RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy11416
         (171 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 =  163 bits (415), Expect = 1e-50
 Identities = 71/142 (50%), Positives = 88/142 (61%), Gaps = 20/142 (14%)

Query: 14  FSDALRDLDDALTLCILIGRMPGLKKQRLGQDKGLMELCQRLPVEFMHAVIHARALRKAF 73
           F DALRDLDDAL++  L   +P   K +     G + LC+RL  EFMH VI +R+LRK F
Sbjct: 122 FIDALRDLDDALSMLFLFSTLPSTHKLK----VGTINLCRRLTAEFMHYVIRSRSLRKVF 177

Query: 74  ISIKGFYFQAEFKGQKITWIIPHLYGHQAHSNMLIMCFLFPQPYDKKQIDIRTMLTFAEF 133
           ISIKG Y+QAE KG+K+TWI+PH + H             P       +D R MLTF EF
Sbjct: 178 ISIKGIYYQAEIKGEKVTWIVPHEFAHN-----------HPT-----DVDFRVMLTFLEF 221

Query: 134 YTSLLGFTLYRLYHTLNLAYPP 155
           YT+LLGF  ++LY  LNL YPP
Sbjct: 222 YTTLLGFVNFKLYQDLNLDYPP 243


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

 Score =  108 bits (271), Expect = 5e-28
 Identities = 52/146 (35%), Positives = 72/146 (49%), Gaps = 24/146 (16%)

Query: 14  FSDALRDLDDALTLCILIGRMPGLKKQRLGQDKGLMELCQRLPVEFMHAVIHARALRKAF 73
           F DA+ D+DDAL++  L   +P     R+     +    Q +   F   V     LRK+F
Sbjct: 125 FGDAVDDIDDALSMLFLFSMLP--LTDRISS--KIANDAQEVCEMFEDYVRRRSLLRKSF 180

Query: 74  ISIKGFYFQAEFKGQKITWIIPHLYGHQAHSNMLIMCFLFPQ--PYDKKQIDIRTMLTFA 131
           +SIKG Y+QA   G+K+ W +P               + FP+  P D   +D R MLTF 
Sbjct: 181 MSIKGVYYQATIGGEKVVWFVP---------------YKFPENIPGD---VDFRIMLTFL 222

Query: 132 EFYTSLLGFTLYRLYHTLNLAYPPCF 157
           EFY++LL F   +LY    L YPP F
Sbjct: 223 EFYSTLLHFVSLKLYVEEGLDYPPKF 248


>gnl|CDD|236891 PRK11278, PRK11278, NADH dehydrogenase I subunit F; Provisional.
          Length = 448

 Score = 28.2 bits (63), Expect = 2.6
 Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 9/51 (17%)

Query: 35  PGLKKQRLGQDKGLMELCQRLPVEFMHAVIHARALR--KAFISIKGFYFQA 83
           PG  K RL     LME    L VE M  +I A AL+  + +I ++G Y +A
Sbjct: 97  PGTYKDRL-----LMEQLPHLLVEGM--LISAFALKAYRGYIFLRGEYIEA 140


>gnl|CDD|218946 pfam06226, DUF1007, Protein of unknown function (DUF1007).  Family
           of conserved bacterial proteins with unknown function.
          Length = 212

 Score = 26.9 bits (60), Expect = 4.7
 Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 4/54 (7%)

Query: 72  AFISIKGF-YF-QAEFKGQKITWIIPHLYGHQAHSNMLIMCFLFP--QPYDKKQ 121
              S+  + YF   +  G+K+ +  P  Y  +     L + F  P  +P D K 
Sbjct: 80  VMASLAEYHYFTYLKADGKKVKFSEPTDYRLEYKGGQLTLHFTLPLAKPVDLKG 133


>gnl|CDD|133000 cd02503, MobA, MobA catalyzes the formation of molybdopterin
          guanine dinucleotide.  The prokaryotic enzyme
          molybdopterin-guanine dinucleotide biosynthesis protein
          A (MobA). All mononuclear molybdoenzymes bind
          molybdenum in complex with an organic cofactor termed
          molybdopterin (MPT). In many bacteria, including
          Escherichia coli, molybdopterin can be further modified
          by attachment of a GMP group to the terminal phosphate
          of molybdopterin to form molybdopterin guanine
          dinucleotide (MGD). This GMP attachment step is
          catalyzed by MobA, by linking a guanosine 5'-phosphate
          to MPT forming molybdopterin guanine dinucleotide. This
          reaction requires GTP, MgCl2, and the MPT form of the
          cofactor. It is a reaction unique to prokaryotes, and
          therefore may represent a potential drug target.
          Length = 181

 Score = 26.0 bits (58), Expect = 8.6
 Identities = 13/30 (43%), Positives = 18/30 (60%), Gaps = 4/30 (13%)

Query: 25 LTLCILIGRMPGLKKQRLGQDKGLMELCQR 54
          +T  IL G   G K +R+G DK L+EL  +
Sbjct: 1  ITGVILAG---G-KSRRMGGDKALLELGGK 26


  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
   0.332    0.145    0.465 

Gapped
Lambda     K      H
   0.267   0.0701    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,033,655
Number of extensions: 830158
Number of successful extensions: 894
Number of sequences better than 10.0: 1
Number of HSP's gapped: 890
Number of HSP's successfully gapped: 15
Length of query: 171
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 81
Effective length of database: 6,945,742
Effective search space: 562605102
Effective search space used: 562605102
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: 55 (25.0 bits)