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= 008862
         (550 letters)

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

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



>pdb|1RKB|A Chain A, The Structure Of Adrenal Gland Protein Ad-004
          Length = 173

 Score = 35.0 bits (79), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 32/59 (54%), Gaps = 3/59 (5%)

Query: 448 VIPLGTDWAAETYYG-EPARKLGLKYIGYTILPRESSLYDQYDK--NDPVLRDPSSVNE 503
           ++  GT    +T  G E A K GLKYI    L RE  LYD YD+  + P+L +   V+E
Sbjct: 7   ILLTGTPGVGKTTLGKELASKSGLKYINVGDLAREEQLYDGYDEEYDCPILDEDRVVDE 65


>pdb|3IIJ|A Chain A, The Structure Of Hcinap-Adp Complex At 1.76 Angstroms
           Resolution.
 pdb|3IIK|A Chain A, The Structure Of Hcinap-So4 Complex At 1.95 Angstroms
           Resolution
 pdb|3IIL|A Chain A, The Structure Of Hcinap-Mgadp-Pi Complex At 2.0 Angstroms
           Resolution
 pdb|3IIM|A Chain A, The Structure Of Hcinap-Dadp Complex At 2.0 Angstroms
           Resolution
          Length = 180

 Score = 34.7 bits (78), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 32/59 (54%), Gaps = 3/59 (5%)

Query: 448 VIPLGTDWAAETYYG-EPARKLGLKYIGYTILPRESSLYDQYDK--NDPVLRDPSSVNE 503
           ++  GT    +T  G E A K GLKYI    L RE  LYD YD+  + P+L +   V+E
Sbjct: 14  ILLTGTPGVGKTTLGKELASKSGLKYINVGDLAREEQLYDGYDEEYDCPILDEDRVVDE 72


>pdb|3BQ9|A Chain A, Crystal Structure Of Predicted Nucleotide-Binding Protein
           From Idiomarina Baltica Os145
 pdb|3BQ9|B Chain B, Crystal Structure Of Predicted Nucleotide-Binding Protein
           From Idiomarina Baltica Os145
          Length = 460

 Score = 31.6 bits (70), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 43/174 (24%), Positives = 71/174 (40%), Gaps = 20/174 (11%)

Query: 348 SLSPSSDPSFKNVKEVQG-DQSKKPKLVILSRNGSRAITNENSLVKMAEDI-----GFQV 401
           S+SP    S  +  E++    S   +L  L RN   A+ N  S    + DI      F+V
Sbjct: 5   SISPQGSMSLLSQLEIERLKASSNSQLYKLFRNCCLAVLNAGSHTDSSADIYDSYKDFEV 64

Query: 402 QVVRPDRTSELAKIY---RALNSSDVMVGVHGAAMTHFLFMKPGSVFIQVIPLGTDWAAE 458
            ++R +R  +L  I     A    +V+VG+              SV   ++  G  ++  
Sbjct: 65  NIIRRERGIKLELIEPPEEAFVDGEVIVGIRELLE---------SVLRDILFTGERYSET 115

Query: 459 TYYGEPARKLGLKYIGYTILPRESSLYDQYDKNDPVLRDPSSVNEKGWQYTKTI 512
               E A    L ++ + IL    +L  Q + N  V     S+NE  ++YTK +
Sbjct: 116 DL--EHADSATLTHVVFDILRNARTLRPQEEPNMVVCWGGHSINEIEYKYTKDV 167


>pdb|3B0P|A Chain A, Trna-Dihydrouridine Synthase From Thermus Thermophilus
 pdb|3B0P|B Chain B, Trna-Dihydrouridine Synthase From Thermus Thermophilus
 pdb|3B0U|X Chain X, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
           Complex With Trna Fragment
 pdb|3B0U|Y Chain Y, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
           Complex With Trna Fragment
          Length = 350

 Score = 30.4 bits (67), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 14/46 (30%), Positives = 27/46 (58%)

Query: 273 RLSDYPPIDFSGDKRTHCFPEAIVGLRIHDELTVDPSLMRGNKNAI 318
           RLS  P +D +         +  +G+R++ E+TVD +++RGN+  +
Sbjct: 5   RLSVAPMVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGNRERL 50


>pdb|3B0V|C Chain C, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
           Complex With Trna
 pdb|3B0V|D Chain D, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
           Complex With Trna
          Length = 363

 Score = 28.9 bits (63), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 14/46 (30%), Positives = 26/46 (56%)

Query: 273 RLSDYPPIDFSGDKRTHCFPEAIVGLRIHDELTVDPSLMRGNKNAI 318
           RLS  P +D +         +  +G+R++ E TVD +++RGN+  +
Sbjct: 26  RLSVAPXVDRTDRHFRFLVRQVSLGVRLYTEXTVDQAVLRGNRERL 71


  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    0.135    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,445,137
Number of Sequences: 62578
Number of extensions: 644526
Number of successful extensions: 1423
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1419
Number of HSP's gapped (non-prelim): 8
length of query: 550
length of database: 14,973,337
effective HSP length: 104
effective length of query: 446
effective length of database: 8,465,225
effective search space: 3775490350
effective search space used: 3775490350
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: 54 (25.4 bits)