RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780814|ref|YP_003065227.1| DNA gyrase subunit B [Candidatus Liberibacter asiaticus str. psy62] (803 letters) >gnl|CDD|184903 PRK14939, gyrB, DNA gyrase subunit B; Provisional. Length = 756 Score = 1312 bits (3397), Expect = 0.0 Identities = 450/807 (55%), Positives = 564/807 (69%), Gaps = 62/807 (7%) Query: 6 QNSSYDADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIIT 65 ++SY A SI++LKGLDAV+KRP MYIGDTD +GLHHM+YEV+DNAIDE+L G+ D IT Sbjct: 3 MSNSYGASSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVYEVVDNAIDEALAGHCDDIT 62 Query: 66 VTLNMDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGV 125 VT++ DGS +VSDNGRGIPTD+H EEG+SAAEVIMT LHAGGKF+Q SYKVSGGLHGVGV Sbjct: 63 VTIHADGSVSVSDNGRGIPTDIHPEEGVSAAEVIMTVLHAGGKFDQNSYKVSGGLHGVGV 122 Query: 126 SVVNALSSWLKLRIKREGNIYEMSFINGILDNPLVVTGSAGNDTGTEVTFLPSSDIFSVQ 185 SVVNALS WL+L I+R+G I+E F +G+ PL V G + TGTEV F PS +IF Sbjct: 123 SVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGET-DKTGTEVRFWPSPEIFENT 181 Query: 186 DFNYDTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYLDRHKKPLMQ 245 +F+YD L RLREL+FLNS V+I L D+R +E Y+GGI+AFV YL+R+K PL Sbjct: 182 EFDYDILAKRLRELAFLNSGVRIRLKDERDG--KEEEFHYEGGIKAFVEYLNRNKTPLHP 239 Query: 246 SPIRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVE 305 + G +D I +++A++WND Y ENVLCFTNNIPQ+DGGTHL+G R+ALTR I +Y+E Sbjct: 240 NIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIE 299 Query: 306 KSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVNDGLS 365 K +KK K S+ GDD REG T+VLS+K+PDP+FSSQTK+KLVSSEVR VES VN+ LS Sbjct: 300 KEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLS 359 Query: 366 AWLEEHPLEAKIIVKKVLDASMVRDAARRARDLTRRKGVLDIASLPGKLADCSERDPKKS 425 +LEE+P EAKIIV K++DA+ R+AAR+AR+LTRRKG LDIA LPGKLADC E+DP S Sbjct: 360 EFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALS 419 Query: 426 ELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTGI 485 EL+LVEGDSAGGSAKQGR R+ QAILPL+GKILNVE+ARFDKMLSSQEIGTLITALG GI Sbjct: 420 ELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGI 479 Query: 486 GQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIKPPLYGIT 545 G+D F+ +KLRYHKIIIMTDADVDG+HIRTLLLTFF+RQMP LI G LYI +PPLY + Sbjct: 480 GRDEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVK 539 Query: 546 RGKSLQYVKDEESLEDYLINQSLSEEIELFCDSKGVISKNDLRNFIDDALKIDKLIKDFY 605 +GK QY+KD+E+L+DYLI +L E L IS L + + + K+I Sbjct: 540 KGKQEQYLKDDEALDDYLIELAL-EGATLHLADGPAISGEALEKLVKEYRAVRKIIDRLE 598 Query: 606 PNHDKTFIEQAVISGVFNCESD------QEINVS-LASKLANRLNFIAEKSEKSWHGSIN 658 + + +E + + + + ++ L S RL +AEK Sbjct: 599 RRYPRAVLEALIYAPALDLDDLADEAAVAALDADFLTSAEYRRLVELAEK---------- 648 Query: 659 NSDILVKRIARGVQEQFVLEGSSIFSFGSKYKRIFSNRIEENYLTILSLICNGDK-IKIT 717 IEE + + G++ ++ Sbjct: 649 ----------------------------------LRGLIEEG-----AYLERGERKQPVS 669 Query: 718 GPCSLLDTIFSIGRKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLF 777 LD + + RKG+S+QRYKGLGEMN QLWETT++P+ R LL+V I DA AD++F Sbjct: 670 SFEEALDWLLAEARKGLSIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIEDAIAADEIF 729 Query: 778 SRLMGDEVEPRREFIQENSLPSA-LDI 803 + LMGDEVEPRREFI+EN+L A LD+ Sbjct: 730 TTLMGDEVEPRREFIEENALNVANLDV 756 >gnl|CDD|180181 PRK05644, gyrB, DNA gyrase subunit B; Validated. Length = 638 Score = 926 bits (2395), Expect = 0.0 Identities = 325/561 (57%), Positives = 422/561 (75%), Gaps = 4/561 (0%) Query: 3 DNIQNSSYDADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYAD 62 + YDA IQ+L+GL+AV+KRP MYIG T GE GLHH++YE++DN+IDE+L GY D Sbjct: 1 KEEKAQEYDASQIQVLEGLEAVRKRPGMYIGST-GERGLHHLVYEIVDNSIDEALAGYCD 59 Query: 63 IITVTLNMDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHG 122 I VT+N DGS TV+DNGRGIP D+H + G A EV++T LHAGGKF YKVSGGLHG Sbjct: 60 HIEVTINEDGSITVTDNGRGIPVDIHPKTGKPAVEVVLTVLHAGGKFGGGGYKVSGGLHG 119 Query: 123 VGVSVVNALSSWLKLRIKREGNIYEMSFINGILDNPLVVTGSAGNDTGTEVTFLPSSDIF 182 VGVSVVNALS+WL++ +KR+G IY + G+ PL V G ++TGT VTF P +IF Sbjct: 120 VGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIGET-DETGTTVTFKPDPEIF 178 Query: 183 SVQDFNYDTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYLDRHKKP 242 +F+YDTL RLREL+FLN ++I+L D+R E +E T Y+GGI+ +V YL+R+K+P Sbjct: 179 ETTEFDYDTLATRLRELAFLNKGLKITLTDEREGEEKEETFHYEGGIKEYVEYLNRNKEP 238 Query: 243 LMQSPIRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITS 302 L + PI +G +D I +++AM++NDGY EN+L F NNI +GGTH G ++ALTR I Sbjct: 239 LHEEPIYFEGEKDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVIND 298 Query: 303 YVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVND 362 Y K+ K+ ++ G+D REG T+V+S+K P+P+F QTK KL +SEVR +V+S V++ Sbjct: 299 YARKNKLLKEKDDNLTGEDVREGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSE 358 Query: 363 GLSAWLEEHPLEAKIIVKKVLDASMVRDAARRARDLTRRKGVLDIASLPGKLADCSERDP 422 LS +LEE+P AK IV+K + A+ R+AAR+AR+LTRRK L+ +SLPGKLADCS +DP Sbjct: 359 ALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALESSSLPGKLADCSSKDP 418 Query: 423 KKSELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALG 482 ++SEL++VEGDSAGGSAKQGR R QAILPLRGKILNVE+AR DK+L ++EI LITALG Sbjct: 419 EESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALG 478 Query: 483 TGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIKPPLY 542 TGIG D FDI+KLRYHKIIIMTDADVDGAHIRTLLLTFF+R M LI G++YI +PPLY Sbjct: 479 TGIGDD-FDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLY 537 Query: 543 GITRGKSLQYVKDEESLEDYL 563 I +G +Y +E L++ L Sbjct: 538 KIKKGGK-EYAYSDEELDEIL 557 Score = 139 bits (354), Expect = 2e-33 Identities = 48/83 (57%), Positives = 63/83 (75%), Gaps = 1/83 (1%) Query: 722 LLDTIFSIGRKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLM 781 +L + G +QRYKGLGEMN QLWETT++P+TR+LL+V I DA++AD++FS LM Sbjct: 556 ILAELKLKGNPKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSILM 615 Query: 782 GDEVEPRREFIQENSLPSA-LDI 803 GD+VEPRREFI+EN+ LDI Sbjct: 616 GDDVEPRREFIEENAKYVRNLDI 638 >gnl|CDD|162180 TIGR01059, gyrB, DNA gyrase, B subunit. This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Proteins scoring above the noise cutoff for this model and below the trusted cutoff for topoisomerase IV models probably should be designated GyrB. Length = 654 Score = 886 bits (2291), Expect = 0.0 Identities = 340/569 (59%), Positives = 436/569 (76%), Gaps = 10/569 (1%) Query: 10 YDADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITVTLN 69 YDA SI++L+GL+AV+KRP MYIG T GE+GLHH++YEV+DN+IDE++ GY D I VT+N Sbjct: 1 YDASSIKVLEGLEAVRKRPGMYIGST-GETGLHHLVYEVVDNSIDEAMAGYCDTINVTIN 59 Query: 70 MDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVN 129 DGS TV DNGRGIP D+H EEGISA EV++T LHAGGKF++ SYKVSGGLHGVGVSVVN Sbjct: 60 DDGSVTVEDNGRGIPVDIHPEEGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVN 119 Query: 130 ALSSWLKLRIKREGNIYEMSFINGILDNPLVVTGSAGNDTGTEVTFLPSSDIFSVQDFNY 189 ALS WL++ + R+G IY F GI PL V G TGT V F P +IF +F++ Sbjct: 120 ALSEWLEVTVFRDGKIYRQEFERGIPLGPLEVVGET-KKTGTTVRFWPDPEIFETTEFDF 178 Query: 190 DTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYLDRHKKPLMQSPIR 249 D L RLREL+FLNS V+ISL D+R + + +T Y+GGI++FV YL+R+K+PL + I Sbjct: 179 DILAKRLRELAFLNSGVKISLEDERDGKGKSVTFHYEGGIKSFVKYLNRNKEPLHEEIIY 238 Query: 250 IQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVEKSFG 309 I+G ++ I +++A++WNDGY EN+L F NNI ++GGTHL G RSALTR I SY + + Sbjct: 239 IKGEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKL 298 Query: 310 SKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVNDGLSAWLE 369 K+ K ++ G+D REG T+V+S+K+PDP+F QTK KL +SEVRS+VES V + L+ + E Sbjct: 299 LKESKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFE 358 Query: 370 EHPLEAKIIVKKVLDASMVRDAARRARDLTRRKGVLDIASLPGKLADCSERDPKKSELFL 429 E+P EAK IV+K + A+ R+AAR+AR+LTRRK LD LPGKLADCS +DP KSEL++ Sbjct: 359 ENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYI 418 Query: 430 VEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTGIGQDS 489 VEGDSAGGSAKQGR R+ QAILPLRGKILNVE+AR DK+LS+QEIG +ITALG GIG+D Sbjct: 419 VEGDSAGGSAKQGRDRKFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKD- 477 Query: 490 FDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIKPPLYGITRGKS 549 FD+ KLRYHKIIIMTDADVDG+HIRTLLLTFF+R M LI NG++YI +PPLY + +GK Sbjct: 478 FDLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKK 537 Query: 550 LQYVKDE-------ESLEDYLINQSLSEE 571 +Y+KD+ E+LED S++ Sbjct: 538 ERYIKDDKEKELVGEALEDLRALYIYSDK 566 Score = 128 bits (324), Expect = 6e-30 Identities = 49/70 (70%), Positives = 60/70 (85%) Query: 728 SIGRKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEP 787 GRKGI +QRYKGLGEMNA QLWETT++P++R+LL+V I DA +AD +FS LMGDEVEP Sbjct: 578 HEGRKGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEP 637 Query: 788 RREFIQENSL 797 RREFI+ N+L Sbjct: 638 RREFIEANAL 647 >gnl|CDD|180127 PRK05559, PRK05559, DNA topoisomerase IV subunit B; Reviewed. Length = 631 Score = 753 bits (1946), Expect = 0.0 Identities = 270/559 (48%), Positives = 365/559 (65%), Gaps = 12/559 (2%) Query: 4 NIQNSSYDADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADI 63 + ++Y+ADSI++L+GL+ V+KRP MYIG TD GLHH++ EV+DN++DE+L G+ Sbjct: 2 AMMTNNYNADSIEVLEGLEPVRKRPGMYIGSTD-TRGLHHLVQEVIDNSVDEALAGHGKR 60 Query: 64 ITVTLNMDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGV 123 I VTL+ DGS +V DNGRGIP +H EEG S EVI+T+LHAGGKF+ K+YK SGGLHGV Sbjct: 61 IEVTLHADGSVSVRDNGRGIPVGIHPEEGKSGVEVILTKLHAGGKFSNKAYKFSGGLHGV 120 Query: 124 GVSVVNALSSWLKLRIKREGNIYEMSFINGILDNPLVVTGSAG-NDTGTEVTFLPSSDIF 182 GVSVVNALSS L++ +KR+G +Y F G PL V G+AG TGT V F P IF Sbjct: 121 GVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGTAGKRKTGTRVRFWPDPKIF 180 Query: 183 SVQDFNYDTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYLDRHKKP 242 F+ + L+ RLR +FL + I+L D+R + T Y+ G++ +++ L+ K+ Sbjct: 181 DSPKFSPERLKERLRSKAFLLPGLTITLNDERERQ----TFHYENGLKDYLAELNEGKET 236 Query: 243 L-MQSPIRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTRQIT 301 L + +G + +++ A++W D EN+ + N IP GGTH +G R L + + Sbjct: 237 LPEEFVGSFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVR 296 Query: 302 SYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVN 361 + EK K K+ + G+D REG +VLS+K+P+P+F QTKEKL S E R V V Sbjct: 297 EFAEKRNLLPKGKK-LEGEDVREGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVK 355 Query: 362 DGLSAWLEEHPLEAKIIVKKVLDASMVRDAARRARDLTRRKGVLDIASLPGKLADCSERD 421 D WL ++P A+ + +K + A+ R A + + R+K +LPGKLADC+ +D Sbjct: 356 DAFDLWLNQNPELAEKLAEKAIKAAQARLRAA--KKVKRKK-KTSGPALPGKLADCTSQD 412 Query: 422 PKKSELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITAL 481 P+++ELFLVEGDSAGGSAKQ R RE QAILPLRGKILN A D +L+++EI +I A+ Sbjct: 413 PERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAI 472 Query: 482 GTGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIKPPL 541 G G G DSFD+ LRY KIIIMTDADVDGAHI TLLLTFF+R P L+ G +YI PPL Sbjct: 473 GIGPG-DSFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPL 531 Query: 542 YGITRGKSLQYVKDEESLE 560 Y + +GK Y DEE E Sbjct: 532 YRVDKGKKKIYALDEEEKE 550 Score = 125 bits (316), Expect = 5e-29 Identities = 38/75 (50%), Positives = 50/75 (66%), Gaps = 1/75 (1%) Query: 721 SLLDTIFSIGRKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRL 780 LL + +QR+KGLGEMN QLWETT++P+TR L+RV I DA + + L L Sbjct: 551 ELLKKLGK-KGGKPEIQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEETEKLVDML 609 Query: 781 MGDEVEPRREFIQEN 795 MG + EPRRE+I+EN Sbjct: 610 MGKKAEPRREWIEEN 624 >gnl|CDD|128710 smart00433, TOP2c, TopoisomeraseII. Eukaryotic DNA topoisomerase II, GyrB, ParE. Length = 594 Score = 675 bits (1745), Expect = 0.0 Identities = 283/527 (53%), Positives = 371/527 (70%), Gaps = 12/527 (2%) Query: 40 GLHHMIYEVLDNAIDESLEGYADIITVTLNMDGSCTVSDNGRGIPTDLHKEEGISAAEVI 99 GLHH++ E++DNA DE+L GY D I VT++ D S +V DNGRGIP ++H +E A EVI Sbjct: 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVI 60 Query: 100 MTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRIKREGNIYEMSFI-NGILDNP 158 T LHAGGKF+ +YKVSGGLHGVG SVVNALS+ ++ + R+G Y+ SF NG + Sbjct: 61 FTVLHAGGKFDDDAYKVSGGLHGVGASVVNALSTEFEVEVARDGKEYKQSFSNNGKPLSE 120 Query: 159 LVVTGSAGNDTGTEVTFLPSSDIFSV-QDFNYDTLQHRLRELSFLNSSVQISLIDKRSPE 217 + G GT+VTF P +IF + D +++ L+ RLREL+FLN V+I+L D+RS E Sbjct: 121 PKIIGDTK-KDGTKVTFKPDLEIFGMTTDDDFELLKRRLRELAFLNKGVKITLNDERSDE 179 Query: 218 PREITMFYKGGIEAFVSYLDRHKKPLMQSPIRIQGSRDNISIDLAMRWNDGYHENVLCFT 277 ++GGI+ +V L+++K+ L P I+G +DNI +++A ++ DGY EN++ F Sbjct: 180 EETF--LFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFV 237 Query: 278 NNIPQKDGGTHLSGLRSALTRQITSYVEKSFGSKKDKRSVI-GDDCREGFTSVLSIKMPD 336 NNI +GGTH +G + ALTR I Y +K KK K I G+D REG T+ +S+K+P+ Sbjct: 238 NNIATTEGGTHENGFKDALTRVINEYAKK---KKKLKEKNIKGEDVREGLTAFISVKIPE 294 Query: 337 PRFSSQTKEKLVSSEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVLDASMVRDAARRAR 396 P+F QTKEKL +SEVR VE V++ L ++LEE+P+EA IV+KVL A+ R AA++AR Sbjct: 295 PQFEGQTKEKLGTSEVRFGVEKIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKAR 354 Query: 397 DLTRRKGVLDIASLPGKLADCSERDPKKSELFLVEGDSAGGSAKQGRSRENQAILPLRGK 456 +LTR+K L SLPGKLAD S PKK ELFLVEGDSAGGSAK GR R+ QAILPLRGK Sbjct: 355 ELTRKKK-LSKISLPGKLADASSAGPKKCELFLVEGDSAGGSAKSGRDRDFQAILPLRGK 413 Query: 457 ILNVERARFDKMLSSQEIGTLITALGTGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTL 516 +LNVE+A DK+L ++EI LITALG GIG+D FDI KLRY KIIIMTDADVDG+HI+ L Sbjct: 414 LLNVEKASLDKILKNEEIQALITALGLGIGKD-FDIEKLRYGKIIIMTDADVDGSHIKGL 472 Query: 517 LLTFFFRQMPSLIHNGFLYIIKPPLYGITRGKSLQYVKDEESLEDYL 563 LLTFF+R MP LI GF+YI PPLY +T+GK SL++Y Sbjct: 473 LLTFFYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVYSF-YSLDEYE 518 Score = 111 bits (281), Expect = 5e-25 Identities = 40/71 (56%), Positives = 53/71 (74%) Query: 725 TIFSIGRKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDE 784 + +QRYKGLGEMNA QLWETT++P+ R+LL V + DA +AD +FS LMGD+ Sbjct: 522 ETKGGNKSKYEIQRYKGLGEMNADQLWETTMDPERRTLLFVTLDDADEADLIFSALMGDK 581 Query: 785 VEPRREFIQEN 795 VEPR+E+I+EN Sbjct: 582 VEPRKEWIEEN 592 >gnl|CDD|130130 TIGR01058, parE_Gpos, DNA topoisomerase IV, B subunit, Gram-positive. Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation step of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason. Length = 637 Score = 594 bits (1534), Expect = e-170 Identities = 267/566 (47%), Positives = 377/566 (66%), Gaps = 13/566 (2%) Query: 8 SSYDADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITVT 67 S Y+AD+I+IL+GLDAV+KRP MYIG TD GLHH+++E++DN++DE L GYAD ITVT Sbjct: 3 SKYNADAIKILEGLDAVRKRPGMYIGSTDS-KGLHHLVWEIVDNSVDEVLAGYADNITVT 61 Query: 68 LNMDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSV 127 L+ D S TV D+GRGIPT +H++ IS E + T LHAGGKF+Q YK +GGLHGVG SV Sbjct: 62 LHKDNSITVQDDGRGIPTGIHQDGNISTVETVFTVLHAGGKFDQGGYKTAGGLHGVGASV 121 Query: 128 VNALSSWLKLRIKREGNIYEMSFIN-GILDNPLVVTGSAGNDTGTEVTFLPSSDIFSVQD 186 VNALSSWL++ +KR+G IY+ F N G + L G+ TGT V F P IF Sbjct: 122 VNALSSWLEVTVKRDGQIYQQRFENGGKIVQSLKKIGTT-KKTGTLVHFHPDPTIFKTTQ 180 Query: 187 FNYDTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYLDRHKKPLMQS 246 FN + ++ RL+E +FL ++++ DKR+ + FY+ G+ FV Y++ K+ L Q Sbjct: 181 FNSNIIKERLKESAFLLKKLKLTFTDKRTNKTTV--FFYENGLVDFVDYINETKETLSQV 238 Query: 247 PIRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVEK 306 +G ++ I +++A ++NDG EN+L F N++ K+GGTH +G + A+T I SY K Sbjct: 239 -TYFEGEKNGIEVEVAFQFNDGDSENILSFANSVKTKEGGTHENGFKLAITDVINSYARK 297 Query: 307 SFGSKKDKRSVIGDDCREGFTSVLSIKMPDP--RFSSQTKEKLVSSEVRSVVESFVNDGL 364 K+ +++ G D REG ++++S+++P+ +F QTK KL S E R+VV+ V D L Sbjct: 298 YNLLKEKDKNLEGSDIREGLSAIISVRIPEELIQFEGQTKSKLFSPEARNVVDEIVQDHL 357 Query: 365 SAWLEEHPLEAKIIVKKVLDASMVRDAARRARDLTR--RKGVLDIASLPGKLADCSERDP 422 +LEE+ +AK+++ K + A ++AA++AR+ + +K + L GKL ++P Sbjct: 358 FFFLEENNNDAKLLIDKAIKARDAKEAAKKAREEKKSGKKPKKEKGILSGKLTPAQSKNP 417 Query: 423 KKSELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALG 482 K+ELFLVEGDSAGGSAKQGR R+ QAILPLRGK+LNVE+A+ +L ++EI T+I +G Sbjct: 418 AKNELFLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKAKLADILKNEEINTIIFCIG 477 Query: 483 TGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIKPPLY 542 TGIG D F I L+Y KIIIMTDAD DGAHI+ LLLTFF+R M LI G +YI PPLY Sbjct: 478 TGIGAD-FSIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELGHVYIALPPLY 536 Query: 543 GITR--GKSLQYVKDEESLEDYLINQ 566 +++ GK ++Y + LE Sbjct: 537 KLSKKDGKKVKYAWSDLELESVKKKL 562 Score = 96.1 bits (239), Expect = 3e-20 Identities = 39/64 (60%), Positives = 54/64 (84%) Query: 732 KGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEPRREF 791 K ++QRYKGLGEMNA QLWETT+NP+TR+L+RVKI D ++A+ + LMGD+VEPR+++ Sbjct: 563 KNYTLQRYKGLGEMNADQLWETTMNPETRTLVRVKIDDLARAERQINTLMGDKVEPRKKW 622 Query: 792 IQEN 795 I+ N Sbjct: 623 IEAN 626 >gnl|CDD|130127 TIGR01055, parE_Gneg, DNA topoisomerase IV, B subunit, proteobacterial. This protein is active as an alpha(2)beta(2) heterotetramer. Length = 625 Score = 465 bits (1197), Expect = e-131 Identities = 234/558 (41%), Positives = 325/558 (58%), Gaps = 14/558 (2%) Query: 8 SSYDADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITVT 67 ++Y A I++L GL+ V+KRP MY T +H++ EV+DN++DE+L G+A II V Sbjct: 2 TNYSAKDIEVLDGLEPVRKRPGMYTDTT----RPNHLVQEVIDNSVDEALAGFASIIMVI 57 Query: 68 LNMDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSV 127 L+ D S V DNGRG+P D+H +EG+SA EVI+T LHAGGKF+ K+Y SGGLHGVG+SV Sbjct: 58 LHQDQSIEVFDNGRGMPVDIHPKEGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGVGISV 117 Query: 128 VNALSSWLKLRIKREGNIYEMSFINGILDNPLVVTGSAGN-DTGTEVTFLPSSDIFSVQD 186 VNALS +K+++ R+G +Y ++F NG L+ G+ G TGT V F P +IF Sbjct: 118 VNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGKRLTGTSVHFTPDPEIFDSLH 177 Query: 187 FNYDTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYLDRHKKPLMQS 246 F+ L H LR + L V+I D+ + Y G++ ++S L Sbjct: 178 FSVSRLYHILRAKAVLCRGVEIEFEDE--VNNTKALWNYPDGLKDYLSEAVNGDNTLPPK 235 Query: 247 PIRIQGSRDNISIDLAMRW-NDGYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVE 305 P D+ +++ A+ W +G + + N IP GGTH++GLR L + + E Sbjct: 236 PFSGNFEGDDEAVEWALLWLPEGGELFMESYVNLIPTPQGGTHVNGLRQGLLDALREFCE 295 Query: 306 KSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVNDGLS 365 + + +D + + VLSIKM DP+F+ QTKE+L S +V V + D Sbjct: 296 MR-NNLPRGVKLTAEDIWDRCSYVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFD 354 Query: 366 AWLEEHPLEAKIIVKKVLDASMVRDAARRARDLTRRKGVLDIASLPGKLADCSERDPKKS 425 WL ++ A+ + + + ++ R R A+ + R+K A LPGKLADC+ +D + + Sbjct: 355 LWLNQNVQLAEHLAEHAISSAQRR--KRAAKKVVRKKLTSGPA-LPGKLADCTRQDLEGT 411 Query: 426 ELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTGI 485 ELFLVEGDSAGGSAKQ R RE QAILPL GKILN DK+L+SQEI + AL GI Sbjct: 412 ELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVAL--GI 469 Query: 486 GQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIKPPLYGIT 545 DS D+++LRY KI I+ DAD DG HI TLL FF P L+ G +Y+ KPPLY I Sbjct: 470 DPDSNDLSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRID 529 Query: 546 RGKSLQYVKDEESLEDYL 563 K + Y DEE E L Sbjct: 530 LSKEVYYALDEEEKEKLL 547 Score = 63.0 bits (153), Expect = 3e-10 Identities = 25/64 (39%), Positives = 42/64 (65%), Gaps = 3/64 (4%) Query: 734 ISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDA--SQADDLFSRLMGDEV-EPRRE 790 ++QR+KGLGEMN +QL ETT++P+TR L+++ + D + D + L+ + E R Sbjct: 557 PNVQRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDDVQDQRVDKIMDMLLAKKRSEDRFN 616 Query: 791 FIQE 794 ++QE Sbjct: 617 WLQE 620 >gnl|CDD|185452 PTZ00109, PTZ00109, DNA gyrase subunit b; Provisional. Length = 903 Score = 456 bits (1175), Expect = e-129 Identities = 233/641 (36%), Positives = 346/641 (53%), Gaps = 97/641 (15%) Query: 7 NSSYDADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITV 66 S YDAD I +L+GL+AV+KRP MYIG+TD E GLH +++E+LDN++DE L G + ITV Sbjct: 97 CSEYDADDIVVLEGLEAVRKRPGMYIGNTD-EKGLHQLLFEILDNSVDEYLAGECNKITV 155 Query: 67 TLNMDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFN---------------- 110 L+ DGS +SDNGRGIP D+ ++ G S E ++T LH+GGKF Sbjct: 156 VLHKDGSVEISDNGRGIPCDVSEKTGKSGLETVLTVLHSGGKFQDTFPKNSRSDKSEDKN 215 Query: 111 ------------------------QKSYKVSGGLHGVGVSVVNALSSWLKLRIKREGNIY 146 + Y+ S GLHGVG+SVVNALSS+LK+ + + G IY Sbjct: 216 DTKSSKKGKSSHVKGPKEAKEKESSQMYEYSSGLHGVGLSVVNALSSFLKVDVFKGGKIY 275 Query: 147 EMSFINGILDNPLVVTGSAGNDTGTEVTFLPS-SDIF--------------SVQDFNYDT 191 + G + PL V GT + FLP IF FN D Sbjct: 276 SIELSKGKVTKPLSVFSCPLKKRGTTIHFLPDYKHIFKTHHQHTETEEEEGCKNGFNLDL 335 Query: 192 LQHRLRELSFLNSSVQISLIDKRS----PEPREITMFYKGGIEAFVSYLDRHKKPLMQSP 247 +++R+ ELS+LN + L+D+R T+ ++GG F+ L + K PL + Sbjct: 336 IKNRIHELSYLNPGLTFYLVDERIANENNFYPYETIKHEGGTREFLEELIKDKTPLYKDI 395 Query: 248 --IRIQGSRDNISIDLAMRWNDG-YHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYV 304 I I+G N+++++++ W+ Y + F NN+ GTH+ G + A+TR + + Sbjct: 396 NIISIRGVIKNVNVEVSLSWSLESYTALIKSFANNV-STTAGTHIDGFKYAITRCVNGNI 454 Query: 305 EKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVNDGL 364 +K+ K + ++ G+ REG T+++S+K+ F QTK KL + +++++ES V + L Sbjct: 455 KKNGYFKGNFVNIPGEFIREGMTAIISVKLNGAEFDGQTKTKLGNHLLKTILESIVFEQL 514 Query: 365 SAWLEEHPLEAKIIVKKVLDASMVRDAARRARDLTRRKGVLDIAS-LPGKLADCSERDPK 423 S LE P I K L A + A+ A+DL R+K ++ LPGKL DC D + Sbjct: 515 SEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYSTILPGKLVDCISDDIE 574 Query: 424 KSELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFD-KMLSSQEIGTLITALG 482 ++ELF+VEG+SA G+AKQ R+RE QA+LPL+GKILN+E+ + + K+ + EI LIT++G Sbjct: 575 RNELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNKKVFENSEIKLLITSIG 634 Query: 483 TGIG-------------------------------QDSFDINKLRYHKIIIMTDADVDGA 511 + ++S LRY KII++TDADVDG Sbjct: 635 LSVNPVTWRQYDLSHGTKASKDESVQNNNSTLTKKKNSLFDTPLRYGKIILLTDADVDGE 694 Query: 512 HIRTLLLTFFFRQMPSLIHNGFLYIIKPPLYGITRGKSLQY 552 H+R LLLT +R PSL +G +Y+ PPLY IT + Q+ Sbjct: 695 HLRILLLTLLYRFCPSLYEHGRVYVACPPLYRITNNRMKQF 735 Score = 84.9 bits (210), Expect = 8e-17 Identities = 35/73 (47%), Positives = 51/73 (69%) Query: 724 DTIFSIGRKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGD 783 + F K +QR+KGLGEM A QLWETT++P R L+R+ ++DA +A +L LMG+ Sbjct: 827 NKAFFKFSKHYEIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDAMRASELIFLLMGE 886 Query: 784 EVEPRREFIQENS 796 +V+ R++FI ENS Sbjct: 887 DVQSRKQFIFENS 899 >gnl|CDD|177398 PHA02569, 39, DNA topoisomerase II large subunit; Provisional. Length = 602 Score = 197 bits (502), Expect = 1e-50 Identities = 168/583 (28%), Positives = 255/583 (43%), Gaps = 105/583 (18%) Query: 13 DSIQILKGLDAVKKRPSMYIGDTDGES----------------GLHHMIYEVLDNAIDES 56 D ++L + + KRP MYIG E+ GL +I E++DN++DE+ Sbjct: 2 DEFKVLSDREHILKRPGMYIGSVAYEAHERFLFGKFTQVEYVPGLVKIIDEIIDNSVDEA 61 Query: 57 LEG---YADIITVTLNMDGSCTVSDNGRGIPTDLHKE---EGISAAEVIMTRLHAGGKFN 110 + +A+ I VT+ + TVSDNGRGIP + E I TR AG F+ Sbjct: 62 IRTNFKFANKIDVTIK-NNQVTVSDNGRGIPQAMVTTPEGEEIPGPVAAWTRTKAGSNFD 120 Query: 111 QKSYKVSGGLHGVGVSVVNALSSWLKLRIKREGNIYEMSFINGILDNPLVVTGSAGNDTG 170 + +V+GG++GVG S+ N S N ++ NG +N T G G Sbjct: 121 DTN-RVTGGMNGVGSSLTNFFSVLFIGETCDGKNEVTVNCSNG-AENISWST-KPGKGKG 177 Query: 171 TEVTFLPSSDIFSVQDFNYDTLQ---HRLRELSFLNSSVQISLIDKRSPEPREITMFYKG 227 T VTF+P F V + L RL+ L+ + ++ + K+ G Sbjct: 178 TSVTFIPDFSHFEVNGLDQQYLDIILDRLQTLAVVFPDIKFTFNGKKVS----------G 227 Query: 228 GIEAFVSYLDRHKKPLMQSPIRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGT 287 + + ++Q DN+SI LA DG+ + L F N + K+GG Sbjct: 228 KFKKYAKQFGDD--TIVQE-------NDNVSIALA-PSPDGFRQ--LSFVNGLHTKNGGH 275 Query: 288 HLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIK-MPDPRFSSQTKEK 346 H+ + + ++ ++K + K V +E T VL ++ M +PRF SQTKE+ Sbjct: 276 HVDCVMDDICEELIPMIKKKHKIEVTKARV-----KECLTIVLFVRNMSNPRFDSQTKER 330 Query: 347 LVSS--EVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVLD----------ASMVRDAARR 394 L S E+R+ ++ L+ K I K++L A++ R A Sbjct: 331 LTSPFGEIRNHID---------------LDYKKIAKQILKTEAIIMPIIEAALARKLAAE 375 Query: 395 ARDLTRR-------KGVLDI-ASLPGKLADCSERDPKKSELFLVEGDSAGGSAKQGRSRE 446 T+ K I A+L GK A+ + LFL EGDSA G + R E Sbjct: 376 KAAETKAAKKAKKAKVAKHIKANLIGKDAE--------TTLFLTEGDSAIGYLIEVRDEE 427 Query: 447 NQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTGIGQDSFDINKLRYHKIIIMTDA 506 PLRGK+LN + +L ++E+ + G +G+ + ++N Y I IMTDA Sbjct: 428 LHGGYPLRGKVLNTWGMSYADILKNKELFDICAITGLVLGEKAENMN---YKNIAIMTDA 484 Query: 507 DVDG-AHIRTLLLTFFFRQMPSLIHNGFLYIIKPPLYGITRGK 548 DVDG I LLL FF R P L G + +K P+ GK Sbjct: 485 DVDGKGSIYPLLLAFFSR-WPELFEQGRIRFVKTPVIIAQVGK 526 >gnl|CDD|185451 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional. Length = 1388 Score = 173 bits (440), Expect = 2e-43 Identities = 148/574 (25%), Positives = 250/574 (43%), Gaps = 80/574 (13%) Query: 11 DADSIQILKGLDAVKKRPSMYIGDTDGES----------------------GLHHMIYEV 48 + Q ++ + RP YIG + ++ GL+ + E+ Sbjct: 6 VEERYQKKTQIEHILLRPDTYIGSIETQTEDMWVYDEEKNRMVYKTITYVPGLYKIFDEI 65 Query: 49 LDNAID----ESLEGYADIITVTLNMD-GSCTVSDNGRGIPTDLHKEEGISAAEVIMTRL 103 L NA D + I VT++ + G +V ++G GIP +HKE I E+I L Sbjct: 66 LVNAADNKARDKGGHRMTYIKVTIDEENGEISVYNDGEGIPVQIHKEHKIYVPEMIFGHL 125 Query: 104 HAGGKFNQKSYKVSGGLHGVGVSVVNALSS--WLKLRIKREGNIYEMSFINGILDN-PLV 160 ++ +V+GG +G G + N S+ ++ + G ++M++ + + Sbjct: 126 LTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECVDSKSGKKFKMTWTDNMSKKSEPR 185 Query: 161 VTGSAGNDTGTEVTFLPSSDIFSVQDFNYDT---LQHRLRELSFLNSSVQISLIDKRSPE 217 +T G T+VTF P F + +F+ D L+ R+ +L+ +++ L +R Sbjct: 186 ITSYDGKKDYTKVTFYPDYAKFGMTEFDDDMLRLLKKRVYDLAGCFGKLKVYLNGERI-- 243 Query: 218 PREITMFYKGGIEAFVSYLDRHKKPLMQSPIRI---QGSRDNISIDLAMRWNDGYHENVL 274 I++F Y+D + + + N ++ + +DG + V Sbjct: 244 ----------AIKSFKDYVDLYLPDGEEGKKPPYPFVYTSVNGRWEVVVSLSDGQFQQV- 292 Query: 275 CFTNNIPQKDGGTHLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDD-CREGFTSVLSIK 333 F N+I GGTH++ + Q+ S +++ KK K I + + ++ Sbjct: 293 SFVNSICTTKGGTHVN----YILDQLISKLQEKAKKKKKKGKEIKPNQIKNHLWVFVNCL 348 Query: 334 MPDPRFSSQTKEKLVSSEV-----RSVVESFVNDGL-SAWLEEHPLEAKIIVKKVLDASM 387 + +P F SQTKE L + + E + L S LE A+ + L+ M Sbjct: 349 IVNPSFDSQTKETLTTKPSKFGSTCELSEKLIKYVLKSPILENIVEWAQAKLAAELNKKM 408 Query: 388 VRDAARRARDLTRRKGVLDIASLPGKLADCSERDPKKSE---LFLVEGDSAGGSAKQGRS 444 A +++R I +P KL D ++ K SE L L EGDSA A G S Sbjct: 409 --KAGKKSR----------ILGIP-KLDDANDAGGKNSEECTLILTEGDSAKALALAGLS 455 Query: 445 ---RENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTGIGQDSFDINKLRYHKII 501 R+ + PLRGK+LNV A ++++++EI L LG IG+ D LRY ++ Sbjct: 456 VVGRDYYGVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYEDPKGLRYGSLM 515 Query: 502 IMTDADVDGAHIRTLLLTFFFRQMPSLI-HNGFL 534 IMTD D DG+HI+ LL+ PSL+ + GFL Sbjct: 516 IMTDQDHDGSHIKGLLINMIHHFWPSLLKNPGFL 549 >gnl|CDD|178674 PLN03128, PLN03128, DNA topoisomerase 2; Provisional. Length = 1135 Score = 161 bits (409), Expect = 6e-40 Identities = 156/590 (26%), Positives = 257/590 (43%), Gaps = 88/590 (14%) Query: 27 RPSMYIGDT-----------DGE---------SGLHHMIYEVLDNAIDESL-EGYADIIT 65 RP YIG T GE GL+ + E+L NA D + D + Sbjct: 19 RPDTYIGSTEKHTQTLWVYEGGEMVNREVTYVPGLYKIFDEILVNAADNKQRDPSMDSLK 78 Query: 66 VTLNMD-GSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVG 124 V ++++ + +V +NG+GIP ++HKEEG+ E+I L F+ K +GG +G G Sbjct: 79 VDIDVEQNTISVYNNGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYG 138 Query: 125 VSVVNALSSWLKLRIK--REGNIYEMSFINGI--LDNPLVVTGSAGNDTGTEVTFLPSSD 180 + N S+ + G Y+ F N + P + + A ++ T++TF P Sbjct: 139 AKLANIFSTEFTVETADGNRGKKYKQVFTNNMSVKSEPKITSCKA-SENWTKITFKPDLA 197 Query: 181 IFSVQDFNYDT---LQHRLRELS-FLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYL 236 F++ + D + R+ +++ L +++ L K+ P +++F Y+ Sbjct: 198 KFNMTRLDEDVVALMSKRVYDIAGCLGKKLKVELNGKKLP------------VKSFQDYV 245 Query: 237 D--RHKKPLMQSPIRI---QGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSG 291 RI R + + L+ DG + V F N+I GGTH+ Sbjct: 246 GLYLGPNSREDPLPRIYEKVNDRWEVCVSLS----DGSFQQV-SFVNSIATIKGGTHV-- 298 Query: 292 LRSALTRQITSYVEKSFGSKKDKR--SVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVS 349 + QI ++++ KK+K V + ++ + +P F SQTKE L + Sbjct: 299 --DYVADQIVKHIQEKV-KKKNKNATHVKPFQIKNHLWVFVNCLIENPTFDSQTKETLTT 355 Query: 350 SEVRSVVESFVNDG-LSAWLEEHPLEAKIIVKKVLDASMVRDAARRAR-DLTRRKGVLDI 407 SF + LS + + +V+ +L + + + D +R+ + I Sbjct: 356 RP-----SSFGSKCELSEEFLKKVEKCG-VVENILSWAQFKQQKELKKKDGAKRQRLTGI 409 Query: 408 ASLPGKLADCSERDPKKSE---LFLVEGDSAGGSAKQGRS---RENQAILPLRGKILNVE 461 KL D ++ KKS+ L L EGDSA A G S R++ + PLRGK+LNV Sbjct: 410 P----KLDDANDAGGKKSKDCTLILTEGDSAKALAMSGLSVVGRDHYGVFPLRGKLLNVR 465 Query: 462 RARFDKMLSSQEIGTLITALGTGIGQ--DSFDINKLRYHKIIIMTDADVDGAHIRTLLLT 519 A +++ + EI + LG G+ D + LRY ++IMTD D DG+HI+ L++ Sbjct: 466 EASHKQIMKNAEITNIKQILGLQFGKTYDEENTKSLRYGHLMIMTDQDHDGSHIKGLIIN 525 Query: 520 FFFRQMPSLIH-NGFLYIIKPPLYGITRGKSLQ-------YVKDEESLED 561 FF PSL+ GFL P+ T+G Y +ESLE Sbjct: 526 FFHSFWPSLLKIPGFLVEFITPIVKATKGGKSLSFYTMPEYEAWKESLEG 575 >gnl|CDD|178775 PLN03237, PLN03237, DNA topoisomerase 2; Provisional. Length = 1465 Score = 141 bits (357), Expect = 7e-34 Identities = 147/548 (26%), Positives = 249/548 (45%), Gaps = 83/548 (15%) Query: 40 GLHHMIYEVLDNAIDESL-EGYADIITVTLNMDGSC-TVSDNGRGIPTDLHKEEGISAAE 97 GL+ + E+L NA D + D + V ++++ + +V +NG G+P ++H+EEG+ E Sbjct: 77 GLYKIFDEILVNAADNKQRDPKMDSLRVVIDVEQNLISVYNNGDGVPVEIHQEEGVYVPE 136 Query: 98 VIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRI---KREGNIYEMSFIN-- 152 +I L ++ K +GG +G G + N S+ + KR+ Y+ F N Sbjct: 137 MIFGHLLTSSNYDDNEKKTTGGRNGYGAKLTNIFSTEFVIETADGKRQKK-YKQVFSNNM 195 Query: 153 GILDNPLVVTGSAGNDTGTEVTFLPSSDIFSVQDFNYDT---LQHRLRELS-FLNSSVQI 208 G P V+T ++ T+VTF P F++ D ++ R+ +++ L +V++ Sbjct: 196 GKKSEP-VITKCKKSENWTKVTFKPDLAKFNMTHLEDDVVALMKKRVVDIAGCLGKTVKV 254 Query: 209 SLIDKRSPEPREITMFYKGGIEAFVSYLDRH----KKPLMQSPIRIQ---GSRDNISIDL 261 L KR P +++F Y+D + K ++ RI R + + L Sbjct: 255 ELNGKRIP------------VKSFSDYVDLYLESANKSRPENLPRIYEKVNDRWEVCVSL 302 Query: 262 AMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDD 321 + +G + V F N+I GGTH+ +T QI ++V ++ K ++ + Sbjct: 303 S----EGQFQQV-SFVNSIATIKGGTHVD----YVTNQIANHVMEAVNKKNKNANIKAHN 353 Query: 322 CREGFTSVLSIKMPDPRFSSQTKEKLVSSE-------------VRSVVESFVNDGLSAWL 368 + ++ + +P F SQTKE L + ++ V++S + + L +W Sbjct: 354 VKNHLWVFVNALIDNPAFDSQTKETLTLRQSSFGSKCELSEDFLKKVMKSGIVENLLSW- 412 Query: 369 EEHPLEAKIIVKKVLDASMVRDAARRARDLTRRKGVLDIASLPGKLADCSE---RDPKKS 425 A K L + D A+ R + +P KL D +E ++ +K Sbjct: 413 ------ADFKQSKELKKT---DGAKTTR----------VTGIP-KLEDANEAGGKNSEKC 452 Query: 426 ELFLVEGDSAGGSAKQGRS---RENQAILPLRGKILNVERARFDKMLSSQEIGTLITALG 482 L L EGDSA A G S R + PLRGK+LNV A +++++ EI + LG Sbjct: 453 TLILTEGDSAKALAVAGLSVVGRNYYGVFPLRGKLLNVREASHKQIMNNAEIENIKQILG 512 Query: 483 TGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIH-NGFLY-IIKPP 540 G+ + LRY ++IMTD D DG+HI+ LL+ F PSL+ FL I P Sbjct: 513 LQHGKQYESVKSLRYGHLMIMTDQDHDGSHIKGLLINFIHSFWPSLLKVPSFLVEFITPI 572 Query: 541 LYGITRGK 548 + RGK Sbjct: 573 VKATRRGK 580 >gnl|CDD|128669 smart00387, HATPase_c, Histidine kinase-like ATPases. Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. Length = 111 Score = 66.5 bits (163), Expect = 2e-11 Identities = 32/110 (29%), Positives = 44/110 (40%), Gaps = 18/110 (16%) Query: 38 ESGLHHMIYEVLDNAIDESLEGYADIITVTL---NMDGSCTVSDNGRGIPTDLHKEEGIS 94 L ++ +LDNAI + EG ITVTL TV DNG GIP Sbjct: 3 PDRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGDHLEITVEDNGPGIP---------- 50 Query: 95 AAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRIKREGN 144 E + + + +S K+ G G+G+S+V L I E Sbjct: 51 -PEDLEKIFEPFFRTDGRSRKIGG--TGLGLSIVKKLVELHGGEISVESE 97 >gnl|CDD|182952 PRK11086, PRK11086, sensory histidine kinase DcuS; Provisional. Length = 542 Score = 34.5 bits (80), Expect = 0.10 Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 11/74 (14%) Query: 31 YIGDTDGESGLHHMIYEVLDNAIDESLEGYADI----ITVTLN-MDG--SCTVSDNGRGI 83 + D+ E +H +I +L N I+ +LE I+V+L+ +G C VSD+G GI Sbjct: 421 QLPDSGDEDQVHELI-TILGNLIENALEAVGGEEGGEISVSLHYRNGWLHCEVSDDGPGI 479 Query: 84 PTDLHK---EEGIS 94 D ++G S Sbjct: 480 APDEIDAIFDKGYS 493 >gnl|CDD|148352 pfam06697, DUF1191, Protein of unknown function (DUF1191). This family contains hypothetical plant proteins of unknown function. Length = 275 Score = 33.9 bits (78), Expect = 0.15 Identities = 17/34 (50%), Positives = 20/34 (58%), Gaps = 1/34 (2%) Query: 383 LDASMVRDAARRARDLTRRKGVLDIASLPGKLAD 416 LDA ++RD A RA RR GVL SLP L+ Sbjct: 13 LDA-LLRDYAFRAFTTRRRTGVLYRVSLPSNLSG 45 >gnl|CDD|182962 PRK11100, PRK11100, sensory histidine kinase CreC; Provisional. Length = 475 Score = 33.7 bits (78), Expect = 0.19 Identities = 21/52 (40%), Positives = 28/52 (53%), Gaps = 6/52 (11%) Query: 37 GESGLHHM-IYEVLDNAIDESLEGYADIITVTLNMDGS---CTVSDNGRGIP 84 G+ L + +LDNAID S EG IT++ +DG +V D G GIP Sbjct: 364 GDPFLLRQALGNLLDNAIDFSPEG--GTITLSAEVDGEQVALSVEDQGPGIP 413 >gnl|CDD|162668 TIGR02032, GG-red-SF, geranylgeranyl reductase family. This model represents a subfamily which includes geranylgeranyl reductases involved in chlorophyll and bacteriochlorophyll biosynthesis as well as other related enzymes which may also act on geranylgeranyl groups or related substrates. Length = 295 Score = 31.9 bits (73), Expect = 0.70 Identities = 16/95 (16%), Positives = 27/95 (28%), Gaps = 22/95 (23%) Query: 391 AARRARDLTRRKGVLDIASLPGKLADCSERDPKKSELFLVEGDSA-------------GG 437 AA R D R +L+ S P C + L G Sbjct: 15 AAYRLADKGLRVLLLEKKSFPRYKP-CGGALSPRVLEELDLPLELIVNLVRGARFFSPNG 73 Query: 438 SAKQGRSRENQAILPLRGKILNVERARFDKMLSSQ 472 + + A + ++R FD+ L+ + Sbjct: 74 DSVEIPIETELAYV--------IDRDAFDEQLAER 100 >gnl|CDD|181295 PRK08213, PRK08213, gluconate 5-dehydrogenase; Provisional. Length = 259 Score = 31.5 bits (72), Expect = 0.88 Identities = 20/86 (23%), Positives = 39/86 (45%), Gaps = 20/86 (23%) Query: 343 TKEKLVSSEVRSVVESF------VNDGLSAW---LEEHPLEAKIIVKKVLDAS------M 387 E + +E F VN+ + W E+HP+EA KV++ + + Sbjct: 71 ADEADIERLAEETLERFGHVDILVNNAGATWGAPAEDHPVEA---WDKVMNLNVRGLFLL 127 Query: 388 VRDAARRARDLTRRKG-VLDIASLPG 412 + A+R+ + R G ++++AS+ G Sbjct: 128 SQAVAKRSM-IPRGYGRIINVASVAG 152 >gnl|CDD|151584 pfam11140, DUF2913, Protein of unknown function (DUF2913). This family of proteins with unknown function appear to be restricted to Gammaproteobacteria. Length = 207 Score = 30.0 bits (68), Expect = 2.7 Identities = 11/57 (19%), Positives = 24/57 (42%), Gaps = 2/57 (3%) Query: 568 LSEEIELFCDSKG--VISKNDLRNFIDDALKIDKLIKDFYPNHDKTFIEQAVISGVF 622 +SE+++L D + V+ D+ ++ K I + + F + A G+ Sbjct: 119 VSEKLKLDSDGQNSLVLCAEQYEQHFDETGELIKPISLYVRGDEALFAKLAFAHGLL 175 >gnl|CDD|173330 PTZ00032, PTZ00032, 60S ribosomal protein L18; Provisional. Length = 211 Score = 29.4 bits (66), Expect = 3.6 Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 2/47 (4%) Query: 454 RGKILNVERARFDKMLSSQEIGTLI--TALGTGIGQDSFDINKLRYH 498 K N R + ++ E+G LI AL GI + FD +Y Sbjct: 148 PTKTTNRVRNNGGTIKAAYELGKLIGRKALSKGISKVRFDRAHYKYA 194 >gnl|CDD|178433 PLN02840, PLN02840, tRNA dimethylallyltransferase. Length = 421 Score = 29.4 bits (66), Expect = 4.0 Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 5/45 (11%) Query: 12 ADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDES 56 ADS+Q+ +GLD +PS ++ + HH+I ++L + D S Sbjct: 52 ADSVQVYRGLDVGSAKPS----LSERKEVPHHLI-DILHPSDDYS 91 >gnl|CDD|181772 PRK09303, PRK09303, adaptive-response sensory kinase; Validated. Length = 380 Score = 29.1 bits (66), Expect = 4.1 Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 6/42 (14%) Query: 49 LDNAIDESLEGYADIITVTL----NMDGSCTVSDNGRGIPTD 86 LDNAI + EG IT+++ ++ D G GIP + Sbjct: 281 LDNAIKYTPEG--GTITLSMLHRTTQKVQVSICDTGPGIPEE 320 >gnl|CDD|148605 pfam07093, SGT1, SGT1 protein. This family consists of several eukaryotic SGT1 proteins. Human SGT1 or hSGT1 is known to suppress GCR2 and is highly expressed in the muscle and heart. The function of this family is unknown although it has been speculated that SGT1 may be functionally analogous to the Gcr2p protein of Saccharomyces cerevisiae which is known to be a regulatory factor of glycolytic gene expression. Length = 485 Score = 29.3 bits (66), Expect = 4.5 Identities = 13/70 (18%), Positives = 26/70 (37%), Gaps = 7/70 (10%) Query: 529 IHNGFLYIIKPPLYGITRGKSLQYVKDEESLEDYLINQSLSEEIELFCDSKGVIS--KND 586 IHNG L+II P + + + +L++ L + L S + Sbjct: 123 IHNGELHIIPPS---QSSKSNENLPDEPLTLDEAL--ELLRSSPSKLRASPEIQEAIFKR 177 Query: 587 LRNFIDDALK 596 L+ + + + Sbjct: 178 LKGYPEQIKE 187 >gnl|CDD|179744 PRK04132, PRK04132, replication factor C small subunit; Provisional. Length = 846 Score = 28.7 bits (64), Expect = 5.7 Identities = 21/62 (33%), Positives = 28/62 (45%), Gaps = 7/62 (11%) Query: 560 EDYLINQSLSEEIELFCDSKGVISKNDLRNFIDDALKIDKLIKDFYPNHDKTFIEQAVIS 619 E Y + S SE ++ F D G + L K KLIK PN D I++ +IS Sbjct: 306 EKYHVIISGSENLKRFLDEIGFSQEEKLE-------KALKLIKKENPNLDGLTIDKELIS 358 Query: 620 GV 621 V Sbjct: 359 YV 360 >gnl|CDD|178618 PLN03069, PLN03069, magnesiumprotoporphyrin-IX chelatase subunit H; Provisional. Length = 1220 Score = 28.2 bits (63), Expect = 7.7 Identities = 11/26 (42%), Positives = 18/26 (69%) Query: 10 YDADSIQILKGLDAVKKRPSMYIGDT 35 +D+D ++++ L KK+PS YI DT Sbjct: 1170 FDSDPTKLVQSLRKDKKKPSSYIADT 1195 >gnl|CDD|132030 TIGR02985, Sig70_bacteroi1, RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium. Length = 161 Score = 28.3 bits (64), Expect = 7.9 Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 3/65 (4%) Query: 537 IKPPLYGITRGKSLQYVKDEESLEDYLINQSLSEEIEL-FCDSKGVISKNDLRNFIDDAL 595 K L+ I + +SL Y++ ++ E Y E EL D + + +L+ I A Sbjct: 52 FKAYLFTIVKNRSLNYLRHKQVEEKYQEEILEIEVDELSENDPEEELEAKELQLIIYKA- 110 Query: 596 KIDKL 600 I+KL Sbjct: 111 -IEKL 114 >gnl|CDD|148410 pfam06788, UPF0257, Uncharacterized protein family (UPF0257). Length = 236 Score = 28.3 bits (63), Expect = 8.0 Identities = 21/61 (34%), Positives = 27/61 (44%), Gaps = 6/61 (9%) Query: 356 VESFVNDGLSA-----WLEEHPLEAKIIVKKVLDASMVRDAARRARDLTRRKGVLDIASL 410 V V LS LE H LE + VLDA+ RDA + + R +G +A L Sbjct: 60 VTKRVTGTLSQEGCFDTLELHDLENNTGLALVLDANYYRDAETLEKRV-RLQGKCQLAEL 118 Query: 411 P 411 P Sbjct: 119 P 119 >gnl|CDD|180964 PRK07406, PRK07406, RNA polymerase sigma factor RpoD; Validated. Length = 373 Score = 28.2 bits (63), Expect = 8.5 Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 9/44 (20%) Query: 331 SIKMPDPRFSS------QTKEKLVSSEVRSVV---ESFVNDGLS 365 + MP P+F + KEK+V S +R VV + ++N GLS Sbjct: 119 LVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLS 162 >gnl|CDD|182581 PRK10600, PRK10600, nitrate/nitrite sensor protein NarX; Provisional. Length = 569 Score = 28.1 bits (63), Expect = 9.2 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 6/49 (12%) Query: 41 LHHMIYEVLDNAIDESLEGYADIITVTLNMDGS---CTVSDNGRGIPTD 86 L + E L NA+ + A + VT+ + + +V DNG G+P + Sbjct: 470 LLQIAREALSNALKHA---QASEVVVTVAQNQNQVKLSVQDNGCGVPEN 515 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.317 0.135 0.383 Gapped Lambda K H 0.267 0.0788 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 12,935,110 Number of extensions: 857928 Number of successful extensions: 1700 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1629 Number of HSP's successfully gapped: 48 Length of query: 803 Length of database: 5,994,473 Length adjustment: 101 Effective length of query: 702 Effective length of database: 3,812,065 Effective search space: 2676069630 Effective search space used: 2676069630 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 (27.2 bits)