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= 038559
         (137 letters)

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

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



>pdb|1R3D|A Chain A, Crystal Structure Of Protein Vc1974 From Vibrio Cholerae,
           Pfam Abhydrolase
          Length = 264

 Score = 26.2 bits (56), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 22/88 (25%), Positives = 38/88 (43%), Gaps = 8/88 (9%)

Query: 53  HVLEEWTEIEEGALPSLKYLQLHKCLKLRM------LLEDLQFVATLKQLQILPLLDEHK 106
           HVL +W   ++    SL + Q    +  R       +   L   +  KQ  +LP L   K
Sbjct: 151 HVLSDW--YQQAVFSSLNHEQRQTLIAQRSANLGSSVAHXLLATSLAKQPYLLPALQALK 208

Query: 107 ERLKPYGGEENYKIRHIPQTPGRGYSRV 134
             +    GE++ K + + ++ G  YS+V
Sbjct: 209 LPIHYVCGEQDSKFQQLAESSGLSYSQV 236


>pdb|4ES1|A Chain A, Double-Stranded Endonuclease Activity In B. Halodurans
           Clustered Regularly Interspaced Short Palindromic
           Repeats (Crispr)-Associated Cas2 Protein
 pdb|4ES2|A Chain A, Double-Stranded Endonuclease Activity In B. Halodurans
           Clustered Regularly Interspaced Short Palindromic
           Repeats (Crispr)-Associated Cas2 Protein
 pdb|4ES3|A Chain A, Double-Stranded Endonuclease Activity In B. Halodurans
           Clustered Regularly Interspaced Short Palindromic
           Repeats (Crispr)-Associated Cas2 Protein
          Length = 100

 Score = 25.4 bits (54), Expect = 9.2,   Method: Compositional matrix adjust.
 Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 2/35 (5%)

Query: 95  QLQILPLLDEHKERLKPYGGEENY--KIRHIPQTP 127
           +L++  L+DE K+ L+ Y    NY  K+ HI   P
Sbjct: 56  KLELTSLIDEEKDSLRIYRLGNNYKTKVEHIGAKP 90


  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
   0.320    0.139    0.402 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,830,266
Number of Sequences: 62578
Number of extensions: 136595
Number of successful extensions: 231
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 231
Number of HSP's gapped (non-prelim): 2
length of query: 137
length of database: 14,973,337
effective HSP length: 89
effective length of query: 48
effective length of database: 9,403,895
effective search space: 451386960
effective search space used: 451386960
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: 46 (22.3 bits)