RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5915
         (89 letters)



>gnl|CDD|224968 COG2057, AtoA, Acyl CoA:acetate/3-ketoacid CoA transferase, beta
           subunit [Lipid metabolism].
          Length = 225

 Score = 40.0 bits (94), Expect = 3e-05
 Identities = 15/42 (35%), Positives = 25/42 (59%)

Query: 43  CVFEVDKERGLTLIEIAEGVEVPEIIVSTGCDFAVSPDLKPM 84
            VFE D    LTL+E+A GV + +++  TG +F V+  ++  
Sbjct: 179 AVFEFDPGGELTLVELAPGVTIEDVVEKTGAEFKVADAVEET 220


>gnl|CDD|188219 TIGR02428, pcaJ_scoB_fam, 3-oxoacid CoA-transferase, B subunit.
           Various members of this family are characterized as the
           B subunits of succinyl-CoA:3-ketoacid-CoA transferase
           (EC 2.8.3.5), beta-ketoadipate:succinyl-CoA transferase
           (EC 2.8.3.6), acetyl-CoA:acetoacetate CoA transferase
           (EC 2.8.3.8), and butyrate-acetoacetate CoA-transferase
           (EC 2.8.3.9). This represents a very distinct clade with
           strong sequence conservation within the larger family
           defined by pfam01144. The A subunit represents a
           different clade in pfam01144.
          Length = 207

 Score = 37.3 bits (87), Expect = 3e-04
 Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 3/52 (5%)

Query: 28  RLGLTALS--SDVLSRDCVFEVDKERGLTLIEIAEGVEVPEIIVSTGCDFAV 77
            L LT       +++   VFEV    GL L E+A GV V E+   T  D  +
Sbjct: 157 TLPLTGAKCVDRIVTELAVFEVTDG-GLILRELAPGVTVEELQAKTEADLII 207


>gnl|CDD|227016 COG4670, COG4670, Acyl CoA:acetate/3-ketoacid CoA transferase
           [Lipid metabolism].
          Length = 527

 Score = 34.6 bits (80), Expect = 0.002
 Identities = 18/44 (40%), Positives = 27/44 (61%), Gaps = 4/44 (9%)

Query: 43  CVFEVDKERGLTLIEIAEGVEVPEIIVSTGCDF--AVSPDLKPM 84
            VF++    GLTLIEIA GV++ + I+    +F   ++ DLK M
Sbjct: 464 AVFKL-TPDGLTLIEIAPGVDLEKDILDQ-MEFEPIIADDLKEM 505


>gnl|CDD|227655 COG5352, COG5352, Uncharacterized protein conserved in bacteria
          [Function unknown].
          Length = 169

 Score = 28.4 bits (63), Expect = 0.33
 Identities = 12/29 (41%), Positives = 16/29 (55%)

Query: 10 SNPRPSAYKADALPTKPTRLGLTALSSDV 38
          S PR     A ++   PTR G TAL ++V
Sbjct: 63 SAPRAPVRAAQSVRHTPTRTGATALQAEV 91


>gnl|CDD|215835 pfam00278, Orn_DAP_Arg_deC, Pyridoxal-dependent decarboxylase,
          C-terminal sheet domain.  These pyridoxal-dependent
          decarboxylases act on ornithine, lysine, arginine and
          related substrates.
          Length = 110

 Score = 26.5 bits (59), Expect = 1.2
 Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 11/57 (19%)

Query: 7  GRESNPRPSAY----------KADALPTKPTRL-GLTALSSDVLSRDCVFEVDKERG 52
          G   +P P+ Y          + D  P +P  L G T  S DVL+RD    ++ E G
Sbjct: 24 GVYGSPDPALYDALHPILPVSRLDDEPLRPYTLAGPTCDSGDVLARDVSLPLELEVG 80


>gnl|CDD|151748 pfam11307, DUF3109, Protein of unknown function (DUF3109).  This
           bacterial family of proteins has no known function.
          Length = 183

 Score = 25.6 bits (57), Expect = 3.5
 Identities = 12/22 (54%), Positives = 13/22 (59%), Gaps = 2/22 (9%)

Query: 40  SRDCVFEVDKERGLTL--IEIA 59
            R+CVF    E G TL  IEIA
Sbjct: 87  GRECVFVTYDEDGTTLCGIEIA 108


>gnl|CDD|214491 smart00052, EAL, Putative diguanylate phosphodiesterase.  Putative
           diguanylate phosphodiesterase, present in a variety of
           bacteria.
          Length = 242

 Score = 25.3 bits (56), Expect = 4.1
 Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 3/29 (10%)

Query: 51  RGLTLIEIAEGVEVPE---IIVSTGCDFA 76
           + L L  +AEGVE PE   ++ S GCD+ 
Sbjct: 201 QKLGLQVVAEGVETPEQLDLLRSLGCDYG 229


>gnl|CDD|224684 COG1770, PtrB, Protease II [Amino acid transport and metabolism].
          Length = 682

 Score = 24.6 bits (54), Expect = 8.5
 Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 2/64 (3%)

Query: 21  ALPTKPTRLGLTALSSDVLSRDCVFEVDKERGLTLI--EIAEGVEVPEIIVSTGCDFAVS 78
           A       LG  ++S D        +V  +   TL   ++A G E+P+ I +T   FA +
Sbjct: 123 AEGHDFFSLGAASISPDHNLLAYSVDVLGDEQYTLRFKDLATGEELPDEITNTSGSFAWA 182

Query: 79  PDLK 82
            D K
Sbjct: 183 ADGK 186


  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
   0.314    0.134    0.382 

Gapped
Lambda     K      H
   0.267   0.0778    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,482,278
Number of extensions: 355823
Number of successful extensions: 255
Number of sequences better than 10.0: 1
Number of HSP's gapped: 255
Number of HSP's successfully gapped: 13
Length of query: 89
Length of database: 10,937,602
Length adjustment: 57
Effective length of query: 32
Effective length of database: 8,409,424
Effective search space: 269101568
Effective search space used: 269101568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.1 bits)