RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy8810
         (218 letters)



>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 491

 Score = 82.3 bits (203), Expect = 2e-18
 Identities = 52/186 (27%), Positives = 83/186 (44%), Gaps = 4/186 (2%)

Query: 1   MRSLGLPLISFGLTGAVVANAYYQKKQFYPSVVYITK-SNSSMAVIYIQALILVILAGKL 59
           MR +   L S  L G  V  + Y     Y ++V  ++ S   + +     L+L  L    
Sbjct: 1   MRFILYVLASLVLFGLSVLLSLYSSATVYSALVMTSQLSPVHITIGLNVILLLFFLIANA 60

Query: 60  VKKIFFGQLRAAEFEHLMERSWYAVTETCLAFTVFKDDFSPKFVALFTLLLFLKAFHWLT 119
           +K + FG LR  E E L E+ W  +TE  LA +VF++  S  F  L + LLF K FHW+ 
Sbjct: 61  LKTLLFGSLRTFELELLYEQLWITLTEILLAISVFREAISFSFFMLLSTLLFAKVFHWIL 120

Query: 120 EDRV--DFMERSPMISYIFHIRIIVLLTVLGLLDLYFVVGAYQTTVTKGASVMIVFGFEY 177
             R     ++ +    +IF  R      +L +LD   +     +      S + +F  E+
Sbjct: 121 SFRTERLQIQSTDQRFHIFS-RFSCAYFLLSILDASLIYLCISSEHLIDKSTLFLFVCEF 179

Query: 178 AILLTV 183
           ++LL  
Sbjct: 180 SVLLLN 185


>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT
          transcription complex subunit 4 (NOT4) and similar
          proteins.  This subfamily corresponds to the RRM of
          NOT4, also termed CCR4-associated factor 4, or E3
          ubiquitin-protein ligase CNOT4, or potential
          transcriptional repressor NOT4Hp, a component of the
          CCR4-NOT complex, a global negative regulator of RNA
          polymerase II transcription. NOT4 functions as an
          ubiquitin-protein ligase (E3). It contains an
          N-terminal C4C4 type RING finger motif, followed by a
          RNA recognition motif (RRM), also termed RBD (RNA
          binding domain) or RNP (ribonucleoprotein domain). The
          RING fingers may interact with a subset of
          ubiquitin-conjugating enzymes (E2s), including UbcH5B,
          and mediate protein-protein interactions. T.
          Length = 98

 Score = 27.1 bits (61), Expect = 2.8
 Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)

Query: 30 PSV-VYITKSNSSMAVIYIQALILVILAGKLVK 61
          PS   Y+T S    A+  IQA+    L G+L+K
Sbjct: 52 PSASAYVTYSRKEDALRCIQAVDGFYLDGRLLK 84


>gnl|CDD|180413 PRK06128, PRK06128, oxidoreductase; Provisional.
          Length = 300

 Score = 28.3 bits (63), Expect = 3.2
 Identities = 11/40 (27%), Positives = 18/40 (45%)

Query: 51  ILVILAGKLVKKIFFGQLRAAEFEHLMERSWYAVTETCLA 90
           ILV +AGK         +   +F+   + + YA+   C A
Sbjct: 137 ILVNIAGKQTAVKDIADITTEQFDATFKTNVYAMFWLCKA 176


>gnl|CDD|107306 cd06311, PBP1_ABC_sugar_binding_like_3, Periplasmic sugar-binding
          domain of uncharacterized ABC-type transport systems.
          Periplasmic sugar-binding domain of uncharacterized
          ABC-type transport systems that share homology with a
          family of pentose/hexose sugar-binding proteins of the
          type I periplasmic binding protein superfamily, which
          consists of two domains connected by a three-stranded
          hinge. The substrate specificity of this group is not
          known, but it is predicted to be involved in the
          transport of sugar-containing molecules and chemotaxis.
          Length = 274

 Score = 28.1 bits (63), Expect = 3.9
 Identities = 18/56 (32%), Positives = 24/56 (42%), Gaps = 12/56 (21%)

Query: 12 GLTGAVVANAYYQKKQF---YPSVVYI--TKSNSSMAVIYIQALI-------LVIL 55
          G T  +V +A    K+    YP V +I  T SN +      Q L+       LVIL
Sbjct: 12 GWTAGIVWHAQAAAKKLEAAYPDVEFILVTASNDTEQQNAQQDLLINRKIDALVIL 67


>gnl|CDD|223956 COG1025, Ptr, Secreted/periplasmic Zn-dependent peptidases,
           insulinase-like [Posttranslational modification, protein
           turnover, chaperones].
          Length = 937

 Score = 27.7 bits (62), Expect = 5.0
 Identities = 28/108 (25%), Positives = 41/108 (37%), Gaps = 20/108 (18%)

Query: 22  YYQKKQFYPSVVYITKSNSSMAVIY-------IQALILVILAGKLVKKIFFGQLRAAE-- 72
           Y  K           +S+S+ A I        I++  L  L G+L+   FF QLR  E  
Sbjct: 718 YLLKGGTRIFETVGGESDSANAAILYPQQYDEIKSSALSSLLGQLIHPWFFDQLRTKEQL 777

Query: 73  ----FEHLMERSWYAVTET-CLAFTVFKDDFSPKFVALFTLLLFLKAF 115
               F    E     V  T  + F V  +  SP ++ L  +  FL+  
Sbjct: 778 GYAVFSGPRE-----VGRTPGIGFLVQSNSKSPSYL-LERINAFLETA 819


>gnl|CDD|213289 cd05922, FACL_like_6, Uncharacterized subfamily of fatty acid CoA
           ligase (FACL).  Fatty acyl-CoA ligases catalyze the
           ATP-dependent activation of fatty acids in a two-step
           reaction. The carboxylate substrate first reacts with
           ATP to form an acyl-adenylate intermediate, which then
           reacts with CoA to produce an acyl-CoA ester. This is a
           required step before free fatty acids can participate in
           most catabolic and anabolic reactions.
          Length = 350

 Score = 27.2 bits (61), Expect = 7.5
 Identities = 8/33 (24%), Positives = 14/33 (42%), Gaps = 2/33 (6%)

Query: 145 TVLGLLDLYFVVGAYQ--TTVTKGASVMIVFGF 175
            +L +L   F  G  Q  T    G ++++   F
Sbjct: 45  RILAVLPFSFDYGLSQLLTAFRVGGTLVLESRF 77


  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
   0.333    0.144    0.428 

Gapped
Lambda     K      H
   0.267   0.0760    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,413,023
Number of extensions: 1116915
Number of successful extensions: 1473
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1468
Number of HSP's successfully gapped: 61
Length of query: 218
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 125
Effective length of database: 6,812,680
Effective search space: 851585000
Effective search space used: 851585000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 57 (25.7 bits)