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)