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)