RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254781031|ref|YP_003065444.1| exsB protein [Candidatus Liberibacter asiaticus str. psy62] (240 letters) >3bl5_A Queuosine biosynthesis protein QUEC; PREQ1 biosynthesis, RNA modification, tRNA, hydrolase; 2.95A {Bacillus subtilis} Length = 219 Score = 207 bits (527), Expect = 2e-54 Identities = 98/226 (43%), Positives = 150/226 (66%), Gaps = 22/226 (9%) Query: 11 ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70 A+++FSGGQDS+TCL WAL F+ VET++F Y QR+ E+E + +K Sbjct: 6 AIVVFSGGQDSTTCLLWALKEFEEVETVTFHYNQRHSQEVEVAKSIAEK----------- 54 Query: 71 LG-EDHILPLAILGDISHSSLTK-NVAMKIQDNNLPNTFVPGRNIIFLVFAATLAYRLGI 128 LG ++H+L +++L ++ ++LT+ ++ ++++D LP+TFVPGRN++FL FA+ LAY++G Sbjct: 55 LGVKNHLLDMSLLNQLAPNALTRNDIEIEVKDGELPSTFVPGRNLVFLSFASILAYQIGA 114 Query: 129 TNIVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHVTVHTPLMWLKKYETWKLAQDIG 188 +I+ GVCETD+SGYPDCR + +++ +NL ME +HTPLMWL K ETWKLA ++G Sbjct: 115 RHIITGVCETDFSGYPDCRDEFVKSCNVTVNLAMEKPFVIHTPLMWLNKAETWKLADELG 174 Query: 189 GQDLVNLILEESHTCYLGKRDKRYEWGYGCNSCPACYLRQKGWMEF 234 ++ + + TCY G GC CPAC+LR KG+ E+ Sbjct: 175 ---ALDFVKNNTLTCYNG------IIADGCGECPACHLRSKGYEEY 211 >2pg3_A Queuosine biosynthesis protein QUEC; YP_049261.1, hypothetical protein, structural genomics; 2.40A {Pectobacterium atrosepticum SCRI1043} SCOP: c.26.2.1 Length = 232 Score = 150 bits (378), Expect = 3e-37 Identities = 86/227 (37%), Positives = 124/227 (54%), Gaps = 14/227 (6%) Query: 11 ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70 A+++FSGGQDS+TCL AL +D V ++FDYGQR++ E+E + +K+ K Sbjct: 5 AVVVFSGGQDSTTCLIQALQDYDDVHCITFDYGQRHRAEIEVAQELSQKLGAAAHKVL-- 62 Query: 71 LGEDHILPLAILGDISHSSLTKNVAMKIQDNNLPNTFVPGRNIIFLVFAATLAYRLGITN 130 D L + +PNTFVPGRNI+FL A+ AY++G Sbjct: 63 ---DVGLLNELATSSLTRDSIPVPDYDANAQGIPNTFVPGRNILFLTLASIYAYQVGAEA 119 Query: 131 IVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHVTVHTPLMWLKKYETWKLAQDIGGQ 190 ++ GVCETD+SGYPDCR + ++A+ AI LG+ + TPLMWL K ETW LA Sbjct: 120 VITGVCETDFSGYPDCRDEFVKALNQAIVLGIARDIRFETPLMWLNKAETWALADYYQQ- 178 Query: 191 DLVNLILEESHTCYLGKRDKRYEWGYGCNSCPACYLRQKGWMEFKEK 237 ++ + + TCY G + G GC C AC+LR G ++++ Sbjct: 179 --LDTVRYHTLTCYNGIK------GDGCGQCAACHLRANGLAQYQKD 217 >2c5s_A THII, probable thiamine biosynthesis protein THII; RNA-binding protein, RNA binding protein, tRNA modification, 4-thiouridine synthase; HET: AMP; 2.5A {Bacillus anthracis} SCOP: c.26.2.6 d.308.1.1 Length = 413 Score = 52.0 bits (124), Expect = 1e-07 Identities = 30/198 (15%), Positives = 58/198 (29%), Gaps = 25/198 (12%) Query: 11 ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70 ++L SGG DS + R VE + F ++ + + Sbjct: 190 VMVLLSGGIDSPVAAYLTMKRGVSVEAVHFHSPP----------FTSERAKQKVIDLAQE 239 Query: 71 LGEDHILPLAILGDISHSSLTKNVAMKIQDNNLPNTFVPGRNIIFLVFAATLAYRLGITN 130 L + + T+ ++ + R ++ +A Sbjct: 240 LTKYCKRV-----TLHLVPFTEVQKTINKEIPSSYSMTVMRRMMM-RITERIAEERNALA 293 Query: 131 IVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHVTVHTPLMWLKKYETWKLAQDIGGQ 190 I G D++ I N + PL+ + K E K+A++IG Sbjct: 294 ITTGESLGQ---VASQTLDSMHTINEVTNYPV------IRPLITMDKLEIIKIAEEIGTY 344 Query: 191 DLVNLILEESHTCYLGKR 208 D+ E+ T + Sbjct: 345 DISIRPYEDCCTVFTPAS 362 >3k32_A Uncharacterized protein MJ0690; predicted subunit of tRNA methyltransferase, methanocaldococcus jannaschii DSM , PSI- 2; 2.50A {Methanocaldococcus jannaschii} Length = 203 Score = 48.5 bits (115), Expect = 1e-06 Identities = 26/177 (14%), Positives = 47/177 (26%), Gaps = 32/177 (18%) Query: 12 LLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDSL 71 +LFSGG+DSS ++ ++G +L Sbjct: 10 HVLFSGGKDSSLSAVILKKLGYNPHLITINFGVIPSYKLAEETAKILGF----------- 58 Query: 72 GEDHILPLAILGDISHSSLTKNVAMKIQDNNLPNTFVPGRNIIFLVFAATLAYRLGITNI 131 + ++ + + K M I+ PG I ++ + + Sbjct: 59 -KHKVI------TLDRKIVEKAADMIIEHKY------PGPAIQYVHKTVLEILADEYSIL 105 Query: 132 VIGVCETDYSGYPDCRHDTIRAIETAINLGMESHVTVHTPLMWLKKYETWKLAQDIG 188 G D +L M ++ TPLM LA + Sbjct: 106 ADGTRRDDRVPKLSYSEIQ--------SLEMRKNIQYITPLMGFGYKTLRHLASEFF 154 >1k92_A Argininosuccinate synthase, argininosuccinate; N-type ATP pyrophosphatase, ligase; 1.60A {Escherichia coli} SCOP: c.26.2.1 d.210.1.1 PDB: 1k97_A* 1kp2_A* 1kp3_A* Length = 455 Score = 36.0 bits (83), Expect = 0.008 Identities = 10/39 (25%), Positives = 19/39 (48%) Query: 13 LLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELE 51 + FSGG D+S L W + + + GQ ++ + + Sbjct: 15 IAFSGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYD 53 >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 = 31.5 bits (71), Expect = 0.16 Identities = 41/224 (18%), Positives = 63/224 (28%), Gaps = 107/224 (47%) Query: 8 APSALLLFSGGQDS--------STCLSWA-LDRFDRVET----------------LSFDY 42 PS L +DS S LS + L + ++V+ +S Sbjct: 320 PPSIL------EDSLENNEGVPSPMLSISNLTQ-EQVQDYVNKTNSHLPAGKQVEISLVN 372 Query: 43 GQRNKV------ELECRLCVR-KKIVELMPKWKDSLGED--HI-------------LPLA 80 G +N V L L + +K K G D I LP Sbjct: 373 GAKNLVVSGPPQSL-YGLNLTLRKA-------KAPSGLDQSRIPFSERKLKFSNRFLP-- 422 Query: 81 ILGDIS---HSSLTKNVAMKI-QDNNLPNTFVPGRNIIFLVFAATLAYRLGITNIVIGVC 136 ++ HS L + I +D + N+ F A + I V Sbjct: 423 ----VASPFHSHLLVPASDLINKD-------LVKNNVSFN--AKDIQ---------IPVY 460 Query: 137 ETDYSGYPDCR-------HDTIRAI-------ETAINLGMESHV 166 +T + G D R + I ET +H+ Sbjct: 461 DT-FDG-SDLRVLSGSISERIVDCIIRLPVKWETTTQFKA-THI 501 >1vl2_A Argininosuccinate synthase; TM1780, structural genomics, JCSG, protein structure initiative, PSI, joint center for structural genomics; 1.65A {Thermotoga maritima} SCOP: c.26.2.1 d.210.1.1 Length = 421 Score = 31.1 bits (70), Expect = 0.26 Identities = 11/37 (29%), Positives = 18/37 (48%) Query: 13 LLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVE 49 L +SGG D+S L W ++ V + GQ++ Sbjct: 19 LAYSGGLDTSVILKWLCEKGFDVIAYVANVGQKDDFV 55 >2ntx_A EMB|CAB41934.1, prone8; dimer, guanine nucleotide exchange factor, signaling protein; HET: MSE; 2.20A {Arabidopsis thaliana} PDB: 2nty_A* 2wbl_A Length = 365 Score = 30.9 bits (70), Expect = 0.27 Identities = 10/34 (29%), Positives = 17/34 (50%) Query: 34 RVETLSFDYGQRNKVELECRLCVRKKIVELMPKW 67 +++ + D R K E++ L V IVE +P Sbjct: 57 KLQPMPQDRQARWKKEIDWLLSVTDHIVEFVPSQ 90 >2dpl_A GMP synthetase, GMP synthase [glutamine-hydrolyzing] subunit B; structural genomics, NPPSFA; 1.43A {Pyrococcus horikoshii OT3} PDB: 2z0c_A 3a4i_A Length = 308 Score = 30.9 bits (69), Expect = 0.28 Identities = 31/180 (17%), Positives = 62/180 (34%), Gaps = 25/180 (13%) Query: 10 SALLLFSGGQDSSTCLSWALDRF-DRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWK 68 A++ SGG DSST A DR+ + + G K E E + + + + Sbjct: 22 KAIIALSGGVDSSTAAVLAHKAIGDRLHAVFVNTGFLRKGEPEFVVKTFRDEFGMNLHYV 81 Query: 69 DSLGEDHILPLAILGDISHSSLTKNVAMKIQDNNLPNTFVPGRNIIFLVFAATLAYRLGI 128 D+ + + V +++ + +A ++G Sbjct: 82 DAQDRFFSALKGVTDPEEKRKIIGRVFIEVFEE--------------------VAKKIGA 121 Query: 129 TNIVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHVTVHTPLMWLKKYETWKLAQDIG 188 ++ G D+ I++ L + ++ + PL L K E +LA+ +G Sbjct: 122 EYLIQGTIAPDWIES----QGKIKSHHNVGGLPEKLNLKLIEPLRDLYKDEVRELAKFLG 177 >2nz2_A Argininosuccinate synthase; amino-acid biosynthesis, aspartate, citrulline, structural genomics, structural genomics consortium, SGC, ligase; HET: CIR; 2.40A {Homo sapiens} Length = 413 Score = 29.9 bits (67), Expect = 0.47 Identities = 12/37 (32%), Positives = 18/37 (48%) Query: 13 LLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVE 49 L +SGG D+S L W ++ V + GQ+ E Sbjct: 10 LAYSGGLDTSCILVWLKEQGYDVIAYLANIGQKEDFE 46 >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 = 30.0 bits (66), Expect = 0.49 Identities = 7/22 (31%), Positives = 14/22 (63%), Gaps = 2/22 (9%) Query: 5 IKKAPSALLLFSGGQDSSTCLS 26 +KK ++L L++ DS+ L+ Sbjct: 22 LKKLQASLKLYA--DDSAPALA 41 Score = 28.4 bits (62), Expect = 1.5 Identities = 8/18 (44%), Positives = 9/18 (50%), Gaps = 2/18 (11%) Query: 216 YGCNSCPACYLRQKGWME 233 Y +S PA L K ME Sbjct: 32 YADDSAPA--LAIKATME 47 >1kor_A Argininosuccinate synthetase; ligase, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: ANP ARG; 1.95A {Thermus thermophilus} SCOP: c.26.2.1 d.210.1.1 PDB: 1j1z_A* 1j21_A* 1kh1_A 1kh2_A* 1kh3_A* 1j20_A* Length = 400 Score = 29.8 bits (67), Expect = 0.58 Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 1/38 (2%) Query: 13 LLFSGGQDSSTCLSWALDRFD-RVETLSFDYGQRNKVE 49 L +SGG D+S L W + + V + D GQ +VE Sbjct: 5 LAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVE 42 >3fiu_A NH(3)-dependent NAD(+) synthetase; rossman fold, adenine nucleotide alpha hydrolase-like, ATP- binding, ligase, nucleotide-binding; HET: AMP; 1.85A {Francisella tularensis subsp} Length = 249 Score = 29.6 bits (65), Expect = 0.75 Identities = 10/49 (20%), Positives = 17/49 (34%) Query: 7 KAPSALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLC 55 A ++ SGG DS+ S A+ L +++ L Sbjct: 28 PAEGFVIGLSGGIDSAVAASLAVKTGLPTTALILPSDNNQHQDMQDALE 76 >2r79_A Periplasmic binding protein; heme transport, transport protein; HET: HEM; 2.40A {Pseudomonas aeruginosa} Length = 283 Score = 28.8 bits (63), Expect = 1.1 Identities = 10/75 (13%), Positives = 26/75 (34%), Gaps = 5/75 (6%) Query: 108 VPGRNIIFLVFAAT-LAYRLGITNIVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHV 166 +P R + + + LG + ++GV S +P + ++ L E + Sbjct: 1 LPQR-WVSAGGSLSEWVVALGGESKLVGV--DTTSQHPQ-ALKQLPSVGYQRQLAAEGVL 56 Query: 167 TVHTPLMWLKKYETW 181 + ++ + Sbjct: 57 ALRPDILIGTEEMGP 71 >1jyk_A LICC protein, CTP:phosphocholine cytidylytransferase; 3D structure, CTP:phosphocholine cytidylyltransferase; 1.50A {Streptococcus pneumoniae} SCOP: c.68.1.13 PDB: 1jyl_A* Length = 254 Score = 27.9 bits (61), Expect = 1.8 Identities = 11/119 (9%), Positives = 29/119 (24%) Query: 96 MKIQDNNLPNTFVPGRNIIFLVFAATLAYRLGITNIVIGVCETDYSGYPDCRHDTIRAIE 155 ++ N P V + + GI +I+I V +R + Sbjct: 39 LRPLTENTPKALVQVNQKPLIEYQIEFLKEKGINDIIIIVGYLKEQFDYLKEKYGVRLVF 98 Query: 156 TAINLGMESHVTVHTPLMWLKKYETWKLAQDIGGQDLVNLILEESHTCYLGKRDKRYEW 214 + +++ L + N + ++ + + Sbjct: 99 NDKYADYNNFYSLYLVKEELANSYVIDADNYLFKNMFRNDLTRSTYFSVYREDCTNEWF 157 >3a2k_A TRNA(Ile)-lysidine synthase; ligase, pseudo-knot, ligase/RNA complex; 3.65A {Geobacillus kaustophilus} Length = 464 Score = 27.7 bits (60), Expect = 2.5 Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 9/68 (13%) Query: 2 NDIIKKAPSALLLFSGGQDSSTCLSWALDRFDR----VETLSFDYGQRNK-----VELEC 52 + ++ + + ++ SGG DS L L D V D+ R + +E Sbjct: 12 HQLLSEGAAVIVGVSGGPDSLALLHVFLSLRDEWKLQVIAAHVDHMFRGRESEEEMEFVK 71 Query: 53 RLCVRKKI 60 R CV ++I Sbjct: 72 RFCVERRI 79 >2gm3_A Unknown protein; AT3G01520, putative ethylene-responsive protein, USP domain, nucleotide binding domain, AMP, protein structure initiative; HET: MSE AMP; 2.46A {Arabidopsis thaliana} SCOP: c.26.2.4 Length = 175 Score = 27.2 bits (59), Expect = 3.1 Identities = 9/46 (19%), Positives = 19/46 (41%) Query: 129 TNIVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHVTVHTPLMW 174 T +++ V + YP+ RA E + + S+ + L+ Sbjct: 6 TKVMVAVNASTIKDYPNPSISCKRAFEWTLEKIVRSNTSDFKILLL 51 >2vld_A NUCS, UPF0286 protein pyrab01260; endonuclease, hydrolase; 2.60A {Pyrococcus abyssi} Length = 251 Score = 26.7 bits (59), Expect = 4.3 Identities = 6/23 (26%), Positives = 9/23 (39%) Query: 120 ATLAYRLGITNIVIGVCETDYSG 142 LA + G + C+ Y G Sbjct: 19 LDLAEKHGGVVTIFARCKVHYEG 41 >2phn_A F420-0:gamma-glutamyl ligase; coenzyme F420 biosynthesis, amide bond forming enzyme, metal dependent, NEW fold, GDP binding MCSG; HET: GDP; 1.35A {Archaeoglobus fulgidus dsm 4304} SCOP: d.340.1.1 PDB: 2g9i_A Length = 254 Score = 26.7 bits (59), Expect = 4.6 Identities = 7/42 (16%), Positives = 13/42 (30%), Gaps = 4/42 (9%) Query: 121 TLAYRLGITNIVIGVCE----TDYSGYPDCRHDTIRAIETAI 158 +R G+ IG+ D+ G D + + Sbjct: 156 GRCFRRGVVGFAIGISGVKAMKDWIGRKDLYGRELEVTVECV 197 >2e18_A NH(3)-dependent NAD(+) synthetase; ligase, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.10A {Pyrococcus horikoshii OT3} Length = 257 Score = 26.1 bits (56), Expect = 8.4 Identities = 15/71 (21%), Positives = 27/71 (38%), Gaps = 4/71 (5%) Query: 3 DIIKK--APSALLLFSGGQDSSTCLSWALDRF--DRVETLSFDYGQRNKVELECRLCVRK 58 + I++ ++ SGG DS+T A ++V L Y + VE + + Sbjct: 15 EFIREKGNNGVVIGISGGVDSATVAYLATKALGKEKVLGLIMPYFENKDVEDAKLVAEKL 74 Query: 59 KIVELMPKWKD 69 I + K Sbjct: 75 GIGYKVINIKP 85 >3dpi_A NAD+ synthetase; ssgcid, decode, structural genomics, PSI, protein structure initiative; 2.20A {Burkholderia pseudomallei 1710B} Length = 285 Score = 26.0 bits (56), Expect = 8.4 Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 2/44 (4%) Query: 1 MNDIIKKA--PSALLLFSGGQDSSTCLSWALDRFDRVETLSFDY 42 + D ++ A + +L SGG DSST A +R+ +D Sbjct: 37 VADYLRTAGLRACVLGISGGIDSSTAGRLAQLAVERLRASGYDA 80 >2gw6_A TRNA-splicing endonuclease subunit SEN15; SEN15_human, tRNA endonuclease, structural genomics, PSI, protein structure initiative; NMR {Homo sapiens} SCOP: c.52.2.1 Length = 123 Score = 26.0 bits (57), Expect = 8.5 Identities = 9/62 (14%), Positives = 26/62 (41%) Query: 45 RNKVELECRLCVRKKIVELMPKWKDSLGEDHILPLAILGDISHSSLTKNVAMKIQDNNLP 104 ++ E+ C +++ L+ + G ++P I +SH+ + + + + P Sbjct: 40 KSWHEVNCVGLPELQLICLVGTEIEGEGLQTVVPTPITASLSHNRIREILKASRKLQGDP 99 Query: 105 NT 106 + Sbjct: 100 DL 101 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 0.322 0.138 0.438 Gapped Lambda K H 0.267 0.0544 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,150,595 Number of extensions: 96386 Number of successful extensions: 286 Number of sequences better than 10.0: 1 Number of HSP's gapped: 281 Number of HSP's successfully gapped: 29 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: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 55 (25.4 bits)