RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12093
         (118 letters)



>gnl|CDD|214532 smart00136, LamNT, Laminin N-terminal domain (domain VI).
           N-terminal domain of laminins and laminin-related
           protein such as Unc-6/ netrins.
          Length = 238

 Score = 47.7 bits (114), Expect = 1e-07
 Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 4/49 (8%)

Query: 34  WQYFAVSDDECWTQYGILASPANPLFLSDSDVICTSHYSKLKPLEGGEL 82
           WQYF+    +C   +G           ++ +VICTS YS + PLEGGE+
Sbjct: 129 WQYFSS---DCRRTFGRPPRGPITKG-NEDEVICTSEYSDIVPLEGGEI 173


>gnl|CDD|215682 pfam00055, Laminin_N, Laminin N-terminal (Domain VI). 
          Length = 237

 Score = 47.9 bits (114), Expect = 1e-07
 Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 3/49 (6%)

Query: 34  WQYFAVSDDECWTQYGILASPANPLFLSDSDVICTSHYSKLKPLEGGEL 82
           +QY+A S   C + Y  +         ++ DVICTS YS ++PL  GE+
Sbjct: 127 YQYYAYS---CESTYPGIPRRPIRTGRAEDDVICTSRYSDIEPLTEGEV 172


>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in
          granule-associated RNA binding proteins p40-TIA-1 and
          TIAR.  This subfamily corresponds to the RRM1 of
          nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
          nucleolysin TIA-1-related protein (TIAR), both of which
          are granule-associated RNA binding proteins involved in
          inducing apoptosis in cytotoxic lymphocyte (CTL) target
          cells. TIA-1 and TIAR share high sequence similarity.
          They are expressed in a wide variety of cell types.
          TIA-1 can be phosphorylated by a serine/threonine
          kinase that is activated during Fas-mediated
          apoptosis.TIAR is mainly localized in the nucleus of
          hematopoietic and nonhematopoietic cells. It is
          translocated from the nucleus to the cytoplasm in
          response to exogenous triggers of apoptosis. Both,
          TIA-1 and TIAR, bind specifically to poly(A) but not to
          poly(C) homopolymers. They are composed of three
          N-terminal highly homologous RNA recognition motifs
          (RRMs), also termed RBDs (RNA binding domains) or RNPs
          (ribonucleoprotein domains), and a glutamine-rich
          C-terminal auxiliary domain containing a
          lysosome-targeting motif. TIA-1 and TIAR interact with
          RNAs containing short stretches of uridylates and their
          RRM2 can mediate the specific binding to uridylate-rich
          RNAs. The C-terminal auxiliary domain may be
          responsible for interacting with other proteins. In
          addition, TIA-1 and TIAR share a potential serine
          protease-cleavage site (Phe-Val-Arg) localized at the
          junction between their RNA binding domains and their
          C-terminal auxiliary domains.
          Length = 72

 Score = 25.7 bits (57), Expect = 3.0
 Identities = 9/19 (47%), Positives = 10/19 (52%)

Query: 5  YVGNKDPGTTEVFVTSRFS 23
          YVGN D   TE  +   FS
Sbjct: 2  YVGNLDRTVTEDLLAELFS 20


>gnl|CDD|221056 pfam11277, Med24_N, Mediator complex subunit 24 N-terminal.  This
          subunit of the Mediator complex appears to be conserved
          only from insects to humans. It is essential for
          correct retinal development in fish. Subunit
          composition of the mediator contributes to the control
          of differentiation in the vertebrate CNS as there are
          divergent functions of the mediator subunits
          Crsp34/Med27, Trap100/Med24, and Crsp150/Med14.
          Length = 991

 Score = 26.7 bits (59), Expect = 3.1
 Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 11/42 (26%)

Query: 29 WVIN---------SWQYFAVSDDECWTQYGILASPANPLFLS 61
          W IN         S   + ++D     Q  ++ S ANPL LS
Sbjct: 23 WGINVKKVLPRGVSGDVYNLAD--ALLQQAMIGSGANPLILS 62


>gnl|CDD|226328 COG3806, ChrR, Transcriptional activator [Transcription].
          Length = 216

 Score = 25.6 bits (56), Expect = 7.3
 Identities = 8/44 (18%), Positives = 12/44 (27%), Gaps = 3/44 (6%)

Query: 5   YVGNKDPGTTEVFVTSRFSHGIQHWVINSWQYFAV---SDDECW 45
            + N D       V      G   W+    +   V   +DD   
Sbjct: 86  RLRNPDGSIHLPSVLEGALLGPWRWLGPGGRVEPVRLPTDDSRR 129


>gnl|CDD|235006 PRK02126, PRK02126, ribonuclease Z; Provisional.
          Length = 334

 Score = 25.6 bits (57), Expect = 8.2
 Identities = 6/9 (66%), Positives = 7/9 (77%)

Query: 98  GKLSSYTWN 106
            KL+ YTWN
Sbjct: 92  HKLAGYTWN 100


>gnl|CDD|180864 PRK07168, PRK07168, bifunctional uroporphyrinogen-III
           methyltransferase/uroporphyrinogen-III synthase;
           Reviewed.
          Length = 474

 Score = 25.3 bits (55), Expect = 8.9
 Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 2/31 (6%)

Query: 35  QYFAVSDDECWTQYGILASPANPLFLSDSDV 65
           Q+  V+  E   QYG+L+  A   F SD+ V
Sbjct: 334 QHMNVATQEKLMQYGLLSKEAK--FSSDTTV 362


  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    0.133    0.426 

Gapped
Lambda     K      H
   0.267   0.0704    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,786,502
Number of extensions: 461506
Number of successful extensions: 306
Number of sequences better than 10.0: 1
Number of HSP's gapped: 306
Number of HSP's successfully gapped: 11
Length of query: 118
Length of database: 10,937,602
Length adjustment: 81
Effective length of query: 37
Effective length of database: 7,344,928
Effective search space: 271762336
Effective search space used: 271762336
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)