RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6948
         (69 letters)



>gnl|CDD|219277 pfam07039, DUF1325, SGF29 tudor-like domain.  This domain is found
           in the yeast protein SAGA-associated factor 29. This
           domain is related to members of the Tudor domain
           superfamily such as pfam05641. The SAGA complex is
           involved in RNA polymerase II-dependent transcriptional
           regulation. The membership of the tudor domain
           superfamily suggests this domain may bind to RNA.
          Length = 130

 Score = 84.7 bits (210), Expect = 3e-23
 Identities = 33/55 (60%), Positives = 41/55 (74%), Gaps = 1/55 (1%)

Query: 13  MALYPQTTCFYKAIVNSLPTTGTDDYELLFEDNSYADNYAPPLGVPQRYVIAYKK 67
           +ALYPQTTCFY+AIV+S P   +D+Y L FED+  AD Y PP  VPQRYV+A+  
Sbjct: 77  LALYPQTTCFYRAIVHSPPKRKSDEYRLRFEDDEDADGY-PPREVPQRYVVAFPG 130


>gnl|CDD|211333 cd02563, PseudoU_synth_TruC, tRNA pseudouridine isomerase C.
           Pseudouridine synthases catalyze the isomerization of
           specific uridines in an tRNA molecule to pseudouridines
           (5-ribosyluracil, psi).  No cofactors are required. TruC
           makes psi65 in tRNAs.  This psi residue is not
           universally conserved.
          Length = 223

 Score = 27.7 bits (62), Expect = 0.37
 Identities = 20/72 (27%), Positives = 28/72 (38%), Gaps = 14/72 (19%)

Query: 10  ILLMALYPQTT---CF----------YKAIVNS-LPTTGTDDYELLFEDNSYADNYAPPL 55
           +LL AL  +                 Y A+V   +P +GT DY L  E +  AD +A   
Sbjct: 59  VLLFALSSEVARKLGEQFTEHRVHKTYLAVVRGYVPESGTIDYPLSEELDKLADKFASDD 118

Query: 56  GVPQRYVIAYKK 67
             PQ     Y+ 
Sbjct: 119 KAPQAATTHYRL 130


>gnl|CDD|130850 TIGR01790, carotene-cycl, lycopene cyclase family protein.  This
           family includes lycopene beta and epsilion cyclases
           (which form beta and delta carotene, respectively) from
           bacteria and plants as well as the plant
           capsanthin/capsorubin and neoxanthin cyclases which
           appear to have evolved from the plant lycopene cyclases.
           The plant lycopene epsilon cyclases also transform
           neurosporene to alpha zeacarotene.
          Length = 388

 Score = 25.9 bits (57), Expect = 1.6
 Identities = 9/39 (23%), Positives = 18/39 (46%), Gaps = 3/39 (7%)

Query: 27  VNSLPTTGTDDYELLFEDNSYADNYAPPLGVPQRYVIAY 65
           + ++P   T    +  E+ S AD  A P    ++ ++A 
Sbjct: 197 LYAMPLGSTR---VFIEETSLADRPALPRDRLRQRILAR 232


>gnl|CDD|182971 PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional.
          Length = 257

 Score = 25.8 bits (57), Expect = 1.8
 Identities = 22/71 (30%), Positives = 26/71 (36%), Gaps = 14/71 (19%)

Query: 10  ILLMALYP-------------QTTCFYKAIVNS-LPTTGTDDYELLFEDNSYADNYAPPL 55
           +LLMAL               Q    Y AIV   L      DY L  E +  AD +A   
Sbjct: 60  VLLMALSSEVARLLAQQFEQHQIQKTYHAIVRGWLMEEAVLDYPLKEELDKIADKFARED 119

Query: 56  GVPQRYVIAYK 66
             PQ  V  Y+
Sbjct: 120 KAPQPAVTHYR 130


>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 = 23.7 bits (52), Expect = 4.2
 Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 2/32 (6%)

Query: 13 MALYPQTTCFYKAIVNSLPTTGTDDYELLFED 44
          +A Y     +Y+A + S+ + G    E+ F D
Sbjct: 5  LAKYSDDGKWYRAKITSILSDGK--VEVFFVD 34


  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
   0.316    0.134    0.390 

Gapped
Lambda     K      H
   0.267   0.0786    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,460,249
Number of extensions: 250848
Number of successful extensions: 151
Number of sequences better than 10.0: 1
Number of HSP's gapped: 150
Number of HSP's successfully gapped: 6
Length of query: 69
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 30
Effective length of database: 9,207,796
Effective search space: 276233880
Effective search space used: 276233880
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 (21.6 bits)
S2: 53 (24.1 bits)