RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780836|ref|YP_003065249.1| putative type I restriction-modification system DNA methylase [Candidatus Liberibacter asiaticus str. psy62] (674 letters) >3lkd_A Type I restriction-modification system methyltransferase subunit; Q5M500_STRT2, STU0711, NESG, SUR80, structural genomics, PSI-2; 2.25A {Streptococcus thermophilus} Length = 542 Score = 231 bits (589), Expect = 4e-61 Identities = 113/497 (22%), Positives = 196/497 (39%), Gaps = 65/497 (13%) Query: 1 MTEFTGSAASLANFIWKNAEDLWGDFKHTDFGKVILPFTLLRRLECALEPTRSAVREK-- 58 M+E T ++ SL +W +A+ L D+ +L + L + + E+ Sbjct: 1 MSETTQTSQSLYQALWNSADVLRSKMDANDYKSYLLGMVFYKYLSDKMLFFVAETMEEET 60 Query: 59 ---------YLAFGGSNIDLESFVKVA--GYSFYNTSEYSLSTLGS--TNTRNNLESYIA 105 Y + E + V S+ + + + L + LE Sbjct: 61 ESLDEALAVYRKYYEDEETHEDLLAVITDEMSYAIHPDLTFTALVERVNDGSFQLEDLAQ 120 Query: 106 SFSDNAKA------IFEDFDFSST---IARLEKAGLLYKICKNFSGIELHPDTVPDRVMS 156 F D ++ +FED D S ++ + + K + +++ ++ Sbjct: 121 GFRDIEQSDELYENLFEDIDLYSKKLGATPQKQNQTVAAVMKELAVLDVAGH--AGDMLG 178 Query: 157 NIYEHLIRRFGSEVSEGAEDFMTPRDVVHLATALLLDPDDALFKESPGMIRTLYDPTCGT 216 + YE+LI +F ++ + A +F TP+ V L T + + TLYD T G+ Sbjct: 179 DAYEYLIGQFATDSGKKAGEFYTPQPVAKLMTQIAFLGRE------DKQGFTLYDATMGS 232 Query: 217 GGFLTDAMNHVADCGSHHKIPPILVPHGQELEPETHAVCVAGMLIRRLESDPRRDLSKNI 276 G L +A + + +V GQEL T+ + M++ + + + + Sbjct: 233 GSLLLNAKRYSRQPQT-------VVYFGQELNTSTYNLARMNMILHGVPIENQF-----L 280 Query: 277 QQGSTLSKDLFT--GKRFHYCLSNPPFGKKWEKDKDAVEKEHKNGELGRFGPGLPKISDG 334 TL +D T F L NPP+ KW ++ L S Sbjct: 281 HNADTLDEDWPTQEPTNFDGVLMNPPYSAKWSASSGFMDDPRF-----SPFGKLAPKSKA 335 Query: 335 SMLFLMHLANKLELPPNGGGRAAIVLSSSPLFNGRAGSGESEIRRWLLENDLIEAIVALP 394 FL+H L+ G AIVL LF G A E IR+ LLE I+ ++ LP Sbjct: 336 DFAFLLHGYYHLKQDN---GVMAIVLPHGVLFRGNA---EGTIRKALLEEGAIDTVIGLP 389 Query: 395 TDLFFRTNIATYLWILSNRKTEERRGKVQLINATDLWTSIRNEGKKRRIINDDQRRQILD 454 ++FF T+I T + IL +T V I+A+ + ++GK + I+ D +IL+ Sbjct: 390 ANIFFNTSIPTTVIILKKNRTNR---DVYFIDASKEF----DKGKNQNIMTDAHIEKILN 442 Query: 455 IYVSRENG-KFSRMLDY 470 Y SRE+ KF+ + + Sbjct: 443 AYKSREDIDKFAHLASF 459 >3khk_A Type I restriction-modification system methylation subunit; structural genomics, PSI-2, protein structure initiative; 2.55A {Methanosarcina mazei} Length = 544 Score = 217 bits (554), Expect = 6e-57 Identities = 94/515 (18%), Positives = 175/515 (33%), Gaps = 85/515 (16%) Query: 11 LANFIWKNAEDLWGDFKHTDFGKVILPFTLLRRLECALEPTRSAVREKYLAFGGSNID-- 68 L N +W+ A+ L + ++ V+L L+ + A E + + E + NI Sbjct: 13 LDNQLWRAADKLRSNLDAANYKHVVLGLIFLKYVSDAFEERQQELTELFQKDDDDNIYYL 72 Query: 69 -LESFVKVAGYS------------------FYNTSEYSLSTLGSTNTRNNLESYIA-SFS 108 E + Y F+ + L T Sbjct: 73 PREDYDSDEAYQQAIAEELEIGDYYTEKNVFWVPKTARWNKLRDVITLPTGSVIWQDEQG 132 Query: 109 DNAKAIFEDFDFSSTIARLEKAG-LLYKICKNFSGIELHPDTVPDR-------------- 153 ++ K + + +EKA L I S +L D + Sbjct: 133 EDVKLRSVSWLIDNAFDDIEKANPKLKGILNRISQYQLDADKLIGLINEFSLTSFNNPEY 192 Query: 154 -----------VMSNIYEHLIRRFGSEVSEGAEDFMTPRDVVHLATALLLDPDDALFKES 202 ++ ++YE+ + +F + + TP+ +V L + + Sbjct: 193 NGEKLNLKSKDILGHVYEYFLGQFALAEGKQGGQYYTPKSIVTL-----------IVEML 241 Query: 203 PGMIRTLYDPTCGTGGFLTDAMNHVADCGSHHKIPPILVP-----HGQELEPETHAVCVA 257 +YDP G+GGF + + + +GQE P T + Sbjct: 242 EPYKGRVYDPAMGSGGFFVSSDKFIEKHANVKHYNASEQKKQISVYGQESNPTTWKLAAM 301 Query: 258 GMLIRRLESDPRRDLSKNIQQGSTLSKDLFTGKRFHYCLSNPPFGKKWEKDKDAVEKEH- 316 M+IR ++ + + + D R + ++NPPF K + + Sbjct: 302 NMVIRGIDFNF------GKKNADSFLDDQHPDLRADFVMTNPPFNMKDWWHEKLADDPRW 355 Query: 317 KNGELGRFGPGLPKISDGSMLFLMHLANKLELPPNGGGRAAIVLSSSPLFNGRAGSGESE 376 G P + + +++H+ L G A ++ + S N + E E Sbjct: 356 TINTNGEKRILTPPTGNANFAWMLHM---LYHLAPTGSMALLLANGSMSSNT---NNEGE 409 Query: 377 IRRWLLENDLIEAIVALPTDLFFRTNIATYLWILSNRKT-----EERRGKVQLINATDLW 431 IR+ L+E DL+E +VALP LF T I +W L+ K +RRG+V I+A L Sbjct: 410 IRKTLVEQDLVECMVALPGQLFTNTQIPACIWFLTKDKNAKNGKRDRRGQVLFIDARKLG 469 Query: 432 TSIRNEGKKRRIINDDQRRQILDIYVSRENGKFSR 466 + + R D+ +++ D + + + Sbjct: 470 YM---KDRVLRDFKDEDIQKLADTFHNWQQEWSEE 501 >2ar0_A M.ecoki, type I restriction enzyme ecoki M protein; structural genomics, protein structure initiative, nysgxrc; 2.80A {Escherichia coli} SCOP: c.66.1.45 Length = 541 Score = 140 bits (354), Expect = 7e-34 Identities = 91/470 (19%), Positives = 164/470 (34%), Gaps = 74/470 (15%) Query: 11 LANFIWKNAEDLW-GDFKHTDFGKVILPFTLLRRLECALEPTRSAVREKYLAFGGSNIDL 69 L +WK ++L G + ++ + L+ + + +YL G DL Sbjct: 8 LVAKLWKLCDNLRDGGVSYQNYVNELASLLFLKMCKETGQ------EAEYLPEGYRWDDL 61 Query: 70 ESFVKVAGYSFYNTSEYSLSTLGSTNTRNNLESYIASFSDNAKAIFEDFDFSSTIARLEK 129 +S + FY L +A+F + + + Sbjct: 62 KSRIGQEQLQFYR---------------KMLVHLGEDDKKLVQAVFHNVST-----TITE 101 Query: 130 AGLLYKICKNFSGIELH--PDTVPDRVMSNIYEHLIRRFGSEVSEGAEDFMTPRDVVHLA 187 + + N ++ + ++YE L+++ +E GA + TPR ++ Sbjct: 102 PKQITALVSNMDSLDWYNGAHGKSRDDFGDMYEGLLQKNANETKSGAGQYFTPRPLIKTI 161 Query: 188 TALLLDPDDALFKESPGMIRTLYDPTCGTGGFLTDAMNHVAD--------CGSHHKIPPI 239 LL P + DP GT GFL +A +V G Sbjct: 162 IHLL----------KPQPREVVQDPAAGTAGFLIEADRYVKSQTNDLDDLDGDTQDFQIH 211 Query: 240 LVPHGQELEPETHAVCVAGMLIRRLESDPRRDLSKNIQQGSTLSKDLFTGKRFHYCLSNP 299 G EL P T + + L+ +E + D I+ G+TL D + H +NP Sbjct: 212 RAFIGLELVPGTRRLALMNCLLHDIEGN--LDHGGAIRLGNTLGSDGENLPKAHIVATNP 269 Query: 300 PFGKKWEKDKDAVEKEHKNGELGRFGPGLPKISDGSMLFLMHLANKLELPPNGGGRAAIV 359 PFG + + S+ + F+ H+ L + GGRAA+V Sbjct: 270 PFGSAAGTN--------------ITRTFVHPTSNKQLCFMQHIIETL----HPGGRAAVV 311 Query: 360 LSSSPLFNGRAGSGESEIRRWLLENDLIEAIVALPTDLFFRTNIATYLWILSNRKTEERR 419 + + LF G ++IRR L++ + I+ LPT +F+ + T + + Sbjct: 312 VPDNVLFEGGK---GTDIRRDLMDKCHLHTILRLPTGIFYAQGVKTNVLFFTKGTVANPN 368 Query: 420 GKVQLINAT---DLWTSIRNEGKKRRIINDDQRRQILDIYVSRENGKFSR 466 + DL T++ + KR D+ + +Y +G R Sbjct: 369 QDKNCTDDVWVYDLRTNMPS-FGKRTPFTDEHLQPFERVYGEDPHGLSPR 417 >2okc_A Type I restriction enzyme stysji M protein; NP_813429.1, N-6 DNA methylase, structural genomics; HET: SAM; 2.20A {Bacteroides thetaiotaomicron vpi-5482} SCOP: c.66.1.45 Length = 445 Score = 128 bits (322), Expect = 4e-30 Identities = 79/466 (16%), Positives = 144/466 (30%), Gaps = 64/466 (13%) Query: 1 MTEFTGSAASLANFIWKNAEDLWGDFKHTDFGKVILPFTLLRRLECALEPTRSAVREKYL 60 M + + SL +W A L G F I T L L+ E E + Sbjct: 2 MATNSSTEQSLTKKVWNLATTLAGQ--GIGFTDYITQLTYLLFLKMDAENVEMFGEESAI 59 Query: 61 AFGGSNIDLESFVKVAGYSFYNTSEYSLSTLGSTNTRNNLESYIASFSDNAKAIFEDFDF 120 GY + + + L ++ + I+ Sbjct: 60 P--------------TGYQWADLIAFDGLDLV--KQYEETLKLLSELDNLIGTIYTKAQN 103 Query: 121 SSTIARLEKAGLLYKICKNFSGIELHPDTVPDRVMSNIYEHLIRRFGSEVSEGAEDFMTP 180 +++K L K+ E + V IYE ++ + G + GA + TP Sbjct: 104 -----KIDKPVYLKKVITMID--EEQWLIMDGDVKGAIYESILEKNGQDKKSGAGQYFTP 156 Query: 181 RDVVHLATALLLDPDDALFKESPGMIRTLYDPTCGTGGFLTDAMNHVADCGSHHKIPPIL 240 R ++ + +P M T+ DP CGTGGFL A +++ + + Sbjct: 157 RPLIQAMVDCI----------NPQMGETVCDPACGTGGFLLTAYDYMKGQSASKEK---- 202 Query: 241 VPHGQELEPETHAVCVAGMLIRRLESDPRRDLSKNIQQGSTLSKDLFTGKRFHYCLSNPP 300 ++ + + + + S + L+NPP Sbjct: 203 RDFLRDKALHGVDNTPLVVTLASMNLYLHGIGTDRSPIVCEDSLEKEPSTLVDVILANPP 262 Query: 301 FGKKWEKDKDAVEKEHKNGELGRFGPGLPKISDGSMLFLMHLANKLELPPNGGGRAAIVL 360 FG + D + + + FL H+ L GGRAA+VL Sbjct: 263 FGTRPAGSVDI-----------NRPDFYVETKNNQLNFLQHMMLML----KTGGRAAVVL 307 Query: 361 SSSPLFNGRAGSGESEIRRWLLENDLIEAIVALPTDLFFRTNIATYLWILSNRKTEERRG 420 + LF A IR+ LL++ + I+ LPT +F+ + + S + + Sbjct: 308 PDNVLFEAGA---GETIRKRLLQDFNLHTILRLPTGIFYAQGVKANVLFFSKGQPTK--- 361 Query: 421 KVQLINATDLWTSIRNEGKKRRIINDDQRRQILDIYVSRENGKFSR 466 ++ + + + Y +R + Sbjct: 362 EIWFYDYRTDI----KHTLATNKLERHHLDDFVSCYNNRVEIYDAE 403 >2f8l_A Hypothetical protein LMO1582; 16411011, structural genomics, PSI, protein structure initiative, joint center for structural genomics; HET: MSE SAM; 2.20A {Listeria monocytogenes} SCOP: c.66.1.45 Length = 344 Score = 116 bits (290), Expect = 2e-26 Identities = 45/346 (13%), Positives = 106/346 (30%), Gaps = 50/346 (14%) Query: 102 SYIASFSDNAKAIFEDFDFSSTIARLEKAGLLYKICKNFSGIELHPDTVPDRVMSNIYEH 161 SY+ + + + +F+ EK L ++ + + + Sbjct: 39 SYLEAVYETGENLFQKEVLQKEELSSEKQLKLQASYESIELENFSNEE-----IRKGLQL 93 Query: 162 LIRRFGSEVSEGAEDFMTPRDVVHLATALLLDPDDALFKESPGMIRTLYDPTCGTGGFLT 221 + + + MTP + + LL + + ++ + ++ DP CGT LT Sbjct: 94 ALLKGMKHGIQVNH-QMTPDSIGFIVAYLL----EKVIQKKKNV--SILDPACGTANLLT 146 Query: 222 DAMNHVADCGSHHKIPPILVPHGQELEPETHAVCVAGMLIRRLESDPRRDLSKNIQQGST 281 +N + + G +++ ++ + G ++R + Sbjct: 147 TVINQLE----LKGDVDVHA-SGVDVDDLLISLALVGADLQRQKMTLLH----------Q 191 Query: 282 LSKDLFTGKRFHYCLSNPPFGKKWEKDKDAVEKEHKNGELGRFGPGLPKISDGSMLFLMH 341 +S+ P G + + + + S LF+ Sbjct: 192 DGLANLLVDPVDVVISDLPVGYYPDDENAKTFELCRE----------EGHSFAHFLFIEQ 241 Query: 342 LANKLELPPNGGGRAAIVLSSSPLFNGRAGSGESEIRRWLLENDLIEAIVALPTDLFFRT 401 GG ++ + +++ +++ +N IE I+ LP LF Sbjct: 242 GMRYT----KPGGYLFFLVPDAMFGTS----DFAKVDKFIKKNGHIEGIIKLPETLFKSE 293 Query: 402 NIATYLWILSNRKTEERR-GKVQLINATDLWTSIRNEGKKRRIIND 446 + IL + + +V L N + L + I+ + Sbjct: 294 QARKSILILEKADVDVKPPKEVLLANLSSL----TDPSVTAPILAE 335 >2ih2_A Modification methylase TAQI; DNA, DNA methyltransferase, target base partner, 5- methylpyrimidin-2(1H)-ONE, base flipping; HET: 5PY 6MA NEA; 1.61A {Thermus aquaticus} SCOP: c.66.1.27 d.287.1.1 PDB: 2ibs_A* 2ibt_A* 2ih4_A* 2ih5_A* 2jg3_A* 2np6_A* 2np7_A* 1aqj_A* 1aqi_A* 2adm_A* 1g38_A* Length = 421 Score = 90.7 bits (224), Expect = 1e-18 Identities = 36/261 (13%), Positives = 67/261 (25%), Gaps = 48/261 (18%) Query: 159 YEHLIRRFGSEVSEGAEDFMTPRDVVHLATALLLDPDDALFKESPGMIRTLYDPTCGTGG 218 L+ + TP +VV +L P + +P C G Sbjct: 3 LPPLLSLPSNSAPRSLGRVETPPEVVDFMVSLAEAPRGG----------RVLEPACAHGP 52 Query: 219 FLTDAMNHVADCGSHHKIPPILVPHGQELEPETHAVCVAGMLIRRLESDPRRDLSKNIQQ 278 FL ++ G E++P+ + I Sbjct: 53 FLRAFREAHGT---AYRF------VGVEIDPKALDLPPWAEGI----------------L 87 Query: 279 GSTLSKDLFTGKRFHYCLSNPPFGKKWEKDKDAVEK-EHKNGELGRFGPGLPKISDGSML 337 L + G+ F L NPP+G E K + + + + Sbjct: 88 ADFLLWEP--GEAFDLILGNPPYGIVGEASKYPIHVFKAVKDLYKKAFSTWKGKYNLYGA 145 Query: 338 FLMHLANKLELPPNGGGRAAIVLSSSPLFNGRAGSGESEIRRWLLENDLIEAIVALPTDL 397 FL L GG V+ ++ L + +R +L ++ Sbjct: 146 FLEKAVRLL----KPGGVLVFVVPATWLV----LEDFALLREFLAREGKTSVY--YLGEV 195 Query: 398 FFRTNIATYLWILSNRKTEER 418 F + ++ + Sbjct: 196 FPQKKVSAVVIRFQKSGKGLS 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 = 83.1 bits (205), Expect = 2e-16 Identities = 98/608 (16%), Positives = 168/608 (27%), Gaps = 246/608 (40%) Query: 7 SAASLANFI----------------WKNAEDLWGDFKHT------------DFGKVI--- 35 A S + A L F + Sbjct: 2 DAYSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELV 61 Query: 36 ---LPFTLLRRLE-----CALEPTRSAVRE---KYLAFGGSNI-----DLES-----FVK 74 L + + +E + + E YL G++I L VK Sbjct: 62 GKFLGY-VSSLVEPSKVGQFDQVLNLCLTEFENCYL--EGNDIHALAAKLLQENDTTLVK 118 Query: 75 VAGY--SFYNTSEYSLSTLGSTNTRNNLESYIASFSDNAK--AIF------ED-FD---- 119 ++ + + + L + A NA+ AIF +D F+ Sbjct: 119 TKELIKNYITARIMAKRPF-DKKSNSAL--FRAVGEGNAQLVAIFGGQGNTDDYFEELRD 175 Query: 120 ----FSSTIARL--EKAGLLYKICKN-------FS-GIEL-----HPDTVPDRVMSNIYE 160 + + L A L ++ + F+ G+ + +P PD+ + Sbjct: 176 LYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDK------D 229 Query: 161 HLIRRFGSEVSE---GAEDFMTPRDVVHLA----TALLLDPDDALFKESPGMIRTLYDPT 213 +L+ +S G V+ LA TA LL +PG +R+ Sbjct: 230 YLL---SIPISCPLIG---------VIQLAHYVVTAKLLG-------FTPGELRSYL--- 267 Query: 214 CG-TG---GFLTDAMNHVAD------------------CG--SHHKIPPILVPHGQELEP 249 G TG G +T D G + P +P P Sbjct: 268 KGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLP------P 321 Query: 250 ETHAVCVAG-------ML-IRRLESDPRRDLSKNIQQ-GSTLSKD------LFTGKRFHY 294 + ML I L + + + + S L L G + + Sbjct: 322 SILEDSLENNEGVPSPMLSISNL---TQEQVQDYVNKTNSHLPAGKQVEISLVNGAK-NL 377 Query: 295 CLSNPP-----FGKKWEKDKDAVE--------KEHK----NGELGRFGPGLPKIS----- 332 +S PP K K E K N RF LP ++ Sbjct: 378 VVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSN----RF---LP-VASPFHS 429 Query: 333 ----DGSMLFLMHLANK-LELPPNGGGRAAIVLSSSPLFNGRAGS-----GESEIRRWLL 382 S L L + I P+++ GS S + Sbjct: 430 HLLVPASDLINKDLVKNNVSFNAK---DIQI-----PVYDTFDGSDLRVLSGS-----IS 476 Query: 383 ENDLIEAIVALPTD----LFFR-TNIATY-------LWILSNRKTEERRGK-VQLINATD 429 E +++ I+ LP F+ T+I + L +L++R + G V++I A Sbjct: 477 E-RIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKD---GTGVRVIVAGT 532 Query: 430 LWTSIRNE 437 L + ++ Sbjct: 533 LDINPDDD 540 Score = 32.2 bits (73), Expect = 0.42 Identities = 48/323 (14%), Positives = 88/323 (27%), Gaps = 130/323 (40%) Query: 372 SGESEIRRWLLENDLIEAIVALPTDLFFRTNIATYLW--ILSNRKTEERRGKVQLINATD 429 S R L + +E ++ +PT FF A+ L L T+ Sbjct: 2 DAYS-TRPLTLSHGSLEHVLLVPTASFFI---ASQLQEQFNK-----------ILPEPTE 46 Query: 430 LWTSIRNEGKKRRIINDDQRRQILDIYVSRENGKFSRMLDYRTFGYRRIKVLRPLRMSFI 489 + + DD+ ++ GKF + ++ Sbjct: 47 GFAA------------DDEPTTPAELV-----GKF---------------------LGYV 68 Query: 490 LDKTGLARLEADITWRKLSPLHQSFWLDILKPMMQQIYPYGWAE----------SFVKES 539 + P + +L + + E + + Sbjct: 69 SSL--------------VEPSKVGQFDQVLNLCLTEF------ENCYLEGNDIHALAAKL 108 Query: 540 IKSNEAKTLKVKASKSFIVAFINAF---GRKDPRADPVTDVNGEWIPDTNLTEY---ENV 593 ++ N+ +K K I +I A R + ++ L N Sbjct: 109 LQENDTTLVKT---KELIKNYITARIMAKRPFDK-----------KSNSALFRAVGEGNA 154 Query: 594 PYLESI---Q----DYF--VREV----SPHVPDAYIDKIFIDEKDKEIGRVGYEINFNRF 640 L +I Q DYF +R++ V D I F E E+ R ++ + Sbjct: 155 Q-LVAIFGGQGNTDDYFEELRDLYQTYHVLVGD-LIK--FSAETLSELIRT--TLDAEKV 208 Query: 641 FYQYQPSRKLQDIDAELKGVEAQ 663 F Q L +I L+ Sbjct: 209 FTQG-----L-NILEWLENPSNT 225 Score = 29.9 bits (67), Expect = 1.7 Identities = 37/235 (15%), Positives = 68/235 (28%), Gaps = 80/235 (34%) Query: 481 LRPLRMSFILDKTGLARLEADIT-----WRKLSPLHQSFWLDILKP---MMQQIYPYGWA 532 RPL +S LE + + S L + F + +P P A Sbjct: 6 TRPLTLSH-------GSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPA 58 Query: 533 E------SFVKESIKSNEAKT----LKVKASKSFIVAF-----INAFGRKDPRADPVTDV 577 E +V ++ ++ L + F + I+A + Sbjct: 59 ELVGKFLGYVSSLVEPSKVGQFDQVLNL-CLTEFENCYLEGNDIHAL---------AAKL 108 Query: 578 NGEWIPDTNLTEYENVPYLESIQDYF------VREVSPHVPDAYIDKIFIDEKDKEIGRV 631 E DT L + + + I++Y R A +F + ++ Sbjct: 109 LQE--NDTTLVKTKEL-----IKNYITARIMAKRPFDKKSNSA----LFRAVGEGNA-QL 156 Query: 632 GYEI-----NFNRFF------YQ-YQPSRKLQDIDAELKGVEAQIATLLEEMATE 674 I N + +F YQ Y + D+ ++ A L E+ Sbjct: 157 -VAIFGGQGNTDDYFEELRDLYQTYHVL--VGDL------IKF-SAETLSELIRT 201 Score = 28.4 bits (63), Expect = 4.9 Identities = 34/225 (15%), Positives = 60/225 (26%), Gaps = 94/225 (41%) Query: 5 TGSAASLANF-IW----KNAEDLWGDFKHTDFGKVILPFTLLRRLECA------------ 47 +G SL + K L D ++ PF+ R+L+ + Sbjct: 380 SGPPQSLYGLNLTLRKAKAPSGL-------DQSRI--PFSE-RKLKFSNRFLPVASPFHS 429 Query: 48 --LEPTRSAVRE----KYLAFGGSNIDLESFVKVAGYSFYNTSEYSLSTLGSTNTRNNLE 101 L P + + ++F D+ ++ Y T ++L Sbjct: 430 HLLVPASDLINKDLVKNNVSFNAK--DI----QIPVYD--------------TFDGSDLR 469 Query: 102 SYIAS-FSDNAKAIFED-FDFSSTIARLEKAGLLYKICKNFSGIELHPDTVPDRVMSNIY 159 S I + E F T Sbjct: 470 VLSGSISERIVDCIIRLPVKW-------ETT-------TQF------KAT---------- 499 Query: 160 EHLIRRFGSEVSEGAEDFMTPRDV------VHLATALLLDPDDAL 198 H++ FG + G +T R+ V +A L ++PDD Sbjct: 500 -HILD-FGPGGASGLGV-LTHRNKDGTGVRVIVAGTLDINPDDDY 541 >3k0b_A Predicted N6-adenine-specific DNA methylase; methylase,PF01170, putative RNA methylase, PSI,MCSG, structural genomics; 1.50A {Listeria monocytogenes str} Length = 393 Score = 35.8 bits (82), Expect = 0.033 Identities = 24/134 (17%), Positives = 43/134 (32%), Gaps = 20/134 (14%) Query: 197 ALFKESPGMIRTLYDPTCGTGGFLTDAMNHVAD---CGSHHKIPPILVPHGQEL------ 247 + S R YDP CG+G +A + + + +++ Sbjct: 193 LVLLTSWHPDRPFYDPVCGSGTIPIEAALIGQNIAPGFNREFVSETWDWMPKQVWADARQ 252 Query: 248 EPETHAVCVAGMLIRRLESDPRRD-----------LSKNIQQGSTLSKDLFTGKRFHYCL 296 E E A + I + D R L I D T + + Sbjct: 253 EAEDLANYDQPLNIIGGDIDARLIEIAKQNAVEAGLGDLITFRQLQVADFQTEDEYGVVV 312 Query: 297 SNPPFGKKWEKDKD 310 +NPP+G++ E ++ Sbjct: 313 ANPPYGERLEDEEA 326 >3ldu_A Putative methylase; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; HET: MSE GTP; 1.70A {Clostridium difficile} Length = 385 Score = 31.9 bits (72), Expect = 0.47 Identities = 25/138 (18%), Positives = 50/138 (36%), Gaps = 23/138 (16%) Query: 207 RTLYDPTCGTGGFLTDA-------MNHVADCGSHHKIPPILVPHGQELEPETHAVCVAGM 259 R L DP CG+G L +A + K + ++ + Sbjct: 197 RVLVDPMCGSGTILIEAAMIGINMAPGLNREFISEKWRTLDKKIWWDVRKDAFNKIDNES 256 Query: 260 LIRRLESDPRRD-------------LSKNIQQGSTLSKDLFTGKRFHYCLSNPPFGKKWE 306 + D + + + I+ + + F + ++NPP+G++ Sbjct: 257 KFKIYGYDIDEESIDIARENAEIAGVDEYIEFNVGDATQFKSEDEFGFIITNPPYGERL- 315 Query: 307 KDKDAVEKEHKNGELGRF 324 +DKD+V++ +K ELG Sbjct: 316 EDKDSVKQLYK--ELGYA 331 >3key_A Protein STN1; butterfly WING-shaped, helix, chromosomal protein, phosphoprotein, telomere; 2.10A {Saccharomyces cerevisiae} PDB: 3k10_A Length = 185 Score = 31.5 bits (71), Expect = 0.68 Identities = 27/132 (20%), Positives = 47/132 (35%), Gaps = 25/132 (18%) Query: 80 FYNTSEYS--LSTLGSTNTRNNLESYIASFSDNAKAIFEDFDFSSTIARLEKAGLLYKIC 137 Y E +++L S + + SF K F D + RL GL+ Sbjct: 27 LYKLKEVRSVVTSLASFLFQQQNVGVMKSFDSLEKEAFRDL-----VNRLVSQGLIGLKD 81 Query: 138 KNFSGIELHPDTVPDRVMSNIYEHLIRRFGS----EVSEGAEDFMTPRDVVHL---ATAL 190 K +L P + N++E+ +R + G ++ +HL T Sbjct: 82 KTSETFDLLP-------LKNLFEYAEKRISVLMKLQCYTGTVQLSHVQEKLHLPYITTNG 134 Query: 191 LLDPDDALFKES 202 ++D +FKE Sbjct: 135 IVD----VFKEC 142 >3dmg_A Probable ribosomal RNA small subunit methyltransferase; monomethyltranserase, 16S rRNA methyltransferase, N2 G1207 methyltransferase; HET: SAH; 1.55A {Thermus thermophilus} PDB: 3dmf_A* 3dmh_A* Length = 381 Score = 30.6 bits (68), Expect = 1.1 Identities = 26/161 (16%), Positives = 40/161 (24%), Gaps = 26/161 (16%) Query: 159 YEHLIRRFGSEVSEGAEDFMTP-----RDVVHLATALLLDPDDALFKESPGMIRTLYDPT 213 L R F + + F V A+ LLL+ R + D Sbjct: 182 LPSLWRAFSARILGAEYTFHHLPGVFSAGKVDPASLLLLEALQERLGPEGVRGRQVLDLG 241 Query: 214 CGTGGFLTDAMNHVADCGSHHKIPPILVPHGQELEPETHAVCVAGMLIRRLESDPRRDLS 273 G G + E V + L+ + Sbjct: 242 AGYGAL---------------------TLPLARMGAEVVGVEDDLASVLSLQKGLEANAL 280 Query: 274 KNIQQGSTLSKDLFTGKRFHYCLSNPPFGKKWEKDKDAVEK 314 K S + + L RF ++NPPF D + Sbjct: 281 KAQALHSDVDEALTEEARFDIIVTNPPFHVGGAVILDVAQA 321 >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 = 1.3 Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 14/39 (35%) Query: 491 DKTGLARLEADITWRKL-----SPLHQSFWLDILKPMMQ 524 +K L +L+A + KL +P L I K M+ Sbjct: 18 EKQALKKLQASL---KLYADDSAPA-----LAI-KATME 47 >3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752 Score = 30.1 bits (67), Expect = 1.6 Identities = 12/81 (14%), Positives = 32/81 (39%), Gaps = 3/81 (3%) Query: 525 QIYPYGWAESFVKESIKSNEAKTLKVKASKSFIVAFINAFGRKDPRADPVTDVNGEWIPD 584 + E ++I+ + +++ ++ + ++ D + EW+ + Sbjct: 1254 EDDDNMIEEDVFLKTIEGHMLESISLRGVPNITRVYMMEHKIVRQIEDGTFERADEWVLE 1313 Query: 585 T---NLTEYENVPYLESIQDY 602 T NLTE V +++ + Y Sbjct: 1314 TDGINLTEAMTVEGVDATRTY 1334 >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 = 29.8 bits (66), Expect = 2.2 Identities = 31/130 (23%), Positives = 52/130 (40%), Gaps = 33/130 (25%) Query: 545 AKTLKVKASKSF-IVAFINAFGRKDPRADPV----------TDVNGEWIPDTNLTEYENV 593 +KTLK ++ I +F FG+K +A V D E++ + E Sbjct: 1429 SKTLKTDGVRAVSITSF--GFGQKGGQAIVVHPDYLYGAITEDRYNEYVAKVSAREKSAY 1486 Query: 594 PYLESIQDY---FV-REVSPHV----PDAYIDKIFIDEKDKEIGRVGYEINFNRFFYQYQ 645 + + Y FV +E +P+ D Y+D + KDK+ G + FN Sbjct: 1487 KFFHNGMIYNKLFVSKEHAPYTDELEEDVYLDPLARVSKDKKSG----SLTFN------- 1535 Query: 646 PSRKLQDIDA 655 S+ +Q D+ Sbjct: 1536 -SKNIQSKDS 1544 >3kxe_A Toxin protein PARE-1; complex, TA system, protein binding; 2.60A {Caulobacter crescentus NA1000} Length = 110 Score = 29.1 bits (65), Expect = 3.0 Identities = 6/66 (9%), Positives = 17/66 (25%), Gaps = 4/66 (6%) Query: 596 LESIQDYFVREVSPHVPDAYIDKIF--ID--EKDKEIGRVGYEINFNRFFYQYQPSRKLQ 651 L+ I Y + Y ++ I+ + +G+ + Sbjct: 28 LDDIWTYSEQRWGVEQAADYARELQATIEMIAEHPGMGQPDENLRAGYRRCASGSHVVFY 87 Query: 652 DIDAEL 657 + + Sbjct: 88 RVGVRV 93 >1o9g_A RRNA methyltransferase; antibiotic resistance, Se-MAD; 1.5A {Streptomyces viridochromogenes} SCOP: c.66.1.29 PDB: 1o9h_A Length = 250 Score = 28.0 bits (62), Expect = 8.0 Identities = 9/14 (64%), Positives = 11/14 (78%) Query: 208 TLYDPTCGTGGFLT 221 TL+DP CG+G LT Sbjct: 54 TLWDPCCGSGYLLT 67 >2cvx_A Ribonucleoside-diphosphate reductase large chain 1; eukaryotic, ribonucleotide reductase, DNTP regulation, oxidoreductase; HET: DGT ADP; 2.20A {Saccharomyces cerevisiae} PDB: 1zyz_A 2cvs_A 2cvt_A* 2cvu_A* 2cvv_A* 1zzd_A* 2cvw_A* 2cvy_A* 2eud_A* 2zlf_A 2zlg_A* Length = 888 Score = 27.9 bits (61), Expect = 8.2 Identities = 10/45 (22%), Positives = 16/45 (35%), Gaps = 6/45 (13%) Query: 116 EDFDFSSTIARLEKAGLLYKICKNFSGIELHPDTVPDRVMSNIYE 160 E F AR+ + C + V R++S +YE Sbjct: 11 EPVQFDKITARISRL------CYGLDPKHIDAVKVTQRIISGVYE 49 >2o8b_A DNA mismatch repair protein MSH2; DNA damage response, somatic hypermutation, protein-DNA complex, DNA mispair, cancer, ABC transporter ATPase; HET: DNA ADP; 2.75A {Homo sapiens} PDB: 2o8c_A* 2o8d_A* 2o8f_A* 2o8e_A* Length = 934 Score = 27.7 bits (60), Expect = 8.6 Identities = 20/161 (12%), Positives = 46/161 (28%), Gaps = 13/161 (8%) Query: 33 KVILPFTLLRRLECALEPTRSAVREKYLAFGGSNIDLESFVKVAGYSFYN--TSEYSLST 90 P L + + + G + + G + + + L Sbjct: 121 YKASPGNLS---QFEDILFGNNDMSASIGVVGVKMSAVDGQRQVGVGYVDSIQRKLGLCE 177 Query: 91 LGSTNTRNNLESYIASFSDNAKAIFEDFDFSSTIARLEKAGLLYKICKNFSGIELHPDTV 150 + +NLE+ + + + + + + +L + GI + Sbjct: 178 FPDNDQFSNLEALLIQIGP-KECVLPGGETAGDMGKLRQ-------IIQRGGILITERKK 229 Query: 151 PDRVMSNIYEHLIRRFGSEVSEGAEDFMTPRDVVHLATALL 191 D +IY+ L R + E + P +A + L Sbjct: 230 ADFSTKDIYQDLNRLLKGKKGEQMNSAVLPEMENQVAVSSL 270 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 0.320 0.137 0.409 Gapped Lambda K H 0.267 0.0480 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 6,080,087 Number of extensions: 298518 Number of successful extensions: 887 Number of sequences better than 10.0: 1 Number of HSP's gapped: 848 Number of HSP's successfully gapped: 30 Length of query: 674 Length of database: 5,693,230 Length adjustment: 99 Effective length of query: 575 Effective length of database: 3,293,074 Effective search space: 1893517550 Effective search space used: 1893517550 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: 60 (27.5 bits)