RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6947
         (92 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 =  119 bits (300), Expect = 1e-36
 Identities = 55/90 (61%), Positives = 68/90 (75%), Gaps = 2/90 (2%)

Query: 1   KGPHQLSRKQIIPLPTKRANPETEPEALFPIGSVVMALYPQTTCFYKAIVNSLPTTGTDD 60
           K  ++LSRK +IPLP K ANPET P ALFP G++V+ALYPQTTCFY+AIV+S P   +D+
Sbjct: 43  KKRYKLSRKDLIPLP-KTANPETSPHALFPKGTIVLALYPQTTCFYRAIVHSPPKRKSDE 101

Query: 61  YELLFEDNSYADNYAPPLGVPQRYVIAYKK 90
           Y L FED+  AD Y PP  VPQRYV+A+  
Sbjct: 102 YRLRFEDDEDADGY-PPREVPQRYVVAFPG 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 = 29.5 bits (67), Expect = 0.043
 Identities = 10/36 (27%), Positives = 18/36 (50%), Gaps = 2/36 (5%)

Query: 32 GSVVMALYPQTTCFYKAIVNSLPTTGTDDYELLFED 67
          G + +A Y     +Y+A + S+ + G    E+ F D
Sbjct: 1  GDLCLAKYSDDGKWYRAKITSILSDGK--VEVFFVD 34


>gnl|CDD|216534 pfam01499, Herpes_UL25, Herpesvirus UL25 family.  The herpesvirus
           UL25 gene product is a virion component involved in
           virus penetration and capsid assembly. The product of
           the UL25 gene is required for packaging but not cleavage
           of replicated viral DNA. This family includes a number
           of herpesvirus proteins: EHV-1 36, EBV BVRF1, HCMV UL77,
           ILTV ORF2, and VZV gene 34.
          Length = 538

 Score = 26.2 bits (58), Expect = 3.1
 Identities = 13/25 (52%), Positives = 15/25 (60%), Gaps = 1/25 (4%)

Query: 14  LPTKRANPETEPEALFPIGSVVMAL 38
           +PT RANP  E   LFP G   +AL
Sbjct: 435 VPTYRANPNVELSQLFP-GLAALAL 458


>gnl|CDD|215161 PLN02287, PLN02287, 3-ketoacyl-CoA thiolase.
          Length = 452

 Score = 25.9 bits (57), Expect = 3.4
 Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 1/34 (2%)

Query: 10  QIIPLPTKRANPETEPEALFPIGSVVMALYPQTT 43
           +I+P+ TK  +P+T  E    I SV   + P TT
Sbjct: 233 EIVPVHTKIVDPKTGEEKPIVI-SVDDGIRPNTT 265


>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 = 25.8 bits (57), Expect = 3.9
 Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 1/46 (2%)

Query: 46  YKAIVNS-LPTTGTDDYELLFEDNSYADNYAPPLGVPQRYVIAYKK 90
           Y A+V   +P +GT DY L  E +  AD +A     PQ     Y+ 
Sbjct: 85  YLAVVRGYVPESGTIDYPLSEELDKLADKFASDDKAPQAATTHYRL 130


>gnl|CDD|118003 pfam09465, LBR_tudor, Lamin-B receptor of TUDOR domain.  The
          Lamin-B receptor, found on the TUDOR domain pfam00567,
          is a chromatin and lamin binding protein in the inner
          nuclear membrane. It is one of the integral inner
          Nuclear Envelope membrane proteins responsible for
          targeting nuclear membranes to chromatin, being a
          downstream effector of Ran, a small Ras-like nuclear
          GTPase which regulates NE assembly. Lamin-B receptor
          interacts with Importin beta, a Ran-binding protein,
          thereby directly contributing to the fusion of membrane
          vesicles and the formation of the NE.
          Length = 55

 Score = 24.4 bits (53), Expect = 4.6
 Identities = 11/43 (25%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 25 PEALFPIGSVVMALYPQTTCFYKAIVNSLPTTGTDDYELLFED 67
          P   +  G VVM  +P ++ +Y+  V S  +  +  Y + ++D
Sbjct: 2  PGRKYADGEVVMGRWPGSSLYYEVQVLSFDSK-SQLYTVKYKD 43


>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 = 25.1 bits (55), Expect = 7.3
 Identities = 9/39 (23%), Positives = 18/39 (46%), Gaps = 3/39 (7%)

Query: 50  VNSLPTTGTDDYELLFEDNSYADNYAPPLGVPQRYVIAY 88
           + ++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 = 24.6 bits (54), Expect = 8.1
 Identities = 16/45 (35%), Positives = 19/45 (42%), Gaps = 1/45 (2%)

Query: 46  YKAIVNS-LPTTGTDDYELLFEDNSYADNYAPPLGVPQRYVIAYK 89
           Y AIV   L      DY L  E +  AD +A     PQ  V  Y+
Sbjct: 86  YHAIVRGWLMEEAVLDYPLKEELDKIADKFAREDKAPQPAVTHYR 130


  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
   0.315    0.134    0.399 

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: 4,769,096
Number of extensions: 380613
Number of successful extensions: 185
Number of sequences better than 10.0: 1
Number of HSP's gapped: 183
Number of HSP's successfully gapped: 11
Length of query: 92
Length of database: 10,937,602
Length adjustment: 59
Effective length of query: 33
Effective length of database: 8,320,716
Effective search space: 274583628
Effective search space used: 274583628
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: 42 (22.0 bits)
S2: 53 (24.1 bits)