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)