RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13340
         (121 letters)



>gnl|CDD|203750 pfam07738, Sad1_UNC, Sad1 / UNC-like C-terminal.  The C. elegans
           UNC-84 protein is a nuclear envelope protein that is
           involved in nuclear anchoring and migration during
           development. The S. pombe Sad1 protein localises at the
           spindle pole body. UNC-84 and and Sad1 share a common
           C-terminal region, that is often termed the SUN (Sad1
           and UNC) domain. In mammals, the SUN domain is present
           in two proteins, Sun1 and Sun2. The SUN domain of Sun2
           has been demonstrated to be in the periplasm.
          Length = 135

 Score = 93.1 bits (232), Expect = 1e-25
 Identities = 42/89 (47%), Positives = 54/89 (60%), Gaps = 4/89 (4%)

Query: 1   MEHIPKTLTPNGIIDSAPKKFAVWGLREKYDENPTLLGEFMYDSEGPTLQYFEAKMVAD- 59
           +EH+ K++ P     SAPK F V G     D    LLG+F YD +G T+Q F+ +   D 
Sbjct: 49  LEHVEKSVAP---YSSAPKDFEVSGSDRYPDTKWVLLGKFTYDLDGKTIQTFQLENPPDI 105

Query: 60  TFDMVELKILSNHGNIEYTCLYRFRVHGN 88
               V+L+ILSN+GN  YTCLYRFRVHG 
Sbjct: 106 WVKYVKLRILSNYGNEHYTCLYRFRVHGT 134


>gnl|CDD|239821 cd04329, RNAP_II_Rpb7_N, RNAP_II_Rpb7_N: Rpb7, N-terminal
          ribonucleoprotein (RNP) domain. Rpb7 is a subunit of
          eukaryotic RNA polymerase (RNAP) II that is homologous
          to Rpc25 of RNAP III, RpoE of archaeal RNAP, and Rpa43
          of eukaryotic RNAP I. Rpb7 heterodimerizes with Rpb4
          and this heterodimer binds the 10-subunit core of RNAP
          II, forming part of the floor of the DNA-binding cleft.
          Rpb7 has two domains, an N-terminal RNP domain and a
          C-terminal oligonucleotide-binding (OB) domain, both of
          which bind single-stranded RNA. Rpb7 is thought to
          interact with the nascent RNA strand as it exits the
          RNAP II complex during transcription elongation. The
          Rpb7/Rpb4 heterodimer is also thought to serve as an
          upstream interface between the C-terminal domain of
          Rpb1 and the transcription factor IIB (TFIIB),
          recruiting pol II to the pol II promoter.
          Length = 80

 Score = 24.4 bits (54), Expect = 8.4
 Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 1/41 (2%)

Query: 43 DSEG-PTLQYFEAKMVADTFDMVELKILSNHGNIEYTCLYR 82
          + EG  T  Y     V D  D+ E KIL   G++E+   Y+
Sbjct: 32 EVEGTCTGDYGYIIAVTDIDDIGEGKILPGTGSVEFPVKYK 72


  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
   0.317    0.134    0.411 

Gapped
Lambda     K      H
   0.267   0.0729    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,116,937
Number of extensions: 514075
Number of successful extensions: 318
Number of sequences better than 10.0: 1
Number of HSP's gapped: 317
Number of HSP's successfully gapped: 3
Length of query: 121
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 37
Effective length of database: 7,211,866
Effective search space: 266839042
Effective search space used: 266839042
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.2 bits)