RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy9841
         (125 letters)



>gnl|CDD|217658 pfam03650, UPF0041, Uncharacterized protein family (UPF0041). 
          Length = 120

 Score =  116 bits (293), Expect = 5e-35
 Identities = 47/82 (57%), Positives = 58/82 (70%)

Query: 17 VPSKARPLWEHPAGPKTVFFWAPMFKWGLVIAGIGDLTRPAEKLSISQSSALAATGLIWS 76
            +  +  W H AGPKTV FWAP  KWGLV+AG+GDL RP EK+S  Q+SAL AT  IW+
Sbjct: 2  FRAAFKRFWNHEAGPKTVHFWAPTLKWGLVLAGLGDLKRPPEKISGPQNSALLATSAIWT 61

Query: 77 RYSLVIIPKNWSLFSVNMFVAL 98
          R+SLV+ PKN+ L SVN F+  
Sbjct: 62 RWSLVVKPKNYLLASVNFFLEC 83


>gnl|CDD|182544 PRK10555, PRK10555, aminoglycoside/multidrug efflux system;
           Provisional.
          Length = 1037

 Score = 27.1 bits (60), Expect = 3.2
 Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 8/65 (12%)

Query: 58  EKLSISQSSALAATGLIWSRYSLVIIPKNWSL-FSVNMFVALPCVKLELEDLGECLSNLL 116
           E+LS +Q+ AL A  L+     L  + ++WS+ FSV + V L         +G  L+  +
Sbjct: 864 ERLSGAQAPALYAISLLVVFLCLAALYESWSVPFSVMLVVPLGV-------IGALLATWM 916

Query: 117 AGIEN 121
            G+EN
Sbjct: 917 RGLEN 921


>gnl|CDD|185081 PRK15127, PRK15127, multidrug efflux system protein AcrB;
           Provisional.
          Length = 1049

 Score = 26.8 bits (59), Expect = 3.8
 Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 8/65 (12%)

Query: 58  EKLSISQSSALAATGLIWSRYSLVIIPKNWSL-FSVNMFVALPCVKLELEDLGECLSNLL 116
           E+LS +Q+ AL A  LI     L  + ++WS+ FSV + V L  +       G  L+   
Sbjct: 866 ERLSGNQAPALYAISLIVVFLCLAALYESWSIPFSVMLVVPLGVI-------GALLAATF 918

Query: 117 AGIEN 121
            G+ N
Sbjct: 919 RGLTN 923


>gnl|CDD|181674 PRK09148, PRK09148, aminotransferase; Validated.
          Length = 405

 Score = 26.6 bits (59), Expect = 4.7
 Identities = 10/27 (37%), Positives = 14/27 (51%)

Query: 14  DRFVPSKARPLWEHPAGPKTVFFWAPM 40
           D  V S  R  W+ P    ++F WAP+
Sbjct: 302 DVLVESFGRAGWDIPPPAASMFAWAPI 328


>gnl|CDD|226697 COG4246, COG4246, Uncharacterized protein conserved in bacteria
          [Function unknown].
          Length = 340

 Score = 26.0 bits (57), Expect = 6.9
 Identities = 16/46 (34%), Positives = 19/46 (41%)

Query: 2  ASAIYRAAISAVDRFVPSKARPLWEHPAGPKTVFFWAPMFKWGLVI 47
           +A  RA   A    VP K R +   P G  T  F    F  GLV+
Sbjct: 21 TAAAARAPPVAAAEPVPVKVRTITPFPVGTTTTLFGGLEFVGGLVM 66


>gnl|CDD|200489 cd11352, AmyAc_5, Alpha amylase catalytic domain found in an
          uncharacterized protein family.  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 = 443

 Score = 25.7 bits (57), Expect = 8.5
 Identities = 11/31 (35%), Positives = 11/31 (35%)

Query: 13 VDRFVPSKARPLWEHPAGPKTVFFWAPMFKW 43
          VDRF   K RP          V  W   F W
Sbjct: 7  VDRFSDGKERPRPLFDGNDPAVATWEDNFGW 37


>gnl|CDD|236425 PRK09240, thiH, thiamine biosynthesis protein ThiH; Reviewed.
          Length = 371

 Score = 25.5 bits (57), Expect = 9.2
 Identities = 5/11 (45%), Positives = 6/11 (54%)

Query: 27  HPAGPKTVFFW 37
           H  GPK  F +
Sbjct: 193 HLRGPKRDFEY 203


  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
   0.322    0.135    0.430 

Gapped
Lambda     K      H
   0.267   0.0575    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,314,392
Number of extensions: 539410
Number of successful extensions: 438
Number of sequences better than 10.0: 1
Number of HSP's gapped: 438
Number of HSP's successfully gapped: 20
Length of query: 125
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 40
Effective length of database: 7,167,512
Effective search space: 286700480
Effective search space used: 286700480
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: 53 (24.5 bits)