RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12811
         (74 letters)



>gnl|CDD|162300 TIGR01317, GOGAT_sm_gam, glutamate synthases, NADH/NADPH, small
           subunit.  This model represents one of three built for
           the NADPH-dependent or NADH-dependent glutamate synthase
           (EC 1.4.1.13 and 1.4.1.14, respectively) small subunit
           or homologous region. TIGR01316 describes a family in
           several archaeal and deeply branched bacterial lineages
           of a homotetrameric form for which there is no large
           subunit. Another model describes glutamate synthase
           small subunit from gamma and some alpha subdivision
           Proteobacteria plus paralogs of unknown function. This
           model describes the small subunit, or homologous region
           of longer forms proteins, of eukaryotes, Gram-positive
           bacteria, cyanobacteria, and some other lineages. All
           members with known function participate in NADH or
           NADPH-dependent reactions to interconvert between
           glutamine plus 2-oxoglutarate and two molecules of
           glutamate.
          Length = 485

 Score = 83.0 bits (205), Expect = 1e-20
 Identities = 27/53 (50%), Positives = 38/53 (71%)

Query: 5   GAQSIVSFEILPQPNPKRSQDNPWPQFPRILKVDYGHEEVKVKHNHDPREFCI 57
           GA S+  FEI+P+P   R++DNPWP++PR+ +VDY HEE    +  DPRE+ I
Sbjct: 306 GAASVHQFEIMPKPPEARAKDNPWPEWPRVYRVDYAHEEAAAHYGRDPREYSI 358


>gnl|CDD|237213 PRK12810, gltD, glutamate synthase subunit beta; Reviewed.
          Length = 471

 Score = 60.2 bits (147), Expect = 1e-12
 Identities = 21/52 (40%), Positives = 34/52 (65%), Gaps = 1/52 (1%)

Query: 5   GAQSIVSFEILPQPNPKRSQDNPWPQFPRILKVDYGHEE-VKVKHNHDPREF 55
           GA+S+   +I+P P  +R+++NPWP +P  L+V   HEE V+ + N   +EF
Sbjct: 304 GAKSVTQRDIMPMPPSRRNKNNPWPYWPMKLEVSNAHEEGVEREFNVQTKEF 355


>gnl|CDD|223567 COG0493, GltD, NADPH-dependent glutamate synthase beta chain and
           related oxidoreductases [Amino acid transport and
           metabolism / General function prediction only].
          Length = 457

 Score = 35.7 bits (83), Expect = 7e-04
 Identities = 14/66 (21%), Positives = 21/66 (31%), Gaps = 10/66 (15%)

Query: 1   MNLFGAQSIVSFEILPQPNPKRSQDNPWPQFPRILKVDYGHEEVKVKHNHDPREFCIFEL 60
               GA+S+  F        +  + N WP +   L+V    EE         R   +   
Sbjct: 281 ALRLGAKSVTCFY----REDRDDETNEWPTWAAQLEVRSAGEEG------VERLPFVQPK 330

Query: 61  RFPFEE 66
            F   E
Sbjct: 331 AFIGNE 336


>gnl|CDD|197271 cd09174, PLDc_Nuc_like_unchar2, Putative catalytic domain of
          uncharacterized hypothetical proteins closely related
          to Nuc, , an endonuclease from Salmonella typhimurium. 
          Putative catalytic domain of uncharacterized
          hypothetical proteins, which show high sequence
          homology to the endonuclease from Salmonella
          typhimurium and vertebrate phospholipase D6. Nuc and
          PLD6 belong to the phospholipase D (PLD) superfamily.
          They contain a short conserved sequence motif, the HKD
          motif (H-x-K-x(4)-D, where x represents any amino acid
          residue), which characterizes the PLD superfamily and
          is essential for catalysis. Nuc and PLD6 utilize a
          two-step mechanism to cleave phosphodiester bonds: Upon
          substrate binding, the bond is first attacked by a
          histidine residue from one HKD motif to form a covalent
          phosphohistidine intermediate, which is then hydrolyzed
          by water with the aid of a second histidine residue
          from the other HKD motif in the opposite subunit.
          However, proteins in this subfamily have two HKD
          motifs in a single polypeptide chain.
          Length = 136

 Score = 24.6 bits (54), Expect = 4.4
 Identities = 6/45 (13%), Positives = 16/45 (35%), Gaps = 6/45 (13%)

Query: 24 QDNPWPQFPRILKVDYGHEEVKVKHNHDPR------EFCIFELRF 62
           D+   +   ++  +   E  K+  N          +FC+ + + 
Sbjct: 54 NDDDINKKDVLILDEDSFEIYKLPGNGSRYGNLMHNKFCVIDFKT 98


>gnl|CDD|227946 COG5659, COG5659, FOG: Transposase [DNA replication, recombination,
           and repair].
          Length = 385

 Score = 24.4 bits (53), Expect = 6.2
 Identities = 10/37 (27%), Positives = 11/37 (29%), Gaps = 3/37 (8%)

Query: 18  PNPKRSQDNPWPQF---PRILKVDYGHEEVKVKHNHD 51
                   NPW      P   +   G E VK K   D
Sbjct: 225 GKTSPLPANPWIGRDRDPSAGRRLSGGEGVKGKRLED 261


  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
   0.323    0.142    0.487 

Gapped
Lambda     K      H
   0.267   0.0731    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,776,051
Number of extensions: 278116
Number of successful extensions: 170
Number of sequences better than 10.0: 1
Number of HSP's gapped: 170
Number of HSP's successfully gapped: 6
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 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.2 bits)