RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13357
(833 letters)
>gnl|CDD|237860 PRK14939, gyrB, DNA gyrase subunit B; Provisional.
Length = 756
Score = 1223 bits (3166), Expect = 0.0
Identities = 424/821 (51%), Positives = 577/821 (70%), Gaps = 65/821 (7%)
Query: 13 DTQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAIDESLAGYCTK 72
+SY ASSI++L+GL+AVRKRP MYIGDT DGTGLHH+V+E++DNAIDE+LAG+C
Sbjct: 1 SMMSNSYGASSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVYEVVDNAIDEALAGHCDD 60
Query: 73 INVTIYSDNSISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGG 132
I VTI++D S+S+SDNGRGIP DI + SAAE++MT LHAGGKF++NSYK+SGG
Sbjct: 61 ITVTIHADGSVSVSDNGRGIPTDIH----PEEGVSAAEVIMTVLHAGGKFDQNSYKVSGG 116
Query: 133 LHGIGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNK 192
LHG+G+S VN LS +L+LTI R+ KIH EF +G+ V+P+K++G+T+K
Sbjct: 117 LHGVGVSVVNALSEWLELTIRRDGKIHEQEFE------------HGVPVAPLKVVGETDK 164
Query: 193 QGTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKGGTS 252
GT++ FW +IF N EF Y+IL KR+REL+FLN+GV I L DER K+E F ++GG
Sbjct: 165 TGTEVRFWPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRLKDERDGKEEEFHYEGGIK 224
Query: 253 GFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQVDG 312
FV Y+N++K +HP IF S +K+ I ++V++QWN+SY EN+LCFTNNI Q DG
Sbjct: 225 AFVEYLNRNKTPLHPNIFY-----FSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDG 279
Query: 313 GTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKN 372
GTHL G R+ +TR IN YIE+ KK+K+ + G+D REGLT VLS+K+PDPKF+SQTK+
Sbjct: 280 GTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKD 339
Query: 373 KLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTRKKNLI 432
KLVSSEVR VE ++ + L +FL+ENP E+K+I KII+AAR+REAARK RELTR+K +
Sbjct: 340 KLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGAL 399
Query: 433 DDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARF 492
D L KLADCQEK+P L ELY+VEGDSAGGS KQGRDR+FQA+LPL+GK+LN+EKARF
Sbjct: 400 DIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARF 459
Query: 493 EKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKM 552
+K++ S++I TLI+ LG GI +DEFN +KLRYH+IIIMTDAD+DG+HIR LLLTFFYR+M
Sbjct: 460 DKMLSSQEIGTLITALGCGIGRDEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQM 519
Query: 553 PKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKNVKLISIENGDIIKEN 612
P+LIE G++YIAQPPLYK+K G E YL+DD + Y++++A + L + +G I
Sbjct: 520 PELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDYLIELALEGATLH-LADGPAISGE 578
Query: 613 YFFKLIDKYNKTIEIVHRLKQIIDISILSAIMSDVILNLDTRENAEQFAKKIIKKLNDSN 672
KL+ +Y +I+ RL++ ++L A++ L+LD + A
Sbjct: 579 ALEKLVKEYRAVRKIIDRLERRYPRAVLEALIYAPALDLDDLADEAAVAA---------- 628
Query: 673 IEIIVEFDQLNNKYLLNIKKKFLKKKNYIIDINFINNKDYKKLVSIISTFKKIIGKGVII 732
+D +F+ + +Y++LV + + +I +G +
Sbjct: 629 -----------------------------LDADFLTSAEYRRLVELAEKLRGLIEEGAYL 659
Query: 733 QKSIGEKIKKYTANNFYKIINYLRNEAENMVIKQRYKGLGEMNPGQLWETTMNPMIRCLL 792
++ GE +K ++F + +++L EA + QRYKGLGEMNP QLWETTM+P R LL
Sbjct: 660 ER--GE--RKQPVSSFEEALDWLLAEARKGLSIQRYKGLGEMNPEQLWETTMDPENRRLL 715
Query: 793 KVKIKDAISADKIFMTLMGDNVELRRKFIELNALHAKNIDI 833
+V I+DAI+AD+IF TLMGD VE RR+FIE NAL+ N+D+
Sbjct: 716 QVTIEDAIAADEIFTTLMGDEVEPRREFIEENALNVANLDV 756
>gnl|CDD|235542 PRK05644, gyrB, DNA gyrase subunit B; Validated.
Length = 638
Score = 860 bits (2224), Expect = 0.0
Identities = 313/593 (52%), Positives = 413/593 (69%), Gaps = 28/593 (4%)
Query: 14 TQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAIDESLAGYCTKI 73
+ Y AS IQ+LEGLEAVRKRP MYIG T + GLHHLV+EI+DN+IDE+LAGYC I
Sbjct: 3 EKAQEYDASQIQVLEGLEAVRKRPGMYIGSTGE-RGLHHLVYEIVDNSIDEALAGYCDHI 61
Query: 74 NVTIYSDNSISISDNGRGIPIDIKIDDKH-KPKRSAAEIVMTELHAGGKFNKNSYKISGG 132
VTI D SI+++DNGRGIP+DI H K + A E+V+T LHAGGKF YK+SGG
Sbjct: 62 EVTINEDGSITVTDNGRGIPVDI-----HPKTGKPAVEVVLTVLHAGGKFGGGGYKVSGG 116
Query: 133 LHGIGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNK 192
LHG+G+S VN LS +L++ + R+ KI+Y E+ G+ V+P+++IG+T++
Sbjct: 117 LHGVGVSVVNALSTWLEVEVKRDGKIYYQEYE------------RGVPVTPLEVIGETDE 164
Query: 193 QGTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDER--IKKKEIFEFKGG 250
GT + F D +IF EF Y+ L R+REL+FLN G+ ITL DER +K+E F ++GG
Sbjct: 165 TGTTVTFKPDPEIFETTEFDYDTLATRLRELAFLNKGLKITLTDEREGEEKEETFHYEGG 224
Query: 251 TSGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQV 310
+V Y+N++K +H +K+ I ++V+MQ+N+ Y+ENIL F NNI
Sbjct: 225 IKEYVEYLNRNKEPLHEEPIY-----FEGEKDGIEVEVAMQYNDGYSENILSFANNINTH 279
Query: 311 DGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQT 370
+GGTH G ++ +TR IN Y +N+ LK+ + GED+REGLT V+S+K P+P+F QT
Sbjct: 280 EGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVREGLTAVISVKHPEPQFEGQT 339
Query: 371 KNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTRKKN 430
K KL +SEVR V+ ++ + L +FL+ENP +K I EK I AAR+REAARK RELTR+K+
Sbjct: 340 KTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKS 399
Query: 431 LIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKA 490
++ L KLADC K+PE ELYIVEGDSAGGS KQGRDRRFQA+LPLRGK+LN+EKA
Sbjct: 400 ALESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKA 459
Query: 491 RFEKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYR 550
R +KI+ +E+I LI+ LG GI D+F++ KLRYH+IIIMTDAD+DGAHIR LLLTFFYR
Sbjct: 460 RLDKILKNEEIRALITALGTGIG-DDFDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYR 518
Query: 551 KMPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKNVKLISI 603
M LIE GY+YIAQPPLYKIK G E Y D E + + ++ K I
Sbjct: 519 YMRPLIEAGYVYIAQPPLYKIKKGGKE-YAYSDEELDEILAELKLKGNPKYGI 570
Score = 131 bits (332), Expect = 1e-31
Identities = 48/84 (57%), Positives = 61/84 (72%)
Query: 750 KIINYLRNEAENMVIKQRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTL 809
+I+ L+ + QRYKGLGEMNP QLWETTM+P R LL+V I+DA AD+IF L
Sbjct: 555 EILAELKLKGNPKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSIL 614
Query: 810 MGDNVELRRKFIELNALHAKNIDI 833
MGD+VE RR+FIE NA + +N+DI
Sbjct: 615 MGDDVEPRREFIEENAKYVRNLDI 638
>gnl|CDD|223265 COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), B subunit [DNA replication,
recombination, and repair].
Length = 635
Score = 828 bits (2142), Expect = 0.0
Identities = 326/588 (55%), Positives = 428/588 (72%), Gaps = 29/588 (4%)
Query: 14 TQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAIDESLAGYCTKI 73
++ ++Y ASSIQ+LEGLEAVRKRP MYIG T DG GLHHLV+E++DN+IDE+LAGY +I
Sbjct: 1 SKTNNYDASSIQVLEGLEAVRKRPGMYIGSTGDGRGLHHLVWEVVDNSIDEALAGYADRI 60
Query: 74 NVTIYSDNSISISDNGRGIPIDIKIDDKH-KPKRSAAEIVMTELHAGGKFNKNSYKISGG 132
+VT++ D SIS+ DNGRGIP+DI H K K SA E++ T LHAGGKF+ +SYK+SGG
Sbjct: 61 DVTLHEDGSISVEDNGRGIPVDI-----HPKEKVSAVEVIFTVLHAGGKFDNDSYKVSGG 115
Query: 133 LHGIGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTN- 191
LHG+G+S VN LS +L++ + R+ KI+ F G+ V+P+++IG T+
Sbjct: 116 LHGVGVSVVNALSTWLEVEVKRDGKIYRQRFE------------RGVPVTPLEVIGSTDT 163
Query: 192 -KQGTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERI-KKKEIFEFKG 249
K GTK+ F D +IF EF YEILK+R+REL+FLN GV ITL DER ++K+ F ++G
Sbjct: 164 KKTGTKVRFKPDPEIFGETEFDYEILKRRLRELAFLNKGVKITLTDERTGEEKKEFHYEG 223
Query: 250 GTSGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQ 309
G +V Y+NK K +H IF G +K+ I ++V++QWN+ Y+ENIL F NNI
Sbjct: 224 GLKDYVEYLNKGKTPLHEEIFYFNG-----EKDGIAVEVALQWNDGYSENILSFVNNIPT 278
Query: 310 VDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQ 369
+GGTH G RS +TRAIN+Y ++ LK+ + G+DIREGLT V+S+KIPDP+F Q
Sbjct: 279 REGGTHEAGFRSALTRAINEYAKKKNLLKEGDLT--GDDIREGLTAVISVKIPDPQFEGQ 336
Query: 370 TKNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTRKK 429
TK KL +SEVR VE+++ + FL+ENP E+K I EK I AA++REAARK RELTR+K
Sbjct: 337 TKEKLGNSEVRSIVEKLVSEAFSLFLEENPQEAKKIVEKAIAAAKAREAARKARELTRRK 396
Query: 430 NLIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEK 489
+ +D L KLADC K+PE EL++VEGDSAGGS KQGRDR FQA+LPLRGK+LN+EK
Sbjct: 397 SALDIPGLPGKLADCTSKDPEKSELFLVEGDSAGGSAKQGRDREFQAILPLRGKILNVEK 456
Query: 490 ARFEKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFY 549
AR +KI+ +E+I T+I+ LG GI +F+LEKLRYH+IIIMTDAD+DGAHIR LLLTFFY
Sbjct: 457 ARLDKILKNEEIQTIITALGTGI-GKDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFY 515
Query: 550 RKMPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKN 597
R MP LIE G++YIAQPPLYK+K G Y DD E E+ + ++ K
Sbjct: 516 RYMPPLIENGHVYIAQPPLYKVKKGKKTFYAYDDEELEKLLERLGKKK 563
Score = 122 bits (309), Expect = 7e-29
Identities = 48/68 (70%), Positives = 54/68 (79%)
Query: 766 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNA 825
QRYKGLGEMNP QLWETTM+P R LL+V I+DA AD+IF TLMGD VE RR FIE NA
Sbjct: 568 QRYKGLGEMNPDQLWETTMDPETRRLLQVTIEDADEADEIFSTLMGDKVEPRRNFIEENA 627
Query: 826 LHAKNIDI 833
L +N+DI
Sbjct: 628 LFVENLDI 635
>gnl|CDD|233254 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 [DNA metabolism, DNA
replication, recombination, and repair].
Length = 654
Score = 810 bits (2094), Expect = 0.0
Identities = 323/572 (56%), Positives = 421/572 (73%), Gaps = 27/572 (4%)
Query: 19 YSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAIDESLAGYCTKINVTIY 78
Y ASSI++LEGLEAVRKRP MYIG T + TGLHHLV+E++DN+IDE++AGYC INVTI
Sbjct: 1 YDASSIKVLEGLEAVRKRPGMYIGSTGE-TGLHHLVYEVVDNSIDEAMAGYCDTINVTIN 59
Query: 79 SDNSISISDNGRGIPIDIKIDDKH-KPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIG 137
D S+++ DNGRGIP+DI H + SA E+V+T LHAGGKF+K+SYK+SGGLHG+G
Sbjct: 60 DDGSVTVEDNGRGIPVDI-----HPEEGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVG 114
Query: 138 LSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKI 197
+S VN LS +L++T+ R+ KI+ EF GI + P++++G+T K GT +
Sbjct: 115 VSVVNALSEWLEVTVFRDGKIYRQEFE------------RGIPLGPLEVVGETKKTGTTV 162
Query: 198 HFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIK--KKEIFEFKGGTSGFV 255
FW D +IF EF ++IL KR+REL+FLN+GV I+L DER K F ++GG FV
Sbjct: 163 RFWPDPEIFETTEFDFDILAKRLRELAFLNSGVKISLEDERDGKGKSVTFHYEGGIKSFV 222
Query: 256 SYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQVDGGTH 315
Y+N++K +H I I +K I ++V++QWN+ Y+ENIL F NNI +GGTH
Sbjct: 223 KYLNRNKEPLHEEIIY-----IKGEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTH 277
Query: 316 LTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKNKLV 375
L G RS +TR IN Y + N+ LK+SK + GEDIREGLT V+S+K+PDP+F QTK KL
Sbjct: 278 LEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLG 337
Query: 376 SSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTRKKNLIDDI 435
+SEVR VE ++ + L +F +ENP E+K I EK I AA++REAARK RELTR+K+ +D
Sbjct: 338 NSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSG 397
Query: 436 ELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKI 495
L KLADC K+P ELYIVEGDSAGGS KQGRDR+FQA+LPLRGK+LN+EKAR +KI
Sbjct: 398 GLPGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRKFQAILPLRGKILNVEKARLDKI 457
Query: 496 ILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKL 555
+ +++I +I+ LG GI +D F+LEKLRYH+IIIMTDAD+DG+HIR LLLTFFYR M L
Sbjct: 458 LSNQEIGAIITALGCGIGKD-FDLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPL 516
Query: 556 IEYGYIYIAQPPLYKIKYGNNECYLRDDIEEE 587
IE GY+YIAQPPLYK+K G E Y++DD E+E
Sbjct: 517 IENGYVYIAQPPLYKVKKGKKERYIKDDKEKE 548
Score = 123 bits (311), Expect = 4e-29
Identities = 48/68 (70%), Positives = 55/68 (80%)
Query: 766 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNA 825
QRYKGLGEMN QLWETTM+P R LLKV I+DA+ AD+IF TLMGD VE RR+FIE NA
Sbjct: 587 QRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEPRREFIEANA 646
Query: 826 LHAKNIDI 833
L KN+D+
Sbjct: 647 LDVKNLDV 654
>gnl|CDD|235501 PRK05559, PRK05559, DNA topoisomerase IV subunit B; Reviewed.
Length = 631
Score = 705 bits (1823), Expect = 0.0
Identities = 255/589 (43%), Positives = 370/589 (62%), Gaps = 32/589 (5%)
Query: 14 TQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAIDESLAGYCTKI 73
++Y+A SI++LEGLE VRKRP MYIG T D GLHHLV E++DN++DE+LAG+ +I
Sbjct: 3 MMTNNYNADSIEVLEGLEPVRKRPGMYIGST-DTRGLHHLVQEVIDNSVDEALAGHGKRI 61
Query: 74 NVTIYSDNSISISDNGRGIPIDIKIDDKH-KPKRSAAEIVMTELHAGGKFNKNSYKISGG 132
VT+++D S+S+ DNGRGIP+ I H + +S E+++T+LHAGGKF+ +YK SGG
Sbjct: 62 EVTLHADGSVSVRDNGRGIPVGI-----HPEEGKSGVEVILTKLHAGGKFSNKAYKFSGG 116
Query: 133 LHGIGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDT-- 190
LHG+G+S VN LS L++ + R+ K++ F G V P++++G
Sbjct: 117 LHGVGVSVVNALSSRLEVEVKRDGKVYRQRFE------------GGDPVGPLEVVGTAGK 164
Query: 191 NKQGTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKGG 250
K GT++ FW D KIF + +F E LK+R+R +FL G+ ITL DER +++ F ++ G
Sbjct: 165 RKTGTRVRFWPDPKIFDSPKFSPERLKERLRSKAFLLPGLTITLNDER--ERQTFHYENG 222
Query: 251 TSGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQV 310
+++ +N+ K + + ++ ++QW + ENI + N I
Sbjct: 223 LKDYLAELNEGKETLPEEFVG----SFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTP 278
Query: 311 DGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQT 370
GGTH G R G+ +A+ ++ E+ L K K ++ GED+REGL VLS+KIP+P+F QT
Sbjct: 279 QGGTHENGFREGLLKAVREFAEKRNLLPKGK-KLEGEDVREGLAAVLSVKIPEPQFEGQT 337
Query: 371 KNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTRKKN 430
K KL S E R+ V ++ +L +NP ++ + EK I+AA++R A K + RKK
Sbjct: 338 KEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEKAIKAAQARLRAAKKVK--RKKK 395
Query: 431 LIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKA 490
L KLADC ++PE EL++VEGDSAGGS KQ RDR FQA+LPLRGK+LN +A
Sbjct: 396 T-SGPALPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEA 454
Query: 491 RFEKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYR 550
+ ++ +E+I +I +GIG D F+LE LRY +IIIMTDAD+DGAHI LLLTFFYR
Sbjct: 455 SLDDVLANEEIHDIIVAIGIGP-GDSFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYR 513
Query: 551 KMPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKNVK 599
P L+E G++YIA PPLY++ G + Y D+ E+E + K+ K K
Sbjct: 514 HFPPLVEAGHVYIALPPLYRVDKGKKKIYALDEEEKEELLKKLGKKGGK 562
Score = 102 bits (257), Expect = 2e-22
Identities = 34/60 (56%), Positives = 42/60 (70%)
Query: 766 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNA 825
QR+KGLGEMNP QLWETTM+P R L++V I DA +K+ LMG E RR++IE N
Sbjct: 566 QRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEETEKLVDMLMGKKAEPRREWIEENG 625
>gnl|CDD|214659 smart00433, TOP2c, TopoisomeraseII. Eukaryotic DNA topoisomerase
II, GyrB, ParE.
Length = 594
Score = 631 bits (1630), Expect = 0.0
Identities = 277/554 (50%), Positives = 373/554 (67%), Gaps = 27/554 (4%)
Query: 49 GLHHLVFEILDNAIDESLAGYCTKINVTIYSDNSISISDNGRGIPIDIKIDDKHKPKRSA 108
GLHHLV EI+DNA DE+LAGY I VTI DNSIS+ DNGRGIP++I K K+ A
Sbjct: 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHP----KEKKYA 56
Query: 109 AEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVL 168
E++ T LHAGGKF+ ++YK+SGGLHG+G S VN LS ++ + R+ K + F
Sbjct: 57 PEVIFTVLHAGGKFDDDAYKVSGGLHGVGASVVNALSTEFEVEVARDGKEYKQSFSN--- 113
Query: 169 QNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVDEKIFSNI-EFHYEILKKRIRELSFLN 227
NG +S KIIGDT K GTK+ F D +IF + +E+LK+R+REL+FLN
Sbjct: 114 --------NGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGMTTDDDFELLKRRLRELAFLN 165
Query: 228 NGVCITLIDERIKKKEIFEFKGGTSGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINID 287
GV ITL DER +++ F F+GG +V +NK+K ++ P I +K+NI ++
Sbjct: 166 KGVKITLNDERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPT-----YIEGEKDNIRVE 220
Query: 288 VSMQWNNSYNENILCFTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGE 347
V+ Q+ + Y+ENI+ F NNI +GGTH G + +TR IN+Y ++ + LK+ I+ GE
Sbjct: 221 VAFQYTDGYSENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKKKLKEKNIK--GE 278
Query: 348 DIREGLTCVLSIKIPDPKFNSQTKNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICE 407
D+REGLT +S+KIP+P+F QTK KL +SEVR VE+I+ + L FL+ENP E+ I E
Sbjct: 279 DVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIVSECLLSFLEENPVEASKIVE 338
Query: 408 KIIEAARSREAARKTRELTRKKNLIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVK 467
K++ AA++R AA+K RELTRKK L I L KLAD P+ CEL++VEGDSAGGS K
Sbjct: 339 KVLLAAKARAAAKKARELTRKKKL-SSISLPGKLADASSAGPKKCELFLVEGDSAGGSAK 397
Query: 468 QGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRI 527
GRDR FQA+LPLRGK+LN+EKA +KI+ +E+I LI+ LG+GI +F++EKLRY +I
Sbjct: 398 SGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIG-KDFDIEKLRYGKI 456
Query: 528 IIMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQPPLYKIKYGNNECYLRD--DIE 585
IIMTDAD+DG+HI+ LLLTFFYR MP LIE G++YIA PPLYK+ G + E
Sbjct: 457 IIMTDADVDGSHIKGLLLTFFYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVYSFYSLDE 516
Query: 586 EERYMLKIAFKNVK 599
E+++ K K
Sbjct: 517 YEKWLEKTEGNKSK 530
Score = 97.2 bits (243), Expect = 7e-21
Identities = 39/60 (65%), Positives = 44/60 (73%)
Query: 766 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNA 825
QRYKGLGEMN QLWETTM+P R LL V + DA AD IF LMGD VE R+++IE NA
Sbjct: 534 QRYKGLGEMNADQLWETTMDPERRTLLFVTLDDADEADLIFSALMGDKVEPRKEWIEENA 593
>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 [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 564 bits (1455), Expect = 0.0
Identities = 274/590 (46%), Positives = 376/590 (63%), Gaps = 31/590 (5%)
Query: 17 SSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAIDESLAGYCTKINVT 76
S Y+A +I+ILEGL+AVRKRP MYIG T D GLHHLV+EI+DN++DE LAGY I VT
Sbjct: 3 SKYNADAIKILEGLDAVRKRPGMYIGST-DSKGLHHLVWEIVDNSVDEVLAGYADNITVT 61
Query: 77 IYSDNSISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGI 136
++ DNSI++ D+GRGIP I D S E V T LHAGGKF++ YK +GGLHG+
Sbjct: 62 LHKDNSITVQDDGRGIPTGIHQDGN----ISTVETVFTVLHAGGKFDQGGYKTAGGLHGV 117
Query: 137 GLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTK 196
G S VN LS +L++T+ R+ +I+ F G G V +K IG T K GT
Sbjct: 118 GASVVNALSSWLEVTVKRDGQIYQQRFENG-----------GKIVQSLKKIGTTKKTGTL 166
Query: 197 IHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKGGTSGFVS 256
+HF D IF +F+ I+K+R++E +FL + +T D+R K +F ++ G FV
Sbjct: 167 VHFHPDPTIFKTTQFNSNIIKERLKESAFLLKKLKLTFTDKRTNKTTVFFYENGLVDFVD 226
Query: 257 YINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQVDGGTHL 316
YIN++K + + +KN I ++V+ Q+N+ +ENIL F N++ +GGTH
Sbjct: 227 YINETKETLSQVTY------FEGEKNGIEVEVAFQFNDGDSENILSFANSVKTKEGGTHE 280
Query: 317 TGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDP--KFNSQTKNKL 374
G + IT IN Y + LK+ + G DIREGL+ ++S++IP+ +F QTK+KL
Sbjct: 281 NGFKLAITDVINSYARKYNLLKEKDKNLEGSDIREGLSAIISVRIPEELIQFEGQTKSKL 340
Query: 375 VSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTR--KKNLI 432
S E R V+EI+ LF FL+EN ++KL+ +K I+A ++EAA+K RE + KK
Sbjct: 341 FSPEARNVVDEIVQDHLFFFLEENNNDAKLLIDKAIKARDAKEAAKKAREEKKSGKKPKK 400
Query: 433 DDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARF 492
+ LS KL Q KNP EL++VEGDSAGGS KQGRDR+FQA+LPLRGKVLN+EKA+
Sbjct: 401 EKGILSGKLTPAQSKNPAKNELFLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKAKL 460
Query: 493 EKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKM 552
I+ +E+I T+I +G GI D F+++ L+Y +IIIMTDAD DGAHI+ LLLTFFYR M
Sbjct: 461 ADILKNEEINTIIFCIGTGIGAD-FSIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYM 519
Query: 553 PKLIEYGYIYIAQPPLYKIKYGNNE--CYLRDDIEEERYMLKIAFKNVKL 600
LIE G++YIA PPLYK+ + + Y D+E E +K KN L
Sbjct: 520 RPLIELGHVYIALPPLYKLSKKDGKKVKYAWSDLELES--VKKKLKNYTL 567
Score = 87.2 bits (216), Expect = 1e-17
Identities = 39/70 (55%), Positives = 50/70 (71%), Gaps = 1/70 (1%)
Query: 755 LRNEAENMVIKQRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNV 814
++ + +N + QRYKGLGEMN QLWETTMNP R L++VKI D A++ TLMGD V
Sbjct: 558 VKKKLKNYTL-QRYKGLGEMNADQLWETTMNPETRTLVRVKIDDLARAERQINTLMGDKV 616
Query: 815 ELRRKFIELN 824
E R+K+IE N
Sbjct: 617 EPRKKWIEAN 626
>gnl|CDD|130127 TIGR01055, parE_Gneg, DNA topoisomerase IV, B subunit,
proteobacterial. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation 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. This protein is active as an
alpha(2)beta(2) heterotetramer [DNA metabolism, DNA
replication, recombination, and repair].
Length = 625
Score = 423 bits (1090), Expect = e-138
Identities = 217/587 (36%), Positives = 335/587 (57%), Gaps = 36/587 (6%)
Query: 17 SSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAIDESLAGYCTKINVT 76
++YSA I++L+GLE VRKRP MY D T +HLV E++DN++DE+LAG+ + I V
Sbjct: 2 TNYSAKDIEVLDGLEPVRKRPGMYT----DTTRPNHLVQEVIDNSVDEALAGFASIIMVI 57
Query: 77 IYSDNSISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGI 136
++ D SI + DNGRG+P+DI K SA E+++T LHAGGKF+ +Y SGGLHG+
Sbjct: 58 LHQDQSIEVFDNGRGMPVDIH----PKEGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGV 113
Query: 137 GLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQ--G 194
G+S VN LS+ +++ + R K++ + F NG V+ + G K+ G
Sbjct: 114 GISVVNALSKRVKIKVYRQGKLYSIAFE------------NGAKVTDLISAGTCGKRLTG 161
Query: 195 TKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKGGTSGF 254
T +HF D +IF ++ F L +R + L GV I DE K ++ + G +
Sbjct: 162 TSVHFTPDPEIFDSLHFSVSRLYHILRAKAVLCRGVEIEFEDEVNNTKALWNYPDGLKDY 221
Query: 255 VS-YINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENIL-CFTNNILQVDG 312
+S +N + P F GN + ++ ++ ++ W E + + N I G
Sbjct: 222 LSEAVNGDNTLP-PKPF--SGNF---EGDDEAVEWALLWLPEGGELFMESYVNLIPTPQG 275
Query: 313 GTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKN 372
GTH+ GLR G+ A+ ++ E L + +++ EDI + + VLSIK+ DP+F QTK
Sbjct: 276 GTHVNGLRQGLLDALREFCEMRNNLPRG-VKLTAEDIWDRCSYVLSIKMQDPQFAGQTKE 334
Query: 373 KLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTRKKNLI 432
+L S +V K V +I +L +N ++ + E I +A+ R+ R +++ RKK L
Sbjct: 335 RLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAEHAISSAQRRK--RAAKKVVRKK-LT 391
Query: 433 DDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARF 492
L KLADC ++ E EL++VEGDSAGGS KQ RDR +QA+LPL GK+LN +
Sbjct: 392 SGPALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSL 451
Query: 493 EKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKM 552
+K++ S++I + + +GI+ D +L +LRY +I I+ DAD DG HI LL F+
Sbjct: 452 DKVLNSQEIHDI--EVALGIDPDSNDLSQLRYGKICILADADSDGLHIATLLCALFFLHF 509
Query: 553 PKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKNVK 599
PKL+E G++Y+A+PPLY+I Y D+ E+E+ + K+ K K
Sbjct: 510 PKLVEEGHVYVAKPPLYRIDLSKEVYYALDEEEKEKLLYKLKKKKGK 556
Score = 55.3 bits (133), Expect = 9e-08
Identities = 26/60 (43%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 766 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDA--ISADKIFMTLMGDNV-ELRRKFIE 822
QR+KGLGEMNP QL ETTM+P R L+++ + D DKI L+ E R +++
Sbjct: 560 QRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDDVQDQRVDKIMDMLLAKKRSEDRFNWLQ 619
>gnl|CDD|240272 PTZ00109, PTZ00109, DNA gyrase subunit b; Provisional.
Length = 903
Score = 428 bits (1101), Expect = e-136
Identities = 241/668 (36%), Positives = 350/668 (52%), Gaps = 121/668 (18%)
Query: 3 LKNKNSYDIQDTQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAI 62
+ + +Q E Y A I +LEGLEAVRKRP MYIG+T D GLH L+FEILDN++
Sbjct: 86 QQKERVPQLQRCSE--YDADDIVVLEGLEAVRKRPGMYIGNT-DEKGLHQLLFEILDNSV 142
Query: 63 DESLAGYCTKINVTIYSDNSISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKF 122
DE LAG C KI V ++ D S+ ISDNGRGIP D+ K +S E V+T LH+GGKF
Sbjct: 143 DEYLAGECNKITVVLHKDGSVEISDNGRGIPCDVS----EKTGKSGLETVLTVLHSGGKF 198
Query: 123 N----------------------------------------KNSYKISGGLHGIGLSCVN 142
Y+ S GLHG+GLS VN
Sbjct: 199 QDTFPKNSRSDKSEDKNDTKSSKKGKSSHVKGPKEAKEKESSQMYEYSSGLHGVGLSVVN 258
Query: 143 GLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVD 202
LS FL++ + + KI+ +E G ++ K ++ + P+K K+GT IHF D
Sbjct: 259 ALSSFLKVDVFKGGKIYSIELSKG----KVTKPLS-VFSCPLK------KRGTTIHFLPD 307
Query: 203 EK-IFSN--------------IEFHYEILKKRIRELSFLNNGVCITLIDERIKKK----- 242
K IF F+ +++K RI ELS+LN G+ L+DERI +
Sbjct: 308 YKHIFKTHHQHTETEEEEGCKNGFNLDLIKNRIHELSYLNPGLTFYLVDERIANENNFYP 367
Query: 243 -EIFEFKGGTSGFVSYINKSKLVVHPTIFQAIGN-KISEKKNNINIDVSMQWN-NSYNEN 299
E + +GGT F+ + K K +++ I I N+N++VS+ W+ SY
Sbjct: 368 YETIKHEGGTREFLEELIKDKT----PLYKDINIISIRGVIKNVNVEVSLSWSLESYTAL 423
Query: 300 ILCFTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSI 359
I F NN+ GTH+ G + ITR +N I++N + K + + I GE IREG+T ++S+
Sbjct: 424 IKSFANNV-STTAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISV 482
Query: 360 KIPDPKFNSQTKNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAA 419
K+ +F+ QTK KL + ++ +E I+ + L + L+ P I K + A ++ E A
Sbjct: 483 KLNGAEFDGQTKTKLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEA 542
Query: 420 RKTRELTRKKN--LIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAV 477
+ ++L R+KN I L KL DC + E EL+IVEG+SA G+ KQ R+R FQAV
Sbjct: 543 KAAKDLIRQKNNQYYSTI-LPGKLVDCISDDIERNELFIVEGESAAGNAKQARNREFQAV 601
Query: 478 LPLRGKVLNIEKARFEKIIL-SEQITTLISTLGIGI------------------------ 512
LPL+GK+LNIEK + K + + +I LI+++G+ +
Sbjct: 602 LPLKGKILNIEKIKNNKKVFENSEIKLLITSIGLSVNPVTWRQYDLSHGTKASKDESVQN 661
Query: 513 -------EQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQ 565
+++ LRY +II++TDAD+DG H+R LLLT YR P L E+G +Y+A
Sbjct: 662 NNSTLTKKKNSLFDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVAC 721
Query: 566 PPLYKIKY 573
PPLY+I
Sbjct: 722 PPLYRITN 729
Score = 70.3 bits (172), Expect = 2e-12
Identities = 29/60 (48%), Positives = 44/60 (73%)
Query: 766 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNA 825
QR+KGLGEM QLWETTM+P R L+++ + DA+ A ++ LMG++V+ R++FI N+
Sbjct: 840 QRFKGLGEMMADQLWETTMDPKKRILIRITVSDAMRASELIFLLMGEDVQSRKQFIFENS 899
>gnl|CDD|238419 cd00822, TopoII_Trans_DNA_gyrase, TopoIIA_Trans_DNA_gyrase:
Transducer domain, having a ribosomal S5 domain 2-like
fold, of the type found in proteins of the type IIA
family of DNA topoisomerases similar to the B subunits
of E. coli DNA gyrase and E. coli Topoisomerase IV which
are heterodimers composed of two subunits. The type
IIA enzymes are the predominant form of topoisomerase
and are found in some bacteriophages, viruses and
archaea, and in all bacteria and eukaryotes. All type
IIA topoisomerases are related to each other at amino
acid sequence level, though their oligomeric
organization sometimes differs. TopoIIA enzymes cut
both strands of the duplex DNA to remove (relax) both
positive and negative supercoils in DNA. These enzymes
covalently attach to the 5' ends of the cut DNA,
separate the free ends of the cleaved strands, pass
another region of the duplex through this gap, then
rejoin the ends. TopoIIA enzymes also catenate/
decatenate duplex rings. E.coli DNA gyrase is a
heterodimer composed of two subunits. E. coli DNA gyrase
B subunit is known to be important in nucleotide
hydrolysis and the transduction of structural signals
from ATP-binding site to the DNA breakage/reunion
regions of the enzymes.
Length = 172
Score = 230 bits (589), Expect = 5e-71
Identities = 87/177 (49%), Positives = 122/177 (68%), Gaps = 5/177 (2%)
Query: 249 GGTSGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNIL 308
GG FV +NK K +H I +K+ + ++V++QW +SY+ENIL F NNI
Sbjct: 1 GGLKDFVEELNKDKEPLHEEPI-----YIEGEKDGVEVEVALQWTDSYSENILSFVNNIP 55
Query: 309 QVDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNS 368
+GGTH TG R+ +TRAIN Y ++N LKK +++ G+DIREGLT V+S+K+P+P+F
Sbjct: 56 TPEGGTHETGFRAALTRAINDYAKKNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEG 115
Query: 369 QTKNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTREL 425
QTK+KL +SEVR VE + + L ++L+ENP E+K I EK I AA++REAARK REL
Sbjct: 116 QTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAILAAKAREAARKAREL 172
>gnl|CDD|173786 cd03366, TOPRIM_TopoIIA_GyrB, TOPRIM_TopoIIA_GyrB:
topoisomerase-primase (TOPRIM) nucleotidyl
transferase/hydrolase domain of the type found in
proteins of the type IIA family of DNA topoisomerases
similar to the Escherichia coli GyrB subunit. TopoIIA
enzymes cut both strands of the duplex DNA to remove
(relax) both positive and negative supercoils in DNA.
These enzymes covalently attach to the 5' ends of the
cut DNA, separate the free ends of the cleaved strands,
pass another region of the duplex through this gap, then
rejoin the ends. These proteins also catenate/
decatenate duplex rings. DNA gyrase is more effective
at relaxing supercoils than decatentating DNA. DNA
gyrase in addition inserts negative supercoils in the
presence of ATP. The TOPRIM domain has two conserved
motifs, one of which centers at a conserved glutamate
and the other one at two conserved aspartates (DxD). The
conserved glutamate may act as a general base in strand
joining and as a general acid in strand cleavage by
topisomerases. The DXD motif may co-ordinate Mg2+, a
cofactor required for full catalytic function.
Length = 114
Score = 212 bits (543), Expect = 2e-65
Identities = 84/115 (73%), Positives = 100/115 (86%), Gaps = 1/115 (0%)
Query: 452 CELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIG 511
ELYIVEGDSAGGS KQGRDRRFQA+LPLRGK+LN+EKAR +KI+ +E+I LI+ LG G
Sbjct: 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTG 60
Query: 512 IEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQP 566
I ++F+LEKLRYH+IIIMTDAD+DGAHIR LLLTFF+R M LIE G++YIAQP
Sbjct: 61 I-GEDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
>gnl|CDD|173780 cd01030, TOPRIM_TopoIIA_like, TOPRIM_TopoIIA_like:
topoisomerase-primase (TOPRIM) nucleotidyl
transferase/hydrolase domain of the type found in
proteins of the type IIA family of DNA topoisomerases
similar to Saccharomyces cerevisiae Topoisomerase II.
TopoIIA enzymes cut both strands of the duplex DNA to
remove (relax) both positive and negative supercoils in
DNA. These enzymes covalently attach to the 5' ends of
the cut DNA, separate the free ends of the cleaved
strands, pass another region of the duplex through this
gap, then rejoin the ends. These proteins also catenate/
decatenate duplex rings. The TOPRIM domain has two
conserved motifs, one of which centers at a conserved
glutamate and the other one at two conserved aspartates
(DxD). The conserved glutamate may act as a general base
in strand joining and as a general acid in strand
cleavage by topisomerases. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 115
Score = 198 bits (506), Expect = 5e-60
Identities = 77/115 (66%), Positives = 96/115 (83%)
Query: 452 CELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIG 511
CEL +VEGDSAGGS KQGRDR FQAV PLRGK+LN+EKA +KI+ +E+I +I LG+G
Sbjct: 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLG 60
Query: 512 IEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQP 566
I +D+F+L+KLRY +IIIMTDAD+DG+HIR LLLTFFYR P L+E G++YIAQ
Sbjct: 61 IGKDDFDLDKLRYGKIIIMTDADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
>gnl|CDD|215785 pfam00204, DNA_gyraseB, DNA gyrase B. This family represents the
second domain of DNA gyrase B which has a ribosomal S5
domain 2-like fold. This family is structurally related
to PF01119.
Length = 173
Score = 197 bits (504), Expect = 6e-59
Identities = 83/176 (47%), Positives = 119/176 (67%), Gaps = 3/176 (1%)
Query: 250 GTSGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQ 309
G +V +NK K +HP + G + + I ++V++QWN+SY+ENI+ F NNI
Sbjct: 1 GLKDYVKELNKDKTPLHPEVIYFEGEE--AFDDRIEVEVALQWNDSYSENIVSFVNNIPT 58
Query: 310 VDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQ 369
DGGTH+ G R+ +TRA+N+Y ++ LKK K +I G+DIREGLT V+S+KIP+P+F Q
Sbjct: 59 PDGGTHVDGFRAALTRALNEYAKKKGLLKK-KDKITGDDIREGLTAVVSVKIPNPQFEGQ 117
Query: 370 TKNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTREL 425
TK KL +SEVR VE ++ + FL++NP +K I EK + AA++R AARK REL
Sbjct: 118 TKEKLGNSEVRSAVESVVSEKFAKFLEKNPEIAKKILEKALAAAKARLAARKAREL 173
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 181 bits (462), Expect = 5e-47
Identities = 158/617 (25%), Positives = 262/617 (42%), Gaps = 109/617 (17%)
Query: 14 TQESSYSASSIQILEGLEAVRKRPEMYIG------------DTSDGT----------GLH 51
T E Y Q +E + RP+ YIG D GL+
Sbjct: 5 TVEERY-----QKKTQIEHILLRPDTYIGSIETQTEDMWVYDEEKNRMVYKTITYVPGLY 59
Query: 52 HLVFEILDNAID----ESLAGYCTKINVTI-YSDNSISISDNGRGIPIDIKIDDKHK--- 103
+ EIL NA D + T I VTI + IS+ ++G GIP+ I +HK
Sbjct: 60 KIFDEILVNAADNKARDKGGHRMTYIKVTIDEENGEISVYNDGEGIPVQI--HKEHKIYV 117
Query: 104 PKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLS-RF-LQLTINRNKKIHYM 161
P E++ L ++ +++GG +G G N S +F ++ +++ K M
Sbjct: 118 P-----EMIFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECVDSKSGKKFKM 172
Query: 162 EFRYGVLQNR--IIKTINGISVSPIKIIGDTNKQGTKIHFWVDEKIFSNIEF---HYEIL 216
+ + + I + +G K TK+ F+ D F EF +L
Sbjct: 173 TWTDNMSKKSEPRITSYDG------------KKDYTKVTFYPDYAKFGMTEFDDDMLRLL 220
Query: 217 KKRIRELSFLNNGVCITLIDERIKKKEIFEFKGGTSGFVSYINKSKLVVHPTIFQAIGNK 276
KKR+ +L+ + + L ERI K F Y++ L +
Sbjct: 221 KKRVYDLAGCFGKLKVYLNGERIAIKS----------FKDYVD---LYLPD-----GEEG 262
Query: 277 ISEKKNNINIDVSMQWN--NSYNE---NILCFTNNILQVDGGTHLTGLRSGITRAINKYI 331
+ V+ +W S ++ + F N+I GGTH+ + + + +
Sbjct: 263 KKPPYPFVYTSVNGRWEVVVSLSDGQFQQVSFVNSICTTKGGTHVNYILDQLISKLQEKA 322
Query: 332 EENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKNKLVSSEVRKPVEEIIIKTL 391
++ KK EI I+ L ++ I +P F+SQTK L + + + + L
Sbjct: 323 KK---KKKKGKEIKPNQIKNHLWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKL 379
Query: 392 FDFLQENPGESKLICEKIIEAARSREAARKTREL-TRKKNLIDDIELSTKLADCQE---K 447
++ ++P I E I+E A+++ AA +++ KK+ I I KL D + K
Sbjct: 380 IKYVLKSP-----ILENIVEWAQAKLAAELNKKMKAGKKSRILGI---PKLDDANDAGGK 431
Query: 448 NPELCELYIVEGDSA------GGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQI 501
N E C L + EGDSA G SV GRD V PLRGK+LN+ A ++++ +++I
Sbjct: 432 NSEECTLILTEGDSAKALALAGLSVV-GRDY--YGVFPLRGKLLNVRDASLKQLMNNKEI 488
Query: 502 TTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEY-GY 560
L LG+ I + + + LRY ++IMTD D DG+HI+ LL+ + P L++ G+
Sbjct: 489 QNLFKILGLDIGKKYEDPKGLRYGSLMIMTDQDHDGSHIKGLLINMIHHFWPSLLKNPGF 548
Query: 561 IYIAQPPLYKIKYGNNE 577
+ P+ K N+
Sbjct: 549 LKEFITPIVKATKKGNQ 565
>gnl|CDD|177398 PHA02569, 39, DNA topoisomerase II large subunit; Provisional.
Length = 602
Score = 167 bits (424), Expect = 1e-43
Identities = 161/604 (26%), Positives = 267/604 (44%), Gaps = 97/604 (16%)
Query: 24 IQILEGLEAVRKRPEMYIGDTSDGT----------------GLHHLVFEILDNAIDESLA 67
++L E + KRP MYIG + GL ++ EI+DN++DE++
Sbjct: 4 FKVLSDREHILKRPGMYIGSVAYEAHERFLFGKFTQVEYVPGLVKIIDEIIDNSVDEAIR 63
Query: 68 G---YCTKINVTIYSDNSISISDNGRGIPIDIKIDDKHK--PKRSAAEIVMTELHAGGKF 122
+ KI+VTI +N +++SDNGRGIP + + + P AA T AG F
Sbjct: 64 TNFKFANKIDVTI-KNNQVTVSDNGRGIPQAMVTTPEGEEIPGPVAA---WTRTKAGSNF 119
Query: 123 NKNSYKISGGLHGIGLSCVNGLSR-FLQLTINRNKKIHYMEFRYGVLQNRIIKTING--- 178
+ ++ +++GG++G+G S N S F+ T + ++ + NG
Sbjct: 120 D-DTNRVTGGMNGVGSSLTNFFSVLFIGETCDGKNEV-------------TVNCSNGAEN 165
Query: 179 ISVSPIKIIGDTNKQGTKIHFWVDEKIFS--NIEFHY-EILKKRIRELSFLNNGVCITLI 235
IS S +GT + F D F ++ Y +I+ R++ L+ + + T
Sbjct: 166 ISWSTKP----GKGKGTSVTFIPDFSHFEVNGLDQQYLDIILDRLQTLAVVFPDIKFTFN 221
Query: 236 DERIKKKEIFEFKGGTSGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNS 295
+++ K F Y +K TI Q E N VS+ S
Sbjct: 222 GKKVSGK-----------FKKY---AKQFGDDTIVQ-------ENDN-----VSIALAPS 255
Query: 296 YNE-NILCFTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLT 354
+ L F N + +GG H+ + I + I+ KK KIE+ ++E LT
Sbjct: 256 PDGFRQLSFVNGLHTKNGGHHVDCVMDDICEELIPMIK-----KKHKIEVTKARVKECLT 310
Query: 355 CVLSIK-IPDPKFNSQTKNKLVSS--EVRKPVEEIIIKTLFDFLQENPGESKLICEKIIE 411
VL ++ + +P+F+SQTK +L S E+R ++ + K + + + I IIE
Sbjct: 311 IVLFVRNMSNPRFDSQTKERLTSPFGEIRNHID-LDYKKIAKQILKTEA----IIMPIIE 365
Query: 412 AARSREAARKTRELTRKKNLIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRD 471
AA +R+ A + T+ +++ + L++ EGDSA G + + RD
Sbjct: 366 AALARKLAAEKAAETKAAKKAKKAKVAKHIKANLIGKDAETTLFLTEGDSAIGYLIEVRD 425
Query: 472 RRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMT 531
PLRGKVLN + I+ ++++ + + G+ + + N + Y I IMT
Sbjct: 426 EELHGGYPLRGKVLNTWGMSYADILKNKELFDICAITGLVLGEKAEN---MNYKNIAIMT 482
Query: 532 DADIDG-AHIRALLLTFFYRKMPKLIEYGYIYIAQPPLYKIKYGNNE--CYLRDDIEEER 588
DAD+DG I LLL FF R P+L E G I + P+ + G Y D+ E+ +
Sbjct: 483 DADVDGKGSIYPLLLAFFSR-WPELFEQGRIRFVKTPVIIAQVGKETKWFYSLDEFEKAK 541
Query: 589 YMLK 592
LK
Sbjct: 542 DSLK 545
>gnl|CDD|215593 PLN03128, PLN03128, DNA topoisomerase 2; Provisional.
Length = 1135
Score = 148 bits (376), Expect = 1e-36
Identities = 155/578 (26%), Positives = 253/578 (43%), Gaps = 104/578 (17%)
Query: 30 LEAVRKRPEMYIGDTSDGT--------------------GLHHLVFEILDNAIDESLAG- 68
LE + RP+ YIG T T GL+ + EIL NA D
Sbjct: 13 LEHILLRPDTYIGSTEKHTQTLWVYEGGEMVNREVTYVPGLYKIFDEILVNAADNKQRDP 72
Query: 69 YCTKINVTIYSD-NSISISDNGRGIPIDIKIDDKHKPKRS-AAEIVMTELHAGGKFNKNS 126
+ V I + N+IS+ +NG+GIP++I HK + E++ L F+ N
Sbjct: 73 SMDSLKVDIDVEQNTISVYNNGKGIPVEI-----HKEEGVYVPELIFGHLLTSSNFDDNE 127
Query: 127 YKISGGLHGIGLSCVNGLS-RFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIK 185
K +GG +G G N S F T + N+ Y + + T N S K
Sbjct: 128 KKTTGGRNGYGAKLANIFSTEFTVETADGNRGKKY----------KQVFTNNMSVKSEPK 177
Query: 186 IIG-DTNKQGTKIHFWVDEKIFSNIEFH---YEILKKRIRELS-FLNNGVCITLIDERIK 240
I ++ TKI F D F+ ++ KR+ +++ L + + L +++
Sbjct: 178 ITSCKASENWTKITFKPDLAKFNMTRLDEDVVALMSKRVYDIAGCLGKKLKVELNGKKLP 237
Query: 241 KKEIFEFKGGTSGFVSYINKSKLVVHPTIFQAIGNKISEKKNN---INIDVSMQWNNSYN 297
K F Y+ L + P + +I EK N+ + + +S + S+
Sbjct: 238 VK----------SFQDYVG---LYLGPNSREDPLPRIYEKVNDRWEVCVSLS---DGSFQ 281
Query: 298 ENILCFTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLKKSK--IEIIGEDIREGLTC 355
+ + F N+I + GGTH+ + I + I + ++ KK+K + I+ L
Sbjct: 282 Q--VSFVNSIATIKGGTHVDYVADQIVKHIQEKVK-----KKNKNATHVKPFQIKNHLWV 334
Query: 356 VLSIKIPDPKFNSQTKNKLVSSEVR-----KPVEEIIIKTLFDFLQENPGESKLICEKII 410
++ I +P F+SQTK L + + EE + K E G + E I+
Sbjct: 335 FVNCLIENPTFDSQTKETLTTRPSSFGSKCELSEEFLKKV------EKCG----VVENIL 384
Query: 411 EAARSREAARKTRELTRKKNLIDDIELSTKLADCQE---KNPELCELYIVEGDSA----- 462
A+ ++ ++ K+ + I KL D + K + C L + EGDSA
Sbjct: 385 SWAQFKQQKELKKKDGAKRQRLTGIP---KLDDANDAGGKKSKDCTLILTEGDSAKALAM 441
Query: 463 -GGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGI--GIEQDEFNL 519
G SV GRD V PLRGK+LN+ +A ++I+ + +IT + LG+ G DE N
Sbjct: 442 SGLSV-VGRD--HYGVFPLRGKLLNVREASHKQIMKNAEITNIKQILGLQFGKTYDEENT 498
Query: 520 EKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIE 557
+ LRY ++IMTD D DG+HI+ L++ FF+ P L++
Sbjct: 499 KSLRYGHLMIMTDQDHDGSHIKGLIINFFHSFWPSLLK 536
>gnl|CDD|201537 pfam00986, DNA_gyraseB_C, DNA gyrase B subunit, carboxyl terminus.
The amino terminus of eukaryotic and prokaryotic DNA
topoisomerase II are similar, but they have a different
carboxyl terminus. The amino-terminal portion of the DNA
gyrase B protein is thought to catalyze the
ATP-dependent super-coiling of DNA. See pfam00204. The
carboxyl-terminal end supports the complexation with the
DNA gyrase A protein and the ATP-independent relaxation.
This family also contains Topoisomerase IV. This is a
bacterial enzyme that is closely related to DNA gyrase.
Length = 65
Score = 108 bits (271), Expect = 2e-28
Identities = 39/57 (68%), Positives = 47/57 (82%)
Query: 766 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIE 822
QR+KGLGEMNP QLWETTM+P R LL+V I+DA AD++F TLMG +VE RR+FIE
Sbjct: 9 QRFKGLGEMNPEQLWETTMDPETRRLLQVTIEDAEEADEMFSTLMGKDVEPRREFIE 65
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 109 bits (273), Expect = 3e-24
Identities = 147/578 (25%), Positives = 243/578 (42%), Gaps = 105/578 (18%)
Query: 30 LEAVRKRPEMYIGDTSDGT--------------------GLHHLVFEILDNAIDE----- 64
LE + RP+ YIG T GL+ + EIL NA D
Sbjct: 38 LEHILLRPDTYIGSIEKHTQTLWVYETDKMVQRSVTYVPGLYKIFDEILVNAADNKQRDP 97
Query: 65 SLAGYCTKINVTIYSDNSISISDNGRGIPIDIKIDDKHKPKR-SAAEIVMTELHAGGKFN 123
+ I+V N IS+ +NG G+P++I H+ + E++ L ++
Sbjct: 98 KMDSLRVVIDV---EQNLISVYNNGDGVPVEI-----HQEEGVYVPEMIFGHLLTSSNYD 149
Query: 124 KNSYKISGGLHGIGLSCVNGLS-RFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVS 182
N K +GG +G G N S F+ T + ++ Y + V N + G
Sbjct: 150 DNEKKTTGGRNGYGAKLTNIFSTEFVIETADGKRQKKYKQ----VFSNNM-----GKKSE 200
Query: 183 PIKIIGDTNKQGTKIHFWVDEKIFSNIEFHYEI---LKKRIRELS-FLNNGVCITLIDER 238
P+ ++ TK+ F D F+ ++ +KKR+ +++ L V + L +R
Sbjct: 201 PVITKCKKSENWTKVTFKPDLAKFNMTHLEDDVVALMKKRVVDIAGCLGKTVKVELNGKR 260
Query: 239 IKKKEIFEFKGGTSGFVSYIN---KSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNS 295
I K F Y++ +S P I K++++ + VS+
Sbjct: 261 IPVK----------SFSDYVDLYLESANKSRPENLPRIYEKVNDR---WEVCVSLSEGQF 307
Query: 296 YNENILCFTNNILQVDGGTHLTGLRSGIT----RAINKYIEENEFLKKSKIEIIGEDIRE 351
+ F N+I + GGTH+ + + I A+NK K I +++
Sbjct: 308 QQ---VSFVNSIATIKGGTHVDYVTNQIANHVMEAVNK--------KNKNANIKAHNVKN 356
Query: 352 GLTCVLSIKIPDPKFNSQTKNKLV--SSEVRKPVEEIIIKTLFDFLQENPGESKLICEKI 409
L ++ I +P F+SQTK L S E DFL+ K++ I
Sbjct: 357 HLWVFVNALIDNPAFDSQTKETLTLRQSSFGSKCELSE-----DFLK------KVMKSGI 405
Query: 410 IEAARSREAARKTRELTR----KKNLIDDIELSTKLADCQE---KNPELCELYIVEGDSA 462
+E S ++++EL + K + I KL D E KN E C L + EGDSA
Sbjct: 406 VENLLSWADFKQSKELKKTDGAKTTRVTGIP---KLEDANEAGGKNSEKCTLILTEGDSA 462
Query: 463 GGSVKQGR---DRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIGIEQDEFNL 519
G R + V PLRGK+LN+ +A ++I+ + +I + LG+ + ++
Sbjct: 463 KALAVAGLSVVGRNYYGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYESV 522
Query: 520 EKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIE 557
+ LRY ++IMTD D DG+HI+ LL+ F + P L++
Sbjct: 523 KSLRYGHLMIMTDQDHDGSHIKGLLINFIHSFWPSLLK 560
>gnl|CDD|173785 cd03365, TOPRIM_TopoIIA, TOPRIM_TopoIIA: topoisomerase-primase
(TOPRIM) nucleotidyl transferase/hydrolase domain of the
type found in proteins of the type IIA family of DNA
topoisomerases similar to Saccharomyces cerevisiae
Topoisomerase II. TopoIIA enzymes cut both strands of
the duplex DNA to remove (relax) both positive and
negative supercoils in DNA. These enzymes covalently
attach to the 5' ends of the cut DNA, separate the free
ends of the cleaved strands, pass another region of the
duplex through this gap, then rejoin the ends. These
proteins also catenate/ decatenate duplex rings. The
TOPRIM domain has two conserved motifs, one of which
centers at a conserved glutamate and the other one at
two conserved aspartates (DxD). This glutamate and two
aspartates, cluster together to form a highly acid
surface patch. The conserved glutamate may act as a
general base in strand joining and as a general acid in
strand cleavage by topisomerases. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 120
Score = 86.6 bits (215), Expect = 3e-20
Identities = 40/109 (36%), Positives = 64/109 (58%), Gaps = 4/109 (3%)
Query: 452 CELYIVEGDSAGGSVKQGR---DRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTL 508
C L + EGDSA G R + V PLRGK+LN+ +A ++I+ + +I + L
Sbjct: 1 CTLILTEGDSAKALAVAGLSVVGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKIL 60
Query: 509 GIGIEQDEF-NLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLI 556
G+ + ++ + + LRY R++IMTD D DG+HI+ LL+ F + P L+
Sbjct: 61 GLQHGKSDYESTKSLRYGRLMIMTDQDHDGSHIKGLLINFIHSFWPSLL 109
>gnl|CDD|238202 cd00329, TopoII_MutL_Trans, MutL_Trans: transducer domain, having a
ribosomal S5 domain 2-like fold, conserved in the
C-terminal domain of type II DNA topoisomerases (Topo
II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins.
This transducer domain is homologous to the second
domain of the DNA gyrase B subunit, which is known to be
important in nucleotide hydrolysis and the transduction
of structural signals from ATP-binding site to the DNA
breakage/reunion regions of the enzymes. The GyrB
dimerizes in response to ATP binding, and is homologous
to the N-terminal half of eukaryotic Topo II and the
ATPase fragment of MutL. Type II DNA topoisomerases
catalyze the ATP-dependent transport of one DNA duplex
through another, in the process generating transient
double strand breaks via covalent attachments to both
DNA strands at the 5' positions. Included in this group
are proteins similar to human MLH1 and PMS2. MLH1 forms
a heterodimer with PMS2 which functions in meiosis and
in DNA mismatch repair (MMR). Cells lacking either hMLH1
or hPMS2 have a strong mutator phenotype and display
microsatellite instability (MSI). Mutation in hMLH1
accounts for a large fraction of Lynch syndrome (HNPCC)
families.
Length = 107
Score = 66.9 bits (164), Expect = 2e-13
Identities = 24/104 (23%), Positives = 43/104 (41%), Gaps = 23/104 (22%)
Query: 277 ISEKKNNINIDVSMQWNN---SYNENILCFTNNILQVDGGTHLTGLRSGITRAINKYIEE 333
+ + + ++ ++ + + S + F N +GGTH+ +R TRA+N
Sbjct: 20 VEGESDGFRVEGAISYPDSGRSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN----- 74
Query: 334 NEFLKKSKIEIIGEDIREGLTCVLSIKIPD--PKFN-SQTKNKL 374
G+D+R VLS+KIP N TK ++
Sbjct: 75 ------------GDDVRRYPVAVLSLKIPPSLVDVNVHPTKEEV 106
>gnl|CDD|216679 pfam01751, Toprim, Toprim domain. This is a conserved region from
DNA primase. This corresponds to the Toprim domain
common to DnaG primases, topoisomerases, OLD family
nucleases and RecR proteins. Both DnaG motifs IV and V
are present in the alignment, the DxD (V) motif may be
involved in Mg2+ binding and mutations to the conserved
glutamate (IV) completely abolish DnaG type primase
activity. DNA primase EC:2.7.7.6 is a
nucleotidyltransferase it synthesises the
oligoribonucleotide primers required for DNA replication
on the lagging strand of the replication fork; it can
also prime the leading stand and has been implicated in
cell division. This family also includes the atypical
archaeal A subunit from type II DNA topoisomerases. Type
II DNA topoisomerases catalyze the relaxation of DNA
supercoiling by causing transient double strand breaks.
Length = 86
Score = 66.1 bits (162), Expect = 2e-13
Identities = 25/114 (21%), Positives = 39/114 (34%), Gaps = 28/114 (24%)
Query: 453 ELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIGI 512
EL IVEG S ++++ AV+ G L++E + L L
Sbjct: 1 ELIIVEGPSDAIALEKAGGVLGGAVVATSGHALDLEHIK-----------ELKKALK--- 46
Query: 513 EQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQP 566
+I+ TD D +G I LL P G + I++
Sbjct: 47 ----------GAKEVILATDPDREGEAIALKLLELLKPLGP----IGRVEISEL 86
>gnl|CDD|217081 pfam02518, HATPase_c, Histidine kinase-, DNA gyrase B-, and
HSP90-like ATPase. This family represents the
structurally related ATPase domains of histidine kinase,
DNA gyrase B and HSP90.
Length = 111
Score = 65.4 bits (160), Expect = 6e-13
Identities = 32/113 (28%), Positives = 46/113 (40%), Gaps = 22/113 (19%)
Query: 46 DGTGLHHLVFEILDNAIDESLAGYCTKINVTIYSD---NSISISDNGRGIPIDIKIDDKH 102
D L ++ +LDNAI + AG +I VT+ D I++ DNG GIP
Sbjct: 2 DEDRLRQVLSNLLDNAIKHAPAG--GEIEVTLERDGGRLRITVEDNGIGIP--------- 50
Query: 103 KPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFLQLTINRN 155
E + + + +S K+ G G+GLS V L TI
Sbjct: 51 ------PEDLPKIFEPFFRTDSSSRKVGG--TGLGLSIVRKLVELHGGTITVE 95
>gnl|CDD|214643 smart00387, HATPase_c, Histidine kinase-like ATPases. Histidine
kinase-, DNA gyrase B-, phytochrome-like ATPases.
Length = 111
Score = 65.0 bits (159), Expect = 9e-13
Identities = 32/113 (28%), Positives = 45/113 (39%), Gaps = 22/113 (19%)
Query: 46 DGTGLHHLVFEILDNAIDESLAGYCTKINVTIYSDN---SISISDNGRGIPIDIKIDDKH 102
D L ++ +LDNAI + G +I VT+ D I++ DNG GIP
Sbjct: 2 DPDRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGDHVEITVEDNGPGIP--------- 50
Query: 103 KPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFLQLTINRN 155
E + + +K S KI G G+GLS V L I+
Sbjct: 51 ------PEDLEKIFEPFFRTDKRSRKIGG--TGLGLSIVKKLVELHGGEISVE 95
>gnl|CDD|238030 cd00075, HATPase_c, Histidine kinase-like ATPases; This family
includes several ATP-binding proteins for example:
histidine kinase, DNA gyrase B, topoisomerases, heat
shock protein HSP90, phytochrome-like ATPases and DNA
mismatch repair proteins.
Length = 103
Score = 58.4 bits (142), Expect = 1e-10
Identities = 26/106 (24%), Positives = 39/106 (36%), Gaps = 22/106 (20%)
Query: 50 LHHLVFEILDNAIDESLAGYCTKINVTIYSDN---SISISDNGRGIPIDIKIDDKHKPKR 106
L ++ +L NAI + G +I +++ D I + DNG GIP +
Sbjct: 1 LQQVLLNLLSNAIKHTPEG-GGRITISVERDGDHLEIRVEDNGPGIPEEDL--------- 50
Query: 107 SAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFLQLTI 152
+F+ S GG G+GLS V L I
Sbjct: 51 ---------ERIFERFSDGSRSRKGGGTGLGLSIVKKLVELHGGRI 87
>gnl|CDD|173773 cd00188, TOPRIM, Topoisomerase-primase domain. This is a
nucleotidyl transferase/hydrolase domain found in type
IA, type IIA and type IIB topoisomerases, bacterial
DnaG-type primases, small primase-like proteins from
bacteria and archaea, OLD family nucleases from
bacterial and archaea, and bacterial DNA repair proteins
of the RecR/M family. This domain has two conserved
motifs, one of which centers at a conserved glutamate
and the other one at two conserved aspartates (DxD).
This glutamate and two aspartates, cluster together to
form a highly acid surface patch. The conserved
glutamate may act as a general base in nucleotide
polymerization by primases and in strand joining in
topoisomerases and, as a general acid in strand cleavage
by topisomerases and nucleases. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 83
Score = 38.9 bits (91), Expect = 6e-04
Identities = 24/105 (22%), Positives = 35/105 (33%), Gaps = 26/105 (24%)
Query: 452 CELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIG 511
+L IVEG S ++ Q AV+ L G LN + +++
Sbjct: 1 KKLIIVEGPSDALALAQAGGYG-GAVVALGGHALNKTRELLKRL---------------- 43
Query: 512 IEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLI 556
+II TDAD +G I LL K+
Sbjct: 44 ---------LGEAKEVIIATDADREGEAIALRLLELLKSLGKKVR 79
>gnl|CDD|239563 cd03481, TopoIIA_Trans_ScTopoIIA, TopoIIA_Trans_ScTopoIIA:
Transducer domain, having a ribosomal S5 domain 2-like
fold, of the type found in proteins of the type IIA
family of DNA topoisomerases similar to Saccharomyces
cerevisiae Topo IIA. S. cerevisiae Topo IIA is a
homodimer encoded by a single gene. The type IIA enzymes
are the predominant form of topoisomerase and are found
in some bacteriophages, viruses and archaea, and in all
bacteria and eukaryotes. All type IIA topoisomerases
are related to each other at amino acid sequence level,
though their oligomeric organization sometimes differs.
TopoIIA enzymes cut both strands of the duplex DNA to
remove (relax) both positive and negative supercoils in
DNA. These enzymes covalently attach to the 5' ends of
the cut DNA, separate the free ends of the cleaved
strands, pass another region of the duplex through this
gap, then rejoin the ends. TopoIIA enzymes also
catenate/ decatenate duplex rings. This transducer
domain is homologous to the second domain of the DNA
gyrase B subunit, which is known to be important in
nucleotide hydrolysis and the transduction of structural
signals from ATP-binding site to the DNA
breakage/reunion regions of the enzymes.
Length = 153
Score = 40.3 bits (95), Expect = 9e-04
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 303 FTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIP 362
F N+I GGTH+ + I + +++ +++ K I + ++ L ++ I
Sbjct: 49 FVNSIATTKGGTHVDYVADQIVKKLDEVVKK---KNKGGINVKPFQVKNHLWIFVNCLIE 105
Query: 363 DPKFNSQTKNKLVS 376
+P F+SQTK L +
Sbjct: 106 NPSFDSQTKETLTT 119
>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated.
Length = 1437
Score = 41.4 bits (98), Expect = 0.002
Identities = 27/176 (15%), Positives = 59/176 (33%), Gaps = 13/176 (7%)
Query: 579 YLRDDIEEERYMLKIAFKNVKLISIENGDIIKENYFFKLIDKYNKTIEIVHRLKQIIDIS 638
+ K+ + KLI N +I ++ L K+ + + +
Sbjct: 105 KNSPLFKSLLKKQKVEVEGNKLIIKVNNEIERD----HLKKKHLPKLIKQYEKFGFGILK 160
Query: 639 ILSAIMSDVILNLDTRENAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKK 698
I D++E E+F + ++ E + +L + K K+
Sbjct: 161 I-------DFEIDDSKEELEKFEAQKEEEDEKLAKEALEAMKKLEAEKKKQSKNFDPKEG 213
Query: 699 NYIIDINFINNKDYKKLVSIISTFKKIIGKGVIIQKSIGEKIKKYTANNFYKIINY 754
I I+ ++ + I ++++ +G + + I E F KI +Y
Sbjct: 214 PVQIGKK-IDKEEITPMKEINEEERRVVVEGYVFKVEIKELKSGRHILTF-KITDY 267
>gnl|CDD|223400 COG0323, MutL, DNA mismatch repair enzyme (predicted ATPase) [DNA
replication, recombination, and repair].
Length = 638
Score = 36.9 bits (86), Expect = 0.044
Identities = 13/42 (30%), Positives = 24/42 (57%), Gaps = 6/42 (14%)
Query: 56 EILDNAIDESLAGYCTKINVTI--YSDNSISISDNGRGIPID 95
E+++N++D AG T+I++ + I + DNG GI +
Sbjct: 30 ELVENSLD---AG-ATRIDIEVEGGGLKLIRVRDNGSGIDKE 67
>gnl|CDD|225115 COG2205, KdpD, Osmosensitive K+ channel histidine kinase [Signal
transduction mechanisms].
Length = 890
Score = 35.7 bits (83), Expect = 0.13
Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 7/61 (11%)
Query: 46 DGTGLHHLVFEILDNAIDESLAGYCTKINVTIYSDNS---ISISDNGRGIPIDI--KIDD 100
D + ++ +L+NA+ A ++I + + S+ D G GIP +I D
Sbjct: 772 DSPLIEQVLINLLENAL--KYAPPGSEIRINAGVERENVVFSVIDEGPGIPEGELERIFD 829
Query: 101 K 101
K
Sbjct: 830 K 830
>gnl|CDD|234630 PRK00095, mutL, DNA mismatch repair protein; Reviewed.
Length = 617
Score = 35.2 bits (82), Expect = 0.15
Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 6/40 (15%)
Query: 56 EILDNAIDESLAGYCTKINVTIYSD--NSISISDNGRGIP 93
E+++NA+D AG T+I++ I I + DNG GI
Sbjct: 29 ELVENALD---AG-ATRIDIEIEEGGLKLIRVRDNGCGIS 64
>gnl|CDD|233035 TIGR00585, mutl, DNA mismatch repair protein MutL. All proteins
in this family for which the functions are known are
involved in the process of generalized mismatch repair.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and
repair].
Length = 312
Score = 33.8 bits (78), Expect = 0.30
Identities = 17/44 (38%), Positives = 26/44 (59%), Gaps = 6/44 (13%)
Query: 54 VFEILDNAIDESLAGYCTKINVTI--YSDNSISISDNGRGIPID 95
V E+++N++D AG T+I+V I I +SDNG GI +
Sbjct: 27 VKELVENSLD---AG-ATRIDVEIEEGGLKLIEVSDNGSGIDKE 66
>gnl|CDD|222246 pfam13589, HATPase_c_3, Histidine kinase-, DNA gyrase B-, and
HSP90-like ATPase. This family represents,
additionally, the structurally related ATPase domains
of histidine kinase, DNA gyrase B and HSP90.
Length = 134
Score = 32.6 bits (75), Expect = 0.30
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 7/45 (15%)
Query: 54 VFEILDNAIDESLAGYCTKINVTIYSDN---SISISDNGRGIPID 95
+ E++DN+ID T + ++I D ISI DNG G+ +
Sbjct: 7 IAELIDNSID----ADATNVKISIDPDRGEDGISIEDNGGGMSYE 47
>gnl|CDD|223715 COG0642, BaeS, Signal transduction histidine kinase [Signal
transduction mechanisms].
Length = 336
Score = 33.6 bits (76), Expect = 0.45
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 6/56 (10%)
Query: 45 SDGTGLHHLVFEILDNAIDESLAGYCTKINVTIYSDNS---ISISDNGRGIPIDIK 97
D L ++ +L NAI + G +I +++ D+ IS+ D G GIP +
Sbjct: 224 GDPERLRQVLVNLLSNAIKYTPGG---EITISVRQDDEQVTISVEDTGPGIPEEEL 276
>gnl|CDD|224307 COG1389, COG1389, DNA topoisomerase VI, subunit B [DNA replication,
recombination, and repair].
Length = 538
Score = 33.5 bits (77), Expect = 0.47
Identities = 52/226 (23%), Positives = 85/226 (37%), Gaps = 58/226 (25%)
Query: 31 EAVRKRPEMYIGDTSDGTGLHHLVFEILDNAIDES-LAGYCTKINVTIYSDN----SISI 85
E RK EM +G L V E++ N++D AG I V I + +
Sbjct: 19 EFFRKNKEM-LGFDGPIRSLTTTVHELVTNSLDACEEAGILPDIKVEIERIGKDHYKVIV 77
Query: 86 SDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLS 145
DNG GIP ++ PK V ++ G KF++N S G GIG+S
Sbjct: 78 EDNGPGIP------EEQIPK------VFGKMLYGSKFHRN--IQSRGQQGIGIS---AAV 120
Query: 146 RFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVDEKI 205
+ Q+T + P+++I T GT + + +
Sbjct: 121 LYSQMTTGK----------------------------PVRVISSTGDSGTAYEYELKIDV 152
Query: 206 FSNIEFHYEILKKRIRELSFLNNGVCITL-IDE---RIKKKEIFEF 247
N EI+++ E +G + L + R K++ I+E+
Sbjct: 153 QKN---EPEIVERGEVENPGGWHGTRVELELKGVWYRAKRQGIYEY 195
>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A'';
Validated.
Length = 383
Score = 32.5 bits (75), Expect = 0.95
Identities = 30/112 (26%), Positives = 49/112 (43%), Gaps = 28/112 (25%)
Query: 654 RENAEQFAKKIIK-KLND---------SNIEIIVEFDQ--LNNKYLL--NIKKKFLKKK- 698
RE AE+ A+KI L + +N+ II+E D+ L ++ L ++K+ KKK
Sbjct: 126 REKAEEVARKIEATTLENLAKDISVDLANMTIIIELDEEMLEDRGLTVDDVKEAIEKKKG 185
Query: 699 ------NYIIDINFINNKDYKKLVSIISTFKKIIGKG------VIIQKSIGE 738
+ I+ Y++L + + I KG VII+K E
Sbjct: 186 GEVEIEGNTLIIS-PKEPSYRELRKLAEKIRNIKIKGIKGIKRVIIRKEGDE 236
>gnl|CDD|238394 cd00771, ThrRS_core, Threonyl-tRNA synthetase (ThrRS) class II core
catalytic domain. ThrRS is a homodimer. It is
responsible for the attachment of threonine to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. Class II assignment is
based upon its structure and the presence of three
characteristic sequence motifs in the core domain.
Length = 298
Score = 32.1 bits (74), Expect = 1.1
Identities = 17/66 (25%), Positives = 22/66 (33%), Gaps = 15/66 (22%)
Query: 537 GAHIRALLLTFFYRKMPKLIEYGYIYIAQPPLYKI----------KYGNNECYLRDDIEE 586
GA IR L F + GY + P +Y Y N + E+
Sbjct: 29 GAIIRNELEDFLRELQ---RKRGYQEVETPIIYNKELWETSGHWDHYRENM--FPFEEED 83
Query: 587 ERYMLK 592
E Y LK
Sbjct: 84 EEYGLK 89
>gnl|CDD|221957 pfam13175, AAA_15, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 320
Score = 32.0 bits (73), Expect = 1.1
Identities = 25/180 (13%), Positives = 53/180 (29%), Gaps = 9/180 (5%)
Query: 545 LTFFYRKMPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKNVKLISIE 604
Y + KIK ++I+ + + + +
Sbjct: 48 KKKIYISISDNKADIDKENLNKKSKKIKISIIIELSSNEIKSFSIKFYLNYYLEIINNDV 107
Query: 605 NGDIIKENYFFKLIDKYNKTIEIVHRLKQIIDISILSAIMSDVILNLDTRENAEQFAKKI 664
+I + L K ++ + + +I S I +D I
Sbjct: 108 EDEIELLLFSKNLEYILKKILDKIEKFDEIKGAKKKDFFKSINIYEID---------NFI 158
Query: 665 IKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYIIDINFINNKDYKKLVSIISTFKK 724
K L+ + IV D L + F +K + + + N+ K +++ I+ K
Sbjct: 159 DKTLSKILDDNIVFQDNLEKNIDDKLSNIFNEKLSNLKNEKISINEKIKSILNEINPDSK 218
>gnl|CDD|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366). This
family of proteins is found in bacteria and eukaryotes.
Proteins in this family are typically between 227 and
387 amino acids in length.
Length = 213
Score = 31.2 bits (71), Expect = 1.6
Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 13/68 (19%)
Query: 579 YLRDDIEEERYMLKIAFKNVKLISIENGDIIKENYFFKLIDKYNKTIEIVHRLKQIIDIS 638
L DD + + I++ N F+ +ID E VH L Q +D +
Sbjct: 62 TLVDDATDA--------SGKQFITVTTKS---GNTFYIVID-RAAEGENVHFLNQ-VDEA 108
Query: 639 ILSAIMSD 646
L A+M +
Sbjct: 109 DLLALMEE 116
>gnl|CDD|226368 COG3850, NarQ, Signal transduction histidine kinase,
nitrate/nitrite-specific [Signal transduction
mechanisms].
Length = 574
Score = 31.5 bits (72), Expect = 2.2
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 9/48 (18%)
Query: 52 HLVF---EILDNAIDESLAGYCTKINVTIYS---DNSISISDNGRGIP 93
HL+ E L NAI + A ++I VT+ ++++ DNG GI
Sbjct: 481 HLLQIVREALSNAIKHAQA---SEIKVTVSQNDGQVTLTVEDNGVGID 525
>gnl|CDD|223127 COG0049, RpsG, Ribosomal protein S7 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 30.2 bits (69), Expect = 2.3
Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 4/68 (5%)
Query: 360 KIPDPKFNSQTKNKLVSSEVR---KPVEEIIIKTLFDFLQENPGESKL-ICEKIIEAARS 415
+PDPK+NS +L++ +R K + E I+ FD +++ G++ L + EK IE +
Sbjct: 11 VLPDPKYNSVIVERLINKIMRDGKKSLAEKIVYGAFDIIEKKTGQNPLQVFEKAIENVKP 70
Query: 416 REAARKTR 423
RE + R
Sbjct: 71 REEVKSRR 78
>gnl|CDD|235947 PRK07152, nadD, putative nicotinate-nucleotide adenylyltransferase;
Validated.
Length = 342
Score = 31.1 bits (71), Expect = 2.4
Identities = 41/190 (21%), Positives = 72/190 (37%), Gaps = 43/190 (22%)
Query: 583 DIEEERY-MLKIAFKNVKLISIENGDIIKENYFFKLIDKYNKTIEIVHRLKQIIDISILS 641
E R MLK+A KN+ + + + +I ++N + TI+ + K+ +
Sbjct: 50 SNGEHRLNMLKLALKNLPKMEVSDFEIKRQNVSY--------TIDTIKYFKKKYPNDEIY 101
Query: 642 AIM-SDVILNLDTRENAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKK-KFLKKKN 699
I+ SD + +N E+ KK+ IV F + N N+KK L KN
Sbjct: 102 FIIGSDNLEKFKKWKNIEEILKKV----------QIVVFKRKKNINKKNLKKYNVLLLKN 151
Query: 700 YIIDINFINNKDYKKLVSIISTFKKIIGKGVIIQKSIGEKIKKYTANNFYKIINYLRNEA 759
I++ +K + + K+ Y NF YL +
Sbjct: 152 ---KNLNISSTKIRKG---------------NLLGKLDPKVNDYINENFL----YLEDIL 189
Query: 760 ENMVIKQRYK 769
++ + + RYK
Sbjct: 190 KSFLDEYRYK 199
>gnl|CDD|214359 CHL00085, ycf24, putative ABC transporter.
Length = 485
Score = 31.1 bits (71), Expect = 2.8
Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 12/82 (14%)
Query: 662 KKIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYIIDINFINNKDYKKLVSIIST 721
KK + L++ + E++ F++L LN +K+ N +D F + VSI +T
Sbjct: 96 KKKLNSLDEVDPELLDTFEKLGIS--LNEQKRL---ANVAVDAVFDS-------VSIGTT 143
Query: 722 FKKIIGKGVIIQKSIGEKIKKY 743
FK+ + K +I SI E I+KY
Sbjct: 144 FKEELAKAGVIFCSISEAIQKY 165
>gnl|CDD|139929 PRK13869, PRK13869, plasmid-partitioning protein RepA; Provisional.
Length = 405
Score = 30.8 bits (69), Expect = 3.1
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 378 EVRKPVEEIIIKTLFDFLQENPGESKLI-CEKIIEAARSREAARKTRELTRKKNLIDDI 435
+ R+P+ ++I T FD L PG +L+ E A S + R TR D++
Sbjct: 190 DTRRPLRDVIRPTYFDGLHLVPGNLELMEFEHTTPKALSDKGTRDGLFFTRVAQAFDEV 248
>gnl|CDD|223074 PHA03396, lef-9, late expression factor 9; Provisional.
Length = 493
Score = 30.7 bits (70), Expect = 3.3
Identities = 23/103 (22%), Positives = 45/103 (43%), Gaps = 20/103 (19%)
Query: 671 SNIEIIVEFDQLNNKYLLNIK--KKFLKKKNYIIDINFINNKDYKKLVSII--------- 719
++ +++ + ++L+N + +NI+ KKFL +N I D+ I + L+ +
Sbjct: 13 TSFDLLTDPNKLDNVFFINIEEFKKFL--RNLISDLKKIKINYFNSLIEQLISVYQECEL 70
Query: 720 -----STFKKIIGKGVIIQKSIGEKI--KKYTANNFYKIINYL 755
KII ++ + + KK N F I+YL
Sbjct: 71 RNEHTDLLSKIILATNVVVTDLPSNVFLKKLKTNKFTDNIDYL 113
>gnl|CDD|226475 COG3966, DltD, Protein involved in D-alanine esterification of
lipoteichoic acid and wall teichoic acid (D-alanine
transfer protein) [Cell envelope biogenesis, outer
membrane].
Length = 415
Score = 30.5 bits (69), Expect = 3.5
Identities = 27/117 (23%), Positives = 48/117 (41%), Gaps = 21/117 (17%)
Query: 609 IKENYFFKLIDKYNKTIEIVHRLKQIIDISILSAIMSDVILNLDTRENAEQFAKKIIKKL 668
+++ F K I LK + D + + E+ A +I KK
Sbjct: 210 ERKDLLFSATSKSGPLKHIKKALKDLPDQF--------------SYKELEKLAVEIGKKS 255
Query: 669 NDSNIEIIVEFDQLNNK-YLLNIKKKFLKKKNYIIDINFINNKDYKKLVSIISTFKK 724
+N F + NK Y+ IK K+ K K+ + ++ + +Y+ L ++ TFKK
Sbjct: 256 TTNN-----PF-GIKNKYYIKKIKPKYKKLKDSQKNFTYLESPEYQDLQLLLDTFKK 306
>gnl|CDD|233238 TIGR01029, rpsG_bact, ribosomal protein S7, bacterial/organelle.
This model describes the bacterial and organellar branch
of the ribosomal protein S7 family (includes prokaroytic
S7 and eukaryotic S5). The eukaryotic and archaeal
branch is described by model TIGR01028 [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 154
Score = 29.6 bits (67), Expect = 4.0
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 362 PDPKFNSQTKNKLVS---SEVRKPVEEIIIKTLFDFLQENPGESKLIC-EKIIEAAR 414
PDP + S NK ++ + +K + E I+ F+ + + GE L E+ +E +
Sbjct: 12 PDPVYGSVLLNKFINRVMKDGKKSLAESIVYKAFERIAKKTGEDPLEVFEQALENVK 68
>gnl|CDD|221018 pfam11186, DUF2972, Protein of unknown function (DUF2972). Some
members in this family of proteins with unknown function
are annotated as sugar transferase proteins, however
this cannot be confirmed.
Length = 197
Score = 29.6 bits (67), Expect = 4.9
Identities = 20/99 (20%), Positives = 41/99 (41%), Gaps = 6/99 (6%)
Query: 663 KIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYIID--INFINNKDYKKLVSIIS 720
K + + F ++ Y+ +I K+ K N I+D I I +D++ L
Sbjct: 57 KENNISITKTNRVFIIFLEIKENYI-DITKELFNK-NDILDNIIICIKKEDFEILKQDEK 114
Query: 721 TFKKIIGKGVIIQKSIGEKIKKYTANNFY--KIINYLRN 757
FKKI +++ +++K + ++ YL+
Sbjct: 115 LFKKIKKYLKKFIEALEKQVKIEESKKLKEKDVLEYLKE 153
>gnl|CDD|236359 PRK08974, PRK08974, long-chain-fatty-acid--CoA ligase; Validated.
Length = 560
Score = 30.4 bits (69), Expect = 5.2
Identities = 11/41 (26%), Positives = 25/41 (60%), Gaps = 2/41 (4%)
Query: 707 INNKDYKKLVSIISTFKKIIGKGVIIQKSIGEKIKKYTANN 747
+NN+++++L S+ K +G G+ +Q+++ E+ K T
Sbjct: 314 LNNEEFQELD--FSSLKLSVGGGMAVQQAVAERWVKLTGQY 352
>gnl|CDD|219694 pfam08008, Viral_cys_rich, Viral cysteine rich. Members of this
family are polydna viral proteins that contain a
cysteine rich motif. Some members of this family have
multiple copies of this domain.
Length = 86
Score = 28.1 bits (63), Expect = 5.3
Identities = 10/37 (27%), Positives = 23/37 (62%), Gaps = 7/37 (18%)
Query: 656 NAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKK 692
N + + ++K+LND+N F++L+N+Y +++
Sbjct: 54 NLTLYLE-LVKQLNDTN------FEELSNQYWKDLQP 83
>gnl|CDD|173015 PRK14550, rnhB, ribonuclease HII; Provisional.
Length = 204
Score = 29.5 bits (66), Expect = 5.3
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 189 DTNKQGTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERI 239
D+ K K F++++KI ++ E + ++KK E+ L G C+ L + I
Sbjct: 39 DSKKLSPKKRFFLEDKIKTHGEVGFFVVKKSANEIDSLGLGACLKLAIQEI 89
>gnl|CDD|223138 COG0060, IleS, Isoleucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 933
Score = 30.3 bits (69), Expect = 5.7
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 451 LCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLN-IEKARFEKIILSE 499
L + E D V+ R++A+L LR V +E AR EK+I S
Sbjct: 789 LEDWP--EVDEELIDVEAALAARWEALLKLRDPVNKALEAARLEKVIGSS 836
>gnl|CDD|202547 pfam03129, HGTP_anticodon, Anticodon binding domain. This domain
is found in histidyl, glycyl, threonyl and prolyl tRNA
synthetases it is probably the anticodon binding domain.
Length = 93
Score = 27.9 bits (63), Expect = 5.9
Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 10/60 (16%)
Query: 647 VILNLDTRENAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKF----LKKKNYII 702
V++ L ++ E +A+K+ ++L ++ I VE D N + KKF L + +
Sbjct: 3 VVIPLGEKDELEDYAQKLAEELREAGIR--VELDDRNES----LGKKFRDADLIGIPFRL 56
>gnl|CDD|236846 PRK11100, PRK11100, sensory histidine kinase CreC; Provisional.
Length = 475
Score = 29.8 bits (68), Expect = 6.0
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 5/40 (12%)
Query: 57 ILDNAIDESLAGYCTKINVTIYSDNS---ISISDNGRGIP 93
+LDNAID S G I ++ D +S+ D G GIP
Sbjct: 376 LLDNAIDFSPEGGT--ITLSAEVDGEQVALSVEDQGPGIP 413
>gnl|CDD|235319 PRK04914, PRK04914, ATP-dependent helicase HepA; Validated.
Length = 956
Score = 29.8 bits (68), Expect = 6.9
Identities = 22/94 (23%), Positives = 42/94 (44%), Gaps = 22/94 (23%)
Query: 357 LSIKIPDPKFNSQ-------TKNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKI 409
LS ++ N Q T +KLV + V++ + +++ K E E++ ++
Sbjct: 842 LSAQVEFESLNRQLSAVNRHTASKLVKA-VQQDIHKLLQKA------EAQAEAQA--REL 892
Query: 410 IEAARSREAARKTRELTRKKNL------IDDIEL 437
IE A+ + + EL+R + L I D E+
Sbjct: 893 IEQAKQEADEKLSAELSRLEALKAVNPNIRDDEI 926
>gnl|CDD|134567 PRK01530, PRK01530, hypothetical protein; Reviewed.
Length = 105
Score = 27.9 bits (62), Expect = 7.4
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 679 FDQLNNKYLLNIKKKFLKKKNYIIDINFINNKDYKKL 715
++ +++ LLN+K K K+N I + INN Y KL
Sbjct: 7 YNSSSHQALLNLKVKPNAKQNLISNFVIINNIPYLKL 43
>gnl|CDD|236462 PRK09303, PRK09303, adaptive-response sensory kinase; Validated.
Length = 380
Score = 29.5 bits (67), Expect = 8.1
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 6/42 (14%)
Query: 58 LDNAIDESLAGYCTKINVTIYSDNS----ISISDNGRGIPID 95
LDNAI + G I +++ + +SI D G GIP +
Sbjct: 281 LDNAIKYTPEG--GTITLSMLHRTTQKVQVSICDTGPGIPEE 320
>gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP).
Archaeal RNA polymerase (RNAP), like bacterial RNAP, is
a large multi-subunit complex responsible for the
synthesis of all RNAs in the cell. The relative
positioning of the RNAP core is highly conserved between
archaeal RNAP and the three classes of eukaryotic RNAPs.
In archaea, the largest subunit is split into two
polypeptides, A' and A'', which are encoded by separate
genes in an operon. Sequence alignments reveal that the
archaeal A'' subunit corresponds to the C-terminal
one-third of the RNAPII largest subunit (Rpb1). In
subunit A'', several loops in the jaw domain are
shorter. The RNAPII Rpb1 interacts with the
second-largest subunit (Rpb2) to form the DNA entry and
RNA exit channels in addition to the catalytic center of
RNA synthesis.
Length = 363
Score = 29.5 bits (67), Expect = 8.3
Identities = 25/113 (22%), Positives = 43/113 (38%), Gaps = 28/113 (24%)
Query: 654 RENAEQFAKKIIK-KLND---------SNIEIIVEFDQ--LNNKYL-----LN-IKKKFL 695
RE AE+ A+KI + L + N+ I +E D+ L ++ + L I+K
Sbjct: 107 REKAEEVARKIEETTLENLAEDISIDLFNMRITIELDEEMLEDRGITVDDVLKAIEKLKK 166
Query: 696 KKK----NYIIDINFINNKDYKKLVSIISTFKKIIGKG------VIIQKSIGE 738
K + + + K+L + KG VI++K E
Sbjct: 167 GKVGEEGDVTLIVLKAEEPSIKELRKLAEKILNTKIKGIKGIKRVIVRKEEDE 219
>gnl|CDD|220920 pfam10977, DUF2797, Protein of unknown function (DUF2797). This
family of proteins has no known function.
Length = 233
Score = 29.2 bits (66), Expect = 8.5
Identities = 25/85 (29%), Positives = 40/85 (47%), Gaps = 4/85 (4%)
Query: 409 IIEAARSREAARKTRELTRKKNLIDDIELSTKLADCQEKNP-ELCELYIVEGDSAGGSVK 467
I+E A A KT K L++D++L+ + A E+ EL EL + G+ A +
Sbjct: 117 IVEVALKAHVADKTNWRKMLKGLVEDVDLAAERARLLEEIAEELKELRLEYGEDAIEEDE 176
Query: 468 QGRDRRFQAVL--PLRGKVLNIEKA 490
+ VL P + K LN++K
Sbjct: 177 AVFSINY-PVLEYPTKVKSLNLDKT 200
>gnl|CDD|99904 cd00133, PTS_IIB, PTS_IIB: subunit IIB of enzyme II (EII) is the
central energy-coupling domain of the
phosphoenolpyruvate:carbohydrate phosphotransferase
system (PTS). In the multienzyme PTS complex, EII is a
carbohydrate-specific permease consisting of two
cytoplasmic domains (IIA and IIB) and a transmembrane
channel IIC domain. The IIB domain fold includes a
central four-stranded parallel open twisted beta-sheet
flanked by alpha-helices on both sides. The seven major
PTS systems with this IIB fold include
chitobiose/lichenan, ascorbate, lactose, galactitol,
mannitol, fructose, and a sensory system with similarity
to the bacterial bgl system. The PTS is found only in
bacteria, where it catalyzes the transport and
phosphorylation of numerous monosaccharides,
disaccharides, polyols, amino sugars, and other sugar
derivatives. The four proteins (domains) forming the PTS
phosphorylation cascade (EI, HPr, EIIA, and EIIB), can
phosphorylate or interact with numerous non-PTS proteins
thereby regulating their activity.
Length = 84
Score = 27.2 bits (61), Expect = 8.7
Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 11/69 (15%)
Query: 661 AKKIIKKLNDSNIEIIVEFDQLNNKYLLN----------IKKKFLKKKNYIIDINFINNK 710
A+K+ K + IE+ VE L+ L + +FL K ++ +N K
Sbjct: 17 AEKLEKAAKELGIEVKVEAQGLSEVIDLADADLIISTVPLAARFLGKPVIVVSP-LLNEK 75
Query: 711 DYKKLVSII 719
D +K++ +
Sbjct: 76 DGEKILEKL 84
>gnl|CDD|215933 pfam00466, Ribosomal_L10, Ribosomal protein L10.
Length = 100
Score = 27.5 bits (62), Expect = 9.1
Identities = 10/45 (22%), Positives = 22/45 (48%)
Query: 653 TRENAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKK 697
TRE E+ ++ + L + ++V++ L L ++KK +
Sbjct: 2 TREKKEEIVAELKELLKEYKSVVVVDYRGLTVAQLTELRKKLREA 46
>gnl|CDD|240419 PTZ00440, PTZ00440, reticulocyte binding protein 2-like protein;
Provisional.
Length = 2722
Score = 29.8 bits (67), Expect = 9.3
Identities = 36/164 (21%), Positives = 67/164 (40%), Gaps = 18/164 (10%)
Query: 618 IDKYNKTIE-IVHRLKQIIDISILSAIMSDVILNLDTRENAEQFAKKIIKKLNDSNIEII 676
I+ + I+ + ++ +I L M + I N K I LND II
Sbjct: 538 IEGLIELIKYYLQSIETLIKDEKLKRSMKNDIKNKIKYIEENVDHIKDIISLNDEIDNII 597
Query: 677 VEFDQLNNKYLLNIKKKFLKKKNYIIDINFINNK----DYKKLVSIISTF---------- 722
+ ++L N+ L N +K +K + + +I NK D ++L+ +S F
Sbjct: 598 QQIEELINEALFNKEKFINEKNDLQEKVKYILNKFYKGDLQELLDELSHFLDDHKYLYHE 657
Query: 723 KKIIGKGVIIQKSIG---EKIKKYTANNFYKIINYLRNEAENMV 763
K + + EK++ ++N II L+ E +N++
Sbjct: 658 AKSKEDLQTLLNTSKNEYEKLEFMKSDNIDNIIKNLKKELQNLL 701
>gnl|CDD|181988 PRK09609, PRK09609, hypothetical protein; Provisional.
Length = 312
Score = 29.2 bits (66), Expect = 9.4
Identities = 14/65 (21%), Positives = 26/65 (40%), Gaps = 1/65 (1%)
Query: 586 EERYMLKIA-FKNVKLISIENGDIIKENYFFKLIDKYNKTIEIVHRLKQIIDISILSAIM 644
+RY KI K ++EN + K + I K + + + + + S I
Sbjct: 114 IKRYDNKIFKQKEQYDFALENPNSEKIQKIKQKIILLEKKKKKLEKTNEEKSLLNFSWIA 173
Query: 645 SDVIL 649
+ +IL
Sbjct: 174 ALIIL 178
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.139 0.387
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 43,525,665
Number of extensions: 4606557
Number of successful extensions: 5840
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5599
Number of HSP's successfully gapped: 387
Length of query: 833
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 728
Effective length of database: 6,280,432
Effective search space: 4572154496
Effective search space used: 4572154496
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 63 (28.1 bits)