RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

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

Query= psy16549
         (60 letters)



>gnl|CDD|216011 pfam00589, Phage_integrase, Phage integrase family.  Members of
           this family cleave DNA substrates by a series of
           staggered cuts, during which the protein becomes
           covalently linked to the DNA through a catalytic
           tyrosine residue at the carboxy end of the alignment.
           The catalytic site residues in CRE recombinase are
           Arg-173, His-289, Arg-292 and Tyr-324.
          Length = 170

 Score = 26.5 bits (59), Expect = 0.62
 Identities = 10/30 (33%), Positives = 13/30 (43%), Gaps = 5/30 (16%)

Query: 20  FGPHYLELGVNLQE-----GHENVSMDETY 44
           F  H  E G  L+      GH ++SM   Y
Sbjct: 134 FATHLAENGAPLRVIQKLLGHSSISMTMRY 163


>gnl|CDD|238587 cd01182, INT_REC_C, DNA breaking-rejoining enzymes,
           intergrase/recombinases, C-terminal catalytic domain.
           The tyrosine recombinase/integrase family share the same
           catalytic domain containing six conserved active site
           residues. The best-studied members of this diverse
           family include the bacteriophage lambda integrase, the
           bacteriophage P1 Cre recombinase, the yeast Flp
           recombinase and the bacterial XerD/C recombinases. Their
           overall reaction mechanism is essentially identical and
           involves cleavage of a single strand of a DNA duplex by
           nucleophilic attack of a conserved tyrosine to give a 3'
           phosphotyrosyl protein-DNA adduct. In the second
           rejoining step, a terminal 5' hydroxyl attacks the
           covalent adduct to release the enzyme and generate
           duplex DNA. Many intergrase/recombinases also have
           N-terminal domains, which show little sequence or
           structure similarity.
          Length = 162

 Score = 24.4 bits (53), Expect = 3.5
 Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 5/28 (17%)

Query: 23  HYLELGVNLQE-----GHENVSMDETYL 45
             LE GV L+      GH ++S  E YL
Sbjct: 134 RLLEAGVPLEVIQELLGHSSISTTERYL 161


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.326    0.142    0.445 

Gapped
Lambda     K      H
   0.267   0.0716    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,043,249
Number of extensions: 206093
Number of successful extensions: 284
Number of sequences better than 10.0: 1
Number of HSP's gapped: 284
Number of HSP's successfully gapped: 3
Length of query: 60
Length of database: 10,937,602
Length adjustment: 31
Effective length of query: 29
Effective length of database: 9,562,628
Effective search space: 277316212
Effective search space used: 277316212
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.2 bits)