RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 009294
(538 letters)
>gnl|CDD|235542 PRK05644, gyrB, DNA gyrase subunit B; Validated.
Length = 638
Score = 763 bits (1974), Expect = 0.0
Identities = 264/460 (57%), Positives = 341/460 (74%), Gaps = 12/460 (2%)
Query: 70 ENPVSKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASN 129
+ ++ Y + QIQVLEGLEAVRKRP MYIGSTG RGLHHLVYEI+DN++DEA AGY +
Sbjct: 1 KEEKAQEYDASQIQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDH 60
Query: 130 IEVALLADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLH 189
IEV + D S++V DNGRGIP+D+HP T K A+E VLTVLHAGGKFGG GY VSGGLH
Sbjct: 61 IEVTINEDGSITVTDNGRGIPVDIHPKTGKPAVEVVLTVLHAGGKFGGG--GYKVSGGLH 118
Query: 190 GVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPD 249
GVG+SVVNALS LEV V RDG Y+Q+Y RG PVT L + D GT + F PD
Sbjct: 119 GVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEV----IGETDETGTTVTFKPD 174
Query: 250 KQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQW 309
++F T +FD++T+A R+RELAFLN L I L D + + + + GG++EYV++
Sbjct: 175 PEIFET-TEFDYDTLATRLRELAFLNKGLKITLT--DEREGEEKEETFHYEGGIKEYVEY 231
Query: 310 LNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKA 368
LN +K+PLH + + F + DGI +++A+Q+ D YS+ +L +AN+I T +GGTH EG K
Sbjct: 232 LNRNKEPLHEEPIYFEGEKDGIEVEVAMQYN-DGYSENILSFANNINTHEGGTHEEGFKT 290
Query: 369 SLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRK 428
+LTR +N +K+K +K+KD +L+GE VREGLT +ISV+ P P+FEGQTKT+LGN EVR
Sbjct: 291 ALTRVINDYARKNKLLKEKDDNLTGEDVREGLTAVISVKHPEPQFEGQTKTKLGNSEVRG 350
Query: 429 VVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKL 488
+VD V E L+E+LE +P+V I+ K++ A +A AA++AR+L R+KS L SSSLPGKL
Sbjct: 351 IVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALESSSLPGKL 410
Query: 489 ADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQVIINPL 528
ADCSS PEESE++IVEGDSAGGSAKQGRDRRFQ I+ PL
Sbjct: 411 ADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAIL-PL 449
>gnl|CDD|237860 PRK14939, gyrB, DNA gyrase subunit B; Provisional.
Length = 756
Score = 667 bits (1725), Expect = 0.0
Identities = 228/460 (49%), Positives = 318/460 (69%), Gaps = 15/460 (3%)
Query: 71 NPVSKTYGSEQIQVLEGLEAVRKRPAMYIGSTG-PRGLHHLVYEILDNAVDEAQAGYASN 129
+ +S +YG+ I+VL+GL+AVRKRP MYIG T GLHH+VYE++DNA+DEA AG+ +
Sbjct: 1 SMMSNSYGASSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVYEVVDNAIDEALAGHCDD 60
Query: 130 IEVALLADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLH 189
I V + AD SVSV+DNGRGIP D+HP SA E ++TVLHAGGKF +S Y VSGGLH
Sbjct: 61 ITVTIHADGSVSVSDNGRGIPTDIHPEEGVSAAEVIMTVLHAGGKFDQNS--YKVSGGLH 118
Query: 190 GVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPD 249
GVG+SVVNALSE LE+T+ RDG + Q++ G PV L V D+ GT +RFWP
Sbjct: 119 GVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKV----VGETDKTGTEVRFWPS 174
Query: 250 KQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQW 309
++F +FD++ +A R+RELAFLN + I L+ E E E+ + GG++ +V++
Sbjct: 175 PEIFEN-TEFDYDILAKRLRELAFLNSGVRIRLKDERDGKE----EEFHYEGGIKAFVEY 229
Query: 310 LNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKA 368
LN +K PLH ++ F + DGI +++ALQW +D+Y + +L + N+I DGGTH+ G +A
Sbjct: 230 LNRNKTPLHPNIFYFSGEKDGIGVEVALQW-NDSYQENVLCFTNNIPQRDGGTHLAGFRA 288
Query: 369 SLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRK 428
+LTRT+N+ +K K +SL+G+ REGLT ++SV+VP+P+F QTK +L + EVR
Sbjct: 289 ALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRP 348
Query: 429 VVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKL 488
V+ V E L+E+LE +P+ I+ K + A +A AA++AR+L R+K L + LPGKL
Sbjct: 349 AVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKL 408
Query: 489 ADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQVIINPL 528
ADC P SE+++VEGDSAGGSAKQGRDR+FQ I+ PL
Sbjct: 409 ADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAIL-PL 447
>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 = 654 bits (1688), Expect = 0.0
Identities = 246/457 (53%), Positives = 332/457 (72%), Gaps = 12/457 (2%)
Query: 77 YGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLA 136
Y + I+VLEGLEAVRKRP MYIGSTG GLHHLVYE++DN++DEA AGY I V +
Sbjct: 1 YDASSIKVLEGLEAVRKRPGMYIGSTGETGLHHLVYEVVDNSIDEAMAGYCDTINVTIND 60
Query: 137 DNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVV 196
D SV+V DNGRGIP+D+HP SA+E VLTVLHAGGKF S Y VSGGLHGVG+SVV
Sbjct: 61 DGSVTVEDNGRGIPVDIHPEEGISAVEVVLTVLHAGGKFDKDS--YKVSGGLHGVGVSVV 118
Query: 197 NALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTA 256
NALSE LEVTV+RDG Y Q++ RG P+ L V+ + GT +RFWPD ++F T
Sbjct: 119 NALSEWLEVTVFRDGKIYRQEFERGIPLGPL--EVVGET--KKTGTTVRFWPDPEIFET- 173
Query: 257 IQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKP 316
+FD + +A R+RELAFLN + I+L E K+ + + GG++ +V++LN +K+P
Sbjct: 174 TEFDFDILAKRLRELAFLNSGVKISLEDERDGKGKS--VTFHYEGGIKSFVKYLNRNKEP 231
Query: 317 LH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLN 375
LH +++ + + +GI +++ALQW D YS+ +L + N+I T +GGTH+EG +++LTR +N
Sbjct: 232 LHEEIIYIKGEKEGIEVEVALQWN-DGYSENILSFVNNINTREGGTHLEGFRSALTRVIN 290
Query: 376 SLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQ 435
S K +K +K+ +L+GE +REGLT +ISV+VP+P+FEGQTKT+LGN EVR +V+ V
Sbjct: 291 SYAKNNKLLKESKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLVY 350
Query: 436 EYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTT 495
E LTE+ E +P +I+ K++ A +A AA++AR+L R+KS L S LPGKLADCSS
Sbjct: 351 EKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKD 410
Query: 496 PEESEIFIVEGDSAGGSAKQGRDRRFQVIINPLQESI 532
P +SE++IVEGDSAGGSAKQGRDR+FQ I+ PL+ I
Sbjct: 411 PSKSELYIVEGDSAGGSAKQGRDRKFQAIL-PLRGKI 446
>gnl|CDD|223265 COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), B subunit [DNA replication,
recombination, and repair].
Length = 635
Score = 652 bits (1685), Expect = 0.0
Identities = 242/454 (53%), Positives = 321/454 (70%), Gaps = 14/454 (3%)
Query: 77 YGSEQIQVLEGLEAVRKRPAMYIGSTGP-RGLHHLVYEILDNAVDEAQAGYASNIEVALL 135
Y + IQVLEGLEAVRKRP MYIGSTG RGLHHLV+E++DN++DEA AGYA I+V L
Sbjct: 6 YDASSIQVLEGLEAVRKRPGMYIGSTGDGRGLHHLVWEVVDNSIDEALAGYADRIDVTLH 65
Query: 136 ADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSV 195
D S+SV DNGRGIP+D+HP SA+E + TVLHAGGKF S Y VSGGLHGVG+SV
Sbjct: 66 EDGSISVEDNGRGIPVDIHPKEKVSAVEVIFTVLHAGGKFDNDS--YKVSGGLHGVGVSV 123
Query: 196 VNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTT 255
VNALS LEV V RDG Y Q++ RG PVT L V+ + GT++RF PD ++F
Sbjct: 124 VNALSTWLEVEVKRDGKIYRQRFERGVPVTPL--EVIGSTDTKKTGTKVRFKPDPEIFGE 181
Query: 256 AIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKK 315
+FD+ + R+RELAFLN + I L E + EK E+ + GGL++YV++LN K
Sbjct: 182 -TEFDYEILKRRLRELAFLNKGVKITLTDERTGEEKK---EFHYEGGLKDYVEYLNKGKT 237
Query: 316 PLHDVVGFRKD-VDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTL 374
PLH+ + + DGI +++ALQW +D YS+ +L + N+I T +GGTH G +++LTR +
Sbjct: 238 PLHEEIFYFNGEKDGIAVEVALQW-NDGYSENILSFVNNIPTREGGTHEAGFRSALTRAI 296
Query: 375 NSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSV 434
N KK +K+ D L+G+ +REGLT +ISV++P+P+FEGQTK +LGN EVR +V++ V
Sbjct: 297 NEYAKKKNLLKEGD--LTGDDIREGLTAVISVKIPDPQFEGQTKEKLGNSEVRSIVEKLV 354
Query: 435 QEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSST 494
E + +LE +P I+ K+++A KA AA++AR+L R+KS L LPGKLADC+S
Sbjct: 355 SEAFSLFLEENPQEAKKIVEKAIAAAKAREAARKARELTRRKSALDIPGLPGKLADCTSK 414
Query: 495 TPEESEIFIVEGDSAGGSAKQGRDRRFQVIINPL 528
PE+SE+F+VEGDSAGGSAKQGRDR FQ I+ PL
Sbjct: 415 DPEKSELFLVEGDSAGGSAKQGRDREFQAIL-PL 447
>gnl|CDD|235501 PRK05559, PRK05559, DNA topoisomerase IV subunit B; Reviewed.
Length = 631
Score = 577 bits (1491), Expect = 0.0
Identities = 212/453 (46%), Positives = 280/453 (61%), Gaps = 18/453 (3%)
Query: 74 SKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVA 133
+ Y ++ I+VLEGLE VRKRP MYIGST RGLHHLV E++DN+VDEA AG+ IEV
Sbjct: 5 TNNYNADSIEVLEGLEPVRKRPGMYIGSTDTRGLHHLVQEVIDNSVDEALAGHGKRIEVT 64
Query: 134 LLADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGL 193
L AD SVSV DNGRGIP+ +HP KS +E +LT LHAGGKF + Y SGGLHGVG+
Sbjct: 65 LHADGSVSVRDNGRGIPVGIHPEEGKSGVEVILTKLHAGGKFSNKA--YKFSGGLHGVGV 122
Query: 194 SVVNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVF 253
SVVNALS LEV V RDG Y Q++ G PV L V+ K + GTR+RFWPD ++F
Sbjct: 123 SVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPL--EVVGTAGKRKTGTRVRFWPDPKIF 180
Query: 254 TTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTD 313
+ +F + R+R AFL P LTI L E + + GL++Y+ LN
Sbjct: 181 DSP-KFSPERLKERLRSKAFLLPGLTITLNDERERQ------TFHYENGLKDYLAELNEG 233
Query: 314 KKPLHD--VVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLT 371
K+ L + V F + +G ++ ALQW +D + + Y N I T GGTH G + L
Sbjct: 234 KETLPEEFVGSFEGEAEGEAVEWALQW-TDEGGENIESYVNLIPTPQGGTHENGFREGLL 292
Query: 372 RTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVD 431
+ + +K + K L GE VREGL ++SV++P P+FEGQTK +LG+ E R+ V
Sbjct: 293 KAVREFAEKRNLLP-KGKKLEGEDVREGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVS 351
Query: 432 QSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADC 491
V++ +L +P++ + + K A+KAA A RA V++K +LPGKLADC
Sbjct: 352 GVVKDAFDLWLNQNPELAEKLAEK---AIKAAQARLRAAKKVKRKKKTSGPALPGKLADC 408
Query: 492 SSTTPEESEIFIVEGDSAGGSAKQGRDRRFQVI 524
+S PE +E+F+VEGDSAGGSAKQ RDR FQ I
Sbjct: 409 TSQDPERTELFLVEGDSAGGSAKQARDREFQAI 441
>gnl|CDD|214659 smart00433, TOP2c, TopoisomeraseII. Eukaryotic DNA topoisomerase
II, GyrB, ParE.
Length = 594
Score = 521 bits (1344), Expect = 0.0
Identities = 213/425 (50%), Positives = 275/425 (64%), Gaps = 17/425 (4%)
Query: 106 GLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHPATNKSALETV 165
GLHHLV EI+DNA DEA AGY I+V + DNS+SV DNGRGIP+++HP K A E +
Sbjct: 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVI 60
Query: 166 LTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSR-GKPV 224
TVLHAGGKF + Y VSGGLHGVG SVVNALS EV V RDG EY Q +S GKP+
Sbjct: 61 FTVLHAGGKFDDDA--YKVSGGLHGVGASVVNALSTEFEVEVARDGKEYKQSFSNNGKPL 118
Query: 225 TTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRK 284
+ ++ KD GT++ F PD ++F D + R+RELAFLN + I L
Sbjct: 119 SEP--KIIGDTKKD--GTKVTFKPDLEIFGMTTDDDFELLKRRLRELAFLNKGVKITLND 174
Query: 285 EDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFR-KDVDGITIDLALQWCSDAY 343
E SD EK + F GG+++YV+ LN +K+ L + + D I +++A Q+ +D Y
Sbjct: 175 ERSDEEK----TFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQY-TDGY 229
Query: 344 SDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCI 403
S+ ++ + N+I T +GGTH G K +LTR +N KK K K K+ ++ GE VREGLT
Sbjct: 230 SENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKK--KLKEKNIKGEDVREGLTAF 287
Query: 404 ISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAA 463
ISV++P P+FEGQTK +LG EVR V++ V E L +LE +P I+ K L A KA
Sbjct: 288 ISVKIPEPQFEGQTKEKLGTSEVRFGVEKIVSECLLSFLEENPVEASKIVEKVLLAAKAR 347
Query: 464 LAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQV 523
AAK+AR+L R K L S SLPGKLAD SS P++ E+F+VEGDSAGGSAK GRDR FQ
Sbjct: 348 AAAKKARELTR-KKKLSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAKSGRDRDFQA 406
Query: 524 IINPL 528
I+ PL
Sbjct: 407 IL-PL 410
>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 = 474 bits (1222), Expect = e-162
Identities = 214/462 (46%), Positives = 300/462 (64%), Gaps = 18/462 (3%)
Query: 73 VSKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEV 132
++ Y ++ I++LEGL+AVRKRP MYIGST +GLHHLV+EI+DN+VDE AGYA NI V
Sbjct: 1 MASKYNADAIKILEGLDAVRKRPGMYIGSTDSKGLHHLVWEIVDNSVDEVLAGYADNITV 60
Query: 133 ALLADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVG 192
L DNS++V D+GRGIP +H N S +ETV TVLHAGGKF GY +GGLHGVG
Sbjct: 61 TLHKDNSITVQDDGRGIPTGIHQDGNISTVETVFTVLHAGGKFD--QGGYKTAGGLHGVG 118
Query: 193 LSVVNALSESLEVTVWRDGMEYHQKYSR-GKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQ 251
SVVNALS LEVTV RDG Y Q++ GK V +L + + + GT + F PD
Sbjct: 119 ASVVNALSSWLEVTVKRDGQIYQQRFENGGKIVQSLK----KIGTTKKTGTLVHFHPDPT 174
Query: 252 VFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLN 311
+F T QF+ N I R++E AFL KL + +D N+ +F+ GL ++V ++N
Sbjct: 175 IFKTT-QFNSNIIKERLKESAFLLKKLKLTF----TDKRTNKTTVFFYENGLVDFVDYIN 229
Query: 312 TDKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLT 371
K+ L V F + +GI +++A Q+ +D S+ +L +ANS++T +GGTH G K ++T
Sbjct: 230 ETKETLSQVTYFEGEKNGIEVEVAFQF-NDGDSENILSFANSVKTKEGGTHENGFKLAIT 288
Query: 372 RTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVP--NPEFEGQTKTRLGNPEVRKV 429
+NS +K +K+KD +L G +REGL+ IISVR+P +FEGQTK++L +PE R V
Sbjct: 289 DVINSYARKYNLLKEKDKNLEGSDIREGLSAIISVRIPEELIQFEGQTKSKLFSPEARNV 348
Query: 430 VDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSS--SLPGK 487
VD+ VQ++L +LE + + ++ K++ A A AAK+AR+ + + L GK
Sbjct: 349 VDEIVQDHLFFFLEENNNDAKLLIDKAIKARDAKEAAKKAREEKKSGKKPKKEKGILSGK 408
Query: 488 LADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQVIINPLQ 529
L S P ++E+F+VEGDSAGGSAKQGRDR+FQ I+ PL+
Sbjct: 409 LTPAQSKNPAKNELFLVEGDSAGGSAKQGRDRKFQAIL-PLR 449
>gnl|CDD|240272 PTZ00109, PTZ00109, DNA gyrase subunit b; Provisional.
Length = 903
Score = 460 bits (1186), Expect = e-153
Identities = 216/516 (41%), Positives = 299/516 (57%), Gaps = 63/516 (12%)
Query: 75 KTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVAL 134
Y ++ I VLEGLEAVRKRP MYIG+T +GLH L++EILDN+VDE AG + I V L
Sbjct: 98 SEYDADDIVVLEGLEAVRKRPGMYIGNTDEKGLHQLLFEILDNSVDEYLAGECNKITVVL 157
Query: 135 LADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKF------------------- 175
D SV ++DNGRGIP D+ T KS LETVLTVLH+GGKF
Sbjct: 158 HKDGSVEISDNGRGIPCDVSEKTGKSGLETVLTVLHSGGKFQDTFPKNSRSDKSEDKNDT 217
Query: 176 -------------------GGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQ 216
SS Y S GLHGVGLSVVNALS L+V V++ G Y
Sbjct: 218 KSSKKGKSSHVKGPKEAKEKESSQMYEYSSGLHGVGLSVVNALSSFLKVDVFKGGKIYSI 277
Query: 217 KYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPD-KQVFTTAIQ-------------FDHN 262
+ S+GK L+ P+ ++GT I F PD K +F T Q F+ +
Sbjct: 278 ELSKGKVTKPLSVFSCPLK---KRGTTIHFLPDYKHIFKTHHQHTETEEEEGCKNGFNLD 334
Query: 263 TIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNE--YFFAGGLEEYVQWLNTDKKPLH-- 318
I RI EL++LNP LT L E E N Y GG E+++ L DK PL+
Sbjct: 335 LIKNRIHELSYLNPGLTFYLVDERIANENNFYPYETIKHEGGTREFLEELIKDKTPLYKD 394
Query: 319 -DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSL 377
+++ R + + ++++L W ++Y+ + +AN++ T GTHI+G K ++TR +N
Sbjct: 395 INIISIRGVIKNVNVEVSLSWSLESYTALIKSFANNVSTT-AGTHIDGFKYAITRCVNGN 453
Query: 378 GKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEY 437
KK+ K +++ GE +REG+T IISV++ EF+GQTKT+LGN ++ +++ V E
Sbjct: 454 IKKNGYFKGNFVNIPGEFIREGMTAIISVKLNGAEFDGQTKTKLGNHLLKTILESIVFEQ 513
Query: 438 LTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSV-LRSSSLPGKLADCSSTTP 496
L+E LE P++L +I +KSL+A KA AK A+DL+RQK+ S+ LPGKL DC S
Sbjct: 514 LSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYSTILPGKLVDCISDDI 573
Query: 497 EESEIFIVEGDSAGGSAKQGRDRRFQVIINPLQESI 532
E +E+FIVEG+SA G+AKQ R+R FQ ++ PL+ I
Sbjct: 574 ERNELFIVEGESAAGNAKQARNREFQAVL-PLKGKI 608
>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 = 329 bits (846), Expect = e-106
Identities = 173/468 (36%), Positives = 252/468 (53%), Gaps = 26/468 (5%)
Query: 76 TYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALL 135
Y ++ I+VL+GLE VRKRP MY +T P +HLV E++DN+VDEA AG+AS I V L
Sbjct: 3 NYSAKDIEVLDGLEPVRKRPGMYTDTTRP---NHLVQEVIDNSVDEALAGFASIIMVILH 59
Query: 136 ADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSV 195
D S+ V DNGRG+P+D+HP SA+E +LT LHAGGKF S+ Y SGGLHGVG+SV
Sbjct: 60 QDQSIEVFDNGRGMPVDIHPKEGVSAVEVILTTLHAGGKF--SNKNYHFSGGLHGVGISV 117
Query: 196 VNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTT 255
VNALS+ +++ V+R G Y + G VT L K GT + F PD ++F +
Sbjct: 118 VNALSKRVKIKVYRQGKLYSIAFENGAKVTDL--ISAGTCGKRLTGTSVHFTPDPEIFDS 175
Query: 256 AIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEY----VQWLN 311
F + + +R A L + I D N + + GL++Y V N
Sbjct: 176 L-HFSVSRLYHILRAKAVLCRGVEIEFE----DEVNNTKALWNYPDGLKDYLSEAVNGDN 230
Query: 312 T-DKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASL 370
T KP G + D ++ AL W + M Y N I T GGTH+ G++ L
Sbjct: 231 TLPPKPF---SGNFEG-DDEAVEWALLWLPEGGELFMESYVNLIPTPQGGTHVNGLRQGL 286
Query: 371 TRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVV 430
L + + + + L+ E + + + ++S+++ +P+F GQTK RL + +V K V
Sbjct: 287 LDALREFC-EMRNNLPRGVKLTAEDIWDRCSYVLSIKMQDPQFAGQTKERLSSRQVAKFV 345
Query: 431 DQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLAD 490
+++ + L+ +V + + A + A+ +VR K + +LPGKLAD
Sbjct: 346 SGVIKDAFDLW--LNQNVQLAEHLAEHAISSAQRRKRAAKKVVR-KKLTSGPALPGKLAD 402
Query: 491 CSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQVIINPLQESIFAFASA 538
C+ E +E+F+VEGDSAGGSAKQ RDR +Q I+ PL I
Sbjct: 403 CTRQDLEGTELFLVEGDSAGGSAKQARDREYQAIL-PLWGKILNTWEV 449
>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 = 237 bits (606), Expect = 5e-76
Identities = 83/173 (47%), Positives = 126/173 (72%), Gaps = 2/173 (1%)
Query: 301 GGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDG 359
GGL+++V+ LN DK+PLH + + + DG+ +++ALQW D+YS+ +L + N+I T +G
Sbjct: 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWT-DSYSENILSFVNNIPTPEG 59
Query: 360 GTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKT 419
GTH G +A+LTR +N KK+ +K KD+ L+G+ +REGLT +ISV+VP P+FEGQTK
Sbjct: 60 GTHETGFRAALTRAINDYAKKNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKD 119
Query: 420 RLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDL 472
+LGN EVR +V+ +V+E L E+LE +P+ IL K++ A KA AA++AR+L
Sbjct: 120 KLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAILAAKAREAARKAREL 172
>gnl|CDD|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 = 203 bits (519), Expect = 5e-63
Identities = 83/175 (47%), Positives = 120/175 (68%), Gaps = 6/175 (3%)
Query: 302 GLEEYVQWLNTDKKPLHDVV----GFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTI 357
GL++YV+ LN DK PLH V G D I +++ALQW YS+ ++ + N+I T
Sbjct: 1 GLKDYVKELNKDKTPLHPEVIYFEGEEAFDDRIEVEVALQWNDS-YSENIVSFVNNIPTP 59
Query: 358 DGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQT 417
DGGTH++G +A+LTR LN KK +K KD ++G+ +REGLT ++SV++PNP+FEGQT
Sbjct: 60 DGGTHVDGFRAALTRALNEYAKKKGLLKKKD-KITGDDIREGLTAVVSVKIPNPQFEGQT 118
Query: 418 KTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDL 472
K +LGN EVR V+ V E ++LE +P++ IL K+L+A KA LAA++AR+L
Sbjct: 119 KEKLGNSEVRSAVESVVSEKFAKFLEKNPEIAKKILEKALAAAKARLAARKAREL 173
>gnl|CDD|177398 PHA02569, 39, DNA topoisomerase II large subunit; Provisional.
Length = 602
Score = 142 bits (361), Expect = 2e-36
Identities = 136/488 (27%), Positives = 210/488 (43%), Gaps = 103/488 (21%)
Query: 79 SEQIQVLEGLEAVRKRPAMYIGSTGPR-----------------GLHHLVYEILDNAVDE 121
++ +VL E + KRP MYIGS GL ++ EI+DN+VDE
Sbjct: 1 KDEFKVLSDREHILKRPGMYIGSVAYEAHERFLFGKFTQVEYVPGLVKIIDEIIDNSVDE 60
Query: 122 A---QAGYASNIEVALLADNSVSVADNGRGIPIDLHPATNKSAL---ETVLTVLHAGGKF 175
A +A+ I+V + +N V+V+DNGRGIP + + T AG F
Sbjct: 61 AIRTNFKFANKIDVTI-KNNQVTVSDNGRGIPQAMVTTPEGEEIPGPVAAWTRTKAGSNF 119
Query: 176 GGSSSGYSVSGGLHGVGLSVVNALSESL---------EVTV-WRDGMEYHQKYSRGKPVT 225
++ V+GG++GVG S+ N S EVTV +G E KP
Sbjct: 120 DDTN---RVTGGMNGVGSSLTNFFSVLFIGETCDGKNEVTVNCSNGAE--NISWSTKP-- 172
Query: 226 TLTCHVLPVDSKDRQGTRIRFWPDKQVF--TTAIQFDHNTIAGRIRELAFLNPKLTIALR 283
K +GT + F PD F Q + I R++ LA + P +
Sbjct: 173 ----------GKG-KGTSVTFIPDFSHFEVNGLDQQYLDIILDRLQTLAVVFPDIKFTFN 221
Query: 284 KEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQWCSDAY 343
+ + +Y + F G + VQ D + +AL D +
Sbjct: 222 GKKVSGKFKKYAKQF---GDDTIVQ--ENDN-----------------VSIALAPSPDGF 259
Query: 344 SDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCI 403
L + N + T +GG H++ V + L + KK K K I ++ V+E LT +
Sbjct: 260 RQ--LSFVNGLHTKNGGHHVDCVMDDICEELIPMIKK----KHK-IEVTKARVKECLTIV 312
Query: 404 ISVR-VPNPEFEGQTKTRLGNP--EVRKVVDQSVQEYLTEYLELHPDVLDSI----LSKS 456
+ VR + NP F+ QTK RL +P E+R +D ++ + L+ ++ I L++
Sbjct: 313 LFVRNMSNPRFDSQTKERLTSPFGEIRNHIDLDYKKIAKQILK-TEAIIMPIIEAALARK 371
Query: 457 LSALKAAL--AAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAK 514
L+A KAA AAK+A+ K + ++L GK A+ TT +F+ EGDSA G
Sbjct: 372 LAAEKAAETKAAKKAKKAKVAKHI--KANLIGKDAE---TT-----LFLTEGDSAIGYLI 421
Query: 515 QGRDRRFQ 522
+ RD
Sbjct: 422 EVRDEELH 429
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 97.0 bits (242), Expect = 5e-21
Identities = 116/493 (23%), Positives = 191/493 (38%), Gaps = 92/493 (18%)
Query: 80 EQIQVLEGLEAVRKRPAMYIGSTGPR-----------------------GLHHLVYEILD 116
E+ Q +E + RP YIGS + GL+ + EIL
Sbjct: 8 ERYQKKTQIEHILLRPDTYIGSIETQTEDMWVYDEEKNRMVYKTITYVPGLYKIFDEILV 67
Query: 117 NAVD----EAQAGYASNIEVAL-LADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHA 171
NA D + + I+V + + +SV ++G GIP+ +H E +
Sbjct: 68 NAADNKARDKGGHRMTYIKVTIDEENGEISVYNDGEGIPVQIHKEHKIYVPEMI------ 121
Query: 172 GGKFGG--SSSGY-----SVSGGLHGVGLSVVNALSESLEVTVW--RDGMEYHQKYSRGK 222
FG +SS Y V+GG +G G + N S V + G ++ ++
Sbjct: 122 ---FGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECVDSKSGKKFKMTWTDNM 178
Query: 223 PVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIA---GRIRELAFLNPKLT 279
+ + D K T++ F+PD F +FD + + R+ +LA KL
Sbjct: 179 SKKS-EPRITSYDGKKDY-TKVTFYPDYAKFGMT-EFDDDMLRLLKKRVYDLAGCFGKLK 235
Query: 280 IALRKEDSDPEKN--QYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQ 337
+ L E K+ Y + + G E ++ R +V ++
Sbjct: 236 VYLNGE-RIAIKSFKDYVDLYLPDGEEGKKPPYPFVYTSVNG----RWEV-VVS------ 283
Query: 338 WCSDAYSDT---MLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGE 394
SD + + NSI T GGTH V L + ++ L +K+K K K +
Sbjct: 284 -----LSDGQFQQVSFVNSICTTKGGTH---VNYILDQLISKLQEKAKKKKKKGKEIKPN 335
Query: 395 HVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILS 454
++ L ++ + NP F+ QTK L + + E L +Y+ L +L++I+
Sbjct: 336 QIKNHLWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKLIKYV-LKSPILENIVE 394
Query: 455 KSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEI---FIVEGDSA-- 509
+ + L A L K +KS R +P KL D + + SE + EGDSA
Sbjct: 395 WAQAKLAAELNKKMK---AGKKS--RILGIP-KLDDANDAGGKNSEECTLILTEGDSAKA 448
Query: 510 ---GGSAKQGRDR 519
G + GRD
Sbjct: 449 LALAGLSVVGRDY 461
>gnl|CDD|215593 PLN03128, PLN03128, DNA topoisomerase 2; Provisional.
Length = 1135
Score = 85.1 bits (211), Expect = 3e-17
Identities = 113/483 (23%), Positives = 182/483 (37%), Gaps = 120/483 (24%)
Query: 88 LEAVRKRPAMYIGSTGPR---------------------GLHHLVYEILDNAVDEAQAGY 126
LE + RP YIGST GL+ + EIL NA D Q
Sbjct: 13 LEHILLRPDTYIGSTEKHTQTLWVYEGGEMVNREVTYVPGLYKIFDEILVNAADNKQRDP 72
Query: 127 ASN-IEVALLAD-NSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSV 184
+ + ++V + + N++SV +NG+GIP+++H E + L F +
Sbjct: 73 SMDSLKVDIDVEQNTISVYNNGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEK--KT 130
Query: 185 SGGLHGVGLSVVNALSESLEV------------TVWRDGMEYHQKYSRGKPVTTLTCHVL 232
+GG +G G + N S V V+ + M K +P T +C
Sbjct: 131 TGGRNGYGAKLANIFSTEFTVETADGNRGKKYKQVFTNNM--SVK---SEPKIT-SC--- 181
Query: 233 PVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIA---GRIRELA-FLNPKLTIALRKEDSD 288
T+I F PD F + D + +A R+ ++A L KL + L +
Sbjct: 182 ---KASENWTKITFKPDLAKFNMT-RLDEDVVALMSKRVYDIAGCLGKKLKVELNGKKLP 237
Query: 289 PEKNQYNEYFFAGGLEEYVQ-WLNTDKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTM 347
++YV +L + + + K D + ++L SD S
Sbjct: 238 -----------VKSFQDYVGLYLGPNSREDPLPRIYEKVNDRWEVCVSL---SDG-SFQQ 282
Query: 348 LGYANSIRTIDGGTHIEGVKASLT-RTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISV 406
+ + NSI TI GGTH++ V + + KK+K + ++ L ++
Sbjct: 283 VSFVNSIATIKGGTHVDYVADQIVKHIQEKVKKKNK----NATHVKPFQIKNHLWVFVNC 338
Query: 407 RVPNPEFEGQTK----TR---------LGNPEVRKVVDQSVQEYLTEYLELHPDVLDSIL 453
+ NP F+ QTK TR L ++KV V+++IL
Sbjct: 339 LIENPTFDSQTKETLTTRPSSFGSKCELSEEFLKKV--------------EKCGVVENIL 384
Query: 454 S----KSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESE---IFIVEG 506
S K LK AKR R +P KL D + ++S+ + + EG
Sbjct: 385 SWAQFKQQKELKKKDGAKRQRLT----------GIP-KLDDANDAGGKKSKDCTLILTEG 433
Query: 507 DSA 509
DSA
Sbjct: 434 DSA 436
>gnl|CDD|217081 pfam02518, HATPase_c, Histidine kinase-, DNA gyrase B-, and
HSP90-like ATPase. This family represents the
structurally related ATPase domains of histidine kinase,
DNA gyrase B and HSP90.
Length = 111
Score = 75.4 bits (186), Expect = 1e-16
Identities = 38/151 (25%), Positives = 53/151 (35%), Gaps = 45/151 (29%)
Query: 104 PRGLHHLVYEILDNAVDEAQAGYASNIEVALLAD---NSVSVADNGRGIPIDLHPATNKS 160
L ++ +LDNA+ A AG IEV L D ++V DNG GIP
Sbjct: 3 EDRLRQVLSNLLDNAIKHAPAG--GEIEVTLERDGGRLRITVEDNGIGIPP--------- 51
Query: 161 ALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSR 220
E + + + SS V G G+GLS+V L E T+
Sbjct: 52 --EDLPKIFEPFFRTDSSS--RKVGG--TGLGLSIVRKLVELHGGTIT------------ 93
Query: 221 GKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQ 251
V+S+ GT F +
Sbjct: 94 -------------VESEPGGGTTFTFTLPLE 111
>gnl|CDD|214643 smart00387, HATPase_c, Histidine kinase-like ATPases. Histidine
kinase-, DNA gyrase B-, phytochrome-like ATPases.
Length = 111
Score = 74.6 bits (184), Expect = 3e-16
Identities = 32/151 (21%), Positives = 47/151 (31%), Gaps = 45/151 (29%)
Query: 104 PRGLHHLVYEILDNAVDEAQAGYASNIEVALLADN---SVSVADNGRGIPIDLHPATNKS 160
P L ++ +LDNA+ G I V L D ++V DNG GIP +
Sbjct: 3 PDRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGDHVEITVEDNGPGIPPEDLE----- 55
Query: 161 ALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSR 220
+ + S GG G+GLS+V L E +
Sbjct: 56 ------KIFEPFFRTDKRSRKI---GG-TGLGLSIVKKLVELHGGEIS------------ 93
Query: 221 GKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQ 251
V+S+ GT +
Sbjct: 94 -------------VESEPGGGTTFTITLPLE 111
>gnl|CDD|238202 cd00329, TopoII_MutL_Trans, MutL_Trans: transducer domain, having a
ribosomal S5 domain 2-like fold, conserved in the
C-terminal domain of type II DNA topoisomerases (Topo
II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins.
This transducer domain is homologous to the second
domain of the DNA gyrase B subunit, which is known to be
important in nucleotide hydrolysis and the transduction
of structural signals from ATP-binding site to the DNA
breakage/reunion regions of the enzymes. The GyrB
dimerizes in response to ATP binding, and is homologous
to the N-terminal half of eukaryotic Topo II and the
ATPase fragment of MutL. Type II DNA topoisomerases
catalyze the ATP-dependent transport of one DNA duplex
through another, in the process generating transient
double strand breaks via covalent attachments to both
DNA strands at the 5' positions. Included in this group
are proteins similar to human MLH1 and PMS2. MLH1 forms
a heterodimer with PMS2 which functions in meiosis and
in DNA mismatch repair (MMR). Cells lacking either hMLH1
or hPMS2 have a strong mutator phenotype and display
microsatellite instability (MSI). Mutation in hMLH1
accounts for a large fraction of Lynch syndrome (HNPCC)
families.
Length = 107
Score = 71.9 bits (177), Expect = 2e-15
Identities = 24/125 (19%), Positives = 50/125 (40%), Gaps = 23/125 (18%)
Query: 303 LEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQWCSD--AYSDTMLGYANSIRTIDGG 360
L++ + + DK ++ + DG ++ A+ + + D + N +GG
Sbjct: 1 LKDRLAEILGDKV-ADKLIYVEGESDGFRVEGAISYPDSGRSSKDRQFSFVNGRPVREGG 59
Query: 361 THIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPN--PEFE-GQT 417
TH++ V+ + TR LN G+ VR ++S+++P + T
Sbjct: 60 THVKAVREAYTRALN-----------------GDDVRRYPVAVLSLKIPPSLVDVNVHPT 102
Query: 418 KTRLG 422
K +
Sbjct: 103 KEEVR 107
>gnl|CDD|238030 cd00075, HATPase_c, Histidine kinase-like ATPases; This family
includes several ATP-binding proteins for example:
histidine kinase, DNA gyrase B, topoisomerases, heat
shock protein HSP90, phytochrome-like ATPases and DNA
mismatch repair proteins.
Length = 103
Score = 68.4 bits (168), Expect = 2e-14
Identities = 30/145 (20%), Positives = 45/145 (31%), Gaps = 45/145 (31%)
Query: 107 LHHLVYEILDNAVDEAQAGYASNIEVALLADN---SVSVADNGRGIPIDLHPATNKSALE 163
L ++ +L NA+ G I +++ D + V DNG GIP +
Sbjct: 1 LQQVLLNLLSNAIKHTPEG-GGRITISVERDGDHLEIRVEDNGPGIPEEDLE-------- 51
Query: 164 TVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKP 223
+F S S GG G+GLS+V L E +
Sbjct: 52 ------RIFERF--SDGSRSRKGGGTGLGLSIVKKLVELHGGRIE--------------- 88
Query: 224 VTTLTCHVLPVDSKDRQGTRIRFWP 248
V+S+ GT
Sbjct: 89 ----------VESEPGGGTTFTITL 103
>gnl|CDD|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 = 66.5 bits (163), Expect = 2e-13
Identities = 26/34 (76%), Positives = 30/34 (88%), Gaps = 1/34 (2%)
Query: 499 SEIFIVEGDSAGGSAKQGRDRRFQVIINPLQESI 532
SE++IVEGDSAGGSAKQGRDRRFQ I+ PL+ I
Sbjct: 1 SELYIVEGDSAGGSAKQGRDRRFQAIL-PLRGKI 33
>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 = 57.1 bits (139), Expect = 3e-10
Identities = 21/31 (67%), Positives = 25/31 (80%), Gaps = 1/31 (3%)
Query: 499 SEIFIVEGDSAGGSAKQGRDRRFQVIINPLQ 529
E+ +VEGDSAGGSAKQGRDR FQ + PL+
Sbjct: 1 CELILVEGDSAGGSAKQGRDRVFQAVF-PLR 30
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 61.4 bits (149), Expect = 9e-10
Identities = 114/490 (23%), Positives = 189/490 (38%), Gaps = 108/490 (22%)
Query: 88 LEAVRKRPAMYIGS---------------------TGPRGLHHLVYEILDNAVDEAQAGY 126
LE + RP YIGS T GL+ + EIL NA D Q
Sbjct: 38 LEHILLRPDTYIGSIEKHTQTLWVYETDKMVQRSVTYVPGLYKIFDEILVNAADNKQRD- 96
Query: 127 ASNIEVALLAD---NSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGG--SSSG 181
+ ++ D N +SV +NG G+P+++H E + FG +SS
Sbjct: 97 PKMDSLRVVIDVEQNLISVYNNGDGVPVEIHQEEGVYVPEMI---------FGHLLTSSN 147
Query: 182 YS-----VSGGLHGVGLSVVNALSES--LEVTVWRDGMEYHQKYS-----RGKPVTTLTC 229
Y +GG +G G + N S +E + +Y Q +S + +PV T C
Sbjct: 148 YDDNEKKTTGGRNGYGAKLTNIFSTEFVIETADGKRQKKYKQVFSNNMGKKSEPVIT-KC 206
Query: 230 HVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIA---GRIRELAFLNPKLTIALRKED 286
K T++ F PD F + + +A R+ ++A K
Sbjct: 207 ------KKSENWTKVTFKPDLAKFNMT-HLEDDVVALMKKRVVDIAGCLGKTVKVELNGK 259
Query: 287 SDPEK--NQYNEYFFAGGLEEYVQWLNTDKKP-LHDVVGFRKDVDGITIDLALQWCSDAY 343
P K + Y + + + + P +++ V R +V + Q S
Sbjct: 260 RIPVKSFSDYVDLYLESANK-----SRPENLPRIYEKVNDRWEVCVSLSEGQFQQVS--- 311
Query: 344 SDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCI 403
+ NSI TI GGTH++ V + + K K+K+ ++ +V+ L
Sbjct: 312 ------FVNSIATIKGGTHVDYVTNQIANHVMEAVNK----KNKNANIKAHNVKNHLWVF 361
Query: 404 ISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLE--LHPDVLDSILS----KSL 457
++ + NP F+ QTK L +R+ S E ++L+ + +++++LS K
Sbjct: 362 VNALIDNPAFDSQTKETL---TLRQSSFGSKCELSEDFLKKVMKSGIVENLLSWADFKQS 418
Query: 458 SALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESE---IFIVEGDSA----- 509
LK AK R + +P KL D + + SE + + EGDSA
Sbjct: 419 KELKKTDGAKTT----------RVTGIP-KLEDANEAGGKNSEKCTLILTEGDSAKALAV 467
Query: 510 GGSAKQGRDR 519
G + GR+
Sbjct: 468 AGLSVVGRNY 477
>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 = 4e-04
Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 6/83 (7%)
Query: 342 AYSD---TMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVRE 398
A SD + + NSI T GGTH++ V + + L+ + KK I++ V+
Sbjct: 38 ALSDGQFQQVSFVNSIATTKGGTHVDYVADQIVKKLDEVVKKKNK---GGINVKPFQVKN 94
Query: 399 GLTCIISVRVPNPEFEGQTKTRL 421
L ++ + NP F+ QTK L
Sbjct: 95 HLWIFVNCLIENPSFDSQTKETL 117
>gnl|CDD|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 = 34.9 bits (81), Expect = 0.011
Identities = 6/26 (23%), Positives = 12/26 (46%)
Query: 500 EIFIVEGDSAGGSAKQGRDRRFQVII 525
E+ IVEG S + ++ ++
Sbjct: 1 ELIIVEGPSDAIALEKAGGVLGGAVV 26
>gnl|CDD|222246 pfam13589, HATPase_c_3, Histidine kinase-, DNA gyrase B-, and
HSP90-like ATPase. This family represents,
additionally, the structurally related ATPase domains of
histidine kinase, DNA gyrase B and HSP90.
Length = 134
Score = 35.3 bits (82), Expect = 0.023
Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 15/72 (20%)
Query: 113 EILDNAVDEAQAGYASNIEVALLADN---SVSVADNGRGIPID-----LHPATNKSALET 164
E++DN++D A+N+++++ D +S+ DNG G+ + L + E
Sbjct: 9 ELIDNSID----ADATNVKISIDPDRGEDGISIEDNGGGMSYEELRNALKLGRSSKEGER 64
Query: 165 VLTVLHAGGKFG 176
T L G+ G
Sbjct: 65 DSTTL---GRKG 73
>gnl|CDD|223400 COG0323, MutL, DNA mismatch repair enzyme (predicted ATPase) [DNA
replication, recombination, and repair].
Length = 638
Score = 36.9 bits (86), Expect = 0.025
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 6/44 (13%)
Query: 111 VYEILDNAVDEAQAGYASNIEVALLAD--NSVSVADNGRGIPID 152
V E+++N++D AG A+ I++ + + V DNG GI +
Sbjct: 28 VKELVENSLD---AG-ATRIDIEVEGGGLKLIRVRDNGSGIDKE 67
>gnl|CDD|224307 COG1389, COG1389, DNA topoisomerase VI, subunit B [DNA replication,
recombination, and repair].
Length = 538
Score = 35.5 bits (82), Expect = 0.073
Identities = 29/93 (31%), Positives = 42/93 (45%), Gaps = 21/93 (22%)
Query: 64 ATEAFKENPVSKTYGSEQIQVLEGLEAVRKRPAMYIGSTGP-RGLHHLVYEILDNAVDEA 122
E F+E V+ E RK M +G GP R L V+E++ N++D
Sbjct: 8 FKEKFRELSVA--------------EFFRKNKEM-LGFDGPIRSLTTTVHELVTNSLDAC 52
Query: 123 Q-AGYASNI--EVALLADN--SVSVADNGRGIP 150
+ AG +I E+ + + V V DNG GIP
Sbjct: 53 EEAGILPDIKVEIERIGKDHYKVIVEDNGPGIP 85
>gnl|CDD|233250 TIGR01052, top6b, DNA topoisomerase VI, B subunit. This model
describes DNA topoisomerase VI, an archaeal type II DNA
topoisomerase (DNA gyrase) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 488
Score = 35.2 bits (81), Expect = 0.100
Identities = 25/83 (30%), Positives = 45/83 (54%), Gaps = 7/83 (8%)
Query: 79 SEQIQVLEGLEAVRKRPAMYIGSTGP-RGLHHLVYEILDNAVDEAQ-AGYASNIEVAL-- 134
E+ + + E RK M +G +G R L +++E++ N++D + AG +I+V +
Sbjct: 1 KEKFREMSVAEFFRKNKHM-LGYSGKIRSLTTVIHELVTNSLDACEEAGILPDIKVEIEK 59
Query: 135 LADN--SVSVADNGRGIPIDLHP 155
+ + V+V DNG GIP + P
Sbjct: 60 IGKDHYKVTVEDNGPGIPEEYIP 82
>gnl|CDD|234630 PRK00095, mutL, DNA mismatch repair protein; Reviewed.
Length = 617
Score = 33.3 bits (77), Expect = 0.32
Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 18/70 (25%)
Query: 111 VYEILDNAVDEAQAGYASNIEVALLAD--NSVSVADNGRGIP-IDL------HPATNK-- 159
V E+++NA+D AG A+ I++ + + V DNG GI DL H AT+K
Sbjct: 27 VKELVENALD---AG-ATRIDIEIEEGGLKLIRVRDNGCGISKEDLALALARH-ATSKIA 81
Query: 160 --SALETVLT 167
LE + T
Sbjct: 82 SLDDLEAIRT 91
>gnl|CDD|237946 PRK15337, PRK15337, type III secretion system protein InvA;
Provisional.
Length = 686
Score = 33.4 bits (77), Expect = 0.33
Identities = 23/95 (24%), Positives = 41/95 (43%), Gaps = 6/95 (6%)
Query: 385 KDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSV-QEYLTEYLE 443
++KD+ + EHVR L I + G+ + + + EV + + + Q +L
Sbjct: 560 REKDVIMLVEHVRGALARYICHKFAA---GGELRAVVLSAEVEDAIRKGIRQTSGGTFLN 616
Query: 444 LHPDVLDSILSKSLSALKAALAAKRARDLVRQKSV 478
L P ++++ AL A RD+V SV
Sbjct: 617 LDPAESENLMDLLTLALDDLGIA--HRDIVLLVSV 649
>gnl|CDD|223715 COG0642, BaeS, Signal transduction histidine kinase [Signal
transduction mechanisms].
Length = 336
Score = 32.4 bits (73), Expect = 0.55
Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 6/52 (11%)
Query: 104 PRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNS---VSVADNGRGIPID 152
P L ++ +L NA+ I +++ D+ +SV D G GIP +
Sbjct: 226 PERLRQVLVNLLSNAIK---YTPGGEITISVRQDDEQVTISVEDTGPGIPEE 274
>gnl|CDD|182388 PRK10337, PRK10337, sensor protein QseC; Provisional.
Length = 449
Score = 31.9 bits (73), Expect = 0.77
Identities = 37/125 (29%), Positives = 50/125 (40%), Gaps = 29/125 (23%)
Query: 95 PAMYIGSTG-PRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDL 153
A + TG P L LV +LDNA+ + G S ++V L A + +V DNG G+
Sbjct: 340 NAHPVIRTGQPLLLSLLVRNLLDNAIRYSPQG--SVVDVTLNA-RNFTVRDNGPGV---- 392
Query: 154 HPATNKSALETVLTVLHAGGKF--------GGSSSGYSVS---GGLHGVGLSVVNALSES 202
AL G +F GS G S+ LHG+ +S NA
Sbjct: 393 ----TPEALA------RIGERFYRPPGQEATGSGLGLSIVRRIAKLHGMNVSFGNAPEGG 442
Query: 203 LEVTV 207
E V
Sbjct: 443 FEAKV 447
>gnl|CDD|233035 TIGR00585, mutl, DNA mismatch repair protein MutL. All proteins in
this family for which the functions are known are
involved in the process of generalized mismatch repair.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 312
Score = 31.5 bits (72), Expect = 0.93
Identities = 15/44 (34%), Positives = 26/44 (59%), Gaps = 6/44 (13%)
Query: 111 VYEILDNAVDEAQAGYASNIEVALLAD--NSVSVADNGRGIPID 152
V E+++N++D AG A+ I+V + + V+DNG GI +
Sbjct: 27 VKELVENSLD---AG-ATRIDVEIEEGGLKLIEVSDNGSGIDKE 66
>gnl|CDD|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 = 1.0
Identities = 17/82 (20%), Positives = 30/82 (36%), Gaps = 11/82 (13%)
Query: 415 GQTKTRLGNPEVRKVVDQSVQ------EYLTEYLELHPDVLDSILSKSLSALKAALAAKR 468
G + RL N + Y E++E P+ + + +S+ L+
Sbjct: 614 GAHRDRLKNLQQTAQFLDGFYPVAKKLIYTLEHIEEIPEAIFNQQQESIETLELRKQEMT 673
Query: 469 ARD-----LVRQKSVLRSSSLP 485
A + LV Q+ L + LP
Sbjct: 674 AEERAVFSLVYQQLNLITQLLP 695
>gnl|CDD|225115 COG2205, KdpD, Osmosensitive K+ channel histidine kinase [Signal
transduction mechanisms].
Length = 890
Score = 31.5 bits (72), Expect = 1.2
Identities = 28/129 (21%), Positives = 44/129 (34%), Gaps = 23/129 (17%)
Query: 114 ILDNAVDEAQAGYASNIEVALLADN-SVSVADNGRGIPIDLHPATNKSALETVLTVLHAG 172
+L+NA+ A G I + +N SV D G GIP LE + + G
Sbjct: 783 LLENALKYAPPGSEIRINAGVERENVVFSVIDEGPGIPEG--------ELERIFDKFYRG 834
Query: 173 GKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPVT-TLTCHV 231
K + G+ G+GL++ + E+ T+ G TL
Sbjct: 835 NKESA-------TRGV-GLGLAICRGIVEAHGGTIS-----AENNPGGGAIFVFTLPVEE 881
Query: 232 LPVDSKDRQ 240
P +
Sbjct: 882 DPPLEDFEE 890
>gnl|CDD|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 = 29.6 bits (67), Expect = 1.3
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 6/74 (8%)
Query: 334 LALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSG 393
LA SD Y D S++T D EG+ L R SLG K+ +VK ++ +
Sbjct: 18 LAGLIDSDGYVDKAKNITASVKTEDKSVM-EGI-VKLAR---SLGIKA-SVKTREEKIDA 71
Query: 394 EHVREGLTCIISVR 407
+ V T I++
Sbjct: 72 KGVNLQFTYPITLS 85
>gnl|CDD|226369 COG3851, UhpB, Signal transduction histidine kinase,
glucose-6-phosphate specific [Signal transduction
mechanisms].
Length = 497
Score = 31.3 bits (71), Expect = 1.4
Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 6/51 (11%)
Query: 107 LHHLVYEILDNAVDEAQAGYASNIEVALLADNSV---SVADNGRGIPIDLH 154
L+ L E+L+N A A S + + L + + D+G G+P
Sbjct: 411 LYRLCQELLNNICKHADA---SAVTIQLWQQDERLMLEIEDDGSGLPPGSG 458
>gnl|CDD|182581 PRK10600, PRK10600, nitrate/nitrite sensor protein NarX;
Provisional.
Length = 569
Score = 31.2 bits (71), Expect = 1.4
Identities = 19/46 (41%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 107 LHHLVYEILDNAVDEAQAGYASNIEVALLADNSV--SVADNGRGIP 150
L + E L NA+ AQA + VA N V SV DNG G+P
Sbjct: 470 LLQIAREALSNALKHAQASEVV-VTVAQ-NQNQVKLSVQDNGCGVP 513
>gnl|CDD|226368 COG3850, NarQ, Signal transduction histidine kinase,
nitrate/nitrite-specific [Signal transduction
mechanisms].
Length = 574
Score = 30.8 bits (70), Expect = 1.9
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 6/50 (12%)
Query: 110 LVYEILDNAVDEAQAGYASNIEVALL---ADNSVSVADNGRGIPIDLHPA 156
+V E L NA+ AQA S I+V + +++V DNG GI P+
Sbjct: 485 IVREALSNAIKHAQA---SEIKVTVSQNDGQVTLTVEDNGVGIDEAAEPS 531
>gnl|CDD|219571 pfam07779, Cas1_AcylT, 10 TM Acyl Transferase domain found in
Cas1p. Cas1p protein of Cryptococcus neoformans is
required for the synthesis of O-acetylated
glucuronoxylomannans, a consitutent of the capsule, and
is critical for its virulence. The multi TM domain of
the Cas1p was unified with the 10 TM Sugar
Acyltransferase superfamily. This superfamily is
comprised of members from the OatA, MdoC, OpgC, NolL and
GumG families in addition to the Cas1p family. The Cas1p
protein has a N terminal PC-Esterase domain with the
opposing Acyl esterase activity.
Length = 496
Score = 30.5 bits (69), Expect = 2.8
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|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 = 29.9 bits (67), Expect = 3.3
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 236 SKDRQGTRIRFWPDKQVFTTAIQFDHNTIA 265
D G R+ F PD +++ T + N A
Sbjct: 143 GNDHNGGRLVFGPDGKIYYTIGEQGRNQGA 172
>gnl|CDD|235246 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated.
Length = 535
Score = 29.9 bits (68), Expect = 3.6
Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 9/67 (13%)
Query: 92 RKRPAMYIGSTGP-RGLHHLVYEILDNAVDEAQ-AGYASNI--EVALLADN----SVSVA 143
K + +G P R L+ V E++DN++D + AG +I E+ + + V+V
Sbjct: 22 EKNKEL-LGFDNPARALYTTVKELVDNSLDACEEAGILPDIKIEIKRVDEGKDHYRVTVE 80
Query: 144 DNGRGIP 150
DNG GIP
Sbjct: 81 DNGPGIP 87
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 30.2 bits (69), Expect = 3.8
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 5/48 (10%)
Query: 445 HPDVLDSILSKSLSALKAALAAKRARDLVRQK--SVLRSSSLPGKLAD 490
+V DS S+ L ++ L K++R +R+K S++RS SL L D
Sbjct: 142 EGEVKDSA-SEKLRGIRRQLRRKKSR--IREKLESIIRSKSLQKYLQD 186
>gnl|CDD|236846 PRK11100, PRK11100, sensory histidine kinase CreC; Provisional.
Length = 475
Score = 29.8 bits (68), Expect = 4.1
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 5/47 (10%)
Query: 107 LHHLVYEILDNAVDEAQAGYASNIEVALLADNS---VSVADNGRGIP 150
L + +LDNA+D + G I ++ D +SV D G GIP
Sbjct: 369 LRQALGNLLDNAIDFSPEG--GTITLSAEVDGEQVALSVEDQGPGIP 413
>gnl|CDD|227447 COG5117, NOC3, Protein involved in the nuclear export of
pre-ribosomes [Translation, ribosomal structure and
biogenesis / Intracellular trafficking and secretion].
Length = 657
Score = 29.6 bits (66), Expect = 4.6
Identities = 31/141 (21%), Positives = 48/141 (34%), Gaps = 29/141 (20%)
Query: 381 SKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLG--NPEVRKVVDQSVQEYL 438
+ DK +S + R+ L CI++ FE + T G N ++ VD +
Sbjct: 455 NDNPLDK---ISSDARRQALLCILTA------FEIASATLYGKENYDLGGFVDLLYS--M 503
Query: 439 TEYLELHPDVLDSILSKSLS-------------ALKAALAAKRARDL---VRQKSVLRSS 482
+ L PD ++ K L K R L +Q R
Sbjct: 504 VHPMNLEPDADLNLKIKRLKDPDAPSKPFVVNATTDNEELLKIVRLLFFKSKQPVHRRHV 563
Query: 483 SLPGKLADCSSTTPEESEIFI 503
+L C S +PEE + I
Sbjct: 564 IFKKRLLYCCSRSPEEFKGAI 584
>gnl|CDD|237841 PRK14867, PRK14867, DNA topoisomerase VI subunit B; Provisional.
Length = 659
Score = 29.8 bits (67), Expect = 4.9
Identities = 26/93 (27%), Positives = 42/93 (45%), Gaps = 19/93 (20%)
Query: 68 FKENPVSKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVD---EAQA 124
FKE+ +S E RK M S R + +++E++ N++D EA+
Sbjct: 12 FKEHSIS--------------EFFRKNKHMLGYSGKLRSMTTIIHELVTNSLDACEEAEI 57
Query: 125 GYASNIEVALLADN--SVSVADNGRGIPIDLHP 155
+E+ L + V+V DNG GIP + P
Sbjct: 58 LPDIKVEIEKLGSDHYKVAVEDNGPGIPPEFVP 90
>gnl|CDD|172541 PRK14049, PRK14049, ferrioxamine B receptor precursor protein;
Provisional.
Length = 726
Score = 29.1 bits (65), Expect = 6.6
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|225827 COG3290, CitA, Signal transduction histidine kinase regulating
citrate/malate metabolism [Signal transduction
mechanisms].
Length = 537
Score = 29.2 bits (66), Expect = 6.7
Identities = 27/114 (23%), Positives = 41/114 (35%), Gaps = 30/114 (26%)
Query: 104 PRGLHHLVY---EILDNAVDEAQAGYASN-IEVALLADNS---VSVADNGRGIPIDL-HP 155
H LV ++DNA++ A + IE++L + VAD G GIP ++
Sbjct: 422 ELQPHDLVTILGNLIDNALEALLAPEENKEIELSLSDRGDELVIEVADTGPGIPPEVRDK 481
Query: 156 ATNKSALETVLTVLHAGGKFGGSSSGYSVSGGL-HGVGLSVVNALSESLEVTVW 208
K G S G+GL +V L E L ++
Sbjct: 482 IFEK---------------------GVSTKNTGGRGIGLYLVKQLVERLGGSIE 514
>gnl|CDD|226951 COG4585, COG4585, Signal transduction histidine kinase [Signal
transduction mechanisms].
Length = 365
Score = 28.6 bits (64), Expect = 8.2
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 6/43 (13%)
Query: 113 EILDNAVDEAQAGYASNIEVALLADNS---VSVADNGRGIPID 152
E L NA+ AQA + + V L + + V DNG G D
Sbjct: 286 EALTNAIRHAQA---TEVRVTLERTDDELRLEVIDNGVGFDPD 325
>gnl|CDD|180530 PRK06328, PRK06328, type III secretion system protein; Validated.
Length = 223
Score = 28.2 bits (63), Expect = 9.4
Identities = 12/28 (42%), Positives = 20/28 (71%)
Query: 433 SVQEYLTEYLELHPDVLDSILSKSLSAL 460
SV++ + + LELHP+ + SI++ SL L
Sbjct: 101 SVKKIIGKELELHPETIVSIIANSLKEL 128
>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 = 28.1 bits (62), Expect = 9.5
Identities = 36/148 (24%), Positives = 56/148 (37%), Gaps = 22/148 (14%)
Query: 359 GGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTK 418
G T E +K SL T SL T ++ + VR+ + V V N
Sbjct: 63 GTTTSELLKTSLMSTATSL-----TTPKHELKTTTTGVRKNESSTSKVTVTNVTLSNAVS 117
Query: 419 TRLGNPEVRKVVDQSVQEYLTEYL---ELHPDVLDSILSKSLSALKAALAAKRARDLVRQ 475
T L + + + S++ TE L PD + ++L A +++D
Sbjct: 118 T-LQSSQNKTENQSSIRT--TEISPTSVLQPDASPKKTGTTSASLTTAETTSQSQD---- 170
Query: 476 KSVLRSSSLPGKLADCSSTTPEESEIFI 503
+ GK+A SSTTP S I +
Sbjct: 171 -------TEDGKIASTSSTTPSYSSIIL 191
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.133 0.379
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: 27,024,697
Number of extensions: 2644684
Number of successful extensions: 2414
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2315
Number of HSP's successfully gapped: 68
Length of query: 538
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 436
Effective length of database: 6,413,494
Effective search space: 2796283384
Effective search space used: 2796283384
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 (21.6 bits)
S2: 61 (27.1 bits)