RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy14411
         (85 letters)



>gnl|CDD|115393 pfam06732, Pescadillo_N, Pescadillo N-terminus.  This family
          represents the N-terminal region of Pescadillo.
          Pescadillo protein localises to distinct substructures
          of the interphase nucleus including nucleoli, the site
          of ribosome biogenesis. During mitosis pescadillo
          closely associates with the periphery of metaphase
          chromosomes and by late anaphase is associated with
          nucleolus-derived foci and prenucleolar bodies.
          Blastomeres in mouse embryos lacking pescadillo arrest
          at morula stages of development, the nucleoli fail to
          differentiate and accumulation of ribosomes is
          inhibited. It has been proposed that in mammalian cells
          pescadillo is essential for ribosome biogenesis and
          nucleologenesis and that disruption to its function
          results in cell cycle arrest. This family is often
          found in conjunction with a pfam00533 domain.
          Length = 282

 Score =  106 bits (267), Expect = 5e-30
 Identities = 44/80 (55%), Positives = 55/80 (68%)

Query: 6  KKYEAGEAVRYITRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYY 65
          KKYE G A +YITR  AL+KLQ++L  FR LCILKG+YPREP  +K+A +G    K  Y 
Sbjct: 2  KKYERGNATKYITRNQALRKLQLSLADFRRLCILKGIYPREPKHKKKANKGSTAPKTFYL 61

Query: 66 RKDINFLLHEPNLVIMRQQR 85
           KDI FLLHEP +   R+ +
Sbjct: 62 AKDIRFLLHEPIVNKFREYK 81


>gnl|CDD|227492 COG5163, NOP7, Protein required for biogenesis of the 60S
          ribosomal subunit [Translation, ribosomal structure and
          biogenesis].
          Length = 591

 Score = 83.6 bits (206), Expect = 1e-20
 Identities = 43/85 (50%), Positives = 53/85 (62%), Gaps = 1/85 (1%)

Query: 1  MVIRQKKYEAGEAVRYITRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGV 60
          M I+ K Y  G A +YITR  A+KKLQ+ L  FR LCILKGVYPREP  +K+A +G    
Sbjct: 1  MRIKGKNY-IGPARKYITRGQAMKKLQLRLADFRRLCILKGVYPREPKNKKKANKGSTAP 59

Query: 61 KILYYRKDINFLLHEPNLVIMRQQR 85
             YY KDI +L HEP     R+ +
Sbjct: 60 GTFYYIKDIQYLAHEPVYRKFRENK 84


>gnl|CDD|235470 PRK05444, PRK05444, 1-deoxy-D-xylulose-5-phosphate synthase;
           Provisional.
          Length = 580

 Score = 25.4 bits (57), Expect = 3.5
 Identities = 7/14 (50%), Positives = 11/14 (78%)

Query: 68  DINFLLHEPNLVIM 81
           D+++L   PN+VIM
Sbjct: 396 DLSYLRCIPNMVIM 409


>gnl|CDD|188230 TIGR02510, NrdE-prime, ribonucleoside-diphosphate reductase, alpha
           chain.  This model represents a small clade of
           ribonucleoside-diphosphate reductase, alpha chains which
           are sufficiently divergent from the usual Class I RNR
           alpha chains (NrdE or NrdA, TIGR02506) as to warrant
           their own model. The genes from Thermus thermophilus,
           Dichelobacter and Salinibacter are adjacent to the usual
           RNR beta chain [Purines, pyrimidines, nucleosides, and
           nucleotides, 2'-Deoxyribonucleotide metabolism].
          Length = 548

 Score = 24.9 bits (54), Expect = 6.7
 Identities = 15/54 (27%), Positives = 21/54 (38%)

Query: 17  ITRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDIN 70
           I R  A ++  +   Q   L I     P       RA    PG+K LYY++   
Sbjct: 478 IIRLAAARQKHIDQAQSLNLFISPDEKPSVDANVLRAFAWDPGLKSLYYQRSER 531


>gnl|CDD|224555 COG1640, MalQ, 4-alpha-glucanotransferase [Carbohydrate transport
           and metabolism].
          Length = 520

 Score = 24.6 bits (54), Expect = 7.8
 Identities = 12/39 (30%), Positives = 15/39 (38%), Gaps = 5/39 (12%)

Query: 41  GVYPREPIKRKRAQRGKPGVKILY----YRKDINFLLHE 75
           G  P E ++   A  G PG+KIL           FL   
Sbjct: 354 GTVPAE-VRDLLAHLGIPGMKILRFEADNEDPSPFLPPN 391


>gnl|CDD|129308 TIGR00204, dxs, 1-deoxy-D-xylulose-5-phosphate synthase.  DXP
           synthase is a thiamine diphosphate-dependent enzyme
           related to transketolase and the pyruvate dehydrogenase
           E1-beta subunit. By an acyloin condensation of pyruvate
           with glyceraldehyde 3-phosphate, it produces
           1-deoxy-D-xylulose 5-phosphate, a precursor of thiamine
           diphosphate (TPP), pyridoxal phosphate, and the
           isoprenoid building block isopentenyl diphosphate (IPP)
           [Biosynthesis of cofactors, prosthetic groups, and
           carriers, Other, Biosynthesis of cofactors, prosthetic
           groups, and carriers, Pyridoxine, Biosynthesis of
           cofactors, prosthetic groups, and carriers, Thiamine].
          Length = 617

 Score = 24.7 bits (54), Expect = 8.1
 Identities = 8/14 (57%), Positives = 11/14 (78%)

Query: 68  DINFLLHEPNLVIM 81
           DI++L   PN+VIM
Sbjct: 427 DISYLRCIPNMVIM 440


>gnl|CDD|224076 COG1154, Dxs, Deoxyxylulose-5-phosphate synthase [Coenzyme
           metabolism / Lipid metabolism].
          Length = 627

 Score = 24.5 bits (54), Expect = 9.9
 Identities = 8/14 (57%), Positives = 11/14 (78%)

Query: 68  DINFLLHEPNLVIM 81
           D++FL   PN+VIM
Sbjct: 433 DLSFLRCIPNMVIM 446


  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
   0.327    0.143    0.412 

Gapped
Lambda     K      H
   0.267   0.0697    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,405,730
Number of extensions: 357178
Number of successful extensions: 425
Number of sequences better than 10.0: 1
Number of HSP's gapped: 425
Number of HSP's successfully gapped: 16
Length of query: 85
Length of database: 10,937,602
Length adjustment: 53
Effective length of query: 32
Effective length of database: 8,586,840
Effective search space: 274778880
Effective search space used: 274778880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.3 bits)