RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|254781148|ref|YP_003065561.1| hypothetical protein
CLIBASIA_05275 [Candidatus Liberibacter asiaticus str. psy62]
         (69 letters)



>gnl|CDD|144390 pfam00772, DnaB, DnaB-like helicase N terminal domain.  The
          hexameric helicase DnaB unwinds the DNA duplex at the
          Escherichia coli chromosome replication fork. Although
          the mechanism by which DnaB both couples ATP hydrolysis
          to translocation along DNA and denatures the duplex is
          unknown, a change in the quaternary structure of the
          protein involving dimerization of the N-terminal domain
          has been observed and may occur during the enzymatic
          cycle. This N-terminal domain is required both for
          interaction with other proteins in the primosome and
          for DnaB helicase activity.
          Length = 103

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 1/42 (2%)

Query: 21 IGLEQEILGSLLL-KGNLQPIISFLDAQHFIDPIHSEVFRAI 61
          I  EQ +LG+LLL    +  +   L  + F DP H  +F AI
Sbjct: 6  IEAEQAVLGALLLDPEAIDEVADILKPEDFYDPAHRLIFEAI 47


>gnl|CDD|30653 COG0305, DnaB, Replicative DNA helicase [DNA replication,
          recombination, and repair].
          Length = 435

 Score = 32.1 bits (73), Expect = 0.035
 Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 21 IGLEQEILGSLLLKGN-LQPIISFLDAQHFIDPIHSEVFRAITR 63
          I  EQ +LG +LL  + ++ +   L  + F  P H  +++AI  
Sbjct: 7  IEAEQAVLGGILLDPDAIERVSERLRPEDFYRPAHRLIYQAILD 50


>gnl|CDD|147709 pfam05704, Caps_synth, Capsular polysaccharide synthesis protein.
           This family consists of several capsular polysaccharide
           proteins. Capsular polysaccharide (CPS) is a major
           virulence factor in Streptococcus pneumoniae.
          Length = 279

 Score = 25.3 bits (56), Expect = 4.0
 Identities = 7/21 (33%), Positives = 12/21 (57%)

Query: 1   MLSDFSKKYYSRNNNSIYYFI 21
            L D   +Y+ + N+ I YF+
Sbjct: 183 FLRDLLLEYWKKYNSLIDYFL 203


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.323    0.140    0.403 

Gapped
Lambda     K      H
   0.267   0.0746    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 824,443
Number of extensions: 34860
Number of successful extensions: 98
Number of sequences better than 10.0: 1
Number of HSP's gapped: 97
Number of HSP's successfully gapped: 6
Length of query: 69
Length of database: 6,263,737
Length adjustment: 40
Effective length of query: 29
Effective length of database: 5,399,377
Effective search space: 156581933
Effective search space used: 156581933
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 (22.0 bits)
S2: 51 (23.4 bits)