RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4429
         (186 letters)



>gnl|CDD|223113 COG0035, Upp, Uracil phosphoribosyltransferase [Nucleotide
           transport and metabolism].
          Length = 210

 Score =  100 bits (251), Expect = 1e-26
 Identities = 45/151 (29%), Positives = 67/151 (44%), Gaps = 27/151 (17%)

Query: 36  QVRELQTILRDKNTSRSDFKFFADRLIRLVIEESLNQLPFSKMDIVTPTGATYHGLKYER 95
            V+   TILRDKNT   +F+   D + RL+  E+   LP  K++I TP G T       +
Sbjct: 11  LVKHKLTILRDKNTGTKEFRELLDEIGRLLAYEATRDLPLEKVEIETPLGPTEGVQIAGK 70

Query: 96  GNCGVSVIRSGEAMEQGLRDCCRSIRIGKILIESDADTHEARIGLRDCCRSIRIGKILIE 155
               V ++R+G  M +GL     S R+G I I  D    E                    
Sbjct: 71  KIVIVPILRAGLGMVEGLLKLIPSARVGHIGIYRD---EE-------------------- 107

Query: 156 SDADTHEARIVYARFPEDIAQRKVLLMYPIM 186
               T E  + Y + PEDI +R V+++ P++
Sbjct: 108 ----TLEPVLYYEKLPEDIDERTVIVLDPML 134


>gnl|CDD|130163 TIGR01091, upp, uracil phosphoribosyltransferase.  A fairly deep
           split in phylogenetic and UPGMA trees separates this
           mostly prokaryotic set of uracil
           phosphoribosyltransferases from a mostly eukaryotic set
           that includes uracil phosphoribosyltransferase, uridine
           kinases, and other, uncharacterized proteins [Purines,
           pyrimidines, nucleosides, and nucleotides, Salvage of
           nucleosides and nucleotides].
          Length = 207

 Score = 49.6 bits (119), Expect = 1e-07
 Identities = 38/148 (25%), Positives = 66/148 (44%), Gaps = 27/148 (18%)

Query: 37  VRELQTILRDKNTSRSDFKFFADRLIRLVIEESLNQLPFSKMDIVTPTGATYHGLKYERG 96
           ++   T+LRDKNT   +F+     L RL+  E+   L   ++++ TP G T  G    + 
Sbjct: 10  IKHKLTLLRDKNTDTKEFRELLRELGRLLAYEATRDLELEEVEVETPLGETEGGRILGKK 69

Query: 97  NCGVSVIRSGEAMEQGLRDCCRSIRIGKILIESDADTHEARIGLRDCCRSIRIGKILIES 156
              V ++R+G  M  G+            LI       EA++G         +G      
Sbjct: 70  IVLVPILRAGLGMVDGVLK----------LIP------EAKVGH--------VG---AYR 102

Query: 157 DADTHEARIVYARFPEDIAQRKVLLMYP 184
           + +T +    Y++ PEDI +R V+++ P
Sbjct: 103 NEETLKPVPYYSKLPEDIDERTVIVLDP 130


>gnl|CDD|234653 PRK00129, upp, uracil phosphoribosyltransferase; Reviewed.
          Length = 209

 Score = 44.7 bits (107), Expect = 6e-06
 Identities = 44/141 (31%), Positives = 64/141 (45%), Gaps = 29/141 (20%)

Query: 42  TILRDKNTSRSDFKFFADRLIRLVIEESLNQLPFSKMDIVTPTGATYHGLKYERGNCG-V 100
           T+LRDKNTS   F+   + L RL+  E+   LP  +++I TP G T  G +        V
Sbjct: 17  TLLRDKNTSTKRFRELLEELGRLLAYEATRDLPLEEVEIETPLGKT-TGKRIAGKKLVIV 75

Query: 101 SVIRSGEAMEQGLRDCCRSIRIGKILIESDADTHEARIGLRDCCRSIRIGKILIESDADT 160
            ++R+G  M  G+            LI S      AR+G         IG   +  D +T
Sbjct: 76  PILRAGLGMVDGVLK----------LIPS------ARVGH--------IG---LYRDEET 108

Query: 161 HEARIVYARFPEDIAQRKVLL 181
            E    Y + PEDI +R V++
Sbjct: 109 LEPVEYYVKLPEDIDERTVIV 129


>gnl|CDD|182975 PRK11118, PRK11118, putative monooxygenase; Provisional.
          Length = 100

 Score = 26.4 bits (59), Expect = 3.7
 Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 6/36 (16%)

Query: 106 GEAMEQGLRDCCRSIR-----IGKILIESDADTHEA 136
           GE M + L+    SI      I KI  E++  T EA
Sbjct: 16  GEEMAKALKPLAESINEEPGFIWKIWTENE-KTQEA 50


>gnl|CDD|233261 TIGR01073, pcrA, ATP-dependent DNA helicase PcrA.  Designed to
           identify pcrA members of the uvrD/rep subfamily [DNA
           metabolism, DNA replication, recombination, and repair].
          Length = 726

 Score = 27.8 bits (62), Expect = 4.5
 Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 3/47 (6%)

Query: 27  NLKILPSNDQVRELQTILRDKNTSRSDFKFFADRLIRLVIEESLNQL 73
           N  I+   DQ+  ++TIL+DKN    D K F  R I   I  + N+L
Sbjct: 105 NFSIIDPTDQLSLMKTILKDKNL---DPKKFEPRSILGTISNAKNEL 148


>gnl|CDD|132763 cd07349, NR_LBD_SHP, The ligand binding domain of DAX1 protein, a
          nuclear receptor lacking DNA binding domain.  The
          ligand binding domain of the Small Heterodimer Partner
          (SHP): SHP is a member of the nuclear receptor
          superfamily. SHP has a ligand binding domain, but lacks
          the DNA binding domain, typical to almost all of the
          nuclear receptors. It functions as a transcriptional
          coregulator by directly interacting with other nuclear
          receptors through its AF-2 motif. The closest relative
          of SHP is DAX1 and they can form heterodimer. SHP is an
          orphan receptor, lacking an identified ligand.
          Length = 222

 Score = 27.1 bits (60), Expect = 5.1
 Identities = 10/25 (40%), Positives = 15/25 (60%)

Query: 17 KYVSFTEDIPNLKILPSNDQVRELQ 41
          K V+F  ++P+   LP  DQ+  LQ
Sbjct: 34 KTVAFMRNLPSFWQLPPQDQLLLLQ 58


>gnl|CDD|225128 COG2218, FwdC, Formylmethanofuran dehydrogenase subunit C [Energy
           production and conversion].
          Length = 264

 Score = 26.6 bits (59), Expect = 7.5
 Identities = 10/37 (27%), Positives = 18/37 (48%), Gaps = 8/37 (21%)

Query: 123 GKILIESDADTHEARIGLRDCCRSIRIGKILIESDAD 159
           G+I++E D   H            ++ GKI++  +AD
Sbjct: 86  GEIIVEGDVGMH--------VGAGMKGGKIVVNGNAD 114


>gnl|CDD|211427 cd11602, Ndc10, Ndc10 component of the yeast centromere-binding
           factor 3.  Ndc10 is a multidomain protein conserved in
           Saccharomycotina that interacts with kinetochore
           components. This model characterizes the majority of the
           protein; some family members may have an additional
           C-terminal domain that is homologous to transcriptional
           activators (GCR1_C). Ndc10 is part of the
           centromere-binding factor 3 (CBF3) complex in budding
           yeast. The CBF3 complex contains four essential
           proteins, Ndc10, Cep3, Ctf13, and Skp1. CBF3/Ndc10 is
           essential for the recruitment of the centromeric
           nucleosome and formation of the kinetochore. The
           Kinetochore is the large, multiprotein assembly that
           serves to connect condensed sister chromatids to the
           mitotic spindle.  Ndc10 forms a dimer and it has
           non-sequence-specific DNA binding activity via the DNA
           backbone. Ndc10 also plays an important role in the
           coordination of cell division. It has been noted that
           the protein bears resemblance to the tyrosine
           recombinases (type IB topoisomerase/lambda-integrase).
          Length = 413

 Score = 26.6 bits (59), Expect = 8.2
 Identities = 9/34 (26%), Positives = 16/34 (47%), Gaps = 1/34 (2%)

Query: 43  ILRDKNTSRSDFK-FFADRLIRLVIEESLNQLPF 75
           I +D      +F+ +F D +        ++QLPF
Sbjct: 379 IFKDPILQNPEFQSYFNDVIGLENQSNGMDQLPF 412


>gnl|CDD|236293 PRK08568, PRK08568, preprotein translocase subunit SecY; Reviewed.
          Length = 462

 Score = 26.7 bits (60), Expect = 8.2
 Identities = 9/22 (40%), Positives = 17/22 (77%), Gaps = 1/22 (4%)

Query: 165 IVYARFPEDIAQRKVLLMYPIM 186
           IVY +  E+IA+ +++ MYP++
Sbjct: 436 IVY-QLYEEIAREQLMEMYPLL 456


>gnl|CDD|112329 pfam03506, Flu_C_NS1, Influenza C non-structural protein (NS1).
           The influenza C virus genome consists of seven
           single-stranded RNA segments. The shortest RNA segment
           encodes a 286 amino acid non-structural protein NS1.
           This protein contains 6 conserved cysteines that may be
           functionally important, perhaps binding to a metal ion.
          Length = 162

 Score = 26.2 bits (57), Expect = 8.8
 Identities = 9/29 (31%), Positives = 16/29 (55%)

Query: 98  CGVSVIRSGEAMEQGLRDCCRSIRIGKIL 126
           CG  + +    +E G+R C R I+ G ++
Sbjct: 111 CGYLIAKQVAGIETGIRKCFRCIKSGFVM 139


>gnl|CDD|132749 cd06951, NR_LBD_Dax1_like, The ligand binding domain of DAX1
          protein, a nuclear receptor lacking DNA binding domain.
           The ligand binding domain of DAX1-like proteins: This
          orphan nuclear receptor family includes  DAX1
          (dosage-sensitive sex reversal adrenal hypoplasia
          congenita critical region on chromosome X gene 1) and
          the Small Heterodimer Partner (SHP). Both receptors
          have a typical ligand binding domain, but lack the DNA
          binding domain, typical to almost all of the nuclear
          receptors. They function as a transcriptional
          coregulator by directly interacting with other nuclear
          receptors. DAX1 and SHP can form heterodimers with each
          other, as well as with many other nuclear receptors. In
          addition, DAX1 can also form homodimers. DAX1 plays an
          important role in the normal development of several
          hormone-producing tissues.  SHP has shown to regulate a
          variety of target genes.
          Length = 222

 Score = 26.3 bits (58), Expect = 9.8
 Identities = 9/25 (36%), Positives = 15/25 (60%)

Query: 17 KYVSFTEDIPNLKILPSNDQVRELQ 41
          K + F  ++P    LP +DQ+R L+
Sbjct: 34 KTIRFVRNLPCFTYLPPDDQLRLLR 58


  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
   0.321    0.138    0.397 

Gapped
Lambda     K      H
   0.267   0.0524    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,471,836
Number of extensions: 888159
Number of successful extensions: 728
Number of sequences better than 10.0: 1
Number of HSP's gapped: 725
Number of HSP's successfully gapped: 19
Length of query: 186
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 95
Effective length of database: 6,901,388
Effective search space: 655631860
Effective search space used: 655631860
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (25.8 bits)