RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780814|ref|YP_003065227.1| DNA gyrase subunit B [Candidatus Liberibacter asiaticus str. psy62] (803 letters) >1ei1_A DNA gyrase B, GYRB; ATPase domain, dimer, isomerase; HET: DNA ANP; 2.30A {Escherichia coli} SCOP: d.14.1.3 d.122.1.2 Length = 391 Score = 535 bits (1379), Expect = e-152 Identities = 223/394 (56%), Positives = 298/394 (75%), Gaps = 4/394 (1%) Query: 7 NSSYDADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITV 66 ++S D+ SI++LKGLDAV+KRP MYIGDTD +GLHHM++EV+DNAIDE+L G+ I V Sbjct: 1 SNSSDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIV 60 Query: 67 TLNMDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVS 126 T++ D S +V D+GRGIPT +H EEG+SAAEVIMT LHAGGKF+ SYKVSGGLHGVGVS Sbjct: 61 TIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVS 120 Query: 127 VVNALSSWLKLRIKREGNIYEMSFINGILDNPLVVTGSAGNDTGTEVTFLPSSDIFS-VQ 185 VVNALS L+L I+REG I+ + +G+ PL VTG TGT V F PS + F+ V Sbjct: 121 VVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETE-KTGTMVRFWPSLETFTNVT 179 Query: 186 DFNYDTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYLDRHKKPLMQ 245 +F Y+ L RLRELSFL+S V I L DKR + +E Y+GGI+AFV YL+++K P+ Sbjct: 180 EFEYEILAKRLRELSFLDSGVSIRLRDKR--DGKEDHFHYEGGIKAFVEYLNKNKTPIHP 237 Query: 246 SPIRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVE 305 + +D I +++A++WNDG+ EN+ CFTNNIPQ+DGGTHL+G R+A+TR + +Y++ Sbjct: 238 NIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMD 297 Query: 306 KSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVNDGLS 365 K SKK K S GDD REG +V+S+K+PDP+FSSQTK+KLVSSEV+S VE +N+ L+ Sbjct: 298 KEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLA 357 Query: 366 AWLEEHPLEAKIIVKKVLDASMVRDAARRARDLT 399 +L E+P +AKI+V K++DA+ R+AARRAR++T Sbjct: 358 EYLLENPTDAKIVVGKIIDAARAREAARRAREMT 391 >3nuh_B DNA gyrase subunit B; topoisomerase, supercoiling, specialization, isomera; HET: DNA; 3.10A {Escherichia coli} Length = 420 Score = 466 bits (1199), Expect = e-131 Identities = 189/420 (45%), Positives = 261/420 (62%), Gaps = 8/420 (1%) Query: 392 ARRARDLTRRKGVLDIASLPGKLADCSERDPKKSELFLVEGDSAGGSAKQGRSRENQAIL 451 + AR++TRRKG LD+A LPGKLADC ERDP SEL+LVEGDSAGGSAKQGR+R+NQAIL Sbjct: 1 SNAAREMTRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAIL 60 Query: 452 PLRGKILNVERARFDKMLSSQEIGTLITALGTGIGQDSFDINKLRYHKIIIMTDADVDGA 511 PL+GKILNVE+ARFDKMLSSQE+ TLITALG GIG+D ++ +KLRYH IIIMTDADVDG+ Sbjct: 61 PLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGS 120 Query: 512 HIRTLLLTFFFRQMPSLIHNGFLYIIKPPLYGITRGKSLQYVKDEESLEDYLINQSLSEE 571 HIRTLLLTFF+RQMP ++ G +YI +PPLY + +GK QY+KD+E+++ Y I+ +L Sbjct: 121 HIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIALDGA 180 Query: 572 IELFCDSKGVISKNDLRNFIDDALKIDKLIKDFYPNHDKTFIEQAVISGVFNCE--SDQE 629 S ++ L + + K+I + K +++ + SD++ Sbjct: 181 TLHTNASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKELIYQPTLTEADLSDEQ 240 Query: 630 INVSLASKLANRLNFIAEKSEKSWHGSINNSD-----ILVKRIARGVQEQFVLEGSSIFS 684 + L + LN + + N++ +V+ GV + L+ I Sbjct: 241 TVTRWVNALVSELNDKEQHGSQWKFDVHTNAEQNLFEPIVRVRTHGVDTDYPLDHEFITG 300 Query: 685 FGSKYKRIFSNRIEENYLTILSLICNGDKIKITGPCSLLDTIFSIGRKGISMQRYKGLGE 744 + ++ + + + LD + R+G+S+QRYKGLGE Sbjct: 301 GEYRRICTLGEKLRGLLEEDAFIERGERRQPVASFEQALDWLVKESRRGLSIQRYKGLGE 360 Query: 745 MNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEPRREFIQENSLPSA-LDI 803 MN QLWETT++P++R +LRV + DA AD LF+ LMGD VEPRR FI+EN+L +A +DI Sbjct: 361 MNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAANIDI 420 >1kij_A DNA gyrase subunit B; topoisomerase, gyrase B-coumarin complex; HET: DNA NOV; 2.30A {Thermus thermophilus} SCOP: d.14.1.3 d.122.1.2 Length = 390 Score = 440 bits (1132), Expect = e-124 Identities = 171/391 (43%), Positives = 242/391 (61%), Gaps = 4/391 (1%) Query: 9 SYDADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITVTL 68 SYDA +I++LKGL+ V+ RP+MYIG T G HH+ E+LDNA+DE+L GYA I V L Sbjct: 2 SYDASAIRVLKGLEGVRHRPAMYIGGTG-VEGYHHLFKEILDNAVDEALAGYATEILVRL 60 Query: 69 NMDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVV 128 N DGS TV DNGRGIP DL EEG A EVI LH+GGKF Q +YKVSGGLHGVG SVV Sbjct: 61 NEDGSLTVEDNGRGIPVDLMPEEGKPAVEVIYNTLHSGGKFEQGAYKVSGGLHGVGASVV 120 Query: 129 NALSSWLKLRIKREGNIYEMSFINGILDNPLVVTGSAGND-TGTEVTFLPSSDIFSVQDF 187 NALS W + + REG + ++F G + PL V G A TGT VTF P +IF F Sbjct: 121 NALSEWTVVEVFREGKHHRIAFSRGEVTEPLRVVGEAPRGKTGTRVTFKPDPEIFGNLRF 180 Query: 188 NYDTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYLDRHKKPLMQSP 247 + ++ RLRE+++L + +++ D++ + KGG+ +F L + L + P Sbjct: 181 DPSKIRARLREVAYLVAGLKLVFQDRQHGKE--EVFLDKGGVASFAKALAEGEDLLYEKP 238 Query: 248 IRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVEKS 307 I+G+ + +++ GY+ +L + N IP +DGGTHL+ +SA +R + Y +K+ Sbjct: 239 FLIRGTHGEVEVEVGFLHTQGYNAEILTYANMIPTRDGGTHLTAFKSAYSRALNQYAKKA 298 Query: 308 FGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVNDGLSAW 367 +K+ GDD EG +V+S+K+P+P+F QTK KL++ E + V V + L Sbjct: 299 GLNKEKGPQPTGDDLLEGLYAVVSVKLPNPQFEGQTKGKLLNPEAGTAVGQVVYERLLEI 358 Query: 368 LEEHPLEAKIIVKKVLDASMVRDAARRARDL 398 LEE+P AK + +K L A+ R+AAR+AR+L Sbjct: 359 LEENPRIAKAVYEKALRAAQAREAARKAREL 389 >1s16_A Topoisomerase IV subunit B; two-domain protein complexed with ADPNP; HET: ANP; 2.10A {Escherichia coli} SCOP: d.14.1.3 d.122.1.2 Length = 390 Score = 367 bits (942), Expect = e-102 Identities = 136/398 (34%), Positives = 217/398 (54%), Gaps = 11/398 (2%) Query: 7 NSSYDADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITV 66 +Y+AD+I++L GL+ V++RP MY T +H+ EV+DN++DE+L G+A + V Sbjct: 2 TQTYNADAIEVLTGLEPVRRRPGMYTDTT----RPNHLGQEVIDNSVDEALAGHAKRVDV 57 Query: 67 TLNMDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVS 126 L+ D S V D+GRG+P D+H EEG+ A E+I+ RLHAGGKF+ K+Y+ SGGLHGVG+S Sbjct: 58 ILHADQSLEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGIS 117 Query: 127 VVNALSSWLKLRIKREGNIYEMSFINGILDNP-LVVTGSAGNDTGTEVTFLPSSDIFSVQ 185 VVNALS +++ ++R+G +Y ++F NG VV +TGT V F P F Sbjct: 118 VVNALSKRVEVNVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSP 177 Query: 186 DFNYDTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYLDRHKKPLMQ 245 F+ L H L+ + L V+I+ D+ + + Y+ G+ +++ L + Sbjct: 178 RFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQR--WCYQDGLNDYLAEAVNGLPTLPE 235 Query: 246 SPIRIQGSRDNISIDLAMRWND-GYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYV 304 P + D ++D A+ W G + N IP GGTH++GLR L + + Sbjct: 236 KPFIGNFAGDTEAVDWALLWLPEGGELLTESYVNLIPTMQGGTHVNGLRQGLLDAMREFC 295 Query: 305 EKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVNDGL 364 E + +D + VLS+KM DP+F+ QTKE+L S + + V V D Sbjct: 296 EYR-NILPRGVKLSAEDIWDRCAYVLSVKMQDPQFAGQTKERLSSRQCAAFVSGVVKDAF 354 Query: 365 SAWLEEHPLEAKIIVKKVLDASMVRDAARRARDLTRRK 402 WL ++ A+++ + + ++ R R A+ + R+K Sbjct: 355 ILWLNQNVQAAELLAEMAISSAQRR--MRAAKKVVRKK 390 >1pvg_A DNA topoisomerase II; GHKL ATPase domain; HET: DNA ANP; 1.80A {Saccharomyces cerevisiae} SCOP: d.14.1.3 d.122.1.2 PDB: 1qzr_A* Length = 418 Score = 322 bits (825), Expect = 3e-88 Identities = 81/421 (19%), Positives = 156/421 (37%), Gaps = 51/421 (12%) Query: 1 MSDNIQNSSYDADSIQILKGLDAVKKRPSMYIGDTDGES--------------------- 39 M +D Q + L+ + KRP YIG + + Sbjct: 3 MVTMSTEPVSASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIV 62 Query: 40 -GLHHMIYEVLDNAIDESLEGYA-DIITVTLN-MDGSCTVSDNGRGIPTDLHKEEGISAA 96 GL + E+L NA D + + I V ++ + + V ++G+GIP ++H +E I Sbjct: 63 PGLFKIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIP 122 Query: 97 EVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKL--RIKREGNIYEMSFIN-G 153 E+I L ++ KV+GG +G G + N S+ L G Y + N Sbjct: 123 EMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNM 182 Query: 154 ILDNPLVVTGSAGNDTGTEVTFLPSSDIFSVQDFNYDTLQHRLRELSFLNSSVQISLIDK 213 + +P +T + T+VTF P F +++ + D L R + +N SV+ + Sbjct: 183 SICHPPKITSYKKGPSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDINGSVRDINVYL 242 Query: 214 RSPEPREITM-----FYKGGIEAFVSYLDRHKKPLMQSPIRIQGSRDNISIDLAMRWNDG 268 + Y +E + I R N ++A +D Sbjct: 243 NGKSLKIRNFKNYVELYLKSLEKKRQLDNGEDGAAKSDIPTILYERINNRWEVAFAVSDI 302 Query: 269 YHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTS 328 + + F N+I GGTH++ + + ++I+ + V + Sbjct: 303 SFQQI-SFVNSIATTMGGTHVNYITDQIVKKISEILXXXXXXS-----VKSFQIKNNMFI 356 Query: 329 VLSIKMPDPRFSSQTKEKLVS-------------SEVRSVVESFVNDGLSAWLEEHPLEA 375 ++ + +P F+SQTKE+L + + ++++ + + + + A Sbjct: 357 FINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKIMKTDLATRMFEIADANEENA 416 Query: 376 K 376 Sbjct: 417 L 417 >3cwv_A DNA gyrase, B subunit, truncated; structural genomics, unknown function, ATP-binding, isomerase, nucleotide-binding, topoisomerase; HET: DNA; 1.95A {Myxococcus xanthus dk 1622} Length = 369 Score = 295 bits (755), Expect = 3e-80 Identities = 80/373 (21%), Positives = 147/373 (39%), Gaps = 29/373 (7%) Query: 20 GLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITVTLNMDGSCTVSDN 79 ++ V+KRP MY GD E GLHH++Y +LD A +E+ G + + + DGS + Sbjct: 11 IVENVRKRPGMYCGDVG-EYGLHHLVYFLLDVAYEEARRGECRDVVLEVGGDGSIALFCT 69 Query: 80 GRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRI 139 R + + + R+ G F + G + V ALSS ++ I Sbjct: 70 SRTVTAE------------NLVRVATGAGFLGRPPGD-GWGWDSMLVVSLALSSRYQVDI 116 Query: 140 KREGNIYEMSFINGILDNPLVVTGS-----AGNDTGTEVTFLPSSDIFSVQDFNYDTLQH 194 +G + + +G + G V F+P + IF V F+ L Sbjct: 117 WADGRQWRVMGEHGHPQGEGAAVTPMEPMPVSAERGVRVHFVPDATIFEVLAFDRARLSR 176 Query: 195 RLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYLDRHKKPLMQSPIRIQGSR 254 R EL+ L +++S D + E GG+ + L + L P+ + Sbjct: 177 RCNELAALAPGLRVSFADLQRGERTL--WHLPGGVAQWAHVLTEARPQLHPEPVVFDFTW 234 Query: 255 DNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVEKSFGSKKDK 314 D + + A++W + +L F N + G H+ G+ AL + ++ G+ Sbjct: 235 DGLRVQCALQWCEDEDSTLLSFANAVRTVRHGAHVKGVTQALRGALAKLSGETRGAFP-- 292 Query: 315 RSVIGDDCREGFTSVLSIKMPDP--RFSSQTKEKLVSSEVRSVVESFVNDGLSAWLEEHP 372 +G T+++++ P F+ TKE L + + + L EHP Sbjct: 293 ----WARVAQGLTAIVAVSGPRRQMAFAGPTKELLAIPGLEEAIRKQLQPLFIELLREHP 348 Query: 373 LEAKIIVKKVLDA 385 + ++ ++ + Sbjct: 349 VTPALLARRTSGS 361 >2xkj_E Topoisomerase IV; type IIA topoisomerase; 2.20A {Acinetobacter baumannii} PDB: 2xkk_A* Length = 767 Score = 280 bits (717), Expect = 1e-75 Identities = 83/177 (46%), Positives = 111/177 (62%), Gaps = 2/177 (1%) Query: 390 DAARRARDLTRRKGVLDIASLPGKLADCSERDPKKSELFLVEGDSAGGSAKQGRSRENQA 449 +A RK ++ +LPGKLADC + ++SELF+VEGDSAGGSAKQ R + QA Sbjct: 9 GRRLKAAKKVERKKIVSGPALPGKLADCVGQTREESELFIVEGDSAGGSAKQARDKNFQA 68 Query: 450 ILPLRGKILNVERARFDKMLSSQEIGTLITALGTGIGQDSFDINKLRYHKIIIMTDADVD 509 I+P+RGKILN D++L+SQE+ + A+G G D D+++LRY KI I+ DAD D Sbjct: 69 IMPIRGKILNTWEVSSDEVLASQEVHDIAIAIGVDPGSD--DLSELRYGKICILADADSD 126 Query: 510 GAHIRTLLLTFFFRQMPSLIHNGFLYIIKPPLYGITRGKSLQYVKDEESLEDYLINQ 566 G HI TLL F + P+L+ G LY+ PPL+ I GK + Y D+E LE L N Sbjct: 127 GLHIATLLCALFVKHFPALVEEGHLYVAMPPLFRIDIGKDVHYALDDEELETILKNV 183 Score = 59.7 bits (144), Expect = 2e-09 Identities = 25/75 (33%), Positives = 44/75 (58%), Gaps = 1/75 (1%) Query: 730 GRKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRL-MGDEVEPR 788 G K + R+KGLGEMNA QL ETT++P+TR L+++ + DA L +L R Sbjct: 185 GNKNPQITRFKGLGEMNAIQLRETTMDPNTRRLVQLDLDDAHLTAGLLDKLLAKKRAADR 244 Query: 789 REFIQENSLPSALDI 803 ++++++ + + + Sbjct: 245 KQWLEQKGNLADITV 259 >3fv5_A DNA topoisomerase 4 subunit B; topoisomerase IV B subunit complex, antibiotic resistance, ATP-binding, nucleotide-binding; HET: DNA 1EU; 1.80A {Escherichia coli} PDB: 1s14_A* Length = 201 Score = 255 bits (653), Expect = 3e-68 Identities = 88/207 (42%), Positives = 128/207 (61%), Gaps = 7/207 (3%) Query: 20 GLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITVTLNMDGSCTVSDN 79 GL+ V++RP MY T +H+ EV+DN++DE+L G+A + V L+ D S V D+ Sbjct: 1 GLEPVRRRPGMYTDTT----RPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDD 56 Query: 80 GRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRI 139 GRG+P D+H EEG+ A E+I+ RLHAGGKF+ K+Y+ SGGLHGVG+SVVNALS +++ + Sbjct: 57 GRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSKRVEVNV 116 Query: 140 KREGNIYEMSFINGILDNPLVVTGSAGN-DTGTEVTFLPSSDIFSVQDFNYDTLQHRLRE 198 +R+G +Y ++F NG L V G+ G +TGT V F P F F+ L H L+ Sbjct: 117 RRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSPRFSVSRLTHVLKA 176 Query: 199 LSFLNSSVQISLIDKRSPEPREITMFY 225 + L V+I+ D+ + E Y Sbjct: 177 KAVLCPGVEITFKDEINNT--EQRWCY 201 >3g7e_A DNA gyrase subunit B; isomerase; HET: DNA B46; 2.20A {Escherichia coli} PDB: 1kzn_A* 1aj6_A* Length = 203 Score = 250 bits (640), Expect = 9e-67 Identities = 122/199 (61%), Positives = 147/199 (73%), Gaps = 2/199 (1%) Query: 20 GLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITVTLNMDGSCTVSDN 79 GLDAV+KRP MYIGDTD +GLHHM++EV+DNAIDE+L G+ I VT++ D S +V D+ Sbjct: 1 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDD 60 Query: 80 GRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRI 139 GRGIPT +H EEG+SAAEVIMT LHAGGKF+ SYKVSGGLHGVGVSVVNALS L+L I Sbjct: 61 GRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVI 120 Query: 140 KREGNIYEMSFINGILDNPLVVTGSAGNDTGTEVTFLPSSDI-FSVQDFNYDTLQHRLRE 198 +REG I+ + +G+ PL VTG TGT V F PS + +V +F Y+ L RLRE Sbjct: 121 QREGKIHRQIYEHGVPQAPLAVTGETEK-TGTMVRFWPSLETFTNVTEFEYEILAKRLRE 179 Query: 199 LSFLNSSVQISLIDKRSPE 217 LSFLNS V I L DKR + Sbjct: 180 LSFLNSGVSIRLRDKRDGK 198 >3l4j_A DNA topoisomerase 2; topoisomerase, protein-DNA complex, covalently linked comple supercoiling; HET: DNA PTR TSP; 2.48A {Saccharomyces cerevisiae} PDB: 3l4k_A* 1bjt_A 1bgw_A 2rgr_A* Length = 757 Score = 248 bits (633), Expect = 4e-66 Identities = 54/163 (33%), Positives = 81/163 (49%), Gaps = 8/163 (4%) Query: 407 IASLPGKLADCSE---RDPKKSELFLVEGDSAGGSAKQGRS---RENQAILPLRGKILNV 460 I + P KL D ++ ++ K L L EGDSA A G + R+ PLRGK+LNV Sbjct: 3 ITNYP-KLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNV 61 Query: 461 ERARFDKMLSSQEIGTLITALGTGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTF 520 A D++L + EI + +G + D LRY ++IMTD D DG+HI+ L++ F Sbjct: 62 REASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINF 121 Query: 521 FFRQMPSLIH-NGFLYIIKPPLYGITRGKSLQYVKDEESLEDY 562 P L+ GFL P+ ++ K + ++ DY Sbjct: 122 LESSFPGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDY 164 Score = 41.3 bits (96), Expect = 9e-04 Identities = 14/73 (19%), Positives = 30/73 (41%), Gaps = 1/73 (1%) Query: 730 GRKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEPRR 789 + + YKGLG A ++ E N D + + + D + + + R+ Sbjct: 173 HKFTWKQKYYKGLGTSLAQEVREYFSNLDRHLKIFHSLQG-NDKDYIDLAFSKKKADDRK 231 Query: 790 EFIQENSLPSALD 802 E++++ + LD Sbjct: 232 EWLRQYEPGTVLD 244 >2xcs_B DNA gyrase subunit B, DNA gyrase subunit A; isomerase, type IIA topoisomerase; HET: DNA 5UA RXV; 2.10A {Staphylococcus aureus} PDB: 2xcr_B* 2xcq_A* 2xco_A* Length = 692 Score = 242 bits (619), Expect = 2e-64 Identities = 95/148 (64%), Positives = 114/148 (77%), Gaps = 1/148 (0%) Query: 405 LDIASLPGKLADCSERDPKKSELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERAR 464 +D+ASLPGKLADCS + P++ E+FLVEGDSAGGS K GR QAILPLRGKILNVE+AR Sbjct: 1 MDVASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKAR 60 Query: 465 FDKMLSSQEIGTLITALGTGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQ 524 D++L++ EI +ITA GTGIG D FD+ K RYHKI+IMTDADVDGAHIRTLLLTFF+R Sbjct: 61 LDRILNNNEIRQMITAFGTGIGGD-FDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRF 119 Query: 525 MPSLIHNGFLYIIKPPLYGITRGKSLQY 552 M LI G++YI +PP G+ Sbjct: 120 MRPLIEAGYVYIAQPPTGYKGLGEMNAD 147 Score = 57.6 bits (139), Expect = 1e-08 Identities = 40/66 (60%), Positives = 52/66 (78%) Query: 737 QRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEPRREFIQENS 796 YKGLGEMNA QLWETT+NP+ R+LL+VK+ DA +AD F LMGD VE RR+FI++N+ Sbjct: 136 TGYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNA 195 Query: 797 LPSALD 802 + + LD Sbjct: 196 VYANLD 201 >1bjt_A Topoisomerase II; quaternary change, DNA-binding, DNA topology; 2.50A {Saccharomyces cerevisiae} SCOP: e.11.1.1 PDB: 1bgw_A 2rgr_A* Length = 793 Score = 236 bits (603), Expect = 1e-62 Identities = 59/204 (28%), Positives = 91/204 (44%), Gaps = 14/204 (6%) Query: 390 DAARRARDLTRRKGVLDIASLPGKLADCSE---RDPKKSELFLVEGDSAGGSAKQGRS-- 444 + A + D TR+ + + KL D ++ ++ K L L EGDSA A G + Sbjct: 1 ENALKKSDGTRKSRITNYP----KLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVV 56 Query: 445 -RENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTGIGQDSFDINKLRYHKIIIM 503 R+ PLRGK+LNV A D++L + EI + +G + D LRY ++IM Sbjct: 57 GRDYYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIM 116 Query: 504 TDADVDGAHIRTLLLTFFFRQMPSLI-HNGFLYIIKPPLYGITRGKSLQYVKDEESLEDY 562 TD D DG+HI+ L++ F L+ GFL P+ ++ K + ++ DY Sbjct: 117 TDQDHDGSHIKGLIINFLESSFLGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDY 176 Query: 563 LINQSLSEEIELFCDSKGVISKND 586 + EE K K Sbjct: 177 EKWR---EEESHKFTWKQKYYKGL 197 Score = 30.2 bits (67), Expect = 2.0 Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 2/57 (3%) Query: 736 MQRYKGLGEMNASQLWETTLNPDTR--SLLRVKITDASQADDLFSRLMGDEVEPRRE 790 + YKGLG A ++ E N D ++ D D FS+ D+ + Sbjct: 191 QKYYKGLGTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWLR 247 >2q2e_B Type 2 DNA topoisomerase 6 subunit B; DNA-binding, SPO11, ATPase; 4.00A {Methanosarcina mazei} Length = 621 Score = 229 bits (585), Expect = 2e-60 Identities = 67/548 (12%), Positives = 149/548 (27%), Gaps = 60/548 (10%) Query: 12 ADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDE-SLEGYADIITVTLNM 70 A + + + +K + D+ S L + E +DNA+D G I V + Sbjct: 10 AKKQKSISVAEFFEKNRQILGFDSAPRS-LITTVKEAVDNALDACEEAGILPDILVQVER 68 Query: 71 DG----SCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVS 126 G + + DNG GI + + +L G +F+ + K S G G+G+S Sbjct: 69 TGPDYVTVIIEDNGPGIVREQI--------PKVFAKLLYGSRFH--ALKQSRGQQGIGIS 118 Query: 127 VVNALSSW-------LKLRIKREGNIYEMSFINGILDN-PLVVTGSAGNDTGTEVTFLPS 178 + + + + + N P ++ + T + Sbjct: 119 AAVLYAQMTAGRHTKILSKTSPTAPAHYYELMINTSTNEPDILVDEVRDWFRPHGTQIEL 178 Query: 179 SDIFSVQDFNYDTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYLDR 238 + ++ L+ + +N +I+LID E E + Sbjct: 179 EMRAAYVKGRRQSIYEYLKATAIVNPHARITLIDPDGNEEV---------FERATDKMPE 229 Query: 239 HKKPLMQSPIRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTR 298 + ++ P I+ L + + + F K G + A Sbjct: 230 PAEEILPHPEGIELG------TLMKMLHYTERQKLAPFLRYSFCKIGLLTAEEICKA--- 280 Query: 299 QITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVES 358 + D ++ + R+ + +K+ P + + + +E Sbjct: 281 -------AGLDPEIDPHALGRHEARKLIEAFEKVKIMAP--PTDCLSPIGEDLIYRGLEK 331 Query: 359 FVNDGLSAWLEEHPLEAKIIVKKVLDASMVRDAARRARDLTRRKGVLDIASLPGKLADCS 418 A P V + ++ + + L + + Sbjct: 332 ETTVDFIATSTRKPAVYSGNPFVVEVGMAYGGNLPKEEKISIMRFANRVPLLYQQGGCVT 391 Query: 419 ERDPKKSELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLI 478 + + + GG G + + + + + I I Sbjct: 392 THAVEDIKWKQYGLNQPGGGIPVGPVILLIHVASINVPFTSESKDA---IADIPVIKEEI 448 Query: 479 TALGTGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIK 538 + + Y + I T +L ++ ++ I Sbjct: 449 DLAIKEVARK-----LKHYLSKQSNLKKRREKEIIITKVLPKLAAKVAHVLEKDVPD-IN 502 Query: 539 PPLYGITR 546 P + I Sbjct: 503 PVVAKIMG 510 Score = 79.1 bits (194), Expect = 3e-15 Identities = 10/63 (15%), Positives = 23/63 (36%), Gaps = 3/63 (4%) Query: 730 GRKGISMQRYKGLGEMNASQL--WETTLNPDTRSLLRVKITDASQADDL-FSRLMGDEVE 786 K + + M W+ + + + +L KI AS+ + +L+ + +E Sbjct: 549 PCKVSGAKPEPKVVTMGNDYDYVWDISASAGSSKVLSYKIESASEEELQKLPQLIVEGIE 608 Query: 787 PRR 789 Sbjct: 609 EEL 611 >3m4i_A DNA gyrase subunit B; GYRB, toprim, type II topoisomerase, tuberculosi quinolone binding site, DNA binding site, ATP-binding; HET: DNA; 1.95A {Mycobacterium tuberculosis} PDB: 3ig0_A* 2zjt_A* Length = 242 Score = 220 bits (561), Expect = 1e-57 Identities = 91/234 (38%), Positives = 132/234 (56%), Gaps = 10/234 (4%) Query: 414 LADCSERDPKKSELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQE 473 + D + DP+KSEL++VEGDSAGGSAK GR QAILPLRGKI+NVE+AR D++L + E Sbjct: 9 VDDDDKTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTE 68 Query: 474 IGTLITALGTGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGF 533 + +ITALGTGI + FDI KLRYHKI++M DADVDG HI TLLLT FR M LI NG Sbjct: 69 VQAIITALGTGIHDE-FDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGH 127 Query: 534 LYIIKPPLYGITRGKSLQYVKDEESLEDYLINQSLSEEIELFCDSKGVISKNDLRNFIDD 593 +++ +PPLY + +S + D L+ K + ++ ++ + Sbjct: 128 VFLAQPPLYKLKWQRSDPEFAYSDRERDGLLE-------AGLKAGKKINKEDGIQRYKGL 180 Query: 594 ALKIDKLIKDFYPNHDKTFIEQAVISGVFNCESDQEINVSLASKLANRLNFIAE 647 K + + + + Q + +D+ ++ + + R +FI Sbjct: 181 GEMDAKELWETTMDPSVRVLRQVTLDD--AAAADELFSILMGEDVDARRSFITR 232 Score = 99.3 bits (247), Expect = 3e-21 Identities = 38/74 (51%), Positives = 52/74 (70%), Gaps = 1/74 (1%) Query: 731 RKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEPRRE 790 K +QRYKGLGEM+A +LWETT++P R L +V + DA+ AD+LFS LMG++V+ RR Sbjct: 169 NKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRS 228 Query: 791 FIQENSLP-SALDI 803 FI N+ LD+ Sbjct: 229 FITRNAKDVRFLDV 242 >1zxm_A TOPO IIA ATPase, DNA topoisomerase II, alpha isozyme; GHKL nucleotide-binding fold; HET: DNA ANP; 1.87A {Homo sapiens} PDB: 1zxn_A* Length = 400 Score = 212 bits (541), Expect = 2e-55 Identities = 68/411 (16%), Positives = 153/411 (37%), Gaps = 56/411 (13%) Query: 13 DSIQILKGLDAVKKRPSMYIGDTDGES---------------------GLHHMIYEVLDN 51 Q L+ + RP YIG + + GL+ + E+L N Sbjct: 4 RIYQKKTQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYREVTFVPGLYKIFDEILVN 63 Query: 52 AIDESLEG-YADIITVTLNMD-GSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKF 109 A D I VT++ + ++ +NG+GIP HK E + +I +L + Sbjct: 64 AADNKQRDPKMSCIRVTIDPENNLISIWNNGKGIPVVEHKVEKMYVPALIFGQLLTSSNY 123 Query: 110 NQKSYKVSGGLHGVGVSVVNALSSWLKLR--IKREGNIYEMSFINGILDNPLVVTGSAGN 167 + KV+GG +G G + N S+ + + +++ ++++ + + Sbjct: 124 DDDEKKVTGGRNGYGAKLCNIFSTKFTVETASREYKKMFKQTWMDNMGRAGEMELKPFNG 183 Query: 168 DTGTEVTFLPSSDIFSVQDFNYDTLQHRL---RELSFLNSSVQISLIDKRSPEPREITMF 224 + T +TF P F +Q + D + + +++ V++ L + Sbjct: 184 EDYTCITFQPDLSKFKMQSLDKDIVALMVRRAYDIAGSTKDVKVFLNGNK---------L 234 Query: 225 YKGGIEAFVSYLDRHKKPLMQSPIRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKD 284 G ++V + K + +++ + N ++ + ++ + + F N+I Sbjct: 235 PVKGFRSYVDMYLKDKLDETGNSLKVIHEQVNHRWEVCLTMSEKGFQQI-SFVNSIATSK 293 Query: 285 GGTHLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTK 344 GG H+ + + ++ V+K K +V + ++ + +P F SQTK Sbjct: 294 GGRHVDYVADQIVTKLVDVVKKKN---KGGVAVKAHQVKNHMWIFVNALIENPTFDSQTK 350 Query: 345 EKLVS-------------SEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKV 382 E + +++ + + + + W++ + KK Sbjct: 351 ENMTLQPKSFGSTCQLSEKFIKAAIGCGIVESILNWVKFK--AQVQLNKKC 399 >3g75_A DNA gyrase subunit B; antibiotic resistance, isomerase; HET: DNA B48; 2.30A {Staphylococcus aureus} PDB: 3g7b_A* Length = 184 Score = 207 bits (529), Expect = 6e-54 Identities = 86/209 (41%), Positives = 121/209 (57%), Gaps = 27/209 (12%) Query: 20 GLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITVTLNMDGSCTVSDN 79 GL+AV+KRP MYIG T E GLHH+++E++DN+IDE+L GYA+ I V + D V+DN Sbjct: 1 GLEAVRKRPGMYIGSTS-ERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDN 59 Query: 80 GRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRI 139 GRGIP D+ ++ G A EVI+T SVVNALS L++ + Sbjct: 60 GRGIPVDIQEKMGRPAVEVILT-----------------------SSVVNALSQDLEVYV 96 Query: 140 KREGNIYEMSFINGILDNPLVVTGSAGNDTGTEVTFLPSSDIF-SVQDFNYDTLQHRLRE 198 R IY ++ G+ L G+ + TGT + F +IF +NY+TLQ R+RE Sbjct: 97 HRNETIYHQAYKKGVPQFDLKEVGTT-DKTGTVIRFKADGEIFTETTVYNYETLQQRIRE 155 Query: 199 LSFLNSSVQISLIDKRSPE-PREITMFYK 226 L+FLN +QI+L D+R E RE + Y+ Sbjct: 156 LAFLNKGIQITLRDERDEENVREDSYHYE 184 >3k9f_C DNA topoisomerase 4 subunit B; quinolone, topoisomerase, protein-DNA cleavage complex; HET: DNA LFX; 2.90A {Streptococcus pneumoniae} PDB: 3fof_C* 3foe_C* Length = 268 Score = 199 bits (508), Expect = 1e-51 Identities = 91/239 (38%), Positives = 129/239 (53%), Gaps = 20/239 (8%) Query: 396 RDLTRRKGVLDIASLPGKLADCSERDPKKSELFLVEGDSAGGSAKQGRSRENQAILPLRG 455 D K D L GKL ++P K+EL+LVEGDSAGGSAKQGR R+ QAILPLRG Sbjct: 19 DDDKHMKNKKDKGLLSGKLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRG 78 Query: 456 KILNVERARFDKMLSSQEIGTLITALGTGIGQDSFDINKLRYHKIIIMTDADVDGAHIRT 515 K++N +A+ +L ++EI T+I +G G+G D F I Y KIIIMTDAD DGAHI+T Sbjct: 79 KVINTAKAKMADILKNEEINTMIYTIGAGVGAD-FSIEDANYDKIIIMTDADTDGAHIQT 137 Query: 516 LLLTFFFRQMPSLIHNGFLYIIKPPLYGITRGKSLQYVKDEESLED-------------- 561 LLLTFF+R M L+ G +YI PPLY +++GK + + Sbjct: 138 LLLTFFYRYMRPLVEAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGELEELRKQFGKGAT 197 Query: 562 YLINQSLSE--EIELFCDSKGVISKNDLRNFIDDALKIDKLIKDFY---PNHDKTFIEQ 615 + L E +L+ + ++ +R I+D + ++ + + +IE Sbjct: 198 LQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIED 256 Score = 102 bits (255), Expect = 3e-22 Identities = 40/66 (60%), Positives = 55/66 (83%) Query: 730 GRKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEPRR 789 KG ++QRYKGLGEMNA QLWETT+NP+TR+L+RV I D ++A+ + LMGD+VEPRR Sbjct: 192 FGKGATLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRR 251 Query: 790 EFIQEN 795 ++I++N Sbjct: 252 KWIEDN 257 >2zjt_A DNA gyrase subunit B; GYRB-CTD, toprim, tail, DNA topoisomerase II, G- segment, T-segment, ATP-binding, nucleotide-binding; HET: DNA; 2.80A {Mycobacterium tuberculosis} Length = 247 Score = 197 bits (501), Expect = 9e-51 Identities = 100/248 (40%), Positives = 139/248 (56%), Gaps = 31/248 (12%) Query: 414 LADCSERDPKKSELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQE 473 + + DP+KSEL++VEGDSAGGSAK GR QAILPLRGKI+NVE+AR D++L + E Sbjct: 1 MTPYAFTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTE 60 Query: 474 IGTLITALGTGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGF 533 + +ITALGTGI D FDI KLRYHKI++M DADVDG HI TLLLT FR M LI NG Sbjct: 61 VQAIITALGTGIH-DEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGH 119 Query: 534 LYIIKPPLYGITRGKSLQYVKDEESLEDYLINQSLSEEIELFCD-----SKGVISKN--- 585 +++ +PPLY + +S + D L+ L ++ + KG+ + Sbjct: 120 VFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKE 179 Query: 586 --------DLRNF----IDDALKIDKLIKDFY---PNHDKTFIEQAVISGVFNCESDQEI 630 +R +DDA D+L + ++FI + N + + + Sbjct: 180 LWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITR-------NAKDVRFL 232 Query: 631 NVSLASKL 638 +V LA+ L Sbjct: 233 DVKLAAAL 240 Score = 97.4 bits (242), Expect = 1e-20 Identities = 38/73 (52%), Positives = 52/73 (71%), Gaps = 1/73 (1%) Query: 732 KGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEPRREF 791 K +QRYKGLGEM+A +LWETT++P R L +V + DA+ AD+LFS LMG++V+ RR F Sbjct: 162 KEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSF 221 Query: 792 IQENSLP-SALDI 803 I N+ LD+ Sbjct: 222 ITRNAKDVRFLDV 234 >2zbk_B Type 2 DNA topoisomerase 6 subunit B; DNA binding protein, decatenation, ATPase, drug design, DNA-binding, magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus shibatae} Length = 530 Score = 136 bits (343), Expect = 2e-32 Identities = 61/569 (10%), Positives = 135/569 (23%), Gaps = 80/569 (14%) Query: 12 ADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDE-SLEGYADIITVTLNM 70 + L + K+ P + + L+ + E+++N++D + G I +T+++ Sbjct: 4 KEKFTSLSPAEFFKRNPELAGFPNPARA-LYQTVRELIENSLDATDVHGILPNIKITIDL 62 Query: 71 DG------SCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVG 124 V DNG GIP R+ K+ + + G++G+G Sbjct: 63 IDDARQIYKVNVVDNGIGIPPQ--------EVPNAFGRVLYSSKYVNRQ---TRGMYGLG 111 Query: 125 VSVVNALSS-------WLKLRIKREGNIYEMSFINGILDNPLVVTGSAGNDTGTEVTFLP 177 V S ++ IY I N ++ + Sbjct: 112 VKAAVLYSQMHQDKPIEIETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTS 171 Query: 178 SSDIFSVQDF-NYDTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYL 236 + + ++ + + D Sbjct: 172 VAISIPGDWPKAKSRIYEYIKRTYIITPYAEFIFKDPEG--------------NVTYYPR 217 Query: 237 DRHKKPLMQSPIRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSAL 296 +K P ++ + + N + F N Q G Sbjct: 218 LTNKIPKPPQEVKPHPYGVDREEIKILINNLKRDYTIKEFLVNEFQSIG----------- 266 Query: 297 TRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVV 356 +E + K + ++ ++ D F S + + L + Sbjct: 267 DTTADKILELAGLKPNKKVKNLTEEEIT---RLVETFKKDEDFRSPSADSLSVIGEDLIE 323 Query: 357 ESFVNDGLSAWLEEHPLEAKIIVKKVLDASMVRDAARRARDLTRRKGVLDIASLPGKLAD 416 + + K GV S+P Sbjct: 324 LGLKKIFNPDFAASITRKPKAYQGHPFI---------------VEAGVAFGGSIPVGEEP 368 Query: 417 CSERDPKKSELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGT 476 R K L E + + I + +++ + K+ Sbjct: 369 IVLRYANKIPLIYDEKSDVIWKVVEELDWKRYGIESDQYQMVVMVHLCSTKIPYKSAGKE 428 Query: 477 LITALGTGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYI 536 I N + K +M A ++ ++ + Sbjct: 429 SIAE----------VENIEKEIKNALMEVARKLKQYLSEKRKEQEAKKKLLAYLKYIPEV 478 Query: 537 IKPPLYGITRGKSLQYVKDEESLEDYLIN 565 + + G K + + + L Sbjct: 479 SRSLATFLASGNKELVSKYQNEISEGLFK 507 >1mu5_A Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix two-turns helix; 2.00A {Sulfolobus shibatae} SCOP: a.156.1.3 d.14.1.3 d.122.1.2 PDB: 1mx0_A* 1z5b_A* 1z5a_A* 1z59_A* 1z5c_A* 2hkj_A* Length = 471 Score = 67.3 bits (164), Expect = 1e-11 Identities = 25/193 (12%), Positives = 57/193 (29%), Gaps = 20/193 (10%) Query: 32 IGDTDGESGLHHMIYEVLDNAIDESLE-GYADIITVTLNMDG------SCTVSDNGRGIP 84 G + L+ + E+++N++D + G I +T+++ V DNG GIP Sbjct: 24 AGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIP 83 Query: 85 TDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRIK---- 140 R+ K+ + + GL + + + + I+ Sbjct: 84 PQEVPN--------AFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIEIETSPV 135 Query: 141 REGNIYEMSFINGILDNPLVVTGSAGNDTGTEVTFLPSSDIFSVQDFNYDT-LQHRLREL 199 IY I N ++ + + + + ++ Sbjct: 136 NSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIYEYIKRT 195 Query: 200 SFLNSSVQISLID 212 + + D Sbjct: 196 YIITPYAEFIFKD 208 >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 = 56.1 bits (135), Expect = 3e-08 Identities = 100/697 (14%), Positives = 176/697 (25%), Gaps = 319/697 (45%) Query: 31 YIGD--TDGESGLHHMIYEVLDNAIDES-LEGYADIITVTLNMDGSCTVSDNGRGIPTDL 87 Y+ + G + + + LEG DI + + T L Sbjct: 67 YVSSLVEPSKVGQFDQVLNLCLTEFENCYLEG-NDIHALAAKLLQE---------NDTTL 116 Query: 88 HKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRIKREGN--I 145 K E+I + A + K S +AL R EGN + Sbjct: 117 VK-----TKELIKNYITARIMAKRPFDKKS----------NSAL-----FRAVGEGNAQL 156 Query: 146 YEMSFINGILDNPLVVTGSAGNDTGTEVTFLPSSDIFSVQDFNYDTLQHRLRELSFLNSS 205 + G GN T+ F EL Sbjct: 157 V-------------AIFGGQGN---TDDYF---------------------EEL------ 173 Query: 206 VQISLIDKRSPEPREITMFYKGGIEAFVSYLDRHKKPLMQSP-----IRIQGSRDNISID 260 R++ Y + + + L+++ + QG ++ Sbjct: 174 -------------RDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQG------LN 214 Query: 261 LAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSA--------LTRQITSYVEKSFGSKK 312 + + W + +N P KD +L S + Q+ YV Sbjct: 215 I-LEWLEN--------PSNTPDKD---YLL---SIPISCPLIGVI-QLAHYV-------- 250 Query: 313 DKRSVIGDDCREGFTSVLSIKMPDP-----RFS-----SQTKEKLVSSEVRSVV---ESF 359 V + +L P SQ LV++ + ESF Sbjct: 251 ----VT---AK-----LLGF---TPGELRSYLKGATGHSQ---GLVTAVAIAETDSWESF 292 Query: 360 VNDGLSA-----W--LEEH---PLEAKIIVKKVLDASMVRDAARRA----------RDLT 399 A + + + P L S++ D+ +LT Sbjct: 293 FVSVRKAITVLFFIGVRCYEAYP-------NTSLPPSILEDSLENNEGVPSPMLSISNLT 345 Query: 400 RRKGVLDI-----ASLPGKLADCSERDPKKSELFLVEGDSA---GGSAKQGRSRENQAIL 451 ++ V D + LP K+ E+ LV G G + S Sbjct: 346 -QEQVQDYVNKTNSHLP--------AG-KQVEISLVNGAKNLVVSGPPQ---S------- 385 Query: 452 PLRGKILNVERARFDKMLSSQEIGTLITALGTGIGQDSFDINKLRYHKIIIMTDADVDGA 511 L G LN+ LR K + +D + Sbjct: 386 -LYG--LNL---------------------------------TLR--K--AKAPSGLDQS 405 Query: 512 HIRTLLLTFFFRQMPSLIHNGFLYIIKP---P-LYGITRGKSLQYVKDEESLEDYLINQS 567 I F + N FL + P L + + + + N Sbjct: 406 RIP-------FSERKLKFSNRFLPVASPFHSHLLVPAS-----DLINKDLVKNNVSFNAK 453 Query: 568 -LSEEIELFCDSKGVISKNDLRNFIDDALKIDKLIK---------------------DFY 605 + +I ++ G +DLR ++++ DF Sbjct: 454 DI--QIPVYDTFDG----SDLRVLSGSI--SERIVDCIIRLPVKWETTTQFKATHILDFG 505 Query: 606 P------------NHDKTFIEQAVISGVFNCESDQEI 630 P N D T + + +++G + D + Sbjct: 506 PGGASGLGVLTHRNKDGTGV-RVIVAGTLDINPDDDY 541 Score = 53.8 bits (129), Expect = 1e-07 Identities = 100/729 (13%), Positives = 183/729 (25%), Gaps = 339/729 (46%) Query: 158 PLVVT-GSAGNDTGTEVTFL-PSSDIFSVQDFNYDTLQHRLRELSFLNSSVQISLIDKRS 215 PL ++ GS E L P++ F +L+E F L Sbjct: 8 PLTLSHGS------LEHVLLVPTASFFIAS---------QLQE-QFNKI-----L----- 41 Query: 216 PEPREITMFYKGGIEAFVSYLDRHKKPLMQSPIRIQGSRDNISIDLAMRWNDGYHENVLC 275 PEP E F + + P +P +L ++ L Sbjct: 42 PEP----------TEGFAADDE----P--TTPA-----------ELVGKF--------LG 66 Query: 276 FTNNIPQKDG-GTHLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKM 334 + +++ + G L LT E + Sbjct: 67 YVSSLVEPSKVGQFDQVLNLCLT-----EFENCY-------------------------- 95 Query: 335 PDPRFSSQTKEKLVSSEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVLDASMVRD--AA 392 L +++ ++ + + + L K+++ ++ A Sbjct: 96 ------------LEGNDIHALAAKLLQE------NDTTLVKT---KELI-----KNYITA 129 Query: 393 RRARDLTRRKGVLDIASLPGKLADCSERDPKKSELFLVEGDSAGGSAKQGRSRENQAILP 452 R K L ++L + GG QG Sbjct: 130 RIMAKRPFDKKS------NSALFRAVGEG--NAQLVAI----FGG---QG---------- 164 Query: 453 LRGKILNVERARFDKMLSSQE--------IGTLITALGT---GIGQDSFDINKLRYHKII 501 N + F+++ ++ +G LI + + + D K+ + Sbjct: 165 ------NTDDY-FEEL---RDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLN 214 Query: 502 IM---TDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIK-P---PLYGITRGKSLQYVK 554 I+ + P Y++ P PL G+ Sbjct: 215 ILEWLENPS----------------NTPDK-----DYLLSIPISCPLIGVI--------- 244 Query: 555 DEESLEDYLI-----NQSLSEEIELFC----DSKGVI------SKNDLRNFIDDALKIDK 599 L Y++ + E S+G++ + +F K Sbjct: 245 ---QLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAIT 301 Query: 600 LIKDFYPNHDKTFIEQAVISGVFNCESDQEI-NVSLASKLANRLNFIAEKSEKSWHG--- 655 ++ F FI G + N SL I E S ++ G Sbjct: 302 VL--F-------FI------G---VRCYEAYPNTSLPPS-------ILEDSLENNEGVPS 336 Query: 656 ---SINNSDILVKRIARGV-QEQFVLEGSSIFSFGSKYKRI-FSNRI--EENYLTILSLI 708 SI + QEQ ++ + +N + I SL+ Sbjct: 337 PMLSI-----------SNLTQEQ--VQ-----------DYVNKTNSHLPAGKQVEI-SLV 371 Query: 709 CNG-DKIKITGP-------CSLLDTI------------FSIGRK-GISMQ---------- 737 NG + ++GP L FS RK S + Sbjct: 372 -NGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFS-ERKLKFSNRFLPVASPFHS 429 Query: 738 RYKGLGEMNASQLWETTLNPDTRSL----LRVKITDASQADDLFSRLMGDEVEPRREFIQ 793 L + AS L L + S +++ + D DL R Sbjct: 430 HL--L--VPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDL------------RVL-S 472 Query: 794 ENSLPSALD 802 + +D Sbjct: 473 GSISERIVD 481 Score = 49.2 bits (117), Expect = 4e-06 Identities = 61/403 (15%), Positives = 113/403 (28%), Gaps = 177/403 (43%) Query: 1 MSDNIQNSSYDADSIQIL--KGLDAVK------KRP----------SM----------YI 32 ++ + + + +GL+ ++ P S Y+ Sbjct: 191 SAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYV 250 Query: 33 ------GDTDGE--------SGLHH--------MI---------YEVLDNAID------- 54 G T GE +G H I + + AI Sbjct: 251 VTAKLLGFTPGELRSYLKGATG--HSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGV 308 Query: 55 ESLEGYADI-ITVTLNMDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKS 113 E Y + + ++ D S +N G+P+ + ++ +V Q Sbjct: 309 RCYEAYPNTSLPPSILED-SL---ENNEGVPSPMLSISNLTQEQV------------QD- 351 Query: 114 YKVSGGLHGVGVSVVNALSSWLKLRIKREGNIYEMSFINGILDNPLVVTGSAGNDTGTEV 173 + V+ N+ + + +S +NG N LVV+G Sbjct: 352 -------Y---VNKTNS-------HLPAGKQVE-ISLVNG-AKN-LVVSG---------- 381 Query: 174 TFLPSSDIFSVQDFNYDTLQHRLREL---SFLNSSVQISLIDKRSPEPREITM-FYKGGI 229 P S+ N LR+ S L+ S +I +R + + F + Sbjct: 382 --PPQ----SLYGLN-----LTLRKAKAPSGLDQS-RIPF-SERKL---KFSNRFLP--V 423 Query: 230 EA-FVS-YL----DRHKKPLMQSPIRIQGSRDNISIDLAM---RWNDG-----YHENVL- 274 + F S L D K L+++ + D+ + DG ++ Sbjct: 424 ASPFHSHLLVPASDLINKDLVKNNVSFNAK------DIQIPVYDTFDGSDLRVLSGSISE 477 Query: 275 ----CFTN---NIPQ--KDGGTHL--------SGLRSALTRQI 300 C + TH+ SGL LT + Sbjct: 478 RIVDCIIRLPVKWETTTQFKATHILDFGPGGASGL-GVLTHRN 519 Score = 38.4 bits (89), Expect = 0.007 Identities = 18/92 (19%), Positives = 26/92 (28%), Gaps = 40/92 (43%) Query: 746 NASQLWETTLNPDTRSLLRVKITDASQADD-------LFSRLMG---DEVEPR------- 788 ASQL E + L + T+ ADD L + +G VEP Sbjct: 29 IASQLQEQFN----KIL--PEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQ 82 Query: 789 ----------REFIQEN-------SLPSALDI 803 +++ N L D Sbjct: 83 VLNLCLTEFENCYLEGNDIHALAAKLLQENDT 114 Score = 28.8 bits (64), Expect = 4.7 Identities = 21/105 (20%), Positives = 41/105 (39%), Gaps = 24/105 (22%) Query: 144 NIYEMSFINGILDNPLVVTGSAGNDTGTEV-------TF-------LPSSDIFSVQDFNY 189 + Y S ++ +++NP+ +T G + G + F L + IF ++ N Sbjct: 1655 DTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIF--KEINE 1712 Query: 190 DTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVS 234 + + R L S+ Q + +P +T+ K E S Sbjct: 1713 HSTSYTFRSEKGLLSATQFT-------QP-ALTLMEKAAFEDLKS 1749 >3h4l_A DNA mismatch repair protein PMS1; ATP binding, DNA repair, DNA damage, nucleus, phosphop DNA binding protein, protein binding; HET: DNA ANP; 2.50A {Saccharomyces cerevisiae} Length = 367 Score = 49.3 bits (117), Expect = 3e-06 Identities = 25/173 (14%), Positives = 60/173 (34%), Gaps = 17/173 (9%) Query: 47 EVLDNAIDESLEGYADIITVTLNMDG--SCTVSDNGRGIPTDLHKEEGISAAEVIMTRLH 104 E++DN+ID + A+ I + G S SDNG GI ++ + Sbjct: 32 ELVDNSIDAN----ANQIEIIFKDYGLESIECSDNGDGIDPSNYE------FLALKHYTS 81 Query: 105 AGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRIKREGNIYEMSFI-NGILDNPLVVTG 163 KF + + G G +S + ++ + ++ + G + + + Sbjct: 82 KIAKFQDVAKVQTLGFRGEALSSLCGIAKLSVITTTSPPKADKLEYDMVGHITSKTTTSR 141 Query: 164 SAGNDTGTEVTFLP----SSDIFSVQDFNYDTLQHRLRELSFLNSSVQISLID 212 + G F + + ++ + +N++++ S+ + Sbjct: 142 NKGTTVLVSQLFHNLPVRQKEFSKTFKRQFTKCLTVIQGYAIINAAIKFSVWN 194 >1h7s_A PMS1 protein homolog 2; DNA repair, GHL ATPase, mismatch repair, HNPCC; 1.95A {Homo sapiens} SCOP: d.14.1.3 d.122.1.2 PDB: 1h7u_A* 1ea6_A* Length = 365 Score = 45.9 bits (108), Expect = 4e-05 Identities = 34/240 (14%), Positives = 71/240 (29%), Gaps = 18/240 (7%) Query: 41 LHHMIYEVLDNAIDESLEGYADIITVTLNMDG--SCTVSDNGRGIPTDLHKEEGISAAEV 98 L + E+++N++D A I + L G VSDNG G+ + + + Sbjct: 35 LSTAVKELVENSLDAG----ATNIDLKLKDYGVDLIEVSDNGCGVEEENFE---GLTLKH 87 Query: 99 IMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRIKREGNIYEMSFI--NGILD 156 +++ Q G G +S + ALS + NG + Sbjct: 88 HTSKIQEFADLTQVETF---GFRGEALSSLCALSDVTISTCHASAKVGTRLMFDHNGKII 144 Query: 157 NPLVVTGSAGNDTGTEVTFLPSSDIFSVQDFNYDT----LQHRLRELSFLNSSVQISLID 212 G + F N + L +++ +++S + Sbjct: 145 QKTPYPRPRGTTVSVQQLFSTLPVRHKEFQRNIKKEYAKMVQVLHAYCIISAGIRVSCTN 204 Query: 213 KRSPEPREITMFYKGGIEAFVSYLDRHKKPLMQSPIRIQGSRDNISIDLAMRWNDGYHEN 272 + R+ + G + + +QS I + S+ + + Sbjct: 205 QLGQGKRQPVVCTGGSPSIKENIGSVFGQKQLQSLIPFVQLPPSDSVCEEYGLSCSDALH 264 >3na3_A DNA mismatch repair protein MLH1; MUTL protein homolog 1, DNA damag repair, structural genomics consortium, SGC, protein bindin; HET: DNA ATP; 2.50A {Homo sapiens} Length = 348 Score = 38.1 bits (88), Expect = 0.008 Identities = 14/90 (15%), Positives = 30/90 (33%), Gaps = 12/90 (13%) Query: 47 EVLDNAIDESLEGYADIITVTLNMDG--SCTVSDNGRGIPTDLHKEEGISAAEVIMTRLH 104 E+++N +D + I V + G + DNG GI + Sbjct: 35 EMIENCLDAK----STSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFT------TS 84 Query: 105 AGGKFNQKSYKVSGGLHGVGVSVVNALSSW 134 F + + G G ++ ++ ++ Sbjct: 85 KLQSFEDLASISTYGFRGEALASISHVAHV 114 >2q8g_A [pyruvate dehydrogenase [lipoamide]] kinase isozyme 1; GHKL ATPase/kinase family, pyruvate dehydrogenase complex, mitochondrial kinase; HET: AZX; 1.90A {Homo sapiens} PDB: 2q8f_A* 2q8h_A Length = 407 Score = 37.0 bits (85), Expect = 0.015 Identities = 21/141 (14%), Positives = 49/141 (34%), Gaps = 21/141 (14%) Query: 1 MSDNIQNSSYDADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGY 60 ++ +++ + +P + S L+HM++E+ NA+ ++E + Sbjct: 207 ARRLCDLYYINSPELELEELNAKSPGQPIQVVYV---PSHLYHMVFELFKNAMRATMEHH 263 Query: 61 ADI-----ITVTLNMDGSC---TVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQ- 111 A+ I V + + +SD G G+P + +++ + Sbjct: 264 ANRGVYPPIQVHVTLGNEDLTVKMSDRGGGVPLRKIDR--------LFNYMYSTAPRPRV 315 Query: 112 -KSYKVSGGLHGVGVSVVNAL 131 S V G G+ + Sbjct: 316 ETSRAVPLAGFGYGLPISRLY 336 >3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190 Score = 36.8 bits (84), Expect = 0.020 Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 22/58 (37%) Query: 554 KDEESLEDYLINQSLSEEIELFCDSKGVISKNDLRNFIDDALKIDKLIKDFY--PNHD 609 K ++ LE++ NQ SE++E KN + N I D K FY P+ D Sbjct: 115 KAKKDLEEW--NQRQSEQVE----------KNKINNRIAD--------KAFYQQPDAD 152 >1y8o_A [pyruvate dehydrogenase [lipoamide]] kinase isozyme 3; pyruvate dehydrogenase kinase 3, lipoyl-bearing domain; HET: LPA ADP; 2.48A {Homo sapiens} SCOP: a.29.5.1 d.122.1.4 PDB: 1y8n_A* 1y8p_A* 2pnr_A* 2q8i_A* Length = 419 Score = 34.7 bits (79), Expect = 0.074 Identities = 13/55 (23%), Positives = 25/55 (45%), Gaps = 9/55 (16%) Query: 41 LHHMIYEVLDNAIDESLEGYAD------IITVTLNMDGSC---TVSDNGRGIPTD 86 L HM++E+ N++ ++E Y D + + + +SD G G+P Sbjct: 254 LFHMLFELFKNSMRATVELYEDRKEGYPAVKTLVTLGKEDLSIKISDLGGGVPLR 308 >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 = 34.0 bits (77), Expect = 0.13 Identities = 119/557 (21%), Positives = 202/557 (36%), Gaps = 154/557 (27%) Query: 118 GGLHGVGVSVVNALSSWLKLRIKRE---GNIYEMSFINGILD--NPLVVTGSAGNDT--G 170 G G G+ V+AL K R K E +I + SFIN + N L+++ S T G Sbjct: 1045 GNCSGSGMGGVSALRGMFKDRFKDEPVQNDILQESFINTMSAWVNMLLISSSGPIKTPVG 1104 Query: 171 TEVTFLPSSDIFSVQDF-----------NYDTLQHRLRELSFLNSSVQISLIDK----RS 215 T + S DI V+ YD Q F N + +++ R+ Sbjct: 1105 ACATSVESVDI-GVETILSGKARICIVGGYDDFQEE-GSFEFGNMKATSNTLEEFEHGRT 1162 Query: 216 PE--PREITMFYKGGIEAFVSYLDRHKKPLMQSPIRIQGSRDNISI--DLAMRWNDGYHE 271 P R T G +EA QG+ I + DLA++ Sbjct: 1163 PAEMSRPATTTRNGFMEA-------------------QGAGIQIIMQADLALKM------ 1197 Query: 272 NVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLS 331 G + G+ A+ T + +S + I RE +SV Sbjct: 1198 --------------GVPIYGI-VAMAATATDKIGRSVPAPGKG---ILTTAREHHSSV-- 1237 Query: 332 IKMPDPRFSSQ-TKEKLVSSEVRSVVESFVNDGLSAW---LEEHPLEAK--IIVKKVLD- 384 K P + + K +LV+ E + ++ +V + L A EE P E + ++++ + Sbjct: 1238 -KYASPNLNMKYRKRQLVTREAQ--IKDWVENELEALKLEAEEIPSEDQNEFLLERTREI 1294 Query: 385 ----ASMVRDAARR-ARDLTRRKGVLDIASLPGKLADCSERDPKKSELFLVEGDSAG--- 436 S +R A ++ D +R IA L G LA + + D G Sbjct: 1295 HNEAESQLRAAQQQWGNDFYKRDP--RIAPLRGALAT-----------YGLTIDDLGVAS 1341 Query: 437 --GSAKQGRSRENQAILPLRGKILNVERAR-----FDKMLSSQEIGT--------LITAL 481 G++ + + A + K L F K L+ G + L Sbjct: 1342 FHGTSTKANDKNESATINEMMKHLGRSEGNPVIGVFQKFLTGHPKGAAGAWMMNGALQIL 1401 Query: 482 GTGI---GQDSFDINKL--RYHKIIIMTDA-DVDGAHIRTLLLTFF-FRQMPSLIHNGFL 534 +GI +++ +++K+ ++ ++ + DG +R + +T F F Q G Sbjct: 1402 NSGIIPGNRNADNVDKILEQFEYVLYPSKTLKTDG--VRAVSITSFGFGQ-----KGGQA 1454 Query: 535 YIIKPP-LYG-ITRGKSLQYVKD----EESLEDYLINQSLSEEIELFCDSKGVISKNDLR 588 ++ P LYG IT + +YV E+S + N + +LF +SK Sbjct: 1455 IVVHPDYLYGAITEDRYNEYVAKVSAREKSAYKFFHNGMIYN--KLF------VSK---- 1502 Query: 589 NFIDDALKIDKLIKDFY 605 + A D+L +D Y Sbjct: 1503 ---EHAPYTDELEEDVY 1516 >2e0a_A Pyruvate dehydrogenase kinase isozyme 4; PDK4, ATP-binding, structural genomics, NPPSFA; HET: ANP; 1.86A {Homo sapiens} PDB: 2zdx_A* 2zdy_A* 2zkj_A* 3d2r_A* Length = 394 Score = 33.5 bits (76), Expect = 0.21 Identities = 18/92 (19%), Positives = 35/92 (38%), Gaps = 16/92 (17%) Query: 41 LHHMIYEVLDNAIDESLEGYAD-----IITVTLNMDGS---CTVSDNGRGIPTDLHKEEG 92 LHHM++E+ NA+ ++E + I V + + +SD G G+P + Sbjct: 231 LHHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPLRIIDR-- 288 Query: 93 ISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVG 124 + + ++ + L G G Sbjct: 289 ------LFSYTYSTAPTPVMDNSRNAPLAGFG 314 >2btz_A Pyruvate dehydrogenase kinase isoenzyme 2; GHKL motif regulation, transferase; 2.2A {Homo sapiens} PDB: 2bu2_A* 2bu5_A* 2bu6_A* 2bu7_A* 2bu8_A* 3crk_A* 1jm6_A* 3crl_A* Length = 394 Score = 33.1 bits (75), Expect = 0.25 Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 11/84 (13%) Query: 11 DADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYAD-----IIT 65 + ++I + A K+P + S L+HM++E+ NA+ ++E + I Sbjct: 205 ASPDLEIQEINAANSKQPIHMVYV---PSHLYHMLFELFKNAMRATVESHESSLILPPIK 261 Query: 66 VTLNMDGS---CTVSDNGRGIPTD 86 V + + +SD G G+P Sbjct: 262 VMVALGEEDLSIKMSDRGGGVPLR 285 >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 = 33.1 bits (74), Expect = 0.26 Identities = 13/43 (30%), Positives = 16/43 (37%), Gaps = 15/43 (34%) Query: 16 QILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLE 58 Q LK L A K +Y D D L AI ++E Sbjct: 20 QALKKLQASLK---LY-AD-DSAPAL----------AIKATME 47 >1keh_A Precursor of cephalosporin acylase; glutaryl-7-ACA, hydrolase; 2.50A {Brevundimonas diminuta} SCOP: d.153.1.2 PDB: 1oqz_A Length = 689 Score = 32.9 bits (74), Expect = 0.27 Identities = 14/53 (26%), Positives = 29/53 (54%), Gaps = 4/53 (7%) Query: 349 SSEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVLD---ASMVRDAARRARDL 398 S + R+ +++F G++A+ +++P + V++VL A +V A R L Sbjct: 97 SPDFRANLDAFA-AGINAYAQQNPDDISPEVRQVLPVSGADVVAHAHRLMNFL 148 >1ixm_A SPO0B, protein (sporulation response regulatory protein); phosphotransferase, two component system; 2.60A {Bacillus subtilis} SCOP: d.123.1.1 PDB: 2ftk_A* 1f51_A Length = 192 Score = 32.0 bits (71), Expect = 0.50 Identities = 6/51 (11%), Positives = 15/51 (29%), Gaps = 5/51 (9%) Query: 41 LHHMIYEVLDNAIDESLEGYADIITVTLNMDGSC-----TVSDNGRGIPTD 86 L ++ ++ + +TV+L D + +G Sbjct: 110 LAKLMRKLFHLFDQAVSRESENHLTVSLQTDHPDRQLILYLDFHGAFADPS 160 >1b63_A MUTL; DNA mismatch repair, ATPase; HET: ANP; 1.90A {Escherichia coli} SCOP: d.14.1.3 d.122.1.2 PDB: 1nhh_A* 1nhi_A* 1bkn_A 1nhj_A* 1b62_A* Length = 333 Score = 31.7 bits (71), Expect = 0.67 Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 6/42 (14%) Query: 47 EVLDNAIDESLEGYADIITVTLNMDG--SCTVSDNGRGIPTD 86 E+++N++D A I + + G + DNG GI D Sbjct: 31 ELVENSLDAG----ATRIDIDIERGGAKLIRIRDNGCGIKKD 68 >1m3q_A 8-oxoguanine DNA glycosylase; DNA repair, END product, HOGG, 8-aminoguanine, RE-ligation, hydrolase/DNA complex; HET: DRZ ANG; 1.90A {Homo sapiens} SCOP: a.96.1.3 d.129.1.2 PDB: 1m3h_A* 1n39_A* 1lwy_A* 1hu0_A* 1lwv_A* 1lww_A* 1fn7_A* 1n3a_A* 1n3c_A* 1ebm_A* 1ko9_A 2noe_A* 2noh_A* 2nol_A* 1yqk_A 2noz_A* 2nof_A* 1yqr_A* 1yql_A* 1yqm_A* ... Length = 317 Score = 30.8 bits (69), Expect = 1.0 Identities = 24/215 (11%), Positives = 57/215 (26%), Gaps = 15/215 (6%) Query: 542 YGITRGKSLQYVKDEESLEDYLINQSLSEEIELFCDSKGVISK-----NDLRNFIDDALK 596 G+ + + EE L + S+ D + K L Sbjct: 48 SGVLADQVWTLTQTEEQLHCTVYRGDKSQASRPTPDELEAVRKYFQLDVTLAQLYHHWGS 107 Query: 597 IDKLIKDFYPNHDKTFI-EQAVISGVFNCESDQEINVSLASKLANRLNFIAEKSEKSWHG 655 +D ++ + Q I +F+ N++ + + RL Sbjct: 108 VDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDD 167 Query: 656 SINNSDILVKRIARGVQEQFVLEGSSIFSFGSKYKRIFSNRIEENYLTILSLICNGDKIK 715 + ++ +A E + + G Y+ + + L + +++ Sbjct: 168 VTYHGFPSLQALAGPEVEAHLRKL------GLGYRARYVSASARAILEEQGGLAWLQQLR 221 Query: 716 ITGPCSLLDT---IFSIGRKGISMQRYKGLGEMNA 747 + + +G K L + A Sbjct: 222 ESSYEEAHKALCILPGVGTKVADCICLMALDKPQA 256 >1f0k_A MURG, UDP-N-acetylglucosamine-N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol...; rossmann fold, transferase; 1.90A {Escherichia coli} SCOP: c.87.1.2 PDB: 1nlm_A* Length = 364 Score = 31.1 bits (69), Expect = 1.1 Identities = 9/61 (14%), Positives = 20/61 (32%), Gaps = 2/61 (3%) Query: 357 ESFVNDGLSAWLEEHPLEAKIIVKKV--LDASMVRDAARRARDLTRRKGVLDIASLPGKL 414 G + +E+ L + + + A RAR + +A+ ++ Sbjct: 294 LPLEKAGAAKIIEQPQLSVDAVANTLAGWSRETLLTMAERARAASIPDATERVANEVSRV 353 Query: 415 A 415 A Sbjct: 354 A 354 >3d36_A Sporulation kinase B; GHKL ATPase, four helix bundle, class I two-component histidine kinase, phosphoprotein; HET: ADP; 2.03A {Geobacillus stearothermophilus} Length = 244 Score = 31.0 bits (70), Expect = 1.2 Identities = 9/47 (19%), Positives = 20/47 (42%), Gaps = 1/47 (2%) Query: 41 LHHMIYEVLDNAIDESLEGYADIITVTLNMDG-SCTVSDNGRGIPTD 86 + V+ NAI+ G + V+++ ++D G G+ + Sbjct: 124 FRQCLLNVMKNAIEAMPNGGTLQVYVSIDNGRVLIRIADTGVGMTKE 170 >1kbi_A Cytochrome B2, L-LCR; flavocytochrome B2, electron transfer, oxidoreductase; HET: HEM FMN; 2.30A {Saccharomyces cerevisiae} SCOP: c.1.4.1 d.120.1.1 PDB: 1fcb_A* 1lco_A* 1ldc_A* 1sze_A* 2oz0_A* 1szf_A* 1szg_A* 1ltd_A* 1kbj_A* 1qcw_A* Length = 511 Score = 30.9 bits (69), Expect = 1.3 Identities = 36/216 (16%), Positives = 70/216 (32%), Gaps = 44/216 (20%) Query: 336 DPRFSSQTKEKLVSSEVRS---------VVESFVNDGLSAWLEEHPLEAKIIVK---KVL 383 +P+ K+K+ +EV V+ +V D L+ +L HP +I K Sbjct: 1 EPKLDM-NKQKISPAEVAKHNKPDDCWVVINGYVYD-LTRFLPNHPGGQDVIKFNAGK-- 56 Query: 384 DASMV------RDAARRARDLTRRKGVLDIASLPGKLADCSERDPKKSELFLVEGDSAGG 437 D + + + + ++ G L + P + K + Sbjct: 57 DVTAIFEPLHAPNVIDKYIAPEKKLGPLQGSMPPELVCPPYAPGETKED----------- 105 Query: 438 SAKQGRSRENQAILPLRGKILNVE--RARFDKMLSSQEIGTLITALGTGIGQDSFDINKL 495 R + +++LP I+N+ + L+ Q + + + N Sbjct: 106 ---IARKEQLKSLLPPLDNIINLYDFEYLASQTLTKQAWAYYSSGANDEV---THRENHN 159 Query: 496 RYHKIIIMTDA--DVDGAHIRTLLLTFFFRQMPSLI 529 YH+I DV I T +L +P + Sbjct: 160 AYHRIFFKPKILVDVRKVDISTDMLGSHVD-VPFYV 194 >2ajr_A Sugar kinase, PFKB family; TM0828, possible 1-phosphofructokinase (EC 2.7.1.56), structural genomics, joint center for structural genomics; HET: MSE; 2.46A {Thermotoga maritima} SCOP: c.72.1.1 Length = 331 Score = 30.3 bits (67), Expect = 1.6 Identities = 18/69 (26%), Positives = 27/69 (39%), Gaps = 16/69 (23%) Query: 63 IITVTLN--MDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGK-FNQKSYKVSGG 119 ++TVTLN +D + D ++ T++ GGK N VS Sbjct: 14 VLTVTLNPALDREIFIE--------DFQVNRLYRINDLSKTQMSPGGKGIN-----VSIA 60 Query: 120 LHGVGVSVV 128 L +GV V Sbjct: 61 LSKLGVPSV 69 >1fm2_A Glutaryl 7-aminocephalosporanic acid acylase; cephalosporin acylase, antibiotics, penicillin acylase, N- terminal hydrolase; 2.00A {Brevundimonas diminuta} SCOP: d.153.1.2 PDB: 1ghd_A 3jtq_A 3jtr_A 2adv_A 2ae3_A 2ae5_A 2ae4_A 1or0_A 1jw0_A 1jvz_A 1gk1_A 1gk0_A Length = 169 Score = 30.3 bits (68), Expect = 1.7 Identities = 9/35 (25%), Positives = 23/35 (65%), Gaps = 1/35 (2%) Query: 349 SSEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVL 383 S + R+ +++F G++A+ +++P + V++VL Sbjct: 97 SPDFRANLDAFA-AGINAYAQQNPDDISPEVRQVL 130 >1h72_C HK, homoserine kinase; transferase, threonine biosynthesis; HET: ANP; 1.8A {Methanococcus jannaschii} SCOP: d.14.1.5 d.58.26.1 PDB: 1fwl_A 1fwk_A* 1h73_A* 1h74_A* Length = 296 Score = 30.4 bits (67), Expect = 1.8 Identities = 16/74 (21%), Positives = 28/74 (37%) Query: 57 LEGYADIITVTLNMDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKV 116 L+ D+I V D + + + IPTD K A+ ++ + G K Sbjct: 25 LKEPYDVIEVEAIDDKEIIIEVDDKNIPTDPDKNVAGIVAKKMIDDFNIGKGVKITIKKG 84 Query: 117 SGGLHGVGVSVVNA 130 G+G S ++ Sbjct: 85 VKAGSGLGSSAASS 98 >1ysr_A Sensor-type histidine kinase PRRB; ATP-binding domain, structural genomics, mycobacterium tuberculosis structural proteomics project; 1.78A {Mycobacterium tuberculosis} SCOP: d.122.1.3 PDB: 1ys3_A Length = 150 Score = 30.2 bits (68), Expect = 2.0 Identities = 16/86 (18%), Positives = 33/86 (38%), Gaps = 3/86 (3%) Query: 1 MSDNIQNSSYDADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGY 60 ++D + +++DA I + V + +G +GL + + NA+ Sbjct: 10 ITDLLDRAAHDAARIYPDLDVSLVPSPTCIIVGL---PAGLRLAVDNAIANAVKHGGATL 66 Query: 61 ADIITVTLNMDGSCTVSDNGRGIPTD 86 + V+ + DNG G+P Sbjct: 67 VQLSAVSSRAGVEIAIDDNGSGVPEG 92 >3a0r_A Sensor protein; four helix bundle, PAS fold, kinase, phosphoprotein, transferase, two-component regulatory system; 3.80A {Thermotoga maritima} Length = 349 Score = 30.0 bits (67), Expect = 2.3 Identities = 11/50 (22%), Positives = 23/50 (46%), Gaps = 1/50 (2%) Query: 41 LHHMIYEVLDNAIDESLEGYADIITVTLNMDG-SCTVSDNGRGIPTDLHK 89 + ++ ++ NAI+ + E IT +V ++G IP +L + Sbjct: 245 IKQVLINLVQNAIEATGENGKIKITSEDMYTKVRVSVWNSGPPIPEELKE 294 >1gkz_A [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase; transferase, mitochondrial protein kinase, potassium; HET: ADP; 2.2A {Rattus norvegicus} SCOP: a.29.5.1 d.122.1.4 PDB: 1gjv_A 1gkx_A* Length = 388 Score = 29.8 bits (66), Expect = 2.4 Identities = 19/110 (17%), Positives = 35/110 (31%), Gaps = 21/110 (19%) Query: 41 LHHMIYEVLDNAIDESLEGYADIITVTLNMDGSC---------TVSDNGRGIPTDLH--- 88 L +++ E+L NA+ ++E + D ++ + +SD G GI Sbjct: 239 LDYILPELLKNAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKDLDRV 298 Query: 89 -------KEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNAL 131 E + H +S + G G G+ A Sbjct: 299 MDYHFTTAEASTQDPRISPLFGHLDMHSGGQSGPMHG--FGFGLPTSRAY 346 >2zxr_A Single-stranded DNA specific exonuclease RECJ; DNA repair, hydrolase; 2.15A {Thermus thermophilus} PDB: 2zxo_A 2zxp_A 1ir6_A Length = 666 Score = 29.7 bits (66), Expect = 2.5 Identities = 28/107 (26%), Positives = 39/107 (36%), Gaps = 30/107 (28%) Query: 10 YDADSI----QILKGLDAVKKRPSMYIGD--TDGESGLHHMIYEVLDNAIDESLEGYADI 63 YDAD + +++GL A+ +I +G Y VL + E LE Sbjct: 81 YDADGLTGTAILVRGLAALGADVHPFIPHRLEEG--------YGVLMERVPEHLEASDLF 132 Query: 64 ITVTLNMDGSCTVSDNGRG--IPTDLHKEEGISAAEVIMTRLHAGGK 108 +TV D G E G+ EVI+T H GK Sbjct: 133 LTV-----------DCGITNHAELRELLENGV---EVIVTDHHTPGK 165 >1id0_A PHOQ histidine kinase; PHOQ/PHOP, signal transduction, transferase; HET: ANP; 1.60A {Escherichia coli} SCOP: d.122.1.3 PDB: 3cgz_A 3cgy_A Length = 152 Score = 29.3 bits (66), Expect = 3.1 Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 7/49 (14%) Query: 41 LHHMIYEVLDNAIDESLEGYADIITVTLNMDGSC---TVSDNGRGIPTD 86 ++ VLDNA LE + ++ V D+G GIP Sbjct: 45 FVEVMGNVLDNACKYCLEF----VEISARQTDEHLYIVVEDDGPGIPLS 89 >3lig_A Fructosyltransferase; five bladed beta-propeller fold, hydrolase; 1.80A {Aspergillus japonicus} PDB: 3ldk_A* 3lem_A* 3ldr_A 3lih_A* 3lf7_A 3lfi_A* Length = 634 Score = 29.4 bits (65), Expect = 3.4 Identities = 4/11 (36%), Positives = 6/11 (54%) Query: 353 RSVVESFVNDG 363 +VVE + N Sbjct: 579 NAVVEVYANGR 589 >1bxd_A ENVZ(290-450), protein (osmolarity sensor protein (ENVZ)); histidine kinase, osmosensor, His-Asp phosphorelay system, signal transduction; HET: ANP; NMR {Escherichia coli} SCOP: d.122.1.3 Length = 161 Score = 29.5 bits (66), Expect = 3.4 Identities = 15/91 (16%), Positives = 31/91 (34%), Gaps = 15/91 (16%) Query: 41 LHHMIYEVLDNAIDESLEGYADIITVTLNMDGSCTVSDNGRGIPTDLHKEEGISAAEVIM 100 + + ++ NA G+ + + T V D+G GI + K Sbjct: 48 IKRAVANMVVNAARYG-NGWIKVSSGTEPNRAWFQVEDDGPGIAPEQRK----------- 95 Query: 101 TRLHAGGKFNQKSYKVSGGLHGVGVSVVNAL 131 H F + + G+G+++V + Sbjct: 96 ---HLFQPFVRGDSARTISGTGLGLAIVQRI 123 >2a33_A Hypothetical protein; structural genomics, protein structure initiative, center for eukaryotic structural genomics, CESG, AT2G37210; 1.95A {Arabidopsis thaliana} SCOP: c.129.1.1 PDB: 2q4o_A Length = 215 Score = 28.9 bits (64), Expect = 4.5 Identities = 7/34 (20%), Positives = 17/34 (50%), Gaps = 2/34 (5%) Query: 579 KGVISKNDLRNFI--DDALKIDKLIKDFYPNHDK 610 +G IS + A ++ K ++++ P H++ Sbjct: 164 EGFISPTAREIIVSAPTAKELVKKLEEYAPCHER 197 >3kf3_A Invertase; GH32, glycoprotein, glycosidase, hydrolase; HET: FRU NAG; 1.90A {Schwanniomyces occidentalis} PDB: 3kf5_A* Length = 509 Score = 28.3 bits (62), Expect = 6.7 Identities = 11/61 (18%), Positives = 23/61 (37%), Gaps = 6/61 (9%) Query: 303 YVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVND 362 Y+++ + + R D + L FS +V ++++E + ND Sbjct: 413 YIDRHIPNVEFPRKQFFTDKLAAYLEPLDYDQDLRVFSLYG---IVD---KNIIELYFND 466 Query: 363 G 363 G Sbjct: 467 G 467 >1o60_A 2-dehydro-3-deoxyphosphooctonate aldolase; structural genomics, transferase; 1.80A {Haemophilus influenzae} SCOP: c.1.10.4 PDB: 3e9a_A Length = 292 Score = 28.2 bits (62), Expect = 7.2 Identities = 9/29 (31%), Positives = 13/29 (44%) Query: 576 CDSKGVISKNDLRNFIDDALKIDKLIKDF 604 CD + + L F+ ID L+K F Sbjct: 249 CDGPSALPLSALEGFVSQMKAIDDLVKSF 277 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 0.317 0.135 0.383 Gapped Lambda K H 0.267 0.0546 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 6,700,655 Number of extensions: 320193 Number of successful extensions: 979 Number of sequences better than 10.0: 1 Number of HSP's gapped: 919 Number of HSP's successfully gapped: 76 Length of query: 803 Length of database: 5,693,230 Length adjustment: 100 Effective length of query: 703 Effective length of database: 3,268,830 Effective search space: 2297987490 Effective search space used: 2297987490 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 61 (27.7 bits)