RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780948|ref|YP_003065361.1| DNA repair protein RecO
[Candidatus Liberibacter asiaticus str. psy62]
         (240 letters)



>gnl|CDD|178852 PRK00085, recO, DNA repair protein RecO; Reviewed.
          Length = 247

 Score =  162 bits (412), Expect = 7e-41
 Identities = 77/251 (30%), Positives = 115/251 (45%), Gaps = 19/251 (7%)

Query: 1   MYWQDDAIILGVRSYGEKNIILEVMTRQYGRHLGFVRNGQSHR--MQPILQAGNLVRVNW 58
           M ++D+ I+L  R YGE ++I+ + TR++GR     +  +  +  +  +LQ    + + W
Sbjct: 2   MLYRDEGIVLHTRPYGETSLIVTLFTREHGRVRAVAKGARRPKSRLGAVLQPFTPLDLLW 61

Query: 59  RSRLAQNLGE-FRFEVLESHCAKLLSSSLFLYGLQSIVPLF-RFLPEREPCLELYDMLNI 116
                  LGE  + E +ES+   L      L     +  L  R LPE +P  EL+++L  
Sbjct: 62  S----AGLGELKQLETIESYGGALPLDGFALAAASYLNELLDRLLPEEDPHPELFELLLQ 117

Query: 117 FL---NCHKIPSVIGKIFVQIELMLLKNIGFGLDLTKCVVTGVTQDLLWVSPKSGGAVCR 173
            L        P  + + F   EL LL  +G+GLDL  C V G   D  + SPK GGAVC 
Sbjct: 118 TLRALAEGGDPEPLLRRF---ELRLLAELGYGLDLDHCAVCGAPGDHRYFSPKEGGAVCS 174

Query: 174 SVGLPYAEKMLVLPSFLW-----KEEQTIDADSLKSAFQLTDYFLNKYALQHNIIHCHLL 228
             G PYA K+L LP FL       +   + A  LK   +     L +  L+  +    L 
Sbjct: 175 ECGDPYAIKLLPLPLFLLRLLLGGDLLALAAADLKLETKKELKRLLRAYLEPYLGGRPLK 234

Query: 229 RENFLGKLLEL 239
               L +LL L
Sbjct: 235 SRELLDQLLRL 245


>gnl|CDD|161959 TIGR00613, reco, DNA repair protein RecO.  All proteins in this
           family for which functions are known are DNA binding
           proteins that are involved in the initiation of
           recombination or recombinational repair.
          Length = 241

 Score = 95.5 bits (238), Expect = 1e-20
 Identities = 65/230 (28%), Positives = 107/230 (46%), Gaps = 18/230 (7%)

Query: 3   WQDDAIILGVRSYGEKNIILEVMTRQYGRHLGFVRNGQS--HRMQPILQAGNLVRVNW-- 58
            +D+ I+L  R YGE + I+ + T +YG+     +  +    RM+ +LQ  +L    W  
Sbjct: 1   IKDEGIVLKSRDYGETDKIITLFTEEYGKVSFVAKGARKSKSRMKAVLQPFSLGDFVWYK 60

Query: 59  RSRLAQNLGEFRFEVLESHCAKLLSSSLFLYGLQSIVP--LFRFLPEREPCLELYDMLNI 116
           RS L       + E++ S     + S LFL    S +   + R LPE EP  +L+++L  
Sbjct: 61  RSGL---STLNQGELINSFEG--IKSDLFLLAYASYIAELIDRLLPEGEPNPKLFELLLK 115

Query: 117 FLNCHKIPSVIGKIFVQIELMLLKNIGFGLDLTKCVVTGVTQDLLWVSPKSGGAVCRSVG 176
            L           +    EL LL+ +G+ LDL KC V G  +DL++ S   GGA+CR  G
Sbjct: 116 TLELINEGGNPELLLRLFELKLLQILGYALDLDKCAVCGSKEDLIYFSMTYGGALCRQCG 175

Query: 177 ------LPYAEKMLVLPSFLWKEE-QTIDADSLKSAFQLTDYFLNKYALQ 219
                 +P   K+L L  +L K + + + +  +K   +L    +     +
Sbjct: 176 EKDPHAIPIDPKLLRLLRYLLKLDLEKLLSIEIKPEIKLEARRILDEYYE 225


>gnl|CDD|152402 pfam11967, RecO_N, Recombination protein O N terminal.
          Recombination protein O (RecO) is involved in DNA
          repair and pfam00470 pathway recombination. This domain
          forms a beta barrel structure.
          Length = 80

 Score = 64.9 bits (159), Expect = 2e-11
 Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 2/61 (3%)

Query: 3  WQDDAIILGVRSYGEKNIILEVMTRQYGRHLGFVRNGQS--HRMQPILQAGNLVRVNWRS 60
          W+ + I+L  R YGE + I+ + TR++G+  G  R  +    R++  LQ   L+ +   +
Sbjct: 4  WKTEGIVLHTRDYGESDKIVTLFTREHGKISGVARGARKPKSRLRAALQPFTLLELVLYA 63

Query: 61 R 61
           
Sbjct: 64 G 64


>gnl|CDD|181449 PRK08491, PRK08491, NADH dehydrogenase subunit C; Provisional.
          Length = 263

 Score = 30.0 bits (68), Expect = 0.63
 Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 6/33 (18%)

Query: 91  LQSIVPLFRF--LPEREPCLELYDMLNIFLNCH 121
           LQS+  LF+     ERE    +YDM  I +N H
Sbjct: 125 LQSVSFLFKSANWSERE----MYDMFGIVINNH 153


>gnl|CDD|140327 PTZ00306, PTZ00306, NADH-dependent fumarate reductase; Provisional.
          Length = 1167

 Score = 28.2 bits (63), Expect = 1.8
 Identities = 12/40 (30%), Positives = 22/40 (55%)

Query: 177 LPYAEKMLVLPSFLWKEEQTIDADSLKSAFQLTDYFLNKY 216
           +PY  K++V      ++   +  + L+SAFQ+ D  LN +
Sbjct: 67  VPYTLKVVVAGPVARQDADAVAKEVLRSAFQMVDTHLNSF 106


>gnl|CDD|184977 PRK15016, PRK15016, isochorismate synthase EntC; Provisional.
          Length = 391

 Score = 28.3 bits (63), Expect = 1.9
 Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 1/41 (2%)

Query: 78  CAKLLSSSLFLYGLQSIVPLFRFLPE-REPCLELYDMLNIF 117
           CAKL  + + L+    IVP    L E RE  ++L  MLN+F
Sbjct: 348 CAKLRENQVRLFAGAGIVPASSPLGEWRETGVKLSTMLNVF 388


>gnl|CDD|163146 TIGR03132, malonate_mdcB, triphosphoribosyl-dephospho-CoA synthase
           MdcB.  This protein acts in cofactor biosynthesis,
           preparing the coenzyme A derivative that becomes
           attached to the malonate decarboxylase acyl carrier
           protein (or delta subunit). The closely related protein
           CitG of citrate lyase produces the same molecule, but
           the two families are nonetheless readily separated.
          Length = 272

 Score = 28.1 bits (63), Expect = 2.3
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 5/50 (10%)

Query: 45  QPILQAGNLVRVNWRSRLA---QNLGEFRFEVLESHCAKLLSSSLFLYGL 91
           +  L AG ++  + R  L    Q+    R     S  A LL+++LFL  L
Sbjct: 224 REFLAAGGVLTSDGRRALHALDQDFVARRLSPGGS--ADLLAATLFLDSL 271


>gnl|CDD|150838 pfam10226, DUF2216, Uncharacterized conserved proteins (DUF2216).
           This is the conserved N-terminal half of a proteins
          which are found from worms to humans. some annotation
          suggests it might be PKR, the Hepatitis delta
          antigen-interacting protein A, but this could not be
          confirmed.
          Length = 195

 Score = 27.0 bits (60), Expect = 4.4
 Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 3/35 (8%)

Query: 37 RNGQSHRMQPILQAGNLVR-VNWRSRLAQNLGEFR 70
          R  ++ +M  I++ GNL+R VN   RL  +L E R
Sbjct: 27 RREEAEKMSAIVEHGNLMREVN--RRLQGHLNEIR 59


>gnl|CDD|131643 TIGR02594, TIGR02594, conserved hypothetical protein TIGR02594.
           Members of this protein family known so far are
           restricted to the bacteria, and for the most to the
           proteobacteria. The function is unknown.
          Length = 129

 Score = 27.0 bits (60), Expect = 4.5
 Identities = 10/29 (34%), Positives = 12/29 (41%)

Query: 24  VMTRQYGRHLGFVRNGQSHRMQPILQAGN 52
           V  R  G H+GFV          I+  GN
Sbjct: 81  VKRRGGGGHVGFVVGKDKQTGTIIVLGGN 109


>gnl|CDD|178734 PLN03192, PLN03192, Voltage-dependent potassium channel;
           Provisional.
          Length = 823

 Score = 26.4 bits (58), Expect = 6.1
 Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 4/56 (7%)

Query: 34  GFVRNGQSHRMQPILQAGNLVRVN-WRSRLAQNLGEFRFEVLESHCAKLLSSSLFL 88
           G V+   S+ +  +L+   L RV    +RL +++   RF      CA+LLS +LFL
Sbjct: 160 GTVKLNLSYSLLGLLRFWRLRRVKQLFTRLEKDI---RFSYFWIRCARLLSVTLFL 212


>gnl|CDD|178674 PLN03128, PLN03128, DNA topoisomerase 2; Provisional.
          Length = 1135

 Score = 26.2 bits (58), Expect = 7.7
 Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 2/31 (6%)

Query: 187 PSFLW--KEEQTIDADSLKSAFQLTDYFLNK 215
           P+F    KE  T    S  S  +L++ FL K
Sbjct: 343 PTFDSQTKETLTTRPSSFGSKCELSEEFLKK 373


  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
   0.327    0.143    0.439 

Gapped
Lambda     K      H
   0.267   0.0726    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,940,146
Number of extensions: 245407
Number of successful extensions: 509
Number of sequences better than 10.0: 1
Number of HSP's gapped: 503
Number of HSP's successfully gapped: 14
Length of query: 240
Length of database: 5,994,473
Length adjustment: 91
Effective length of query: 149
Effective length of database: 4,028,145
Effective search space: 600193605
Effective search space used: 600193605
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 56 (25.4 bits)