RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 010553
(507 letters)
>gnl|CDD|235542 PRK05644, gyrB, DNA gyrase subunit B; Validated.
Length = 638
Score = 769 bits (1988), Expect = 0.0
Identities = 276/505 (54%), Positives = 365/505 (72%), Gaps = 14/505 (2%)
Query: 3 YHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAF 62
Y+Q+Y RG PVT L + D GT + F PD ++F T +FD++T+A R+RELAF
Sbjct: 143 YYQEYERGVPVTPLEV----IGETDETGTTVTFKPDPEIFET-TEFDYDTLATRLRELAF 197
Query: 63 LNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITI 121
LN L I L D + + + + GG++EYV++LN +K+PLH + + F + DGI +
Sbjct: 198 LNKGLKITLT--DEREGEEKEETFHYEGGIKEYVEYLNRNKEPLHEEPIYFEGEKDGIEV 255
Query: 122 DLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLS 181
++A+Q+ D YS+ +L +AN+I T +GGTH EG K +LTR +N +K+K +K+KD +L+
Sbjct: 256 EVAMQYN-DGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLT 314
Query: 182 GEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSI 241
GE VREGLT +ISV+ P P+FEGQTKT+LGN EVR +VD V E L+E+LE +P+V I
Sbjct: 315 GEDVREGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKI 374
Query: 242 LSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGS 301
+ K++ A +A AA++AR+L R+KS L SSSLPGKLADCSS PEESE++IVEGDSAGGS
Sbjct: 375 VEKAILAARAREAARKARELTRRKSALESSSLPGKLADCSSKDPEESELYIVEGDSAGGS 434
Query: 302 AKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYH 361
AKQGRDRRFQAILPLRGKILNVE+ + KNEEI+ LI ALG G+ G+DF LRYH
Sbjct: 435 AKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGI-GDDFDISKLRYH 493
Query: 362 KIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAE 421
KIII+TDADVDGAHIRTLLLTFFYRY + L + G +Y+ PPLYK+++G + +Y Y D E
Sbjct: 494 KIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIKKGGK-EYAYSDEE 552
Query: 422 LKKVKSSFP--SNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFS 479
L ++ + N Y IQR+KGLGEM P QLWETT++PE R L Q+ IEDAAEA+ +FS
Sbjct: 553 LDEILAELKLKGNPKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFS 612
Query: 480 SLMGARVDTRKELIQ-NAANLVNLD 503
LMG V+ R+E I+ NA + NLD
Sbjct: 613 ILMGDDVEPRREFIEENAKYVRNLD 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 = 678 bits (1751), Expect = 0.0
Identities = 262/504 (51%), Positives = 353/504 (70%), Gaps = 12/504 (2%)
Query: 2 EYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELA 61
Y Q++ RG PVT L V+ + GT++RF PD ++F +FD+ + R+RELA
Sbjct: 141 IYRQRFERGVPVTPL--EVIGSTDTKKTGTKVRFKPDPEIFGE-TEFDYEILKRRLRELA 197
Query: 62 FLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKD-VDGIT 120
FLN + I L E + EK E+ + GGL++YV++LN K PLH+ + + DGI
Sbjct: 198 FLNKGVKITLTDERTGEEKK---EFHYEGGLKDYVEYLNKGKTPLHEEIFYFNGEKDGIA 254
Query: 121 IDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISL 180
+++ALQW +D YS+ +L + N+I T +GGTH G +++LTR +N KK +K+ D L
Sbjct: 255 VEVALQW-NDGYSENILSFVNNIPTREGGTHEAGFRSALTRAINEYAKKKNLLKEGD--L 311
Query: 181 SGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDS 240
+G+ +REGLT +ISV++P+P+FEGQTK +LGN EVR +V++ V E + +LE +P
Sbjct: 312 TGDDIREGLTAVISVKIPDPQFEGQTKEKLGNSEVRSIVEKLVSEAFSLFLEENPQEAKK 371
Query: 241 ILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGG 300
I+ K+++A KA AA++AR+L R+KS L LPGKLADC+S PE+SE+F+VEGDSAGG
Sbjct: 372 IVEKAIAAAKAREAARKARELTRRKSALDIPGLPGKLADCTSKDPEKSELFLVEGDSAGG 431
Query: 301 SAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRY 360
SAKQGRDR FQAILPLRGKILNVE+ + KNEEIQ +I ALG G+ G+DF E LRY
Sbjct: 432 SAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIQTIITALGTGI-GKDFDLEKLRY 490
Query: 361 HKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDA 420
HKIII+TDADVDGAHIRTLLLTFFYRY L + G +Y+ PPLYKV++GK+ Y YDD
Sbjct: 491 HKIIIMTDADVDGAHIRTLLLTFFYRYMPPLIENGHVYIAQPPLYKVKKGKKTFYAYDDE 550
Query: 421 ELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSS 480
EL+K+ Y IQR+KGLGEM P QLWETT++PE R L Q+ IEDA EA+ +FS+
Sbjct: 551 ELEKLLERLGKKKGYEIQRYKGLGEMNPDQLWETTMDPETRRLLQVTIEDADEADEIFST 610
Query: 481 LMGARVDTRKELIQ-NAANLVNLD 503
LMG +V+ R+ I+ NA + NLD
Sbjct: 611 LMGDKVEPRRNFIEENALFVENLD 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 = 657 bits (1697), Expect = 0.0
Identities = 257/528 (48%), Positives = 361/528 (68%), Gaps = 35/528 (6%)
Query: 2 EYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELA 61
Y Q++ RG P+ L V+ + GT +RFWPD ++F T +FD + +A R+RELA
Sbjct: 135 IYRQEFERGIPLGPL--EVVGET--KKTGTTVRFWPDPEIFET-TEFDFDILAKRLRELA 189
Query: 62 FLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGIT 120
FLN + I+L E K+ + + GG++ +V++LN +K+PLH +++ + + +GI
Sbjct: 190 FLNSGVKISLEDERDGKGKS--VTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKEGIE 247
Query: 121 IDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISL 180
+++ALQW D YS+ +L + N+I T +GGTH+EG +++LTR +NS K +K +K+ +L
Sbjct: 248 VEVALQWN-DGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNL 306
Query: 181 SGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDS 240
+GE +REGLT +ISV+VP+P+FEGQTKT+LGN EVR +V+ V E LTE+ E +P +
Sbjct: 307 TGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKA 366
Query: 241 ILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGG 300
I+ K++ A +A AA++AR+L R+KS L S LPGKLADCSS P +SE++IVEGDSAGG
Sbjct: 367 IVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGG 426
Query: 301 SAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRY 360
SAKQGRDR+FQAILPLRGKILNVE+ + N+EI +I ALG G+ G+DF E LRY
Sbjct: 427 SAKQGRDRKFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGI-GKDFDLEKLRY 485
Query: 361 HKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQ------ 414
HKIII+TDADVDG+HIRTLLLTFFYRY + L + G +Y+ PPLYKV++GK+ +
Sbjct: 486 HKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIKDDK 545
Query: 415 ---------------YCYDDAELKKVKSSFPSNAL---YSIQRFKGLGEMMPVQLWETTL 456
Y Y D E ++ K+ P + IQR+KGLGEM QLWETT+
Sbjct: 546 EKELVGEALEDLRALYIYSDKEKEEAKTQIPVHEGRKGIEIQRYKGLGEMNADQLWETTM 605
Query: 457 NPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ-NAANLVNLD 503
+PE R L ++ IEDA EA+ +FS+LMG V+ R+E I+ NA ++ NLD
Sbjct: 606 DPESRTLLKVTIEDAVEADRIFSTLMGDEVEPRREFIEANALDVKNLD 653
>gnl|CDD|235501 PRK05559, PRK05559, DNA topoisomerase IV subunit B; Reviewed.
Length = 631
Score = 595 bits (1537), Expect = 0.0
Identities = 215/504 (42%), Positives = 301/504 (59%), Gaps = 18/504 (3%)
Query: 3 YHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAF 62
Y Q++ G PV L V+ K + GTR+RFWPD ++F + +F + R+R AF
Sbjct: 143 YRQRFEGGDPVGPL--EVVGTAGKRKTGTRVRFWPDPKIFDSP-KFSPERLKERLRSKAF 199
Query: 63 LNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHD--VVGFRKDVDGIT 120
L P LTI L E + + GL++Y+ LN K+ L + V F + +G
Sbjct: 200 LLPGLTITLNDERERQT------FHYENGLKDYLAELNEGKETLPEEFVGSFEGEAEGEA 253
Query: 121 IDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISL 180
++ ALQW +D + + Y N I T GGTH G + L + + +K + K L
Sbjct: 254 VEWALQW-TDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLP-KGKKL 311
Query: 181 SGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDS 240
GE VREGL ++SV++P P+FEGQTK +LG+ E R+ V V++ +L +P++ +
Sbjct: 312 EGEDVREGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEK 371
Query: 241 ILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGG 300
+ K A+KAA A RA V++K +LPGKLADC+S PE +E+F+VEGDSAGG
Sbjct: 372 LAEK---AIKAAQARLRAAKKVKRKKKTSGPALPGKLADCTSQDPERTELFLVEGDSAGG 428
Query: 301 SAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRY 360
SAKQ RDR FQAILPLRGKILN + NEEI ++I A+G+G G+ F E LRY
Sbjct: 429 SAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIGIGP-GDSFDLEDLRY 487
Query: 361 HKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDA 420
KIII+TDADVDGAHI TLLLTFFYR+ L + G +Y+ +PPLY+V++GK+ Y D+
Sbjct: 488 GKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRVDKGKKKIYALDEE 547
Query: 421 ELKKV-KSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFS 479
E +++ K IQRFKGLGEM P QLWETT++PE R L ++ I+DA E +
Sbjct: 548 EKEELLKKLGKKGGKPEIQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEETEKLVD 607
Query: 480 SLMGARVDTRKELIQNAANLVNLD 503
LMG + + R+E I+ + +
Sbjct: 608 MLMGKKAEPRREWIEENGDFAEEE 631
>gnl|CDD|214659 smart00433, TOP2c, TopoisomeraseII. Eukaryotic DNA topoisomerase
II, GyrB, ParE.
Length = 594
Score = 579 bits (1494), Expect = 0.0
Identities = 243/502 (48%), Positives = 327/502 (65%), Gaps = 18/502 (3%)
Query: 2 EYHQKYSR-GKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIREL 60
EY Q +S GKP++ + + GT++ F PD ++F D + R+REL
Sbjct: 106 EYKQSFSNNGKPLSEPKI----IGDTKKDGTKVTFKPDLEIFGMTTDDDFELLKRRLREL 161
Query: 61 AFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFR-KDVDGI 119
AFLN + I L E SD EK + F GG+++YV+ LN +K+ L + + D I
Sbjct: 162 AFLNKGVKITLNDERSDEEK----TFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNI 217
Query: 120 TIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDIS 179
+++A Q+ +D YS+ ++ + N+I T +GGTH G K +LTR +N KK K K K+ +
Sbjct: 218 RVEVAFQY-TDGYSENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKK--KLKEKN 274
Query: 180 LSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLD 239
+ GE VREGLT ISV++P P+FEGQTK +LG EVR V++ V E L +LE +P
Sbjct: 275 IKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIVSECLLSFLEENPVEAS 334
Query: 240 SILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAG 299
I+ K L A KA AAK+AR+L R K L S SLPGKLAD SS P++ E+F+VEGDSAG
Sbjct: 335 KIVEKVLLAAKARAAAKKARELTR-KKKLSSISLPGKLADASSAGPKKCELFLVEGDSAG 393
Query: 300 GSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALR 359
GSAK GRDR FQAILPLRGKILNVE+ + KNEEIQ LI ALGLG+ G+DF E LR
Sbjct: 394 GSAKSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGI-GKDFDIEKLR 452
Query: 360 YHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCY-- 417
Y KIII+TDADVDG+HI+ LLLTFFYRY L + G +Y+ +PPLYKV +GK+
Sbjct: 453 YGKIIIMTDADVDGSHIKGLLLTFFYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVYSFY 512
Query: 418 -DDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANV 476
D K ++ + + + Y IQR+KGLGEM QLWETT++PE+R L + ++DA EA++
Sbjct: 513 SLDEYEKWLEKTEGNKSKYEIQRYKGLGEMNADQLWETTMDPERRTLLFVTLDDADEADL 572
Query: 477 VFSSLMGARVDTRKELIQNAAN 498
+FS+LMG +V+ RKE I+ A
Sbjct: 573 IFSALMGDKVEPRKEWIEENAP 594
>gnl|CDD|237860 PRK14939, gyrB, DNA gyrase subunit B; Provisional.
Length = 756
Score = 579 bits (1495), Expect = 0.0
Identities = 203/428 (47%), Positives = 285/428 (66%), Gaps = 19/428 (4%)
Query: 2 EYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELA 61
+ Q++ G PV L V D+ GT +RFWP ++F +FD++ +A R+RELA
Sbjct: 142 IHEQEFEHGVPVAPLKV----VGETDKTGTEVRFWPSPEIFEN-TEFDYDILAKRLRELA 196
Query: 62 FLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGIT 120
FLN + I L+ E E E+ + GG++ +V++LN +K PLH ++ F + DGI
Sbjct: 197 FLNSGVRIRLKDERDGKE----EEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIG 252
Query: 121 IDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISL 180
+++ALQW +D+Y + +L + N+I DGGTH+ G +A+LTRT+N+ +K K +SL
Sbjct: 253 VEVALQW-NDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSL 311
Query: 181 SGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDS 240
+G+ REGLT ++SV+VP+P+F QTK +L + EVR V+ V E L+E+LE +P+
Sbjct: 312 TGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKI 371
Query: 241 ILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGG 300
I+ K + A +A AA++AR+L R+K L + LPGKLADC P SE+++VEGDSAGG
Sbjct: 372 IVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGG 431
Query: 301 SAKQGRDRRFQAILPLRGKILNVER----KDEAAMYKNEEIQNLIRALGLGVKGEDFKKE 356
SAKQGRDR+FQAILPL+GKILNVE+ K M ++EI LI ALG G+ ++F +
Sbjct: 432 SAKQGRDRKFQAILPLKGKILNVEKARFDK----MLSSQEIGTLITALGCGIGRDEFNPD 487
Query: 357 ALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYC 416
LRYHKIII+TDADVDG+HIRTLLLTFFYR L + G +Y+ PPLYKV++GKQ QY
Sbjct: 488 KLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYL 547
Query: 417 YDDAELKK 424
DD L
Sbjct: 548 KDDEALDD 555
Score = 103 bits (259), Expect = 3e-23
Identities = 41/69 (59%), Positives = 53/69 (76%), Gaps = 1/69 (1%)
Query: 436 SIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ- 494
SIQR+KGLGEM P QLWETT++PE R L Q+ IEDA A+ +F++LMG V+ R+E I+
Sbjct: 687 SIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIEDAIAADEIFTTLMGDEVEPRREFIEE 746
Query: 495 NAANLVNLD 503
NA N+ NLD
Sbjct: 747 NALNVANLD 755
>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 = 469 bits (1208), Expect = e-160
Identities = 222/512 (43%), Positives = 325/512 (63%), Gaps = 21/512 (4%)
Query: 3 YHQKYSRG-KPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELA 61
Y Q++ G K V +L + + + GT + F PD +F T QF+ N I R++E A
Sbjct: 140 YQQRFENGGKIVQSLK----KIGTTKKTGTLVHFHPDPTIFKTT-QFNSNIIKERLKESA 194
Query: 62 FLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDGITI 121
FL KL + +D N+ +F+ GL ++V ++N K+ L V F + +GI +
Sbjct: 195 FLLKKLKLTF----TDKRTNKTTVFFYENGLVDFVDYINETKETLSQVTYFEGEKNGIEV 250
Query: 122 DLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLS 181
++A Q+ +D S+ +L +ANS++T +GGTH G K ++T +NS +K +K+KD +L
Sbjct: 251 EVAFQF-NDGDSENILSFANSVKTKEGGTHENGFKLAITDVINSYARKYNLLKEKDKNLE 309
Query: 182 GEHVREGLTCIISVRVP--NPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLD 239
G +REGL+ IISVR+P +FEGQTK++L +PE R VVD+ VQ++L +LE + +
Sbjct: 310 GSDIREGLSAIISVRIPEELIQFEGQTKSKLFSPEARNVVDEIVQDHLFFFLEENNNDAK 369
Query: 240 SILSKSLSALKAALAAKRARDLVRQKSVLRSS--SLPGKLADCSSTTPEESEIFIVEGDS 297
++ K++ A A AAK+AR+ + + L GKL S P ++E+F+VEGDS
Sbjct: 370 LLIDKAIKARDAKEAAKKAREEKKSGKKPKKEKGILSGKLTPAQSKNPAKNELFLVEGDS 429
Query: 298 AGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEA 357
AGGSAKQGRDR+FQAILPLRGK+LNVE+ A + KNEEI +I +G G+ G DF +
Sbjct: 430 AGGSAKQGRDRKFQAILPLRGKVLNVEKAKLADILKNEEINTIIFCIGTGI-GADFSIKD 488
Query: 358 LRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVER--GKQVQY 415
L+Y KIII+TDAD DGAHI+ LLLTFFYRY + L + G +Y+ +PPLYK+ + GK+V+Y
Sbjct: 489 LKYDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELGHVYIALPPLYKLSKKDGKKVKY 548
Query: 416 CYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEAN 475
+ D EL+ VK + Y++QR+KGLGEM QLWETT+NPE R L ++ I+D A A
Sbjct: 549 AWSDLELESVKKKLKN---YTLQRYKGLGEMNADQLWETTMNPETRTLVRVKIDDLARAE 605
Query: 476 VVFSSLMGARVDTRKELIQNAANLVNLDHLDI 507
++LMG +V+ RK+ I+ N + L I
Sbjct: 606 RQINTLMGDKVEPRKKWIEANINFSVEEELQI 637
>gnl|CDD|240272 PTZ00109, PTZ00109, DNA gyrase subunit b; Provisional.
Length = 903
Score = 385 bits (991), Expect = e-125
Identities = 178/465 (38%), Positives = 268/465 (57%), Gaps = 56/465 (12%)
Query: 3 YHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPD-KQVFTTAIQ-------------F 48
Y + S+GK L+ P+ ++GT I F PD K +F T Q F
Sbjct: 275 YSIELSKGKVTKPLSVFSCPLK---KRGTTIHFLPDYKHIFKTHHQHTETEEEEGCKNGF 331
Query: 49 DHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNE--YFFAGGLEEYVQWLNTDKKPL 106
+ + I RI EL++LNP LT L E E N Y GG E+++ L DK PL
Sbjct: 332 NLDLIKNRIHELSYLNPGLTFYLVDERIANENNFYPYETIKHEGGTREFLEELIKDKTPL 391
Query: 107 H---DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTL 163
+ +++ R + + ++++L W ++Y+ + +AN++ T GTHI+G K ++TR +
Sbjct: 392 YKDINIISIRGVIKNVNVEVSLSWSLESYTALIKSFANNVSTT-AGTHIDGFKYAITRCV 450
Query: 164 NSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSV 223
N KK+ K +++ GE +REG+T IISV++ EF+GQTKT+LGN ++ +++ V
Sbjct: 451 NGNIKKNGYFKGNFVNIPGEFIREGMTAIISVKLNGAEFDGQTKTKLGNHLLKTILESIV 510
Query: 224 QEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSV-LRSSSLPGKLADCSS 282
E L+E LE P++L +I +KSL+A KA AK A+DL+RQK+ S+ LPGKL DC S
Sbjct: 511 FEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYSTILPGKLVDCIS 570
Query: 283 TTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVER-KDEAAMYKNEEIQNLI 341
E +E+FIVEG+SA G+AKQ R+R FQA+LPL+GKILN+E+ K+ +++N EI+ LI
Sbjct: 571 DDIERNELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNKKVFENSEIKLLI 630
Query: 342 RALGLGVKGEDFKKE-------------------------------ALRYHKIIILTDAD 370
++GL V +++ LRY KII+LTDAD
Sbjct: 631 TSIGLSVNPVTWRQYDLSHGTKASKDESVQNNNSTLTKKKNSLFDTPLRYGKIILLTDAD 690
Query: 371 VDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQY 415
VDG H+R LLLT YR+ +L++ G +YV PPLY++ + Q+
Sbjct: 691 VDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRITNNRMKQF 735
Score = 88.8 bits (220), Expect = 1e-18
Identities = 39/94 (41%), Positives = 54/94 (57%)
Query: 405 YKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLK 464
K E G V EL K+ F + Y IQRFKGLGEMM QLWETT++P++R+L
Sbjct: 807 LKTELGTNVADTEQTDELDINKAFFKFSKHYEIQRFKGLGEMMADQLWETTMDPKKRILI 866
Query: 465 QLVIEDAAEANVVFSSLMGARVDTRKELIQNAAN 498
++ + 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 = 306 bits (784), Expect = 4e-97
Identities = 167/507 (32%), Positives = 252/507 (49%), Gaps = 26/507 (5%)
Query: 3 YHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAF 62
Y + G VT L K GT + F PD ++F + F + + +R A
Sbjct: 136 YSIAFENGAKVTDL--ISAGTCGKRLTGTSVHFTPDPEIFDSL-HFSVSRLYHILRAKAV 192
Query: 63 LNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEY----VQWLNT-DKKPLHDVVGFRKDVD 117
L + I D N + + GL++Y V NT KP G + D
Sbjct: 193 LCRGVEIEFE----DEVNNTKALWNYPDGLKDYLSEAVNGDNTLPPKPF---SGNFEG-D 244
Query: 118 GITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKD 177
++ AL W + M Y N I T GGTH+ G++ L L + + +
Sbjct: 245 DEAVEWALLWLPEGGELFMESYVNLIPTPQGGTHVNGLRQGLLDALREFCE-MRNNLPRG 303
Query: 178 ISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDV 237
+ L+ E + + + ++S+++ +P+F GQTK RL + +V K V +++ +L + +V
Sbjct: 304 VKLTAEDIWDRCSYVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWL--NQNV 361
Query: 238 LDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDS 297
+ + A + A+ +VR K + +LPGKLADC+ E +E+F+VEGDS
Sbjct: 362 QLAEHLAEHAISSAQRRKRAAKKVVR-KKLTSGPALPGKLADCTRQDLEGTELFLVEGDS 420
Query: 298 AGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEA 357
AGGSAKQ RDR +QAILPL GKILN + ++EI ++ ALG+ D
Sbjct: 421 AGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALGIDPDSND--LSQ 478
Query: 358 LRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCY 417
LRY KI IL DAD DG HI TLL F+ + L +EG +YV PPLY+++ K+V Y
Sbjct: 479 LRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRIDLSKEVYYAL 538
Query: 418 DDAELKKVKSSFP-SNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANV 476
D+ E +K+ ++QRFKGLGEM P QL ETT++P R L QL ++D + V
Sbjct: 539 DEEEKEKLLYKLKKKKGKPNVQRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDDVQDQRV 598
Query: 477 --VFSSLMG-ARVDTRKELIQNAANLV 500
+ L+ R + R +Q + +
Sbjct: 599 DKIMDMLLAKKRSEDRFNWLQEKGDQI 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 = 233 bits (598), Expect = 5e-75
Identities = 83/173 (47%), Positives = 126/173 (72%), Gaps = 2/173 (1%)
Query: 90 GGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDG 148
GGL+++V+ LN DK+PLH + + + DG+ +++ALQW D+YS+ +L + N+I T +G
Sbjct: 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWT-DSYSENILSFVNNIPTPEG 59
Query: 149 GTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKT 208
GTH G +A+LTR +N KK+ +K KD+ L+G+ +REGLT +ISV+VP P+FEGQTK
Sbjct: 60 GTHETGFRAALTRAINDYAKKNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKD 119
Query: 209 RLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDL 261
+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 = 227 bits (581), Expect = 2e-73
Identities = 83/115 (72%), Positives = 95/115 (82%), Gaps = 1/115 (0%)
Query: 288 SEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLG 347
SE++IVEGDSAGGSAKQGRDRRFQAILPLRGKILNVE+ + KNEEI+ LI ALG G
Sbjct: 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTG 60
Query: 348 VKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVP 402
+ 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 = 211 bits (541), Expect = 2e-67
Identities = 74/115 (64%), Positives = 91/115 (79%)
Query: 288 SEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLG 347
E+ +VEGDSAGGSAKQGRDR FQA+ PLRGKILNVE+ + KNEEIQN+I+ALGLG
Sbjct: 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLG 60
Query: 348 VKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVP 402
+ +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 = 199 bits (508), Expect = 9e-62
Identities = 83/175 (47%), Positives = 120/175 (68%), Gaps = 6/175 (3%)
Query: 91 GLEEYVQWLNTDKKPLHDVV----GFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTI 146
GL++YV+ LN DK PLH V G D I +++ALQW YS+ ++ + N+I T
Sbjct: 1 GLKDYVKELNKDKTPLHPEVIYFEGEEAFDDRIEVEVALQWNDS-YSENIVSFVNNIPTP 59
Query: 147 DGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQT 206
DGGTH++G +A+LTR LN KK +K KD ++G+ +REGLT ++SV++PNP+FEGQT
Sbjct: 60 DGGTHVDGFRAALTRALNEYAKKKGLLKKKD-KITGDDIREGLTAVVSVKIPNPQFEGQT 118
Query: 207 KTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDL 261
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 = 166 bits (422), Expect = 5e-45
Identities = 143/478 (29%), Positives = 222/478 (46%), Gaps = 64/478 (13%)
Query: 29 QGTRIRFWPDKQVF--TTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEY 86
+GT + F PD F Q + I R++ LA + P + + + +Y +
Sbjct: 176 KGTSVTFIPDFSHFEVNGLDQQYLDIILDRLQTLAVVFPDIKFTFNGKKVSGKFKKYAKQ 235
Query: 87 FFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTI 146
F G + VQ D + +AL D + L + N + T
Sbjct: 236 F---GDDTIVQ--ENDN-----------------VSIALAPSPDGFRQ--LSFVNGLHTK 271
Query: 147 DGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVR-VPNPEFEGQ 205
+GG H++ V + L + KK K K I ++ V+E LT ++ VR + NP F+ Q
Sbjct: 272 NGGHHVDCVMDDICEELIPMIKK----KHK-IEVTKARVKECLTIVLFVRNMSNPRFDSQ 326
Query: 206 TKTRLGNP--EVRKVVDQSVQEYLTEYLELHPDVLDSI----LSKSLSALKAAL--AAKR 257
TK RL +P E+R +D ++ + L+ ++ I L++ L+A KAA AAK+
Sbjct: 327 TKERLTSPFGEIRNHIDLDYKKIAKQILK-TEAIIMPIIEAALARKLAAEKAAETKAAKK 385
Query: 258 ARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLR 317
A+ K + ++L GK A+ TT +F+ EGDSA G + RD PLR
Sbjct: 386 AKKAKVAKHI--KANLIGKDAE---TT-----LFLTEGDSAIGYLIEVRDEELHGGYPLR 435
Query: 318 GKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDG-AHI 376
GK+LN A + KN+E+ ++ GL V GE K E + Y I I+TDADVDG I
Sbjct: 436 GKVLNTWGMSYADILKNKELFDICAITGL-VLGE--KAENMNYKNIAIMTDADVDGKGSI 492
Query: 377 RTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYS 436
LLL FF R+ + LF++G I P+ + GK+ ++ Y E +K K S +S
Sbjct: 493 YPLLLAFFSRWPE-LFEQGRIRFVKTPVIIAQVGKETKWFYSLDEFEKAKDSLKK---WS 548
Query: 437 IQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ 494
I+ KGLG + + NP + +V+ D + +F L G D RK+ +
Sbjct: 549 IRYIKGLGSLRKSEYRRVINNP---VYDVVVLPDDWKE--LFEMLFGDDADLRKDWMS 601
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 140 bits (355), Expect = 3e-35
Identities = 109/392 (27%), Positives = 179/392 (45%), Gaps = 39/392 (9%)
Query: 132 YSDT---MLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREG 188
SD + + NSI T GGTH V L + ++ L +K+K K K + ++
Sbjct: 284 LSDGQFQQVSFVNSICTTKGGTH---VNYILDQLISKLQEKAKKKKKKGKEIKPNQIKNH 340
Query: 189 LTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSA 248
L ++ + NP F+ QTK L + + E L +Y+ L +L++I+ + +
Sbjct: 341 LWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKLIKYV-LKSPILENIVEWAQAK 399
Query: 249 LKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEI---FIVEGDSAGGSAKQG 305
L A L K +KS R +P KL D + + SE + EGDSA A G
Sbjct: 400 LAAELNKKMK---AGKKS--RILGIP-KLDDANDAGGKNSEECTLILTEGDSAKALALAG 453
Query: 306 ---RDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHK 362
R + + PLRGK+LNV + N+EIQNL + LGL + + + LRY
Sbjct: 454 LSVVGRDYYGVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYEDPKGLRYGS 513
Query: 363 IIILTDADVDGAHIRTLLLTFFYRYQKTLFD-EGCIYVGVPPLYKV-ERGKQVQYCYDDA 420
++I+TD D DG+HI+ LL+ + + +L G + + P+ K ++G QV +
Sbjct: 514 LMIMTDQDHDGSHIKGLLINMIHHFWPSLLKNPGFLKEFITPIVKATKKGNQVISFFTIP 573
Query: 421 ELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPE--------QRMLKQLVIEDAA 472
+ +K K + + I+ +KGLG T+ + E + + V D +
Sbjct: 574 DFEKWKQTVG-LKGWKIKYYKGLG---------TSTDKEGKEYFSNIDKHRIRFVYVDDS 623
Query: 473 EANVVFSSLMGARVDTRKELIQNAANLVNLDH 504
+ + + + RV+ RKE I N +DH
Sbjct: 624 DDDSIDLAFSKKRVEDRKEWITNYKGGTYVDH 655
>gnl|CDD|215593 PLN03128, PLN03128, DNA topoisomerase 2; Provisional.
Length = 1135
Score = 127 bits (320), Expect = 6e-31
Identities = 132/498 (26%), Positives = 214/498 (42%), Gaps = 63/498 (12%)
Query: 31 TRIRFWPDKQVFTTAIQFDHNTIA---GRIRELA-FLNPKLTIALRKEDSDPEKNQYNEY 86
T+I F PD F + D + +A R+ ++A L KL + L +
Sbjct: 188 TKITFKPDLAKFNMT-RLDEDVVALMSKRVYDIAGCLGKKLKVELNGKKLP--------- 237
Query: 87 FFAGGLEEYVQ-WLNTDKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRT 145
++YV +L + + + K D + ++L SD S + + NSI T
Sbjct: 238 --VKSFQDYVGLYLGPNSREDPLPRIYEKVNDRWEVCVSL---SDG-SFQQVSFVNSIAT 291
Query: 146 IDGGTHIEGVKASLT-RTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEG 204
I GGTH++ V + + KK+K + ++ L ++ + NP F+
Sbjct: 292 IKGGTHVDYVADQIVKHIQEKVKKKNK----NATHVKPFQIKNHLWVFVNCLIENPTFDS 347
Query: 205 QTKTRLGNPEVRKVVDQSVQEYLTEYLE--LHPDVLDSILS----KSLSALKAALAAKRA 258
QTK L R S E E+L+ V+++ILS K LK AKR
Sbjct: 348 QTKETL---TTRPSSFGSKCELSEEFLKKVEKCGVVENILSWAQFKQQKELKKKDGAKRQ 404
Query: 259 RDLVRQKSVLRSSSLPGKLADCSSTTPEESE---IFIVEGDSAGGSAKQGRD---RRFQA 312
R +P KL D + ++S+ + + EGDSA A G R
Sbjct: 405 RLT----------GIP-KLDDANDAGGKKSKDCTLILTEGDSAKALAMSGLSVVGRDHYG 453
Query: 313 ILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKE---ALRYHKIIILTDA 369
+ PLRGK+LNV + KN EI N+ + LGL G+ + +E +LRY ++I+TD
Sbjct: 454 VFPLRGKLLNVREASHKQIMKNAEITNIKQILGLQ-FGKTYDEENTKSLRYGHLMIMTDQ 512
Query: 370 DVDGAHIRTLLLTFFYRYQKTLFD-EGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSS 428
D DG+HI+ L++ FF+ + +L G + + P+ K +G + Y E + K S
Sbjct: 513 DHDGSHIKGLIINFFHSFWPSLLKIPGFLVEFITPIVKATKGGKSLSFYTMPEYEAWKES 572
Query: 429 FPSNAL-YSIQRFKGLGEMMPVQLWE--TTLNPEQRMLKQLVIEDAAEANVVFSSLMGAR 485
++I+ +KGLG + E + L+ ++ ED ++ FS R
Sbjct: 573 LEGETKGWTIKYYKGLGTSTSEEAKEYFSNLDIHKKEFLWQSDEDGDLIDMAFSK---KR 629
Query: 486 VDTRKELIQNAANLVNLD 503
V+ RK + N LD
Sbjct: 630 VEDRKIWLNNYEPGTFLD 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 = 108 bits (271), Expect = 7e-29
Identities = 37/60 (61%), Positives = 46/60 (76%)
Query: 435 YSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ 494
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 = 116 bits (292), Expect = 2e-27
Identities = 99/323 (30%), Positives = 158/323 (48%), Gaps = 37/323 (11%)
Query: 139 YANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVP 198
+ NSI TI GGTH++ V + + K K+K+ ++ +V+ L ++ +
Sbjct: 312 FVNSIATIKGGTHVDYVTNQIANHVMEAVNK----KNKNANIKAHNVKNHLWVFVNALID 367
Query: 199 NPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLE--LHPDVLDSILS----KSLSALKAA 252
NP F+ QTK L +R+ S E ++L+ + +++++LS K LK
Sbjct: 368 NPAFDSQTKETL---TLRQSSFGSKCELSEDFLKKVMKSGIVENLLSWADFKQSKELKKT 424
Query: 253 LAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESE---IFIVEGDSAGGSAKQGR--- 306
AK R + +P KL D + + SE + + EGDSA A G
Sbjct: 425 DGAKTTR----------VTGIP-KLEDANEAGGKNSEKCTLILTEGDSAKALAVAGLSVV 473
Query: 307 DRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGL--GVKGEDFKKEALRYHKII 364
R + + PLRGK+LNV + N EI+N+ + LGL G + E K +LRY ++
Sbjct: 474 GRNYYGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYESVK--SLRYGHLM 531
Query: 365 ILTDADVDGAHIRTLLLTFFYRYQKTLFD-EGCIYVGVPPLYKV-ERGKQVQYCYDDAEL 422
I+TD D DG+HI+ LL+ F + + +L + + P+ K RGK+V Y E
Sbjct: 532 IMTDQDHDGSHIKGLLINFIHSFWPSLLKVPSFLVEFITPIVKATRRGKKVLSFYSMPEY 591
Query: 423 KKVKSSFPSNAL-YSIQRFKGLG 444
++ 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: 294 EGDSAGGSAKQGR---DRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKG 350
EGDSA A G R + + PLRGK+LNV + +N EIQN+ + LGL
Sbjct: 7 EGDSAKALAVAGLSVVGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGK 66
Query: 351 EDFKK-EALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFD 393
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 = 78.5 bits (194), Expect = 5e-18
Identities = 22/101 (21%), Positives = 36/101 (35%), Gaps = 24/101 (23%)
Query: 289 EIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGV 348
E+ IVEG S + ++ A++ G L++E I+ L +AL
Sbjct: 1 ELIIVEGPSDAIALEKAGGVLGGAVVATSGHALDLEH-----------IKELKKALK--- 46
Query: 349 KGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQK 389
++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: 92 LEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQWCSD--AYSDTMLGYANSIRTIDGG 149
L++ + + DK ++ + DG ++ A+ + + D + N +GG
Sbjct: 1 LKDRLAEILGDKV-ADKLIYVEGESDGFRVEGAISYPDSGRSSKDRQFSFVNGRPVREGG 59
Query: 150 THIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPN--PEFE-GQT 206
TH++ V+ + TR LN G+ VR ++S+++P + T
Sbjct: 60 THVKAVREAYTRALN-----------------GDDVRRYPVAVLSLKIPPSLVDVNVHPT 102
Query: 207 KTRLG 211
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: 288 SEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLG 347
++ IVEG S + Q A++ L G LN + + L R LG
Sbjct: 1 KKLIIVEGPSDALALAQAGGYG-GAVVALGGHALN------------KTRELLKRLLG-- 45
Query: 348 VKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLF 392
++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: 131 AYSD---TMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVRE 187
A SD + + NSI T GGTH++ V + + L+ + KK I++ V+
Sbjct: 38 ALSDGQFQQVSFVNSIATTKGGTHVDYVADQIVKKLDEVVKKKNK---GGINVKPFQVKN 94
Query: 188 GLTCIISVRVPNPEFEGQTKTRL 210
L ++ + NP F+ QTK L
Sbjct: 95 HLWIFVNCLIENPSFDSQTKETL 117
>gnl|CDD|237946 PRK15337, PRK15337, type III secretion system protein InvA;
Provisional.
Length = 686
Score = 33.4 bits (77), Expect = 0.30
Identities = 23/95 (24%), Positives = 41/95 (43%), Gaps = 6/95 (6%)
Query: 174 KDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSV-QEYLTEYLE 232
++KD+ + EHVR L I + G+ + + + EV + + + Q +L
Sbjct: 560 REKDVIMLVEHVRGALARYICHKFAA---GGELRAVVLSAEVEDAIRKGIRQTSGGTFLN 616
Query: 233 LHPDVLDSILSKSLSALKAALAAKRARDLVRQKSV 267
L P ++++ AL A RD+V SV
Sbjct: 617 LDPAESENLMDLLTLALDDLGIA--HRDIVLLVSV 649
>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 = 30.7 bits (70), Expect = 0.44
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 6/74 (8%)
Query: 123 LALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSG 182
LA SD Y D S++T D EG+ L R SLG K+ +VK ++ +
Sbjct: 18 LAGLIDSDGYVDKAKNITASVKTEDKSVM-EGI-VKLAR---SLGIKA-SVKTREEKIDA 71
Query: 183 EHVREGLTCIISVR 196
+ V T I++
Sbjct: 72 KGVNLQFTYPITLS 85
>gnl|CDD|224572 COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA
replication, recombination, and repair].
Length = 127
Score = 31.2 bits (71), Expect = 0.52
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 355 KEALRYHKIIILTDADVDGAHIRTLL 380
K+A +Y +IILTD D G IR L
Sbjct: 50 KKAQKYKGVIILTDPDRKGERIRKKL 75
>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 = 0.97
Identities = 17/82 (20%), Positives = 30/82 (36%), Gaps = 11/82 (13%)
Query: 204 GQTKTRLGNPEVRKVVDQSVQ------EYLTEYLELHPDVLDSILSKSLSALKAALAAKR 257
G + RL N + Y E++E P+ + + +S+ L+
Sbjct: 614 GAHRDRLKNLQQTAQFLDGFYPVAKKLIYTLEHIEEIPEAIFNQQQESIETLELRKQEMT 673
Query: 258 ARD-----LVRQKSVLRSSSLP 274
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 = 30.2 bits (68), Expect = 1.5
Identities = 22/60 (36%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 320 ILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFK--KEALRYHKIIILTDADVDGAHIR 377
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 = 29.3 bits (66), Expect = 1.8
Identities = 18/74 (24%), Positives = 27/74 (36%), Gaps = 5/74 (6%)
Query: 371 VDGAHIRTLLLTFF---YRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKS 427
V+ + LL F + KTL + C + L V + + E K + +
Sbjct: 33 VEFRKLNKKLLKFLKEGIGFYKTLIQKLCAKYNLDLLSPVASFELLTDSLSIGESKVLAA 92
Query: 428 S--FPSNALYSIQR 439
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 = 1.9
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 402 PPLYKVERGKQVQYCYDDAELKKVKSSFPS 431
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 = 2.0
Identities = 36/148 (24%), Positives = 56/148 (37%), Gaps = 22/148 (14%)
Query: 148 GGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTK 207
G T E +K SL T SL T ++ + VR+ + V V N
Sbjct: 63 GTTTSELLKTSLMSTATSL-----TTPKHELKTTTTGVRKNESSTSKVTVTNVTLSNAVS 117
Query: 208 TRLGNPEVRKVVDQSVQEYLTEYL---ELHPDVLDSILSKSLSALKAALAAKRARDLVRQ 264
T L + + + S++ TE L PD + ++L A +++D
Sbjct: 118 T-LQSSQNKTENQSSIRT--TEISPTSVLQPDASPKKTGTTSASLTTAETTSQSQD---- 170
Query: 265 KSVLRSSSLPGKLADCSSTTPEESEIFI 292
+ 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 = 30.0 bits (67), Expect = 2.6
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 402 PPLYKVERGKQVQYCYDDAELKKVKSSFPS 431
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 = 2.9
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 25 SKDRQGTRIRFWPDKQVFTTAIQFDHNTIA 54
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 = 3.6
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 316 LRGKILNVERKDEAAMYKNEEIQ---NLIRALGLGVKGEDF 353
+ G L VE + M + EI ++R +G+G+ +DF
Sbjct: 659 IDGHQLTVEITESMMMEHDTEIFKRIQILRDMGVGLSVDDF 699
>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 = 4.9
Identities = 16/55 (29%), Positives = 21/55 (38%), Gaps = 14/55 (25%)
Query: 467 VIEDAAEANV-VFSSLMGARVDT----------RKELIQNAANLV---NLDHLDI 507
V+ A NV + SL G RK L+ N V NLD +D+
Sbjct: 51 VVNAAHAHNVKILISLAGGSPPEFTAALNDPAKRKALVDKIINYVVSYNLDGIDV 105
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 29.3 bits (66), Expect = 5.4
Identities = 19/83 (22%), Positives = 32/83 (38%), Gaps = 11/83 (13%)
Query: 242 LSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLA--DCSSTTPEESEIFIVEGDSAG 299
L +++ +AA A R + + R+ + K T PE+ I + G
Sbjct: 236 LKNEIASAEAAAAKAREAAAAAEAAAARARAAEAKRTGETYKPTAPEKMLI----SSTGG 291
Query: 300 GSAKQGRDRRFQAILPLRGKILN 322
A +G Q P+ G+IL
Sbjct: 292 FGALRG-----QLAWPVTGRILR 309
>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 = 26.8 bits (60), Expect = 7.4
Identities = 11/24 (45%), Positives = 12/24 (50%)
Query: 357 ALRYHKIIILTDADVDGAHIRTLL 380
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 = 29.0 bits (66), Expect = 7.6
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 5/48 (10%)
Query: 234 HPDVLDSILSKSLSALKAALAAKRARDLVRQK--SVLRSSSLPGKLAD 279
+V DS S+ L ++ L K++R +R+K S++RS SL L D
Sbjct: 142 EGEVKDSA-SEKLRGIRRQLRRKKSR--IREKLESIIRSKSLQKYLQD 186
>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated.
Length = 822
Score = 28.8 bits (65), Expect = 8.2
Identities = 28/103 (27%), Positives = 36/103 (34%), Gaps = 34/103 (33%)
Query: 299 GGSAKQ-----------GRDRRFQAILPLRGKILNVERKDE--------------AAMYK 333
GG AK+ R ++ L G I+ V+ +E A K
Sbjct: 21 GGKAKKKRVNGVPYYEFERKGEKWIVIGLSGHIVTVDFPEEYGDWRDVDPAELIDADPVK 80
Query: 334 NEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHI 376
QN I AL KK A +III TD D +G I
Sbjct: 81 KITKQNYINAL---------KKLAKDADEIIIATDYDREGELI 114
>gnl|CDD|218854 pfam06012, DUF908, Domain of Unknown Function (DUF908).
Length = 309
Score = 28.1 bits (63), Expect = 9.9
Identities = 27/100 (27%), Positives = 39/100 (39%), Gaps = 22/100 (22%)
Query: 178 ISLSGEHVREGLTCI----ISVRV---PNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEY 230
S + R L I IS V P F +K +PE +E L E
Sbjct: 204 KGFSDDSYRRQLLQIRLLAISNLVYLLIEPAF--SSKFLESDPEF-------FEE-LVEL 253
Query: 231 LELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRS 270
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
0.318 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: 26,084,648
Number of extensions: 2610431
Number of successful extensions: 2428
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2335
Number of HSP's successfully gapped: 54
Length of query: 507
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 406
Effective length of database: 6,457,848
Effective search space: 2621886288
Effective search space used: 2621886288
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: 61 (27.1 bits)