RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy17083
         (60 letters)



>gnl|CDD|178528 PLN02940, PLN02940, riboflavin kinase.
          Length = 382

 Score = 26.7 bits (59), Expect = 0.64
 Identities = 9/22 (40%), Positives = 11/22 (50%)

Query: 2   SNRLGRNIRASVQCRPGWRGEF 23
           SN    NI A + C  GW+  F
Sbjct: 116 SNSPRANIEAKISCHQGWKESF 137


>gnl|CDD|176473 cd06444, DNA_pol_A, Family A polymerase primarily fills DNA gaps
           that arise during DNA repair, recombination and
           replication.  DNA polymerase family A, 5'-3' polymerase
           domain. Family A polymerase functions primarily to fill
           DNA gaps that arise during DNA repair, recombination and
           replication. DNA-dependent DNA polymerases can be
           classified into six main groups based upon phylogenetic
           relationships with E. coli polymerase I (classA), E.
           coli polymerase II (class B), E.coli polymerase III
           (class C), euryarchaeota polymerase II (class D), human
           polymerase  beta (class X), E. coli UmuC/DinB and
           eukaryotic RAP 30/Xeroderma pigmentosum variant (class
           Y). Family A polymerases are found primarily in
           organisms related to prokaryotes and include prokaryotic
           DNA polymerase I, mitochondrial polymerase gamma, and
           several bacteriophage polymerases including those from
           odd-numbered phage (T3, T5, and T7). Prokaryotic
           polymerase I (pol I) has two functional domains located
           on the same polypeptide; a 5'-3' polymerase and a 5'-3'
           exonuclease. Pol I uses its 5' nuclease activity to
           remove the ribonucleotide portion of newly synthesized
           Okazaki fragments and the DNA polymerase activity to
           fill in the resulting gap. The structure of these
           polymerases resembles in overall morphology a cupped
           human right hand, with fingers (which bind an incoming
           nucleotide and interact with the single-stranded
           template), palm (which harbors the catalytic amino acid
           residues and also binds an incoming dNTP) and thumb
           (which binds double-stranded DNA) subdomains.
          Length = 347

 Score = 26.6 bits (59), Expect = 0.65
 Identities = 8/19 (42%), Positives = 11/19 (57%)

Query: 2   SNRLGRNIRASVQCRPGWR 20
            + LGR+IR +    PGW 
Sbjct: 86  RDPLGRDIRQAFVADPGWT 104


>gnl|CDD|201250 pfam00476, DNA_pol_A, DNA polymerase family A. 
          Length = 383

 Score = 26.2 bits (58), Expect = 0.83
 Identities = 8/18 (44%), Positives = 10/18 (55%)

Query: 2   SNRLGRNIRASVQCRPGW 19
            N  GR IRA+    PG+
Sbjct: 138 RNEYGREIRAAFIAEPGY 155


>gnl|CDD|161718 TIGR00120, ArgJ, glutamate N-acetyltransferase/amino-acid
           acetyltransferase.  This enzyme can acetylate Glu to
           N-acetyl-Glu by deacetylating N-2-acetyl-ornithine into
           ornithine; the two halves of this reaction represent the
           first and fifth steps in the synthesis of Arg (or
           citrulline) from Glu by way of ornithine (EC 2.3.1.35).
           In Bacillus stearothermophilus, but not in Thermus
           thermophilus HB27, the enzyme is bifunctional and can
           also use acetyl-CoA to acetylate Glu (EC 2.3.1.1) [Amino
           acid biosynthesis, Glutamate family].
          Length = 404

 Score = 25.9 bits (57), Expect = 1.1
 Identities = 6/14 (42%), Positives = 8/14 (57%)

Query: 47  CDTNWGGILCDQGH 60
            D NWG I+   G+
Sbjct: 310 QDPNWGRIIAAAGY 323


>gnl|CDD|216811 pfam01960, ArgJ, ArgJ family.  Members of the ArgJ family catalyze
           the first EC:2.3.1.1 and fifth steps EC:2.3.1.35 in
           arginine biosynthesis.
          Length = 380

 Score = 25.1 bits (56), Expect = 2.0
 Identities = 6/10 (60%), Positives = 6/10 (60%)

Query: 47  CDTNWGGILC 56
            D NWG IL 
Sbjct: 292 EDPNWGRILA 301


>gnl|CDD|219674 pfam07971, Glyco_hydro_92, Glycosyl hydrolase family 92.  Members
           of this family are alpha-1,2-mannosidases, enzymes which
           remove alpha-1,2-linked mannose residues from
           Man(9)(GlcNAc)(2) by hydrolysis. They are critical for
           the maturation of N-linked oligosaccharides and
           ER-associated degradation.
          Length = 497

 Score = 24.8 bits (55), Expect = 2.5
 Identities = 5/24 (20%), Positives = 10/24 (41%), Gaps = 2/24 (8%)

Query: 21  GEFCDQCKPYPGCKHGYCNGSSWQ 44
           G + +   P       +  G++WQ
Sbjct: 285 GSWREPFDPL--SGDDFTEGNAWQ 306


  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
   0.325    0.144    0.569 

Gapped
Lambda     K      H
   0.267   0.0653    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 2,752,460
Number of extensions: 161078
Number of successful extensions: 226
Number of sequences better than 10.0: 1
Number of HSP's gapped: 225
Number of HSP's successfully gapped: 23
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 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.4 bits)