RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 005193
(709 letters)
>gnl|CDD|235542 PRK05644, gyrB, DNA gyrase subunit B; Validated.
Length = 638
Score = 1043 bits (2699), Expect = 0.0
Identities = 369/649 (56%), Positives = 471/649 (72%), Gaps = 25/649 (3%)
Query: 70 ENPVSKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASN 129
+ ++ Y + QIQVLEGLEAVRKRP MYIGSTG RGLHHLVYEI+DN++DEA AGY +
Sbjct: 1 KEEKAQEYDASQIQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDH 60
Query: 130 IEVALLADNS---------IPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLH 180
IEV + D S IP+D+HP T K A+E VLTVLHAGGKFGG GY VSGGLH
Sbjct: 61 IEVTINEDGSITVTDNGRGIPVDIHPKTGKPAVEVVLTVLHAGGKFGGG--GYKVSGGLH 118
Query: 181 GVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPD 240
GVG+SVVNALS LEV V RDG Y+Q+Y RG PVT L + D GT + F PD
Sbjct: 119 GVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEV----IGETDETGTTVTFKPD 174
Query: 241 KQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQW 300
++F T +FD++T+A R+RELAFLN L I L D + + + + GG++EYV++
Sbjct: 175 PEIFET-TEFDYDTLATRLRELAFLNKGLKITLT--DEREGEEKEETFHYEGGIKEYVEY 231
Query: 301 LNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKA 359
LN +K+PLH + + F + DGI +++A+Q+ D YS+ +L +AN+I T +GGTH EG K
Sbjct: 232 LNRNKEPLHEEPIYFEGEKDGIEVEVAMQYN-DGYSENILSFANNINTHEGGTHEEGFKT 290
Query: 360 SLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRK 419
+LTR +N +K+K +K+KD +L+GE VREGLT +ISV+ P P+FEGQTKT+LGN EVR
Sbjct: 291 ALTRVINDYARKNKLLKEKDDNLTGEDVREGLTAVISVKHPEPQFEGQTKTKLGNSEVRG 350
Query: 420 VVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKL 479
+VD V E L+E+LE +P+V I+ K++ A +A AA++AR+L R+KS L SSSLPGKL
Sbjct: 351 IVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALESSSLPGKL 410
Query: 480 ADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEI 539
ADCSS PEESE++IVEGDSAGGSAKQGRDRRFQAILPLRGKILNVE+ + KNEEI
Sbjct: 411 ADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEI 470
Query: 540 QNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCI 599
+ LI ALG G+ G+DF LRYHKIII+TDADVDGAHIRTLLLTFFYRY + L + G +
Sbjct: 471 RALITALGTGI-GDDFDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYV 529
Query: 600 YVGVPPLYKVERGKQVQYCYDDAELKKVKSSFP--SNALYSIQRFKGLGEMMPVQLWETT 657
Y+ PPLYK+++G + +Y Y D EL ++ + N Y IQR+KGLGEM P QLWETT
Sbjct: 530 YIAQPPLYKIKKGGK-EYAYSDEELDEILAELKLKGNPKYGIQRYKGLGEMNPEQLWETT 588
Query: 658 LNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ-NAANLVNLD 705
++PE R L Q+ IEDAAEA+ +FS LMG V+ R+E I+ NA + NLD
Sbjct: 589 MDPETRTLLQVTIEDAAEADEIFSILMGDDVEPRREFIEENAKYVRNLD 637
>gnl|CDD|223265 COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), B subunit [DNA replication,
recombination, and repair].
Length = 635
Score = 913 bits (2362), Expect = 0.0
Identities = 348/641 (54%), Positives = 451/641 (70%), Gaps = 24/641 (3%)
Query: 77 YGSEQIQVLEGLEAVRKRPAMYIGSTGP-RGLHHLVYEILDNAVDEAQAGYASNIEVALL 135
Y + IQVLEGLEAVRKRP MYIGSTG RGLHHLV+E++DN++DEA AGYA I+V L
Sbjct: 6 YDASSIQVLEGLEAVRKRPGMYIGSTGDGRGLHHLVWEVVDNSIDEALAGYADRIDVTLH 65
Query: 136 ADNS---------IPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSV 186
D S IP+D+HP SA+E + TVLHAGGKF S Y VSGGLHGVG+SV
Sbjct: 66 EDGSISVEDNGRGIPVDIHPKEKVSAVEVIFTVLHAGGKFDNDS--YKVSGGLHGVGVSV 123
Query: 187 VNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTT 246
VNALS LEV V RDG Y Q++ RG PVT L V+ + GT++RF PD ++F
Sbjct: 124 VNALSTWLEVEVKRDGKIYRQRFERGVPVTPL--EVIGSTDTKKTGTKVRFKPDPEIFGE 181
Query: 247 AIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKK 306
+FD+ + R+RELAFLN + I L E + EK E+ + GGL++YV++LN K
Sbjct: 182 -TEFDYEILKRRLRELAFLNKGVKITLTDERTGEEKK---EFHYEGGLKDYVEYLNKGKT 237
Query: 307 PLHDVVGFRKD-VDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTL 365
PLH+ + + DGI +++ALQW +D YS+ +L + N+I T +GGTH G +++LTR +
Sbjct: 238 PLHEEIFYFNGEKDGIAVEVALQW-NDGYSENILSFVNNIPTREGGTHEAGFRSALTRAI 296
Query: 366 NSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSV 425
N KK +K+ D L+G+ +REGLT +ISV++P+P+FEGQTK +LGN EVR +V++ V
Sbjct: 297 NEYAKKKNLLKEGD--LTGDDIREGLTAVISVKIPDPQFEGQTKEKLGNSEVRSIVEKLV 354
Query: 426 QEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSST 485
E + +LE +P I+ K+++A KA AA++AR+L R+KS L LPGKLADC+S
Sbjct: 355 SEAFSLFLEENPQEAKKIVEKAIAAAKAREAARKARELTRRKSALDIPGLPGKLADCTSK 414
Query: 486 TPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRA 545
PE+SE+F+VEGDSAGGSAKQGRDR FQAILPLRGKILNVE+ + KNEEIQ +I A
Sbjct: 415 DPEKSELFLVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIQTIITA 474
Query: 546 LGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPP 605
LG G+ G+DF E LRYHKIII+TDADVDGAHIRTLLLTFFYRY L + G +Y+ PP
Sbjct: 475 LGTGI-GKDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMPPLIENGHVYIAQPP 533
Query: 606 LYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRML 665
LYKV++GK+ Y YDD EL+K+ Y IQR+KGLGEM P QLWETT++PE R L
Sbjct: 534 LYKVKKGKKTFYAYDDEELEKLLERLGKKKGYEIQRYKGLGEMNPDQLWETTMDPETRRL 593
Query: 666 KQLVIEDAAEANVVFSSLMGARVDTRKELIQ-NAANLVNLD 705
Q+ IEDA EA+ +FS+LMG +V+ R+ I+ NA + NLD
Sbjct: 594 LQVTIEDADEADEIFSTLMGDKVEPRRNFIEENALFVENLD 634
>gnl|CDD|233254 TIGR01059, gyrB, DNA gyrase, B subunit. This model describes the
common type II DNA topoisomerase (DNA gyrase). Two
apparently independently arising families, one in the
Proteobacteria and one in Gram-positive lineages, are
both designated toposisomerase IV. Proteins scoring
above the noise cutoff for this model and below the
trusted cutoff for topoisomerase IV models probably
should be designated GyrB [DNA metabolism, DNA
replication, recombination, and repair].
Length = 654
Score = 889 bits (2299), Expect = 0.0
Identities = 344/664 (51%), Positives = 460/664 (69%), Gaps = 46/664 (6%)
Query: 77 YGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLA 136
Y + I+VLEGLEAVRKRP MYIGSTG GLHHLVYE++DN++DEA AGY I V +
Sbjct: 1 YDASSIKVLEGLEAVRKRPGMYIGSTGETGLHHLVYEVVDNSIDEAMAGYCDTINVTIND 60
Query: 137 DNS---------IPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVV 187
D S IP+D+HP SA+E VLTVLHAGGKF S Y VSGGLHGVG+SVV
Sbjct: 61 DGSVTVEDNGRGIPVDIHPEEGISAVEVVLTVLHAGGKFDKDS--YKVSGGLHGVGVSVV 118
Query: 188 NALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTA 247
NALSE LEVTV+RDG Y Q++ RG P+ L V+ + GT +RFWPD ++F T
Sbjct: 119 NALSEWLEVTVFRDGKIYRQEFERGIPLGPL--EVVGET--KKTGTTVRFWPDPEIFET- 173
Query: 248 IQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKP 307
+FD + +A R+RELAFLN + I+L E K+ + + GG++ +V++LN +K+P
Sbjct: 174 TEFDFDILAKRLRELAFLNSGVKISLEDERDGKGKS--VTFHYEGGIKSFVKYLNRNKEP 231
Query: 308 LH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLN 366
LH +++ + + +GI +++ALQW D YS+ +L + N+I T +GGTH+EG +++LTR +N
Sbjct: 232 LHEEIIYIKGEKEGIEVEVALQWN-DGYSENILSFVNNINTREGGTHLEGFRSALTRVIN 290
Query: 367 SLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQ 426
S K +K +K+ +L+GE +REGLT +ISV+VP+P+FEGQTKT+LGN EVR +V+ V
Sbjct: 291 SYAKNNKLLKESKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLVY 350
Query: 427 EYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTT 486
E LTE+ E +P +I+ K++ A +A AA++AR+L R+KS L S LPGKLADCSS
Sbjct: 351 EKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKD 410
Query: 487 PEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRAL 546
P +SE++IVEGDSAGGSAKQGRDR+FQAILPLRGKILNVE+ + N+EI +I AL
Sbjct: 411 PSKSELYIVEGDSAGGSAKQGRDRKFQAILPLRGKILNVEKARLDKILSNQEIGAIITAL 470
Query: 547 GLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPL 606
G G+ G+DF E LRYHKIII+TDADVDG+HIRTLLLTFFYRY + L + G +Y+ PPL
Sbjct: 471 GCGI-GKDFDLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPL 529
Query: 607 YKVERGKQVQ---------------------YCYDDAELKKVKSSFPSNAL---YSIQRF 642
YKV++GK+ + Y Y D E ++ K+ P + IQR+
Sbjct: 530 YKVKKGKKERYIKDDKEKELVGEALEDLRALYIYSDKEKEEAKTQIPVHEGRKGIEIQRY 589
Query: 643 KGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ-NAANL 701
KGLGEM QLWETT++PE R L ++ IEDA EA+ +FS+LMG V+ R+E I+ NA ++
Sbjct: 590 KGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEPRREFIEANALDV 649
Query: 702 VNLD 705
NLD
Sbjct: 650 KNLD 653
>gnl|CDD|235501 PRK05559, PRK05559, DNA topoisomerase IV subunit B; Reviewed.
Length = 631
Score = 823 bits (2129), Expect = 0.0
Identities = 296/644 (45%), Positives = 396/644 (61%), Gaps = 29/644 (4%)
Query: 74 SKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVA 133
+ Y ++ I+VLEGLE VRKRP MYIGST RGLHHLV E++DN+VDEA AG+ IEV
Sbjct: 5 TNNYNADSIEVLEGLEPVRKRPGMYIGSTDTRGLHHLVQEVIDNSVDEALAGHGKRIEVT 64
Query: 134 LLADNS---------IPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGL 184
L AD S IP+ +HP KS +E +LT LHAGGKF + Y SGGLHGVG+
Sbjct: 65 LHADGSVSVRDNGRGIPVGIHPEEGKSGVEVILTKLHAGGKFSNKA--YKFSGGLHGVGV 122
Query: 185 SVVNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVF 244
SVVNALS LEV V RDG Y Q++ G PV L V+ K + GTR+RFWPD ++F
Sbjct: 123 SVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPL--EVVGTAGKRKTGTRVRFWPDPKIF 180
Query: 245 TTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTD 304
+ +F + R+R AFL P LTI L E + + GL++Y+ LN
Sbjct: 181 DSP-KFSPERLKERLRSKAFLLPGLTITLNDERERQT------FHYENGLKDYLAELNEG 233
Query: 305 KKPLHD--VVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLT 362
K+ L + V F + +G ++ ALQW +D + + Y N I T GGTH G + L
Sbjct: 234 KETLPEEFVGSFEGEAEGEAVEWALQW-TDEGGENIESYVNLIPTPQGGTHENGFREGLL 292
Query: 363 RTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVD 422
+ + +K + K L GE VREGL ++SV++P P+FEGQTK +LG+ E R+ V
Sbjct: 293 KAVREFAEKRNLLP-KGKKLEGEDVREGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVS 351
Query: 423 QSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADC 482
V++ +L +P++ + + K A+KAA A RA V++K +LPGKLADC
Sbjct: 352 GVVKDAFDLWLNQNPELAEKLAEK---AIKAAQARLRAAKKVKRKKKTSGPALPGKLADC 408
Query: 483 SSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNL 542
+S PE +E+F+VEGDSAGGSAKQ RDR FQAILPLRGKILN + NEEI ++
Sbjct: 409 TSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDI 468
Query: 543 IRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVG 602
I A+G+G G+ F E LRY KIII+TDADVDGAHI TLLLTFFYR+ L + G +Y+
Sbjct: 469 IVAIGIGP-GDSFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIA 527
Query: 603 VPPLYKVERGKQVQYCYDDAELKKV-KSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPE 661
+PPLY+V++GK+ Y D+ E +++ K IQRFKGLGEM P QLWETT++PE
Sbjct: 528 LPPLYRVDKGKKKIYALDEEEKEELLKKLGKKGGKPEIQRFKGLGEMNPDQLWETTMDPE 587
Query: 662 QRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQNAANLVNLD 705
R L ++ I+DA E + LMG + + R+E I+ + +
Sbjct: 588 TRRLVRVTIDDAEETEKLVDMLMGKKAEPRREWIEENGDFAEEE 631
>gnl|CDD|237860 PRK14939, gyrB, DNA gyrase subunit B; Provisional.
Length = 756
Score = 815 bits (2107), Expect = 0.0
Identities = 284/571 (49%), Positives = 387/571 (67%), Gaps = 31/571 (5%)
Query: 71 NPVSKTYGSEQIQVLEGLEAVRKRPAMYIGSTG-PRGLHHLVYEILDNAVDEAQAGYASN 129
+ +S +YG+ I+VL+GL+AVRKRP MYIG T GLHH+VYE++DNA+DEA AG+ +
Sbjct: 1 SMMSNSYGASSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVYEVVDNAIDEALAGHCDD 60
Query: 130 IEVALLADNS---------IPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLH 180
I V + AD S IP D+HP SA E ++TVLHAGGKF +S Y VSGGLH
Sbjct: 61 ITVTIHADGSVSVSDNGRGIPTDIHPEEGVSAAEVIMTVLHAGGKFDQNS--YKVSGGLH 118
Query: 181 GVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPD 240
GVG+SVVNALSE LE+T+ RDG + Q++ G PV L V D+ GT +RFWP
Sbjct: 119 GVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKV----VGETDKTGTEVRFWPS 174
Query: 241 KQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQW 300
++F +FD++ +A R+RELAFLN + I L+ E E E+ + GG++ +V++
Sbjct: 175 PEIFEN-TEFDYDILAKRLRELAFLNSGVRIRLKDERDGKE----EEFHYEGGIKAFVEY 229
Query: 301 LNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKA 359
LN +K PLH ++ F + DGI +++ALQW +D+Y + +L + N+I DGGTH+ G +A
Sbjct: 230 LNRNKTPLHPNIFYFSGEKDGIGVEVALQW-NDSYQENVLCFTNNIPQRDGGTHLAGFRA 288
Query: 360 SLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRK 419
+LTRT+N+ +K K +SL+G+ REGLT ++SV+VP+P+F QTK +L + EVR
Sbjct: 289 ALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRP 348
Query: 420 VVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKL 479
V+ V E L+E+LE +P+ I+ K + A +A AA++AR+L R+K L + LPGKL
Sbjct: 349 AVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKL 408
Query: 480 ADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVER----KDEAAMYK 535
ADC P SE+++VEGDSAGGSAKQGRDR+FQAILPL+GKILNVE+ K M
Sbjct: 409 ADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDK----MLS 464
Query: 536 NEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFD 595
++EI LI ALG G+ ++F + LRYHKIII+TDADVDG+HIRTLLLTFFYR L +
Sbjct: 465 SQEIGTLITALGCGIGRDEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIE 524
Query: 596 EGCIYVGVPPLYKVERGKQVQYCYDDAELKK 626
G +Y+ PPLYKV++GKQ QY DD L
Sbjct: 525 RGHLYIAQPPLYKVKKGKQEQYLKDDEALDD 555
Score = 103 bits (260), Expect = 7e-23
Identities = 41/69 (59%), Positives = 53/69 (76%), Gaps = 1/69 (1%)
Query: 638 SIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ- 696
SIQR+KGLGEM P QLWETT++PE R L Q+ IEDA A+ +F++LMG V+ R+E I+
Sbjct: 687 SIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIEDAIAADEIFTTLMGDEVEPRREFIEE 746
Query: 697 NAANLVNLD 705
NA N+ NLD
Sbjct: 747 NALNVANLD 755
>gnl|CDD|214659 smart00433, TOP2c, TopoisomeraseII. Eukaryotic DNA topoisomerase
II, GyrB, ParE.
Length = 594
Score = 744 bits (1924), Expect = 0.0
Identities = 306/609 (50%), Positives = 398/609 (65%), Gaps = 29/609 (4%)
Query: 106 GLHHLVYEILDNAVDEAQAGYASNIEVALLADNS---------IPIDLHPATNKSALETV 156
GLHHLV EI+DNA DEA AGY I+V + DNS IP+++HP K A E +
Sbjct: 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVI 60
Query: 157 LTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSR-GKPV 215
TVLHAGGKF + Y VSGGLHGVG SVVNALS EV V RDG EY Q +S GKP+
Sbjct: 61 FTVLHAGGKFDDDA--YKVSGGLHGVGASVVNALSTEFEVEVARDGKEYKQSFSNNGKPL 118
Query: 216 TTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRK 275
+ ++ KD GT++ F PD ++F D + R+RELAFLN + I L
Sbjct: 119 SEP--KIIGDTKKD--GTKVTFKPDLEIFGMTTDDDFELLKRRLRELAFLNKGVKITLND 174
Query: 276 EDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFR-KDVDGITIDLALQWCSDAY 334
E SD EK + F GG+++YV+ LN +K+ L + + D I +++A Q+ +D Y
Sbjct: 175 ERSDEEK----TFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQY-TDGY 229
Query: 335 SDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCI 394
S+ ++ + N+I T +GGTH G K +LTR +N KK K K K+ ++ GE VREGLT
Sbjct: 230 SENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKK--KLKEKNIKGEDVREGLTAF 287
Query: 395 ISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAA 454
ISV++P P+FEGQTK +LG EVR V++ V E L +LE +P I+ K L A KA
Sbjct: 288 ISVKIPEPQFEGQTKEKLGTSEVRFGVEKIVSECLLSFLEENPVEASKIVEKVLLAAKAR 347
Query: 455 LAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQA 514
AAK+AR+L R K L S SLPGKLAD SS P++ E+F+VEGDSAGGSAK GRDR FQA
Sbjct: 348 AAAKKARELTR-KKKLSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAKSGRDRDFQA 406
Query: 515 ILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVD 574
ILPLRGKILNVE+ + KNEEIQ LI ALGLG+ G+DF E LRY KIII+TDADVD
Sbjct: 407 ILPLRGKILNVEKASLDKILKNEEIQALITALGLGI-GKDFDIEKLRYGKIIIMTDADVD 465
Query: 575 GAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCY---DDAELKKVKSSF 631
G+HI+ LLLTFFYRY L + G +Y+ +PPLYKV +GK+ D K ++ +
Sbjct: 466 GSHIKGLLLTFFYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVYSFYSLDEYEKWLEKTE 525
Query: 632 PSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTR 691
+ + Y IQR+KGLGEM QLWETT++PE+R L + ++DA EA+++FS+LMG +V+ R
Sbjct: 526 GNKSKYEIQRYKGLGEMNADQLWETTMDPERRTLLFVTLDDADEADLIFSALMGDKVEPR 585
Query: 692 KELIQNAAN 700
KE I+ A
Sbjct: 586 KEWIEENAP 594
>gnl|CDD|130130 TIGR01058, parE_Gpos, DNA topoisomerase IV, B subunit,
Gram-positive. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation step
of chromosome segregation. Not every bacterium has both
a topo II and a topo IV. The topo IV families of the
Gram-positive bacteria and the Gram-negative bacteria
appear not to represent a single clade among the type II
topoisomerases, and are represented by separate models
for this reason [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 656 bits (1693), Expect = 0.0
Identities = 305/653 (46%), Positives = 422/653 (64%), Gaps = 32/653 (4%)
Query: 73 VSKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEV 132
++ Y ++ I++LEGL+AVRKRP MYIGST +GLHHLV+EI+DN+VDE AGYA NI V
Sbjct: 1 MASKYNADAIKILEGLDAVRKRPGMYIGSTDSKGLHHLVWEIVDNSVDEVLAGYADNITV 60
Query: 133 ALLADNSI---------PIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVG 183
L DNSI P +H N S +ETV TVLHAGGKF GY +GGLHGVG
Sbjct: 61 TLHKDNSITVQDDGRGIPTGIHQDGNISTVETVFTVLHAGGKFD--QGGYKTAGGLHGVG 118
Query: 184 LSVVNALSESLEVTVWRDGMEYHQKYSRG-KPVTTLTCHVLPVDSKDRQGTRIRFWPDKQ 242
SVVNALS LEVTV RDG Y Q++ G K V +L + + + GT + F PD
Sbjct: 119 ASVVNALSSWLEVTVKRDGQIYQQRFENGGKIVQSLK----KIGTTKKTGTLVHFHPDPT 174
Query: 243 VFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLN 302
+F T QF+ N I R++E AFL KL + +D N+ +F+ GL ++V ++N
Sbjct: 175 IFKTT-QFNSNIIKERLKESAFLLKKLKLTF----TDKRTNKTTVFFYENGLVDFVDYIN 229
Query: 303 TDKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLT 362
K+ L V F + +GI +++A Q+ +D S+ +L +ANS++T +GGTH G K ++T
Sbjct: 230 ETKETLSQVTYFEGEKNGIEVEVAFQF-NDGDSENILSFANSVKTKEGGTHENGFKLAIT 288
Query: 363 RTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVP--NPEFEGQTKTRLGNPEVRKV 420
+NS +K +K+KD +L G +REGL+ IISVR+P +FEGQTK++L +PE R V
Sbjct: 289 DVINSYARKYNLLKEKDKNLEGSDIREGLSAIISVRIPEELIQFEGQTKSKLFSPEARNV 348
Query: 421 VDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSS--SLPGK 478
VD+ VQ++L +LE + + ++ K++ A A AAK+AR+ + + L GK
Sbjct: 349 VDEIVQDHLFFFLEENNNDAKLLIDKAIKARDAKEAAKKAREEKKSGKKPKKEKGILSGK 408
Query: 479 LADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEE 538
L S P ++E+F+VEGDSAGGSAKQGRDR+FQAILPLRGK+LNVE+ A + KNEE
Sbjct: 409 LTPAQSKNPAKNELFLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKAKLADILKNEE 468
Query: 539 IQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGC 598
I +I +G G+ G DF + L+Y KIII+TDAD DGAHI+ LLLTFFYRY + L + G
Sbjct: 469 INTIIFCIGTGI-GADFSIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELGH 527
Query: 599 IYVGVPPLYKVER--GKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWET 656
+Y+ +PPLYK+ + GK+V+Y + D EL+ VK + Y++QR+KGLGEM QLWET
Sbjct: 528 VYIALPPLYKLSKKDGKKVKYAWSDLELESVKKKLKN---YTLQRYKGLGEMNADQLWET 584
Query: 657 TLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQNAANLVNLDHLDI 709
T+NPE R L ++ I+D A A ++LMG +V+ RK+ I+ N + L I
Sbjct: 585 TMNPETRTLVRVKIDDLARAERQINTLMGDKVEPRKKWIEANINFSVEEELQI 637
>gnl|CDD|240272 PTZ00109, PTZ00109, DNA gyrase subunit b; Provisional.
Length = 903
Score = 542 bits (1397), Expect = 0.0
Identities = 257/642 (40%), Positives = 360/642 (56%), Gaps = 103/642 (16%)
Query: 75 KTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVAL 134
Y ++ I VLEGLEAVRKRP MYIG+T +GLH L++EILDN+VDE AG + I V L
Sbjct: 98 SEYDADDIVVLEGLEAVRKRPGMYIGNTDEKGLHQLLFEILDNSVDEYLAGECNKITVVL 157
Query: 135 LADNS---------IPIDLHPATNKSALETVLTVLHAGGKF------------------- 166
D S IP D+ T KS LETVLTVLH+GGKF
Sbjct: 158 HKDGSVEISDNGRGIPCDVSEKTGKSGLETVLTVLHSGGKFQDTFPKNSRSDKSEDKNDT 217
Query: 167 -------------------GGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQ 207
SS Y S GLHGVGLSVVNALS L+V V++ G Y
Sbjct: 218 KSSKKGKSSHVKGPKEAKEKESSQMYEYSSGLHGVGLSVVNALSSFLKVDVFKGGKIYSI 277
Query: 208 KYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPD-KQVFTTAIQ-------------FDHN 253
+ S+GK L+ P+ ++GT I F PD K +F T Q F+ +
Sbjct: 278 ELSKGKVTKPLSVFSCPLK---KRGTTIHFLPDYKHIFKTHHQHTETEEEEGCKNGFNLD 334
Query: 254 TIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNE--YFFAGGLEEYVQWLNTDKKPLH-- 309
I RI EL++LNP LT L E E N Y GG E+++ L DK PL+
Sbjct: 335 LIKNRIHELSYLNPGLTFYLVDERIANENNFYPYETIKHEGGTREFLEELIKDKTPLYKD 394
Query: 310 -DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSL 368
+++ R + + ++++L W ++Y+ + +AN++ T GTHI+G K ++TR +N
Sbjct: 395 INIISIRGVIKNVNVEVSLSWSLESYTALIKSFANNVSTT-AGTHIDGFKYAITRCVNGN 453
Query: 369 GKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEY 428
KK+ K +++ GE +REG+T IISV++ EF+GQTKT+LGN ++ +++ V E
Sbjct: 454 IKKNGYFKGNFVNIPGEFIREGMTAIISVKLNGAEFDGQTKTKLGNHLLKTILESIVFEQ 513
Query: 429 LTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSV-LRSSSLPGKLADCSSTTP 487
L+E LE P++L +I +KSL+A KA AK A+DL+RQK+ S+ LPGKL DC S
Sbjct: 514 LSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYSTILPGKLVDCISDDI 573
Query: 488 EESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVER-KDEAAMYKNEEIQNLIRAL 546
E +E+FIVEG+SA G+AKQ R+R FQA+LPL+GKILN+E+ K+ +++N EI+ LI ++
Sbjct: 574 ERNELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNKKVFENSEIKLLITSI 633
Query: 547 GLGVKGEDFKKE-------------------------------ALRYHKIIILTDADVDG 575
GL V +++ LRY KII+LTDADVDG
Sbjct: 634 GLSVNPVTWRQYDLSHGTKASKDESVQNNNSTLTKKKNSLFDTPLRYGKIILLTDADVDG 693
Query: 576 AHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQY 617
H+R LLLT YR+ +L++ G +YV PPLY++ + Q+
Sbjct: 694 EHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRITNNRMKQF 735
Score = 89.9 bits (223), Expect = 2e-18
Identities = 39/94 (41%), Positives = 54/94 (57%)
Query: 607 YKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLK 666
K E G V EL K+ F + Y IQRFKGLGEMM QLWETT++P++R+L
Sbjct: 807 LKTELGTNVADTEQTDELDINKAFFKFSKHYEIQRFKGLGEMMADQLWETTMDPKKRILI 866
Query: 667 QLVIEDAAEANVVFSSLMGARVDTRKELIQNAAN 700
++ + 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 = 459 bits (1183), Expect = e-154
Identities = 239/645 (37%), Positives = 345/645 (53%), Gaps = 40/645 (6%)
Query: 76 TYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALL 135
Y ++ I+VL+GLE VRKRP MY +T P +HLV E++DN+VDEA AG+AS I V L
Sbjct: 3 NYSAKDIEVLDGLEPVRKRPGMYTDTTRP---NHLVQEVIDNSVDEALAGFASIIMVILH 59
Query: 136 ADNSI---------PIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSV 186
D SI P+D+HP SA+E +LT LHAGGKF S+ Y SGGLHGVG+SV
Sbjct: 60 QDQSIEVFDNGRGMPVDIHPKEGVSAVEVILTTLHAGGKF--SNKNYHFSGGLHGVGISV 117
Query: 187 VNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTT 246
VNALS+ +++ V+R G Y + G VT L K GT + F PD ++F +
Sbjct: 118 VNALSKRVKIKVYRQGKLYSIAFENGAKVTDL--ISAGTCGKRLTGTSVHFTPDPEIFDS 175
Query: 247 AIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEY----VQWLN 302
F + + +R A L + I D N + + GL++Y V N
Sbjct: 176 L-HFSVSRLYHILRAKAVLCRGVEIEFE----DEVNNTKALWNYPDGLKDYLSEAVNGDN 230
Query: 303 T-DKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASL 361
T KP G + D ++ AL W + M Y N I T GGTH+ G++ L
Sbjct: 231 TLPPKPF---SGNFEG-DDEAVEWALLWLPEGGELFMESYVNLIPTPQGGTHVNGLRQGL 286
Query: 362 TRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVV 421
L + + + + L+ E + + + ++S+++ +P+F GQTK RL + +V K V
Sbjct: 287 LDALREFCE-MRNNLPRGVKLTAEDIWDRCSYVLSIKMQDPQFAGQTKERLSSRQVAKFV 345
Query: 422 DQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLAD 481
+++ +L + +V + + A + A+ +VR K + +LPGKLAD
Sbjct: 346 SGVIKDAFDLWL--NQNVQLAEHLAEHAISSAQRRKRAAKKVVR-KKLTSGPALPGKLAD 402
Query: 482 CSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQN 541
C+ E +E+F+VEGDSAGGSAKQ RDR +QAILPL GKILN + ++EI +
Sbjct: 403 CTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHD 462
Query: 542 LIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYV 601
+ ALG+ D LRY KI IL DAD DG HI TLL F+ + L +EG +YV
Sbjct: 463 IEVALGIDPDSND--LSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYV 520
Query: 602 GVPPLYKVERGKQVQYCYDDAELKKVKSSFP-SNALYSIQRFKGLGEMMPVQLWETTLNP 660
PPLY+++ K+V Y D+ E +K+ ++QRFKGLGEM P QL ETT++P
Sbjct: 521 AKPPLYRIDLSKEVYYALDEEEKEKLLYKLKKKKGKPNVQRFKGLGEMNPAQLRETTMDP 580
Query: 661 EQRMLKQLVIEDAAEANV--VFSSLMG-ARVDTRKELIQNAANLV 702
R L QL ++D + V + L+ R + R +Q + +
Sbjct: 581 NTRRLVQLTLDDVQDQRVDKIMDMLLAKKRSEDRFNWLQEKGDQI 625
>gnl|CDD|238419 cd00822, TopoII_Trans_DNA_gyrase, TopoIIA_Trans_DNA_gyrase:
Transducer domain, having a ribosomal S5 domain 2-like
fold, of the type found in proteins of the type IIA
family of DNA topoisomerases similar to the B subunits
of E. coli DNA gyrase and E. coli Topoisomerase IV which
are heterodimers composed of two subunits. The type
IIA enzymes are the predominant form of topoisomerase
and are found in some bacteriophages, viruses and
archaea, and in all bacteria and eukaryotes. All type
IIA topoisomerases are related to each other at amino
acid sequence level, though their oligomeric
organization sometimes differs. TopoIIA enzymes cut
both strands of the duplex DNA to remove (relax) both
positive and negative supercoils in DNA. These enzymes
covalently attach to the 5' ends of the cut DNA,
separate the free ends of the cleaved strands, pass
another region of the duplex through this gap, then
rejoin the ends. TopoIIA enzymes also catenate/
decatenate duplex rings. E.coli DNA gyrase is a
heterodimer composed of two subunits. E. coli DNA gyrase
B subunit is known to be important in nucleotide
hydrolysis and the transduction of structural signals
from ATP-binding site to the DNA breakage/reunion
regions of the enzymes.
Length = 172
Score = 235 bits (603), Expect = 6e-74
Identities = 83/173 (47%), Positives = 126/173 (72%), Gaps = 2/173 (1%)
Query: 292 GGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDG 350
GGL+++V+ LN DK+PLH + + + DG+ +++ALQW D+YS+ +L + N+I T +G
Sbjct: 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWT-DSYSENILSFVNNIPTPEG 59
Query: 351 GTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKT 410
GTH G +A+LTR +N KK+ +K KD+ L+G+ +REGLT +ISV+VP P+FEGQTK
Sbjct: 60 GTHETGFRAALTRAINDYAKKNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKD 119
Query: 411 RLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDL 463
+LGN EVR +V+ +V+E L E+LE +P+ IL K++ A KA AA++AR+L
Sbjct: 120 KLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAILAAKAREAARKAREL 172
>gnl|CDD|173786 cd03366, TOPRIM_TopoIIA_GyrB, TOPRIM_TopoIIA_GyrB:
topoisomerase-primase (TOPRIM) nucleotidyl
transferase/hydrolase domain of the type found in
proteins of the type IIA family of DNA topoisomerases
similar to the Escherichia coli GyrB subunit. TopoIIA
enzymes cut both strands of the duplex DNA to remove
(relax) both positive and negative supercoils in DNA.
These enzymes covalently attach to the 5' ends of the
cut DNA, separate the free ends of the cleaved strands,
pass another region of the duplex through this gap, then
rejoin the ends. These proteins also catenate/
decatenate duplex rings. DNA gyrase is more effective
at relaxing supercoils than decatentating DNA. DNA
gyrase in addition inserts negative supercoils in the
presence of ATP. The TOPRIM domain has two conserved
motifs, one of which centers at a conserved glutamate
and the other one at two conserved aspartates (DxD). The
conserved glutamate may act as a general base in strand
joining and as a general acid in strand cleavage by
topisomerases. The DXD motif may co-ordinate Mg2+, a
cofactor required for full catalytic function.
Length = 114
Score = 229 bits (585), Expect = 4e-72
Identities = 83/115 (72%), Positives = 95/115 (82%), Gaps = 1/115 (0%)
Query: 490 SEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLG 549
SE++IVEGDSAGGSAKQGRDRRFQAILPLRGKILNVE+ + KNEEI+ LI ALG G
Sbjct: 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTG 60
Query: 550 VKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVP 604
+ 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 (543), Expect = 5e-66
Identities = 74/115 (64%), Positives = 91/115 (79%)
Query: 490 SEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLG 549
E+ +VEGDSAGGSAKQGRDR FQA+ PLRGKILNVE+ + KNEEIQN+I+ALGLG
Sbjct: 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLG 60
Query: 550 VKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVP 604
+ +DF + LRY KIII+TDADVDG+HIRTLLLTFFYR+ +L + G +Y+
Sbjct: 61 IGKDDFDLDKLRYGKIIIMTDADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
>gnl|CDD|215785 pfam00204, DNA_gyraseB, DNA gyrase B. This family represents the
second domain of DNA gyrase B which has a ribosomal S5
domain 2-like fold. This family is structurally related
to PF01119.
Length = 173
Score = 202 bits (515), Expect = 4e-61
Identities = 83/175 (47%), Positives = 120/175 (68%), Gaps = 6/175 (3%)
Query: 293 GLEEYVQWLNTDKKPLHDVV----GFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTI 348
GL++YV+ LN DK PLH V G D I +++ALQW YS+ ++ + N+I T
Sbjct: 1 GLKDYVKELNKDKTPLHPEVIYFEGEEAFDDRIEVEVALQWNDS-YSENIVSFVNNIPTP 59
Query: 349 DGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQT 408
DGGTH++G +A+LTR LN KK +K KD ++G+ +REGLT ++SV++PNP+FEGQT
Sbjct: 60 DGGTHVDGFRAALTRALNEYAKKKGLLKKKD-KITGDDIREGLTAVVSVKIPNPQFEGQT 118
Query: 409 KTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDL 463
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 = 207 bits (528), Expect = 3e-58
Identities = 194/671 (28%), Positives = 294/671 (43%), Gaps = 123/671 (18%)
Query: 79 SEQIQVLEGLEAVRKRPAMYIGSTGPR-----------------GLHHLVYEILDNAVDE 121
++ +VL E + KRP MYIGS GL ++ EI+DN+VDE
Sbjct: 1 KDEFKVLSDREHILKRPGMYIGSVAYEAHERFLFGKFTQVEYVPGLVKIIDEIIDNSVDE 60
Query: 122 A---QAGYASNIEVAL------LADNSIPIDLHPATNKSALETVL-----TVLHAGGKFG 167
A +A+ I+V + ++DN I T E T AG F
Sbjct: 61 AIRTNFKFANKIDVTIKNNQVTVSDNGRGIPQAMVTTPEGEEIPGPVAAWTRTKAGSNFD 120
Query: 168 GSSSGYSVSGGLHGVGLSVVNALSESL---------EVTV-WRDGMEYHQKYSRGKPVTT 217
++ V+GG++GVG S+ N S EVTV +G E KP
Sbjct: 121 DTNR---VTGGMNGVGSSLTNFFSVLFIGETCDGKNEVTVNCSNGAE--NISWSTKP--- 172
Query: 218 LTCHVLPVDSKDRQGTRIRFWPDKQVF--TTAIQFDHNTIAGRIRELAFLNPKLTIALRK 275
K +GT + F PD F Q + I R++ LA + P +
Sbjct: 173 ---------GKG-KGTSVTFIPDFSHFEVNGLDQQYLDIILDRLQTLAVVFPDIKFTFNG 222
Query: 276 EDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQWCSDAYS 335
+ + +Y + F G + VQ D + +AL D +
Sbjct: 223 KKVSGKFKKYAKQF---GDDTIVQ--ENDN-----------------VSIALAPSPDGFR 260
Query: 336 DTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCII 395
L + N + T +GG H++ V + L + KK K K I ++ V+E LT ++
Sbjct: 261 Q--LSFVNGLHTKNGGHHVDCVMDDICEELIPMIKK----KHK-IEVTKARVKECLTIVL 313
Query: 396 SVR-VPNPEFEGQTKTRLGNP--EVRKVVDQSVQEYLTEYLELHPDVLDSI----LSKSL 448
VR + NP F+ QTK RL +P E+R +D ++ + L+ ++ I L++ L
Sbjct: 314 FVRNMSNPRFDSQTKERLTSPFGEIRNHIDLDYKKIAKQILK-TEAIIMPIIEAALARKL 372
Query: 449 SALKAAL--AAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQ 506
+A KAA AAK+A+ K + ++L GK A+ TT +F+ EGDSA G +
Sbjct: 373 AAEKAAETKAAKKAKKAKVAKHI--KANLIGKDAE---TT-----LFLTEGDSAIGYLIE 422
Query: 507 GRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKII 566
RD PLRGK+LN A + KN+E+ ++ GL V GE K E + Y I
Sbjct: 423 VRDEELHGGYPLRGKVLNTWGMSYADILKNKELFDICAITGL-VLGE--KAENMNYKNIA 479
Query: 567 ILTDADVDG-AHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELK 625
I+TDADVDG I LLL FF R+ + LF++G I P+ + GK+ ++ Y E +
Sbjct: 480 IMTDADVDGKGSIYPLLLAFFSRWPE-LFEQGRIRFVKTPVIIAQVGKETKWFYSLDEFE 538
Query: 626 KVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMG 685
K K S +SI+ KGLG + + NP + +V+ D + +F L G
Sbjct: 539 KAKDSLKK---WSIRYIKGLGSLRKSEYRRVINNP---VYDVVVLPDDWKE--LFEMLFG 590
Query: 686 ARVDTRKELIQ 696
D RK+ +
Sbjct: 591 DDADLRKDWMS 601
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 161 bits (410), Expect = 4e-41
Identities = 169/697 (24%), Positives = 281/697 (40%), Gaps = 119/697 (17%)
Query: 80 EQIQVLEGLEAVRKRPAMYIGSTGPR-----------------------GLHHLVYEILD 116
E+ Q +E + RP YIGS + GL+ + EIL
Sbjct: 8 ERYQKKTQIEHILLRPDTYIGSIETQTEDMWVYDEEKNRMVYKTITYVPGLYKIFDEILV 67
Query: 117 NAVD----EAQAGYASNIEVALLADN----------SIPIDLHPATNKSALETVLTVLHA 162
NA D + + I+V + +N IP+ +H E +
Sbjct: 68 NAADNKARDKGGHRMTYIKVTIDEENGEISVYNDGEGIPVQIHKEHKIYVPEMI------ 121
Query: 163 GGKFGG--SSSGY-----SVSGGLHGVGLSVVNALSESLEVTVW--RDGMEYHQKYSRGK 213
FG +SS Y V+GG +G G + N S V + G ++ ++
Sbjct: 122 ---FGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECVDSKSGKKFKMTWTDNM 178
Query: 214 PVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIA---GRIRELAFLNPKLT 270
+ + D K T++ F+PD F +FD + + R+ +LA KL
Sbjct: 179 SKKS-EPRITSYDGKKDY-TKVTFYPDYAKFGMT-EFDDDMLRLLKKRVYDLAGCFGKLK 235
Query: 271 IALRKEDSDPEKN--QYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQ 328
+ L E K+ Y + + G E ++ R +V ++
Sbjct: 236 VYLNGE-RIAIKSFKDYVDLYLPDGEEGKKPPYPFVYTSVNG----RWEV-VVS------ 283
Query: 329 WCSDAYSDT---MLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGE 385
SD + + NSI T GGTH V L + ++ L +K+K K K +
Sbjct: 284 -----LSDGQFQQVSFVNSICTTKGGTH---VNYILDQLISKLQEKAKKKKKKGKEIKPN 335
Query: 386 HVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILS 445
++ L ++ + NP F+ QTK L + + E L +Y+ L +L++I+
Sbjct: 336 QIKNHLWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKLIKYV-LKSPILENIVE 394
Query: 446 KSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEI---FIVEGDSAGG 502
+ + L A L K +KS R +P KL D + + SE + EGDSA
Sbjct: 395 WAQAKLAAELNKKMK---AGKKS--RILGIP-KLDDANDAGGKNSEECTLILTEGDSAKA 448
Query: 503 SAKQG---RDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEA 559
A G R + + PLRGK+LNV + N+EIQNL + LGL + + +
Sbjct: 449 LALAGLSVVGRDYYGVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYEDPKG 508
Query: 560 LRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFD-EGCIYVGVPPLYKV-ERGKQVQY 617
LRY ++I+TD D DG+HI+ LL+ + + +L G + + P+ K ++G QV
Sbjct: 509 LRYGSLMIMTDQDHDGSHIKGLLINMIHHFWPSLLKNPGFLKEFITPIVKATKKGNQVIS 568
Query: 618 CYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPE--------QRMLKQLV 669
+ + +K K + + I+ +KGLG T+ + E + + V
Sbjct: 569 FFTIPDFEKWKQTVG-LKGWKIKYYKGLG---------TSTDKEGKEYFSNIDKHRIRFV 618
Query: 670 IEDAAEANVVFSSLMGARVDTRKELIQNAANLVNLDH 706
D ++ + + + RV+ RKE I N +DH
Sbjct: 619 YVDDSDDDSIDLAFSKKRVEDRKEWITNYKGGTYVDH 655
>gnl|CDD|215593 PLN03128, PLN03128, DNA topoisomerase 2; Provisional.
Length = 1135
Score = 147 bits (372), Expect = 2e-36
Identities = 170/691 (24%), Positives = 270/691 (39%), Gaps = 129/691 (18%)
Query: 88 LEAVRKRPAMYIGSTGPR---------------------GLHHLVYEILDNAVDEAQAGY 126
LE + RP YIGST GL+ + EIL NA D Q
Sbjct: 13 LEHILLRPDTYIGSTEKHTQTLWVYEGGEMVNREVTYVPGLYKIFDEILVNAADNKQRDP 72
Query: 127 ASN-IEVALLAD----------NSIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSV 175
+ + ++V + + IP+++H E + L F +
Sbjct: 73 SMDSLKVDIDVEQNTISVYNNGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEK--KT 130
Query: 176 SGGLHGVGLSVVNALSESLEV------------TVWRDGMEYHQKYSRGKPVTTLTCHVL 223
+GG +G G + N S V V+ + M K +P T +C
Sbjct: 131 TGGRNGYGAKLANIFSTEFTVETADGNRGKKYKQVFTNNM--SVK---SEPKIT-SC--- 181
Query: 224 PVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIA---GRIRELA-FLNPKLTIALRKEDSD 279
T+I F PD F + D + +A R+ ++A L KL + L +
Sbjct: 182 ---KASENWTKITFKPDLAKFNMT-RLDEDVVALMSKRVYDIAGCLGKKLKVELNGKKLP 237
Query: 280 PEKNQYNEYFFAGGLEEYVQ-WLNTDKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTM 338
++YV +L + + + K D + ++L SD S
Sbjct: 238 -----------VKSFQDYVGLYLGPNSREDPLPRIYEKVNDRWEVCVSL---SDG-SFQQ 282
Query: 339 LGYANSIRTIDGGTHIEGVKASLT-RTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISV 397
+ + NSI TI GGTH++ V + + KK+K + ++ L ++
Sbjct: 283 VSFVNSIATIKGGTHVDYVADQIVKHIQEKVKKKNK----NATHVKPFQIKNHLWVFVNC 338
Query: 398 RVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLE--LHPDVLDSILS----KSLSAL 451
+ NP F+ QTK L R S E E+L+ V+++ILS K L
Sbjct: 339 LIENPTFDSQTKETL---TTRPSSFGSKCELSEEFLKKVEKCGVVENILSWAQFKQQKEL 395
Query: 452 KAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESE---IFIVEGDSAGGSAKQGR 508
K AKR R +P KL D + ++S+ + + EGDSA A G
Sbjct: 396 KKKDGAKRQRLT----------GIP-KLDDANDAGGKKSKDCTLILTEGDSAKALAMSGL 444
Query: 509 D---RRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKE------- 558
R + PLRGK+LNV + KN EI N+ + LGL F K
Sbjct: 445 SVVGRDHYGVFPLRGKLLNVREASHKQIMKNAEITNIKQILGL-----QFGKTYDEENTK 499
Query: 559 ALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFD-EGCIYVGVPPLYKVERGKQVQY 617
+LRY ++I+TD D DG+HI+ L++ FF+ + +L G + + P+ K +G +
Sbjct: 500 SLRYGHLMIMTDQDHDGSHIKGLIINFFHSFWPSLLKIPGFLVEFITPIVKATKGGKSLS 559
Query: 618 CYDDAELKKVKSSFPSNAL-YSIQRFKGLGEMMPVQLWE--TTLNPEQRMLKQLVIEDAA 674
Y E + K S ++I+ +KGLG + E + L+ ++ ED
Sbjct: 560 FYTMPEYEAWKESLEGETKGWTIKYYKGLGTSTSEEAKEYFSNLDIHKKEFLWQSDEDGD 619
Query: 675 EANVVFSSLMGARVDTRKELIQNAANLVNLD 705
++ FS RV+ RK + N LD
Sbjct: 620 LIDMAFSK---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 = 110 bits (277), Expect = 2e-29
Identities = 37/60 (61%), Positives = 46/60 (76%)
Query: 637 YSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ 696
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 = 118 bits (298), Expect = 2e-27
Identities = 99/323 (30%), Positives = 158/323 (48%), Gaps = 37/323 (11%)
Query: 341 YANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVP 400
+ NSI TI GGTH++ V + + K K+K+ ++ +V+ L ++ +
Sbjct: 312 FVNSIATIKGGTHVDYVTNQIANHVMEAVNK----KNKNANIKAHNVKNHLWVFVNALID 367
Query: 401 NPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLE--LHPDVLDSILS----KSLSALKAA 454
NP F+ QTK L +R+ S E ++L+ + +++++LS K LK
Sbjct: 368 NPAFDSQTKETL---TLRQSSFGSKCELSEDFLKKVMKSGIVENLLSWADFKQSKELKKT 424
Query: 455 LAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESE---IFIVEGDSAGGSAKQGR--- 508
AK R + +P KL D + + SE + + EGDSA A G
Sbjct: 425 DGAKTTR----------VTGIP-KLEDANEAGGKNSEKCTLILTEGDSAKALAVAGLSVV 473
Query: 509 DRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGL--GVKGEDFKKEALRYHKII 566
R + + PLRGK+LNV + N EI+N+ + LGL G + E K +LRY ++
Sbjct: 474 GRNYYGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYESVK--SLRYGHLM 531
Query: 567 ILTDADVDGAHIRTLLLTFFYRYQKTLFD-EGCIYVGVPPLYKV-ERGKQVQYCYDDAEL 624
I+TD D DG+HI+ LL+ F + + +L + + P+ K RGK+V Y E
Sbjct: 532 IMTDQDHDGSHIKGLLINFIHSFWPSLLKVPSFLVEFITPIVKATRRGKKVLSFYSMPEY 591
Query: 625 KKVKSSFPSNAL-YSIQRFKGLG 646
++ 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 = 90.4 bits (225), Expect = 1e-21
Identities = 40/104 (38%), Positives = 61/104 (58%), Gaps = 4/104 (3%)
Query: 496 EGDSAGGSAKQGR---DRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKG 552
EGDSA A G R + + PLRGK+LNV + +N EIQN+ + LGL
Sbjct: 7 EGDSAKALAVAGLSVVGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGK 66
Query: 553 EDFKK-EALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFD 595
D++ ++LRY +++I+TD D DG+HI+ LL+ F + + +L
Sbjct: 67 SDYESTKSLRYGRLMIMTDQDHDGSHIKGLLINFIHSFWPSLLK 110
>gnl|CDD|216679 pfam01751, Toprim, Toprim domain. This is a conserved region from
DNA primase. This corresponds to the Toprim domain
common to DnaG primases, topoisomerases, OLD family
nucleases and RecR proteins. Both DnaG motifs IV and V
are present in the alignment, the DxD (V) motif may be
involved in Mg2+ binding and mutations to the conserved
glutamate (IV) completely abolish DnaG type primase
activity. DNA primase EC:2.7.7.6 is a
nucleotidyltransferase it synthesises the
oligoribonucleotide primers required for DNA replication
on the lagging strand of the replication fork; it can
also prime the leading stand and has been implicated in
cell division. This family also includes the atypical
archaeal A subunit from type II DNA topoisomerases. Type
II DNA topoisomerases catalyze the relaxation of DNA
supercoiling by causing transient double strand breaks.
Length = 86
Score = 79.2 bits (196), Expect = 4e-18
Identities = 22/101 (21%), Positives = 36/101 (35%), Gaps = 24/101 (23%)
Query: 491 EIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGV 550
E+ IVEG S + ++ A++ G L++E I+ L +AL
Sbjct: 1 ELIIVEGPSDAIALEKAGGVLGGAVVATSGHALDLEH-----------IKELKKALK--- 46
Query: 551 KGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQK 591
++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 = 3e-15
Identities = 24/125 (19%), Positives = 50/125 (40%), Gaps = 23/125 (18%)
Query: 294 LEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQWCSD--AYSDTMLGYANSIRTIDGG 351
L++ + + DK ++ + DG ++ A+ + + D + N +GG
Sbjct: 1 LKDRLAEILGDKV-ADKLIYVEGESDGFRVEGAISYPDSGRSSKDRQFSFVNGRPVREGG 59
Query: 352 THIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPN--PEFE-GQT 408
TH++ V+ + TR LN G+ VR ++S+++P + T
Sbjct: 60 THVKAVREAYTRALN-----------------GDDVRRYPVAVLSLKIPPSLVDVNVHPT 102
Query: 409 KTRLG 413
K +
Sbjct: 103 KEEVR 107
>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 = 58.5 bits (142), Expect = 1e-10
Identities = 34/149 (22%), Positives = 47/149 (31%), Gaps = 50/149 (33%)
Query: 104 PRGLHHLVYEILDNAVDEAQAGYASNIEVALLA----------DNSIPIDLHPATNKSAL 153
L ++ +LDNA+ A AG IEV L DN I I
Sbjct: 3 EDRLRQVLSNLLDNAIKHAPAG--GEIEVTLERDGGRLRITVEDNGIGIP---------P 51
Query: 154 ETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGK 213
E + + + SS V G G+GLS+V L E T+
Sbjct: 52 EDLPKIFEPFFRTDSSS--RKVGG--TGLGLSIVRKLVELHGGTIT-------------- 93
Query: 214 PVTTLTCHVLPVDSKDRQGTRIRFWPDKQ 242
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 = 55.3 bits (134), Expect = 2e-09
Identities = 28/149 (18%), Positives = 41/149 (27%), Gaps = 50/149 (33%)
Query: 104 PRGLHHLVYEILDNAVDEAQAGYASNIEVALLA----------DNSIPIDLHPATNKSAL 153
P L ++ +LDNA+ G I V L DN I
Sbjct: 3 PDRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGDHVEITVEDNGPGIPP--------- 51
Query: 154 ETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGK 213
E + + + S GG G+GLS+V L E +
Sbjct: 52 EDLEKIFEPFFRTDKRSRKI---GG-TGLGLSIVKKLVELHGGEIS-------------- 93
Query: 214 PVTTLTCHVLPVDSKDRQGTRIRFWPDKQ 242
V+S+ GT +
Sbjct: 94 -----------VESEPGGGTTFTITLPLE 111
>gnl|CDD|173773 cd00188, TOPRIM, Topoisomerase-primase domain. This is a
nucleotidyl transferase/hydrolase domain found in type
IA, type IIA and type IIB topoisomerases, bacterial
DnaG-type primases, small primase-like proteins from
bacteria and archaea, OLD family nucleases from
bacterial and archaea, and bacterial DNA repair proteins
of the RecR/M family. This domain has two conserved
motifs, one of which centers at a conserved glutamate
and the other one at two conserved aspartates (DxD).
This glutamate and two aspartates, cluster together to
form a highly acid surface patch. The conserved
glutamate may act as a general base in nucleotide
polymerization by primases and in strand joining in
topoisomerases and, as a general acid in strand cleavage
by topisomerases and nucleases. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 83
Score = 49.7 bits (119), Expect = 9e-08
Identities = 26/105 (24%), Positives = 37/105 (35%), Gaps = 26/105 (24%)
Query: 490 SEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLG 549
++ IVEG S + Q A++ L G LN + + L R LG
Sbjct: 1 KKLIIVEGPSDALALAQAGGYG-GAVVALGGHALN------------KTRELLKRLLG-- 45
Query: 550 VKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLF 594
++II TDAD +G I LL K +
Sbjct: 46 -----------EAKEVIIATDADREGEAIALRLLELLKSLGKKVR 79
>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 = 48.4 bits (116), Expect = 4e-07
Identities = 25/145 (17%), Positives = 39/145 (26%), Gaps = 54/145 (37%)
Query: 107 LHHLVYEILDNAVDEAQAGYASNIEVALLADNS------------IPIDLHPATNKSALE 154
L ++ +L NA+ G I +++ D IP +
Sbjct: 1 LQQVLLNLLSNAIKHTPEG-GGRITISVERDGDHLEIRVEDNGPGIPEEDLE-------- 51
Query: 155 TVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKP 214
+F S S GG G+GLS+V L E +
Sbjct: 52 ------RIFERF--SDGSRSRKGGGTGLGLSIVKKLVELHGGRIE--------------- 88
Query: 215 VTTLTCHVLPVDSKDRQGTRIRFWP 239
V+S+ GT
Sbjct: 89 ----------VESEPGGGTTFTITL 103
>gnl|CDD|239563 cd03481, TopoIIA_Trans_ScTopoIIA, TopoIIA_Trans_ScTopoIIA:
Transducer domain, having a ribosomal S5 domain 2-like
fold, of the type found in proteins of the type IIA
family of DNA topoisomerases similar to Saccharomyces
cerevisiae Topo IIA. S. cerevisiae Topo IIA is a
homodimer encoded by a single gene. The type IIA enzymes
are the predominant form of topoisomerase and are found
in some bacteriophages, viruses and archaea, and in all
bacteria and eukaryotes. All type IIA topoisomerases
are related to each other at amino acid sequence level,
though their oligomeric organization sometimes differs.
TopoIIA enzymes cut both strands of the duplex DNA to
remove (relax) both positive and negative supercoils in
DNA. These enzymes covalently attach to the 5' ends of
the cut DNA, separate the free ends of the cleaved
strands, pass another region of the duplex through this
gap, then rejoin the ends. TopoIIA enzymes also
catenate/ decatenate duplex rings. This transducer
domain is homologous to the second domain of the DNA
gyrase B subunit, which is known to be important in
nucleotide hydrolysis and the transduction of structural
signals from ATP-binding site to the DNA
breakage/reunion regions of the enzymes.
Length = 153
Score = 40.7 bits (96), Expect = 5e-04
Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 6/83 (7%)
Query: 333 AYSD---TMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVRE 389
A SD + + NSI T GGTH++ V + + L+ + KK I++ V+
Sbjct: 38 ALSDGQFQQVSFVNSIATTKGGTHVDYVADQIVKKLDEVVKKKNK---GGINVKPFQVKN 94
Query: 390 GLTCIISVRVPNPEFEGQTKTRL 412
L ++ + NP F+ QTK L
Sbjct: 95 HLWIFVNCLIENPSFDSQTKETL 117
>gnl|CDD|224572 COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA
replication, recombination, and repair].
Length = 127
Score = 31.9 bits (73), Expect = 0.35
Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 519 RGKILNVE-RKDEAAMYK---NEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVD 574
+++ VE + D A++ + I A+ E KK A +Y +IILTD D
Sbjct: 9 LKEVIVVEGKDDTASLKRLGDAGVIITNGSAINSLETIELIKK-AQKYKGVIILTDPDRK 67
Query: 575 GAHIRTLL 582
G IR L
Sbjct: 68 GERIRKKL 75
>gnl|CDD|237946 PRK15337, PRK15337, type III secretion system protein InvA;
Provisional.
Length = 686
Score = 33.4 bits (77), Expect = 0.51
Identities = 23/95 (24%), Positives = 41/95 (43%), Gaps = 6/95 (6%)
Query: 376 KDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSV-QEYLTEYLE 434
++KD+ + EHVR L I + G+ + + + EV + + + Q +L
Sbjct: 560 REKDVIMLVEHVRGALARYICHKFAA---GGELRAVVLSAEVEDAIRKGIRQTSGGTFLN 616
Query: 435 LHPDVLDSILSKSLSALKAALAAKRARDLVRQKSV 469
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 = 30.4 bits (69), Expect = 0.99
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 6/74 (8%)
Query: 325 LALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSG 384
LA SD Y D S++T D EG+ L R SLG K+ +VK ++ +
Sbjct: 18 LAGLIDSDGYVDKAKNITASVKTEDKSVM-EGI-VKLAR---SLGIKA-SVKTREEKIDA 71
Query: 385 EHVREGLTCIISVR 398
+ V T I++
Sbjct: 72 KGVNLQFTYPITLS 85
>gnl|CDD|232924 TIGR00334, 5S_RNA_mat_M5, ribonuclease M5. This family of
orthologous proteins shows a weak but significant
similarity to the central region of the DnaG-type DNA
primase. The region of similarity is termed the Toprim
(topoisomerase-primase) domain and is also shared by
RecR, OLD family nucleases, and type IA and II
topoisomerases [Transcription, RNA processing].
Length = 174
Score = 31.3 bits (71), Expect = 1.1
Identities = 22/60 (36%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 522 ILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFK--KEALRYHKIIILTDADVDGAHIR 579
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 = 1.6
Identities = 18/74 (24%), Positives = 27/74 (36%), Gaps = 5/74 (6%)
Query: 573 VDGAHIRTLLLTFF---YRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKS 629
V+ + LL F + KTL + C + L V + + E K + +
Sbjct: 33 VEFRKLNKKLLKFLKEGIGFYKTLIQKLCAKYNLDLLSPVASFELLTDSLSIGESKVLAA 92
Query: 630 S--FPSNALYSIQR 641
S S AL S R
Sbjct: 93 SSPLVSYALMSCHR 106
>gnl|CDD|130727 TIGR01666, YCCS, TIGR01666 family membrane protein. This model
represents a clade of sequences from gamma and beta
proteobacteria. These proteins are >700 amino acids long
and many have been annotated as putative membrane
proteins. The gene from Salmonella has been annotated as
a putative efflux transporter. The gene from E. coli has
the name yccS [Cell envelope, Other].
Length = 704
Score = 31.8 bits (72), Expect = 1.7
Identities = 17/82 (20%), Positives = 30/82 (36%), Gaps = 11/82 (13%)
Query: 406 GQTKTRLGNPEVRKVVDQSVQ------EYLTEYLELHPDVLDSILSKSLSALKAALAAKR 459
G + RL N + Y E++E P+ + + +S+ L+
Sbjct: 614 GAHRDRLKNLQQTAQFLDGFYPVAKKLIYTLEHIEEIPEAIFNQQQESIETLELRKQEMT 673
Query: 460 ARD-----LVRQKSVLRSSSLP 476
A + LV Q+ L + LP
Sbjct: 674 AEERAVFSLVYQQLNLITQLLP 695
>gnl|CDD|197325 cd09091, INPP5c_SHIP, Catalytic inositol polyphosphate
5-phosphatase (INPP5c) domain of SH2 domain containing
inositol polyphosphate 5-phosphatase-1 and -2, and
related proteins. This subfamily contains the INPP5c
domain of SHIP1 (SH2 domain containing inositol
polyphosphate 5-phosphatase-1, also known as
SHIP/INPP5D), and SHIP2 (also known as INPPL1). It
belongs to a family of Mg2+-dependent inositol
polyphosphate 5-phosphatases, which hydrolyze the
5-phosphate from the inositol ring of various 5-position
phosphorylated phosphoinositides (PIs) and inositol
phosphates (IPs), and to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. Both SHIP1 and -2 catalyze the dephosphorylation
of the PI, phosphatidylinositol 3,4,5-trisphosphate
[PI(3,4,5)P3], to phosphatidylinositol 3,4-bisphosphate
[PI(3,4)P2]. SHIP1 also converts inositol-1,3,4,5-
polyphosphate [I(1,3,4,5)P4] to
inositol-1,3,4-polyphosphate [I(1,3,4)P3]. SHIP1 and
SHIP2 have little overlap in their in vivo functions.
SHIP1 is a negative regulator of cell growth and plays a
major part in mediating the inhibitory signaling in B
cells; it is predominantly expressed in hematopoietic
cells. SHIP2 is as an inhibitor of the insulin signaling
pathway, and is implicated in actin structure
remodeling, cell adhesion and cell spreading, receptor
endocytosis and degradation, and in the JIP1-mediated
JNK pathway. SHIP2 is widely expressed, most
prominently in brain, heart and in skeletal muscle. In
addition to this INPP5c domain, SHIP1 has an N-terminal
SH2 domain, two NPXY motifs, and a C-terminal
proline-rich region (PRD), while SHIP2 has an N-terminal
SH2 domain, a C-terminal proline-rich domain (PRD),
which includes a WW-domain binding motif (PPLP), an NPXY
motif, and a sterile alpha motif (SAM) domain. The gene
encoding SHIP2 is a candidate gene for conferring a
predisposition for type 2 diabetes.
Length = 307
Score = 30.7 bits (69), Expect = 2.5
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 604 PPLYKVERGKQVQYCYDDAELKKVKSSFPS 633
PP Y+ ERG + Y Y + VK + PS
Sbjct: 238 PPTYRYERGSRDTYAYTKQKATGVKYNLPS 267
>gnl|CDD|197334 cd09100, INPP5c_SHIP1-INPP5D, Catalytic inositol polyphosphate
5-phosphatase (INPP5c) domain of SH2 domain containing
inositol polyphosphate 5-phosphatase-1 and related
proteins. This subfamily contains the INPP5c domain of
SHIP1 (SH2 domain containing inositol polyphosphate
5-phosphatase-1, also known as SHIP/INPP5D) and related
proteins. It belongs to a family of Mg2+-dependent
inositol polyphosphate 5-phosphatases, which hydrolyze
the 5-phosphate from the inositol ring of various
5-position phosphorylated phosphoinositides (PIs) and
inositol phosphates (IPs), and to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. SHIP1's enzymic activity is restricted to
phosphatidylinositol 3,4,5-trisphosphate [PI (3,4,5)P3]
and inositol-1,3,4,5- polyphosphate [I(1,3,4,5)P4]. It
converts these two phosphoinositides to
phosphatidylinositol 3,4-bisphosphate [PI (3,4)P2] and
inositol-1,3,4-polyphosphate [I(1,3,4)P3], respectively.
SHIP1 is a negative regulator of cell growth and plays a
major part in mediating the inhibitory signaling in B
cells; it is predominantly expressed in hematopoietic
cells. In addition to this INPP5c domain, SHIP1 has an
N-terminal SH2 domain, two NPXY motifs, and a C-terminal
proline-rich region (PRD). SHIP1's phosphorylated NPXY
motifs interact with proteins with phosphotyrosine
binding (PTB) domains, and facilitate the translocation
of SHIP1 to the plasma membrane to hydrolyze
PI(3,4,5)P3. SHIP1 generally acts to oppose the activity
of phosphatidylinositol 3-kinase (PI3K). It acts as a
negative signaling molecule, reducing the levels of
PI(3,4,5)P3, thereby removing the latter as a
membrane-targeting signal for PH domain-containing
effector molecules. SHIP1 may also, in certain contexts,
amplify PI3K signals. SHIP1 and SHIP2 have little
overlap in their in vivo functions.
Length = 307
Score = 30.3 bits (68), Expect = 3.4
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 604 PPLYKVERGKQVQYCYDDAELKKVKSSFPS 633
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 = 4.1
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 227 SKDRQGTRIRFWPDKQVFTTAIQFDHNTIA 256
D G R+ F PD +++ T + N A
Sbjct: 143 GNDHNGGRLVFGPDGKIYYTIGEQGRNQGA 172
>gnl|CDD|115650 pfam07010, Endomucin, Endomucin. This family consists of several
mammalian endomucin proteins. Endomucin is an early
endothelial-specific antigen that is also expressed on
putative hematopoietic progenitor cells.
Length = 259
Score = 30.1 bits (67), Expect = 4.2
Identities = 36/148 (24%), Positives = 56/148 (37%), Gaps = 22/148 (14%)
Query: 350 GGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTK 409
G T E +K SL T SL T ++ + VR+ + V V N
Sbjct: 63 GTTTSELLKTSLMSTATSL-----TTPKHELKTTTTGVRKNESSTSKVTVTNVTLSNAVS 117
Query: 410 TRLGNPEVRKVVDQSVQEYLTEYL---ELHPDVLDSILSKSLSALKAALAAKRARDLVRQ 466
T L + + + S++ TE L PD + ++L A +++D
Sbjct: 118 T-LQSSQNKTENQSSIRT--TEISPTSVLQPDASPKKTGTTSASLTTAETTSQSQD---- 170
Query: 467 KSVLRSSSLPGKLADCSSTTPEESEIFI 494
+ GK+A SSTTP S I +
Sbjct: 171 -------TEDGKIASTSSTTPSYSSIIL 191
>gnl|CDD|219571 pfam07779, Cas1_AcylT, 10 TM Acyl Transferase domain found in
Cas1p. Cas1p protein of Cryptococcus neoformans is
required for the synthesis of O-acetylated
glucuronoxylomannans, a consitutent of the capsule, and
is critical for its virulence. The multi TM domain of
the Cas1p was unified with the 10 TM Sugar
Acyltransferase superfamily. This superfamily is
comprised of members from the OatA, MdoC, OpgC, NolL and
GumG families in addition to the Cas1p family. The Cas1p
protein has a N terminal PC-Esterase domain with the
opposing Acyl esterase activity.
Length = 496
Score = 30.1 bits (68), Expect = 4.2
Identities = 20/50 (40%), Positives = 28/50 (56%), Gaps = 5/50 (10%)
Query: 10 YLHIRVLMASRCFCS-FSSSLFFKPRTNFAIRGVSSQVLTRSN---VVLP 55
Y+HIRVL+A+ F + + FF + +F + V QVL R N VVL
Sbjct: 171 YMHIRVLVAAYLFMTGYGHFTFFWKKGDFGFKRV-FQVLFRLNFLSVVLC 219
>gnl|CDD|183097 PRK11359, PRK11359, cyclic-di-GMP phosphodiesterase; Provisional.
Length = 799
Score = 30.1 bits (68), Expect = 5.4
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 518 LRGKILNVERKDEAAMYKNEEIQ---NLIRALGLGVKGEDF 555
+ G L VE + M + EI ++R +G+G+ +DF
Sbjct: 659 IDGHQLTVEITESMMMEHDTEIFKRIQILRDMGVGLSVDDF 699
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 29.7 bits (67), Expect = 5.8
Identities = 19/83 (22%), Positives = 32/83 (38%), Gaps = 11/83 (13%)
Query: 444 LSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLA--DCSSTTPEESEIFIVEGDSAG 501
L +++ +AA A R + + R+ + K T PE+ I + G
Sbjct: 236 LKNEIASAEAAAAKAREAAAAAEAAAARARAAEAKRTGETYKPTAPEKMLI----SSTGG 291
Query: 502 GSAKQGRDRRFQAILPLRGKILN 524
A +G Q P+ G+IL
Sbjct: 292 FGALRG-----QLAWPVTGRILR 309
>gnl|CDD|172541 PRK14049, PRK14049, ferrioxamine B receptor precursor protein;
Provisional.
Length = 726
Score = 29.9 bits (67), Expect = 5.9
Identities = 34/103 (33%), Positives = 51/103 (49%), Gaps = 20/103 (19%)
Query: 31 FKPRTN-FAIRG--VSSQVLTRSNVVLPRAFLSSSIATEAFKENPVSKTYGSEQIQVLEG 87
F PR + F +RG V+ + R N+ P A SSSI FK P YG E + +L G
Sbjct: 116 FDPRFDAFFVRGFDVTYTGVFRDNLRQPGA--SSSI----FKTEP----YGLEGVSILRG 165
Query: 88 LEAVRKRPAMYIGSTGPRGLHHLVYE-ILDNAVDEAQAGYASN 129
+ A+Y G++G GL +L+ + + + E Q Y +N
Sbjct: 166 PSS-----ALY-GASGAGGLFNLITKRPTEEPLREVQVQYGTN 202
>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated.
Length = 822
Score = 30.0 bits (68), Expect = 6.1
Identities = 28/103 (27%), Positives = 36/103 (34%), Gaps = 34/103 (33%)
Query: 501 GGSAKQ-----------GRDRRFQAILPLRGKILNVERKDE--------------AAMYK 535
GG AK+ R ++ L G I+ V+ +E A K
Sbjct: 21 GGKAKKKRVNGVPYYEFERKGEKWIVIGLSGHIVTVDFPEEYGDWRDVDPAELIDADPVK 80
Query: 536 NEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHI 578
QN I AL KK A +III TD D +G I
Sbjct: 81 KITKQNYINAL---------KKLAKDADEIIIATDYDREGELI 114
>gnl|CDD|179711 PRK04017, PRK04017, hypothetical protein; Provisional.
Length = 132
Score = 28.4 bits (64), Expect = 6.2
Identities = 22/83 (26%), Positives = 33/83 (39%), Gaps = 29/83 (34%)
Query: 510 RRFQAILPLR-----GKILNVE-RKDEAAMYKNEEIQNLIRALGLGVKGE---------- 553
R + I L+ G + VE ++D ++ K LGV+GE
Sbjct: 8 RFEEIIEELKEFSEAGAPIIVEGKRDVESLRK------------LGVEGEIIKVSRTPLA 55
Query: 554 -DFKKEALRYHKIIILTDADVDG 575
+ A R ++IILTD D G
Sbjct: 56 EIAELIASRGKEVIILTDFDRKG 78
>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: 559 ALRYHKIIILTDADVDGAHIRTLL 582
Y +IILTD D G IR L
Sbjct: 42 KKAYRGVIILTDPDRKGEKIRKKL 65
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 29.4 bits (67), Expect = 7.9
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 5/48 (10%)
Query: 436 HPDVLDSILSKSLSALKAALAAKRARDLVRQK--SVLRSSSLPGKLAD 481
+V DS S+ L ++ L K++R +R+K S++RS SL L D
Sbjct: 142 EGEVKDSA-SEKLRGIRRQLRRKKSR--IREKLESIIRSKSLQKYLQD 186
>gnl|CDD|119362 cd06545, GH18_3CO4_chitinase, The Bacteroides thetaiotaomicron
protein represented by pdb structure 3CO4 is an
uncharacterized bacterial member of the family 18
glycosyl hydrolases with homologs found in
Flavobacterium, Stigmatella, and Pseudomonas.
Length = 253
Score = 29.0 bits (65), Expect = 8.6
Identities = 16/55 (29%), Positives = 21/55 (38%), Gaps = 14/55 (25%)
Query: 669 VIEDAAEANV-VFSSLMGARVDT----------RKELIQNAANLV---NLDHLDI 709
V+ A NV + SL G RK L+ N V NLD +D+
Sbjct: 51 VVNAAHAHNVKILISLAGGSPPEFTAALNDPAKRKALVDKIINYVVSYNLDGIDV 105
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 0.134 0.384
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 36,068,535
Number of extensions: 3606001
Number of successful extensions: 3290
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3161
Number of HSP's successfully gapped: 59
Length of query: 709
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 605
Effective length of database: 6,324,786
Effective search space: 3826495530
Effective search space used: 3826495530
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 63 (27.9 bits)