RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 005028
(718 letters)
>gnl|CDD|235542 PRK05644, gyrB, DNA gyrase subunit B; Validated.
Length = 638
Score = 1070 bits (2771), Expect = 0.0
Identities = 375/649 (57%), Positives = 479/649 (73%), Gaps = 16/649 (2%)
Query: 70 ENPVSKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASN 129
+ ++ Y + QIQVLEGLEAVRKRP MYIGSTG RGLHHLVYEI+DN++DEA AGY +
Sbjct: 1 KEEKAQEYDASQIQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDH 60
Query: 130 IEVALLADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLH 189
IEV + D S++V DNGRGIP+D+HP T K A+E VLTVLHAGGKFGG GY VSGGLH
Sbjct: 61 IEVTINEDGSITVTDNGRGIPVDIHPKTGKPAVEVVLTVLHAGGKFGGG--GYKVSGGLH 118
Query: 190 GVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPD 249
GVG+SVVNALS LEV V RDG Y+Q+Y RG PVT L + D GT + F PD
Sbjct: 119 GVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEV----IGETDETGTTVTFKPD 174
Query: 250 KQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQW 309
++F T +FD++T+A R+RELAFLN L I L D + + + + GG++EYV++
Sbjct: 175 PEIFET-TEFDYDTLATRLRELAFLNKGLKITLT--DEREGEEKEETFHYEGGIKEYVEY 231
Query: 310 LNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKA 368
LN +K+PLH + + F + DGI +++A+Q+ D YS+ +L +AN+I T +GGTH EG K
Sbjct: 232 LNRNKEPLHEEPIYFEGEKDGIEVEVAMQYN-DGYSENILSFANNINTHEGGTHEEGFKT 290
Query: 369 SLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRK 428
+LTR +N +K+K +K+KD +L+GE VREGLT +ISV+ P P+FEGQTKT+LGN EVR
Sbjct: 291 ALTRVINDYARKNKLLKEKDDNLTGEDVREGLTAVISVKHPEPQFEGQTKTKLGNSEVRG 350
Query: 429 VVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKL 488
+VD V E L+E+LE +P+V I+ K++ A +A AA++AR+L R+KS L SSSLPGKL
Sbjct: 351 IVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALESSSLPGKL 410
Query: 489 ADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEI 548
ADCSS PEESE++IVEGDSAGGSAKQGRDRRFQAILPLRGKILNVE+ + KNEEI
Sbjct: 411 ADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEI 470
Query: 549 QNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCI 608
+ LI ALG G+ G+DF LRYHKIII+TDADVDGAHIRTLLLTFFYRY + L + G +
Sbjct: 471 RALITALGTGI-GDDFDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYV 529
Query: 609 YVGVPPLYKVERGKQVQYCYDDAELKKVKSSFP--SNALYSIQRFKGLGEMMPVQLWETT 666
Y+ PPLYK+++G + +Y Y D EL ++ + N Y IQR+KGLGEM P QLWETT
Sbjct: 530 YIAQPPLYKIKKGGK-EYAYSDEELDEILAELKLKGNPKYGIQRYKGLGEMNPEQLWETT 588
Query: 667 LNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ-NAANLVNLD 714
++PE R L Q+ IEDAAEA+ +FS LMG V+ R+E I+ NA + NLD
Sbjct: 589 MDPETRTLLQVTIEDAAEADEIFSILMGDDVEPRREFIEENAKYVRNLD 637
>gnl|CDD|223265 COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), B subunit [DNA replication,
recombination, and repair].
Length = 635
Score = 941 bits (2434), Expect = 0.0
Identities = 355/641 (55%), Positives = 459/641 (71%), Gaps = 15/641 (2%)
Query: 77 YGSEQIQVLEGLEAVRKRPAMYIGSTGP-RGLHHLVYEILDNAVDEAQAGYASNIEVALL 135
Y + IQVLEGLEAVRKRP MYIGSTG RGLHHLV+E++DN++DEA AGYA I+V L
Sbjct: 6 YDASSIQVLEGLEAVRKRPGMYIGSTGDGRGLHHLVWEVVDNSIDEALAGYADRIDVTLH 65
Query: 136 ADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSV 195
D S+SV DNGRGIP+D+HP SA+E + TVLHAGGKF S Y VSGGLHGVG+SV
Sbjct: 66 EDGSISVEDNGRGIPVDIHPKEKVSAVEVIFTVLHAGGKFDNDS--YKVSGGLHGVGVSV 123
Query: 196 VNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTT 255
VNALS LEV V RDG Y Q++ RG PVT L V+ + GT++RF PD ++F
Sbjct: 124 VNALSTWLEVEVKRDGKIYRQRFERGVPVTPL--EVIGSTDTKKTGTKVRFKPDPEIFGE 181
Query: 256 AIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKK 315
+FD+ + R+RELAFLN + I L E + EK E+ + GGL++YV++LN K
Sbjct: 182 -TEFDYEILKRRLRELAFLNKGVKITLTDERTGEEKK---EFHYEGGLKDYVEYLNKGKT 237
Query: 316 PLHDVVGFRKD-VDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTL 374
PLH+ + + DGI +++ALQW +D YS+ +L + N+I T +GGTH G +++LTR +
Sbjct: 238 PLHEEIFYFNGEKDGIAVEVALQW-NDGYSENILSFVNNIPTREGGTHEAGFRSALTRAI 296
Query: 375 NSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSV 434
N KK +K+ D L+G+ +REGLT +ISV++P+P+FEGQTK +LGN EVR +V++ V
Sbjct: 297 NEYAKKKNLLKEGD--LTGDDIREGLTAVISVKIPDPQFEGQTKEKLGNSEVRSIVEKLV 354
Query: 435 QEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSST 494
E + +LE +P I+ K+++A KA AA++AR+L R+KS L LPGKLADC+S
Sbjct: 355 SEAFSLFLEENPQEAKKIVEKAIAAAKAREAARKARELTRRKSALDIPGLPGKLADCTSK 414
Query: 495 TPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRA 554
PE+SE+F+VEGDSAGGSAKQGRDR FQAILPLRGKILNVE+ + KNEEIQ +I A
Sbjct: 415 DPEKSELFLVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIQTIITA 474
Query: 555 LGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPP 614
LG G+ G+DF E LRYHKIII+TDADVDGAHIRTLLLTFFYRY L + G +Y+ PP
Sbjct: 475 LGTGI-GKDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMPPLIENGHVYIAQPP 533
Query: 615 LYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRML 674
LYKV++GK+ Y YDD EL+K+ Y IQR+KGLGEM P QLWETT++PE R L
Sbjct: 534 LYKVKKGKKTFYAYDDEELEKLLERLGKKKGYEIQRYKGLGEMNPDQLWETTMDPETRRL 593
Query: 675 KQLVIEDAAEANVVFSSLMGARVDTRKELIQ-NAANLVNLD 714
Q+ IEDA EA+ +FS+LMG +V+ R+ I+ NA + NLD
Sbjct: 594 LQVTIEDADEADEIFSTLMGDKVEPRRNFIEENALFVENLD 634
>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 = 915 bits (2367), Expect = 0.0
Identities = 351/664 (52%), Positives = 468/664 (70%), Gaps = 37/664 (5%)
Query: 77 YGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLA 136
Y + I+VLEGLEAVRKRP MYIGSTG GLHHLVYE++DN++DEA AGY I V +
Sbjct: 1 YDASSIKVLEGLEAVRKRPGMYIGSTGETGLHHLVYEVVDNSIDEAMAGYCDTINVTIND 60
Query: 137 DNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVV 196
D SV+V DNGRGIP+D+HP SA+E VLTVLHAGGKF S Y VSGGLHGVG+SVV
Sbjct: 61 DGSVTVEDNGRGIPVDIHPEEGISAVEVVLTVLHAGGKFDKDS--YKVSGGLHGVGVSVV 118
Query: 197 NALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTA 256
NALSE LEVTV+RDG Y Q++ RG P+ L V+ + GT +RFWPD ++F T
Sbjct: 119 NALSEWLEVTVFRDGKIYRQEFERGIPLGPL--EVVGET--KKTGTTVRFWPDPEIFET- 173
Query: 257 IQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKP 316
+FD + +A R+RELAFLN + I+L E K+ + + GG++ +V++LN +K+P
Sbjct: 174 TEFDFDILAKRLRELAFLNSGVKISLEDERDGKGKS--VTFHYEGGIKSFVKYLNRNKEP 231
Query: 317 LH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLN 375
LH +++ + + +GI +++ALQW D YS+ +L + N+I T +GGTH+EG +++LTR +N
Sbjct: 232 LHEEIIYIKGEKEGIEVEVALQWN-DGYSENILSFVNNINTREGGTHLEGFRSALTRVIN 290
Query: 376 SLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQ 435
S K +K +K+ +L+GE +REGLT +ISV+VP+P+FEGQTKT+LGN EVR +V+ V
Sbjct: 291 SYAKNNKLLKESKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLVY 350
Query: 436 EYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTT 495
E LTE+ E +P +I+ K++ A +A AA++AR+L R+KS L S LPGKLADCSS
Sbjct: 351 EKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKD 410
Query: 496 PEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRAL 555
P +SE++IVEGDSAGGSAKQGRDR+FQAILPLRGKILNVE+ + N+EI +I AL
Sbjct: 411 PSKSELYIVEGDSAGGSAKQGRDRKFQAILPLRGKILNVEKARLDKILSNQEIGAIITAL 470
Query: 556 GLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPL 615
G G+ G+DF E LRYHKIII+TDADVDG+HIRTLLLTFFYRY + L + G +Y+ PPL
Sbjct: 471 GCGI-GKDFDLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPL 529
Query: 616 YKVERGKQVQ---------------------YCYDDAELKKVKSSFPSNAL---YSIQRF 651
YKV++GK+ + Y Y D E ++ K+ P + IQR+
Sbjct: 530 YKVKKGKKERYIKDDKEKELVGEALEDLRALYIYSDKEKEEAKTQIPVHEGRKGIEIQRY 589
Query: 652 KGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ-NAANL 710
KGLGEM QLWETT++PE R L ++ IEDA EA+ +FS+LMG V+ R+E I+ NA ++
Sbjct: 590 KGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEPRREFIEANALDV 649
Query: 711 VNLD 714
NLD
Sbjct: 650 KNLD 653
>gnl|CDD|235501 PRK05559, PRK05559, DNA topoisomerase IV subunit B; Reviewed.
Length = 631
Score = 851 bits (2202), Expect = 0.0
Identities = 304/644 (47%), Positives = 404/644 (62%), Gaps = 20/644 (3%)
Query: 74 SKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVA 133
+ Y ++ I+VLEGLE VRKRP MYIGST RGLHHLV E++DN+VDEA AG+ IEV
Sbjct: 5 TNNYNADSIEVLEGLEPVRKRPGMYIGSTDTRGLHHLVQEVIDNSVDEALAGHGKRIEVT 64
Query: 134 LLADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGL 193
L AD SVSV DNGRGIP+ +HP KS +E +LT LHAGGKF + Y SGGLHGVG+
Sbjct: 65 LHADGSVSVRDNGRGIPVGIHPEEGKSGVEVILTKLHAGGKFSNKA--YKFSGGLHGVGV 122
Query: 194 SVVNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVF 253
SVVNALS LEV V RDG Y Q++ G PV L V+ K + GTR+RFWPD ++F
Sbjct: 123 SVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPL--EVVGTAGKRKTGTRVRFWPDPKIF 180
Query: 254 TTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTD 313
+ +F + R+R AFL P LTI L E + + GL++Y+ LN
Sbjct: 181 DSP-KFSPERLKERLRSKAFLLPGLTITLNDERERQ------TFHYENGLKDYLAELNEG 233
Query: 314 KKPLHD--VVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLT 371
K+ L + V F + +G ++ ALQW +D + + Y N I T GGTH G + L
Sbjct: 234 KETLPEEFVGSFEGEAEGEAVEWALQW-TDEGGENIESYVNLIPTPQGGTHENGFREGLL 292
Query: 372 RTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVD 431
+ + +K + K L GE VREGL ++SV++P P+FEGQTK +LG+ E R+ V
Sbjct: 293 KAVREFAEKRNLLP-KGKKLEGEDVREGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVS 351
Query: 432 QSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADC 491
V++ +L +P++ + + K A+KAA A RA V++K +LPGKLADC
Sbjct: 352 GVVKDAFDLWLNQNPELAEKLAEK---AIKAAQARLRAAKKVKRKKKTSGPALPGKLADC 408
Query: 492 SSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNL 551
+S PE +E+F+VEGDSAGGSAKQ RDR FQAILPLRGKILN + NEEI ++
Sbjct: 409 TSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDI 468
Query: 552 IRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVG 611
I A+G+G G+ F E LRY KIII+TDADVDGAHI TLLLTFFYR+ L + G +Y+
Sbjct: 469 IVAIGIGP-GDSFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIA 527
Query: 612 VPPLYKVERGKQVQYCYDDAELKKV-KSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPE 670
+PPLY+V++GK+ Y D+ E +++ K IQRFKGLGEM P QLWETT++PE
Sbjct: 528 LPPLYRVDKGKKKIYALDEEEKEELLKKLGKKGGKPEIQRFKGLGEMNPDQLWETTMDPE 587
Query: 671 QRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQNAANLVNLD 714
R L ++ I+DA E + LMG + + R+E I+ + +
Sbjct: 588 TRRLVRVTIDDAEETEKLVDMLMGKKAEPRREWIEENGDFAEEE 631
>gnl|CDD|237860 PRK14939, gyrB, DNA gyrase subunit B; Provisional.
Length = 756
Score = 843 bits (2182), Expect = 0.0
Identities = 292/571 (51%), Positives = 396/571 (69%), Gaps = 22/571 (3%)
Query: 71 NPVSKTYGSEQIQVLEGLEAVRKRPAMYIGSTG-PRGLHHLVYEILDNAVDEAQAGYASN 129
+ +S +YG+ I+VL+GL+AVRKRP MYIG T GLHH+VYE++DNA+DEA AG+ +
Sbjct: 1 SMMSNSYGASSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVYEVVDNAIDEALAGHCDD 60
Query: 130 IEVALLADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLH 189
I V + AD SVSV+DNGRGIP D+HP SA E ++TVLHAGGKF +S Y VSGGLH
Sbjct: 61 ITVTIHADGSVSVSDNGRGIPTDIHPEEGVSAAEVIMTVLHAGGKFDQNS--YKVSGGLH 118
Query: 190 GVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPD 249
GVG+SVVNALSE LE+T+ RDG + Q++ G PV L V D+ GT +RFWP
Sbjct: 119 GVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKV----VGETDKTGTEVRFWPS 174
Query: 250 KQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQW 309
++F +FD++ +A R+RELAFLN + I L+ E E E+ + GG++ +V++
Sbjct: 175 PEIFEN-TEFDYDILAKRLRELAFLNSGVRIRLKDERDGKE----EEFHYEGGIKAFVEY 229
Query: 310 LNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKA 368
LN +K PLH ++ F + DGI +++ALQW +D+Y + +L + N+I DGGTH+ G +A
Sbjct: 230 LNRNKTPLHPNIFYFSGEKDGIGVEVALQW-NDSYQENVLCFTNNIPQRDGGTHLAGFRA 288
Query: 369 SLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRK 428
+LTRT+N+ +K K +SL+G+ REGLT ++SV+VP+P+F QTK +L + EVR
Sbjct: 289 ALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRP 348
Query: 429 VVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKL 488
V+ V E L+E+LE +P+ I+ K + A +A AA++AR+L R+K L + LPGKL
Sbjct: 349 AVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKL 408
Query: 489 ADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVER----KDEAAMYK 544
ADC P SE+++VEGDSAGGSAKQGRDR+FQAILPL+GKILNVE+ K M
Sbjct: 409 ADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDK----MLS 464
Query: 545 NEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFD 604
++EI LI ALG G+ ++F + LRYHKIII+TDADVDG+HIRTLLLTFFYR L +
Sbjct: 465 SQEIGTLITALGCGIGRDEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIE 524
Query: 605 EGCIYVGVPPLYKVERGKQVQYCYDDAELKK 635
G +Y+ PPLYKV++GKQ QY DD L
Sbjct: 525 RGHLYIAQPPLYKVKKGKQEQYLKDDEALDD 555
Score = 103 bits (260), Expect = 7e-23
Identities = 41/69 (59%), Positives = 53/69 (76%), Gaps = 1/69 (1%)
Query: 647 SIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ- 705
SIQR+KGLGEM P QLWETT++PE R L Q+ IEDA A+ +F++LMG V+ R+E I+
Sbjct: 687 SIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIEDAIAADEIFTTLMGDEVEPRREFIEE 746
Query: 706 NAANLVNLD 714
NA N+ NLD
Sbjct: 747 NALNVANLD 755
>gnl|CDD|214659 smart00433, TOP2c, TopoisomeraseII. Eukaryotic DNA topoisomerase
II, GyrB, ParE.
Length = 594
Score = 770 bits (1991), Expect = 0.0
Identities = 313/609 (51%), Positives = 406/609 (66%), Gaps = 20/609 (3%)
Query: 106 GLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHPATNKSALETV 165
GLHHLV EI+DNA DEA AGY I+V + DNS+SV DNGRGIP+++HP K A E +
Sbjct: 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVI 60
Query: 166 LTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSR-GKPV 224
TVLHAGGKF + Y VSGGLHGVG SVVNALS EV V RDG EY Q +S GKP+
Sbjct: 61 FTVLHAGGKFDDDA--YKVSGGLHGVGASVVNALSTEFEVEVARDGKEYKQSFSNNGKPL 118
Query: 225 TTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRK 284
+ ++ KD GT++ F PD ++F D + R+RELAFLN + I L
Sbjct: 119 SEP--KIIGDTKKD--GTKVTFKPDLEIFGMTTDDDFELLKRRLRELAFLNKGVKITLND 174
Query: 285 EDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFR-KDVDGITIDLALQWCSDAY 343
E SD EK + F GG+++YV+ LN +K+ L + + D I +++A Q+ +D Y
Sbjct: 175 ERSDEEK----TFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQY-TDGY 229
Query: 344 SDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCI 403
S+ ++ + N+I T +GGTH G K +LTR +N KK K K K+ ++ GE VREGLT
Sbjct: 230 SENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKK--KLKEKNIKGEDVREGLTAF 287
Query: 404 ISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAA 463
ISV++P P+FEGQTK +LG EVR V++ V E L +LE +P I+ K L A KA
Sbjct: 288 ISVKIPEPQFEGQTKEKLGTSEVRFGVEKIVSECLLSFLEENPVEASKIVEKVLLAAKAR 347
Query: 464 LAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQA 523
AAK+AR+L R K L S SLPGKLAD SS P++ E+F+VEGDSAGGSAK GRDR FQA
Sbjct: 348 AAAKKARELTR-KKKLSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAKSGRDRDFQA 406
Query: 524 ILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVD 583
ILPLRGKILNVE+ + KNEEIQ LI ALGLG+ G+DF E LRY KIII+TDADVD
Sbjct: 407 ILPLRGKILNVEKASLDKILKNEEIQALITALGLGI-GKDFDIEKLRYGKIIIMTDADVD 465
Query: 584 GAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCY---DDAELKKVKSSF 640
G+HI+ LLLTFFYRY L + G +Y+ +PPLYKV +GK+ D K ++ +
Sbjct: 466 GSHIKGLLLTFFYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVYSFYSLDEYEKWLEKTE 525
Query: 641 PSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTR 700
+ + Y IQR+KGLGEM QLWETT++PE+R L + ++DA EA+++FS+LMG +V+ R
Sbjct: 526 GNKSKYEIQRYKGLGEMNADQLWETTMDPERRTLLFVTLDDADEADLIFSALMGDKVEPR 585
Query: 701 KELIQNAAN 709
KE I+ A
Sbjct: 586 KEWIEENAP 594
>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 = 677 bits (1748), Expect = 0.0
Identities = 310/653 (47%), Positives = 430/653 (65%), Gaps = 23/653 (3%)
Query: 73 VSKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEV 132
++ Y ++ I++LEGL+AVRKRP MYIGST +GLHHLV+EI+DN+VDE AGYA NI V
Sbjct: 1 MASKYNADAIKILEGLDAVRKRPGMYIGSTDSKGLHHLVWEIVDNSVDEVLAGYADNITV 60
Query: 133 ALLADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVG 192
L DNS++V D+GRGIP +H N S +ETV TVLHAGGKF GY +GGLHGVG
Sbjct: 61 TLHKDNSITVQDDGRGIPTGIHQDGNISTVETVFTVLHAGGKFD--QGGYKTAGGLHGVG 118
Query: 193 LSVVNALSESLEVTVWRDGMEYHQKYSR-GKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQ 251
SVVNALS LEVTV RDG Y Q++ GK V +L + + + GT + F PD
Sbjct: 119 ASVVNALSSWLEVTVKRDGQIYQQRFENGGKIVQSLK----KIGTTKKTGTLVHFHPDPT 174
Query: 252 VFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLN 311
+F T QF+ N I R++E AFL KL + +D N+ +F+ GL ++V ++N
Sbjct: 175 IFKTT-QFNSNIIKERLKESAFLLKKLKLTF----TDKRTNKTTVFFYENGLVDFVDYIN 229
Query: 312 TDKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLT 371
K+ L V F + +GI +++A Q+ +D S+ +L +ANS++T +GGTH G K ++T
Sbjct: 230 ETKETLSQVTYFEGEKNGIEVEVAFQF-NDGDSENILSFANSVKTKEGGTHENGFKLAIT 288
Query: 372 RTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVP--NPEFEGQTKTRLGNPEVRKV 429
+NS +K +K+KD +L G +REGL+ IISVR+P +FEGQTK++L +PE R V
Sbjct: 289 DVINSYARKYNLLKEKDKNLEGSDIREGLSAIISVRIPEELIQFEGQTKSKLFSPEARNV 348
Query: 430 VDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSS--SLPGK 487
VD+ VQ++L +LE + + ++ K++ A A AAK+AR+ + + L GK
Sbjct: 349 VDEIVQDHLFFFLEENNNDAKLLIDKAIKARDAKEAAKKAREEKKSGKKPKKEKGILSGK 408
Query: 488 LADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEE 547
L S P ++E+F+VEGDSAGGSAKQGRDR+FQAILPLRGK+LNVE+ A + KNEE
Sbjct: 409 LTPAQSKNPAKNELFLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKAKLADILKNEE 468
Query: 548 IQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGC 607
I +I +G G+ G DF + L+Y KIII+TDAD DGAHI+ LLLTFFYRY + L + G
Sbjct: 469 INTIIFCIGTGI-GADFSIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELGH 527
Query: 608 IYVGVPPLYKVER--GKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWET 665
+Y+ +PPLYK+ + GK+V+Y + D EL+ VK + Y++QR+KGLGEM QLWET
Sbjct: 528 VYIALPPLYKLSKKDGKKVKYAWSDLELESVKKKLKN---YTLQRYKGLGEMNADQLWET 584
Query: 666 TLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQNAANLVNLDHLDI 718
T+NPE R L ++ I+D A A ++LMG +V+ RK+ I+ N + L I
Sbjct: 585 TMNPETRTLVRVKIDDLARAERQINTLMGDKVEPRKKWIEANINFSVEEELQI 637
>gnl|CDD|240272 PTZ00109, PTZ00109, DNA gyrase subunit b; Provisional.
Length = 903
Score = 566 bits (1460), Expect = 0.0
Identities = 263/642 (40%), Positives = 368/642 (57%), Gaps = 94/642 (14%)
Query: 75 KTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVAL 134
Y ++ I VLEGLEAVRKRP MYIG+T +GLH L++EILDN+VDE AG + I V L
Sbjct: 98 SEYDADDIVVLEGLEAVRKRPGMYIGNTDEKGLHQLLFEILDNSVDEYLAGECNKITVVL 157
Query: 135 LADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKF------------------- 175
D SV ++DNGRGIP D+ T KS LETVLTVLH+GGKF
Sbjct: 158 HKDGSVEISDNGRGIPCDVSEKTGKSGLETVLTVLHSGGKFQDTFPKNSRSDKSEDKNDT 217
Query: 176 -------------------GGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQ 216
SS Y S GLHGVGLSVVNALS L+V V++ G Y
Sbjct: 218 KSSKKGKSSHVKGPKEAKEKESSQMYEYSSGLHGVGLSVVNALSSFLKVDVFKGGKIYSI 277
Query: 217 KYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPD-KQVFTTAIQ-------------FDHN 262
+ S+GK L+ P+ ++GT I F PD K +F T Q F+ +
Sbjct: 278 ELSKGKVTKPLSVFSCPLK---KRGTTIHFLPDYKHIFKTHHQHTETEEEEGCKNGFNLD 334
Query: 263 TIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNE--YFFAGGLEEYVQWLNTDKKPLH-- 318
I RI EL++LNP LT L E E N Y GG E+++ L DK PL+
Sbjct: 335 LIKNRIHELSYLNPGLTFYLVDERIANENNFYPYETIKHEGGTREFLEELIKDKTPLYKD 394
Query: 319 -DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSL 377
+++ R + + ++++L W ++Y+ + +AN++ T GTHI+G K ++TR +N
Sbjct: 395 INIISIRGVIKNVNVEVSLSWSLESYTALIKSFANNVSTT-AGTHIDGFKYAITRCVNGN 453
Query: 378 GKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEY 437
KK+ K +++ GE +REG+T IISV++ EF+GQTKT+LGN ++ +++ V E
Sbjct: 454 IKKNGYFKGNFVNIPGEFIREGMTAIISVKLNGAEFDGQTKTKLGNHLLKTILESIVFEQ 513
Query: 438 LTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSV-LRSSSLPGKLADCSSTTP 496
L+E LE P++L +I +KSL+A KA AK A+DL+RQK+ S+ LPGKL DC S
Sbjct: 514 LSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYSTILPGKLVDCISDDI 573
Query: 497 EESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVER-KDEAAMYKNEEIQNLIRAL 555
E +E+FIVEG+SA G+AKQ R+R FQA+LPL+GKILN+E+ K+ +++N EI+ LI ++
Sbjct: 574 ERNELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNKKVFENSEIKLLITSI 633
Query: 556 GLGVKGEDFKKE-------------------------------ALRYHKIIILTDADVDG 584
GL V +++ LRY KII+LTDADVDG
Sbjct: 634 GLSVNPVTWRQYDLSHGTKASKDESVQNNNSTLTKKKNSLFDTPLRYGKIILLTDADVDG 693
Query: 585 AHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQY 626
H+R LLLT YR+ +L++ G +YV PPLY++ + Q+
Sbjct: 694 EHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRITNNRMKQF 735
Score = 89.9 bits (223), Expect = 2e-18
Identities = 39/94 (41%), Positives = 54/94 (57%)
Query: 616 YKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLK 675
K E G V EL K+ F + Y IQRFKGLGEMM QLWETT++P++R+L
Sbjct: 807 LKTELGTNVADTEQTDELDINKAFFKFSKHYEIQRFKGLGEMMADQLWETTMDPKKRILI 866
Query: 676 QLVIEDAAEANVVFSSLMGARVDTRKELIQNAAN 709
++ + DA A+ + LMG V +RK+ I +
Sbjct: 867 RITVSDAMRASELIFLLMGEDVQSRKQFIFENSP 900
>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 = 480 bits (1238), Expect = e-162
Identities = 244/645 (37%), Positives = 352/645 (54%), Gaps = 31/645 (4%)
Query: 76 TYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALL 135
Y ++ I+VL+GLE VRKRP MY +T P +HLV E++DN+VDEA AG+AS I V L
Sbjct: 3 NYSAKDIEVLDGLEPVRKRPGMYTDTTRP---NHLVQEVIDNSVDEALAGFASIIMVILH 59
Query: 136 ADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSV 195
D S+ V DNGRG+P+D+HP SA+E +LT LHAGGKF S+ Y SGGLHGVG+SV
Sbjct: 60 QDQSIEVFDNGRGMPVDIHPKEGVSAVEVILTTLHAGGKF--SNKNYHFSGGLHGVGISV 117
Query: 196 VNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTT 255
VNALS+ +++ V+R G Y + G VT L K GT + F PD ++F +
Sbjct: 118 VNALSKRVKIKVYRQGKLYSIAFENGAKVTDL--ISAGTCGKRLTGTSVHFTPDPEIFDS 175
Query: 256 AIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEY----VQWLN 311
F + + +R A L + I D N + + GL++Y V N
Sbjct: 176 L-HFSVSRLYHILRAKAVLCRGVEIEFE----DEVNNTKALWNYPDGLKDYLSEAVNGDN 230
Query: 312 T-DKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASL 370
T KP G + D ++ AL W + M Y N I T GGTH+ G++ L
Sbjct: 231 TLPPKPF---SGNFEG-DDEAVEWALLWLPEGGELFMESYVNLIPTPQGGTHVNGLRQGL 286
Query: 371 TRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVV 430
L + + + + L+ E + + + ++S+++ +P+F GQTK RL + +V K V
Sbjct: 287 LDALREFCE-MRNNLPRGVKLTAEDIWDRCSYVLSIKMQDPQFAGQTKERLSSRQVAKFV 345
Query: 431 DQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLAD 490
+++ +L + +V + + A + A+ +VR K + +LPGKLAD
Sbjct: 346 SGVIKDAFDLWL--NQNVQLAEHLAEHAISSAQRRKRAAKKVVR-KKLTSGPALPGKLAD 402
Query: 491 CSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQN 550
C+ E +E+F+VEGDSAGGSAKQ RDR +QAILPL GKILN + ++EI +
Sbjct: 403 CTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHD 462
Query: 551 LIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYV 610
+ ALG+ D LRY KI IL DAD DG HI TLL F+ + L +EG +YV
Sbjct: 463 IEVALGIDPDSND--LSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYV 520
Query: 611 GVPPLYKVERGKQVQYCYDDAELKKVKSSFP-SNALYSIQRFKGLGEMMPVQLWETTLNP 669
PPLY+++ K+V Y D+ E +K+ ++QRFKGLGEM P QL ETT++P
Sbjct: 521 AKPPLYRIDLSKEVYYALDEEEKEKLLYKLKKKKGKPNVQRFKGLGEMNPAQLRETTMDP 580
Query: 670 EQRMLKQLVIEDAAEANV--VFSSLMG-ARVDTRKELIQNAANLV 711
R L QL ++D + V + L+ R + R +Q + +
Sbjct: 581 NTRRLVQLTLDDVQDQRVDKIMDMLLAKKRSEDRFNWLQEKGDQI 625
>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 = 235 bits (603), Expect = 8e-74
Identities = 83/173 (47%), Positives = 126/173 (72%), Gaps = 2/173 (1%)
Query: 301 GGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDG 359
GGL+++V+ LN DK+PLH + + + DG+ +++ALQW D+YS+ +L + N+I T +G
Sbjct: 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWT-DSYSENILSFVNNIPTPEG 59
Query: 360 GTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKT 419
GTH G +A+LTR +N KK+ +K KD+ L+G+ +REGLT +ISV+VP P+FEGQTK
Sbjct: 60 GTHETGFRAALTRAINDYAKKNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKD 119
Query: 420 RLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDL 472
+LGN EVR +V+ +V+E L E+LE +P+ IL K++ A KA AA++AR+L
Sbjct: 120 KLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAILAAKAREAARKAREL 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 = 229 bits (585), Expect = 5e-72
Identities = 83/115 (72%), Positives = 95/115 (82%), Gaps = 1/115 (0%)
Query: 499 SEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLG 558
SE++IVEGDSAGGSAKQGRDRRFQAILPLRGKILNVE+ + KNEEI+ LI ALG G
Sbjct: 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTG 60
Query: 559 VKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVP 613
+ GEDF E LRYHKIII+TDADVDGAHIRTLLLTFF+RY + L + G +Y+ P
Sbjct: 61 I-GEDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
>gnl|CDD|177398 PHA02569, 39, DNA topoisomerase II large subunit; Provisional.
Length = 602
Score = 230 bits (589), Expect = 1e-66
Identities = 199/672 (29%), Positives = 302/672 (44%), Gaps = 116/672 (17%)
Query: 79 SEQIQVLEGLEAVRKRPAMYIGSTGPR-----------------GLHHLVYEILDNAVDE 121
++ +VL E + KRP MYIGS GL ++ EI+DN+VDE
Sbjct: 1 KDEFKVLSDREHILKRPGMYIGSVAYEAHERFLFGKFTQVEYVPGLVKIIDEIIDNSVDE 60
Query: 122 A---QAGYASNIEVALLADNSVSVADNGRGIPIDLHPATNKSAL---ETVLTVLHAGGKF 175
A +A+ I+V + +N V+V+DNGRGIP + + T AG F
Sbjct: 61 AIRTNFKFANKIDVTI-KNNQVTVSDNGRGIPQAMVTTPEGEEIPGPVAAWTRTKAGSNF 119
Query: 176 GGSSSGYSVSGGLHGVGLSVVNALSESL---------EVTV-WRDGMEYHQKYSRGKPVT 225
++ V+GG++GVG S+ N S EVTV +G E KP
Sbjct: 120 DDTNR---VTGGMNGVGSSLTNFFSVLFIGETCDGKNEVTVNCSNGAE--NISWSTKP-- 172
Query: 226 TLTCHVLPVDSKDRQGTRIRFWPDKQVF--TTAIQFDHNTIAGRIRELAFLNPKLTIALR 283
K +GT + F PD F Q + I R++ LA + P +
Sbjct: 173 ----------GKG-KGTSVTFIPDFSHFEVNGLDQQYLDIILDRLQTLAVVFPDIKFTFN 221
Query: 284 KEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQWCSDAY 343
+ + +Y + F G + VQ D + +AL D +
Sbjct: 222 GKKVSGKFKKYAKQF---GDDTIVQ--ENDN-----------------VSIALAPSPDGF 259
Query: 344 SDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCI 403
L + N + T +GG H++ V + L + KK K K I ++ V+E LT +
Sbjct: 260 RQ--LSFVNGLHTKNGGHHVDCVMDDICEELIPMIKK----KHK-IEVTKARVKECLTIV 312
Query: 404 ISVR-VPNPEFEGQTKTRLGNP--EVRKVVDQSVQEYLTEYLELHPDVLDSI----LSKS 456
+ VR + NP F+ QTK RL +P E+R +D ++ + L+ ++ I L++
Sbjct: 313 LFVRNMSNPRFDSQTKERLTSPFGEIRNHIDLDYKKIAKQILK-TEAIIMPIIEAALARK 371
Query: 457 LSALKAAL--AAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAK 514
L+A KAA AAK+A+ K + ++L GK A+ TT +F+ EGDSA G
Sbjct: 372 LAAEKAAETKAAKKAKKAKVAKHI--KANLIGKDAE---TT-----LFLTEGDSAIGYLI 421
Query: 515 QGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKI 574
+ RD PLRGK+LN A + KN+E+ ++ GL V GE K E + Y I
Sbjct: 422 EVRDEELHGGYPLRGKVLNTWGMSYADILKNKELFDICAITGL-VLGE--KAENMNYKNI 478
Query: 575 IILTDADVDG-AHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAEL 633
I+TDADVDG I LLL FF R+ + LF++G I P+ + GK+ ++ Y E
Sbjct: 479 AIMTDADVDGKGSIYPLLLAFFSRWPE-LFEQGRIRFVKTPVIIAQVGKETKWFYSLDEF 537
Query: 634 KKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLM 693
+K K S +SI+ KGLG + + NP + +V+ D + +F L
Sbjct: 538 EKAKDSLKK---WSIRYIKGLGSLRKSEYRRVINNP---VYDVVVLPDDWKE--LFEMLF 589
Query: 694 GARVDTRKELIQ 705
G D RK+ +
Sbjct: 590 GDDADLRKDWMS 601
>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 = 213 bits (544), Expect = 5e-66
Identities = 74/115 (64%), Positives = 91/115 (79%)
Query: 499 SEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLG 558
E+ +VEGDSAGGSAKQGRDR FQA+ PLRGKILNVE+ + KNEEIQN+I+ALGLG
Sbjct: 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLG 60
Query: 559 VKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVP 613
+ +DF + LRY KIII+TDADVDG+HIRTLLLTFFYR+ +L + G +Y+
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 = 202 bits (515), Expect = 4e-61
Identities = 83/175 (47%), Positives = 120/175 (68%), Gaps = 6/175 (3%)
Query: 302 GLEEYVQWLNTDKKPLHDVV----GFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTI 357
GL++YV+ LN DK PLH V G D I +++ALQW YS+ ++ + N+I T
Sbjct: 1 GLKDYVKELNKDKTPLHPEVIYFEGEEAFDDRIEVEVALQWNDS-YSENIVSFVNNIPTP 59
Query: 358 DGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQT 417
DGGTH++G +A+LTR LN KK +K KD ++G+ +REGLT ++SV++PNP+FEGQT
Sbjct: 60 DGGTHVDGFRAALTRALNEYAKKKGLLKKKD-KITGDDIREGLTAVVSVKIPNPQFEGQT 118
Query: 418 KTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDL 472
K +LGN EVR V+ V E ++LE +P++ IL K+L+A KA LAA++AR+L
Sbjct: 119 KEKLGNSEVRSAVESVVSEKFAKFLEKNPEIAKKILEKALAAAKARLAARKAREL 173
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 175 bits (446), Expect = 1e-45
Identities = 172/697 (24%), Positives = 287/697 (41%), Gaps = 110/697 (15%)
Query: 80 EQIQVLEGLEAVRKRPAMYIGSTGPR-----------------------GLHHLVYEILD 116
E+ Q +E + RP YIGS + GL+ + EIL
Sbjct: 8 ERYQKKTQIEHILLRPDTYIGSIETQTEDMWVYDEEKNRMVYKTITYVPGLYKIFDEILV 67
Query: 117 NAVD----EAQAGYASNIEVAL-LADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHA 171
NA D + + I+V + + +SV ++G GIP+ +H E +
Sbjct: 68 NAADNKARDKGGHRMTYIKVTIDEENGEISVYNDGEGIPVQIHKEHKIYVPEMI------ 121
Query: 172 GGKFGG--SSSGY-----SVSGGLHGVGLSVVNALSESLEVTVW--RDGMEYHQKYSRGK 222
FG +SS Y V+GG +G G + N S V + G ++ ++
Sbjct: 122 ---FGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECVDSKSGKKFKMTWTDNM 178
Query: 223 PVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIA---GRIRELAFLNPKLT 279
+ + D K T++ F+PD F +FD + + R+ +LA KL
Sbjct: 179 SKKS-EPRITSYDGKKDY-TKVTFYPDYAKFGMT-EFDDDMLRLLKKRVYDLAGCFGKLK 235
Query: 280 IALRKEDSDPEKN--QYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQ 337
+ L E K+ Y + + G E ++ R +V ++
Sbjct: 236 VYLNGE-RIAIKSFKDYVDLYLPDGEEGKKPPYPFVYTSVNG----RWEV-VVS------ 283
Query: 338 WCSDAYSDT---MLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGE 394
SD + + NSI T GGTH V L + ++ L +K+K K K +
Sbjct: 284 -----LSDGQFQQVSFVNSICTTKGGTH---VNYILDQLISKLQEKAKKKKKKGKEIKPN 335
Query: 395 HVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILS 454
++ L ++ + NP F+ QTK L + + E L +Y+ L +L++I+
Sbjct: 336 QIKNHLWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKLIKYV-LKSPILENIVE 394
Query: 455 KSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEI---FIVEGDSAGG 511
+ + L A L K +KS R +P KL D + + SE + EGDSA
Sbjct: 395 WAQAKLAAELNKKMK---AGKKS--RILGIP-KLDDANDAGGKNSEECTLILTEGDSAKA 448
Query: 512 SAKQG---RDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEA 568
A G R + + PLRGK+LNV + N+EIQNL + LGL + + +
Sbjct: 449 LALAGLSVVGRDYYGVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYEDPKG 508
Query: 569 LRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFD-EGCIYVGVPPLYKV-ERGKQVQY 626
LRY ++I+TD D DG+HI+ LL+ + + +L G + + P+ K ++G QV
Sbjct: 509 LRYGSLMIMTDQDHDGSHIKGLLINMIHHFWPSLLKNPGFLKEFITPIVKATKKGNQVIS 568
Query: 627 CYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPE--------QRMLKQLV 678
+ + +K K + + I+ +KGLG T+ + E + + V
Sbjct: 569 FFTIPDFEKWKQTVG-LKGWKIKYYKGLG---------TSTDKEGKEYFSNIDKHRIRFV 618
Query: 679 IEDAAEANVVFSSLMGARVDTRKELIQNAANLVNLDH 715
D ++ + + + RV+ RKE I N +DH
Sbjct: 619 YVDDSDDDSIDLAFSKKRVEDRKEWITNYKGGTYVDH 655
>gnl|CDD|215593 PLN03128, PLN03128, DNA topoisomerase 2; Provisional.
Length = 1135
Score = 163 bits (415), Expect = 9e-42
Identities = 176/691 (25%), Positives = 280/691 (40%), Gaps = 120/691 (17%)
Query: 88 LEAVRKRPAMYIGSTGPR---------------------GLHHLVYEILDNAVDEAQAGY 126
LE + RP YIGST GL+ + EIL NA D Q
Sbjct: 13 LEHILLRPDTYIGSTEKHTQTLWVYEGGEMVNREVTYVPGLYKIFDEILVNAADNKQRDP 72
Query: 127 ASN-IEVALLAD-NSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSV 184
+ + ++V + + N++SV +NG+GIP+++H E + L F +
Sbjct: 73 SMDSLKVDIDVEQNTISVYNNGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEK--KT 130
Query: 185 SGGLHGVGLSVVNALSESLEV------------TVWRDGMEYHQKYSRGKPVTTLTCHVL 232
+GG +G G + N S V V+ + M K +P T +C
Sbjct: 131 TGGRNGYGAKLANIFSTEFTVETADGNRGKKYKQVFTNNM--SVK---SEPKIT-SC--- 181
Query: 233 PVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIA---GRIRELA-FLNPKLTIALRKEDSD 288
T+I F PD F + D + +A R+ ++A L KL + L +
Sbjct: 182 ---KASENWTKITFKPDLAKFNMT-RLDEDVVALMSKRVYDIAGCLGKKLKVELNGKKLP 237
Query: 289 PEKNQYNEYFFAGGLEEYVQ-WLNTDKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTM 347
++YV +L + + + K D + ++L SD S
Sbjct: 238 -----------VKSFQDYVGLYLGPNSREDPLPRIYEKVNDRWEVCVSL---SDG-SFQQ 282
Query: 348 LGYANSIRTIDGGTHIEGVKASLT-RTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISV 406
+ + NSI TI GGTH++ V + + KK+K + ++ L ++
Sbjct: 283 VSFVNSIATIKGGTHVDYVADQIVKHIQEKVKKKNK----NATHVKPFQIKNHLWVFVNC 338
Query: 407 RVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLE--LHPDVLDSILS----KSLSAL 460
+ NP F+ QTK L R S E E+L+ V+++ILS K L
Sbjct: 339 LIENPTFDSQTKETL---TTRPSSFGSKCELSEEFLKKVEKCGVVENILSWAQFKQQKEL 395
Query: 461 KAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESE---IFIVEGDSAGGSAKQGR 517
K AKR R +P KL D + ++S+ + + EGDSA A G
Sbjct: 396 KKKDGAKRQRLT----------GIP-KLDDANDAGGKKSKDCTLILTEGDSAKALAMSGL 444
Query: 518 D---RRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKE------- 567
R + PLRGK+LNV + KN EI N+ + LGL F K
Sbjct: 445 SVVGRDHYGVFPLRGKLLNVREASHKQIMKNAEITNIKQILGL-----QFGKTYDEENTK 499
Query: 568 ALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFD-EGCIYVGVPPLYKVERGKQVQY 626
+LRY ++I+TD D DG+HI+ L++ FF+ + +L G + + P+ K +G +
Sbjct: 500 SLRYGHLMIMTDQDHDGSHIKGLIINFFHSFWPSLLKIPGFLVEFITPIVKATKGGKSLS 559
Query: 627 CYDDAELKKVKSSFPSNAL-YSIQRFKGLGEMMPVQLWE--TTLNPEQRMLKQLVIEDAA 683
Y E + K S ++I+ +KGLG + E + L+ ++ ED
Sbjct: 560 FYTMPEYEAWKESLEGETKGWTIKYYKGLGTSTSEEAKEYFSNLDIHKKEFLWQSDEDGD 619
Query: 684 EANVVFSSLMGARVDTRKELIQNAANLVNLD 714
++ FS RV+ RK + N LD
Sbjct: 620 LIDMAFSK---KRVEDRKIWLNNYEPGTFLD 647
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 130 bits (328), Expect = 5e-31
Identities = 165/629 (26%), Positives = 265/629 (42%), Gaps = 113/629 (17%)
Query: 88 LEAVRKRPAMYIGS---------------------TGPRGLHHLVYEILDNAVDEAQAGY 126
LE + RP YIGS T GL+ + EIL NA D Q
Sbjct: 38 LEHILLRPDTYIGSIEKHTQTLWVYETDKMVQRSVTYVPGLYKIFDEILVNAADNKQRD- 96
Query: 127 ASNIEVALLAD---NSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGG--SSSG 181
+ ++ D N +SV +NG G+P+++H E + FG +SS
Sbjct: 97 PKMDSLRVVIDVEQNLISVYNNGDGVPVEIHQEEGVYVPEMI---------FGHLLTSSN 147
Query: 182 YS-----VSGGLHGVGLSVVNALSES--LEVTVWRDGMEYHQKYS-----RGKPVTTLTC 229
Y +GG +G G + N S +E + +Y Q +S + +PV T C
Sbjct: 148 YDDNEKKTTGGRNGYGAKLTNIFSTEFVIETADGKRQKKYKQVFSNNMGKKSEPVIT-KC 206
Query: 230 HVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIA---GRIRELAFLNPKLTIALRKED 286
K T++ F PD F + + +A R+ ++A K
Sbjct: 207 ------KKSENWTKVTFKPDLAKFNMT-HLEDDVVALMKKRVVDIAGCLGKTVKVELNGK 259
Query: 287 SDPEK--NQYNEYFFAGGLEEYVQWLNTDKKP-LHDVVGFRKDVDGITIDLALQWCSDAY 343
P K + Y + + + + P +++ V R +V + Q S
Sbjct: 260 RIPVKSFSDYVDLYLESANK-----SRPENLPRIYEKVNDRWEVCVSLSEGQFQQVS--- 311
Query: 344 SDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCI 403
+ NSI TI GGTH++ V + + K K+K+ ++ +V+ L
Sbjct: 312 ------FVNSIATIKGGTHVDYVTNQIANHVMEAVNK----KNKNANIKAHNVKNHLWVF 361
Query: 404 ISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLE--LHPDVLDSILS----KSL 457
++ + NP F+ QTK L +R+ S E ++L+ + +++++LS K
Sbjct: 362 VNALIDNPAFDSQTKETL---TLRQSSFGSKCELSEDFLKKVMKSGIVENLLSWADFKQS 418
Query: 458 SALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESE---IFIVEGDSAGGSAK 514
LK AK R + +P KL D + + SE + + EGDSA A
Sbjct: 419 KELKKTDGAKTTR----------VTGIP-KLEDANEAGGKNSEKCTLILTEGDSAKALAV 467
Query: 515 QGR---DRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGL--GVKGEDFKKEAL 569
G R + + PLRGK+LNV + N EI+N+ + LGL G + E K +L
Sbjct: 468 AGLSVVGRNYYGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYESVK--SL 525
Query: 570 RYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFD-EGCIYVGVPPLYKV-ERGKQVQYC 627
RY ++I+TD D DG+HI+ LL+ F + + +L + + P+ K RGK+V
Sbjct: 526 RYGHLMIMTDQDHDGSHIKGLLINFIHSFWPSLLKVPSFLVEFITPIVKATRRGKKVLSF 585
Query: 628 YDDAELKKVKSSFPSNAL-YSIQRFKGLG 655
Y E ++ K S NA +SI+ +KGLG
Sbjct: 586 YSMPEYEEWKESLGGNATGWSIKYYKGLG 614
>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 = 110 bits (278), Expect = 2e-29
Identities = 37/60 (61%), Positives = 46/60 (76%)
Query: 646 YSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ 705
IQRFKGLGEM P QLWETT++PE R L Q+ IEDA EA+ +FS+LMG V+ R+E I+
Sbjct: 6 VEIQRFKGLGEMNPEQLWETTMDPETRRLLQVTIEDAEEADEMFSTLMGKDVEPRREFIE 65
>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 = 90.4 bits (225), Expect = 1e-21
Identities = 40/104 (38%), Positives = 61/104 (58%), Gaps = 4/104 (3%)
Query: 505 EGDSAGGSAKQGR---DRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKG 561
EGDSA A G R + + PLRGK+LNV + +N EIQN+ + LGL
Sbjct: 7 EGDSAKALAVAGLSVVGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGK 66
Query: 562 EDFKK-EALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFD 604
D++ ++LRY +++I+TD D DG+HI+ LL+ F + + +L
Sbjct: 67 SDYESTKSLRYGRLMIMTDQDHDGSHIKGLLINFIHSFWPSLLK 110
>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 = 79.2 bits (196), Expect = 4e-18
Identities = 22/101 (21%), Positives = 36/101 (35%), Gaps = 24/101 (23%)
Query: 500 EIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGV 559
E+ IVEG S + ++ A++ G L++E I+ L +AL
Sbjct: 1 ELIIVEGPSDAIALEKAGGVLGGAVVATSGHALDLEH-----------IKELKKALK--- 46
Query: 560 KGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQK 600
++I+ TD D +G I LL
Sbjct: 47 ----------GAKEVILATDPDREGEAIALKLLELLKPLGP 77
>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 = 75.8 bits (187), Expect = 1e-16
Identities = 38/151 (25%), Positives = 53/151 (35%), Gaps = 45/151 (29%)
Query: 104 PRGLHHLVYEILDNAVDEAQAGYASNIEVALLAD---NSVSVADNGRGIPIDLHPATNKS 160
L ++ +LDNA+ A AG IEV L D ++V DNG GIP
Sbjct: 3 EDRLRQVLSNLLDNAIKHAPAG--GEIEVTLERDGGRLRITVEDNGIGIPP--------- 51
Query: 161 ALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSR 220
E + + + SS V G G+GLS+V L E T+
Sbjct: 52 --EDLPKIFEPFFRTDSSS--RKVGG--TGLGLSIVRKLVELHGGTIT------------ 93
Query: 221 GKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQ 251
V+S+ GT F +
Sbjct: 94 -------------VESEPGGGTTFTFTLPLE 111
>gnl|CDD|214643 smart00387, HATPase_c, Histidine kinase-like ATPases. Histidine
kinase-, DNA gyrase B-, phytochrome-like ATPases.
Length = 111
Score = 74.6 bits (184), Expect = 3e-16
Identities = 31/151 (20%), Positives = 47/151 (31%), Gaps = 45/151 (29%)
Query: 104 PRGLHHLVYEILDNAVDEAQAGYASNIEVALLADN---SVSVADNGRGIPIDLHPATNKS 160
P L ++ +LDNA+ G I V L D ++V DNG GIP +
Sbjct: 3 PDRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGDHVEITVEDNGPGIPPEDLE----- 55
Query: 161 ALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSR 220
+ + S + G G+GLS+V L E +
Sbjct: 56 ------KIFEPFFRTDKRS--RKIGG--TGLGLSIVKKLVELHGGEIS------------ 93
Query: 221 GKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQ 251
V+S+ GT +
Sbjct: 94 -------------VESEPGGGTTFTITLPLE 111
>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 = 71.9 bits (177), Expect = 3e-15
Identities = 24/125 (19%), Positives = 50/125 (40%), Gaps = 23/125 (18%)
Query: 303 LEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQWCSD--AYSDTMLGYANSIRTIDGG 360
L++ + + DK ++ + DG ++ A+ + + D + N +GG
Sbjct: 1 LKDRLAEILGDKV-ADKLIYVEGESDGFRVEGAISYPDSGRSSKDRQFSFVNGRPVREGG 59
Query: 361 THIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPN--PEFE-GQT 417
TH++ V+ + TR LN G+ VR ++S+++P + T
Sbjct: 60 THVKAVREAYTRALN-----------------GDDVRRYPVAVLSLKIPPSLVDVNVHPT 102
Query: 418 KTRLG 422
K +
Sbjct: 103 KEEVR 107
>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 = 69.2 bits (170), Expect = 2e-14
Identities = 30/145 (20%), Positives = 45/145 (31%), Gaps = 45/145 (31%)
Query: 107 LHHLVYEILDNAVDEAQAGYASNIEVALLADN---SVSVADNGRGIPIDLHPATNKSALE 163
L ++ +L NA+ G I +++ D + V DNG GIP +
Sbjct: 1 LQQVLLNLLSNAIKHTPEG-GGRITISVERDGDHLEIRVEDNGPGIPEEDLE-------- 51
Query: 164 TVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKP 223
+F S S GG G+GLS+V L E +
Sbjct: 52 ------RIFERF--SDGSRSRKGGGTGLGLSIVKKLVELHGGRIE--------------- 88
Query: 224 VTTLTCHVLPVDSKDRQGTRIRFWP 248
V+S+ GT
Sbjct: 89 ----------VESEPGGGTTFTITL 103
>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 = 49.7 bits (119), Expect = 9e-08
Identities = 26/105 (24%), Positives = 37/105 (35%), Gaps = 26/105 (24%)
Query: 499 SEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLG 558
++ IVEG S + Q A++ L G LN + + L R LG
Sbjct: 1 KKLIIVEGPSDALALAQAGGYG-GAVVALGGHALN------------KTRELLKRLLG-- 45
Query: 559 VKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLF 603
++II TDAD +G I LL K +
Sbjct: 46 -----------EAKEVIIATDADREGEAIALRLLELLKSLGKKVR 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 = 40.7 bits (96), Expect = 5e-04
Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 6/83 (7%)
Query: 342 AYSD---TMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVRE 398
A SD + + NSI T GGTH++ V + + L+ + KK I++ V+
Sbjct: 38 ALSDGQFQQVSFVNSIATTKGGTHVDYVADQIVKKLDEVVKKKNK---GGINVKPFQVKN 94
Query: 399 GLTCIISVRVPNPEFEGQTKTRL 421
L ++ + NP F+ QTK L
Sbjct: 95 HLWIFVNCLIENPSFDSQTKETL 117
>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 = 35.3 bits (82), Expect = 0.029
Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 15/72 (20%)
Query: 113 EILDNAVDEAQAGYASNIEVALLADN---SVSVADNGRGIPID-----LHPATNKSALET 164
E++DN++D A+N+++++ D +S+ DNG G+ + L + E
Sbjct: 9 ELIDNSID----ADATNVKISIDPDRGEDGISIEDNGGGMSYEELRNALKLGRSSKEGER 64
Query: 165 VLTVLHAGGKFG 176
T L G+ G
Sbjct: 65 DSTTL---GRKG 73
>gnl|CDD|223400 COG0323, MutL, DNA mismatch repair enzyme (predicted ATPase) [DNA
replication, recombination, and repair].
Length = 638
Score = 36.9 bits (86), Expect = 0.038
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 6/44 (13%)
Query: 111 VYEILDNAVDEAQAGYASNIEVALLAD--NSVSVADNGRGIPID 152
V E+++N++D AG A+ I++ + + V DNG GI +
Sbjct: 28 VKELVENSLD---AG-ATRIDIEVEGGGLKLIRVRDNGSGIDKE 67
>gnl|CDD|224307 COG1389, COG1389, DNA topoisomerase VI, subunit B [DNA replication,
recombination, and repair].
Length = 538
Score = 35.1 bits (81), Expect = 0.14
Identities = 29/93 (31%), Positives = 42/93 (45%), Gaps = 21/93 (22%)
Query: 64 ATEAFKENPVSKTYGSEQIQVLEGLEAVRKRPAMYIGSTGP-RGLHHLVYEILDNAVDEA 122
E F+E V+ E RK M +G GP R L V+E++ N++D
Sbjct: 8 FKEKFRELSVA--------------EFFRKNKEM-LGFDGPIRSLTTTVHELVTNSLDAC 52
Query: 123 Q-AGYASNI--EVALLADN--SVSVADNGRGIP 150
+ AG +I E+ + + V V DNG GIP
Sbjct: 53 EEAGILPDIKVEIERIGKDHYKVIVEDNGPGIP 85
>gnl|CDD|233250 TIGR01052, top6b, DNA topoisomerase VI, B subunit. This model
describes DNA topoisomerase VI, an archaeal type II DNA
topoisomerase (DNA gyrase) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 488
Score = 34.8 bits (80), Expect = 0.17
Identities = 25/83 (30%), Positives = 45/83 (54%), Gaps = 7/83 (8%)
Query: 79 SEQIQVLEGLEAVRKRPAMYIGSTGP-RGLHHLVYEILDNAVDEAQ-AGYASNIEVAL-- 134
E+ + + E RK M +G +G R L +++E++ N++D + AG +I+V +
Sbjct: 1 KEKFREMSVAEFFRKNKHM-LGYSGKIRSLTTVIHELVTNSLDACEEAGILPDIKVEIEK 59
Query: 135 LADN--SVSVADNGRGIPIDLHP 155
+ + V+V DNG GIP + P
Sbjct: 60 IGKDHYKVTVEDNGPGIPEEYIP 82
>gnl|CDD|224572 COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA
replication, recombination, and repair].
Length = 127
Score = 31.9 bits (73), Expect = 0.34
Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 528 RGKILNVE-RKDEAAMYK---NEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVD 583
+++ VE + D A++ + I A+ E KK A +Y +IILTD D
Sbjct: 9 LKEVIVVEGKDDTASLKRLGDAGVIITNGSAINSLETIELIKK-AQKYKGVIILTDPDRK 67
Query: 584 GAHIRTLL 591
G IR L
Sbjct: 68 GERIRKKL 75
>gnl|CDD|234630 PRK00095, mutL, DNA mismatch repair protein; Reviewed.
Length = 617
Score = 33.3 bits (77), Expect = 0.46
Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 18/70 (25%)
Query: 111 VYEILDNAVDEAQAGYASNIEVALLAD--NSVSVADNGRGIP-IDL------HPATNK-- 159
V E+++NA+D AG A+ I++ + + V DNG GI DL H AT+K
Sbjct: 27 VKELVENALD---AG-ATRIDIEIEEGGLKLIRVRDNGCGISKEDLALALARH-ATSKIA 81
Query: 160 --SALETVLT 167
LE + T
Sbjct: 82 SLDDLEAIRT 91
>gnl|CDD|237946 PRK15337, PRK15337, type III secretion system protein InvA;
Provisional.
Length = 686
Score = 33.4 bits (77), Expect = 0.52
Identities = 23/95 (24%), Positives = 41/95 (43%), Gaps = 6/95 (6%)
Query: 385 KDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSV-QEYLTEYLE 443
++KD+ + EHVR L I + G+ + + + EV + + + Q +L
Sbjct: 560 REKDVIMLVEHVRGALARYICHKFAA---GGELRAVVLSAEVEDAIRKGIRQTSGGTFLN 616
Query: 444 LHPDVLDSILSKSLSALKAALAAKRARDLVRQKSV 478
L P ++++ AL A RD+V SV
Sbjct: 617 LDPAESENLMDLLTLALDDLGIA--HRDIVLLVSV 649
>gnl|CDD|232924 TIGR00334, 5S_RNA_mat_M5, ribonuclease M5. This family of
orthologous proteins shows a weak but significant
similarity to the central region of the DnaG-type DNA
primase. The region of similarity is termed the Toprim
(topoisomerase-primase) domain and is also shared by
RecR, OLD family nucleases, and type IA and II
topoisomerases [Transcription, RNA processing].
Length = 174
Score = 31.3 bits (71), Expect = 1.0
Identities = 22/60 (36%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 531 ILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFK--KEALRYHKIIILTDADVDGAHIR 588
I+ VE KD+ A K ++I G +K E K+A + +IILTD D G IR
Sbjct: 5 IIVVEGKDDQARIKQAFDVDVIETNGSALKDETINLIKKAQKKQGVIILTDPDFPGEKIR 64
>gnl|CDD|223715 COG0642, BaeS, Signal transduction histidine kinase [Signal
transduction mechanisms].
Length = 336
Score = 32.0 bits (72), Expect = 1.1
Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 6/52 (11%)
Query: 104 PRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNS---VSVADNGRGIPID 152
P L ++ +L NA+ I +++ D+ +SV D G GIP +
Sbjct: 226 PERLRQVLVNLLSNAIK---YTPGGEITISVRQDDEQVTISVEDTGPGIPEE 274
>gnl|CDD|218496 pfam05204, Hom_end, Homing endonuclease. Homing endonucleases are
encoded by mobile DNA elements that are found inserted
within host genes in all domains of life.
Length = 110
Score = 30.4 bits (69), Expect = 1.1
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 6/74 (8%)
Query: 334 LALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSG 393
LA SD Y D S++T D EG+ L R SLG K+ +VK ++ +
Sbjct: 18 LAGLIDSDGYVDKAKNITASVKTEDKSVM-EGI-VKLAR---SLGIKA-SVKTREEKIDA 71
Query: 394 EHVREGLTCIISVR 407
+ V T I++
Sbjct: 72 KGVNLQFTYPITLS 85
>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 = 31.8 bits (73), Expect = 1.2
Identities = 15/44 (34%), Positives = 26/44 (59%), Gaps = 6/44 (13%)
Query: 111 VYEILDNAVDEAQAGYASNIEVALLAD--NSVSVADNGRGIPID 152
V E+++N++D AG A+ I+V + + V+DNG GI +
Sbjct: 27 VKELVENSLD---AG-ATRIDVEIEEGGLKLIEVSDNGSGIDKE 66
>gnl|CDD|182388 PRK10337, PRK10337, sensor protein QseC; Provisional.
Length = 449
Score = 31.9 bits (73), Expect = 1.3
Identities = 37/125 (29%), Positives = 50/125 (40%), Gaps = 29/125 (23%)
Query: 95 PAMYIGSTG-PRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDL 153
A + TG P L LV +LDNA+ + G S ++V L A + +V DNG G+
Sbjct: 340 NAHPVIRTGQPLLLSLLVRNLLDNAIRYSPQG--SVVDVTLNA-RNFTVRDNGPGV---- 392
Query: 154 HPATNKSALETVLTVLHAGGKF--------GGSSSGYSVS---GGLHGVGLSVVNALSES 202
AL G +F GS G S+ LHG+ +S NA
Sbjct: 393 ----TPEALA------RIGERFYRPPGQEATGSGLGLSIVRRIAKLHGMNVSFGNAPEGG 442
Query: 203 LEVTV 207
E V
Sbjct: 443 FEAKV 447
>gnl|CDD|220722 pfam10374, EST1, Telomerase activating protein Est1. Est1 is a
protein which recruits or activates telomerase at the
site of polymerisation.
Length = 125
Score = 30.1 bits (68), Expect = 1.5
Identities = 18/74 (24%), Positives = 27/74 (36%), Gaps = 5/74 (6%)
Query: 582 VDGAHIRTLLLTFF---YRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKS 638
V+ + LL F + KTL + C + L V + + E K + +
Sbjct: 33 VEFRKLNKKLLKFLKEGIGFYKTLIQKLCAKYNLDLLSPVASFELLTDSLSIGESKVLAA 92
Query: 639 S--FPSNALYSIQR 650
S S AL S R
Sbjct: 93 SSPLVSYALMSCHR 106
>gnl|CDD|130727 TIGR01666, YCCS, TIGR01666 family membrane protein. This model
represents a clade of sequences from gamma and beta
proteobacteria. These proteins are >700 amino acids long
and many have been annotated as putative membrane
proteins. The gene from Salmonella has been annotated as
a putative efflux transporter. The gene from E. coli has
the name yccS [Cell envelope, Other].
Length = 704
Score = 31.8 bits (72), Expect = 1.6
Identities = 17/82 (20%), Positives = 30/82 (36%), Gaps = 11/82 (13%)
Query: 415 GQTKTRLGNPEVRKVVDQSVQ------EYLTEYLELHPDVLDSILSKSLSALKAALAAKR 468
G + RL N + Y E++E P+ + + +S+ L+
Sbjct: 614 GAHRDRLKNLQQTAQFLDGFYPVAKKLIYTLEHIEEIPEAIFNQQQESIETLELRKQEMT 673
Query: 469 ARD-----LVRQKSVLRSSSLP 485
A + LV Q+ L + LP
Sbjct: 674 AEERAVFSLVYQQLNLITQLLP 695
>gnl|CDD|225115 COG2205, KdpD, Osmosensitive K+ channel histidine kinase [Signal
transduction mechanisms].
Length = 890
Score = 31.5 bits (72), Expect = 2.1
Identities = 28/129 (21%), Positives = 44/129 (34%), Gaps = 23/129 (17%)
Query: 114 ILDNAVDEAQAGYASNIEVALLADN-SVSVADNGRGIPIDLHPATNKSALETVLTVLHAG 172
+L+NA+ A G I + +N SV D G GIP LE + + G
Sbjct: 783 LLENALKYAPPGSEIRINAGVERENVVFSVIDEGPGIPEG--------ELERIFDKFYRG 834
Query: 173 GKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPVT-TLTCHV 231
K + G+ G+GL++ + E+ T+ G TL
Sbjct: 835 NKESA-------TRGV-GLGLAICRGIVEAHGGTIS-----AENNPGGGAIFVFTLPVEE 881
Query: 232 LPVDSKDRQ 240
P +
Sbjct: 882 DPPLEDFEE 890
>gnl|CDD|226369 COG3851, UhpB, Signal transduction histidine kinase,
glucose-6-phosphate specific [Signal transduction
mechanisms].
Length = 497
Score = 31.3 bits (71), Expect = 2.1
Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 6/51 (11%)
Query: 107 LHHLVYEILDNAVDEAQAGYASNIEVALLADNSV---SVADNGRGIPIDLH 154
L+ L E+L+N A A S + + L + + D+G G+P
Sbjct: 411 LYRLCQELLNNICKHADA---SAVTIQLWQQDERLMLEIEDDGSGLPPGSG 458
>gnl|CDD|182581 PRK10600, PRK10600, nitrate/nitrite sensor protein NarX;
Provisional.
Length = 569
Score = 31.2 bits (71), Expect = 2.3
Identities = 19/46 (41%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 107 LHHLVYEILDNAVDEAQAGYASNIEVALLADNSV--SVADNGRGIP 150
L + E L NA+ AQA + VA N V SV DNG G+P
Sbjct: 470 LLQIAREALSNALKHAQASEVV-VTVAQ-NQNQVKLSVQDNGCGVP 513
>gnl|CDD|197325 cd09091, INPP5c_SHIP, Catalytic inositol polyphosphate
5-phosphatase (INPP5c) domain of SH2 domain containing
inositol polyphosphate 5-phosphatase-1 and -2, and
related proteins. This subfamily contains the INPP5c
domain of SHIP1 (SH2 domain containing inositol
polyphosphate 5-phosphatase-1, also known as
SHIP/INPP5D), and SHIP2 (also known as INPPL1). It
belongs to a family of Mg2+-dependent inositol
polyphosphate 5-phosphatases, which hydrolyze the
5-phosphate from the inositol ring of various 5-position
phosphorylated phosphoinositides (PIs) and inositol
phosphates (IPs), and to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. Both SHIP1 and -2 catalyze the dephosphorylation
of the PI, phosphatidylinositol 3,4,5-trisphosphate
[PI(3,4,5)P3], to phosphatidylinositol 3,4-bisphosphate
[PI(3,4)P2]. SHIP1 also converts inositol-1,3,4,5-
polyphosphate [I(1,3,4,5)P4] to
inositol-1,3,4-polyphosphate [I(1,3,4)P3]. SHIP1 and
SHIP2 have little overlap in their in vivo functions.
SHIP1 is a negative regulator of cell growth and plays a
major part in mediating the inhibitory signaling in B
cells; it is predominantly expressed in hematopoietic
cells. SHIP2 is as an inhibitor of the insulin signaling
pathway, and is implicated in actin structure
remodeling, cell adhesion and cell spreading, receptor
endocytosis and degradation, and in the JIP1-mediated
JNK pathway. SHIP2 is widely expressed, most
prominently in brain, heart and in skeletal muscle. In
addition to this INPP5c domain, SHIP1 has an N-terminal
SH2 domain, two NPXY motifs, and a C-terminal
proline-rich region (PRD), while SHIP2 has an N-terminal
SH2 domain, a C-terminal proline-rich domain (PRD),
which includes a WW-domain binding motif (PPLP), an NPXY
motif, and a sterile alpha motif (SAM) domain. The gene
encoding SHIP2 is a candidate gene for conferring a
predisposition for type 2 diabetes.
Length = 307
Score = 30.7 bits (69), Expect = 2.5
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 613 PPLYKVERGKQVQYCYDDAELKKVKSSFPS 642
PP Y+ ERG + Y Y + VK + PS
Sbjct: 238 PPTYRYERGSRDTYAYTKQKATGVKYNLPS 267
>gnl|CDD|226368 COG3850, NarQ, Signal transduction histidine kinase,
nitrate/nitrite-specific [Signal transduction
mechanisms].
Length = 574
Score = 30.8 bits (70), Expect = 3.3
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 6/50 (12%)
Query: 110 LVYEILDNAVDEAQAGYASNIEVALL---ADNSVSVADNGRGIPIDLHPA 156
+V E L NA+ AQA S I+V + +++V DNG GI P+
Sbjct: 485 IVREALSNAIKHAQA---SEIKVTVSQNDGQVTLTVEDNGVGIDEAAEPS 531
>gnl|CDD|197334 cd09100, INPP5c_SHIP1-INPP5D, Catalytic inositol polyphosphate
5-phosphatase (INPP5c) domain of SH2 domain containing
inositol polyphosphate 5-phosphatase-1 and related
proteins. This subfamily contains the INPP5c domain of
SHIP1 (SH2 domain containing inositol polyphosphate
5-phosphatase-1, also known as SHIP/INPP5D) and related
proteins. It belongs to a family of Mg2+-dependent
inositol polyphosphate 5-phosphatases, which hydrolyze
the 5-phosphate from the inositol ring of various
5-position phosphorylated phosphoinositides (PIs) and
inositol phosphates (IPs), and to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. SHIP1's enzymic activity is restricted to
phosphatidylinositol 3,4,5-trisphosphate [PI (3,4,5)P3]
and inositol-1,3,4,5- polyphosphate [I(1,3,4,5)P4]. It
converts these two phosphoinositides to
phosphatidylinositol 3,4-bisphosphate [PI (3,4)P2] and
inositol-1,3,4-polyphosphate [I(1,3,4)P3], respectively.
SHIP1 is a negative regulator of cell growth and plays a
major part in mediating the inhibitory signaling in B
cells; it is predominantly expressed in hematopoietic
cells. In addition to this INPP5c domain, SHIP1 has an
N-terminal SH2 domain, two NPXY motifs, and a C-terminal
proline-rich region (PRD). SHIP1's phosphorylated NPXY
motifs interact with proteins with phosphotyrosine
binding (PTB) domains, and facilitate the translocation
of SHIP1 to the plasma membrane to hydrolyze
PI(3,4,5)P3. SHIP1 generally acts to oppose the activity
of phosphatidylinositol 3-kinase (PI3K). It acts as a
negative signaling molecule, reducing the levels of
PI(3,4,5)P3, thereby removing the latter as a
membrane-targeting signal for PH domain-containing
effector molecules. SHIP1 may also, in certain contexts,
amplify PI3K signals. SHIP1 and SHIP2 have little
overlap in their in vivo functions.
Length = 307
Score = 30.3 bits (68), Expect = 3.3
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 613 PPLYKVERGKQVQYCYDDAELKKVKSSFPS 642
P Y+ ERG + +Y Y + +K + PS
Sbjct: 238 APTYRFERGTRERYAYTKQKATGMKYNLPS 267
>gnl|CDD|219571 pfam07779, Cas1_AcylT, 10 TM Acyl Transferase domain found in
Cas1p. Cas1p protein of Cryptococcus neoformans is
required for the synthesis of O-acetylated
glucuronoxylomannans, a consitutent of the capsule, and
is critical for its virulence. The multi TM domain of
the Cas1p was unified with the 10 TM Sugar
Acyltransferase superfamily. This superfamily is
comprised of members from the OatA, MdoC, OpgC, NolL and
GumG families in addition to the Cas1p family. The Cas1p
protein has a N terminal PC-Esterase domain with the
opposing Acyl esterase activity.
Length = 496
Score = 30.5 bits (69), Expect = 4.0
Identities = 20/50 (40%), Positives = 28/50 (56%), Gaps = 5/50 (10%)
Query: 10 YLHIRVLMASRCFCS-FSSSLFFKPRTNFAIRGVSSQVLTRSN---VVLP 55
Y+HIRVL+A+ F + + FF + +F + V QVL R N VVL
Sbjct: 171 YMHIRVLVAAYLFMTGYGHFTFFWKKGDFGFKRV-FQVLFRLNFLSVVLC 219
>gnl|CDD|115650 pfam07010, Endomucin, Endomucin. This family consists of several
mammalian endomucin proteins. Endomucin is an early
endothelial-specific antigen that is also expressed on
putative hematopoietic progenitor cells.
Length = 259
Score = 30.1 bits (67), Expect = 4.2
Identities = 36/148 (24%), Positives = 56/148 (37%), Gaps = 22/148 (14%)
Query: 359 GGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTK 418
G T E +K SL T SL T ++ + VR+ + V V N
Sbjct: 63 GTTTSELLKTSLMSTATSL-----TTPKHELKTTTTGVRKNESSTSKVTVTNVTLSNAVS 117
Query: 419 TRLGNPEVRKVVDQSVQEYLTEYL---ELHPDVLDSILSKSLSALKAALAAKRARDLVRQ 475
T L + + + S++ TE L PD + ++L A +++D
Sbjct: 118 T-LQSSQNKTENQSSIRT--TEISPTSVLQPDASPKKTGTTSASLTTAETTSQSQD---- 170
Query: 476 KSVLRSSSLPGKLADCSSTTPEESEIFI 503
+ GK+A SSTTP S I +
Sbjct: 171 -------TEDGKIASTSSTTPSYSSIIL 191
>gnl|CDD|234278 TIGR03606, non_repeat_PQQ, dehydrogenase, PQQ-dependent, s-GDH
family. PQQ, or pyrroloquinoline-quinone, serves as a
cofactor for a number of sugar and alcohol
dehydrogenases in a limited number of bacterial species.
Most characterized PQQ-dependent enzymes have multiple
repeats of a sequence region described by pfam01011 (PQQ
enzyme repeat), but this protein family in unusual in
lacking that repeat. Below the noise cutoff are related
proteins mostly from species that lack PQQ biosynthesis.
Length = 454
Score = 30.3 bits (68), Expect = 4.3
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 236 SKDRQGTRIRFWPDKQVFTTAIQFDHNTIA 265
D G R+ F PD +++ T + N A
Sbjct: 143 GNDHNGGRLVFGPDGKIYYTIGEQGRNQGA 172
>gnl|CDD|183097 PRK11359, PRK11359, cyclic-di-GMP phosphodiesterase; Provisional.
Length = 799
Score = 30.1 bits (68), Expect = 5.5
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 527 LRGKILNVERKDEAAMYKNEEIQ---NLIRALGLGVKGEDF 564
+ G L VE + M + EI ++R +G+G+ +DF
Sbjct: 659 IDGHQLTVEITESMMMEHDTEIFKRIQILRDMGVGLSVDDF 699
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 29.7 bits (67), Expect = 5.9
Identities = 19/83 (22%), Positives = 32/83 (38%), Gaps = 11/83 (13%)
Query: 453 LSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLA--DCSSTTPEESEIFIVEGDSAG 510
L +++ +AA A R + + R+ + K T PE+ I + G
Sbjct: 236 LKNEIASAEAAAAKAREAAAAAEAAAARARAAEAKRTGETYKPTAPEKMLI----SSTGG 291
Query: 511 GSAKQGRDRRFQAILPLRGKILN 533
A +G Q P+ G+IL
Sbjct: 292 FGALRG-----QLAWPVTGRILR 309
>gnl|CDD|179711 PRK04017, PRK04017, hypothetical protein; Provisional.
Length = 132
Score = 28.4 bits (64), Expect = 6.0
Identities = 22/83 (26%), Positives = 33/83 (39%), Gaps = 29/83 (34%)
Query: 519 RRFQAILPLR-----GKILNVE-RKDEAAMYKNEEIQNLIRALGLGVKGE---------- 562
R + I L+ G + VE ++D ++ K LGV+GE
Sbjct: 8 RFEEIIEELKEFSEAGAPIIVEGKRDVESLRK------------LGVEGEIIKVSRTPLA 55
Query: 563 -DFKKEALRYHKIIILTDADVDG 584
+ A R ++IILTD D G
Sbjct: 56 EIAELIASRGKEVIILTDFDRKG 78
>gnl|CDD|236846 PRK11100, PRK11100, sensory histidine kinase CreC; Provisional.
Length = 475
Score = 29.8 bits (68), Expect = 6.0
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 5/47 (10%)
Query: 107 LHHLVYEILDNAVDEAQAGYASNIEVALLADNS---VSVADNGRGIP 150
L + +LDNA+D + G I ++ D +SV D G GIP
Sbjct: 369 LRQALGNLLDNAIDFSPEG--GTITLSAEVDGEQVALSVEDQGPGIP 413
>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated.
Length = 822
Score = 30.0 bits (68), Expect = 6.0
Identities = 28/103 (27%), Positives = 36/103 (34%), Gaps = 34/103 (33%)
Query: 510 GGSAKQ-----------GRDRRFQAILPLRGKILNVERKDE--------------AAMYK 544
GG AK+ R ++ L G I+ V+ +E A K
Sbjct: 21 GGKAKKKRVNGVPYYEFERKGEKWIVIGLSGHIVTVDFPEEYGDWRDVDPAELIDADPVK 80
Query: 545 NEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHI 587
QN I AL KK A +III TD D +G I
Sbjct: 81 KITKQNYINAL---------KKLAKDADEIIIATDYDREGELI 114
>gnl|CDD|172541 PRK14049, PRK14049, ferrioxamine B receptor precursor protein;
Provisional.
Length = 726
Score = 29.9 bits (67), Expect = 6.2
Identities = 34/103 (33%), Positives = 51/103 (49%), Gaps = 20/103 (19%)
Query: 31 FKPRTN-FAIRG--VSSQVLTRSNVVLPRAFLSSSIATEAFKENPVSKTYGSEQIQVLEG 87
F PR + F +RG V+ + R N+ P A SSSI FK P YG E + +L G
Sbjct: 116 FDPRFDAFFVRGFDVTYTGVFRDNLRQPGA--SSSI----FKTEP----YGLEGVSILRG 165
Query: 88 LEAVRKRPAMYIGSTGPRGLHHLVYE-ILDNAVDEAQAGYASN 129
+ A+Y G++G GL +L+ + + + E Q Y +N
Sbjct: 166 PSS-----ALY-GASGAGGLFNLITKRPTEEPLREVQVQYGTN 202
>gnl|CDD|235246 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated.
Length = 535
Score = 29.9 bits (68), Expect = 6.4
Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 9/67 (13%)
Query: 92 RKRPAMYIGSTGP-RGLHHLVYEILDNAVDEAQ-AGYASNI--EVALLADN----SVSVA 143
K + +G P R L+ V E++DN++D + AG +I E+ + + V+V
Sbjct: 22 EKNKEL-LGFDNPARALYTTVKELVDNSLDACEEAGILPDIKIEIKRVDEGKDHYRVTVE 80
Query: 144 DNGRGIP 150
DNG GIP
Sbjct: 81 DNGPGIP 87
>gnl|CDD|173777 cd01027, TOPRIM_RNase_M5_like, TOPRIM_ RNase M5_like: The
topoisomerase-primase (TOPRIM) nucleotidyl
transferase/hydrolase domain found in Ribonuclease M5:
(RNase M5) and other small primase-like proteins from
bacteria and archaea. RNase M5 catalyzes the maturation
of 5S rRNA in low G+C Gram-positive bacteria. 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 nucleotide polymerization by primases.
The DXD motif may co-ordinate Mg2+, a cofactor required
for full catalytic function.
Length = 81
Score = 27.2 bits (61), Expect = 6.6
Identities = 11/24 (45%), Positives = 12/24 (50%)
Query: 568 ALRYHKIIILTDADVDGAHIRTLL 591
Y +IILTD D G IR L
Sbjct: 42 KKAYRGVIILTDPDRKGEKIRKKL 65
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 29.4 bits (67), Expect = 7.7
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 5/48 (10%)
Query: 445 HPDVLDSILSKSLSALKAALAAKRARDLVRQK--SVLRSSSLPGKLAD 490
+V DS S+ L ++ L K++R +R+K S++RS SL L D
Sbjct: 142 EGEVKDSA-SEKLRGIRRQLRRKKSR--IREKLESIIRSKSLQKYLQD 186
>gnl|CDD|119362 cd06545, GH18_3CO4_chitinase, The Bacteroides thetaiotaomicron
protein represented by pdb structure 3CO4 is an
uncharacterized bacterial member of the family 18
glycosyl hydrolases with homologs found in
Flavobacterium, Stigmatella, and Pseudomonas.
Length = 253
Score = 29.0 bits (65), Expect = 9.3
Identities = 16/55 (29%), Positives = 21/55 (38%), Gaps = 14/55 (25%)
Query: 678 VIEDAAEANV-VFSSLMGARVDT----------RKELIQNAANLV---NLDHLDI 718
V+ A NV + SL G RK L+ N V NLD +D+
Sbjct: 51 VVNAAHAHNVKILISLAGGSPPEFTAALNDPAKRKALVDKIINYVVSYNLDGIDV 105
>gnl|CDD|237841 PRK14867, PRK14867, DNA topoisomerase VI subunit B; Provisional.
Length = 659
Score = 29.0 bits (65), Expect = 9.4
Identities = 26/93 (27%), Positives = 42/93 (45%), Gaps = 19/93 (20%)
Query: 68 FKENPVSKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVD---EAQA 124
FKE+ +S E RK M S R + +++E++ N++D EA+
Sbjct: 12 FKEHSIS--------------EFFRKNKHMLGYSGKLRSMTTIIHELVTNSLDACEEAEI 57
Query: 125 GYASNIEVALLADN--SVSVADNGRGIPIDLHP 155
+E+ L + V+V DNG GIP + P
Sbjct: 58 LPDIKVEIEKLGSDHYKVAVEDNGPGIPPEFVP 90
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
0.317 0.134 0.383
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 36,497,088
Number of extensions: 3652477
Number of successful extensions: 3366
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3234
Number of HSP's successfully gapped: 79
Length of query: 718
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 614
Effective length of database: 6,324,786
Effective search space: 3883418604
Effective search space used: 3883418604
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 (21.7 bits)
S2: 63 (27.9 bits)