RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3259
         (69 letters)



>gnl|CDD|215507 PLN02939, PLN02939, transferase, transferring glycosyl groups.
          Length = 977

 Score = 28.7 bits (64), Expect = 0.19
 Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 7/71 (9%)

Query: 2   SLLGFEPESFPDSPQHSLTVLLLGESGLVYCMEQIFLYGFKSS----RLFSRNLNI---W 54
           S+  F+ E+ P   ++  T L   E GL   +E+ F Y  +      +L  +++NI   W
Sbjct: 894 SVFDFDDETIPVELRNGFTFLTPDEQGLNSALERAFNYYKRKPEVWKQLVQKDMNIDFSW 953

Query: 55  DLFIKIYQEIF 65
           D     Y+E++
Sbjct: 954 DSSASQYEELY 964


>gnl|CDD|233958 TIGR02636, galM_Leloir, galactose mutarotase.  Members of this
           protein family act as galactose mutarotase (D-galactose
           1-epimerase) and participate in the Leloir pathway for
           galactose/glucose interconversion. All members of the
           seed alignment for this model are found in gene clusters
           with other enzymes of the Leloir pathway. This enzyme
           family belongs to the aldose 1-epimerase family,
           described by Pfam model pfam01263. However, the enzyme
           described as aldose 1-epimerase itself (EC 5.1.3.3) is
           called broadly specific for D-glucose, L-arabinose,
           D-xylose, D-galactose, maltose and lactose. The
           restricted genome context for genes in this family
           suggests members should act primarily on D-galactose.
          Length = 336

 Score = 25.0 bits (55), Expect = 3.7
 Identities = 6/14 (42%), Positives = 8/14 (57%)

Query: 4   LGFEPESFPDSPQH 17
           +  E +  PDSP H
Sbjct: 298 IALETQFLPDSPNH 311


>gnl|CDD|216115 pfam00780, CNH, CNH domain.  Domain found in NIK1-like kinase,
           mouse citron and yeast ROM1, ROM2. Unpublished
           observations.
          Length = 266

 Score = 24.5 bits (54), Expect = 4.3
 Identities = 6/36 (16%), Positives = 12/36 (33%)

Query: 1   MSLLGFEPESFPDSPQHSLTVLLLGESGLVYCMEQI 36
           + L     +S  D    SL      E+     + ++
Sbjct: 153 VDLDTGATQSLLDPADQSLDFAARKENLKPLAVVRL 188


>gnl|CDD|234013 TIGR02785, addA_Gpos, helicase-exonuclease AddAB, AddA subunit,
           Firmicutes type.  AddAB, also called RexAB, substitutes
           for RecBCD in several bacterial lineages. These DNA
           recombination proteins act before synapse and are
           particularly important for DNA repair of double-stranded
           breaks by homologous recombination. The term AddAB is
           used broadly, with AddA homologous between the
           Firmicutes (as modeled here) and the
           alphaproteobacteria, while the partner AddB proteins
           show no strong homology across the two groups of species
           [DNA metabolism, DNA replication, recombination, and
           repair].
          Length = 1230

 Score = 24.7 bits (54), Expect = 4.4
 Identities = 10/33 (30%), Positives = 17/33 (51%)

Query: 37  FLYGFKSSRLFSRNLNIWDLFIKIYQEIFSYTF 69
           FL   +  R F+R  ++ +L  KIY +   Y +
Sbjct: 688 FLDSLQKWREFARTHSVSELIWKIYNDTGYYDY 720


>gnl|CDD|182931 PRK11055, galM, galactose-1-epimerase; Provisional.
          Length = 342

 Score = 24.5 bits (54), Expect = 5.5
 Identities = 7/14 (50%), Positives = 8/14 (57%)

Query: 4   LGFEPESFPDSPQH 17
           L  E +  PDSP H
Sbjct: 302 LALESQFLPDSPNH 315


>gnl|CDD|182778 PRK10851, PRK10851, sulfate/thiosulfate transporter subunit;
           Provisional.
          Length = 353

 Score = 24.3 bits (53), Expect = 5.6
 Identities = 10/39 (25%), Positives = 22/39 (56%), Gaps = 1/39 (2%)

Query: 15  PQHSLTVLLLGESGLVYCMEQIFLYGFKSSRLFSRNLNI 53
               LTV++ G+       E++F+ G +++RL++ +  I
Sbjct: 316 YNEPLTVVMHGDIDAPQRGERLFV-GLQNARLYNGDERI 353


>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain. 
          Length = 168

 Score = 24.3 bits (54), Expect = 5.6
 Identities = 7/10 (70%), Positives = 8/10 (80%)

Query: 19 LTVLLLGESG 28
           TVL+ GESG
Sbjct: 23 ATVLITGESG 32


>gnl|CDD|215384 PLN02724, PLN02724, Molybdenum cofactor sulfurase.
          Length = 805

 Score = 24.4 bits (53), Expect = 6.7
 Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 2/38 (5%)

Query: 19  LTVLLLGESGLVYCMEQIFLYGFKSSRLFSRNLNIWDL 56
           L VL   ES   + ++ I +Y  KS   FS  +  W L
Sbjct: 506 LPVLERKESFDSHRLKSITVYPIKSCAGFS--VERWPL 541


>gnl|CDD|185710 cd07900, Adenylation_DNA_ligase_I_Euk, Adenylation domain of
          eukaryotic DNA Ligase I.  ATP-dependent polynucleotide
          ligases catalyze phosphodiester bond formation using
          nicked nucleic acid substrates with the high energy
          nucleotide of ATP as a cofactor in a three step
          reaction mechanism. DNA ligases play a vital role in
          the diverse processes of DNA replication, recombination
          and repair. ATP-dependent ligases are present in many
          organisms such as viruses, bacteriophages, eukarya,
          archaea and bacteria. Some organisms express a variety
          of different ligases which appear to be targeted to
          specific functions. There are three classes of
          ATP-dependent DNA ligases in eukaryotic cells (I, III
          and IV). DNA ligase I is required for the ligation of
          Okazaki fragments during lagging-strand DNA synthesis
          and for base excision repair (BER). DNA ligases have a
          highly modular architecture consisting of a unique
          arrangement of two or more discrete domains. The
          adenylation and C-terminal
          oligonucleotide/oligosaccharide binding (OB)-fold
          domains comprise a catalytic core unit that is common
          to most members of the ATP-dependent DNA ligase family.
          The adenylation domain binds ATP and contains many of
          the active-site residues. DNA ligase I is the main
          replicative ligase in eukaryotes. The common catalytic
          core unit comprises six conserved sequence motifs (I,
          III, IIIa, IV, V and VI) that define this family of
          related nucleotidyltransferases.
          Length = 219

 Score = 24.1 bits (53), Expect = 7.8
 Identities = 8/17 (47%), Positives = 10/17 (58%)

Query: 35 QIFLYGFKSSRLFSRNL 51
          QI L      ++FSRNL
Sbjct: 45 QIHLLEDGKVKIFSRNL 61


  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
   0.328    0.144    0.442 

Gapped
Lambda     K      H
   0.267   0.0765    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,536,987
Number of extensions: 264289
Number of successful extensions: 282
Number of sequences better than 10.0: 1
Number of HSP's gapped: 282
Number of HSP's successfully gapped: 12
Length of query: 69
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 30
Effective length of database: 9,207,796
Effective search space: 276233880
Effective search space used: 276233880
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 (24.1 bits)