RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13017
         (74 letters)



>gnl|CDD|216769 pfam01894, UPF0047, Uncharacterized protein family UPF0047.  This
           family has no known function. The alignment contains a
           conserved aspartate and histidine that may be
           functionally important.
          Length = 118

 Score = 83.3 bits (207), Expect = 8e-23
 Identities = 26/49 (53%), Positives = 37/49 (75%), Gaps = 1/49 (2%)

Query: 4   PAHVKACFLGSSLTIPISDGKLNLGMWQGIWLCEHRDQAGSRKLVVTLN 52
           PAH+K+  LG SLT+P+++G+L LG WQGI+LCE      SR++VVT+ 
Sbjct: 71  PAHLKSSLLGPSLTVPVTNGRLALGTWQGIYLCEFDG-PRSRRVVVTIL 118


>gnl|CDD|223509 COG0432, COG0432, Uncharacterized conserved protein [Function
           unknown].
          Length = 137

 Score = 80.3 bits (199), Expect = 2e-21
 Identities = 26/50 (52%), Positives = 34/50 (68%)

Query: 4   PAHVKACFLGSSLTIPISDGKLNLGMWQGIWLCEHRDQAGSRKLVVTLNG 53
           PAH+KA  LG SLTIP+ +G+L LG WQGI+L E       R++VV + G
Sbjct: 88  PAHLKASLLGPSLTIPVINGRLVLGTWQGIFLVEFDGPRHRRRVVVKIIG 137


>gnl|CDD|129253 TIGR00149, TIGR00149_YjbQ, secondary thiamine-phosphate synthase
           enzyme.  Members of this protein family have been
           studied extensively by crystallography. Members from
           several different species have been shown to have
           sufficient thiamin phosphate synthase activity (EC
           2.5.1.3) to complement thiE mutants. However, it is
           presumed that this is a secondary activity, and the
           primary function of this enzyme remains unknown [Unknown
           function, Enzymes of unknown specificity].
          Length = 132

 Score = 65.9 bits (161), Expect = 8e-16
 Identities = 20/50 (40%), Positives = 33/50 (66%), Gaps = 1/50 (2%)

Query: 4   PAHVKACFLGSSLTIPISDGKLNLGMWQGIWLCEHRDQAGSRKLVVTLNG 53
            AH+K+  LG+S  +P+ +G+L LG WQGI+  E  D   +R+++V + G
Sbjct: 83  DAHIKSSLLGTSQHVPVENGRLQLGTWQGIFFAEF-DGPRTRRIIVKVQG 131


>gnl|CDD|200456 cd11317, AmyAc_bac_euk_AmyA, Alpha amylase catalytic domain found
           in bacterial and eukaryotic Alpha amylases (also called
           1,4-alpha-D-glucan-4-glucanohydrolase).  AmyA (EC
           3.2.1.1) catalyzes the hydrolysis of alpha-(1,4)
           glycosidic linkages of glycogen, starch, related
           polysaccharides, and some oligosaccharides. This group
           includes AmyA proteins from bacteria, fungi, mammals,
           insects, mollusks, and nematodes. The Alpha-amylase
           family comprises the largest family of glycoside
           hydrolases (GH), with the majority of enzymes acting on
           starch, glycogen, and related oligo- and
           polysaccharides. These proteins catalyze the
           transformation of alpha-1,4 and alpha-1,6 glucosidic
           linkages with retention of the anomeric center. The
           protein is described as having 3 domains: A, B, C. A is
           a (beta/alpha) 8-barrel; B is a loop between the beta 3
           strand and alpha 3 helix of A; C is the C-terminal
           extension characterized by a Greek key. The majority of
           the enzymes have an active site cleft found between
           domains A and B where a triad of catalytic residues
           (Asp, Glu and Asp) performs catalysis. Other members of
           this family have lost the catalytic activity as in the
           case of the human 4F2hc, or only have 2 residues that
           serve as the catalytic nucleophile and the acid/base,
           such as Thermus A4 beta-galactosidase with 2 Glu
           residues (GH42) and human alpha-galactosidase with 2 Asp
           residues (GH31). The family members are quite extensive
           and include: alpha amylase, maltosyltransferase,
           cyclodextrin glycotransferase, maltogenic amylase,
           neopullulanase, isoamylase, 1,4-alpha-D-glucan
           maltotetrahydrolase, 4-alpha-glucotransferase,
           oligo-1,6-glucosidase, amylosucrase, sucrose
           phosphorylase, and amylomaltase.
          Length = 329

 Score = 25.2 bits (56), Expect = 3.0
 Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 4/30 (13%)

Query: 13  GSSLTIPISDGKLNLGMWQGIWLCEHRDQA 42
           G++L++ I+D     G   G W+CEHR  A
Sbjct: 293 GNTLSVTINDD----GTCGGGWVCEHRWPA 318


>gnl|CDD|131814 TIGR02767, TraG-Ti, Ti-type conjugative transfer system protein
           TraG.  This protein is found in the Agrobacterium
           tumefaciens Ti plasmid tra region responsible for
           conjugative transfer of the entire plasmid among
           Agrobacterium strains. The protein is distantly related
           to the F-type conjugation system TraG protein. Both of
           these systems are examples of type IV secretion systems.
          Length = 623

 Score = 24.8 bits (54), Expect = 5.4
 Identities = 10/15 (66%), Positives = 14/15 (93%)

Query: 35  LCEHRDQAGSRKLVV 49
           +CEHR QAG+RK++V
Sbjct: 253 VCEHRRQAGNRKVIV 267


  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
   0.317    0.133    0.413 

Gapped
Lambda     K      H
   0.267   0.0855    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,519,311
Number of extensions: 248220
Number of successful extensions: 157
Number of sequences better than 10.0: 1
Number of HSP's gapped: 157
Number of HSP's successfully gapped: 5
Length of query: 74
Length of database: 10,937,602
Length adjustment: 44
Effective length of query: 30
Effective length of database: 8,986,026
Effective search space: 269580780
Effective search space used: 269580780
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.0 bits)