RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780948|ref|YP_003065361.1| DNA repair protein RecO [Candidatus Liberibacter asiaticus str. psy62] (240 letters) >1u5k_A Hypothetical protein; OBD-fold, Zn-binding, recombination,replication; 2.00A {Deinococcus radiodurans R1} SCOP: b.40.4.13 g.45.1.2 PDB: 1w3s_A 2v1c_C Length = 244 Score = 86.0 bits (212), Expect = 7e-18 Identities = 34/221 (15%), Positives = 65/221 (29%), Gaps = 10/221 (4%) Query: 2 YWQDDAIILGVRSYGEKNIILEVMTRQYGRHLGFVRNGQSHRMQPILQAGNLVRVNWRSR 61 I++ R +II+ ++T Q G+ R G + L + V V Sbjct: 5 TANRSGIVIRRRVTPAGDIIVTLLTPQ-GKLKAIARGGVKGPLSSSLNLFHHVGVQVYQG 63 Query: 62 LAQNLGEFRFEVLESHCAKLLSSSLFLYGLQSIVPLFRFLPEREPCLELYDMLNIFLNCH 121 +L + VLE L + + E E + +D+ L Sbjct: 64 PHNDLASVKQAVLEGALPTLAEPERYAFAHLMAEFADALFQEGEFSEQAFDLFAASLRGV 123 Query: 122 KIPSVIGKIFVQIELMLLKNIGFGLDLTKCVVTGVTQDLLWVSPKSGGAVCR-------- 173 + + + LL G +C G D P G +C Sbjct: 124 AHQPDPEWVALVMSYKLLGLAGVIPQTARCARCG-APDPEHPDPLGGQLLCSKCAALPPY 182 Query: 174 SVGLPYAEKMLVLPSFLWKEEQTIDADSLKSAFQLTDYFLN 214 + + V + EQ + + + ++ + F+ Sbjct: 183 PPAVLDFLRHAVRRTVRASFEQPVPSADRPALWRALEKFVT 223 >2pff_B Fatty acid synthase subunit beta; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 2006 Score = 38.0 bits (88), Expect = 0.002 Identities = 27/260 (10%), Positives = 57/260 (21%), Gaps = 119/260 (45%) Query: 21 ILEVMTRQYGRHLGFVRNGQSH----RMQPILQAGNLVRVNW-------RSRLAQNLGEF 69 +L + ++ ++ H ++ + R + + Sbjct: 83 VLNLCLTEFENC--YLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKK 140 Query: 70 R----FEVLESHCAKLLSSSLFLYGLQSIVPLFRFLPEREPCL----ELYDMLNIFLNCH 121 F + A+L++ ++G Q + +LY ++ + Sbjct: 141 SNSALFRAVGEGNAQLVA----IFGGQGNT---------DDYFEELRDLYQTYHVLV--- 184 Query: 122 KIPSVIGKIFVQIELMLLKNI-----------GFGLDLTKCVVTGVTQDLLWVSPKSGGA 170 ++ L + GL++ + W Sbjct: 185 -------GDLIKFSAETLSELIRTTLDAEKVFTQGLNILE-----------W-------- 218 Query: 171 VCRSVGLPYAEKMLVLPSFLWKEEQTIDADSLKSA---------FQLTDYFLNKYALQHN 221 L T D D L S QL Y Sbjct: 219 -------------------LENPSNTPDKDYLLSIPISCPLIGVIQLAHY---------- 249 Query: 222 IIHCHLL-------RENFLG 234 ++ LL R G Sbjct: 250 VVTAKLLGFTPGELRSYLKG 269 Score = 33.4 bits (76), Expect = 0.052 Identities = 46/230 (20%), Positives = 75/230 (32%), Gaps = 86/230 (37%) Query: 30 GRHLGFVRN------GQSHRMQPILQAGNLVRV-NWRS--RLAQNLGEFRFEV-LESHCA 79 G G +R+ G S Q ++ A + +W S + F + + + A Sbjct: 257 GFTPGELRSYLKGATGHS---QGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEA 313 Query: 80 ---KLLSSSLFLYGLQ-SI-----VP---L-FRFLPEREPCLELYDMLNIFLNCHKIPSV 126 L S+ L+ S+ VP L L +E + + N L K Sbjct: 314 YPNTSLPPSI----LEDSLENNEGVPSPMLSISNLT-QEQVQDYVNKTNSHLPAGK---- 364 Query: 127 IGKIFVQIELMLL---KNIGFGLDLTKCVVTGVTQDL----LW---VSPKSGGAVCRSVG 176 Q+E+ L+ KN+ VV+G Q L L SG R Sbjct: 365 ------QVEISLVNGAKNL---------VVSGPPQSLYGLNLTLRKAKAPSGLDQSR--- 406 Query: 177 LPYAEKMLV-----LP---SF---------------LWKEEQTIDADSLK 203 +P++E+ L LP F L K + +A ++ Sbjct: 407 IPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQ 456 Score = 27.6 bits (61), Expect = 2.3 Identities = 11/50 (22%), Positives = 18/50 (36%), Gaps = 15/50 (30%) Query: 197 IDADSLKSAFQLTDYFLNKYA-LQHNI-------IHCHLLRENFLGKLLE 238 +DA S + L+ + L+H + L+E F L E Sbjct: 1 MDAYSTRP-LTLS------HGSLEHVLLVPTASFFIASQLQEQFNKILPE 43 >3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190 Score = 31.8 bits (71), Expect = 0.13 Identities = 9/33 (27%), Positives = 17/33 (51%) Query: 37 RNGQSHRMQPILQAGNLVRVNWRSRLAQNLGEF 69 R Q R+Q + A ++ WR + ++L E+ Sbjct: 91 REEQRKRLQELDAASKVMEQEWREKAKKDLEEW 123 >1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154 Score = 30.4 bits (67), Expect = 0.38 Identities = 9/22 (40%), Positives = 10/22 (45%), Gaps = 1/22 (4%) Query: 75 ESHCAKLLSSSLFLYGLQSIVP 96 E K L +SL LY S P Sbjct: 18 EKQALKKLQASLKLYADDS-AP 38 >1efd_N Ferrichrome-binding periplasmic protein; periplasmic binding protein-siderophore complex, FHUD complex with gallichrome; HET: GCR; 1.90A {Escherichia coli} SCOP: c.92.2.1 PDB: 1k7s_N* 1k2v_N* 1esz_A* Length = 266 Score = 28.3 bits (62), Expect = 1.5 Identities = 9/64 (14%), Positives = 23/64 (35%), Gaps = 5/64 (7%) Query: 3 WQDDAIILGVRSYGEKNIILEVMTRQYGRHLGFVRNGQSHRMQPILQAGNLVRVNWRSRL 62 ++D ++ + + +M + + FVR G+ R+ + G + Sbjct: 200 YKDVDVLCF--DHDNSKDMDALMATPLWQAMPFVRAGRFQRVPAVWFYGATLSAM---HF 254 Query: 63 AQNL 66 + L Sbjct: 255 VRVL 258 >3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} Length = 197 Score = 28.0 bits (62), Expect = 2.3 Identities = 12/57 (21%), Positives = 17/57 (29%), Gaps = 16/57 (28%) Query: 145 GLDL---TKCVVTGVTQDLLWVSPKSGGAVCRSVGLPYAEKMLVLPSFLWKEEQTID 198 G +L C V + G VC G LVL ++ +D Sbjct: 15 GPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCG-------LVL------SDKLVD 58 >1mhy_B Methane monooxygenase hydroxylase; oxidoreductase, NADP, one-carbon metabolism; 2.00A {Methylosinus trichosporium} SCOP: a.25.1.2 PDB: 1mhz_B Length = 395 Score = 27.9 bits (62), Expect = 2.4 Identities = 18/110 (16%), Positives = 30/110 (27%), Gaps = 24/110 (21%) Query: 2 YWQDDAIILGVRSYGEKNII-----LEVMTRQYGRHLGFVRNGQSHRMQPILQAGNLVRV 56 W D I G R+ ++ E++ V G R Sbjct: 220 IWTTDPIYSGARATVQEIWQGVQDWNEILWAG-----HAV-------YDATF--GQFARR 265 Query: 57 NWRSRLAQNLGEFRFEVLESHCAKLLSSSLFLYGLQSIVPLFRFLPEREP 106 + RLA G+ + S + F +I LF + + Sbjct: 266 EFFQRLATVYGDTLTPFFTAQ-----SQTYFQTTRGAIDDLFVYCLANDS 310 >1gnf_A Transcription factor GATA-1; zinc finger, transcription regulation; NMR {Mus musculus} SCOP: g.39.1.1 PDB: 1y0j_A Length = 46 Score = 26.2 bits (57), Expect = 7.2 Identities = 11/33 (33%), Positives = 17/33 (51%) Query: 145 GLDLTKCVVTGVTQDLLWVSPKSGGAVCRSVGL 177 G + +CV G T LW ++G +C + GL Sbjct: 1 GSEARECVNCGATATPLWRRDRTGHYLCNACGL 33 Database: pdb70 Posted date: Jan 26, 2011 11:21 AM Number of letters in database: 5,693,230 Number of sequences in database: 24,244 Lambda K H 0.327 0.143 0.439 Gapped Lambda K H 0.267 0.0450 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,077,389 Number of extensions: 90888 Number of successful extensions: 398 Number of sequences better than 10.0: 1 Number of HSP's gapped: 394 Number of HSP's successfully gapped: 13 Length of query: 240 Length of database: 5,693,230 Length adjustment: 90 Effective length of query: 150 Effective length of database: 3,511,270 Effective search space: 526690500 Effective search space used: 526690500 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: 55 (25.7 bits)