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= 040491
         (497 letters)

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

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



>pdb|1UJ5|A Chain A, Crystal Structure Of Thermus Thermophilus
           Ribose-5-Phosphate Isomerase Complexed With
           Ribose-5-Phosphate
          Length = 227

 Score = 29.6 bits (65), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 17/54 (31%), Positives = 27/54 (50%)

Query: 441 ILDEHVEVRKLELEGLVKMFEQEAESHAQVRKSVPHSTLPPTAADLLPDGASYV 494
           +L+    +R+ EL+G+V +    A      R+ +P   LPP   DL  DGA  +
Sbjct: 38  VLELARRLREGELKGVVGVPTSRATEELAKREGIPLVDLPPEGVDLAIDGADEI 91


>pdb|1UJ4|A Chain A, Crystal Structure Of Thermus Thermophilus
           Ribose-5-phosphate Isomerase
 pdb|1UJ6|A Chain A, Crystal Structure Of Thermus Thermophilus
           Ribose-5-Phosphate Isomerase Complexed With
           Arabinose-5-Phosphate
          Length = 227

 Score = 29.6 bits (65), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 17/54 (31%), Positives = 27/54 (50%)

Query: 441 ILDEHVEVRKLELEGLVKMFEQEAESHAQVRKSVPHSTLPPTAADLLPDGASYV 494
           +L+    +R+ EL+G+V +    A      R+ +P   LPP   DL  DGA  +
Sbjct: 38  VLELARRLREGELKGVVGVPTSRATEELAKREGIPLVDLPPEGVDLAIDGADEI 91


>pdb|3FCR|A Chain A, Crystal Structure Of Putative Aminotransferase
           (Yp_614685.1) From Silicibacter Sp. Tm1040 At 1.80 A
           Resolution
          Length = 459

 Score = 29.3 bits (64), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 12/38 (31%), Positives = 20/38 (52%)

Query: 35  GDLWTDGLICAFEFVRGHKKMVKSKPGSKVEPSLTPKV 72
           GD+  +GL+CA EFV+            K+ P ++ K+
Sbjct: 376 GDVRGEGLLCAVEFVKDRDSRTFFDAADKIGPQISAKL 413


  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    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,097,894
Number of Sequences: 62578
Number of extensions: 553407
Number of successful extensions: 1033
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1023
Number of HSP's gapped (non-prelim): 19
length of query: 497
length of database: 14,973,337
effective HSP length: 103
effective length of query: 394
effective length of database: 8,527,803
effective search space: 3359954382
effective search space used: 3359954382
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: 53 (25.0 bits)