RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2693
         (122 letters)



>gnl|CDD|219240 pfam06957, COPI_C, Coatomer (COPI) alpha subunit C-terminus.  This
           family represents the C-terminus (approximately 500
           residues) of the eukaryotic coatomer alpha subunit.
           Coatomer (COPI) is a large cytosolic protein complex
           which forms a coat around vesicles budding from the
           Golgi apparatus. Such coatomer-coated vesicles have been
           proposed to play a role in many distinct steps of
           intracellular transport. Note that many family members
           also contain the pfam04053 domain.
          Length = 421

 Score =  116 bits (291), Expect = 5e-32
 Identities = 44/84 (52%), Positives = 56/84 (66%), Gaps = 2/84 (2%)

Query: 12  VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
           VA QARK+L  C  NPTD H ++YDEHNPF +C  SY PIY G+    C YCGAS+ P +
Sbjct: 334 VAQQARKVLQACEKNPTDAHQLNYDEHNPFVVCGASYVPIYRGKPDVKCPYCGASFSPGF 393

Query: 72  KGELCAVCTVSVIDTHRNAYGLQI 95
           +G LC VC V+ I   ++  GL+I
Sbjct: 394 EGNLCTVCEVAEIG--KDVIGLRI 415


>gnl|CDD|149388 pfam08313, SCA7, SCA7, zinc-binding domain.  This domain is found
          in the protein Sgf73/Sca7 which is a component of the
          multihistone acetyltransferase complexes SAGA and SILK.
          This domain is also found in Ataxin-7, a human protein
          which in its polyglutamine expanded pathological form,
          is responsible for the neurodegenerative disease
          spinocerebellar ataxia 7 (SCA7). Ataxin-7 is an
          integral component of the mammalian SAGA-like
          complexes, the TATA-binding protein-free TAF-containing
          complex (TFTC) and the SPT3/TAF9/GCN5 acetyltransferase
          complex (STAGA). This domain is a minimal domain in
          ataxin-7-like proteins that is required for interaction
          with TFTC/STAGA subunits and is conserved highly
          through evolution. The domain contains a conserved
          Cys(3)His motif that binds zinc, thus indicating this
          to be a new zinc-binding domain.
          Length = 73

 Score = 25.8 bits (57), Expect = 2.7
 Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 5/29 (17%)

Query: 26 NPTDEHTIDYDEH----NP-FQICARSYT 49
          NP  +  +D D+      P  + CARS T
Sbjct: 11 NPKAKKPVDVDKQCGVILPEGKPCARSLT 39


>gnl|CDD|218988 pfam06321, P_gingi_FimA, Major fimbrial subunit protein (FimA).
           This family consists of several Porphyromonas gingivalis
           major fimbrial subunit protein (FimA) sequences.
           Fimbriae of Porphyromonas gingivalis, a
           periodontopathogen, play an important role in its
           adhesion to and invasion of host cells. The fimA genes
           encoding fimbrillin (FimA), a subunit protein of
           fimbriae, have been classified into five types, types I
           to V, based on nucleotide sequences. It has been found
           that type II FimA can bind to epithelial cells most
           efficiently through specific host receptors. Human
           dental plaque is a multispecies microbial biofilm that
           is associated with two common oral diseases, dental
           caries and periodontal disease. There is an
           inter-species contact-dependent communication system
           between P. gingivalis and S. cristatus that involces the
           Arc-A enzyme.
          Length = 265

 Score = 26.7 bits (59), Expect = 3.1
 Identities = 7/33 (21%), Positives = 11/33 (33%)

Query: 5   AKFQIIPVATQARKLLAICNANPTDEHTIDYDE 37
                IPV   A+ ++ I N    D       +
Sbjct: 75  TNVDFIPVTAGAKTIVVIANVGELDAGGKTLAD 107


>gnl|CDD|223242 COG0164, RnhB, Ribonuclease HII [DNA replication, recombination,
           and repair].
          Length = 199

 Score = 25.3 bits (56), Expect = 8.9
 Identities = 8/26 (30%), Positives = 11/26 (42%), Gaps = 1/26 (3%)

Query: 27  PTDEHTIDYDEHNPFQICAR-SYTPI 51
           PTD HT    +        R S+ P+
Sbjct: 159 PTDPHTEALLKKGGTPGIHRRSFAPV 184


  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
   0.322    0.134    0.422 

Gapped
Lambda     K      H
   0.267   0.0710    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,917,194
Number of extensions: 472865
Number of successful extensions: 305
Number of sequences better than 10.0: 1
Number of HSP's gapped: 304
Number of HSP's successfully gapped: 10
Length of query: 122
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 38
Effective length of database: 7,211,866
Effective search space: 274050908
Effective search space used: 274050908
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 (22.0 bits)
S2: 53 (24.2 bits)