RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12593
         (122 letters)



>gnl|CDD|216332 pfam01151, ELO, GNS1/SUR4 family.  Members of this family are
           involved in long chain fatty acid elongation systems
           that produce the 26-carbon precursors for ceramide and
           sphingolipid synthesis. Predicted to be integral
           membrane proteins, in eukaryotes they are probably
           located on the endoplasmic reticulum. Yeast ELO3 affects
           plasma membrane H+-ATPase activity, and may act on a
           glucose-signaling pathway that controls the expression
           of several genes that are transcriptionally regulated by
           glucose such as PMA1.
          Length = 244

 Score = 64.6 bits (158), Expect = 1e-13
 Identities = 25/57 (43%), Positives = 35/57 (61%), Gaps = 1/57 (1%)

Query: 66  FLMSGPLPTVCICLSYAFIVKIVGPKLMEDRKPFQLRKTLIVYNFLQVLFSSWLFYE 122
            L+S P P + I + Y   V + GPK+M +RKPF L++ LIV+N   VL S + FY 
Sbjct: 1   PLLSSPWPVILIIVLYLVFVFL-GPKIMRNRKPFDLKRLLIVHNLFLVLLSLYGFYG 56


>gnl|CDD|107267 cd06272, PBP1_hexuronate_repressor_like, Ligand-binding domain of
           DNA transcription repressor for the hexuronate
           utilization operon from Bacillus species and its close
           homologs from other bacteria, all of which are a member
           of the LacI-GalR family of bacterial transcription
           regulators.  Ligand-binding domain of DNA transcription
           repressor for the hexuronate utilization operon from
           Bacillus species and its close homologs from other
           bacteria, all of which are a member of the LacI-GalR
           family of bacterial transcription regulators. The
           LacI-GalR family repressors are composed of two
           functional domains: an N-terminal HTH (helix-turn-helix)
           domain, which is responsible for the DNA-binding
           specificity, and a C-terminal ligand-binding domain,
           which is homologous to the sugar-binding domain of
           ABC-type transport systems that contain the type I
           periplasmic binding protein-like fold. As also observed
           in the periplasmic binding proteins, the C-terminal
           domain of the bacterial transcription repressor
           undergoes a conformational change upon ligand binding
           which in turn changes the DNA binding affinity of the
           repressor.
          Length = 261

 Score = 26.9 bits (60), Expect = 2.4
 Identities = 14/52 (26%), Positives = 19/52 (36%), Gaps = 9/52 (17%)

Query: 39  FKGILESVQDFYFDVMNNRSDPRVKDW---------FLMSGPLPTVCICLSY 81
           FKG LE+  +    + ++  D                L    LPT  IC SY
Sbjct: 130 FKGFLETCDENGISISDSHIDVDGLSAEGGDNAAKKLLKESDLPTAIICGSY 181


>gnl|CDD|215460 PLN02855, PLN02855, Bifunctional selenocysteine lyase/cysteine
           desulfurase.
          Length = 424

 Score = 26.6 bits (59), Expect = 3.5
 Identities = 12/31 (38%), Positives = 16/31 (51%)

Query: 16  EVLQDVFCAESTMATTPFPRSAGFKGILESV 46
           E++ DVF   ST A  P    AG   I E++
Sbjct: 263 EMISDVFLDHSTYAPPPSRFEAGTPAIGEAI 293


>gnl|CDD|129983 TIGR00905, 2A0302, transporter, basic amino acid/polyamine
           antiporter (APA) family.  This family includes several
           families of antiporters that, rather commonly, are
           encoded next to decarboxylases that convert one of the
           antiporter substrates into the other. This arrangement
           allows a cycle that can remove proteins from the
           cytoplasm and thereby protect against acidic conditions
           [Transport and binding proteins, Amino acids, peptides
           and amines].
          Length = 473

 Score = 26.2 bits (58), Expect = 4.9
 Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 4/47 (8%)

Query: 75  VCICLSYAFIVKIVGPKLMEDRKPFQLRKTLIVYNFLQVLFSSWLFY 121
           V   LS A+++K+         K    RK LIV   +  ++S WL Y
Sbjct: 369 VPYLLSAAYLLKLAKVGTYPKIKN---RKALIV-GVIACVYSIWLLY 411


>gnl|CDD|236269 PRK08462, PRK08462, biotin carboxylase; Validated.
          Length = 445

 Score = 25.9 bits (57), Expect = 6.0
 Identities = 12/23 (52%), Positives = 15/23 (65%), Gaps = 1/23 (4%)

Query: 36  SAG-FKGILESVQDFYFDVMNNR 57
            AG F+ +L+S  DFYF  MN R
Sbjct: 272 GAGTFEFLLDSNLDFYFMEMNTR 294


>gnl|CDD|234415 TIGR03955, rSAM_HydG, [FeFe] hydrogenase H-cluster radical SAM
           maturase HydG.  This model describes the radical SAM
           protein HydG. It is part of an enzyme metallocenter
           maturation system, working together with GTP-binding
           protein HydF and another radical SAM enzyme, HydE, in
           H-cluster maturation in [FeFe] hydrogenases [Protein
           fate, Protein modification and repair].
          Length = 471

 Score = 25.8 bits (57), Expect = 6.7
 Identities = 10/26 (38%), Positives = 16/26 (61%)

Query: 51  FDVMNNRSDPRVKDWFLMSGPLPTVC 76
           FDV +NR+   V +W +  G +P+ C
Sbjct: 360 FDVSDNRTLDEVVNWLMDLGYIPSFC 385


  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    0.141    0.460 

Gapped
Lambda     K      H
   0.267   0.0713    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,209,696
Number of extensions: 513798
Number of successful extensions: 501
Number of sequences better than 10.0: 1
Number of HSP's gapped: 500
Number of HSP's successfully gapped: 12
Length of query: 122
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 38
Effective length of database: 7,211,866
Effective search space: 274050908
Effective search space used: 274050908
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 (21.8 bits)
S2: 53 (24.2 bits)