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)