RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy939
         (67 letters)



>gnl|CDD|235000 PRK02106, PRK02106, choline dehydrogenase; Validated.
          Length = 560

 Score = 69.1 bits (170), Expect = 8e-16
 Identities = 24/51 (47%), Positives = 36/51 (70%), Gaps = 1/51 (1%)

Query: 7   GKVMGGTTVLNGLMYCRGDSSDYDEYEKL-GATGWGYKNVLPYFLKSEHNL 56
           GKV+GG++ +NG++Y RG++ DYD + +L G  GW Y + LPYF K+E   
Sbjct: 85  GKVLGGSSSINGMVYIRGNAMDYDNWAELPGLEGWSYADCLPYFKKAETRD 135


>gnl|CDD|225186 COG2303, BetA, Choline dehydrogenase and related flavoproteins
           [Amino acid transport and metabolism].
          Length = 542

 Score = 67.5 bits (165), Expect = 3e-15
 Identities = 24/51 (47%), Positives = 37/51 (72%), Gaps = 1/51 (1%)

Query: 7   GKVMGGTTVLNGLMYCRGDSSDYDEY-EKLGATGWGYKNVLPYFLKSEHNL 56
           GKV+GG++ +NG++Y RG   D+D + ++ GA GW Y +VLPYF ++E  L
Sbjct: 84  GKVLGGSSSINGMVYVRGHPEDFDAWAQESGAPGWPYDDVLPYFKRAEDLL 134


>gnl|CDD|233581 TIGR01810, betA, choline dehydrogenase.  Choline dehydrogenase
           catalyzes the conversion of exogenously supplied choline
           into the intermediate glycine betaine aldehyde, as part
           of a two-step oxidative reaction leading to the
           formation of osmoprotectant betaine. This enzymatic
           system can be found in both gram-positive and
           gram-negative bacteria. As in Escherichia coli ,
           Staphylococcus xylosus , and Sinorhizobium meliloti,
           this enzyme is found associated in a transciptionally
           co-induced gene cluster with betaine aldehyde
           dehydrogenase, the second catalytic enzyme in this
           reaction. Other gram-positive organisms have been shown
           to employ a different enzymatic system, utlizing a
           soluable choline oxidase or type III alcohol
           dehydrogenase instead of choline dehydrogenase. This
           enzyme is a member of the GMC oxidoreductase family
           (pfam00732 and pfam05199), sharing a common
           evoluntionary origin and enzymatic reaction with alcohol
           dehydrogenase. Outgrouping from this model, Caulobacter
           crescentus shares sequence homology with choline
           dehydrogenase, yet other genes participating in this
           enzymatic reaction have not currently been identified
           [Cellular processes, Adaptations to atypical
           conditions].
          Length = 532

 Score = 61.0 bits (148), Expect = 5e-13
 Identities = 20/49 (40%), Positives = 33/49 (67%), Gaps = 1/49 (2%)

Query: 7   GKVMGGTTVLNGLMYCRGDSSDYDEYEK-LGATGWGYKNVLPYFLKSEH 54
           GKV+GG++ +NG++Y RG+  DY+++ K  G   W Y + LPY+ + E 
Sbjct: 79  GKVLGGSSSINGMIYQRGNPMDYEKWAKPEGMESWDYADCLPYYKRLET 127


>gnl|CDD|216089 pfam00732, GMC_oxred_N, GMC oxidoreductase.  This family of
          proteins bind FAD as a cofactor.
          Length = 218

 Score = 56.1 bits (136), Expect = 1e-11
 Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 1/48 (2%)

Query: 7  GKVMGGTTVLNGLMYCRGDSSDYDE-YEKLGATGWGYKNVLPYFLKSE 53
          G  +GG + +N     R  ++  DE   + G  GWGY + LPY  K E
Sbjct: 24 GSTVGGGSSVNWSACIRTPAAVLDEWASEFGLEGWGYDDYLPYMDKVE 71


>gnl|CDD|234421 TIGR03970, Rv0697, dehydrogenase, Rv0697 family.  This model
           describes a set of dehydrogenases belonging to the
           glucose-methanol-choline oxidoreductase (GMC
           oxidoreductase) family. Members of the present family
           are restricted to Actinobacterial genome contexts
           containing also members of families TIGR03962 and
           TIGR03969 (the mycofactocin system), and are proposed to
           be uniform in function.
          Length = 487

 Score = 52.1 bits (125), Expect = 7e-10
 Identities = 19/55 (34%), Positives = 32/55 (58%), Gaps = 3/55 (5%)

Query: 4   IFDGKVMGGTTVLNGLMYCRGDSSDYDEYEKLGATGWGYKNVLPYFLKSEHNLQY 58
           I  G+V+GG+  +NG  +CR   +D+D +      GW + +VLP+F   E +L +
Sbjct: 78  IVRGRVLGGSGAVNGGYFCRALPADFDAW---PIPGWSWDDVLPHFRAIETDLDF 129


>gnl|CDD|137204 PRK09310, aroDE, bifunctional 3-dehydroquinate
           dehydratase/shikimate dehydrogenase protein; Reviewed.
          Length = 477

 Score = 28.2 bits (63), Expect = 0.24
 Identities = 15/30 (50%), Positives = 16/30 (53%)

Query: 37  ATGWGYKNVLPYFLKSEHNLQYNYQSYSAQ 66
           A G G   V P  L  EH L YNY + SAQ
Sbjct: 185 AAGIGAPPVAPGQLSLEHLLFYNYANLSAQ 214


>gnl|CDD|147262 pfam04993, TfoX_N, TfoX N-terminal domain.  TfoX may play a key
          role in the development of genetic competence by
          regulating the expression of late competence-specific
          genes. This family corresponds to the N-terminal
          presumed domain of TfoX. The domain is found as an
          isolated domain in some proteins suggesting this is an
          autonomous domain.
          Length = 94

 Score = 26.4 bits (59), Expect = 0.77
 Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 7/57 (12%)

Query: 6  DGKVMGGTTVLNGLMYCRGDSSDYDEYEKLGATGWGYK-----NVLPYFLKSEHNLQ 57
          DG +     V +G +Y + D      +E  G   + Y        L Y+L  E  L+
Sbjct: 23 DGVMFAL--VSDGELYLKADDETRAYFEAAGCEPYVYVKRGRPVTLNYYLVPEELLE 77


>gnl|CDD|233850 TIGR02402, trehalose_TreZ, malto-oligosyltrehalose
           trehalohydrolase.  Members of this family are the
           trehalose biosynthetic enzyme malto-oligosyltrehalose
           trehalohydrolase, formally known as
           4-alpha-D-{(1->4)-alpha-D-glucano}trehalose
           trehalohydrolase (EC 3.2.1.141). It is the TreZ protein
           of the TreYZ pathway for trehalose biosynthesis, and
           alternative to the OtsAB system [Energy metabolism,
           Biosynthesis and degradation of polysaccharides].
          Length = 544

 Score = 26.1 bits (58), Expect = 1.1
 Identities = 9/13 (69%), Positives = 9/13 (69%)

Query: 36  GATGWGYKNVLPY 48
           G  GWGY  VLPY
Sbjct: 138 GTRGWGYDGVLPY 150


>gnl|CDD|222548 pfam14109, GldH_lipo, GldH lipoprotein.  Members of this protein
          family are predicted lipoproteins, exclusive to the
          Bacteroidetes phylum. Proteins in this family are
          typically between 155 and 167 amino acids in length.
          Members include GldH, a protein linked to a type of
          rapid surface gliding motility found in certain
          Bacteroidetes, such as Flavobacterium johnsoniae and
          Cytophaga hutchinsonii. Gliding motility appears
          closely linked to chitin utilization in the model
          species Flavobacterium johnsoniae. Not all
          Bacteroidetes with members of this protein family may
          have gliding motility.
          Length = 131

 Score = 24.1 bits (53), Expect = 5.3
 Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 13/51 (25%)

Query: 25 DSSDYDEYEKLGATGWGYKNVL-----------PY--FLKSEHNLQYNYQS 62
          +++ YDEY+ +  +GW   + L           PY  FL   +N  Y Y +
Sbjct: 1  ENTVYDEYQSVPDSGWEKNDTLSFEFPITDTSGPYNLFLNLRNNNDYPYSN 51


  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
   0.316    0.136    0.418 

Gapped
Lambda     K      H
   0.267   0.0784    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,299,620
Number of extensions: 230001
Number of successful extensions: 174
Number of sequences better than 10.0: 1
Number of HSP's gapped: 169
Number of HSP's successfully gapped: 10
Length of query: 67
Length of database: 10,937,602
Length adjustment: 38
Effective length of query: 29
Effective length of database: 9,252,150
Effective search space: 268312350
Effective search space used: 268312350
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.1 bits)