RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780995|ref|YP_003065408.1|
Endonuclease/exonuclease/phosphatase [Candidatus Liberibacter
asiaticus str. psy62]
         (125 letters)



>gnl|CDD|140318 PTZ00297, PTZ00297, pantothenate kinase; Provisional.
          Length = 1452

 Score = 28.7 bits (64), Expect = 0.37
 Identities = 13/16 (81%), Positives = 13/16 (81%), Gaps = 2/16 (12%)

Query: 21  IPFVIAGDFNRKINSI 36
           IPFVIAGDFN  IN I
Sbjct: 196 IPFVIAGDFN--INGI 209


>gnl|CDD|185163 PRK15251, PRK15251, cytolethal distending toxin subunit CdtB;
           Provisional.
          Length = 271

 Score = 27.3 bits (61), Expect = 1.2
 Identities = 26/96 (27%), Positives = 40/96 (41%), Gaps = 18/96 (18%)

Query: 21  IPFVIAGDFNRKINSIGDTDDFWQKMDPDGL--LIRFPQEKESTCNVIKRNKSSLDYFVI 78
           I ++IAGDFNR  + +  T      +D + L   +      E T    +R+  +LDY V 
Sbjct: 185 INWMIAGDFNRSPDRLEST------LDTEHLRNRVNIVAPTEPT----QRSGGTLDYAVT 234

Query: 79  DRDNKNFLIDNSFSIVSYDQSDLDTRRSKL-STHCP 113
              N+ F      + +          RS+L S H P
Sbjct: 235 GNSNQTFGPPLLAASLMLAS-----LRSQLASDHFP 265


>gnl|CDD|177627 PHA03391, p47, viral transcription regulator p47; Provisional.
          Length = 395

 Score = 26.7 bits (60), Expect = 1.5
 Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 6/36 (16%)

Query: 65  VIKRNKSSLDYFV--IDRDN----KNFLIDNSFSIV 94
           +IKR+K S  Y V  +D +N    K  L D  F+++
Sbjct: 197 IIKRHKFSKKYIVLELDANNWTAIKELLQDEFFTVI 232


>gnl|CDD|162892 TIGR02504, NrdJ_Z, ribonucleoside-diphosphate reductase,
           adenosylcobalamin-dependent.  This model identifies
           genes in a wide range of deeply branching bacteria. All
           are structurally related to the class I (non-heme iron
           dependent) RNRs. In most species this gene is known as
           NrdJ, while in mycobacteria it is called NrdZ.
          Length = 586

 Score = 26.5 bits (59), Expect = 1.9
 Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 4/52 (7%)

Query: 29  FNRKINSIGDTDDFWQKMDPDGLL-IRFPQEKESTCNVIKRNKSSLDYFVID 79
           FN    S+G TD F + ++ D    +R P+  E    + + +  +  Y  + 
Sbjct: 183 FN---ISVGVTDAFMEAVEADEEYKLRNPRTGEEIEELAELDPKNKVYKEVP 231


>gnl|CDD|152552 pfam12117, DUF3580, Protein of unknown function (DUF3580).  This
          domain is found in viruses, and is about 120 amino
          acids in length. It is found in association with
          pfam01057.
          Length = 120

 Score = 24.9 bits (54), Expect = 5.5
 Identities = 10/35 (28%), Positives = 14/35 (40%), Gaps = 12/35 (34%)

Query: 7  EWLKKWADQKIKTGIPFVIAGDFNRKINSIGDTDD 41
          +W + WA+ KI+T             INS G    
Sbjct: 8  DWSENWAEPKIQTP------------INSPGSARS 30


>gnl|CDD|131789 TIGR02742, TrbC_Ftype, type-F conjugative transfer system pilin
          assembly protein TrbC.  This protein is an essential
          component of the F-type conjugative pilus assembly
          system for the transfer of plasmid DNA. The N-terminal
          portion of these proteins are heterogeneous and are not
          covered by this model.
          Length = 130

 Score = 24.7 bits (54), Expect = 6.2
 Identities = 11/32 (34%), Positives = 12/32 (37%), Gaps = 4/32 (12%)

Query: 9  LKKWADQKIKTGIPFVIAG----DFNRKINSI 36
          LK+  DQ    G P VI G     F      I
Sbjct: 14 LKQLLDQAEALGAPLVIRGLLDNGFKATATRI 45


>gnl|CDD|117424 pfam08857, ParBc_2, Putative ParB-like nuclease.  This domain is
           probably distantly related to pfam02195. Suggesting
           these uncharacterized proteins have a nuclease function.
          Length = 162

 Score = 24.5 bits (54), Expect = 6.6
 Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 5/45 (11%)

Query: 8   WLKKWADQKIKTGIPFVIAGDFNRKINSIGDTDDFWQKMDPDGLL 52
            L+   +  +   +P  +  D      S  D D FW KMD +G +
Sbjct: 64  LLRALLELGVGGTVPVTVVADL-----SDLDKDAFWNKMDNNGWV 103


>gnl|CDD|183921 PRK13255, PRK13255, thiopurine S-methyltransferase; Reviewed.
          Length = 218

 Score = 24.8 bits (55), Expect = 6.6
 Identities = 5/14 (35%), Positives = 8/14 (57%)

Query: 4  QQGEWLKKWADQKI 17
              W +KWA+ +I
Sbjct: 2  DPDFWHEKWAENQI 15


>gnl|CDD|180231 PRK05743, ileS, isoleucyl-tRNA synthetase; Reviewed.
          Length = 912

 Score = 24.7 bits (55), Expect = 6.7
 Identities = 4/11 (36%), Positives = 7/11 (63%)

Query: 7  EWLKKWADQKI 17
          E LK+W +  +
Sbjct: 27 EILKRWEENDL 37


>gnl|CDD|178689 PLN03144, PLN03144, Carbon catabolite repressor protein 4 homolog;
           Provisional.
          Length = 606

 Score = 24.7 bits (54), Expect = 7.3
 Identities = 6/10 (60%), Positives = 8/10 (80%)

Query: 21  IPFVIAGDFN 30
           IP ++ GDFN
Sbjct: 456 IPMLVCGDFN 465


>gnl|CDD|162079 TIGR00871, zwf, glucose-6-phosphate 1-dehydrogenase.  This is a
           well-studied enzyme family, with sequences available
           from well over 50 species. The trusted cutoff is set
           above the score for the Drosophila melanogaster CG7140
           gene product, a homolog of unknown function. G6PD
           homologs from the bacteria Aquifex aeolicus and
           Helicobacter pylori lack several motifs well conserved
           most other members, were omitted from the seed
           alignment, and score well below the trusted cutoff.
          Length = 482

 Score = 24.6 bits (54), Expect = 7.8
 Identities = 9/45 (20%), Positives = 15/45 (33%), Gaps = 6/45 (13%)

Query: 83  KNFLIDNSFSIVSYDQSDLDT------RRSKLSTHCPLTIEYDFE 121
           +N L+   F IV   + DL         R  +       I+   +
Sbjct: 28  RNGLLPPDFRIVGVARRDLSVEDFRKQVREAIIKFETEEIDEQLD 72


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.319    0.137    0.416 

Gapped
Lambda     K      H
   0.267   0.0690    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,035,932
Number of extensions: 115178
Number of successful extensions: 235
Number of sequences better than 10.0: 1
Number of HSP's gapped: 234
Number of HSP's successfully gapped: 25
Length of query: 125
Length of database: 5,994,473
Length adjustment: 82
Effective length of query: 43
Effective length of database: 4,222,617
Effective search space: 181572531
Effective search space used: 181572531
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 (21.7 bits)
S2: 51 (23.5 bits)