RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780743|ref|YP_003065156.1| putative uracil-DNA
glycosylase [Candidatus Liberibacter asiaticus str. psy62]
         (261 letters)



>gnl|CDD|129841 TIGR00758, UDG_fam4, uracil-DNA glycosylase, family 4.  This
           well-conserved family of proteins is about 200 residues
           in length and homologous to the N-terminus of the DNA
           polymerase of phage SPO1 of Bacillus subtilis. The
           member from Thermus thermophilus HB8 is known to act as
           uracil-DNA glycosylase, an enzyme of DNA base excision
           repair. Its appearance as a domain of phage DNA
           polymerases could be consistent with uracil-DNA
           glycosylase activity.
          Length = 173

 Score =  102 bits (255), Expect = 1e-22
 Identities = 43/156 (27%), Positives = 76/156 (48%), Gaps = 9/156 (5%)

Query: 109 DLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEIMRTQIHISMISPWHPPGNRNLSN 168
           ++M +G  P   ++  G+PF G+ G +LD+ML +I + R  ++I+ +    PP NR+ + 
Sbjct: 23  NIMFVGEAPGREEDRKGRPFVGRAGKLLDEMLAAIGLSRENVYITNVVKCRPPNNRDPTP 82

Query: 169 IEMEICRPIIMRQIELISPKILLFIGNKTKNFFFNNDAQKTYQNLGKWSNLCTPHSI--- 225
            E+E C P +++QIELI PK+++ +G                  + K       +     
Sbjct: 83  EEVEACAPYLVKQIELIRPKVIICLGRTAAQSILG-----KNDGITKIRGRVFEYRYIGT 137

Query: 226 -IPTLATVHPQELIQYPLIKKNTWHALITLKKALKN 260
            I   AT HP  L++ P +++        LK+ L N
Sbjct: 138 KIKITATYHPAALLRNPQLRRELEEDFKKLKELLSN 173


>gnl|CDD|161940 TIGR00584, mug, mismatch-specific thymine-DNA glycosylate (mug).
           All proteins in this family for whcih functions are
           known are G-T or G-U mismatch glycosylases that function
           in base excision repair. This family is based on the
           phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
           Stanford University). Used 2pf model.
          Length = 328

 Score = 29.6 bits (66), Expect = 0.88
 Identities = 28/125 (22%), Positives = 46/125 (36%), Gaps = 28/125 (22%)

Query: 105 TEGQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEIMRTQ--------------I 150
           T   D++IIG  P       G  + G  GN   K L    +   Q              I
Sbjct: 128 TFNLDIVIIGINPGLMAAYKGHHYPGP-GNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGI 186

Query: 151 HISMISPWHPPGNRNLSNIEMEICRPIIMRQIELISPKILLFIGN-------------KT 197
             + +     PG+++LS+ E      I++++++   P+I +F G              K 
Sbjct: 187 GFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKV 246

Query: 198 KNFFF 202
           KN  F
Sbjct: 247 KNLEF 251


>gnl|CDD|162269 TIGR01246, dapE_proteo, succinyl-diaminopimelate desuccinylase,
           proteobacterial clade.  This model describes a
           proteobacterial subset of succinyl-diaminopimelate
           desuccinylases. An experimentally confirmed
           Gram-positive lineage succinyl-diaminopimelate
           desuccinylase has been described for Corynebacterium
           glutamicum, and a neighbor-joining tree shows the seed
           members, SP:Q59284, and putative archaeal members such
           as TrEMBL:O58003 in a single clade. However, the
           archaeal members differ substantially, share a number of
           motifs with acetylornithine deacetylases rather than
           succinyl-diaminopimelate desuccinylases, and are not
           taken as trusted examples of succinyl-diaminopimelate
           desuccinylases. This model is limited to proteobacterial
           members for this reason.
          Length = 370

 Score = 27.8 bits (62), Expect = 3.1
 Identities = 9/23 (39%), Positives = 16/23 (69%)

Query: 122 NISGKPFSGKTGNMLDKMLQSIE 144
           ++SG+PF    G ++DK  ++IE
Sbjct: 284 SLSGEPFLTNDGKLIDKAREAIE 306


>gnl|CDD|183403 PRK12285, PRK12285, tryptophanyl-tRNA synthetase; Reviewed.
          Length = 368

 Score = 26.4 bits (59), Expect = 8.5
 Identities = 9/15 (60%), Positives = 9/15 (60%)

Query: 54  TNIRHIHSPLVQQAD 68
           TNI HI  P  Q AD
Sbjct: 178 TNIGHIFYPATQAAD 192


  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    0.133    0.397 

Gapped
Lambda     K      H
   0.267   0.0715    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,042,944
Number of extensions: 238630
Number of successful extensions: 367
Number of sequences better than 10.0: 1
Number of HSP's gapped: 366
Number of HSP's successfully gapped: 9
Length of query: 261
Length of database: 5,994,473
Length adjustment: 91
Effective length of query: 170
Effective length of database: 4,028,145
Effective search space: 684784650
Effective search space used: 684784650
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 (21.8 bits)
S2: 56 (25.4 bits)