RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5357
         (181 letters)



>gnl|CDD|147520 pfam05380, Peptidase_A17, Pao retrotransposon peptidase.
           Corresponds to Merops family A17. These proteins are
           homologous to aspartic proteinases encoded by
           retroposons and retroviruses.
          Length = 159

 Score = 63.2 bits (154), Expect = 4e-13
 Identities = 30/89 (33%), Positives = 47/89 (52%), Gaps = 6/89 (6%)

Query: 2   IDSMNFVSNIPVARYFDVPNNHDDQSVRYEPHAFSDACSYSYASVVYLRSVSHSGDIRTN 61
              ++ +  I V RY         +++  + H F DA   +YA+ VY R V    +I+ +
Sbjct: 57  RKQLSTLQQIRVPRYV---PYSPARNI--QLHGFCDASEKAYAAAVYWR-VEEGEEIQVS 110

Query: 62  IVFAKSRVAPTNKPTLPRLELLGALIAYR 90
           +V AK+RVAP    ++PRLEL  AL+  R
Sbjct: 111 LVAAKTRVAPLKTVSIPRLELCAALLLTR 139


>gnl|CDD|187696 cd09272, RNase_HI_RT_Ty1, Ty1/Copia family of RNase HI in long-term
           repeat retroelements.  Ribonuclease H (RNase H) enzymes
           are divided into two major families, Type 1 and Type 2,
           based on amino acid sequence similarities and
           biochemical properties. RNase H is an endonuclease that
           cleaves the RNA strand of an RNA/DNA hybrid in a
           sequence non-specific manner in the presence of divalent
           cations. RNase H is widely present in various organisms,
           including bacteria, archaea and eukaryotes.  RNase HI
           has also been observed as adjunct domains to the reverse
           transcriptase gene in retroviruses, in long-term repeat
           (LTR)-bearing 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.
           Phylogenetic patterns of RNase HI of LTR retroelements
           is classified into five major families, Ty3/Gypsy,
           Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate
           retroviruses.  Ty1/Copia family is widely distributed
           among the genomes of plants, fungi and animals. RNase H
           inhibitors have been explored as an anti-HIV drug target
           because RNase H inactivation inhibits reverse
           transcription.
          Length = 142

 Score = 30.9 bits (71), Expect = 0.20
 Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 7/57 (12%)

Query: 95  LWIDNQCVIHWLTGNKVF---TTFVNNRVKALKE-IKASVFPIVYKYIPTDSNPADL 147
           ++ DNQ  I  L  N VF   T  ++ R   ++E ++     I  +YIPT+   AD+
Sbjct: 79  IYCDNQSAIA-LAKNPVFHERTKHIDIRYHFIREKVEKGE--IKLEYIPTEEQLADI 132


>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
           Provisional.
          Length = 2849

 Score = 29.2 bits (65), Expect = 1.6
 Identities = 11/38 (28%), Positives = 15/38 (39%)

Query: 103 IHWLTGNKVFTTFVNNRVKALKEIKASVFPIVYKYIPT 140
             W    K     +N  V   K+ KA  F + Y +IP 
Sbjct: 491 EKWDKEKKSLGNLINGAVVYNKDFKAKYFNVKYFHIPK 528


>gnl|CDD|216028 pfam00621, RhoGEF, RhoGEF domain.  Guanine nucleotide exchange
           factor for Rho/Rac/Cdc42-like GTPases Also called
           Dbl-homologous (DH) domain. It appears that pfam00169
           domains invariably occur C-terminal to RhoGEF/DH
           domains.
          Length = 179

 Score = 27.2 bits (61), Expect = 4.4
 Identities = 13/51 (25%), Positives = 24/51 (47%), Gaps = 7/51 (13%)

Query: 81  ELLGALIAYRNKCYLWIDNQCV----IHWLTGNKVFTTFVNNRVKALKEIK 127
           E L  L     +   W D Q +    + +    KV++T+ +N  +AL+ +K
Sbjct: 54  EFLEEL---EERLEEWPDIQRIGDIFLKFAPFFKVYSTYCSNYPRALELLK 101


>gnl|CDD|215519 PLN02960, PLN02960, alpha-amylase.
          Length = 897

 Score = 26.7 bits (59), Expect = 8.3
 Identities = 9/23 (39%), Positives = 15/23 (65%)

Query: 109 NKVFTTFVNNRVKALKEIKASVF 131
           ++ F  F+  R KALK++K  +F
Sbjct: 82  DRAFAQFLRERHKALKDLKWEIF 104


>gnl|CDD|131316 TIGR02263, benz_CoA_red_C, benzoyl-CoA reductase, subunit C.  This
           model describes C subunit of benzoyl-CoA reductase, a
           4-subunit enzyme. Many aromatic compounds are
           metabolized by way of benzoyl-CoA. This enzyme acts
           under anaerobic conditions.
          Length = 380

 Score = 26.5 bits (58), Expect = 9.0
 Identities = 9/12 (75%), Positives = 11/12 (91%)

Query: 14  ARYFDVPNNHDD 25
           ARYFD+P+N DD
Sbjct: 122 ARYFDLPHNFDD 133


  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
   0.322    0.136    0.438 

Gapped
Lambda     K      H
   0.267   0.0652    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,123,730
Number of extensions: 792473
Number of successful extensions: 461
Number of sequences better than 10.0: 1
Number of HSP's gapped: 459
Number of HSP's successfully gapped: 14
Length of query: 181
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 90
Effective length of database: 6,901,388
Effective search space: 621124920
Effective search space used: 621124920
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 (21.9 bits)
S2: 56 (25.5 bits)