RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= 047640
         (111 letters)



>gnl|CDD|173833 cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphate Synthases,
           head-to-tail.  These trans-Isoprenyl Diphosphate
           Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4)
           condensation reactions. This CD includes all-trans
           (E)-isoprenyl diphosphate synthases which synthesize
           various chain length (C10, C15, C20, C25, C30, C35, C40,
           C45, and C50) linear isoprenyl diphosphates from
           precursors,  isopentenyl diphosphate (IPP) and
           dimethylallyl diphosphate (DMAPP). They catalyze the
           successive 1'-4 condensation of the 5-carbon IPP to
           allylic substrates geranyl-, farnesyl-, or
           geranylgeranyl-diphosphate. Isoprenoid chain elongation
           reactions proceed via electrophilic alkylations in which
           a new carbon-carbon single bond is generated through
           interaction between a highly reactive electron-deficient
           allylic carbocation and an electron-rich carbon-carbon
           double bond. The catalytic site consists of a large
           central cavity formed by mostly antiparallel alpha
           helices with two aspartate-rich regions (DDXX(XX)D)
           located on opposite walls. These residues mediate
           binding of prenyl phosphates via bridging Mg2+ ions,
           inducing proposed conformational changes that close the
           active site to solvent, protecting and stabilizing
           reactive carbocation intermediates. Farnesyl diphosphate
           synthases produce the precursors of steroids,
           cholesterol, sesquiterpenes, farnsylated proteins, heme,
           and vitamin K12; and geranylgeranyl diphosphate and
           longer chain synthases produce the precursors of
           carotenoids, retinoids, diterpenes, geranylgeranylated
           chlorophylls, ubiquinone, and archaeal ether linked
           lipids. Isoprenyl diphosphate synthases are widely
           distributed among archaea, bacteria, and eukareya.
          Length = 259

 Score = 40.6 bits (96), Expect = 3e-05
 Identities = 27/95 (28%), Positives = 35/95 (36%), Gaps = 12/95 (12%)

Query: 2   ADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTY 61
            D +L    ELLA   NP      R L +  E    +     VEGQ  +L      ++T 
Sbjct: 87  GDYLLARAFELLARLGNPYYP---RALELFSEAILEL-----VEGQLLDLLSEYDTDVTE 138

Query: 62  ETYKKNE----GGLHTCGAACGAILGGGSVEEIEK 92
           E Y +        L       GA+L G   EE E 
Sbjct: 139 EEYLRIIRLKTAALFAAAPLLGALLAGADEEEAEA 173


>gnl|CDD|132850 cd07211, Pat_PNPLA8, Patatin-like phospholipase domain containing
           protein 8.  PNPLA8 is a Ca-independent myocardial
           phospholipase which maintains mitochondrial integrity.
           PNPLA8 is also known as iPLA2-gamma. In humans, it is
           predominantly expressed in heart tissue. iPLA2-gamma can
           catalyze both phospholipase A1 and A2 reactions (PLA1
           and PLA2 respectively). This family includes PNPLA8
           (iPLA2-gamma) from Homo sapiens and iPLA2-2 from Mus
           musculus.
          Length = 308

 Score = 26.8 bits (60), Expect = 2.5
 Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 6/34 (17%)

Query: 74  CGAACGAILG------GGSVEEIEKKFRGLIIKI 101
           CG + GAIL         S++E E+ +R L   +
Sbjct: 46  CGVSTGAILAFLLGLKKMSLDECEELYRKLGKDV 79


>gnl|CDD|222521 pfam14066, DUF4256, Protein of unknown function (DUF4256).  This
           family of proteins is functionally uncharacterized. This
           family of proteins is found in bacteria. Proteins in
           this family are approximately 190 amino acids in length.
          Length = 173

 Score = 26.0 bits (58), Expect = 4.2
 Identities = 10/21 (47%), Positives = 13/21 (61%)

Query: 32  VEMTRAMGSQGVVEGQYNELQ 52
           V+M   MG + + E QY ELQ
Sbjct: 96  VDMAAEMGIELLTEEQYRELQ 116


>gnl|CDD|240318 PTZ00224, PTZ00224, protein phosphatase 2C; Provisional.
          Length = 381

 Score = 25.9 bits (57), Expect = 5.7
 Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 1/43 (2%)

Query: 31 MVEMTRAMGSQGVVEGQYNELQCSQYVEMTYETYKKNEGGLHT 73
          ++ +T   G  GV +G  N+ +CSQY+   +    + E    T
Sbjct: 41 LLYLTDDWGFFGVFDGHVND-ECSQYLARAWPQALEKEPEPMT 82


>gnl|CDD|213978 TIGR04365, spare_glycyl, autonomous glycyl radical cofactor GrcA.
           This small protein, previously designated YfiD in E.
          coli, is closely homologous to pyruvate formate_lyase
          (PFL) in a region surrounding the stable glycyl radical
          that is prepared by the action of pyruvate
          formate-lyase activase, a radical SAM enzyme. When
          damage at the site of this radical breaks the main
          chain of PFL, this protein acts as a spare part that
          reintroduces the needed stable glycyl radical. Cutoffs
          for this model are set to exclude a set of closely
          related phage proteins that appear to have a
          corresponding function.
          Length = 124

 Score = 25.5 bits (56), Expect = 5.7
 Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 4/61 (6%)

Query: 16 SDNPAGNNSGRILRVMVEMTRAMGSQ-GVVEGQ---YNELQCSQYVEMTYETYKKNEGGL 71
          + N A  NS  +L       R + ++ G    Q    +EL   +Y E+  E   K EGG 
Sbjct: 9  AANQALLNSFWLLDEETNQARCLVAKAGFAADQVVPLSELGDFEYREIAIEAPAKVEGGQ 68

Query: 72 H 72
          H
Sbjct: 69 H 69


>gnl|CDD|227263 COG4926, PblB, Phage-related protein [Function unknown].
          Length = 698

 Score = 25.6 bits (56), Expect = 7.8
 Identities = 13/61 (21%), Positives = 20/61 (32%), Gaps = 2/61 (3%)

Query: 35  TRAMGSQGVVEGQYNELQCSQYVEMTYETYKKNEGGL--HTCGAACGAILGGGSVEEIEK 92
                S G  +G+Y   + S   + + E Y KN   +     G     +     V  I  
Sbjct: 570 RYTGVSGGGPQGRYVPHRASNREKASSEEYAKNIRKVKKTAFGKTAKNVQTETDVYHIAD 629

Query: 93  K 93
           K
Sbjct: 630 K 630


>gnl|CDD|223717 COG0644, FixC, Dehydrogenases (flavoproteins) [Energy production
           and conversion].
          Length = 396

 Score = 25.1 bits (55), Expect = 8.7
 Identities = 11/45 (24%), Positives = 16/45 (35%), Gaps = 3/45 (6%)

Query: 65  KKNEGGLHTCGAACGAILGGGSVEEIEKKFRGLIIKITKMMIRNS 109
           K +E G   C   CG  L   ++EE+   F   I +         
Sbjct: 34  KGSEPGAKPC---CGGGLSPRALEELIPDFDEEIERKVTGARIYF 75


  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
   0.318    0.135    0.390 

Gapped
Lambda     K      H
   0.267   0.0790    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,509,043
Number of extensions: 453521
Number of successful extensions: 424
Number of sequences better than 10.0: 1
Number of HSP's gapped: 423
Number of HSP's successfully gapped: 10
Length of query: 111
Length of database: 10,937,602
Length adjustment: 75
Effective length of query: 36
Effective length of database: 7,611,052
Effective search space: 273997872
Effective search space used: 273997872
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 (21.7 bits)
S2: 53 (24.1 bits)