RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12540
         (79 letters)



>gnl|CDD|227365 COG5032, TEL1, Phosphatidylinositol kinase and protein kinases of the
            PI-3 kinase family [Signal transduction mechanisms / Cell
            division and chromosome partitioning / Chromatin
            structure and dynamics / DNA replication, recombination,
            and repair / Intracellular trafficking and secretion].
          Length = 2105

 Score = 42.1 bits (99), Expect = 5e-06
 Identities = 21/52 (40%), Positives = 28/52 (53%)

Query: 26   VQAYLSDIGKRHPQALVYPLTVASKSNSSSRRNAANKILQSMCDLSPLLVKL 77
             Q+ LS IGK HPQALV+ L  A +S + S+ + A  +        P LVK 
Sbjct: 1568 AQSLLSKIGKEHPQALVFTLRSAIESTALSKESVALSLENKSRTHDPSLVKE 1619


>gnl|CDD|233974 TIGR02682, cas_csx11, CRISPR-associated protein, Csx11 family.
          Members of this uncommon, sporadically distributed
          protein family are large (>900 amino acids) and
          strictly associated, so far, with CRISPR-associated
          (Cas) gene clusters. Nearby Cas genes always include
          members of the RAMP superfamily and the six-gene
          CRISPR-associated RAMP module. Species in which it is
          found, so far, include three archaea (Methanosarcina
          mazei, M. barkeri and Methanobacterium
          thermoautotrophicum) and two bacteria
          (Thermodesulfovibrio yellowstonii DSM 11347 and
          Sulfurihydrogenibium azorense) [Mobile and
          extrachromosomal element functions, Other].
          Length = 918

 Score = 26.8 bits (59), Expect = 1.3
 Identities = 7/25 (28%), Positives = 12/25 (48%)

Query: 15 RKRKSKLIGGPVQAYLSDIGKRHPQ 39
          +  K +++   + AYL   GK  P 
Sbjct: 7  KNNKDEILLAEIGAYLHLWGKLSPS 31


>gnl|CDD|175980 cd04013, C2_SynGAP_like, C2 domain present in Ras GTPase activating
           protein (GAP) family.  SynGAP, GAP1, RasGAP, and
           neurofibromin are all members of the Ras-specific GAP
           (GTPase-activating protein) family.  SynGAP regulates
           the MAP kinase signaling pathway and is critical for
           cognition and synapse function.  Mutations in this gene
           causes mental retardation in humans.   SynGAP contains a
           PH-like domain, a C2 domain, and a  Ras-GAP domain.  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.
          Length = 146

 Score = 25.7 bits (57), Expect = 2.2
 Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 14  KRKRKSKLIGGPVQAYLSDIGKRHPQALVYPLTVASKSNSSSRRN 58
           K+K KS+LIG  V   ++D+  R      YP++    +  S  + 
Sbjct: 81  KKKDKSQLIG-TVNIPVTDVSSRQFVEKWYPVSTPKGNGKSGGKE 124


>gnl|CDD|235995 PRK07338, PRK07338, hypothetical protein; Provisional.
          Length = 402

 Score = 24.9 bits (55), Expect = 4.7
 Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 12/68 (17%)

Query: 6   LVALCAFLKRKRKSKL-----------IGGPV-QAYLSDIGKRHPQALVYPLTVASKSNS 53
           L AL AF +     KL           IG P     L+++ +    AL Y   +   + +
Sbjct: 138 LAALLAFERSPLADKLGYDVLINPDEEIGSPASAPLLAELARGKHAALTYEPALPDGTLA 197

Query: 54  SSRRNAAN 61
            +R+ + N
Sbjct: 198 GARKGSGN 205


>gnl|CDD|214353 CHL00073, chlN, photochlorophyllide reductase subunit N.
          Length = 457

 Score = 24.6 bits (54), Expect = 6.2
 Identities = 9/13 (69%), Positives = 10/13 (76%)

Query: 13  LKRKRKSKLIGGP 25
           L R+RK KLIG P
Sbjct: 256 LMRRRKCKLIGAP 268


  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    0.132    0.368 

Gapped
Lambda     K      H
   0.267   0.0708    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,699,390
Number of extensions: 268980
Number of successful extensions: 240
Number of sequences better than 10.0: 1
Number of HSP's gapped: 240
Number of HSP's successfully gapped: 8
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: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.2 bits)