RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16397
         (60 letters)



>gnl|CDD|220655 pfam10255, Paf67, RNA polymerase I-associated factor PAF67.  RNA
           polymerase I is a multisubunit enzyme and its
           transcription competence is dependent on the presence of
           PAF67. This family of proteins is conserved from worms
           to humans.
          Length = 402

 Score = 58.1 bits (141), Expect = 4e-12
 Identities = 23/36 (63%), Positives = 29/36 (80%)

Query: 14  TAMLDFYIDNEMIHIADTKVAHRYGDFFIRKIIKFE 49
           ++ LDFYID +MIHI +TKV  RYGDFFIR+I K +
Sbjct: 367 SSDLDFYIDGDMIHIKETKVQKRYGDFFIRQINKCK 402


>gnl|CDD|237197 PRK12770, PRK12770, putative glutamate synthase subunit beta;
           Provisional.
          Length = 352

 Score = 25.7 bits (57), Expect = 1.5
 Identities = 11/31 (35%), Positives = 16/31 (51%)

Query: 30  DTKVAHRYGDFFIRKIIKFEELNKKLQAIKI 60
              +    GD F+ +I+  EEL KK  A+ I
Sbjct: 94  GEPLHEEEGDEFVERIVSLEELVKKYDAVLI 124


>gnl|CDD|232981 TIGR00456, argS, arginyl-tRNA synthetase.  This model recognizes
           arginyl-tRNA synthetase in every completed genome to
           date. An interesting feature of the alignment of all
           arginyl-tRNA synthetases is a fairly deep split between
           two families. One family includes archaeal, eukaryotic
           and organellar, spirochete, E. coli, and Synechocystis
           sp. The second, sharing a deletion of about 25 residues
           in the central region relative to the first, includes
           Bacillus subtilis, Aquifex aeolicus, the Mycoplasmas and
           Mycobacteria, and the Gram-negative bacterium
           Helicobacter pylori [Protein synthesis, tRNA
           aminoacylation].
          Length = 566

 Score = 25.0 bits (55), Expect = 2.8
 Identities = 10/43 (23%), Positives = 17/43 (39%), Gaps = 3/43 (6%)

Query: 11  GTLTAMLDFYI---DNEMIHIADTKVAHRYGDFFIRKIIKFEE 50
           G    +L   +    NE ++ A  K  H    F++    + EE
Sbjct: 162 GRQFGLLALGVEKFGNEKLNEAVKKPDHGLEGFYVEINKRLEE 204


>gnl|CDD|131426 TIGR02373, photo_yellow, photoactive yellow protein.  Members of
           this family are photoactive yellow protein, a cytosolic,
           14-kDa light-sensing protein which has a
           4-hydroxycinnamyl (p-coumaric acid) chromophore
           covalently linked to a Cys residue. The enzyme
           4-coumarate--CoA ligase as described by TIGR02372 is
           required for its biosynthesis. The modified Cys is in a
           PAS (pfam00989) domain, frequently found in signal
           transducing proteins. Members are known in alpha and
           gamma Proteobacteria that include Rhodobacter
           capsulatus, Halorhodospira halophila, Rhodospirillum
           centenum, etc.
          Length = 124

 Score = 24.0 bits (52), Expect = 5.5
 Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 7/46 (15%)

Query: 6   QGLTEGTLTAMLDFYIDNEM------IHIADTKVAHRYGDFFIRKI 45
           +G+  GTL AM D+  D +M      IH+ +  V   Y   F++++
Sbjct: 80  EGVASGTLNAMFDYVFDYQMAPVKVKIHMKNAGVGDSYW-IFVKRV 124


>gnl|CDD|131042 TIGR01987, HI0074, nucleotidyltransferase substrate binding
           protein, HI0074 family.  The member of this family from
           Haemophilus influenzae, HI0074, has been shown by
           crystal structure to resemble nucleotidyltransferase
           substrate binding proteins. It forms a complex with
           HI0073, encoded by the adjacent gene and containing a
           nucleotidyltransferase nucleotide binding domain
           (pfam01909).
          Length = 123

 Score = 23.6 bits (51), Expect = 6.5
 Identities = 8/35 (22%), Positives = 14/35 (40%)

Query: 23  NEMIHIADTKVAHRYGDFFIRKIIKFEELNKKLQA 57
           N   H  D + A          + +FE L ++L+ 
Sbjct: 89  NITSHTYDQEKAREIYAQIRDYVPEFEFLLEQLRQ 123


>gnl|CDD|232830 TIGR00113, queA, S-adenosylmethionine:tRNA
          ribosyltransferase-isomerase.  This model describes the
          enzyme for S-adenosylmethionine:tRNA
          ribosyltransferase-isomerase (QueA). QueA synthesizes
          Queuosine which is usually in the first position of the
          anticodon of tRNAs specific for asparagine, aspartate,
          histidine, and tyrosine [Protein synthesis, tRNA and
          rRNA base modification].
          Length = 344

 Score = 24.0 bits (52), Expect = 6.8
 Identities = 8/29 (27%), Positives = 17/29 (58%)

Query: 5  NQGLTEGTLTAMLDFYIDNEMIHIADTKV 33
             +T  T   +LDF+ + +++ + +TKV
Sbjct: 34 TGKITHSTFKDVLDFFNEGDLLVLNNTKV 62


>gnl|CDD|151980 pfam11544, Spc42p, Spindle pole body component Spc42p.  Spc42p is
          a 42-kD component of the S.cerevisiae spindle body that
          localises to the electron dense central region of the
          SPB.Spc42p is a phosphoprotein which forms a polymeric
          layer at the periphery of the SPB central plaque. This
          functions during SPB duplication and also facilitates
          the attachment of the SPB to the nuclear membrane.
          Length = 74

 Score = 23.3 bits (50), Expect = 8.0
 Identities = 9/14 (64%), Positives = 12/14 (85%)

Query: 44 KIIKFEELNKKLQA 57
          K+IK+ ELNKKL+ 
Sbjct: 32 KLIKYTELNKKLED 45


  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
   0.326    0.142    0.395 

Gapped
Lambda     K      H
   0.267   0.0624    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,080,854
Number of extensions: 224948
Number of successful extensions: 325
Number of sequences better than 10.0: 1
Number of HSP's gapped: 325
Number of HSP's successfully gapped: 13
Length of query: 60
Length of database: 10,937,602
Length adjustment: 31
Effective length of query: 29
Effective length of database: 9,562,628
Effective search space: 277316212
Effective search space used: 277316212
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 (24.4 bits)