RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy678
         (60 letters)



>gnl|CDD|235427 PRK05354, PRK05354, arginine decarboxylase; Provisional.
          Length = 634

 Score = 25.8 bits (58), Expect = 1.1
 Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 7/44 (15%)

Query: 13  AAKLLEVVHDLF-------EEQTSIEQVVVKIMQRAQSLLKCEN 49
           A + LE    LF       +E+   EQ+   I ++ Q LL  +N
Sbjct: 400 AQQDLEEALTLFALGYLSLQERAWAEQLYWAICRKIQKLLDPKN 443


>gnl|CDD|137624 PRK09978, PRK09978, DNA-binding transcriptional regulator GadX;
           Provisional.
          Length = 274

 Score = 24.5 bits (53), Expect = 3.4
 Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 1/31 (3%)

Query: 23  LFEEQTSIEQVVVKI-MQRAQSLLKCENAAV 52
           L EE+TS  Q++ +  MQRA  L+     ++
Sbjct: 179 LREEETSYSQLLTECRMQRALQLIVIHGFSI 209


>gnl|CDD|221964 pfam13185, GAF_2, GAF domain. 
          Length = 105

 Score = 24.3 bits (53), Expect = 3.9
 Identities = 8/32 (25%), Positives = 16/32 (50%)

Query: 27 QTSIEQVVVKIMQRAQSLLKCENAAVLLIDES 58
            S+E+++  I++    L   E   + L+DE 
Sbjct: 1  ALSLEELLEAILEALLELTGSEAGFIGLVDED 32


>gnl|CDD|222174 pfam13492, GAF_3, GAF domain. 
          Length = 129

 Score = 23.5 bits (51), Expect = 6.4
 Identities = 6/29 (20%), Positives = 18/29 (62%)

Query: 29 SIEQVVVKIMQRAQSLLKCENAAVLLIDE 57
            ++++ ++++    +L  + AA+ L+DE
Sbjct: 1  DPDELLERLLELLAEILGADRAALYLLDE 29


>gnl|CDD|234013 TIGR02785, addA_Gpos, helicase-exonuclease AddAB, AddA subunit,
           Firmicutes type.  AddAB, also called RexAB, substitutes
           for RecBCD in several bacterial lineages. These DNA
           recombination proteins act before synapse and are
           particularly important for DNA repair of double-stranded
           breaks by homologous recombination. The term AddAB is
           used broadly, with AddA homologous between the
           Firmicutes (as modeled here) and the
           alphaproteobacteria, while the partner AddB proteins
           show no strong homology across the two groups of species
           [DNA metabolism, DNA replication, recombination, and
           repair].
          Length = 1230

 Score = 23.9 bits (52), Expect = 6.5
 Identities = 8/22 (36%), Positives = 12/22 (54%)

Query: 11  ENAAKLLEVVHDLFEEQTSIEQ 32
           E    + EV+ D+FEE+   E 
Sbjct: 125 EQLLLIKEVLDDVFEEEYYKED 146


>gnl|CDD|235845 PRK06647, PRK06647, DNA polymerase III subunits gamma and tau;
           Validated.
          Length = 563

 Score = 23.6 bits (51), Expect = 8.6
 Identities = 11/35 (31%), Positives = 21/35 (60%)

Query: 11  ENAAKLLEVVHDLFEEQTSIEQVVVKIMQRAQSLL 45
           E+A +LL V+  +F    S+EQ ++  ++  + LL
Sbjct: 259 EDAKELLCVLDSVFLSGVSVEQFLLDCIEFFRELL 293


  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
   0.316    0.126    0.317 

Gapped
Lambda     K      H
   0.267   0.0675    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 2,662,766
Number of extensions: 175551
Number of successful extensions: 200
Number of sequences better than 10.0: 1
Number of HSP's gapped: 200
Number of HSP's successfully gapped: 11
Length of query: 60
Length of database: 10,937,602
Length adjustment: 31
Effective length of query: 29
Effective length of database: 9,562,628
Effective search space: 277316212
Effective search space used: 277316212
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.3 bits)