RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy10544
         (181 letters)



>gnl|CDD|216043 pfam00651, BTB, BTB/POZ domain.  The BTB (for BR-C, ttk and bab) or
           POZ (for Pox virus and Zinc finger) domain is present
           near the N-terminus of a fraction of zinc finger
           (pfam00096) proteins and in proteins that contain the
           pfam01344 motif such as Kelch and a family of pox virus
           proteins. The BTB/POZ domain mediates homomeric
           dimerisation and in some instances heteromeric
           dimerisation. The structure of the dimerised PLZF
           BTB/POZ domain has been solved and consists of a tightly
           intertwined homodimer. The central scaffolding of the
           protein is made up of a cluster of alpha-helices flanked
           by short beta-sheets at both the top and bottom of the
           molecule. POZ domains from several zinc finger proteins
           have been shown to mediate transcriptional repression
           and to interact with components of histone deacetylase
           co-repressor complexes including N-CoR and SMRT. The POZ
           or BTB domain is also known as BR-C/Ttk or ZiN.
          Length = 101

 Score =  106 bits (266), Expect = 2e-30
 Identities = 35/94 (37%), Positives = 58/94 (61%), Gaps = 2/94 (2%)

Query: 21  FDQLLHDESFVDVTLAVDGRYLKAHKIVLSACSPYFQALFVGHPDRHPIVILKDIPYVDM 80
            ++L  +    DVTL V  +   AHK VL+ACSPYF+ALF G+ +    + L+D+   D 
Sbjct: 1   LNELRENGELCDVTLVVGDKEFHAHKAVLAACSPYFKALFTGNKEVE--ITLEDVSPEDF 58

Query: 81  RSLLDFMYRGEVSVDQDRLTTFLKVAESLRIKAL 114
            +LL+F+Y G++ + ++ +   L +A+ L+I AL
Sbjct: 59  EALLEFIYTGKLEITEENVDDLLALADKLQIPAL 92


>gnl|CDD|197585 smart00225, BTB, Broad-Complex, Tramtrack and Bric a brac.  Domain
           in Broad-Complex, Tramtrack and Bric a brac. Also known
           as POZ (poxvirus and zinc finger) domain. Known to be a
           protein-protein interaction motif found at the N-termini
           of several C2H2-type transcription factors as well as
           Shaw-type potassium channels. Known structure reveals a
           tightly intertwined dimer formed via interactions
           between N-terminal strand and helix structures. However
           in a subset of BTB/POZ domains, these two secondary
           structures appear to be missing. Be aware SMART predicts
           BTB/POZ domains without the beta1- and alpha1-secondary
           structures.
          Length = 97

 Score = 89.3 bits (222), Expect = 1e-23
 Identities = 33/85 (38%), Positives = 51/85 (60%), Gaps = 2/85 (2%)

Query: 32  DVTLAVDGRYLKAHKIVLSACSPYFQALFVGHP--DRHPIVILKDIPYVDMRSLLDFMYR 89
           DVTL V G+   AHK VL+A SPYF+ALF           + L D+   D R+LL+F+Y 
Sbjct: 1   DVTLVVGGKKFHAHKAVLAAHSPYFKALFSSDFKESDKSEIYLDDVSPEDFRALLNFLYT 60

Query: 90  GEVSVDQDRLTTFLKVAESLRIKAL 114
           G++ + ++ +   L++A+ L+I  L
Sbjct: 61  GKLDLPEENVEELLELADYLQIPGL 85


>gnl|CDD|222983 PHA03098, PHA03098, kelch-like protein; Provisional.
          Length = 534

 Score = 45.1 bits (107), Expect = 7e-06
 Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 2/84 (2%)

Query: 31  VDVTLAVDGRYLKAHKIVLSACSPYFQALFVGHPDRHPIVILKDIPYVDMRSLLDFMYRG 90
             + +   G  +K HKI+LS+ S YF+ +F  +   + I +  D    +   ++ ++Y G
Sbjct: 12  ESIIIVNGGGIIKVHKIILSSSSEYFKKMFKNNFKENEINLNIDYDSFN--EVIKYIYTG 69

Query: 91  EVSVDQDRLTTFLKVAESLRIKAL 114
           ++++  + +   L +A  L I  L
Sbjct: 70  KINITSNNVKDILSIANYLIIDFL 93


>gnl|CDD|165086 PHA02713, PHA02713, hypothetical protein; Provisional.
          Length = 557

 Score = 40.4 bits (94), Expect = 3e-04
 Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 13 HQSNLLSVFDQLLHDESFVDVTLAV-DGRYLKAHKIVLSACSPYFQALF 60
          H   ++S    LL D+   DV + + DG  +KAHK +L+A S YF+ LF
Sbjct: 8  HNRRVVSNISNLLDDDILCDVIITIGDGEEIKAHKTILAAGSKYFRTLF 56


>gnl|CDD|217554 pfam03432, Relaxase, Relaxase/Mobilisation nuclease domain.
           Relaxases/mobilisation proteins are required for the
           horizontal transfer of genetic information contained on
           plasmids that occurs during bacterial conjugation. The
           relaxase, in conjunction with several auxiliary
           proteins, forms the relaxation complex or relaxosome.
           Relaxases nick duplex DNA in a specific manner by
           catalyzing trans-esterification.
          Length = 240

 Score = 28.5 bits (64), Expect = 1.5
 Identities = 13/44 (29%), Positives = 16/44 (36%), Gaps = 3/44 (6%)

Query: 138 ESLRIKELVSNVKAERDTEGNSGGDQTERTSPTPERFPPGLLKP 181
               +    S  KA R+  G   GDQ      +   F PG L P
Sbjct: 30  NGCDVDYAKSEFKATRELYGKVDGDQVHHIIQS---FSPGELTP 70


>gnl|CDD|218324 pfam04912, Dynamitin, Dynamitin.  Dynamitin is a subunit of the
           microtubule-dependent motor complex and in implicated in
           cell adhesion by binding to macrophage-enriched
           myristoylated alanine-rice C kinase substrate
           (MacMARCKS).
          Length = 376

 Score = 27.4 bits (61), Expect = 4.3
 Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 11/87 (12%)

Query: 79  DMRSLLDFMYRGEVSV--DQDRLTTFLKVAESL-------RIKALSALLYRGEVSVDQDR 129
            +  L   +++ E ++  D D+L+      ESL       RI A +ALL    +   + R
Sbjct: 198 KLAELEKRLHKLEAAIGNDPDKLSRLTADTESLPLLEAVSRISAKAALLDPDHLDHIEQR 257

Query: 130 LTTFLKVAESLRIKELVSNVKAERDTE 156
           L + L   ES  I E  +   A+ +TE
Sbjct: 258 LQSVLGKMES--IDEKKAASLADANTE 282


>gnl|CDD|175975 cd00276, C2B_Synaptotagmin, C2 domain second repeat present in
          Synaptotagmin.  Synaptotagmin is a membrane-trafficking
          protein characterized by a N-terminal transmembrane
          region, a linker, and 2 C-terminal C2 domains. There
          are several classes of Synaptotagmins. Previously all
          synaptotagmins were thought to be calcium sensors in
          the regulation of neurotransmitter release and hormone
          secretion, but it has been shown that not all of them
          bind calcium.  Of the 17 identified synaptotagmins only
          8 bind calcium (1-3, 5-7, 9, 10).  The function of the
          two C2 domains that bind calcium are: regulating the
          fusion step of synaptic vesicle exocytosis (C2A) and
          binding to phosphatidyl-inositol-3,4,5-triphosphate
          (PIP3) in the absence of calcium ions and to
          phosphatidylinositol bisphosphate (PIP2) in their
          presence (C2B).  C2B also regulates also the recycling
          step of synaptic vesicles. C2 domains fold into an
          8-standed beta-sandwich that can adopt 2 structural
          arrangements: Type I and Type II, distinguished by a
          circular permutation involving their N- and C-terminal
          beta strands. Many C2 domains are Ca2+-dependent
          membrane-targeting modules that bind a wide variety of
          substances including bind phospholipids, inositol
          polyphosphates, and intracellular proteins.  Most C2
          domain proteins are either signal transduction enzymes
          that contain a single C2 domain, such as protein kinase
          C, or membrane trafficking proteins which contain at
          least two C2 domains, such as synaptotagmin 1.
          However, there are a few exceptions to this including
          RIM isoforms and some splice variants of
          piccolo/aczonin and intersectin which only have a
          single C2 domain.  C2 domains with a calcium binding
          region have negatively charged residues, primarily
          aspartates, that serve as ligands for calcium ions.
          This cd contains the second C2 repeat, C2B, and has a
          type-I topology.
          Length = 134

 Score = 26.4 bits (59), Expect = 5.8
 Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 3/48 (6%)

Query: 16 NLLSVFDQLLHDESFVDVTLAVDGRYLKAHK--IVLSACSPYFQALFV 61
          NL     + L D  +V V+L   G+ LK  K  +     +P F   F 
Sbjct: 25 NLPPSDGKGLSD-PYVKVSLLQGGKKLKKKKTSVKKGTLNPVFNEAFS 71


>gnl|CDD|218253 pfam04765, DUF616, Protein of unknown function (DUF616).  Family of
           uncharacterized proteins.
          Length = 306

 Score = 26.9 bits (60), Expect = 6.2
 Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 14/53 (26%)

Query: 30  FVD-VTLAVDGRYLKAHKIVLSACSPYFQALFVGHPDRHPIVILKDIPYVDMR 81
           FVD  TL      LK+   V            VG      IV++K++PY D R
Sbjct: 98  FVDEETL----STLKSEGHVPD------DNGRVG---LWRIVVVKNLPYTDPR 137


  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    0.137    0.397 

Gapped
Lambda     K      H
   0.267   0.0732    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,152,955
Number of extensions: 844916
Number of successful extensions: 680
Number of sequences better than 10.0: 1
Number of HSP's gapped: 678
Number of HSP's successfully gapped: 20
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 (25.3 bits)