RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 008738
(555 letters)
>gnl|CDD|235542 PRK05644, gyrB, DNA gyrase subunit B; Validated.
Length = 638
Score = 865 bits (2239), Expect = 0.0
Identities = 312/554 (56%), Positives = 404/554 (72%), Gaps = 16/554 (2%)
Query: 2 IVTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPV 61
++TVLHAGGKFGG GY VSGGLHGVG+SVVNALS LEV V RDG Y+Q+Y RG PV
Sbjct: 96 VLTVLHAGGKFGGG--GYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPV 153
Query: 62 TTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRK 121
T L + D GT + F PD ++F T +FD++T+A R+RELAFLN L I L
Sbjct: 154 TPLEV----IGETDETGTTVTFKPDPEIFET-TEFDYDTLATRLRELAFLNKGLKITLT- 207
Query: 122 EDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAY 180
D + + + + GG++EYV++LN +K+PLH + + F + DGI +++A+Q+ D Y
Sbjct: 208 -DEREGEEKEETFHYEGGIKEYVEYLNRNKEPLHEEPIYFEGEKDGIEVEVAMQYN-DGY 265
Query: 181 SDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCI 240
S+ +L +AN+I T +GGTH EG K +LTR +N +K+K +K+KD +L+GE VREGLT +
Sbjct: 266 SENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVREGLTAV 325
Query: 241 ISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAA 300
ISV+ P P+FEGQTKT+LGN EVR +VD V E L+E+LE +P+V I+ K++ A +A
Sbjct: 326 ISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAR 385
Query: 301 LAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQA 360
AA++AR+L R+KS L SSSLPGKLADCSS PEESE++IVEGDSAGGSAKQGRDRRFQA
Sbjct: 386 EAARKARELTRRKSALESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQA 445
Query: 361 ILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVD 420
ILPLRGKILNVE+ + KNEEI+ LI ALG G+ G+DF LRYHKIII+TDADVD
Sbjct: 446 ILPLRGKILNVEKARLDKILKNEEIRALITALGTGI-GDDFDISKLRYHKIIIMTDADVD 504
Query: 421 GAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFP-- 478
GAHIRTLLLTFFYRY + L + G +Y+ PPLYK+++G + +Y Y D EL ++ +
Sbjct: 505 GAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIKKGGK-EYAYSDEELDEILAELKLK 563
Query: 479 SNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRK 538
N Y IQR+KGLGEM P QLWETT++PE R L Q+ IEDAAEA+ +FS LMG V+ R+
Sbjct: 564 GNPKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSILMGDDVEPRR 623
Query: 539 ELIQ-NAANLVNLD 551
E I+ NA + NLD
Sbjct: 624 EFIEENAKYVRNLD 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 = 768 bits (1986), Expect = 0.0
Identities = 297/553 (53%), Positives = 390/553 (70%), Gaps = 14/553 (2%)
Query: 1 MIVTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKP 60
+I TVLHAGGKF S Y VSGGLHGVG+SVVNALS LEV V RDG Y Q++ RG P
Sbjct: 94 VIFTVLHAGGKFDNDS--YKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYRQRFERGVP 151
Query: 61 VTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALR 120
VT L V+ + GT++RF PD ++F +FD+ + R+RELAFLN + I L
Sbjct: 152 VTPL--EVIGSTDTKKTGTKVRFKPDPEIFGE-TEFDYEILKRRLRELAFLNKGVKITLT 208
Query: 121 KEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKD-VDGITIDLALQWCSDA 179
E + EK E+ + GGL++YV++LN K PLH+ + + DGI +++ALQW +D
Sbjct: 209 DERTGEEKK---EFHYEGGLKDYVEYLNKGKTPLHEEIFYFNGEKDGIAVEVALQW-NDG 264
Query: 180 YSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTC 239
YS+ +L + N+I T +GGTH G +++LTR +N KK +K+ D L+G+ +REGLT
Sbjct: 265 YSENILSFVNNIPTREGGTHEAGFRSALTRAINEYAKKKNLLKEGD--LTGDDIREGLTA 322
Query: 240 IISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKA 299
+ISV++P+P+FEGQTK +LGN EVR +V++ V E + +LE +P I+ K+++A KA
Sbjct: 323 VISVKIPDPQFEGQTKEKLGNSEVRSIVEKLVSEAFSLFLEENPQEAKKIVEKAIAAAKA 382
Query: 300 ALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQ 359
AA++AR+L R+KS L LPGKLADC+S PE+SE+F+VEGDSAGGSAKQGRDR FQ
Sbjct: 383 REAARKARELTRRKSALDIPGLPGKLADCTSKDPEKSELFLVEGDSAGGSAKQGRDREFQ 442
Query: 360 AILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADV 419
AILPLRGKILNVE+ + KNEEIQ +I ALG G+ G+DF E LRYHKIII+TDADV
Sbjct: 443 AILPLRGKILNVEKARLDKILKNEEIQTIITALGTGI-GKDFDLEKLRYHKIIIMTDADV 501
Query: 420 DGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPS 479
DGAHIRTLLLTFFYRY L + G +Y+ PPLYKV++GK+ Y YDD EL+K+
Sbjct: 502 DGAHIRTLLLTFFYRYMPPLIENGHVYIAQPPLYKVKKGKKTFYAYDDEELEKLLERLGK 561
Query: 480 NALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKE 539
Y IQR+KGLGEM P QLWETT++PE R L Q+ IEDA EA+ +FS+LMG +V+ R+
Sbjct: 562 KKGYEIQRYKGLGEMNPDQLWETTMDPETRRLLQVTIEDADEADEIFSTLMGDKVEPRRN 621
Query: 540 LIQ-NAANLVNLD 551
I+ NA + NLD
Sbjct: 622 FIEENALFVENLD 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 = 743 bits (1920), Expect = 0.0
Identities = 293/577 (50%), Positives = 402/577 (69%), Gaps = 37/577 (6%)
Query: 1 MIVTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKP 60
+++TVLHAGGKF S Y VSGGLHGVG+SVVNALSE LEVTV+RDG Y Q++ RG P
Sbjct: 88 VVLTVLHAGGKFDKDS--YKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIP 145
Query: 61 VTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALR 120
+ L V+ + GT +RFWPD ++F T +FD + +A R+RELAFLN + I+L
Sbjct: 146 LGPL--EVVGET--KKTGTTVRFWPDPEIFET-TEFDFDILAKRLRELAFLNSGVKISLE 200
Query: 121 KEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDA 179
E K+ + + GG++ +V++LN +K+PLH +++ + + +GI +++ALQW D
Sbjct: 201 DERDGKGKS--VTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKEGIEVEVALQWN-DG 257
Query: 180 YSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTC 239
YS+ +L + N+I T +GGTH+EG +++LTR +NS K +K +K+ +L+GE +REGLT
Sbjct: 258 YSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTA 317
Query: 240 IISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKA 299
+ISV+VP+P+FEGQTKT+LGN EVR +V+ V E LTE+ E +P +I+ K++ A +A
Sbjct: 318 VISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQA 377
Query: 300 ALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQ 359
AA++AR+L R+KS L S LPGKLADCSS P +SE++IVEGDSAGGSAKQGRDR+FQ
Sbjct: 378 REAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRKFQ 437
Query: 360 AILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADV 419
AILPLRGKILNVE+ + N+EI +I ALG G+ G+DF E LRYHKIII+TDADV
Sbjct: 438 AILPLRGKILNVEKARLDKILSNQEIGAIITALGCGI-GKDFDLEKLRYHKIIIMTDADV 496
Query: 420 DGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQ----------------- 462
DG+HIRTLLLTFFYRY + L + G +Y+ PPLYKV++GK+ +
Sbjct: 497 DGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIKDDKEKELVGEALED 556
Query: 463 ----YCYDDAELKKVKSSFPSNAL---YSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLV 515
Y Y D E ++ K+ P + IQR+KGLGEM QLWETT++PE R L ++
Sbjct: 557 LRALYIYSDKEKEEAKTQIPVHEGRKGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVT 616
Query: 516 IEDAAEANVVFSSLMGARVDTRKELIQ-NAANLVNLD 551
IEDA EA+ +FS+LMG V+ R+E I+ NA ++ NLD
Sbjct: 617 IEDAVEADRIFSTLMGDEVEPRREFIEANALDVKNLD 653
>gnl|CDD|235501 PRK05559, PRK05559, DNA topoisomerase IV subunit B; Reviewed.
Length = 631
Score = 688 bits (1778), Expect = 0.0
Identities = 247/554 (44%), Positives = 337/554 (60%), Gaps = 20/554 (3%)
Query: 1 MIVTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKP 60
+I+T LHAGGKF + Y SGGLHGVG+SVVNALS LEV V RDG Y Q++ G P
Sbjct: 95 VILTKLHAGGKFSNKA--YKFSGGLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDP 152
Query: 61 VTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALR 120
V L V+ K + GTR+RFWPD ++F + +F + R+R AFL P LTI L
Sbjct: 153 VGPL--EVVGTAGKRKTGTRVRFWPDPKIFDSP-KFSPERLKERLRSKAFLLPGLTITLN 209
Query: 121 KEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHD--VVGFRKDVDGITIDLALQWCSD 178
E + + GL++Y+ LN K+ L + V F + +G ++ ALQW +D
Sbjct: 210 DERERQT------FHYENGLKDYLAELNEGKETLPEEFVGSFEGEAEGEAVEWALQW-TD 262
Query: 179 AYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLT 238
+ + Y N I T GGTH G + L + + +K + K L GE VREGL
Sbjct: 263 EGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLP-KGKKLEGEDVREGLA 321
Query: 239 CIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALK 298
++SV++P P+FEGQTK +LG+ E R+ V V++ +L +P++ + + K A+K
Sbjct: 322 AVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEK---AIK 378
Query: 299 AALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRF 358
AA A RA V++K +LPGKLADC+S PE +E+F+VEGDSAGGSAKQ RDR F
Sbjct: 379 AAQARLRAAKKVKRKKKTSGPALPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREF 438
Query: 359 QAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDAD 418
QAILPLRGKILN + NEEI ++I A+G+G G+ F E LRY KIII+TDAD
Sbjct: 439 QAILPLRGKILNTWEASLDDVLANEEIHDIIVAIGIGP-GDSFDLEDLRYGKIIIMTDAD 497
Query: 419 VDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKV-KSSF 477
VDGAHI TLLLTFFYR+ L + G +Y+ +PPLY+V++GK+ Y D+ E +++ K
Sbjct: 498 VDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRVDKGKKKIYALDEEEKEELLKKLG 557
Query: 478 PSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTR 537
IQRFKGLGEM P QLWETT++PE R L ++ I+DA E + LMG + + R
Sbjct: 558 KKGGKPEIQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEETEKLVDMLMGKKAEPR 617
Query: 538 KELIQNAANLVNLD 551
+E I+ + +
Sbjct: 618 REWIEENGDFAEEE 631
>gnl|CDD|237860 PRK14939, gyrB, DNA gyrase subunit B; Provisional.
Length = 756
Score = 671 bits (1733), Expect = 0.0
Identities = 238/477 (49%), Positives = 326/477 (68%), Gaps = 21/477 (4%)
Query: 1 MIVTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKP 60
+I+TVLHAGGKF +S Y VSGGLHGVG+SVVNALSE LE+T+ RDG + Q++ G P
Sbjct: 95 VIMTVLHAGGKFDQNS--YKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVP 152
Query: 61 VTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALR 120
V L V D+ GT +RFWP ++F +FD++ +A R+RELAFLN + I L+
Sbjct: 153 VAPLKV----VGETDKTGTEVRFWPSPEIFEN-TEFDYDILAKRLRELAFLNSGVRIRLK 207
Query: 121 KEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDA 179
E E E+ + GG++ +V++LN +K PLH ++ F + DGI +++ALQW +D+
Sbjct: 208 DERDGKE----EEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQW-NDS 262
Query: 180 YSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTC 239
Y + +L + N+I DGGTH+ G +A+LTRT+N+ +K K +SL+G+ REGLT
Sbjct: 263 YQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTA 322
Query: 240 IISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKA 299
++SV+VP+P+F QTK +L + EVR V+ V E L+E+LE +P+ I+ K + A +A
Sbjct: 323 VLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARA 382
Query: 300 ALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQ 359
AA++AR+L R+K L + LPGKLADC P SE+++VEGDSAGGSAKQGRDR+FQ
Sbjct: 383 REAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQ 442
Query: 360 AILPLRGKILNVER----KDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILT 415
AILPL+GKILNVE+ K M ++EI LI ALG G+ ++F + LRYHKIII+T
Sbjct: 443 AILPLKGKILNVEKARFDK----MLSSQEIGTLITALGCGIGRDEFNPDKLRYHKIIIMT 498
Query: 416 DADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKK 472
DADVDG+HIRTLLLTFFYR L + G +Y+ PPLYKV++GKQ QY DD L
Sbjct: 499 DADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDD 555
Score = 103 bits (259), Expect = 4e-23
Identities = 41/69 (59%), Positives = 53/69 (76%), Gaps = 1/69 (1%)
Query: 484 SIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ- 542
SIQR+KGLGEM P QLWETT++PE R L Q+ IEDA A+ +F++LMG V+ R+E I+
Sbjct: 687 SIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIEDAIAADEIFTTLMGDEVEPRREFIEE 746
Query: 543 NAANLVNLD 551
NA N+ NLD
Sbjct: 747 NALNVANLD 755
>gnl|CDD|214659 smart00433, TOP2c, TopoisomeraseII. Eukaryotic DNA topoisomerase
II, GyrB, ParE.
Length = 594
Score = 661 bits (1709), Expect = 0.0
Identities = 276/551 (50%), Positives = 362/551 (65%), Gaps = 20/551 (3%)
Query: 1 MIVTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSR-GK 59
+I TVLHAGGKF + Y VSGGLHGVG SVVNALS EV V RDG EY Q +S GK
Sbjct: 59 VIFTVLHAGGKFDDDA--YKVSGGLHGVGASVVNALSTEFEVEVARDGKEYKQSFSNNGK 116
Query: 60 PVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIAL 119
P++ + + GT++ F PD ++F D + R+RELAFLN + I L
Sbjct: 117 PLSEPKI----IGDTKKDGTKVTFKPDLEIFGMTTDDDFELLKRRLRELAFLNKGVKITL 172
Query: 120 RKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFR-KDVDGITIDLALQWCSD 178
E SD EK + F GG+++YV+ LN +K+ L + + D I +++A Q+ +D
Sbjct: 173 NDERSDEEK----TFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQY-TD 227
Query: 179 AYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLT 238
YS+ ++ + N+I T +GGTH G K +LTR +N KK K K K+ ++ GE VREGLT
Sbjct: 228 GYSENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKK--KLKEKNIKGEDVREGLT 285
Query: 239 CIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALK 298
ISV++P P+FEGQTK +LG EVR V++ V E L +LE +P I+ K L A K
Sbjct: 286 AFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIVSECLLSFLEENPVEASKIVEKVLLAAK 345
Query: 299 AALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRF 358
A AAK+AR+L R K L S SLPGKLAD SS P++ E+F+VEGDSAGGSAK GRDR F
Sbjct: 346 ARAAAKKARELTR-KKKLSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAKSGRDRDF 404
Query: 359 QAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDAD 418
QAILPLRGKILNVE+ + KNEEIQ LI ALGLG+ G+DF E LRY KIII+TDAD
Sbjct: 405 QAILPLRGKILNVEKASLDKILKNEEIQALITALGLGI-GKDFDIEKLRYGKIIIMTDAD 463
Query: 419 VDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCY---DDAELKKVKS 475
VDG+HI+ LLLTFFYRY L + G +Y+ +PPLYKV +GK+ D K ++
Sbjct: 464 VDGSHIKGLLLTFFYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVYSFYSLDEYEKWLEK 523
Query: 476 SFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVD 535
+ + + Y IQR+KGLGEM QLWETT++PE+R L + ++DA EA+++FS+LMG +V+
Sbjct: 524 TEGNKSKYEIQRYKGLGEMNADQLWETTMDPERRTLLFVTLDDADEADLIFSALMGDKVE 583
Query: 536 TRKELIQNAAN 546
RKE I+ A
Sbjct: 584 PRKEWIEENAP 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 = 540 bits (1392), Expect = 0.0
Identities = 255/561 (45%), Positives = 360/561 (64%), Gaps = 23/561 (4%)
Query: 2 IVTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRG-KP 60
+ TVLHAGGKF GY +GGLHGVG SVVNALS LEVTV RDG Y Q++ G K
Sbjct: 93 VFTVLHAGGKFD--QGGYKTAGGLHGVGASVVNALSSWLEVTVKRDGQIYQQRFENGGKI 150
Query: 61 VTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALR 120
V +L + + + GT + F PD +F T QF+ N I R++E AFL KL +
Sbjct: 151 VQSLK----KIGTTKKTGTLVHFHPDPTIFKTT-QFNSNIIKERLKESAFLLKKLKLTF- 204
Query: 121 KEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQWCSDAY 180
+D N+ +F+ GL ++V ++N K+ L V F + +GI +++A Q+ +D
Sbjct: 205 ---TDKRTNKTTVFFYENGLVDFVDYINETKETLSQVTYFEGEKNGIEVEVAFQF-NDGD 260
Query: 181 SDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCI 240
S+ +L +ANS++T +GGTH G K ++T +NS +K +K+KD +L G +REGL+ I
Sbjct: 261 SENILSFANSVKTKEGGTHENGFKLAITDVINSYARKYNLLKEKDKNLEGSDIREGLSAI 320
Query: 241 ISVRVP--NPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALK 298
ISVR+P +FEGQTK++L +PE R VVD+ VQ++L +LE + + ++ K++ A
Sbjct: 321 ISVRIPEELIQFEGQTKSKLFSPEARNVVDEIVQDHLFFFLEENNNDAKLLIDKAIKARD 380
Query: 299 AALAAKRARDLVRQKSVLRSS--SLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDR 356
A AAK+AR+ + + L GKL S P ++E+F+VEGDSAGGSAKQGRDR
Sbjct: 381 AKEAAKKAREEKKSGKKPKKEKGILSGKLTPAQSKNPAKNELFLVEGDSAGGSAKQGRDR 440
Query: 357 RFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTD 416
+FQAILPLRGK+LNVE+ A + KNEEI +I +G G+ G DF + L+Y KIII+TD
Sbjct: 441 KFQAILPLRGKVLNVEKAKLADILKNEEINTIIFCIGTGI-GADFSIKDLKYDKIIIMTD 499
Query: 417 ADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVER--GKQVQYCYDDAELKKVK 474
AD DGAHI+ LLLTFFYRY + L + G +Y+ +PPLYK+ + GK+V+Y + D EL+ VK
Sbjct: 500 ADTDGAHIQVLLLTFFYRYMRPLIELGHVYIALPPLYKLSKKDGKKVKYAWSDLELESVK 559
Query: 475 SSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARV 534
+ Y++QR+KGLGEM QLWETT+NPE R L ++ I+D A A ++LMG +V
Sbjct: 560 KKLKN---YTLQRYKGLGEMNADQLWETTMNPETRTLVRVKIDDLARAERQINTLMGDKV 616
Query: 535 DTRKELIQNAANLVNLDHLDI 555
+ RK+ I+ N + L I
Sbjct: 617 EPRKKWIEANINFSVEEELQI 637
>gnl|CDD|240272 PTZ00109, PTZ00109, DNA gyrase subunit b; Provisional.
Length = 903
Score = 430 bits (1108), Expect = e-141
Identities = 208/552 (37%), Positives = 304/552 (55%), Gaps = 94/552 (17%)
Query: 2 IVTVLHAGGKF--------------------------------------GGSSSGYSVSG 23
++TVLH+GGKF SS Y S
Sbjct: 188 VLTVLHSGGKFQDTFPKNSRSDKSEDKNDTKSSKKGKSSHVKGPKEAKEKESSQMYEYSS 247
Query: 24 GLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRF 83
GLHGVGLSVVNALS L+V V++ G Y + S+GK L+ P+ ++GT I F
Sbjct: 248 GLHGVGLSVVNALSSFLKVDVFKGGKIYSIELSKGKVTKPLSVFSCPLK---KRGTTIHF 304
Query: 84 WPD-KQVFTTAIQ-------------FDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKN 129
PD K +F T Q F+ + I RI EL++LNP LT L E E N
Sbjct: 305 LPDYKHIFKTHHQHTETEEEEGCKNGFNLDLIKNRIHELSYLNPGLTFYLVDERIANENN 364
Query: 130 QYNE--YFFAGGLEEYVQWLNTDKKPLH---DVVGFRKDVDGITIDLALQWCSDAYSDTM 184
Y GG E+++ L DK PL+ +++ R + + ++++L W ++Y+ +
Sbjct: 365 FYPYETIKHEGGTREFLEELIKDKTPLYKDINIISIRGVIKNVNVEVSLSWSLESYTALI 424
Query: 185 LGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVR 244
+AN++ T GTHI+G K ++TR +N KK+ K +++ GE +REG+T IISV+
Sbjct: 425 KSFANNVSTT-AGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISVK 483
Query: 245 VPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAK 304
+ EF+GQTKT+LGN ++ +++ V E L+E LE P++L +I +KSL+A KA AK
Sbjct: 484 LNGAEFDGQTKTKLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAK 543
Query: 305 RARDLVRQKSV-LRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILP 363
A+DL+RQK+ S+ LPGKL DC S E +E+FIVEG+SA G+AKQ R+R FQA+LP
Sbjct: 544 AAKDLIRQKNNQYYSTILPGKLVDCISDDIERNELFIVEGESAAGNAKQARNREFQAVLP 603
Query: 364 LRGKILNVER-KDEAAMYKNEEIQNLIRALGLGVKGEDFKKE------------------ 404
L+GKILN+E+ K+ +++N EI+ LI ++GL V +++
Sbjct: 604 LKGKILNIEKIKNNKKVFENSEIKLLITSIGLSVNPVTWRQYDLSHGTKASKDESVQNNN 663
Query: 405 -------------ALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPP 451
LRY KII+LTDADVDG H+R LLLT YR+ +L++ G +YV PP
Sbjct: 664 STLTKKKNSLFDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPP 723
Query: 452 LYKVERGKQVQY 463
LY++ + Q+
Sbjct: 724 LYRITNNRMKQF 735
Score = 89.6 bits (222), Expect = 1e-18
Identities = 39/94 (41%), Positives = 54/94 (57%)
Query: 453 YKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLK 512
K E G V EL K+ F + Y IQRFKGLGEMM QLWETT++P++R+L
Sbjct: 807 LKTELGTNVADTEQTDELDINKAFFKFSKHYEIQRFKGLGEMMADQLWETTMDPKKRILI 866
Query: 513 QLVIEDAAEANVVFSSLMGARVDTRKELIQNAAN 546
++ + 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 = 367 bits (943), Expect = e-120
Identities = 196/557 (35%), Positives = 290/557 (52%), Gaps = 28/557 (5%)
Query: 1 MIVTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKP 60
+I+T LHAGGKF S+ Y SGGLHGVG+SVVNALS+ +++ V+R G Y + G
Sbjct: 88 VILTTLHAGGKF--SNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAK 145
Query: 61 VTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALR 120
VT L K GT + F PD ++F + F + + +R A L + I
Sbjct: 146 VTDL--ISAGTCGKRLTGTSVHFTPDPEIFDSL-HFSVSRLYHILRAKAVLCRGVEIEFE 202
Query: 121 KEDSDPEKNQYNEYFFAGGLEEY----VQWLNT-DKKPLHDVVGFRKDVDGITIDLALQW 175
D N + + GL++Y V NT KP G + D ++ AL W
Sbjct: 203 ----DEVNNTKALWNYPDGLKDYLSEAVNGDNTLPPKPF---SGNFEG-DDEAVEWALLW 254
Query: 176 CSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVRE 235
+ M Y N I T GGTH+ G++ L L + + + + L+ E + +
Sbjct: 255 LPEGGELFMESYVNLIPTPQGGTHVNGLRQGLLDALREFCE-MRNNLPRGVKLTAEDIWD 313
Query: 236 GLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLS 295
+ ++S+++ +P+F GQTK RL + +V K V +++ +L + +V + +
Sbjct: 314 RCSYVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWL--NQNVQLAEHLAEHA 371
Query: 296 ALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRD 355
A + A+ +VR K + +LPGKLADC+ E +E+F+VEGDSAGGSAKQ RD
Sbjct: 372 ISSAQRRKRAAKKVVR-KKLTSGPALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARD 430
Query: 356 RRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILT 415
R +QAILPL GKILN + ++EI ++ ALG+ D LRY KI IL
Sbjct: 431 REYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALGIDPDSND--LSQLRYGKICILA 488
Query: 416 DADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKS 475
DAD DG HI TLL F+ + L +EG +YV PPLY+++ K+V Y D+ E +K+
Sbjct: 489 DADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRIDLSKEVYYALDEEEKEKLLY 548
Query: 476 SFP-SNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANV--VFSSLMG- 531
++QRFKGLGEM P QL ETT++P R L QL ++D + V + L+
Sbjct: 549 KLKKKKGKPNVQRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDDVQDQRVDKIMDMLLAK 608
Query: 532 ARVDTRKELIQNAANLV 548
R + R +Q + +
Sbjct: 609 KRSEDRFNWLQEKGDQI 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 = 234 bits (600), Expect = 8e-75
Identities = 83/173 (47%), Positives = 126/173 (72%), Gaps = 2/173 (1%)
Query: 138 GGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDG 196
GGL+++V+ LN DK+PLH + + + DG+ +++ALQW D+YS+ +L + N+I T +G
Sbjct: 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWT-DSYSENILSFVNNIPTPEG 59
Query: 197 GTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKT 256
GTH G +A+LTR +N KK+ +K KD+ L+G+ +REGLT +ISV+VP P+FEGQTK
Sbjct: 60 GTHETGFRAALTRAINDYAKKNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKD 119
Query: 257 RLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDL 309
+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 = 228 bits (583), Expect = 3e-73
Identities = 83/115 (72%), Positives = 95/115 (82%), Gaps = 1/115 (0%)
Query: 336 SEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLG 395
SE++IVEGDSAGGSAKQGRDRRFQAILPLRGKILNVE+ + KNEEI+ LI ALG G
Sbjct: 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTG 60
Query: 396 VKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVP 450
+ GEDF E LRYHKIII+TDADVDGAHIRTLLLTFF+RY + L + G +Y+ P
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 = 212 bits (542), Expect = 4e-67
Identities = 74/115 (64%), Positives = 91/115 (79%)
Query: 336 SEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLG 395
E+ +VEGDSAGGSAKQGRDR FQA+ PLRGKILNVE+ + KNEEIQN+I+ALGLG
Sbjct: 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLG 60
Query: 396 VKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVP 450
+ +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 = 200 bits (512), Expect = 7e-62
Identities = 83/175 (47%), Positives = 120/175 (68%), Gaps = 6/175 (3%)
Query: 139 GLEEYVQWLNTDKKPLHDVV----GFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTI 194
GL++YV+ LN DK PLH V G D I +++ALQW YS+ ++ + N+I T
Sbjct: 1 GLKDYVKELNKDKTPLHPEVIYFEGEEAFDDRIEVEVALQWNDS-YSENIVSFVNNIPTP 59
Query: 195 DGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQT 254
DGGTH++G +A+LTR LN KK +K KD ++G+ +REGLT ++SV++PNP+FEGQT
Sbjct: 60 DGGTHVDGFRAALTRALNEYAKKKGLLKKKD-KITGDDIREGLTAVVSVKIPNPQFEGQT 118
Query: 255 KTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDL 309
K +LGN EVR V+ V E ++LE +P++ IL K+L+A KA LAA++AR+L
Sbjct: 119 KEKLGNSEVRSAVESVVSEKFAKFLEKNPEIAKKILEKALAAAKARLAARKAREL 173
>gnl|CDD|177398 PHA02569, 39, DNA topoisomerase II large subunit; Provisional.
Length = 602
Score = 176 bits (447), Expect = 4e-48
Identities = 164/561 (29%), Positives = 250/561 (44%), Gaps = 92/561 (16%)
Query: 4 TVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESL---------EVTV-WRDGMEYHQ 53
T AG F ++ V+GG++GVG S+ N S EVTV +G E
Sbjct: 111 TRTKAGSNFDDTNR---VTGGMNGVGSSLTNFFSVLFIGETCDGKNEVTVNCSNGAE--N 165
Query: 54 KYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVF--TTAIQFDHNTIAGRIRELAFL 111
KP +GT + F PD F Q + I R++ LA +
Sbjct: 166 ISWSTKPGKG-------------KGTSVTFIPDFSHFEVNGLDQQYLDIILDRLQTLAVV 212
Query: 112 NPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDGITIDL 171
P + + + +Y + F G + VQ D + +
Sbjct: 213 FPDIKFTFNGKKVSGKFKKYAKQF---GDDTIVQ--ENDN-----------------VSI 250
Query: 172 ALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGE 231
AL D + L + N + T +GG H++ V + L + KK K K I ++
Sbjct: 251 ALAPSPDGFRQ--LSFVNGLHTKNGGHHVDCVMDDICEELIPMIKK----KHK-IEVTKA 303
Query: 232 HVREGLTCIISVR-VPNPEFEGQTKTRLGNP--EVRKVVDQSVQEYLTEYLELHPDVLDS 288
V+E LT ++ VR + NP F+ QTK RL +P E+R +D ++ + L+ ++
Sbjct: 304 RVKECLTIVLFVRNMSNPRFDSQTKERLTSPFGEIRNHIDLDYKKIAKQILK-TEAIIMP 362
Query: 289 I----LSKSLSALKAAL--AAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVE 342
I L++ L+A KAA AAK+A+ K + ++L GK A+ TT +F+ E
Sbjct: 363 IIEAALARKLAAEKAAETKAAKKAKKAKVAKHI--KANLIGKDAE---TT-----LFLTE 412
Query: 343 GDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFK 402
GDSA G + RD PLRGK+LN A + KN+E+ ++ GL V GE K
Sbjct: 413 GDSAIGYLIEVRDEELHGGYPLRGKVLNTWGMSYADILKNKELFDICAITGL-VLGE--K 469
Query: 403 KEALRYHKIIILTDADVDG-AHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQV 461
E + Y I I+TDADVDG I LLL FF R+ + LF++G I P+ + GK+
Sbjct: 470 AENMNYKNIAIMTDADVDGKGSIYPLLLAFFSRWPE-LFEQGRIRFVKTPVIIAQVGKET 528
Query: 462 QYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAE 521
++ Y E +K K S +SI+ KGLG + + NP + +V+ D +
Sbjct: 529 KWFYSLDEFEKAKDSLKK---WSIRYIKGLGSLRKSEYRRVINNP---VYDVVVLPDDWK 582
Query: 522 ANVVFSSLMGARVDTRKELIQ 542
+F L G D RK+ +
Sbjct: 583 E--LFEMLFGDDADLRKDWMS 601
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 148 bits (376), Expect = 1e-37
Identities = 143/569 (25%), Positives = 241/569 (42%), Gaps = 71/569 (12%)
Query: 15 SSSGY-----SVSGGLHGVGLSVVNALSESLEVTVW--RDGMEYHQKYSRGKPVTTLTCH 67
+SS Y V+GG +G G + N S V + G ++ ++ +
Sbjct: 127 TSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECVDSKSGKKFKMTWTDNMSKKS-EPR 185
Query: 68 VLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIA---GRIRELAFLNPKLTIALRKEDS 124
+ D K T++ F+PD F +FD + + R+ +LA KL + L E
Sbjct: 186 ITSYDGKKDY-TKVTFYPDYAKFGMT-EFDDDMLRLLKKRVYDLAGCFGKLKVYLNGE-R 242
Query: 125 DPEKN--QYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQWCSDAYSD 182
K+ Y + + G E ++ R +V ++ SD
Sbjct: 243 IAIKSFKDYVDLYLPDGEEGKKPPYPFVYTSVNG----RWEV-VVS-----------LSD 286
Query: 183 T---MLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTC 239
+ + NSI T GGTH V L + ++ L +K+K K K + ++ L
Sbjct: 287 GQFQQVSFVNSICTTKGGTH---VNYILDQLISKLQEKAKKKKKKGKEIKPNQIKNHLWV 343
Query: 240 IISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKA 299
++ + NP F+ QTK L + + E L +Y+ L +L++I+ + + L A
Sbjct: 344 FVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKLIKYV-LKSPILENIVEWAQAKLAA 402
Query: 300 ALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEI---FIVEGDSAGGSAKQG--- 353
L K +KS R +P KL D + + SE + EGDSA A G
Sbjct: 403 ELNKKMK---AGKKS--RILGIP-KLDDANDAGGKNSEECTLILTEGDSAKALALAGLSV 456
Query: 354 RDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIII 413
R + + PLRGK+LNV + N+EIQNL + LGL + + + LRY ++I
Sbjct: 457 VGRDYYGVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYEDPKGLRYGSLMI 516
Query: 414 LTDADVDGAHIRTLLLTFFYRYQKTLFD-EGCIYVGVPPLYKV-ERGKQVQYCYDDAELK 471
+TD D DG+HI+ LL+ + + +L G + + P+ K ++G QV + + +
Sbjct: 517 MTDQDHDGSHIKGLLINMIHHFWPSLLKNPGFLKEFITPIVKATKKGNQVISFFTIPDFE 576
Query: 472 KVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPE--------QRMLKQLVIEDAAEAN 523
K K + + I+ +KGLG T+ + E + + V D ++ +
Sbjct: 577 KWKQTVG-LKGWKIKYYKGLG---------TSTDKEGKEYFSNIDKHRIRFVYVDDSDDD 626
Query: 524 VVFSSLMGARVDTRKELIQNAANLVNLDH 552
+ + RV+ RKE I N +DH
Sbjct: 627 SIDLAFSKKRVEDRKEWITNYKGGTYVDH 655
>gnl|CDD|215593 PLN03128, PLN03128, DNA topoisomerase 2; Provisional.
Length = 1135
Score = 133 bits (337), Expect = 9e-33
Identities = 145/568 (25%), Positives = 234/568 (41%), Gaps = 87/568 (15%)
Query: 21 VSGGLHGVGLSVVNALSESLEV------------TVWRDGMEYHQKYSRGKPVTTLTCHV 68
+GG +G G + N S V V+ + M K +P T +C
Sbjct: 130 TTGGRNGYGAKLANIFSTEFTVETADGNRGKKYKQVFTNNM--SVK---SEPKIT-SC-- 181
Query: 69 LPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIA---GRIRELA-FLNPKLTIALRKEDS 124
T+I F PD F + D + +A R+ ++A L KL + L +
Sbjct: 182 ----KASENWTKITFKPDLAKFNMT-RLDEDVVALMSKRVYDIAGCLGKKLKVELNGKKL 236
Query: 125 DPEKNQYNEYFFAGGLEEYVQ-WLNTDKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDT 183
++YV +L + + + K D + ++L SD S
Sbjct: 237 P-----------VKSFQDYVGLYLGPNSREDPLPRIYEKVNDRWEVCVSL---SDG-SFQ 281
Query: 184 MLGYANSIRTIDGGTHIEGVKASLT-RTLNSLGKKSKTVKDKDISLSGEHVREGLTCIIS 242
+ + NSI TI GGTH++ V + + KK+K + ++ L ++
Sbjct: 282 QVSFVNSIATIKGGTHVDYVADQIVKHIQEKVKKKNK----NATHVKPFQIKNHLWVFVN 337
Query: 243 VRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLE--LHPDVLDSILS----KSLSA 296
+ NP F+ QTK L R S E E+L+ V+++ILS K
Sbjct: 338 CLIENPTFDSQTKETL---TTRPSSFGSKCELSEEFLKKVEKCGVVENILSWAQFKQQKE 394
Query: 297 LKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESE---IFIVEGDSAGGSAKQG 353
LK AKR R +P KL D + ++S+ + + EGDSA A G
Sbjct: 395 LKKKDGAKRQRLT----------GIP-KLDDANDAGGKKSKDCTLILTEGDSAKALAMSG 443
Query: 354 RD---RRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKE---ALR 407
R + PLRGK+LNV + KN EI N+ + LGL G+ + +E +LR
Sbjct: 444 LSVVGRDHYGVFPLRGKLLNVREASHKQIMKNAEITNIKQILGLQ-FGKTYDEENTKSLR 502
Query: 408 YHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFD-EGCIYVGVPPLYKVERGKQVQYCYD 466
Y ++I+TD D DG+HI+ L++ FF+ + +L G + + P+ K +G + Y
Sbjct: 503 YGHLMIMTDQDHDGSHIKGLIINFFHSFWPSLLKIPGFLVEFITPIVKATKGGKSLSFYT 562
Query: 467 DAELKKVKSSFPSNAL-YSIQRFKGLGEMMPVQLWE--TTLNPEQRMLKQLVIEDAAEAN 523
E + K S ++I+ +KGLG + E + L+ ++ ED +
Sbjct: 563 MPEYEAWKESLEGETKGWTIKYYKGLGTSTSEEAKEYFSNLDIHKKEFLWQSDEDGDLID 622
Query: 524 VVFSSLMGARVDTRKELIQNAANLVNLD 551
+ FS RV+ RK + N LD
Sbjct: 623 MAFSK---KRVEDRKIWLNNYEPGTFLD 647
>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 = 109 bits (274), Expect = 4e-29
Identities = 37/60 (61%), Positives = 46/60 (76%)
Query: 483 YSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ 542
IQRFKGLGEM P QLWETT++PE R L Q+ IEDA EA+ +FS+LMG V+ R+E I+
Sbjct: 6 VEIQRFKGLGEMNPEQLWETTMDPETRRLLQVTIEDAEEADEMFSTLMGKDVEPRREFIE 65
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 117 bits (295), Expect = 2e-27
Identities = 99/323 (30%), Positives = 158/323 (48%), Gaps = 37/323 (11%)
Query: 187 YANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVP 246
+ NSI TI GGTH++ V + + K K+K+ ++ +V+ L ++ +
Sbjct: 312 FVNSIATIKGGTHVDYVTNQIANHVMEAVNK----KNKNANIKAHNVKNHLWVFVNALID 367
Query: 247 NPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLE--LHPDVLDSILS----KSLSALKAA 300
NP F+ QTK L +R+ S E ++L+ + +++++LS K LK
Sbjct: 368 NPAFDSQTKETL---TLRQSSFGSKCELSEDFLKKVMKSGIVENLLSWADFKQSKELKKT 424
Query: 301 LAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESE---IFIVEGDSAGGSAKQGR--- 354
AK R + +P KL D + + SE + + EGDSA A G
Sbjct: 425 DGAKTTR----------VTGIP-KLEDANEAGGKNSEKCTLILTEGDSAKALAVAGLSVV 473
Query: 355 DRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGL--GVKGEDFKKEALRYHKII 412
R + + PLRGK+LNV + N EI+N+ + LGL G + E K +LRY ++
Sbjct: 474 GRNYYGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYESVK--SLRYGHLM 531
Query: 413 ILTDADVDGAHIRTLLLTFFYRYQKTLFD-EGCIYVGVPPLYKV-ERGKQVQYCYDDAEL 470
I+TD D DG+HI+ LL+ F + + +L + + P+ K RGK+V Y E
Sbjct: 532 IMTDQDHDGSHIKGLLINFIHSFWPSLLKVPSFLVEFITPIVKATRRGKKVLSFYSMPEY 591
Query: 471 KKVKSSFPSNAL-YSIQRFKGLG 492
++ K S NA +SI+ +KGLG
Sbjct: 592 EEWKESLGGNATGWSIKYYKGLG 614
>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 = 90.1 bits (224), Expect = 1e-21
Identities = 40/104 (38%), Positives = 61/104 (58%), Gaps = 4/104 (3%)
Query: 342 EGDSAGGSAKQGR---DRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKG 398
EGDSA A G R + + PLRGK+LNV + +N EIQN+ + LGL
Sbjct: 7 EGDSAKALAVAGLSVVGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGK 66
Query: 399 EDFKK-EALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFD 441
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 = 78.9 bits (195), Expect = 4e-18
Identities = 22/101 (21%), Positives = 36/101 (35%), Gaps = 24/101 (23%)
Query: 337 EIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGV 396
E+ IVEG S + ++ A++ G L++E I+ L +AL
Sbjct: 1 ELIIVEGPSDAIALEKAGGVLGGAVVATSGHALDLEH-----------IKELKKALK--- 46
Query: 397 KGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQK 437
++I+ TD D +G I LL
Sbjct: 47 ----------GAKEVILATDPDREGEAIALKLLELLKPLGP 77
>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 = 2e-15
Identities = 24/125 (19%), Positives = 50/125 (40%), Gaps = 23/125 (18%)
Query: 140 LEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQWCSD--AYSDTMLGYANSIRTIDGG 197
L++ + + DK ++ + DG ++ A+ + + D + N +GG
Sbjct: 1 LKDRLAEILGDKV-ADKLIYVEGESDGFRVEGAISYPDSGRSSKDRQFSFVNGRPVREGG 59
Query: 198 THIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPN--PEFE-GQT 254
TH++ V+ + TR LN G+ VR ++S+++P + T
Sbjct: 60 THVKAVREAYTRALN-----------------GDDVRRYPVAVLSLKIPPSLVDVNVHPT 102
Query: 255 KTRLG 259
K +
Sbjct: 103 KEEVR 107
>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 = 49.3 bits (118), Expect = 9e-08
Identities = 26/105 (24%), Positives = 37/105 (35%), Gaps = 26/105 (24%)
Query: 336 SEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLG 395
++ IVEG S + Q A++ L G LN + + L R LG
Sbjct: 1 KKLIIVEGPSDALALAQAGGYG-GAVVALGGHALN------------KTRELLKRLLG-- 45
Query: 396 VKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLF 440
++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 = 40.3 bits (95), Expect = 5e-04
Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 6/83 (7%)
Query: 179 AYSD---TMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVRE 235
A SD + + NSI T GGTH++ V + + L+ + KK I++ V+
Sbjct: 38 ALSDGQFQQVSFVNSIATTKGGTHVDYVADQIVKKLDEVVKKKNK---GGINVKPFQVKN 94
Query: 236 GLTCIISVRVPNPEFEGQTKTRL 258
L ++ + NP F+ QTK L
Sbjct: 95 HLWIFVNCLIENPSFDSQTKETL 117
>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 = 37.3 bits (87), Expect = 0.003
Identities = 17/85 (20%), Positives = 25/85 (29%), Gaps = 29/85 (34%)
Query: 4 TVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPVTT 63
+ + SS V G G+GLS+V L E T+
Sbjct: 56 KIFEPFFRTDSSS--RKVGG--TGLGLSIVRKLVELHGGTIT------------------ 93
Query: 64 LTCHVLPVDSKDRQGTRIRFWPDKQ 88
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 = 36.9 bits (86), Expect = 0.004
Identities = 13/85 (15%), Positives = 22/85 (25%), Gaps = 29/85 (34%)
Query: 4 TVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPVTT 63
+ + S + G G+GLS+V L E +
Sbjct: 56 KIFEPFFRTDKRS--RKIGG--TGLGLSIVKKLVELHGGEIS------------------ 93
Query: 64 LTCHVLPVDSKDRQGTRIRFWPDKQ 88
V+S+ GT +
Sbjct: 94 -------VESEPGGGTTFTITLPLE 111
>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 = 33.8 bits (78), Expect = 0.038
Identities = 15/71 (21%), Positives = 20/71 (28%), Gaps = 25/71 (35%)
Query: 15 SSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSK 74
S S GG G+GLS+V L E + V+S+
Sbjct: 58 SDGSRSRKGGGTGLGLSIVKKLVELHGGRIE-------------------------VESE 92
Query: 75 DRQGTRIRFWP 85
GT
Sbjct: 93 PGGGTTFTITL 103
>gnl|CDD|237946 PRK15337, PRK15337, type III secretion system protein InvA;
Provisional.
Length = 686
Score = 33.4 bits (77), Expect = 0.35
Identities = 23/95 (24%), Positives = 41/95 (43%), Gaps = 6/95 (6%)
Query: 222 KDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSV-QEYLTEYLE 280
++KD+ + EHVR L I + G+ + + + EV + + + Q +L
Sbjct: 560 REKDVIMLVEHVRGALARYICHKFAA---GGELRAVVLSAEVEDAIRKGIRQTSGGTFLN 616
Query: 281 LHPDVLDSILSKSLSALKAALAAKRARDLVRQKSV 315
L P ++++ AL A RD+V SV
Sbjct: 617 LDPAESENLMDLLTLALDDLGIA--HRDIVLLVSV 649
>gnl|CDD|224572 COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA
replication, recombination, and repair].
Length = 127
Score = 31.5 bits (72), Expect = 0.42
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 403 KEALRYHKIIILTDADVDGAHIRTLL 428
K+A +Y +IILTD D G IR L
Sbjct: 50 KKAQKYKGVIILTDPDRKGERIRKKL 75
>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 = 0.68
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 6/74 (8%)
Query: 171 LALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSG 230
LA SD Y D S++T D EG+ L R SLG K+ +VK ++ +
Sbjct: 18 LAGLIDSDGYVDKAKNITASVKTEDKSVM-EGI-VKLAR---SLGIKA-SVKTREEKIDA 71
Query: 231 EHVREGLTCIISVR 244
+ V T I++
Sbjct: 72 KGVNLQFTYPITLS 85
>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 = 32.1 bits (73), Expect = 0.98
Identities = 17/82 (20%), Positives = 30/82 (36%), Gaps = 11/82 (13%)
Query: 252 GQTKTRLGNPEVRKVVDQSVQ------EYLTEYLELHPDVLDSILSKSLSALKAALAAKR 305
G + RL N + Y E++E P+ + + +S+ L+
Sbjct: 614 GAHRDRLKNLQQTAQFLDGFYPVAKKLIYTLEHIEEIPEAIFNQQQESIETLELRKQEMT 673
Query: 306 ARD-----LVRQKSVLRSSSLP 322
A + LV Q+ L + LP
Sbjct: 674 AEERAVFSLVYQQLNLITQLLP 695
>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 = 30.9 bits (70), Expect = 1.1
Identities = 22/60 (36%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 368 ILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFK--KEALRYHKIIILTDADVDGAHIR 425
I+ VE KD+ A K ++I G +K E K+A + +IILTD D G IR
Sbjct: 5 IIVVEGKDDQARIKQAFDVDVIETNGSALKDETINLIKKAQKKQGVIILTDPDFPGEKIR 64
>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 = 1.3
Identities = 18/74 (24%), Positives = 27/74 (36%), Gaps = 5/74 (6%)
Query: 419 VDGAHIRTLLLTFF---YRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKS 475
V+ + LL F + KTL + C + L V + + E K + +
Sbjct: 33 VEFRKLNKKLLKFLKEGIGFYKTLIQKLCAKYNLDLLSPVASFELLTDSLSIGESKVLAA 92
Query: 476 S--FPSNALYSIQR 487
S S AL S R
Sbjct: 93 SSPLVSYALMSCHR 106
>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 = 2.0
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 450 PPLYKVERGKQVQYCYDDAELKKVKSSFPS 479
PP Y+ ERG + Y Y + VK + PS
Sbjct: 238 PPTYRYERGSRDTYAYTKQKATGVKYNLPS 267
>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 = 30.5 bits (68), Expect = 2.3
Identities = 36/148 (24%), Positives = 56/148 (37%), Gaps = 22/148 (14%)
Query: 196 GGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTK 255
G T E +K SL T SL T ++ + VR+ + V V N
Sbjct: 63 GTTTSELLKTSLMSTATSL-----TTPKHELKTTTTGVRKNESSTSKVTVTNVTLSNAVS 117
Query: 256 TRLGNPEVRKVVDQSVQEYLTEYL---ELHPDVLDSILSKSLSALKAALAAKRARDLVRQ 312
T L + + + S++ TE L PD + ++L A +++D
Sbjct: 118 T-LQSSQNKTENQSSIRT--TEISPTSVLQPDASPKKTGTTSASLTTAETTSQSQD---- 170
Query: 313 KSVLRSSSLPGKLADCSSTTPEESEIFI 340
+ GK+A SSTTP S I +
Sbjct: 171 -------TEDGKIASTSSTTPSYSSIIL 191
>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 = 2.7
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 450 PPLYKVERGKQVQYCYDDAELKKVKSSFPS 479
P Y+ ERG + +Y Y + +K + PS
Sbjct: 238 APTYRFERGTRERYAYTKQKATGMKYNLPS 267
>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 = 3.3
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 73 SKDRQGTRIRFWPDKQVFTTAIQFDHNTIA 102
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 = 3.9
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 364 LRGKILNVERKDEAAMYKNEEIQ---NLIRALGLGVKGEDF 401
+ 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 = 4.5
Identities = 19/83 (22%), Positives = 32/83 (38%), Gaps = 11/83 (13%)
Query: 290 LSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLA--DCSSTTPEESEIFIVEGDSAG 347
L +++ +AA A R + + R+ + K T PE+ I + G
Sbjct: 236 LKNEIASAEAAAAKAREAAAAAEAAAARARAAEAKRTGETYKPTAPEKMLI----SSTGG 291
Query: 348 GSAKQGRDRRFQAILPLRGKILN 370
A +G Q P+ G+IL
Sbjct: 292 FGALRG-----QLAWPVTGRILR 309
>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated.
Length = 822
Score = 29.2 bits (66), Expect = 6.3
Identities = 28/103 (27%), Positives = 36/103 (34%), Gaps = 34/103 (33%)
Query: 347 GGSAKQ-----------GRDRRFQAILPLRGKILNVERKDE--------------AAMYK 381
GG AK+ R ++ L G I+ V+ +E A K
Sbjct: 21 GGKAKKKRVNGVPYYEFERKGEKWIVIGLSGHIVTVDFPEEYGDWRDVDPAELIDADPVK 80
Query: 382 NEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHI 424
QN I AL KK A +III TD D +G I
Sbjct: 81 KITKQNYINAL---------KKLAKDADEIIIATDYDREGELI 114
>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 = 6.5
Identities = 16/55 (29%), Positives = 21/55 (38%), Gaps = 14/55 (25%)
Query: 515 VIEDAAEANV-VFSSLMGARVDT----------RKELIQNAANLV---NLDHLDI 555
V+ A NV + SL G RK L+ N V NLD +D+
Sbjct: 51 VVNAAHAHNVKILISLAGGSPPEFTAALNDPAKRKALVDKIINYVVSYNLDGIDV 105
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 29.4 bits (67), Expect = 6.6
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 5/48 (10%)
Query: 282 HPDVLDSILSKSLSALKAALAAKRARDLVRQK--SVLRSSSLPGKLAD 327
+V DS S+ L ++ L K++R +R+K S++RS SL L D
Sbjct: 142 EGEVKDSA-SEKLRGIRRQLRRKKSR--IREKLESIIRSKSLQKYLQD 186
>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: 405 ALRYHKIIILTDADVDGAHIRTLL 428
Y +IILTD D G IR L
Sbjct: 42 KKAYRGVIILTDPDRKGEKIRKKL 65
>gnl|CDD|179711 PRK04017, PRK04017, hypothetical protein; Provisional.
Length = 132
Score = 28.0 bits (63), Expect = 7.3
Identities = 22/83 (26%), Positives = 33/83 (39%), Gaps = 29/83 (34%)
Query: 356 RRFQAILPLR-----GKILNVE-RKDEAAMYKNEEIQNLIRALGLGVKGE---------- 399
R + I L+ G + VE ++D ++ K LGV+GE
Sbjct: 8 RFEEIIEELKEFSEAGAPIIVEGKRDVESLRK------------LGVEGEIIKVSRTPLA 55
Query: 400 -DFKKEALRYHKIIILTDADVDG 421
+ A R ++IILTD D G
Sbjct: 56 EIAELIASRGKEVIILTDFDRKG 78
>gnl|CDD|218854 pfam06012, DUF908, Domain of Unknown Function (DUF908).
Length = 309
Score = 28.5 bits (64), Expect = 8.9
Identities = 27/100 (27%), Positives = 39/100 (39%), Gaps = 22/100 (22%)
Query: 226 ISLSGEHVREGLTCI----ISVRV---PNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEY 278
S + R L I IS V P F +K +PE +E L E
Sbjct: 204 KGFSDDSYRRQLLQIRLLAISNLVYLLIEPAF--SSKFLESDPEF-------FEE-LVEL 253
Query: 279 LELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRS 318
L V + + +L AL+ A++ KR V+ VLR+
Sbjct: 254 LSPSDKVPRELRTIALEALE-AISHKR----VKYSDVLRA 288
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 0.135 0.387
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: 28,479,721
Number of extensions: 2849018
Number of successful extensions: 2716
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2607
Number of HSP's successfully gapped: 59
Length of query: 555
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 453
Effective length of database: 6,413,494
Effective search space: 2905312782
Effective search space used: 2905312782
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: 62 (27.5 bits)