RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780423|ref|YP_003064836.1| S-adenosylmethionine synthetase [Candidatus Liberibacter asiaticus str. psy62] (413 letters) >1p7l_A S-adenosylmethionine synthetase; AMPPNP, SAM, transferase; HET: SAM ANP PPK; 2.50A {Escherichia coli} SCOP: d.130.1.1 d.130.1.1 d.130.1.1 PDB: 1fug_A 1mxb_A* 1mxc_A* 1mxa_A* 1rg9_A* 1xra_A 1xrb_A 1xrc_A Length = 383 Score = 467 bits (1202), Expect = e-132 Identities = 197/412 (47%), Positives = 248/412 (60%), Gaps = 33/412 (8%) Query: 3 ADFLFTSESVSEGHPDKICDRISDEIVDLVYREAIESKMDVNSVRVACEVLVTKNKVIVA 62 A LFTSESVSEGHPDKI D+ISD ++D + + D + RVACE V V+V Sbjct: 1 AKHLFTSESVSEGHPDKIADQISDAVLDAILEQ------DPKA-RVACETYVKTGMVLVG 53 Query: 63 GEVRLPHGLSKKDSITGQYVVDKEKFEKVVRSVIRSIGYEQE--GFHWETVDVEVLLHSQ 120 GE IT VD E++ R+ +R IGY GF + V + Q Sbjct: 54 GE------------ITTSAWVD---IEEITRNTVREIGYVHSDMGFDANSCAVLSAIGKQ 98 Query: 121 SSDIAYGVDNASDDCSTLGAGDQGIMFGYACRETADFMPAPIYYAHRILRTLADARKNSG 180 S DI GVD D GAGDQG+MFGYA ET MPAPI YAHR+++ A+ RKN Sbjct: 99 SPDINQGVD--RADPLEQGAGDQGLMFGYATNETDVLMPAPITYAHRLVQRQAEVRKN-- 154 Query: 181 GDVSKLGPDAKSQVTIRYVDNKVCEVKSIVLSIQHFDPTWDRGKVRSVVEPYILKALEDI 240 G + L PDAKSQVT +Y D K+ + ++VLS QH + + +V+E I L Sbjct: 155 GTLPWLRPDAKSQVTFQYDDGKIVGIDAVVLSTQHSEEIDQKSLQEAVMEEIIKPILPAE 214 Query: 241 KISPDCSWYINPAGKFVIGGPCSDAGLTGRKIIVDTYGGASPHGGGAFSGKDITKVDRAA 300 ++ ++INP G+FVIGGP D GLTGRKIIVDTYGG + HGGGAFSGKD +KVDR+A Sbjct: 215 WLTSATKFFINPTGRFVIGGPMGDCGLTGRKIIVDTYGGMARHGGGAFSGKDPSKVDRSA 274 Query: 301 AYAARYLAKNIVAAGLADRCTIQLSYAIGISRPLSIFVDLHDSGKVSESCVANAINKVMD 360 AYAARY+AKNIVAAGLADRC IQ+SYAIG++ P SI V+ + KV + + + D Sbjct: 275 AYAARYVAKNIVAAGLADRCEIQVSYAIGVAEPTSIMVETFGTEKVPSEQLTLLVREFFD 334 Query: 361 LSVSGIRDHLNLSRPIYAQTSAYGHFGRSANQDGFFPWEALDLIEPLKKAIG 412 L G+ L+L PIY +T+AYGHFGR FPWE D + L+ A G Sbjct: 335 LRPYGLIQMLDLLHPIYKETAAYGHFGREH-----FPWEKTDKAQLLRDAAG 381 >3iml_A S-adenosylmethionine synthetase; structural genomics, ATP- binding, cobalt, cytoplasm, magnesium, metal-binding, nucleotide-binding; 2.35A {Burkholderia pseudomallei} Length = 399 Score = 432 bits (1111), Expect = e-122 Identities = 195/414 (47%), Positives = 252/414 (60%), Gaps = 29/414 (7%) Query: 1 MSADFLFTSESVSEGHPDKICDRISDEIVDLVYREAIESKMDVNSVRVACEVLVTKNKVI 60 M+ D+LFTSESVSEGHPDK+ D+ISD I+D + + D S RVA E L V+ Sbjct: 5 MANDYLFTSESVSEGHPDKVADQISDAILDAILAQ------DKYS-RVAAETLCNTGLVV 57 Query: 61 VAGEVRLPHGLSKKDSITGQYVVDKEKFEKVVRSVIRSIGYEQE--GFHWETVDVEVLLH 118 +AGE+ + ++ R I+ IGY+ G + V V Sbjct: 58 LAGEITTTA---------------NIDYIQIARDTIKRIGYDNTDYGIDYRGCAVLVAYD 102 Query: 119 SQSSDIAYGVDNASDDCSTLGAGDQGIMFGYACRETADFMPAPIYYAHRILRTLADARKN 178 QS DIA GVD A D+ GAGDQG+MFGYAC ET + MP PI+ +HR++ A+ R++ Sbjct: 103 KQSPDIAQGVDRAHDNNLDQGAGDQGLMFGYACDETPELMPLPIHLSHRLVERQANLRRD 162 Query: 179 SGGDVSKLGPDAKSQVTIRYVDNKVCEVKSIVLSIQHFDPTWDRGKVRSVVEPYILKALE 238 G + L PDAKSQVT+RYVD K + ++VLS QH +V+E I L Sbjct: 163 --GRLPWLRPDAKSQVTVRYVDGKPHSIDTVVLSTQHAPEIDLPALREAVIEEVIKPTLP 220 Query: 239 DIKISPDCSWYINPAGKFVIGGPCSDAGLTGRKIIVDTYGGASPHGGGAFSGKDITKVDR 298 I D + +NP G+FVIGGP D GLTGRKIIVDTYGGA+PHGGGAFSGKD +KVDR Sbjct: 221 ADLIKGDIKFLVNPTGRFVIGGPQGDCGLTGRKIIVDTYGGAAPHGGGAFSGKDPSKVDR 280 Query: 299 AAAYAARYLAKNIVAAGLADRCTIQLSYAIGISRPLSIFVDLHDSGKVSESCVANAINKV 358 +AAYA RY+AKNIVAAGLA R IQ+SYAIG++ P S+ V+ +G+VS+ + + + Sbjct: 281 SAAYAGRYVAKNIVAAGLASRALIQVSYAIGVAEPTSVMVNTFGTGRVSDETITKLVREH 340 Query: 359 MDLSVSGIRDHLNLSRPIYAQTSAYGHFGRSANQDGFFPWEALDLIEPLKKAIG 412 DL GI L+L RPIY +T+AYGHFGR ++ F WEA D L +A G Sbjct: 341 FDLRPKGIIQMLDLLRPIYEKTAAYGHFGR---EEPEFSWEAADKALALAEAAG 391 >2p02_A S-adenosylmethionine synthetase isoform type-2; structural genomics, structural genomics consortium, SGC, transferase; HET: SAM; 1.21A {Homo sapiens} SCOP: d.130.1.1 d.130.1.1 d.130.1.1 PDB: 1qm4_A 1o92_A* 1o93_A* 1o90_A* 1o9t_A 2obv_A* Length = 396 Score = 397 bits (1021), Expect = e-111 Identities = 174/411 (42%), Positives = 248/411 (60%), Gaps = 36/411 (8%) Query: 1 MSADFLFTSESVSEGHPDKICDRISDEIVDLVYREAIESKMDVNSVRVACEVLVTKNKVI 60 FLFTSESV EGHPDKICD+ISD ++D ++ D ++ +VACE + ++ Sbjct: 15 EEGTFLFTSESVGEGHPDKICDQISDAVLDAHLQQ------DPDA-KVACETVAKTGMIL 67 Query: 61 VAGEVRLPHGLSKKDSITGQYVVDKEKFEKVVRSVIRSIGY--EQEGFHWETVDVEVLLH 118 +AGE+ VD ++KVVR ++ IGY +GF ++T +V V L Sbjct: 68 LAGEITSRA------------AVD---YQKVVREAVKHIGYDDSSKGFDYKTCNVLVALE 112 Query: 119 SQSSDIAYGVDNASDDCSTLGAGDQGIMFGYACRETADFMPAPIYYAHRILRTLADARKN 178 QS DIA GV ++ +GAGDQG+MFGYA ET + MP I AH++ LA+ R+N Sbjct: 113 QQSPDIAQGVHLDRNE-EDIGAGDQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRN 171 Query: 179 SGGDVSKLGPDAKSQVTIRYVDNKVCEVKSIVLSIQHF---DPTWDRGKVRSVVEPYILK 235 G + L PD+K+QVT++Y+ ++ + V +I D ++R ++ ++K Sbjct: 172 --GTLPWLRPDSKTQVTVQYMQDRGAVLPIRVHTIVISVQHDEEVCLDEMRDALKEKVIK 229 Query: 236 A-LEDIKISPDCSWYINPAGKFVIGGPCSDAGLTGRKIIVDTYGGASPHGGGAFSGKDIT 294 A + + D +++ P+G+FVIGGP DAGLTGRKIIVDTYGG HGGGAFSGKD T Sbjct: 230 AVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDYT 289 Query: 295 KVDRAAAYAARYLAKNIVAAGLADRCTIQLSYAIGISRPLSIFVDLHDSGKVSESCVANA 354 KVDR+AAYAAR++AK++V GL R +Q+SYAIG+S PLSI + + + + SE + Sbjct: 290 KVDRSAAYAARWVAKSLVKGGLCRRVLVQVSYAIGVSHPLSISIFHYGTSQKSERELLEI 349 Query: 355 INKVMDLSVSGIRDHLNLSRPIYAQTSAYGHFGRSANQDGFFPWEALDLIE 405 + K DL I L+L +PIY +T+AYGHFGR + FPWE ++ Sbjct: 350 VKKNFDLRPGVIVRDLDLKKPIYQRTAAYGHFGRDS-----FPWEVPKKLK 395 >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 = 64.2 bits (156), Expect = 5e-11 Identities = 79/502 (15%), Positives = 136/502 (27%), Gaps = 230/502 (45%) Query: 3 ADFL-FTSESVSEGHPDKICDRISDEIVDLVYREAIESKM----DVNSVRVACE-----V 52 FL + S V + D++++L E E+ D++++ Sbjct: 62 GKFLGYVSSLVEPSKVGQ-----FDQVLNLCLTE-FENCYLEGNDIHALAAKLLQENDTT 115 Query: 53 LVTKNKVI--------VAGEVRLPHGLSK--KDSITGQ---YVV------DKEKFEK--- 90 LV ++I +A S + G + + FE+ Sbjct: 116 LVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRD 175 Query: 91 -------VVRSVIRSIG---------------YEQEGF---HW----ETV-DVEVLLHSQ 120 +V +I+ +G W D + LL Sbjct: 176 LYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIP 235 Query: 121 SS-------DIA-YGVDNASDDCSTLG-------------AG-DQGI------------- 145 S +A Y V LG G QG+ Sbjct: 236 ISCPLIGVIQLAHYVVT-----AKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWE 290 Query: 146 ------------MF--GYACRETADFMPAPIYYAHRILR--TLADARKNSGGDVSKLGPD 189 +F G C E Y + L L D+ +N+ G S P Sbjct: 291 SFFVSVRKAITVLFFIGVRCYEA---------YPNTSLPPSILEDSLENNEGVPS---P- 337 Query: 190 AKSQVTIRYVDNKVCEVKSIVLSIQHFDPTWDRGKVRSVVEPYI------LKALEDIKIS 243 +LSI + V+ Y+ L A + ++IS Sbjct: 338 --------------------MLSI--------SNLTQEQVQDYVNKTNSHLPAGKQVEIS 369 Query: 244 PDCSWYINPAGKFVIGGPCSD-AGLTG--RKIIVDTYGGASPHGGGAFSGKDITKV---D 297 +N A V+ GP GL RK A SG D +++ + Sbjct: 370 -----LVNGAKNLVVSGPPQSLYGLNLTLRKA-------------KAPSGLDQSRIPFSE 411 Query: 298 RAAAYAARYLAKNIVAAGLADRCTIQLSYAIGISRPLSIFVDLHDSGKVSESCVANAINK 357 R ++ R+L ++ P F H S + A + Sbjct: 412 RKLKFSNRFLP---------------------VASP---F---H-S-----HLLVPASDL 438 Query: 358 VM-DLSVSGIR-DHLNLSRPIY 377 + DL + + + ++ P+Y Sbjct: 439 INKDLVKNNVSFNAKDIQIPVY 460 Score = 52.3 bits (125), Expect = 2e-07 Identities = 62/443 (13%), Positives = 116/443 (26%), Gaps = 182/443 (41%) Query: 41 MDVNSVR--------VACEVLVTKNKVIVAGEVR------LPHGLSKKDSITGQYVVDKE 86 MD S R + +LV +A +++ LP + + Sbjct: 1 MDAYSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILP---EPTEGFAAD-----D 52 Query: 87 KFEKVVRSVIRSIGY----EQEGFHWETVDV-EVLLHS------QSSDI-AYGVDNASDD 134 + V + +GY + + V + L + +DI A ++ Sbjct: 53 EPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQEN 112 Query: 135 CSTLGAGDQGIMFGYACRETADFMPAPIYYAHRILRTLADARKNSGGDVSKLGPDA---- 190 +TL +++ AR + K A Sbjct: 113 DTTLVK------------------------TKELIKNYITARIMAKRPFDKKSNSALFRA 148 Query: 191 --KSQVTI-----------RYVDNKVCEVKSIVLSIQHFDPTWDRGKVRSVVEPYILKA- 236 + + Y + E++ + + T+ +V I + Sbjct: 149 VGEGNAQLVAIFGGQGNTDDYFE----ELRDL------YQ-TY-----HVLVGDLIKFSA 192 Query: 237 --LEDIKISPDC------------SWYINPAGK----FVIGGP----------------- 261 L ++ + W NP+ +++ P Sbjct: 193 ETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVT 252 Query: 262 CSDAGLT-GRKIIVDTYGGASPHGGGAFSGKDITKVDRAAAYAA-------RYLAKNIVA 313 G T G + GA+ H G +T A A A + + Sbjct: 253 AKLLGFTPGE--LRSYLKGATGHSQGL-----VT----AVAIAETDSWESFFVSVRKAIT 301 Query: 314 A----GLADRCTIQLSYAIGISRPLSIFVDLHDS---GKVSESCVANAINKVMDLSVSGI 366 G+ RC +Y S P SI L DS + S M LS+S + Sbjct: 302 VLFFIGV--RC--YEAYPN-TSLPPSI---LEDSLENNEGVPSP--------M-LSISNL 344 Query: 367 -RD-----------HLNLSRPIY 377 ++ HL + + Sbjct: 345 TQEQVQDYVNKTNSHLPAGKQVE 367 Score = 28.4 bits (63), Expect = 3.2 Identities = 9/20 (45%), Positives = 11/20 (55%), Gaps = 6/20 (30%) Query: 52 VLVTKNK------VIVAGEV 65 VL +NK VIVAG + Sbjct: 514 VLTHRNKDGTGVRVIVAGTL 533 >2o9u_X Monellin chain B and monellin chain A; alternative conformations, 3-10 polyproline II helix, plant protein; 1.15A {Dioscoreophyllum cumminsii} SCOP: d.17.1.1 PDB: 1m9g_A 1fa3_A 1iv7_A 1iv9_A 1mnl_A 1mol_A 1fuw_A 4mon_B 3mon_B 1krl_B 4mon_A 1krl_A 3mon_A 2q33_B* 2q33_A* Length = 97 Score = 30.8 bits (69), Expect = 0.65 Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 11/70 (15%) Query: 79 GQYVVDKEK---------FEKVVRSVIRSIGYEQEGFHWETVDVEVLLHSQSSDIAYGVD 129 G++ VD+E F KV+R ++ YE EGF E E L+ +SD + D Sbjct: 17 GKFAVDEENKIGQYGRLTFNKVIRPCMKKTIYENEGFR-EIKGYEYQLYVYASDKLFRAD 75 Query: 130 NASDDCSTLG 139 S+D T G Sbjct: 76 -ISEDYKTRG 84 >1vma_A Cell division protein FTSY; TM0570, structural genomics, JCSG, protein structure initiative, PSI, joint center for structural genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10 Length = 306 Score = 29.8 bits (66), Expect = 1.1 Identities = 22/156 (14%), Positives = 41/156 (26%), Gaps = 2/156 (1%) Query: 206 VKSIVLSIQHFDPTWDRGKVRSVVEPYI-LKALEDIKISPDCSWYINPAGKFVIGGPCSD 264 +K I+L I +FD + V + + + GK V+ Sbjct: 83 LKEIILEILNFDTKLNVPPEPPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAADT 142 Query: 265 AGLTGRKIIVDTYGGASPHGGGAFSGKDITKVDRAAAYAARYLAKNIVAAGLADRCTIQL 324 + + G D V A A K++V A R + Sbjct: 143 FRAAAIEQLKIWGERVGATVISHSEGADPAAVAFDAVAHALARNKDVVIIDTAGRLHTKK 202 Query: 325 SYAIGISRPLSIFVDLHDSGKVSESCVANAINKVMD 360 + + R + V E+ + + Sbjct: 203 NL-MEELRKVHRVVKKKIPDAPHETLLVIDATTGQN 237 >3ho1_A Argonaute; argonaute, protein-DNA-RNA complex, plasmid; 2.60A {Thermus thermophilus HB27} PDB: 3dlb_A* 3dlh_A* 3f73_A* 3hm9_A 3hvr_A 3hxm_A* 3hk2_A 3hjf_A Length = 685 Score = 28.0 bits (62), Expect = 4.2 Identities = 5/15 (33%), Positives = 12/15 (80%) Query: 158 MPAPIYYAHRILRTL 172 +PAP++ A R+++ + Sbjct: 652 LPAPLHLADRLVKEV 666 >1yvu_A Hypothetical protein AQ_1447; RNAse H fold, RNA binding protein, gene regulation; 2.90A {Aquifex aeolicus VF5} SCOP: b.34.14.1 c.55.3.10 PDB: 2f8s_A 2f8t_A 2nub_A Length = 706 Score = 27.6 bits (61), Expect = 4.7 Identities = 4/11 (36%), Positives = 9/11 (81%) Query: 158 MPAPIYYAHRI 168 +PA ++Y+ +I Sbjct: 675 LPATVHYSDKI 685 >2w42_A PIWI, putative uncharacterized protein; RNAI, RISC, argonaute, PIWI domain, protein/DNA complex; 1.90A {Archaeoglobus fulgidus} PDB: 1ytu_A 2bgg_A 1w9h_A Length = 427 Score = 27.7 bits (61), Expect = 5.0 Identities = 2/11 (18%), Positives = 5/11 (45%) Query: 158 MPAPIYYAHRI 168 +P + Y + Sbjct: 387 LPVTVNYPKLV 397 >3b7k_A Acyl-coenzyme A thioesterase 12; hotdog fold, structural genomics, structural genomics consortium, SGC, cytoplasm, fatty acid metabolism, hydrolase; HET: COA; 2.70A {Homo sapiens} Length = 333 Score = 27.7 bits (61), Expect = 5.1 Identities = 12/65 (18%), Positives = 22/65 (33%), Gaps = 2/65 (3%) Query: 283 HGGGAFSGKDITKVDRAAAYAARYLAKNIVAAGLADRCTIQLSYAIGISRPLSIFVDLHD 342 G +G+ + +D A AA A D IQ + + ++I + Sbjct: 39 ARGELSAGQLLKWIDTTACLAAEKHAGVSCVTASVDD--IQFEETARVGQVITIKAKVTR 96 Query: 343 SGKVS 347 + S Sbjct: 97 AFSTS 101 >2v4n_A Multifunctional protein SUR E; hydrolase, surviVal protein, stationary phase, phosphatase, mononucleotidase, divalent metal ION; 1.7A {Salmonella typhimurium} PDB: 2v4o_A Length = 254 Score = 27.3 bits (60), Expect = 6.0 Identities = 25/119 (21%), Positives = 41/119 (34%), Gaps = 18/119 (15%) Query: 298 RAAAYAARYLAKNIVAAGLADRCTIQLSYAIGISRPLSIFVDLHDSGKVSES----CVAN 353 + A A R A V A +R S ++ + L F + V CV Sbjct: 18 QTLAKALREFADVQVVAPDRNRSGA--SNSLTLESSLRTFTFDNGDIAVQMGTPTDCVYL 75 Query: 354 AINKVM----DLSVSGIRDHLNLSRPIY-------AQTSA-YGHFGRSANQDGFFPWEA 400 +N +M D+ VSGI NL + A G + + +G+ ++ Sbjct: 76 GVNALMRPRPDIVVSGINAGPNLGDDVIYSGTVAAAMEGRHLGFPALAVSLNGYQHYDT 134 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 0.136 0.403 Gapped Lambda K H 0.267 0.0716 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 3,612,722 Number of extensions: 167024 Number of successful extensions: 490 Number of sequences better than 10.0: 1 Number of HSP's gapped: 471 Number of HSP's successfully gapped: 17 Length of query: 413 Length of database: 5,693,230 Length adjustment: 95 Effective length of query: 318 Effective length of database: 3,390,050 Effective search space: 1078035900 Effective search space used: 1078035900 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 (21.7 bits) S2: 58 (26.1 bits)