RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780737|ref|YP_003065150.1| hypothetical protein
CLIBASIA_03120 [Candidatus Liberibacter asiaticus str. psy62]
         (60 letters)



>gnl|CDD|36641 KOG1428, KOG1428, KOG1428, Inhibitor of type V adenylyl
            cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1
            [Signal transduction mechanisms].
          Length = 3738

 Score = 27.4 bits (60), Expect = 0.99
 Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 3/51 (5%)

Query: 11   SFFMITHSYYAFSQDEIKKNNPTLEKKPIV---LMKHEIQEKKTLAAFTSF 58
            S  + + +       ++  +  T E+ P++   L+KH   EK+TLA+ TSF
Sbjct: 1397 SAIIGSLAKIERFAHQLLCSTTTTERFPMLSSLLLKHFNCEKETLASLTSF 1447


>gnl|CDD|145855 pfam02919, Topoisom_I_N, Eukaryotic DNA topoisomerase I, DNA
           binding fragment.  Topoisomerase I promotes the
           relaxation of DNA superhelical tension by introducing a
           transient single-stranded break in duplex DNA and are
           vital for the processes of replication, transcription,
           and recombination. This family may be more than one
           structural domain.
          Length = 215

 Score = 24.5 bits (54), Expect = 7.4
 Identities = 10/37 (27%), Positives = 18/37 (48%), Gaps = 1/37 (2%)

Query: 13  FMITHSYYAFSQDEIKKNNPTLEKKPIVLMKHEIQEK 49
           F   + Y+  ++ E KK     EKK +   K +++E 
Sbjct: 88  FTPIYEYFE-AEKEKKKAMSKEEKKALKEEKDKLEEP 123


>gnl|CDD|48064 cd00660, Topoisomer_IB_N, Topoisomer_IB_N: N-terminal DNA binding
           fragment found in eukaryotic DNA topoisomerase (topo) IB
           proteins similar to the monomeric yeast and human topo I
           and heterodimeric topo I from Leishmania donvanni. Topo
           I enzymes are divided into:  topo type IA (bacterial)
           and type IB (eukaryotic). Topo I relaxes superhelical
           tension in duplex DNA by creating a single-strand nick,
           the broken strand can then rotate around the unbroken
           strand to remove DNA supercoils and, the nick is
           religated, liberating topo I. These enzymes regulate the
           topological changes that accompany DNA replication,
           transcription and other nuclear processes.  Human topo I
           is the target of a diverse set of anticancer drugs
           including camptothecins (CPTs). CPTs bind to the topo
           I-DNA complex and inhibit re-ligation of the
           single-strand nick, resulting in the accumulation of
           topo I-DNA adducts.  In addition to differences in
           structure and some biochemical properties,
           Trypanosomatid parasite topo I differ from human topo I
           in their sensitivity to CPTs and other classical topo I
           inhibitors. Trypanosomatid topos I play putative roles
           in organizing the kinetoplast DNA network unique to
           these parasites.  This family may represent more than
           one structural domain..
          Length = 215

 Score = 24.4 bits (53), Expect = 7.7
 Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 1/37 (2%)

Query: 13  FMITHSYYAFSQDEIKKNNPTLEKKPIVLMKHEIQEK 49
           F   + Y+   + E KK     EKK I   K +++E 
Sbjct: 87  FTPIYQYFE-EEKEKKKAMSKEEKKAIKEEKEKLEEP 122


  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
   0.321    0.128    0.345 

Gapped
Lambda     K      H
   0.267   0.0810    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 663,418
Number of extensions: 24168
Number of successful extensions: 57
Number of sequences better than 10.0: 1
Number of HSP's gapped: 57
Number of HSP's successfully gapped: 5
Length of query: 60
Length of database: 6,263,737
Length adjustment: 32
Effective length of query: 28
Effective length of database: 5,572,249
Effective search space: 156022972
Effective search space used: 156022972
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (23.3 bits)