RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|255764492|ref|YP_003065069.2| hypothetical protein
CLIBASIA_02715 [Candidatus Liberibacter asiaticus str. psy62]
         (56 letters)



>gnl|CDD|72942 cd04657, Piwi_ago-like, Piwi_ago-like: PIWI domain, Argonaute-like
           subfamily. Argonaute is the central component of the
           RNA-induced silencing complex (RISC) and related
           complexes. The PIWI domain is the C-terminal portion of
           Argonaute and consists of two subdomains, one of which
           provides the 5' anchoring of the guide RNA and the
           other, the catalytic site for slicing..
          Length = 426

 Score = 25.6 bits (56), Expect = 2.8
 Identities = 7/25 (28%), Positives = 13/25 (52%)

Query: 23  NSISSRRQNIPPSSVISDLVVHPHE 47
           +    +  N+PP +V+   + HP E
Sbjct: 330 DDADGKNGNVPPGTVVDRGITHPRE 354


>gnl|CDD|145366 pfam02171, Piwi, Piwi domain.  This domain is found in the protein
           Piwi and its relatives. The function of this domain is
           the dsRNA guided hydrolysis of ssRNA. Determination of
           the crystal structure of Argonaute reveals that PIWI is
           an RNase H domain, and identifies Argonaute as Slicer,
           the enzyme that cleaves mRNA in the RNAi RISC complex.
           In addition, Mg+2 dependence and production of 3'-OH and
           5' phosphate products are shared characteristics of
           RNaseH and RISC. The PIWI domain core has a tertiary
           structure belonging to the RNase H family of enzymes.
           RNase H fold proteins all have a five-stranded mixed
           beta-sheet surrounded by helices. By analogy to RNase H
           enzymes which cleave single-stranded RNA guided by the
           DNA strand in an RNA/DNA hybrid, the PIWI domain can be
           inferred to cleave single-stranded RNA, for example
           mRNA, guided by double stranded siRNA.
          Length = 296

 Score = 25.0 bits (55), Expect = 4.3
 Identities = 6/23 (26%), Positives = 11/23 (47%)

Query: 23  NSISSRRQNIPPSSVISDLVVHP 45
           +      QN PP +V+  ++  P
Sbjct: 199 SGKRDGAQNPPPGTVVDTVITSP 221


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.308    0.125    0.350 

Gapped
Lambda     K      H
   0.267   0.0590    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 624,778
Number of extensions: 19650
Number of successful extensions: 47
Number of sequences better than 10.0: 1
Number of HSP's gapped: 47
Number of HSP's successfully gapped: 5
Length of query: 56
Length of database: 6,263,737
Length adjustment: 28
Effective length of query: 28
Effective length of database: 5,658,685
Effective search space: 158443180
Effective search space used: 158443180
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 51 (23.7 bits)