RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780743|ref|YP_003065156.1| putative uracil-DNA glycosylase [Candidatus Liberibacter asiaticus str. psy62] (261 letters) >1vk2_A Uracil-DNA glycosylase TM0511; structural genomics, JCSG, PSI, protein structure initiative, joint center for structural genomics, hydrolase; 1.90A {Thermotoga maritima} SCOP: c.18.1.2 PDB: 1l9g_A Length = 204 Score = 85.8 bits (211), Expect = 9e-18 Identities = 35/194 (18%), Positives = 80/194 (41%), Gaps = 5/194 (2%) Query: 70 IAQKACSLHELKSLLRSFHDCHLCSTSLSTICATQTEGQDLMIIGYTPSDSDNISGKPFS 129 + + + + ++ C L + + ++ +G P + ++ +G+PF Sbjct: 13 MYTREELMEIVSERVKKCTACPLHLNRTNVVVGEGNLDTRIVFVGEGPGEEEDKTGRPFV 72 Query: 130 GKTGNMLDKMLQSIEIMRTQIHISMISPWHPPGNRNLSNIEMEICRPIIMRQIELISPKI 189 G+ G +L ++L+ I R ++I + PP NR + E C ++ QIE+I+P + Sbjct: 73 GRAGMLLTELLRESGIRREDVYICNVVKCRPPNNRTPTPEEQAACGHFLLAQIEIINPDV 132 Query: 190 LLFIGNKTKNFFFNNDAQKTYQNLGKWSNLCTPHSIIPTLATVHPQELIQYP--LIKKNT 247 ++ +G +FF + + G + + T HP L++ +++ Sbjct: 133 IVALGATALSFFVDGKKVSITKVRGNPIDW---LGGKKVIPTFHPSYLLRNRSNELRRIV 189 Query: 248 WHALITLKKALKNL 261 + K +K Sbjct: 190 LEDIEKAKSFIKKE 203 >1ui0_A Uracil-DNA glycosylase; base excision repair, iron/sulfer cluster, thermophIle, riken structural genomics/proteomics initiative, RSGI; 1.50A {Thermus thermophilus} SCOP: c.18.1.2 PDB: 1ui1_A Length = 205 Score = 85.6 bits (211), Expect = 1e-17 Identities = 54/192 (28%), Positives = 90/192 (46%), Gaps = 11/192 (5%) Query: 76 SLHELKSLLRSFHDCHLCSTSLSTICATQTEGQDLMIIGYTPSDSDNISGKPFSGKTGNM 135 +L L++ ++ C L + LMI+G P + ++ +G+PF GK G + Sbjct: 2 TLELLQAQAQNCTACRLMEGRTRVVFGEGNPDAKLMIVGEGPGEEEDKTGRPFVGKAGQL 61 Query: 136 LDKMLQSIEIMRTQIHISMISPWHPPGNRNLSNIEMEICR-PIIMRQIELISPKILLFIG 194 L+++L++ I R +++I+ I PP NR E +IC +++QIELI+P+I++ +G Sbjct: 62 LNRILEAAGIPREEVYITNIVKCRPPQNRAPLPDEAKICTDKWLLKQIELIAPQIIVPLG 121 Query: 195 NKTKNFFFNNDAQKTYQNLGKWSNLCTPHSIIPTLATVHPQELIQYP-----LIKKNTWH 249 FF T GKW I HP L++ P K TW Sbjct: 122 AVAAEFFLGEKVSITKVR-GKWYEWHG----IKVFPMFHPAYLLRNPSRAPGSPKHLTWL 176 Query: 250 ALITLKKALKNL 261 + +K+AL L Sbjct: 177 DIQEVKRALDAL 188 >3ikb_A Uncharacterized conserved protein; APC63946, streptococcus mutans UA159, structural genomics, PSI-2, protein structure initiative; HET: FLC; 1.67A {Streptococcus mutans} Length = 198 Score = 83.8 bits (207), Expect = 4e-17 Identities = 21/187 (11%), Positives = 57/187 (30%), Gaps = 12/187 (6%) Query: 76 SLHELKSLLRSFHDCHLCSTSLSTICATQTEGQDLMIIGYTPSDSDNISGKPFSGKTGNM 135 SL E+ + + + + + + I+G P S ++ K+G+ Sbjct: 6 SLEEITKAIMADSQNKVFTEKNIEPLFAAPKTARINIVGQAPGIKAQESRLYWNDKSGDR 65 Query: 136 LDKMLQSIEIM---RTQIHISMISPWHPPGNRNLSNIEMEICRPIIMRQI--ELISPKIL 190 L + + + + ++P ++ + + I L ++ Sbjct: 66 LREWMGVDYDTFYHSGYFAVIPMDFYYPGKGKSGDLPPRKGFAQKWHQPILDLLPDIQLT 125 Query: 191 LFIGNKTKNFFFNNDAQKT-YQNLGKWSNLCTPHSIIPTLATVHPQELIQYPLIKKNTWH 249 + IGN + ++ + + + + VHP Q + ++ W Sbjct: 126 ILIGNYAQKYYLHQKSSVKLTDTVAHYKKYLP-----DYFPLVHPSPRNQ-IWMSRHPWF 179 Query: 250 ALITLKK 256 + Sbjct: 180 EAQVVPD 186 >1wyw_A TDG, G/T mismatch-specific thymine DNA glycosylase; hydrolase; 2.10A {Homo sapiens} SCOP: c.18.1.2 PDB: 2d07_A 2rba_A* Length = 230 Score = 72.3 bits (177), Expect = 1e-13 Identities = 20/111 (18%), Positives = 39/111 (35%), Gaps = 13/111 (11%) Query: 106 EGQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEIMR-------------TQIHI 152 D++IIG P G + G + + S I Sbjct: 21 FNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGF 80 Query: 153 SMISPWHPPGNRNLSNIEMEICRPIIMRQIELISPKILLFIGNKTKNFFFN 203 + + PG+++LS+ E I++++++ P+I +F G F Sbjct: 81 TNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSK 131 >1mug_A Protein (G:T/U specific DNA glycosylase); hydrolase; 1.80A {Escherichia coli} SCOP: c.18.1.2 PDB: 1mtl_A 1mwi_A* 1mwj_A Length = 168 Score = 71.6 bits (175), Expect = 1e-13 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 23/166 (13%) Query: 106 EGQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSI------------EIMRTQIHIS 153 G ++ G P S +G PF+ + Q+ ++ + ++ Sbjct: 8 PGLRVVFCGINPGLSSAGTGFPFAHPANRFWKVIYQAGFTDRQLKPQEAQHLLDYRCGVT 67 Query: 154 MISPWHPPGNRNLSNIEMEICRPIIMRQIELISPKILLFIGNKTKNFFFNNDAQKTYQNL 213 + +S E+ ++ +IE P+ L +G + F+ Q Sbjct: 68 KLVDRPTVQANEVSKQELHAGGRKLIEKIEDYQPQALAILGKQAYEQGFS-------QRG 120 Query: 214 GKWSNLCTPHSIIPTLATVHPQELIQYPLIKK-NTWHALITLKKAL 258 +W +P L + L K + L +AL Sbjct: 121 AQWGKQTLTIGSTQIWVLPNPSGLSRVSLEKLVEAYRE---LDQAL 163 >2c2q_A G/U mismatch-specific DNA glycosylase; radiation resistance, DNA repair enzymes, uracil-DNA glycosylase, MUG, hydrolase; 1.7A {Deinococcus radiodurans} PDB: 2c2p_A Length = 199 Score = 59.9 bits (144), Expect = 5e-10 Identities = 19/187 (10%), Positives = 46/187 (24%), Gaps = 25/187 (13%) Query: 95 TSLSTICATQT--------EGQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEI- 145 + + + G L+++G PS + ++ + Sbjct: 5 HDVPDLTGSGEYLVPDVLQPGLTLVLVGTAPSGISARARAYYANPENKFWRTLHAVGLTP 64 Query: 146 -----------MRTQIHISMISPWHPPGNRNLSNIEMEICRPIIMRQIELISPKILLFIG 194 + + ++ ++ H L + R++E P+I+ F Sbjct: 65 RQLVPQEYATLPQYGLGLTDVAKRHSGVAAALPGEAWRPDE--LRRKVEHYRPRIVAFTS 122 Query: 195 NKTKNFFFNNDAQKTYQNLGKWSNLCTPHSIIPTLATVHPQELIQYPLIKKNTWHALITL 254 + + K G + L + W AL Sbjct: 123 KRGASETLGVPTGKL--PYGPQPQPLDWPAETELWVLPSTSPLGHNHF-RLEPWQALGDR 179 Query: 255 KKALKNL 261 + L+ Sbjct: 180 VRELRGA 186 >2d3y_A Uracil-DNA glycosylase; base excision repair, iron/sulfer cluster, thermophIle, structural genomics, NPPSFA; HET: DU; 1.55A {Thermus thermophilus HB8} PDB: 2ddg_A* 2dem_A* 2dp6_A* Length = 219 Score = 54.1 bits (129), Expect = 3e-08 Identities = 17/167 (10%), Positives = 39/167 (23%), Gaps = 16/167 (9%) Query: 109 DLMIIGYTPSDSDNISGKP--FSGKTGNMLDKMLQSIEIMRTQIHISMIS---------- 156 +++ G P + +G L +L + + Sbjct: 52 RILLFGLAPGAHGSNRTGRPFTGDASGAFLYPLLHEAGLSSKPESLPGDDLRLYGVYLTA 111 Query: 157 --PWHPPGNRNLSNIEMEICRPIIMRQIELISPKILLFIGNKTKNFFFNNDAQKTYQNLG 214 PP N+ R + L ++ + +G + + + Sbjct: 112 AVRCAPPKNKPTPEELRACARWTEVELGLLPEVRVYVALGRIALEALLAHFGLRKSAHPF 171 Query: 215 KWSNLCTPHSIIPTLATVHPQELIQYPLIKKNTWHALITLKKALKNL 261 + LA+ H + T + + K L Sbjct: 172 RHGAHYPLPGGRHLLASYHVSRQNTQT--GRLTREMFLEVLMEAKRL 216 >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 = 48.0 bits (114), Expect = 2e-06 Identities = 48/278 (17%), Positives = 89/278 (32%), Gaps = 76/278 (27%) Query: 2 TSKR--ILSQEQILTIALFYADSGVYWVFDEPNNEATYESQRKEKSIDSAIQPITNIRH- 58 S R LS + V P SQ +E+ +P Sbjct: 4 YSTRPLTLSHGSLEH------------VLLVPTASFFIASQLQEQFNKILPEPTEGFAAD 51 Query: 59 --IHSP--LVQQ-----ADSIAQKACSLHE--LKSLLRSFHDCHLCSTSLSTICA----- 102 +P LV + + + + L L F +C+L + + A Sbjct: 52 DEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQE 111 Query: 103 ---TQTEGQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEIMRTQIHISMISPWH 159 T + ++L+ T + ++ +PF K+ + L +++ Q+ I + Sbjct: 112 NDTTLVKTKELIKNYIT---ARIMAKRPFDKKSNSAL---FRAVGEGNAQLV--AI--FG 161 Query: 160 PPGN--------RNLSNIEMEICRPIIMRQIELISPKILLFIGNKTKNFFFNNDAQKTYQ 211 GN R+L ++ I+ + + I DA+K + Sbjct: 162 GQGNTDDYFEELRDLYQTY----HVLVGDLIKFSAETLSELIRTTL-------DAEKVFT 210 Query: 212 ---NLGKWSNLCTPHSIIPT---LATVHPQELIQYPLI 243 N+ +W L P + P L ++ P I PLI Sbjct: 211 QGLNILEW--LENPSN-TPDKDYLLSI-P---ISCPLI 241 Score = 39.2 bits (91), Expect = 9e-04 Identities = 32/161 (19%), Positives = 49/161 (30%), Gaps = 86/161 (53%) Query: 60 HSPLVQ---------QADS------IAQKACSLHELKSL----LRSFHDCHLC--STSLS 98 HS Q + DS +KA ++ L +R C+ +TSL Sbjct: 273 HS---QGLVTAVAIAETDSWESFFVSVRKAITV-----LFFIGVR----CYEAYPNTSLP 320 Query: 99 TICATQTEGQDLMIIGYTPS---DS-DNISGKPFSGKTGNMLD------KMLQSIEIMRT 148 PS DS +N G P ML + +Q + +T Sbjct: 321 ------------------PSILEDSLENNEGVP-----SPMLSISNLTQEQVQDY-VNKT 356 Query: 149 --------QIHISMI-SPWH-----PP----G-NRNLSNIE 170 Q+ IS++ + PP G N L + Sbjct: 357 NSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAK 397 Score = 39.2 bits (91), Expect = 9e-04 Identities = 36/236 (15%), Positives = 58/236 (24%), Gaps = 125/236 (52%) Query: 1 MTSKRILSQEQILTIALFYADSGVYWVFDEPNNEATYESQRKEKSIDSAIQPITNI---- 56 M S L+QEQ+ + ++ TN Sbjct: 338 MLSISNLTQEQV------------------------------QDYVNK-----TNSHLPA 362 Query: 57 -RHIHSPLVQQADS--IAQKACSLHELKSLLRS--------------------------- 86 + + LV A + ++ SL+ L LR Sbjct: 363 GKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLP 422 Query: 87 ----FHDCHLCSTSLSTICATQTEGQDLMIIGYTPSDSDNISGK----P-FSGKTGNMLD 137 FH L A+ +DL ++ + + K P + G+ L Sbjct: 423 VASPFHSHLLVP-------ASDLINKDL------VKNNVSFNAKDIQIPVYDTFDGSDLR 469 Query: 138 KMLQSIEIMRTQIH--ISMI--SP--W---------H----PPG---------NRN 165 + SI + I P W H PG +RN Sbjct: 470 VLSGSI------SERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRN 519 Score = 32.2 bits (73), Expect = 0.12 Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 12/56 (21%) Query: 27 VFDEPNNEATYESQRKEKSIDSAIQPITNIRHIHSPLVQQADSIAQKACSLHELKS 82 +F E N +T + R EK + SA Q Q A ++ +KA + +LKS Sbjct: 1706 IFKEINEHSTSYTFRSEKGLLSATQ-----------FTQPALTLMEKA-AFEDLKS 1749 >2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 1688 Score = 28.2 bits (62), Expect = 2.0 Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 20/64 (31%) Query: 123 ISGKPFSGKTGN-MLDKMLQSIEIMRTQIHISMISPWHPPGNRNLSNIEMEICRPIIMRQ 181 ++G P G G M++ LQ I+ + I PGNRN N++ I+ Q Sbjct: 1381 LTGHP-KGAAGAWMMNGALQ---ILNSGI---------IPGNRNADNVDK------ILEQ 1421 Query: 182 IELI 185 E + Sbjct: 1422 FEYV 1425 >2o9c_A Bacteriophytochrome; phytochrome chromophore, figure-OF-eight knot, phytochromobilin, biliverdin, PAS, GAF, transferase; HET: LBV; 1.45A {Deinococcus radiodurans} SCOP: d.110.2.1 d.110.3.9 PDB: 2o9b_A* 1ztu_A* Length = 342 Score = 28.1 bits (62), Expect = 2.1 Identities = 7/43 (16%), Positives = 15/43 (34%), Gaps = 2/43 (4%) Query: 50 IQPITNIRHIHSPLVQQADSIAQKACSLHELKSLLRSFHDCHL 92 ++ + R PL + L ++LR+ H+ Sbjct: 236 LRLTADTRAAAVPLDPVLNPQTNAPTPLGG--AVLRATSPMHM 276 >2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: b.122.1.1 d.265.1.2 Length = 357 Score = 27.8 bits (61), Expect = 2.7 Identities = 9/61 (14%), Positives = 17/61 (27%), Gaps = 1/61 (1%) Query: 189 ILLFIGNKTKNFFFNNDAQKTYQNLGKWSNLCTPHSIIPTLATVHPQELIQYPLIKKNTW 248 + + + TK + K Y L + I+ + Q P +K Sbjct: 109 LPVALERATKTIPMWHIPPKEYVCLMHLHRDASEEDILRVFKE-FTGRIYQRPPLKAAVK 167 Query: 249 H 249 Sbjct: 168 R 168 >1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Bacteriophage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A* Length = 296 Score = 27.3 bits (59), Expect = 3.5 Identities = 9/147 (6%), Positives = 36/147 (24%), Gaps = 4/147 (2%) Query: 109 DLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQ-SIEIMRTQIHISMISPWHPPGNRNLS 167 + +G + ++ GK+ + + LQ + + + + Sbjct: 26 NDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDLIG 85 Query: 168 NIEMEICRPIIMRQIELISPKILLFIGNK---TKNFFFNNDAQKTYQNLGKWSNLCTPHS 224 R + E+I ++ F + + + Sbjct: 86 LHNRVRLRQSDSLKREIIENGKFDQWFDELFGNDTFHLYDSFAEAETDRLLAKLAYMRSG 145 Query: 225 IIPTLATVHPQELIQYPLIKKNTWHAL 251 + + + ++ + + + Sbjct: 146 LGCDVIILDHISIVVSASGESDERKMI 172 >2ool_A Sensor protein; bacteriophytochrome, photoconversion, photoreceptor, biliverdin, signaling protein; HET: LBV; 2.20A {Rhodopseudomonas palustris CGA009} SCOP: d.110.2.1 d.110.3.9 Length = 337 Score = 27.4 bits (60), Expect = 3.6 Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 2/40 (5%) Query: 53 ITNIRHIHSPLVQQADSIAQKACSLHELKSLLRSFHDCHL 92 I +I + SPLV + L S+LRS HL Sbjct: 233 IPDIGYRPSPLVPDINPRLGGPIDLSF--SVLRSVSPTHL 270 >1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, protein structure initiative; 1.90A {Mycobacterium tuberculosis H37RV} SCOP: b.122.1.1 d.265.1.2 Length = 316 Score = 26.2 bits (57), Expect = 7.2 Identities = 9/73 (12%), Positives = 19/73 (26%), Gaps = 5/73 (6%) Query: 190 LLFIGNKTKNFFFNNDAQKTYQNLGKW-----SNLCTPHSIIPTLATVHPQELIQYPLIK 244 ++ I TK A K+Y + + + A E I + + Sbjct: 50 VIGIERATKILGLLTAAPKSYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMER 109 Query: 245 KNTWHALITLKKA 257 + + Sbjct: 110 LRGEIRQVPSSVS 122 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 0.319 0.133 0.397 Gapped Lambda K H 0.267 0.0592 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,154,352 Number of extensions: 92424 Number of successful extensions: 259 Number of sequences better than 10.0: 1 Number of HSP's gapped: 252 Number of HSP's successfully gapped: 21 Length of query: 261 Length of database: 5,693,230 Length adjustment: 91 Effective length of query: 170 Effective length of database: 3,487,026 Effective search space: 592794420 Effective search space used: 592794420 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 (25.7 bits)