RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12033
         (79 letters)



>gnl|CDD|217613 pfam03556, Cullin_binding, Cullin binding.  This domain binds to
          cullins and to Rbx-1, components of an E3 ubiquitin
          ligase complex for neddylation. Neddylation is the
          process by which the C-terminal glycine of the
          ubiquitin-like protein Nedd8 is covalently linked to
          lysine residues in a protein through an isopeptide
          bond. The structure of this domain is composed entirely
          of alpha helices.
          Length = 117

 Score = 70.7 bits (174), Expect = 1e-17
 Identities = 28/74 (37%), Positives = 39/74 (52%), Gaps = 8/74 (10%)

Query: 6  KFTFRFGLDSSCGQRILPIDMAIILWKLVFSIRVSCDESFILTAWLNFLSQHTHVVRGIP 65
          +FTF F  +   GQ+ L ++ AI  WKL+F  R       +L  W+ FL +     + I 
Sbjct: 27 RFTFDFAREE--GQKSLDLETAIEYWKLLFGSRTFP----LLDQWIEFLEEKHK--KSIS 78

Query: 66 RDTWNMFLTFYDTI 79
          +DTWNM L F  TI
Sbjct: 79 KDTWNMLLEFSKTI 92


>gnl|CDD|217495 pfam03326, Herpes_TAF50, Herpesvirus transcription activation
          factor (transactivator).  This family includes EBV
          BRLF1 and similar ORF 50 proteins from other
          herpesviruses.
          Length = 500

 Score = 26.7 bits (59), Expect = 1.2
 Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 5/46 (10%)

Query: 8  TFRFGLDSSCGQRILPIDMAIILWKLVFSIRVSCDESFILTAWLNF 53
          T RF L + C   +LP  +A  L+KL+   R  C     L AW   
Sbjct: 38 TDRFFLTAPCSGVVLPQPLAKALFKLLKECRKKC-----LGAWRRL 78


>gnl|CDD|239493 cd03399, Band_7_flotillin, Band_7_flotillin: a subgroup of the
          band 7 domain of flotillin (reggie) like proteins. This
          subgroup contains proteins similar to stomatin,
          prohibitin, flotillin, HlfK/C and podicin.  These two
          proteins are lipid raft-associated.  Individual
          proteins of this band 7 domain family may cluster to
          form membrane microdomains which may in turn recruit
          multiprotein complexes. Microdomains formed from
          flotillin proteins may in addition be dynamic units
          with their own regulatory functions.  Flotillins have
          been implicated in signal transduction, vesicle
          trafficking, cytoskeleton rearrangement and, interact
          with a variety of proteins.  Flotillins may play a role
          in the progression of prion disease, in the
          pathogenesis of neurodegenerative diseases such as
          Parkinson's and Alzheimer's disease and, in cancer
          invasion and metastasis.
          Length = 128

 Score = 25.6 bits (57), Expect = 2.4
 Identities = 9/35 (25%), Positives = 16/35 (45%)

Query: 34 VFSIRVSCDESFILTAWLNFLSQHTHVVRGIPRDT 68
          VF ++V   E  I TA   FL +    +  + ++ 
Sbjct: 29 VFQVKVGGTEEAIATAAERFLGKSEEEIEELVKEV 63


>gnl|CDD|215469 PLN02871, PLN02871, UDP-sulfoquinovose:DAG
           sulfoquinovosyltransferase.
          Length = 465

 Score = 25.1 bits (55), Expect = 4.2
 Identities = 9/17 (52%), Positives = 12/17 (70%)

Query: 54  LSQHTHVVRGIPRDTWN 70
           +S HTHV   IPR T++
Sbjct: 173 MSYHTHVPVYIPRYTFS 189


>gnl|CDD|227610 COG5290, COG5290, IkappaB kinase complex, IKAP component
           [Transcription].
          Length = 1243

 Score = 25.0 bits (54), Expect = 4.7
 Identities = 13/29 (44%), Positives = 14/29 (48%), Gaps = 1/29 (3%)

Query: 35  FSIRVSCDESFILTAWLNFLSQHTHVVRG 63
           F +RV CDE   L  W N LS    V  G
Sbjct: 288 FDLRVGCDEKAFLENW-NLLSTVLAVAEG 315


>gnl|CDD|234875 PRK00957, PRK00957, methionine synthase; Provisional.
          Length = 305

 Score = 25.0 bits (55), Expect = 4.8
 Identities = 10/21 (47%), Positives = 13/21 (61%), Gaps = 2/21 (9%)

Query: 13  LDSSCGQRILPIDMAIILWKL 33
           +D  CG R+LP D+A    KL
Sbjct: 276 IDPDCGMRMLPRDVA--FEKL 294


  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
   0.335    0.145    0.493 

Gapped
Lambda     K      H
   0.267   0.0652    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,150,438
Number of extensions: 317631
Number of successful extensions: 390
Number of sequences better than 10.0: 1
Number of HSP's gapped: 387
Number of HSP's successfully gapped: 13
Length of query: 79
Length of database: 10,937,602
Length adjustment: 48
Effective length of query: 31
Effective length of database: 8,808,610
Effective search space: 273066910
Effective search space used: 273066910
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.6 bits)
S2: 53 (24.4 bits)