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= 025542
         (251 letters)

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

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



>pdb|3OQG|A Chain A, Restriction Endonuclease Hpy188i In Complex With Substrate
           Dna
 pdb|3OQG|B Chain B, Restriction Endonuclease Hpy188i In Complex With Substrate
           Dna
 pdb|3OR3|A Chain A, Restriction Endonuclease Hpy188i In Complex With Product
           Dna
 pdb|3OR3|B Chain B, Restriction Endonuclease Hpy188i In Complex With Product
           Dna
          Length = 180

 Score = 29.6 bits (65), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 3/63 (4%)

Query: 170 GRMRGLHNSTALGGHIFLLPYLLRISLICRTYLKLPWKPLISIDGSTVYELNDELKITRH 229
           G++    N T    + F+L  LL+I+ I + Y   P +P  ++ G T     D    ++ 
Sbjct: 101 GKVEYRKNGTCSTTNYFVLQSLLKINKIVQVYAFFPEQPTYTLFGKT---YQDSFSTSKR 157

Query: 230 AES 232
           AE+
Sbjct: 158 AEN 160


>pdb|2V2Q|A Chain A, Ispe In Complex With Ligand
 pdb|2V2Q|B Chain B, Ispe In Complex With Ligand
 pdb|2V2V|A Chain A, Ispe In Complex With Ligand
 pdb|2V2V|B Chain B, Ispe In Complex With Ligand
 pdb|2V2Z|A Chain A, Ispe In Complex With Adp And Cdpme
 pdb|2V2Z|B Chain B, Ispe In Complex With Adp And Cdpme
 pdb|2V34|A Chain A, Ispe In Complex With Cytidine And Ligand
 pdb|2V34|B Chain B, Ispe In Complex With Cytidine And Ligand
 pdb|2V8P|A Chain A, Ispe In Complex With Adp And Cdp
 pdb|2V8P|B Chain B, Ispe In Complex With Adp And Cdp
 pdb|2VF3|A Chain A, Aquifex Aeolicus Ispe In Complex With Ligand
 pdb|2VF3|B Chain B, Aquifex Aeolicus Ispe In Complex With Ligand
          Length = 271

 Score = 27.7 bits (60), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 3/50 (6%)

Query: 193 RISLICRTYLKLPWKPLISIDGSTVY---ELNDELKITRHAESWNVSALE 239
            I+ + R    L +KP +S  GSTVY     ++ELK       W V  LE
Sbjct: 221 EINEVYRFVEYLGFKPFVSGSGSTVYFFGGASEELKKAAKMRGWKVVELE 270


>pdb|1CZF|A Chain A, Endo-Polygalacturonase Ii From Aspergillus Niger
 pdb|1CZF|B Chain B, Endo-Polygalacturonase Ii From Aspergillus Niger
          Length = 362

 Score = 27.3 bits (59), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 29/106 (27%), Positives = 49/106 (46%), Gaps = 10/106 (9%)

Query: 31  GTVNDGNKNTNNKTATPQILKFAVSGVTELLRLFS-SFDKGRLDKVSYKQKYEILVSGID 89
           G+V D    +NN      I    VS     +R+ + S   G + +++Y     I++SGI 
Sbjct: 228 GSVGD---RSNNVVKNVTIEHSTVSNSENAVRIKTISGATGSVSEITYSN---IVMSGIS 281

Query: 90  DIVTILRSDYENAYFVTGIFTSEIYAEDCIFEDPT--IRFRGTELY 133
           D   +++ DYE+    TG  T+ +  +D   E  T  +    TE+Y
Sbjct: 282 DYGVVIQQDYEDGK-PTGKPTNGVTIQDVKLESVTGSVDSGATEIY 326


  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
   0.323    0.140    0.420 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,434,988
Number of Sequences: 62578
Number of extensions: 295860
Number of successful extensions: 500
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 499
Number of HSP's gapped (non-prelim): 5
length of query: 251
length of database: 14,973,337
effective HSP length: 96
effective length of query: 155
effective length of database: 8,965,849
effective search space: 1389706595
effective search space used: 1389706595
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)