RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13437
         (80 letters)



>gnl|CDD|215998 pfam00567, TUDOR, Tudor domain. 
          Length = 118

 Score = 64.3 bits (157), Expect = 3e-15
 Identities = 26/57 (45%), Positives = 37/57 (64%), Gaps = 1/57 (1%)

Query: 2   GGWFRAQILAVDVVNASCQVKFVDYGGYLTLETSALRQIRADFLSLPFQAIECGLAN 58
           G W+RA+IL V + +   +V F+DYG   T+  S LR + ++F SLP QAI+C LA 
Sbjct: 63  GKWYRAKIL-VSLDDGLVEVFFIDYGNTETVPLSDLRPLPSEFASLPPQAIKCSLAG 118


>gnl|CDD|197660 smart00333, TUDOR, Tudor domain.  Domain of unknown function
          present in several RNA-binding proteins. 10 copies in
          the Drosophila Tudor protein. Initial proposal that the
          survival motor neuron gene product contain a Tudor
          domain are corroborated by more recent database search
          techniques such as PSI-BLAST (unpublished).
          Length = 57

 Score = 40.7 bits (96), Expect = 1e-06
 Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 1/41 (2%)

Query: 4  WFRAQILAVDVVNASCQVKFVDYGGYLTLETSALRQIRADF 44
          W+RA+I+ VD      +V F+DYG    +  S LRQ+  + 
Sbjct: 18 WYRARIVKVDG-EQLYEVFFIDYGNEEVVPPSDLRQLPEEL 57


>gnl|CDD|119391 cd04508, TUDOR, Tudor domains are found in many eukaryotic
          organisms and have been implicated in protein-protein
          interactions in which methylated protein substrates
          bind to these domains. For example, the Tudor domain of
          Survival of Motor Neuron (SMN) binds to symmetrically
          dimethylated arginines of arginine-glycine (RG) rich
          sequences found in the C-terminal tails of Sm proteins.
          The SMN protein is linked to spinal muscular atrophy.
          Another example is the tandem tudor domains of 53BP1,
          which bind to histone H4 specifically dimethylated at
          Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA
          damage checkpoint signal.
          Length = 48

 Score = 37.2 bits (87), Expect = 2e-05
 Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 2  GGWFRAQILAVDVVNASCQVKFVDYGGYLTLETSALRQ 39
          G W+RA+I ++   +   +V FVDYG    +  S LR 
Sbjct: 12 GKWYRAKITSILS-DGKVEVFFVDYGNTEVVPLSDLRP 48


>gnl|CDD|216003 pfam00579, tRNA-synt_1b, tRNA synthetases class I (W and Y). 
          Length = 291

 Score = 26.9 bits (60), Expect = 1.1
 Identities = 8/26 (30%), Positives = 13/26 (50%), Gaps = 3/26 (11%)

Query: 57  ANIVPVGTDGEYNIIL---IVERIGK 79
           A++ P G+D   +I L   +  R  K
Sbjct: 150 ADLQPGGSDQWGHIELGRDLARRFNK 175


>gnl|CDD|132268 TIGR03224, benzo_boxA, benzoyl-CoA oxygenase/reductase, BoxA
           protein.  Members of this protein family are BoxA, the A
           component of the BoxAB benzoyl-CoA oxygenase/reductase.
           This oxygen-requiring enzyme acts in an aerobic pathway
           of benzoate catabolism via coenzyme A ligation. BoxA is
           a homodimeric iron-sulphur-flavoprotein and acts as an
           NADPH-dependent reductase for BoxB [Energy metabolism,
           Other].
          Length = 411

 Score = 26.8 bits (59), Expect = 1.4
 Identities = 13/34 (38%), Positives = 17/34 (50%)

Query: 32  LETSALRQIRADFLSLPFQAIECGLANIVPVGTD 65
             +S +  I  DF S PF  +E     I+P GTD
Sbjct: 157 DASSDIHHIVLDFGSHPFPVLEGQSIGILPPGTD 190


>gnl|CDD|234054 TIGR02904, spore_ysxE, spore coat protein YsxE.  Members of this
          family are homologs of the Bacillus subtilis spore coat
          protein CotS. Members of this family, designated YsxE,
          are found only in the family Bacillaceae, from among
          the endospore-forming members of the Firmicutes branch
          of the Bacteria. As a rule, the ysxE gene is found
          immediately downstream of spoVID, a gene necessary for
          spore coat assembly. The protein has been shown to be
          part of the spore coat [Cellular processes, Sporulation
          and germination].
          Length = 309

 Score = 26.3 bits (58), Expect = 1.9
 Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 3/44 (6%)

Query: 28 GYLTLETSALRQIRAD-FLSLPFQAIECGLANIVPV--GTDGEY 68
          G   L+     +   + F+S      E G + IVPV    DG Y
Sbjct: 30 GVFALKKLYADRNTIESFVSQIQVLSEKGFSRIVPVYPTKDGSY 73


>gnl|CDD|237225 PRK12843, PRK12843, putative FAD-binding dehydrogenase; Reviewed.
          Length = 578

 Score = 25.1 bits (55), Expect = 4.1
 Identities = 10/32 (31%), Positives = 16/32 (50%), Gaps = 4/32 (12%)

Query: 11  AVDVVNASCQVKFVDYG---GYLT-LETSALR 38
           A+  + A+ +VKF  Y     Y + L  + LR
Sbjct: 109 AIAFLEANSEVKFRAYASHPDYESDLPGATLR 140


>gnl|CDD|173750 cd07857, STKc_MPK1, Catalytic domain of the Serine/Threonine
           Kinase, Fungal Mitogen-Activated Protein Kinase MPK1.
           Serine/Threonine Kinases (STKs), Fungal
           Mitogen-Activated Protein Kinase (MAPK) MPK1 subfamily,
           catalytic (c) domain. STKs catalyze the transfer of the
           gamma-phosphoryl group from ATP to serine/threonine
           residues on protein substrates. The MPK1 subfamily is
           part of a larger superfamily that includes the catalytic
           domains of other protein STKs, protein tyrosine kinases,
           RIO kinases, aminoglycoside phosphotransferase, choline
           kinase, and phosphoinositide 3-kinase. This subfamily is
           composed of the MAPKs MPK1 from Saccharomyces
           cerevisiae, Pmk1 from Schizosaccharomyces pombe, and
           similar proteins. MAPKs are important mediators of
           cellular responses to extracellular signals. MPK1 (also
           called Slt2) and Pmk1 (also called Spm1) are
           stress-activated MAPKs that regulate the cell wall
           integrity (CWI) pathway, and are therefore important in
           the maintainance of cell shape, cell wall construction,
           morphogenesis, and ion homeostasis. MPK1 is activated in
           response to cell wall stress including heat stimulation,
           osmotic shock, UV irradiation, and any agents that
           interfere with cell wall biogenesis such as chitin
           antagonists, caffeine, or zymolase. MPK1 is regulated by
           the MAP2Ks Mkk1/2, which are regulated by the MAP3K
           Bck1. Pmk1 is also activated by multiple stresses
           including elevated temperatures, hyper- or hypotonic
           stress, glucose deprivation, exposure to cell-wall
           damaging compounds, and oxidative stress. It is
           regulated by the MAP2K Pek1, which is regulated by the
           MAP3K Mkh1.
          Length = 332

 Score = 25.1 bits (55), Expect = 4.4
 Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 14/49 (28%)

Query: 15  VNASCQVKFVDYG-------------GYLTLETSALRQIRADFLSLPFQ 50
           VNA C++K  D+G             G++T E  A R  RA  + L FQ
Sbjct: 138 VNADCELKICDFGLARGFSENPGENAGFMT-EYVATRWYRAPEIMLSFQ 185


>gnl|CDD|227009 COG4663, FcbT1, TRAP-type mannitol/chloroaromatic compound
           transport system, periplasmic component [Secondary
           metabolites biosynthesis, transport, and catabolism].
          Length = 363

 Score = 24.7 bits (54), Expect = 6.6
 Identities = 8/13 (61%), Positives = 11/13 (84%)

Query: 1   MGGWFRAQILAVD 13
           MGGWFR +I +V+
Sbjct: 162 MGGWFRKEINSVE 174


>gnl|CDD|183199 PRK11561, PRK11561, isovaleryl CoA dehydrogenase; Provisional.
          Length = 538

 Score = 24.7 bits (54), Expect = 6.9
 Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 1/26 (3%)

Query: 16  NASCQVKFVDYGGYLT-LETSALRQI 40
           NAS +V+F D  G+L   E   +R I
Sbjct: 266 NASSEVEFQDAIGWLLGEEGEGIRLI 291


  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
   0.325    0.144    0.431 

Gapped
Lambda     K      H
   0.267   0.0748    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,148,311
Number of extensions: 321347
Number of successful extensions: 303
Number of sequences better than 10.0: 1
Number of HSP's gapped: 300
Number of HSP's successfully gapped: 11
Length of query: 80
Length of database: 10,937,602
Length adjustment: 49
Effective length of query: 31
Effective length of database: 8,764,256
Effective search space: 271691936
Effective search space used: 271691936
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.2 bits)