RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy17867
         (81 letters)



>gnl|CDD|198369 cd07798, FGGY_AI-2K_like, Autoinducer-2 kinase-like proteins;
           belongs to the FGGY family of carbohydrate kinases.
           This subgroup consists of uncharacterized hypothetical
           bacterial proteins with similarity to bacterial
           autoinducer-2 (AI-2) kinases, which catalyzes the
           phosphorylation of intracellular AI-2 to phospho-AI-2,
           leading to the inactivation of lsrR, the repressor of
           the lsr operon. Members of this subgroup belong to the
           FGGY family of carbohydrate kinases, the monomers of
           which contain two large domains, which are separated by
           a deep cleft that forms the active site. This model
           includes both the N-terminal domain, which adopts a
           ribonuclease H-like fold, and the structurally related
           C-terminal domain.
          Length = 437

 Score = 26.8 bits (59), Expect = 1.1
 Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 6/62 (9%)

Query: 15  NPNTGIGAFRFMLETNKGRTMLEFQELMTVFQLLHWNGSLKAMRERQCSRQEVVAHYSNR 74
           N +TG G   +++ETN G T L +Q+L  +F   + N S + M E + ++ +   H    
Sbjct: 277 NCHTGGG--TWLVETNPGVTGLNYQKLKAIF---YPNESYEVM-EEEIAKLQKTDHACTA 330

Query: 75  AL 76
           AL
Sbjct: 331 AL 332


>gnl|CDD|129243 TIGR00137, gid_trmFO, tRNA:m(5)U-54 methyltransferase.  This model
           represents an orthologous set of proteins present in
           relatively few bacteria but very tightly conserved where
           it occurs. It is closely related to gidA
           (glucose-inhibited division protein A), which appears to
           be present in all complete eubacterial genomes so far
           and in Saccharomyces cerevisiae. It was designated gid
           but is now recognized as a tRNA:m(5)U-54
           methyltransferase and is now designated trmFO [Protein
           synthesis, tRNA and rRNA base modification].
          Length = 433

 Score = 25.6 bits (56), Expect = 3.1
 Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 11/75 (14%)

Query: 5   LLQGEPEEADNPNTGIGA-FRFMLETNKGRTMLEFQELMTVFQLLHWNGSLKAMRERQCS 63
           L  GEP       T +GA F ++   +       FQ +   F      G L  + ++  +
Sbjct: 361 LALGEPLLTLPAETMMGALFNYISTASPK----HFQPMNPNF------GLLPELPQKIRN 410

Query: 64  RQEVVAHYSNRALDD 78
           ++E    Y++RAL+ 
Sbjct: 411 KKERYEQYADRALET 425


>gnl|CDD|235763 PRK06270, PRK06270, homoserine dehydrogenase; Provisional.
          Length = 341

 Score = 25.2 bits (56), Expect = 4.7
 Identities = 10/40 (25%), Positives = 15/40 (37%), Gaps = 10/40 (25%)

Query: 15  NPNTGIGAFRFMLE----------TNKGRTMLEFQELMTV 44
           N  TG  A     +          +NKG   L ++EL  +
Sbjct: 100 NIETGEPALSHCRKALERGKHVVTSNKGPLALAYKELKEL 139


>gnl|CDD|184208 PRK13649, cbiO, cobalt transporter ATP-binding subunit;
           Provisional.
          Length = 280

 Score = 25.1 bits (55), Expect = 5.2
 Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 5/22 (22%)

Query: 31  KGRTMLEFQELMTVFQLLHWNG 52
           KGR     +ELMT+F+ LH +G
Sbjct: 179 KGR-----KELMTLFKKLHQSG 195


  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    0.134    0.396 

Gapped
Lambda     K      H
   0.267   0.0718    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,128,772
Number of extensions: 314869
Number of successful extensions: 175
Number of sequences better than 10.0: 1
Number of HSP's gapped: 175
Number of HSP's successfully gapped: 6
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
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 (24.2 bits)