RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254781120|ref|YP_003065533.1| radical SAM protein [Candidatus Liberibacter asiaticus str. psy62] (384 letters) >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 = 52.6 bits (126), Expect = 1e-07 Identities = 74/406 (18%), Positives = 116/406 (28%), Gaps = 161/406 (39%) Query: 20 ALLKIGIPQRHVRMRTSQIWKWIYVRGIRDF--QG-MSDISQEVRHLLNQHFSIIYPEIV 76 AL R V +Q+ I F QG D +E+R L Y +V Sbjct: 144 ALF------RAVGEGNAQL----VA--I--FGGQGNTDDYFEELRDLYQ-----TYHVLV 184 Query: 77 DEKISCDGTRKWLLRFPARCIGGPVEIETVYI-----------PEK--SRGTLCVSSQVG 123 + I L R ++ E V+ P + L +S + Sbjct: 185 GDLIKFSAET--LSEL-IRT---TLDAEKVFTQGLNILEWLENPSNTPDKDYL-LSIPIS 237 Query: 124 CSL-----------TC------------SFC-YTG-TQKLVRNLTA---------EEILL 149 C L T TG +Q LV TA E + Sbjct: 238 CPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLV---TAVAIAETDSWESFFV 294 Query: 150 QVLLARSLLGDF-PGCEDIEG---MVIPSVGRK--ISNIVMMGMGEPLCNFDNVKKS--L 201 V A ++L F G E +P + + N G P S L Sbjct: 295 SVRKAITVL--FFIGVRCYEAYPNTSLPPSILEDSLEN----NEGVP---------SPML 339 Query: 202 SIASDSMGLSFSK--RRITLSTSGFVP----------NIAR---VGEEIGVMLAISLHAV 246 SI+ L+ + + T+ +P N A+ V G SL+ + Sbjct: 340 SIS----NLTQEQVQDYVN-KTNSHLPAGKQVEISLVNGAKNLVVS---G--PPQSLYGL 389 Query: 247 SNDLRNILVPIN----------RKYPLEM--L-IDACRHYPGLSNARRITFEYVMLKGIN 293 + LR P RK L + + H L A + + ++ ++ Sbjct: 390 NLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVS 449 Query: 294 DSPRDALNLIKI-------------LKG--IPAKINLIPFNP--WP 322 + +D I+I L G ++ I P W Sbjct: 450 FNAKD----IQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWE 491 Score = 31.1 bits (70), Expect = 0.42 Identities = 46/287 (16%), Positives = 77/287 (26%), Gaps = 109/287 (37%) Query: 119 SSQVGCSLTCSF-CYTGTQKLVRNLTAEEILLQVLLA---RSLLGDFPGCEDIEGMV--- 171 ++ L F Y + + + +L + L L DI + Sbjct: 55 TTPAE--LVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEG----NDIHALAAKL 108 Query: 172 ---IPSVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNI 228 + K + + N+ A F K+ S S Sbjct: 109 LQENDTTLVKTKEL--------IKNYIT-------ARIMAKRPFDKK----SNSALF-RA 148 Query: 229 ARVGEEIGVMLAISLHAV------SND----LRNILVPINRKYP--LEMLIDAC-RHYPG 275 G L A+ ++D LR++ + Y + LI Sbjct: 149 VGEGN-------AQLVAIFGGQGNTDDYFEELRDL----YQTYHVLVGDLIKFSAETLSE 197 Query: 276 LSNARRITFEYVMLKGINDSPRDALNLIKILKGIPAKINLIPFNPWPGCEYLCSDQKDIV 335 L + E V +G LN+++ L+ P+ P +YL Sbjct: 198 LI-RTTLDAEKVFTQG--------LNILEWLEN-PSNT--------PDKDYLL------- 232 Query: 336 TFSECIKRSGYSSPIRTPR-GLDILA----AC-------GQLKS-LS 369 S PI P G+ LA G+L+S L Sbjct: 233 -----------SIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLK 268 Score = 29.5 bits (66), Expect = 1.1 Identities = 59/279 (21%), Positives = 100/279 (35%), Gaps = 104/279 (37%) Query: 34 RTSQIWKWIYVRG---IRDFQGMSDISQEVRHLLNQ--HF-------------SIIYPEI 75 +TS+ + ++ R +D G S + + + +N HF ++I+ I Sbjct: 1637 KTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETI 1696 Query: 76 VDEKISCDG---------------TRKWLL---RF--PARCIGGPVEIETVYIPEKSRGT 115 VD K+ + + K LL +F PA + E + KS+G Sbjct: 1697 VDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDL----KSKGL 1752 Query: 116 LCVSSQ-VGCSLTCSFCYTGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMV--- 171 + + G SL Y L ++ E L++V+ R GM Sbjct: 1753 IPADATFAGHSLGE---YAALASLADVMSIES-LVEVVFYR-------------GMTMQV 1795 Query: 172 -IP--SVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNI 228 +P +GR SN GM ++I + SFS+ + +V + Sbjct: 1796 AVPRDELGR--SN---YGM-------------IAINPGRVAASFSQEALQ-----YV--V 1830 Query: 229 ARVGEEIGVMLAISLHAVSN-------DLR------NIL 254 RVG+ G ++ I + V N DLR N+L Sbjct: 1831 ERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVL 1869 >3c8f_A Pyruvate formate-lyase 1-activating enzyme; adoMet radical, SAM radical, activase, glycyl radical, 4Fe- 4S, carbohydrate metabolism, cytoplasm; HET: MT2 PGE; 2.25A {Escherichia coli} PDB: 3cb8_A* Length = 245 Score = 49.2 bits (116), Expect = 1e-06 Identities = 36/206 (17%), Positives = 74/206 (35%), Gaps = 38/206 (18%) Query: 123 GCSLTCSFCY---TGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMVIPSVGRKI 179 GC + C +C+ T + +T E+++ +V+ R + G Sbjct: 28 GCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRHFMNASGGG--------------- 72 Query: 180 SNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIARVGEE---IG 236 V GE + + V+ L T+GFV V +E + Sbjct: 73 ---VTASGGEAILQAEFVRDWFRACKKEG------IHTCLDTNGFVRRYDPVIDELLEVT 123 Query: 237 VMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNARRITFEYVMLKGINDSP 296 ++ + L +++++ LV ++ LE ++ YV++ G +D Sbjct: 124 DLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKYLANKNV------KVWIRYVVVPGWSDDD 177 Query: 297 RDALNLIKILKGIPA--KINLIPFNP 320 A L + + + KI L+P++ Sbjct: 178 DSAHRLGEFTRDMGNVEKIELLPYHE 203 >2yx0_A Radical SAM enzyme; predicted tRNA modification enzyme, metal binding protein, structural genomics, NPPSFA; 2.21A {Pyrococcus horikoshii} Length = 342 Score = 42.4 bits (99), Expect = 2e-04 Identities = 28/210 (13%), Positives = 57/210 (27%), Gaps = 21/210 (10%) Query: 123 GCSLTCSFCY------TGTQKLVRNLTAEEILLQVLLARSLLGDFPGCEDIEGMVIPSVG 176 C+ C FC+ GT+ I+ + + A+ L Sbjct: 80 WCTHNCIFCWRPMENFLGTELPQPWDDPAFIVEESIKAQRKLLIGYKGNPKVDKKKFEEA 139 Query: 177 RKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNIARVGEEIG 236 ++ + GEP+ + T+G +P + Sbjct: 140 WNPTHAAISLSGEPMLYPYMGDLVEEFHKRGF-------TTFIVTNGTIPERLEEMIKED 192 Query: 237 ---VMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYPGLSNAR-RITFEYVMLKGI 292 L +S+ A + N + E ++ + + R ++KG Sbjct: 193 KLPTQLYVSITAPDIETYNSVNIPMIPDGWERILRFLEL---MRDLPTRTVVRLTLVKGE 249 Query: 293 NDS-PRDALNLIKILKGIPAKINLIPFNPW 321 N P LI + + + F + Sbjct: 250 NMHSPEKYAKLILKARPMFVEAKAYMFVGY 279 >2z2u_A UPF0026 protein MJ0257; metal binding protein; 2.40A {Methanocaldococcus jannaschii} Length = 311 Score = 40.1 bits (93), Expect = 8e-04 Identities = 30/214 (14%), Positives = 66/214 (30%), Gaps = 30/214 (14%) Query: 120 SQVGCSLTCSFCYTGTQKLV----------RNLTAEEILLQVL-LARSLLGDFPGCEDIE 168 S + C C FC+ + + + E + ++L + + ++ + G D Sbjct: 58 SVIWCQQNCIFCWRVLPRDIGIDISQIKEPKWEEPEVVYEKILAMHKRIIMGYAGVLDRV 117 Query: 169 GMVIPSVGRKISNIVMMGMGEPLCNFDNVKKSLSIASDSMGLSFSKRRITLSTSGFVPNI 228 G + ++ + GEP + + F+ ++ Sbjct: 118 GEKKFKEALEPKHVAISLSGEPTLYPYLDE----LIKIFHKNGFTTFVVSNGI-----LT 168 Query: 229 ARVGEEIGVMLAISLHAVSND-LRNILVPINRKYPLEML-IDACRHYPGLSNARRITFEY 286 + + L ISL A D R I + + +D + +R Sbjct: 169 DVIEKIEPTQLYISLDAYDLDSYRRICGGKKEYWESILNTLDILK------EKKRTCIRT 222 Query: 287 VMLKGINDSPRDALNLIKILKGIPAKINLIPFNP 320 +++G ND + L + + I L + Sbjct: 223 TLIRGYNDDILKFVELYE--RADVHFIELKSYMH 254 >3cux_A Malate synthase; TIM barrel, glyoxylate bypass, transferase, tricarboxylic acid cycle; 1.70A {Bacillus anthracis} Length = 528 Score = 29.6 bits (66), Expect = 1.3 Identities = 11/51 (21%), Positives = 21/51 (41%) Query: 31 VRMRTSQIWKWIYVRGIRDFQGMSDISQEVRHLLNQHFSIIYPEIVDEKIS 81 + +Q+W+WI G + G + + + L + + I EI E Sbjct: 446 AEISRAQVWQWIRHEGGKLNDGRNITLELMEELKEEELAKIEREIGKEAFK 496 >3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation termination, ATP-binding, cytoplasm, hydrolase, membrane; 2.80A {Schizosaccharomyces pombe} Length = 508 Score = 29.3 bits (65), Expect = 1.7 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 13/73 (17%) Query: 19 EALLKIGIP--------QRHVRMRTSQIWKWIYVRGIRDFQGMSDISQEVRHLLNQH--- 67 +A + IG P +R + R +++ + D QG+ D S ++HLL ++ Sbjct: 235 DAQIVIGTPGTVMDLMKRRQLDARDIKVFVLDEADNMLDQQGLGDQSMRIKHLLPRNTQI 294 Query: 68 --FSIIYPEIVDE 78 FS + E V++ Sbjct: 295 VLFSATFSERVEK 307 >2a5h_A L-lysine 2,3-aminomutase; radical SAM, four-iron-four-sulfur cluster, 4Fe4S, FS4, SAM, S-adenosylmethionine, alpha-beta channel; HET: SAM LYS PLP; 2.10A {Clostridium subterminale} Length = 416 Score = 27.7 bits (61), Expect = 4.7 Identities = 23/143 (16%), Positives = 49/143 (34%), Gaps = 12/143 (8%) Query: 215 RRITLSTSGFVPNIARVGEEIGVMLAISLHAVSNDLRNILVPINRKYPLEMLIDACRHYP 274 + + + V R+ E L + + + + +P E+ ++ R Sbjct: 195 EIVRIGSRTPVVLPQRITPE--------LVNMLKKYHPVWLNTHFNHPNEITEESTRACQ 246 Query: 275 GLSNAR-RITFEYVMLKGINDSPRDALNLIKILKGIPAK-INLIPFNPWPGCEYLCSDQK 332 L++A + + V+L+G+ND L+ L I + + + G E+ + Sbjct: 247 LLADAGVPLGNQSVLLRGVNDCVHVMKELVNKLVKIRVRPYYIYQCDLSLGLEHFRTPVS 306 Query: 333 DIVTF--SECIKRSGYSSPIRTP 353 + SGY P Sbjct: 307 KGIEIIEGLRGHTSGYCVPTFVV 329 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 0.323 0.140 0.421 Gapped Lambda K H 0.267 0.0521 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 3,396,284 Number of extensions: 162897 Number of successful extensions: 426 Number of sequences better than 10.0: 1 Number of HSP's gapped: 422 Number of HSP's successfully gapped: 16 Length of query: 384 Length of database: 5,693,230 Length adjustment: 94 Effective length of query: 290 Effective length of database: 3,414,294 Effective search space: 990145260 Effective search space used: 990145260 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 57 (26.2 bits)