query: 98  ELKDDPLVVCVLDGNMLKLFLGNEDDFTMLAENLFA 133
           +LK+    + +  G + +      D   +  EN+FA
Sbjct: 93  DLKNKGFEIWIFSGGLSESIQPFADYLNIPRENIFA 128


>pdb|3UB6|A Chain A, Periplasmic Portion Of The Helicobacter Pylori
           Chemoreceptor Tlpb With Urea Bound
 pdb|3UB6|B Chain B, Periplasmic Portion Of The Helicobacter Pylori
           Chemoreceptor Tlpb With Urea Bound
 pdb|3UB7|A Chain A, Periplasmic Portion Of The Helicobacter Pylori
           Chemoreceptor Tlpb With Acetamide Bound
 pdb|3UB7|B Chain B, Periplasmic Portion Of The Helicobacter Pylori
           Chemoreceptor Tlpb With Acetamide Bound
 pdb|3UB8|A Chain A, Periplasmic Portion Of The Helicobacter Pylori
           Chemoreceptor Tlpb With Formamide Bound
 pdb|3UB8|B Chain B, Periplasmic Portion Of The Helicobacter Pylori
           Chemoreceptor Tlpb With Formamide Bound
 pdb|3UB9|A Chain A, Periplasmic Portion Of The Helicobacter Pylori
           Chemoreceptor Tlpb With Hydroxyurea Bound
 pdb|3UB9|B Chain B, Periplasmic Portion Of The Helicobacter Pylori
           Chemoreceptor Tlpb With Hydroxyurea Bound
          Length = 181

 Score = 27.3 bits (59), Expect = 9.3,   Method: Compositional matrix adjust.
 Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 2/41 (4%)

Query: 77  KEFDRDHASKLASDYITAIADELKDDPLVVCVLDGNMLKLF 117
           K FD D A K+A DY   I D+     + + V+D N + LF
Sbjct: 45  KSFDNDTARKMALDYFKRINDD--KGMIYMVVVDKNGVVLF 83


  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    0.136    0.389 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,599,237
Number of Sequences: 62578
Number of extensions: 242463
Number of successful extensions: 688
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 687
Number of HSP's gapped (non-prelim): 9
length of query: 253
length of database: 14,973,337
effective HSP length: 97
effective length of query: 156
effective length of database: 8,903,271
effective search space: 1388910276
effective search space used: 1388910276
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)