RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16296
         (70 letters)



>gnl|CDD|215754 pfam00153, Mito_carr, Mitochondrial carrier protein. 
          Length = 96

 Score = 43.8 bits (104), Expect = 2e-07
 Identities = 14/31 (45%), Positives = 17/31 (54%)

Query: 38 RVYKGSIDCMLQTIKHEGFMALYKGFIPTWF 68
          R YKG +DC  +  K EG   LYKG +P   
Sbjct: 42 RKYKGILDCFKKIYKEEGIRGLYKGLLPNLL 72


>gnl|CDD|240302 PTZ00169, PTZ00169, ADP/ATP transporter on adenylate translocase;
           Provisional.
          Length = 300

 Score = 32.8 bits (75), Expect = 0.005
 Identities = 11/26 (42%), Positives = 18/26 (69%)

Query: 38  RVYKGSIDCMLQTIKHEGFMALYKGF 63
           R + G  DC+++  K  GF++LY+GF
Sbjct: 151 REFTGLFDCLMKISKQTGFLSLYQGF 176



 Score = 32.4 bits (74), Expect = 0.007
 Identities = 9/23 (39%), Positives = 15/23 (65%)

Query: 40  YKGSIDCMLQTIKHEGFMALYKG 62
           Y G++DC  + +K+EG    +KG
Sbjct: 252 YTGTLDCWKKILKNEGLGGFFKG 274



 Score = 24.3 bits (53), Expect = 6.1
 Identities = 7/23 (30%), Positives = 15/23 (65%)

Query: 40 YKGSIDCMLQTIKHEGFMALYKG 62
          Y G ++C  +  K +G ++L++G
Sbjct: 52 YSGIVNCFRRVSKEQGVLSLWRG 74


>gnl|CDD|187699 cd09275, RNase_HI_RT_DIRS1, DIRS1 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 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. 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. The structural features of
          DIRS1-group elements are different from typical LTR
          elements. RNase H inhibitors have been explored as an
          anti-HIV drug target because RNase H inactivation
          inhibits reverse transcription.
          Length = 120

 Score = 26.1 bits (58), Expect = 1.3
 Identities = 13/41 (31%), Positives = 17/41 (41%), Gaps = 5/41 (12%)

Query: 17 ELLIFLVALPMNQKHLKNQHVRVYKGSIDCM--LQTIKHEG 55
          ELL  L+AL      L N+ V V     D    +  I  +G
Sbjct: 37 ELLAVLLALQHWGARLSNRKVLVR---SDNTTAVAYINRQG 74


>gnl|CDD|237538 PRK13876, PRK13876, conjugal transfer coupling protein TraG;
           Provisional.
          Length = 663

 Score = 24.9 bits (55), Expect = 4.0
 Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 9/37 (24%)

Query: 12  FSYGYELLIFLVALPMNQ-------KH--LKNQHVRV 39
           F  GY +  FL+A  +NQ        +  L N HVRV
Sbjct: 424 FMAGYGIKSFLIAQSLNQIEKAYGQNNSILDNCHVRV 460


  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
   0.332    0.147    0.465 

Gapped
Lambda     K      H
   0.267   0.0714    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,609,408
Number of extensions: 261424
Number of successful extensions: 301
Number of sequences better than 10.0: 1
Number of HSP's gapped: 301
Number of HSP's successfully gapped: 8
Length of query: 70
Length of database: 10,937,602
Length adjustment: 40
Effective length of query: 30
Effective length of database: 9,163,442
Effective search space: 274903260
Effective search space used: 274903260
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 53 (24.2 bits)