RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy405
         (66 letters)



>gnl|CDD|216473 pfam01388, ARID, ARID/BRIGHT DNA binding domain.  This domain is
          know as ARID for AT-Rich Interaction Domain, and also
          known as the BRIGHT domain.
          Length = 90

 Score = 63.4 bits (155), Expect = 2e-15
 Identities = 27/49 (55%), Positives = 31/49 (63%)

Query: 14 KEKESFLRDLQHFHETRGTPCRHVPKIGGKEIDLYLLYCLVTSNGGWVK 62
           EKE+FL  L  F E RGTP   +P IGGK +DLY LY LV   GG+ K
Sbjct: 3  PEKENFLDRLAKFMERRGTPLDKIPVIGGKPLDLYKLYRLVQKLGGFEK 51


>gnl|CDD|198082 smart01014, ARID, ARID/BRIGHT DNA binding domain.  Members of the
          recently discovered ARID (AT-rich interaction domain)
          family of DNA-binding proteins are found in fungi and
          invertebrate and vertebrate metazoans. ARID-encoding
          genes are involved in a variety of biological processes
          including embryonic development, cell lineage gene
          regulation and cell cycle control. Although the
          specific roles of this domain and of ARID-containing
          proteins in transcriptional regulation are yet to be
          elucidated, they include both positive and negative
          transcriptional regulation and a likely involvement in
          the modification of chromatin structure. The basic
          structure of the ARID domain domain appears to be a
          series of six alpha-helices separated by beta-strands,
          loops, or turns, but the structured region may extend
          to an additional helix at either or both ends of the
          basic six. Based on primary sequence homology, they can
          be partitioned into three structural classes: Minimal
          ARID proteins that consist of a core domain formed by
          six alpha helices; ARID proteins that supplement the
          core domain with an N-terminal alpha-helix; and
          Extended-ARID proteins, which contain the core domain
          and additional alpha-helices at their N- and C-termini.
          Length = 88

 Score = 63.0 bits (154), Expect = 3e-15
 Identities = 25/49 (51%), Positives = 31/49 (63%)

Query: 14 KEKESFLRDLQHFHETRGTPCRHVPKIGGKEIDLYLLYCLVTSNGGWVK 62
          +E+E FL  L+ F E RGTP   +P IGGK +DLY LY  V   GG+ K
Sbjct: 1  RERELFLDRLRKFMEKRGTPLDKIPVIGGKPLDLYRLYRAVQKRGGFDK 49


>gnl|CDD|128777 smart00501, BRIGHT, BRIGHT, ARID (A/T-rich interaction domain)
          domain.  DNA-binding domain containing a
          helix-turn-helix structure.
          Length = 93

 Score = 56.5 bits (137), Expect = 1e-12
 Identities = 23/51 (45%), Positives = 31/51 (60%)

Query: 14 KEKESFLRDLQHFHETRGTPCRHVPKIGGKEIDLYLLYCLVTSNGGWVKKC 64
          +E+  FL  L  F E RG+P + +P IGGK +DLY LY LV   GG+ +  
Sbjct: 1  RERVLFLDRLYKFMEERGSPLKKIPVIGGKPLDLYRLYRLVQERGGYDQVT 51


>gnl|CDD|212470 cd01723, LSm4, Like-Sm protein 4.  The eukaryotic LSm proteins
          (LSm2-8 or LSm1-7) assemble into a hetero-heptameric
          ring around the 3'-terminus uridylation tag of the
          gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
          LSm2-8 form the core of the snRNP particle that, in
          turn, assembles with other components onto the pre-mRNA
          to form the spliceosome which is responsible for the
          excision of introns and the ligation of exons. LSm1-7
          is involved in recognition of the 3' uridylation tag
          and recruitment of the decapping machinery. Members of
          this family share a highly conserved Sm fold containing
          an N-terminal helix followed by a strongly bent
          five-stranded antiparallel beta-sheet.
          Length = 76

 Score = 26.4 bits (59), Expect = 0.46
 Identities = 8/20 (40%), Positives = 12/20 (60%)

Query: 2  AKVTKKDGDAYFKEKESFLR 21
             T KDGD ++K  E ++R
Sbjct: 42 VICTSKDGDRFWKMPECYIR 61


>gnl|CDD|233690 TIGR02025, BchH, magnesium chelatase, H subunit.  This model
            represents the H subunit of the magnesium chelatase
            complex responsible for magnesium insertion into the
            protoporphyrin IX ring in the biosynthesis of both
            chlorophyll and bacteriochlorophyll. In
            chlorophyll-utilizing species, this gene is known as
            ChlH, while in bacteriochlorophyll-utilizing spoecies it
            is called BchH. Subunit H is the largest (~140kDa) of the
            three subunits (the others being BchD/ChlD and
            BchI/ChlI), and is known to bind protoporphyrin IX.
            Subunit H is homologous to the CobN subunit of
            cobaltochelatase and by anology with that enzyme, subunit
            H is believed to also bind the magnesium ion which is
            inserted into the ring. In conjunction with the
            hydrolysis of ATP by subunits I and D, a conformation
            change is believed to happen in subunit H causing the
            magnesium ion insertion into the distorted protoporphyrin
            ring [Biosynthesis of cofactors, prosthetic groups, and
            carriers, Chlorophyll and bacteriochlorphyll].
          Length = 1224

 Score = 26.3 bits (58), Expect = 1.3
 Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 3/42 (7%)

Query: 7    KDGDAYFKEKESF---LRDLQHFHETRGTPCRHVPKIGGKEI 45
            K  D  F+  +S    L D+ H+ ++ G   + V +  GK  
Sbjct: 1045 KTVDRTFQNIDSVEIGLTDIDHYFDSLGGLSKAVERQSGKTA 1086


>gnl|CDD|218675 pfam05648, PEX11, Peroxisomal biogenesis factor 11 (PEX11).  This
          family consists of several peroxisomal biogenesis
          factor 11 (PEX11) proteins from several eukaryotic
          species. The PEX11 peroxisomal membrane proteins
          promote peroxisome division in multiple eukaryotes.
          Length = 225

 Score = 24.9 bits (55), Expect = 2.8
 Identities = 8/41 (19%), Positives = 10/41 (24%), Gaps = 7/41 (17%)

Query: 19 FLRDLQHFHETRGTPCRHVPKIGGKEIDLYLLYCLVTSNGG 59
            + L+H                 K  D  L    V  N G
Sbjct: 61 LGKFLEHLQAAAKYY-------DNKLPDPVLRLLAVLRNLG 94


>gnl|CDD|224816 COG1904, UxaC, Glucuronate isomerase [Carbohydrate transport and
           metabolism].
          Length = 463

 Score = 24.6 bits (54), Expect = 3.9
 Identities = 4/21 (19%), Positives = 7/21 (33%)

Query: 16  KESFLRDLQHFHETRGTPCRH 36
           +E +    +      G P  H
Sbjct: 80  REKWRAFAKTVPLFIGNPLYH 100


>gnl|CDD|173484 PTZ00220, PTZ00220, Activator of HSP-90 ATPase; Provisional.
          Length = 132

 Score = 24.4 bits (53), Expect = 5.0
 Identities = 8/27 (29%), Positives = 12/27 (44%)

Query: 17 ESFLRDLQHFHETRGTPCRHVPKIGGK 43
           +FL        + G+P     K+GGK
Sbjct: 10 NAFLDAYTLTRLSLGSPAEMDAKVGGK 36


  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
   0.321    0.139    0.447 

Gapped
Lambda     K      H
   0.267   0.0771    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,253,371
Number of extensions: 227970
Number of successful extensions: 171
Number of sequences better than 10.0: 1
Number of HSP's gapped: 171
Number of HSP's successfully gapped: 8
Length of query: 66
Length of database: 10,937,602
Length adjustment: 37
Effective length of query: 29
Effective length of database: 9,296,504
Effective search space: 269598616
Effective search space used: 269598616
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: 53 (24.1 bits)