RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy8736
         (290 letters)



>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse
           transcriptases.  Ribonuclease H (RNase H) is classified
           into two families, type 1 (prokaryotic RNase HI,
           eukaryotic RNase H1 and viral RNase H) and type 2
           (prokaryotic RNase HII and HIII, and eukaryotic RNase
           H2). Ribonuclease HI (RNase HI) is an endonuclease that
           cleaves the RNA strand of an RNA/DNA hybrid in a
           sequence non-specific manner. RNase H is widely present
           in various organisms, including bacteria, archaea and
           eukaryotes.  RNase HI has also been observed as an
           adjunct domain to the reverse transcriptase gene in
           retroviruses, long-term repeat (LTR)-bearing
           retrotransposons and non-LTR retrotransposons. RNase HI
           in LTR retrotransposons perform degradation of the
           original RNA template, generation of a polypurine tract
           (the primer for plus-strand DNA synthesis), and final
           removal of RNA primers from newly synthesized minus and
           plus strands. The catalytic residues for RNase H
           enzymatic activity, three aspartatic acids and one
           glutamatic acid residue (DEDD), are unvaried across all
           RNase H domains. The position of the RNase domain of
           non-LTR and LTR transposons is at the carboxyl terminal
           of the reverse transcriptase (RT) domain and their RNase
           domains group together, indicating a common evolutionary
           origin. Many non-LTR transposons have lost the RNase
           domain because their activity is at the nucleus and
           cellular RNase may suffice; however LTR retotransposons
           always encode their own RNase domain because it requires
           RNase activity in RNA-protein particles in the
           cytoplasm. RNase H inhibitors have been explored as an
           anti-HIV drug target because RNase H inactivation
           inhibits reverse transcription.
          Length = 128

 Score = 57.3 bits (139), Expect = 2e-10
 Identities = 28/91 (30%), Positives = 40/91 (43%), Gaps = 9/91 (9%)

Query: 137 QIFTDASKNEHSVSSAFCC---EETKFSVKLDPRISICNAELISIQYAISFIISTTPLQV 193
            I+TD SK E    + F          S KL P  S+ +AEL++I  A+   +       
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALRE---GR 57

Query: 194 PTPKFVLYSDSLSA---LQSREQVSLTRLRI 221
              K  ++SDS +A   L+S    S   LRI
Sbjct: 58  RARKITIFSDSQAALKALRSPRSSSPLVLRI 88


>gnl|CDD|131777 TIGR02730, carot_isom, carotene isomerase.  Members of this family,
           including sll0033 (crtH) of Synechocystis sp. PCC 6803,
           catalyze a cis-trans isomerization of carotenes to the
           all-trans lycopene, a reaction that can also occur
           non-enzymatically in light through photoisomerization
           [Biosynthesis of cofactors, prosthetic groups, and
           carriers, Other].
          Length = 493

 Score = 33.6 bits (77), Expect = 0.11
 Identities = 16/42 (38%), Positives = 24/42 (57%)

Query: 96  LNTLRDPRHLHFNLIKNDNVNLHQEIQIGFFELAQKFPNYKQ 137
           L T+ DP  +H++L    NV +H+E      EL  KFP+ K+
Sbjct: 79  LETIPDPVQIHYHLPNGLNVKVHREYDDFIQELVAKFPHEKE 120


>gnl|CDD|215695 pfam00075, RNase_H, RNase H.  RNase H digests the RNA strand of an
           RNA/DNA hybrid. Important enzyme in retroviral
           replication cycle, and often found as a domain
           associated with reverse transcriptases. Structure is a
           mixed alpha+beta fold with three a/b/a layers.
          Length = 126

 Score = 28.8 bits (65), Expect = 1.5
 Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 10/80 (12%)

Query: 133 PNYKQIFTDAS--KNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTP 190
           P    ++TD S   N     + +  +  K   K  P  +   AEL+++  A+        
Sbjct: 1   PEAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGTTNQRAELLALIEALE------- 53

Query: 191 LQVPTPKFVLYSDSLSALQS 210
             +   K  +Y+DS   +  
Sbjct: 54  -ALSGQKVNIYTDSQYVIGG 72


>gnl|CDD|226615 COG4130, COG4130, Predicted sugar epimerase [Carbohydrate transport
           and metabolism].
          Length = 272

 Score = 27.5 bits (61), Expect = 7.2
 Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 1/31 (3%)

Query: 27  SYIRSKLDYASIVYSSASDSSLK-VLDTVHH 56
             +RSK + A  + ++  +   K V DT HH
Sbjct: 148 CSLRSKAEAAEAIRAAGGERVFKLVHDTFHH 178


  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
   0.319    0.133    0.386 

Gapped
Lambda     K      H
   0.267   0.0706    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,828,188
Number of extensions: 1253758
Number of successful extensions: 1024
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1022
Number of HSP's successfully gapped: 11
Length of query: 290
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 194
Effective length of database: 6,679,618
Effective search space: 1295845892
Effective search space used: 1295845892
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.2 bits)