RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780306|ref|YP_003064719.1| DNA topoisomerase I
[Candidatus Liberibacter asiaticus str. psy62]
(837 letters)
>gnl|CDD|181030 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated.
Length = 859
Score = 1137 bits (2944), Expect = 0.0
Identities = 374/857 (43%), Positives = 518/857 (60%), Gaps = 58/857 (6%)
Query: 1 MNVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGS--------------VLPEK 46
+++IVESPAKAKTI+KYLGS+Y V +S GHIRDLP S V P+
Sbjct: 2 KSLVIVESPAKAKTINKYLGSDYVVKASVGHIRDLPTSASSVPAKEKGALWARMGVDPDH 61
Query: 47 EFEMIWNIDPSSQKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTK 106
+FE ++ + P +K + + A K + L LATDPDREGEAI+WH+L+VL
Sbjct: 62 DFEALYEVLPGKEKVVSELKKAAKDADELYLATDPDREGEAIAWHLLEVLGGD----DVP 117
Query: 107 IQRVSFNAITKQVVLNAMKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQKLPGARSA 166
++RV FN ITK + A ++PR+++++LVNA ARR LD LVG+ +SP+LW+K+ SA
Sbjct: 118 VKRVVFNEITKNAIQEAFENPRELDINLVNAQQARRFLDRLVGYMVSPLLWKKIARGLSA 177
Query: 167 GRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISN 226
GRVQSVA+RLI RE +IE+FV EEYW + L TPR D F A LT +G++ + N
Sbjct: 178 GRVQSVAVRLIVEREREIEAFVPEEYWDIHADLTTPRGDAFEARLTHLDGKKFAPVDLLN 237
Query: 227 KKEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQK 286
+ +A+ ++ ++ A YSV +E+KP R P FTTSTLQQ AS +LGFS TMRIAQ+
Sbjct: 238 EAQAEAAVAALEGARYSVASVEDKPTTRKPSAPFTTSTLQQEASRKLGFSVKKTMRIAQR 297
Query: 287 LYEGIDVNGEIVGLITYMRTDGVHMSPDALEAVRRSITSHYGDHYLPEKPRIYSSKSKNA 346
LYE G ITYMRTD ++S +A+ A R I +YG YLPEKPR YSSK+KNA
Sbjct: 298 LYE--------AGYITYMRTDSTNLSQEAINAARGYIGDNYGKKYLPEKPRQYSSKAKNA 349
Query: 347 QEAHEAIRPNDFDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYN 406
QEAHEAIRP+D P ++K L+ D +LY LIWKR VASQMA A+++ TTV I A
Sbjct: 350 QEAHEAIRPSDVFRTPDQLK-GLEGDAQRLYELIWKRFVASQMAPARYDSTTVTIAAGDA 408
Query: 407 DQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTE 466
+ LR TG +L FDGFLKV+ D + +ED LP + + L + + +QHFT+
Sbjct: 409 E----LRATGRVLRFDGFLKVYVEGRDDALD-DEDRRLPALKVGDALTLEKLDPTQHFTK 463
Query: 467 PPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLEN 526
PP RYSE+SL+K++E++GIGRPSTYA+I+ T+ R YV E R+ P+ GRIVT LE
Sbjct: 464 PPARYSEASLVKELEKLGIGRPSTYASIISTIQDRGYVRLENRRFYPEKMGRIVTDRLEE 523
Query: 527 FFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILND 586
FF + V+YDFTA +EE+LD+I+ G+ +WK VL +F+++F ++++ ++LR +
Sbjct: 524 FFPRLVDYDFTARMEEELDDIANGEADWKPVLDDFYKDFSQQLEKAEELREEGGMR---- 579
Query: 587 TLSSVIFPPKENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNY---PECKYTRQLTSNP 643
P + R CP C + ++ K G F+GC+ Y CK TR LT
Sbjct: 580 --------PNQMVITDRDCPTCGR-GMGIRT-GKTGVFLGCSGYALKERCKTTRNLTPEE 629
Query: 644 QDIP----EMKESVLLGNDLETKESVTLRSGRFGLYVQRGDGKDAKRCSLPKTWKSDSVD 699
+ + E E+ LG D E ++ LRSGRFG YVQ G+G +R SLPK + V
Sbjct: 630 ETLNVLEGEDAETRALGADPECGTAMVLRSGRFGPYVQEGEGDKPRRLSLPKGNNPECVG 689
Query: 700 YDKAMSLLSLPREIGIHPETQKNIIAGTGKYGYYLNHDGAYTKLESIEQVLTIDLEQAIS 759
+ A+ LLSLPR +G HPE I A G++G Y+ G Y L++ +VLTI L +A+
Sbjct: 690 LEIALGLLSLPRPVGEHPECGSEIQAKIGRFGPYVKCGGTYASLKNTRKVLTIGLNRAVE 749
Query: 760 CITEKKKIEKSSRKNSKNQGHVIGTHPEGGSITVHNGRYGPYLHWKKINASLSKEESPDT 819
+ E K+ K +G G + +GRYGPY+ K NA+L K
Sbjct: 750 LLAEPKR-----PKEDPVPLPELGCPKSGAPFVLRDGRYGPYVKHGKANATLPKGRETRA 804
Query: 820 VDLEKALKILNIKKQKK 836
+E+AL++L K +K
Sbjct: 805 PTVEEALELLAEKPEKL 821
>gnl|CDD|180637 PRK06599, PRK06599, DNA topoisomerase I; Validated.
Length = 675
Score = 947 bits (2450), Expect = 0.0
Identities = 344/692 (49%), Positives = 460/692 (66%), Gaps = 20/692 (2%)
Query: 1 MNVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQK 60
++IVESPAKAKTI KYLG +YKVL+SFGH+RDLP KKG V P+ +F + I +K
Sbjct: 3 KKLVIVESPAKAKTIKKYLGKDYKVLASFGHVRDLPKKKGGVDPDNDFAPKYEIIEGKEK 62
Query: 61 HLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVV 120
+ + A K + + LATDPDREGEAI+WH+ +VL++ L +K ++RV FN ITK+ V
Sbjct: 63 VVDALKKAAKKADAVYLATDPDREGEAIAWHIAEVLKEAKLKDK-NVKRVVFNEITKKAV 121
Query: 121 LNAMKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQKLPGARSAGRVQSVALRLICNR 180
A+++PRDI++DLV+A ARRALDYLVGF LSP+LW+K+ SAGRVQSVALRLIC R
Sbjct: 122 QEAIENPRDIDMDLVDAQQARRALDYLVGFKLSPLLWKKVRRGLSAGRVQSVALRLICER 181
Query: 181 ENQIESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKA 240
E++IE+F+ +EYW++ L T + FTA L + NG+++EK SI+N+++A L+ ++
Sbjct: 182 EDEIEAFIPQEYWTIEADLATSNGEPFTAKLVEVNGKKLEKFSITNEEQAKALVKALEGQ 241
Query: 241 TYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGL 300
Y+V+KIE K KRNP P F TSTLQQ AS +LGFSA TMRIAQKLYEGID+ VGL
Sbjct: 242 AYTVDKIEKKERKRNPPPPFITSTLQQEASRKLGFSAKKTMRIAQKLYEGIDLGEGTVGL 301
Query: 301 ITYMRTDGVHMSPDALEAVRRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPNDFDF 360
ITYMRTD V +S +AL+ R+ IT YG YLP KPR+Y KSKNAQEAHEAIRP +
Sbjct: 302 ITYMRTDSVRLSNEALDEARKYITKKYGKEYLPAKPRVYKKKSKNAQEAHEAIRPTSINR 361
Query: 361 LPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLC 420
P +K +L DQF+LY LIWKR+VASQMA A ++T+V+I + + R TGS++
Sbjct: 362 TPESLKPYLTPDQFKLYELIWKRTVASQMAPAILDQTSVDIASENGKYV--FRATGSVIL 419
Query: 421 FDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKM 480
F GFLKV+ D E+ +E LLP + E+L E QHFTEPPPRYSE+SL+KK+
Sbjct: 420 FPGFLKVYGESKDDEEEDDEK-LLPPLKEGEKLKLDELLPEQHFTEPPPRYSEASLVKKL 478
Query: 481 EEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADL 540
EE GIGRPSTYA+I+ TL R+YV EK++ +P + GRIV FL F +YV+YDFTA L
Sbjct: 479 EEYGIGRPSTYASIISTLQDREYVELEKKRFIPTDLGRIVNDFLVEHFPKYVDYDFTAGL 538
Query: 541 EEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNE 600
E++LDEI+ GK +WK VL EFWE FI ++ +++ + + E
Sbjct: 539 EDELDEIAEGKKDWKPVLREFWEPFISNLEKVEEDVRTEKV---------------TQEE 583
Query: 601 DSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLTSNPQDIPEMKESVLLGNDLE 660
TCP+C L LKL K G F+GC+ YPECKYT+ +T + + E +E V +
Sbjct: 584 TDETCPKCGGGPLVLKL-GKNGKFLGCSGYPECKYTKNITRDEDEPIEEEEIVEEEKCPK 642
Query: 661 TKESVTLRSGRFGLYVQRGDGKDAKRCSLPKT 692
+ L+ GR+G ++ + K +
Sbjct: 643 CGGPLVLKKGRYGKFLACSGYPECKHIKPLEK 674
>gnl|CDD|180146 PRK05582, PRK05582, DNA topoisomerase I; Validated.
Length = 650
Score = 743 bits (1922), Expect = 0.0
Identities = 278/639 (43%), Positives = 396/639 (61%), Gaps = 37/639 (5%)
Query: 2 NVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKH 61
++IVESPAKAKTI KYLG NYKV++S GHIRDLP + + E FE +
Sbjct: 4 KLVIVESPAKAKTIEKYLGKNYKVVASMGHIRDLPKSQLGIDIENNFEPKYITIRGKGPV 63
Query: 62 LQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVL 121
++ + A K + + LATDPDREGEAI+WH+ +L +++ + R+ FN ITK +
Sbjct: 64 IKELKKAAKKAKKVYLATDPDREGEAIAWHLAHILG----LDEKEKNRIVFNEITKDAIK 119
Query: 122 NAMKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQKLPGARSAGRVQSVALRLICNRE 181
NA K+PR I+++LV+A ARR LD LVG+ LSP+LW+K+ SAGRVQSVAL+LI +RE
Sbjct: 120 NAFKNPRKIDMNLVDAQQARRILDRLVGYKLSPLLWKKVKKGLSAGRVQSVALKLIIDRE 179
Query: 182 NQIESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKAT 241
+I +FV EEYW++ + KF A + G +K + N+++ ++++ +KK
Sbjct: 180 KEIRAFVPEEYWTIDAEFK-KGKKKFEASFYGYKG---KKIELKNEEDVKEILAELKKKD 235
Query: 242 YSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGE-IVGL 300
+ V K++ K KRNP P FTTSTLQQ A+ +L FS TM IAQ+LYEGID+ + VGL
Sbjct: 236 FKVSKVKKKERKRNPPPPFTTSTLQQEAARKLNFSTKKTMMIAQQLYEGIDLGKQGTVGL 295
Query: 301 ITYMRTDGVHMSPDALEAVRRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPNDFDF 360
ITYMRTD +S A E R I YG YLP+KP++Y K AQ+AHEAIRP
Sbjct: 296 ITYMRTDSTRISDTAQEEAREFIEEKYGKEYLPKKPKVYKKK-SGAQDAHEAIRPTSVFL 354
Query: 361 LPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLC 420
P K++L DQ +LY LIW R VASQMA A F+ +V++ N R +GS +
Sbjct: 355 TPESAKKYLTKDQLKLYKLIWNRFVASQMAPAVFDTVSVDLEN--NGVK--FRASGSKVK 410
Query: 421 FDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKM 480
FDGF+KV+ + E+D +LP + E++ + QHFT+PP RY+E+SLIK +
Sbjct: 411 FDGFMKVYV------GDEEKDKMLPELEEGEKVKLKKIEPEQHFTQPPARYTEASLIKTL 464
Query: 481 EEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADL 540
EE+GIGRPSTYA + T+ KR YV EK++++P G IV LE FF V+ +FTA++
Sbjct: 465 EELGIGRPSTYAPTISTIQKRGYVKLEKKRLVPTELGEIVNELLEEFFPDIVDVEFTAEM 524
Query: 541 EEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNE 600
EEKLDEI GK +WK+VL +F++ F ++I+ +K + + + E
Sbjct: 525 EEKLDEIEEGKEDWKKVLDDFYKPFEKEIEKAEK------------EIEKIKIKDEPAGE 572
Query: 601 DSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQL 639
D CP+C + +K+ +YG F+ C+N+P+C+ T+ +
Sbjct: 573 D---CPKCG-SPMVIKM-GRYGKFIACSNFPDCRNTKPI 606
>gnl|CDD|162175 TIGR01051, topA_bact, DNA topoisomerase I, bacterial. This model
describes DNA topoisomerase I among the members of
bacteria. DNA topoisomerase I transiently cleaves one
DNA strand and thus relaxes negatively supercoiled DNA
during replication, transcription and recombination
events.
Length = 610
Score = 734 bits (1897), Expect = 0.0
Identities = 292/637 (45%), Positives = 399/637 (62%), Gaps = 28/637 (4%)
Query: 4 IIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQ 63
+IVESPAKAKTI KYLG Y+V +S GHIRDLP + V EK+FE + + +K ++
Sbjct: 2 VIVESPAKAKTIKKYLGDEYEVEASMGHIRDLPKSRLGVDIEKDFEPEYVVSKGKKKVVK 61
Query: 64 NIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNA 123
+ K + + LATDPDREGEAI+WH+ +VL+ K+ + K R+ FN ITK+ + A
Sbjct: 62 ELKTLAKKADEVYLATDPDREGEAIAWHLAEVLKPKDPVYK----RIVFNEITKKAIRAA 117
Query: 124 MKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQKLPGARSAGRVQSVALRLICNRENQ 183
+K+PR+I+++LVNA ARR LD LVG+ LSP+LW+K+ SAGRVQSVALRLI +RE +
Sbjct: 118 LKNPREIDMNLVNAQQARRILDRLVGYTLSPLLWKKVAKGLSAGRVQSVALRLIVDRERE 177
Query: 184 IESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKATYS 243
I+ FV EEYW++ + + F A LT+ NG++++ S ++ EA L +K
Sbjct: 178 IKRFVPEEYWTIDATFQKG-EETFEALLTEVNGKKLKAGSDLDEAEATALKEQLKGEELV 236
Query: 244 VEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITY 303
VE+IE KP K P P FTTSTLQQ AS +LGFSA TM IAQ+LYEG+ +GLITY
Sbjct: 237 VEEIEKKPKKSRPPPPFTTSTLQQEASRKLGFSAKKTMMIAQRLYEGVSTGDGTIGLITY 296
Query: 304 MRTDGVHMSPDALEAVRRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPNDFDFLPS 363
MRTD +S A+ R I +YG YL KP+ Y SK KNAQEAHEAIRP P
Sbjct: 297 MRTDSTRLSNQAVNEARNLIDKNYGKEYLGPKPKRYKSKEKNAQEAHEAIRPTSVFRTPE 356
Query: 364 KMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDG 423
++K +L D+F+LY LIWKR VASQMA A+++ T+V + + + + TG L FDG
Sbjct: 357 ELKDYLKRDEFRLYELIWKRFVASQMADARYDSTSVRLTNEDGEYV--FKATGRKLIFDG 414
Query: 424 FLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEI 483
+ KV+ D E+D +LP + + + E +QHFT+PP RY+E+SL+K++EE+
Sbjct: 415 YYKVYVEGSDDPLE-EKDRILPPLKEGDAVKLVEVKPNQHFTQPPARYTEASLVKELEEL 473
Query: 484 GIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEK 543
GIGRPSTYA+I+ T+ R YV E +++ P G VT LE F V+YDFTA +E+
Sbjct: 474 GIGRPSTYASIISTIQDRGYVKKENKRLYPTELGFAVTDLLEKHFGDVVDYDFTAKMEKD 533
Query: 544 LDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSR 603
LDEI+ GK WK VL F+ F K+ ++ +RI I K S+
Sbjct: 534 LDEIAEGKAEWKPVLKNFYTGFSSKVKKLRNMRI--------------IVDFKT----SQ 575
Query: 604 TCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLT 640
CP C + +KL KYG F+ C+N+PECKYT+ +
Sbjct: 576 DCPLCGR-PMVVKL-GKYGPFLACSNFPECKYTKSIV 610
>gnl|CDD|181555 PRK08780, PRK08780, DNA topoisomerase I; Provisional.
Length = 780
Score = 665 bits (1718), Expect = 0.0
Identities = 280/575 (48%), Positives = 383/575 (66%), Gaps = 10/575 (1%)
Query: 2 NVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKH 61
+++IVESPAKAKTI+KYLG ++ VL+S+GH+RDL K+G+V PE F M +++ ++KH
Sbjct: 4 HLVIVESPAKAKTINKYLGKDFTVLASYGHVRDLVPKEGAVDPENGFAMRYDLIDKNEKH 63
Query: 62 LQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVL 121
++ I A KS+ L LATDPDREGEAISWH+ ++L+++ L++ +QRV F IT + +
Sbjct: 64 VEAIAKAAKSADDLYLATDPDREGEAISWHLAEILKERGLLKDKPMQRVVFTEITPRAIK 123
Query: 122 NAMKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQKLPGARSAGRVQSVALRLICNRE 181
AM PRDI DLV+A ARRALDYLVGFNLSP+LW+K+ SAGRVQS ALR+I RE
Sbjct: 124 EAMAKPRDIASDLVDAQQARRALDYLVGFNLSPLLWRKIQRGLSAGRVQSPALRMIVERE 183
Query: 182 NQIESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKA- 240
+IE+F++ EYWS+ P F A L +GQ+ E+ +I++ A+ +++A
Sbjct: 184 EEIEAFIAREYWSIEADCAHPSQ-PFNAKLIKLDGQKFEQFTITDGDTAEAARLRIQQAA 242
Query: 241 --TYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGE-I 297
T V +E+K KRNP P FTTSTLQQ AS +LGF+ TM++AQKLYEG+D+ E
Sbjct: 243 QGTLHVTDVESKERKRNPAPPFTTSTLQQEASRKLGFTTRRTMQVAQKLYEGVDLGDEGS 302
Query: 298 VGLITYMRTDGVHMSPDALEAVRRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPND 357
VGLITYMRTD V++S DAL +R I YG LP++P Y +KSKNAQEAHEA+RP
Sbjct: 303 VGLITYMRTDSVNLSQDALAEIRDVIARDYGTASLPDQPNTYKTKSKNAQEAHEAVRPTS 362
Query: 358 FDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGS 417
P+++ +FL DQ +LY LIWKR+VA QM A +V+ +A ++ + R TGS
Sbjct: 363 ALRTPAQVARFLSDDQRRLYELIWKRAVACQMIPATLNTVSVD-LAAGSEHV--FRATGS 419
Query: 418 LLCFDGFLKVWENQYDQEKNSEEDI--LLPYISANEQLIATETNASQHFTEPPPRYSESS 475
+ GFL V+E D + +ED LP + + + A QHFTEPPPRY+E+S
Sbjct: 420 TVVVPGFLAVYEEGKDDKSAEDEDEGRKLPPMKEGDNVPLERIRAEQHFTEPPPRYTEAS 479
Query: 476 LIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYD 535
L+K +EE GIGRPSTYA+I+ TL RKYV E R+ P + GR V FL F++YV+YD
Sbjct: 480 LVKALEEYGIGRPSTYASIISTLQFRKYVEMEGRRFRPTDVGRAVNKFLTGHFTRYVDYD 539
Query: 536 FTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKID 570
FTA LE+ LD +S G+ W ++ +FW F E ++
Sbjct: 540 FTARLEDDLDAVSRGEKEWIPLMEKFWGPFKELVE 574
Score = 103 bits (258), Expect = 2e-22
Identities = 59/192 (30%), Positives = 96/192 (50%), Gaps = 14/192 (7%)
Query: 648 EMKESVLLGNDLETKESVTLRSGRFGLYVQRGDGKDAKR---CSLPKTWKSDSVDYDKAM 704
E + LG D ++ + V++R GRFG VQ G D ++ SL DS+ ++A+
Sbjct: 584 EAGQVRELGTDPKSGKPVSVRIGRFGPMVQIGTKDDEEKPRFASLRPGQSIDSITLEEAL 643
Query: 705 SLLSLPREIGIHPETQKNIIAGTGKYGYYLNHDGAYTKLESIEQVLTIDLEQAISCITEK 764
L LPR +G E + + G G++G ++ Y L+ + TIDL +A+ I EK
Sbjct: 644 ELFKLPRALGETDEGED-VSVGIGRFGPFVKRGSKYASLKKEDDPYTIDLARALFLIEEK 702
Query: 765 KKIEKSSRKNSKNQGHVIGTHPEGGSITVHNGRYGPYLHWKKINASLSKEESPDTVDLEK 824
++I ++ VI G I V NGRYGPY+ K+N + K+ P ++ LE+
Sbjct: 703 EEIARN---------RVIKDFEGSG-IQVLNGRYGPYITDGKLNGKIPKDREPASLTLEE 752
Query: 825 ALKILNIKKQKK 836
++L +K
Sbjct: 753 VQQLLADAPVRK 764
Score = 61.7 bits (150), Expect = 7e-10
Identities = 44/155 (28%), Positives = 70/155 (45%), Gaps = 38/155 (24%)
Query: 694 KSDSVDYDKAMSLLSLPREIGIHPETQKNIIAGTGKYGYYLNHDGAYTKLESIEQVLTID 753
K DSVD +A RE+G P++ K + G++G + Q+ T D
Sbjct: 576 KKDSVDRTEAGQ----VRELGTDPKSGKPVSVRIGRFGPMV-------------QIGTKD 618
Query: 754 LE-----------QAISCITEKKKIE--KSSRKNSKNQGHVIGTHPEGGSITVHNGRYGP 800
E Q+I IT ++ +E K R +G EG ++V GR+GP
Sbjct: 619 DEEKPRFASLRPGQSIDSITLEEALELFKLPRA--------LGETDEGEDVSVGIGRFGP 670
Query: 801 YLHWKKINASLSKEESPDTVDLEKALKILNIKKQK 835
++ ASL KE+ P T+DL +AL ++ K++
Sbjct: 671 FVKRGSKYASLKKEDDPYTIDLARALFLIEEKEEI 705
>gnl|CDD|180527 PRK06319, PRK06319, DNA topoisomerase I/SWI domain fusion protein;
Validated.
Length = 860
Score = 587 bits (1514), Expect = e-168
Identities = 302/696 (43%), Positives = 428/696 (61%), Gaps = 56/696 (8%)
Query: 3 VIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHL 62
+IIVESPAK KT+ K LG + SS GHI DLPAK+ + E +FE + I P ++ +
Sbjct: 5 LIIVESPAKIKTLQKLLGEGFIFASSLGHIVDLPAKEFGIDIENDFEPDYQILPDKEEVI 64
Query: 63 QNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLN 122
I K ++ L+ DPDREGEAI+WH+ + L KN TKIQR+SFNAITK V
Sbjct: 65 NKICKLAKKCDVVYLSPDPDREGEAIAWHIANQL-PKN----TKIQRISFNAITKGAVTE 119
Query: 123 AMKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQKLP--GARSAGRVQSVALRLICNR 180
A+K PR+I++ LVNA ARR LD +VG+ +SPIL +KL SAGRVQSVAL+L+ +R
Sbjct: 120 ALKHPREIDMALVNAQQARRLLDRIVGYKISPILSRKLQRRSGVSAGRVQSVALKLVVDR 179
Query: 181 ENQIESFVSEEYWSLSVLLETPRNDK-FTAHLTDFNGQRIEKKS-----------ISNKK 228
E IE+FV EYW++ V L+ P+ K F AHL +G++ EK+ I++K+
Sbjct: 180 EKAIEAFVPVEYWNIRVHLKDPKTQKTFWAHLYSVDGKKWEKEIPEGKTEDEVLLINSKE 239
Query: 229 EADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLY 288
+AD ++ ++ ATY+V ++E+K +RN +P F TSTLQQ AS FS+S TM IAQ LY
Sbjct: 240 KADHIVELLESATYTVTRVESKEKRRNAYPPFITSTLQQEASRHFRFSSSRTMNIAQTLY 299
Query: 289 EGIDVNGE-IVGLITYMRTDGVHMSPDALEAVRRSITSHYGDHYLPEKPRIYSSKSKNAQ 347
EG+D++ E GLITYMRTD V P+AL+ VR+ I +G +LP P +Y++K K AQ
Sbjct: 300 EGVDLDSEGATGLITYMRTDSVRTDPEALKQVRKYIEGTFGKEFLPSSPNVYTTK-KMAQ 358
Query: 348 EAHEAIRPNDFDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYND 407
+AHEAIRP D P K++ L DQ++LY+LIWKR VASQM A ++ T+ I T N
Sbjct: 359 DAHEAIRPTDITLTPEKLRSKLTEDQYKLYSLIWKRFVASQMIPAIYD--TLAIRITTNK 416
Query: 408 QIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEP 467
I LR TGSLL F GFL V+E + D E + EE+I LP + + L E +A Q FT+P
Sbjct: 417 GI-DLRATGSLLKFKGFLAVYEEKRDDEGDEEENIHLPKLHEQDVLTKEELSAEQAFTKP 475
Query: 468 PPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENF 527
PR++E+SL+K++E+ GIGRPSTYATI+ + R+Y + E +++ P G+I++ FLE
Sbjct: 476 LPRFTEASLVKELEKSGIGRPSTYATIMNKIQSREYTLKENQRLRPTELGKIISQFLETN 535
Query: 528 FSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDT 587
F + ++ FTA +E++L+ I+ K WK +L EFWE F+ + + +K + I+ +
Sbjct: 536 FPRIMDIGFTALMEDELELIADNKKPWKLLLQEFWELFLPVVVTAEKEAF--IPRIVTEI 593
Query: 588 LSSVIFPPKENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYT---RQLTSNPQ 644
CP+CH L +K+ +K F GC+ YPEC Y +LT N +
Sbjct: 594 ----------------DCPKCHKGKL-VKIWAKNRYFYGCSEYPECDYKTSEEELTFNKE 636
Query: 645 D----IPEMKESVLLGNDLETKESVTLRSGRFGLYV 676
D P L G +++ +R GRFG ++
Sbjct: 637 DYAEDTPWDSPCPLCGGEMK------VRHGRFGTFL 666
>gnl|CDD|181823 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 303 bits (779), Expect = 9e-83
Identities = 188/631 (29%), Positives = 286/631 (45%), Gaps = 126/631 (19%)
Query: 3 VIIVESPAKAKTISKYLG----------SNYKV---------LSSFGHIRDLPAKKG--S 41
++IVESP KA+TI+ + G Y+ +S GH+ DL + G
Sbjct: 604 LLIVESPTKARTIANFFGRPSRRRIGGLVVYETVTGDRILTITASKGHVYDLTTEIGYYG 663
Query: 42 VLPE-KEFEMIWN-IDPSSQKHLQ-------------NIIH------------AVKSSTI 74
VL + F +++ I Q I A++ +
Sbjct: 664 VLVKDGGFVPVYDTIKRCRDCGYQFTDESDKCPRCGSTNIEDKEEIIEALRELALEVDEV 723
Query: 75 LILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDL 134
LI ATDPD EGE I+W + +L N + I+R+ F+ +T++ +L A+++PRD+N +L
Sbjct: 724 LI-ATDPDTEGEKIAWDLYLLLSPYN----SNIKRIEFHEVTRKAILEALRNPRDVNENL 778
Query: 135 VNAYLARRALDYLVGFNLSPILWQKLPGAR--SAGRVQSVALRLICNRENQIESFVSEEY 192
V A + RR D +GF LS L +K G R SAGRVQ+ L I R + + +
Sbjct: 779 VKAQIVRRIEDRWIGFELSQKLQKKF-GKRNLSAGRVQTPVLGWIVERY---KEYKKSKG 834
Query: 193 WSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKATYSVEKIENKPI 252
+ L + LE + + S K+EA+ + + + VEK+E K
Sbjct: 835 YVLVIKLENGGGLEL-------------EGEFSEKEEAEKFYNNLIE----VEKVEEKEE 877
Query: 253 KRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMS 312
+ NP P +TT TL AS +L SA TMRIAQ L+E +GLITY RTD +S
Sbjct: 878 ELNPLPPYTTDTLLSDASRKLRLSAQETMRIAQDLFE--------LGLITYHRTDSTRVS 929
Query: 313 PDALEAVRRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPN---DFDFL-------P 362
+ + + G+ Y PR + AHEAIRP D + L
Sbjct: 930 DVGISVAKEYLEKRGGEEYF--VPRSWG-----EGGAHEAIRPTRPLDAEELRQMIEEGI 982
Query: 363 SKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSL-LCF 421
K+ + L + +LY+LI++R +ASQM AK L + +
Sbjct: 983 LKLSEGLTKNHLRLYDLIFRRFMASQMKPAKVRY----QKVLIKADGKELELELVVEILE 1038
Query: 422 DGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPP-PRYSESSLIKKM 480
DGF KV + + + + + P Y++ LI +M
Sbjct: 1039 DGFNKVLPLKLYPLLEGKVKVKEKKT----------------YKKSKVPLYTQGDLISEM 1082
Query: 481 EEIGIGRPSTYATILETLYKRKYVIAEKR--KILPQNTGRIVTAFLENFFSQYVEYDFTA 538
+E GIGRPSTYA I+ETL +R YVI K +++P G V +L + V + T
Sbjct: 1083 KERGIGRPSTYAKIVETLLRRGYVIESKGKKRLIPTKLGIKVYEYLSEKYKDLVSEERTR 1142
Query: 539 DLEEKLDEISTGKLNWKEVLHEFWEEFIEKI 569
LEEK+D++ GK +++EVL E +EE I+++
Sbjct: 1143 KLEEKMDKVEEGKEDYQEVLKELYEE-IKEL 1172
>gnl|CDD|180891 PRK07219, PRK07219, DNA topoisomerase I; Validated.
Length = 822
Score = 294 bits (754), Expect = 8e-80
Identities = 195/692 (28%), Positives = 309/692 (44%), Gaps = 101/692 (14%)
Query: 1 MNVIIVESPAKAKTISKYL---------------------GSNYKVLSSFGHI--RDLPA 37
+II E A+ I+ L G + V+ GHI D P
Sbjct: 1 TELIIAEKNNAARRIADILSGGKAKKKRVNGVPYYEFERKGEKWIVIGLSGHIVTVDFPE 60
Query: 38 KKGSVLPEKEFEMIWNIDPSSQKHL--QNIIHAVKS----STILILATDPDREGEAISWH 91
+ G ++ + ID K + QN I+A+K + +I+ATD DREGE I
Sbjct: 61 EYGDW---RDVDPAELIDADPVKKITKQNYINALKKLAKDADEIIIATDYDREGELIGKE 117
Query: 92 VLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNAYLARRALDYLVGFN 151
+LR+ + ++R F+++TK+ + A ++P +I+ +L +A AR+ +D G
Sbjct: 118 AYHILREVC---QVPVKRARFSSLTKKEIRKAFENPDEIDFNLADAGEARQIIDLYWGAA 174
Query: 152 LSPILWQ-----KLPGARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDK 206
L+ L S GRVQ+ L I +RE +I +F E+YW + LL + +
Sbjct: 175 LTRFLSLSVRQLGRWDFLSVGRVQTPTLAFIVDREREIRAFDPEDYWKIEALL----DKE 230
Query: 207 FTAHLTDFNGQRIEKKSISNKKEADDLISFVKKA-TYSVEKIENKPIKRNPWPAFTTSTL 265
D G E + +++EA+++ +K A +V ++ + +P F T+
Sbjct: 231 AQYFYRDLIGGH-EAEKFWDEEEAEEIYEKLKGAKEATVSSVKKRERTISPPAPFNTTEF 289
Query: 266 QQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPD--ALEAVRRSI 323
+ AS G S M IA+KLY G I+Y RTD + PD + + + +
Sbjct: 290 LREASKIFGISPKRAMEIAEKLYTA--------GYISYPRTDN-TVYPDDLDPKELLKKL 340
Query: 324 TSH--YGDHY--LPEKPRIYSSKSKNAQEAHEAIRPNDFDFLPSKMKQFLDSDQFQLYNL 379
+ YG + + E+ I ++ K H I P D +P + + L D++++Y L
Sbjct: 341 SKKKEYGPYAESILEQENIKPTEGKKETTDHPPIHPVD---VPKREE--LSDDEWKVYEL 395
Query: 380 IWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSE 439
I +R +A+ A++E V + N +I + +GS L +G+ +V Y EK E
Sbjct: 396 IVRRFLATLADPAEWEYLKVELDV--NGEI--FKASGSRLVEEGWHEV----YPYEKFDE 447
Query: 440 EDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLY 499
LP + E+L + T+PP RY++SSLIK+ME+ G+G +T I+E LY
Sbjct: 448 --KELPDLEEGEKLKVNKIEIEAKETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEKLY 505
Query: 500 KRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEV-- 557
KR YVI E P + G V LE + + V + TA LE + I GK ++V
Sbjct: 506 KRGYVI-EGDPPRPTDLGIAVIEALEKYAPEIVSEEMTAQLEADMQAIEDGKKKKEDVTE 564
Query: 558 -----LHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSR--TCPECHT 610
L E E EK I D L +L + EN CPEC
Sbjct: 565 ESREMLKEILSELKEKRKEIG--------DHLAGSLKA------ENRSLKTIGKCPEC-G 609
Query: 611 HSLSLKLSSKYGAFVGCTNYPECKYTRQLTSN 642
L + + K FVGC+ YP+C+ T L S
Sbjct: 610 GDLIIIRTDKGSRFVGCSGYPDCRNTFPLPST 641
Score = 52.3 bits (126), Expect = 5e-07
Identities = 22/47 (46%), Positives = 28/47 (59%), Gaps = 5/47 (10%)
Query: 593 FPPKENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQL 639
P E CP+C L++K KYG+F+GCTNYP+CKYT L
Sbjct: 682 EDPDEVI---GPCPKCGG-ELAIK-QLKYGSFLGCTNYPKCKYTLPL 723
Score = 33.1 bits (76), Expect = 0.32
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 4/46 (8%)
Query: 595 PKENNEDSR--TCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQ 638
P+ CPEC L++ +G +GC N P+C YT +
Sbjct: 724 PRRGKITVTDEKCPECG--LPLLRVKGGFGDELGCCNNPKCNYTEK 767
>gnl|CDD|128714 smart00437, TOP1Ac, Bacterial DNA topoisomerase I DNA-binding
domain. Bacterial DNA topoisomerase I and III,
Eukaryotic DNA topoisomeraes III, reverse gyrase alpha
subunit.
Length = 259
Score = 275 bits (705), Expect = 4e-74
Identities = 126/277 (45%), Positives = 157/277 (56%), Gaps = 22/277 (7%)
Query: 248 ENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTD 307
E K K+NP P FTTSTLQQ AS +LGFSA TM+IAQKLYE GLITY RTD
Sbjct: 1 EEKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEK--------GLITYPRTD 52
Query: 308 GVHMSPDALEAVRRSITSHYGDHYLPE----KPRIYSSKSKNAQEAHEAIRPNDFDFLPS 363
+S +A+ R I+ HYG YLP K Q AHEAIRP P
Sbjct: 53 STRLSEEAVLEARNYISKHYGKEYLPLAVSLLKPRKPRWGKKEQGAHEAIRPTKPIPTPE 112
Query: 364 KMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDG 423
++ L D+ +LY LIW+R +ASQM AK+E T V I + G L FDG
Sbjct: 113 L-EKELSEDEKKLYELIWRRFLASQMPDAKYEETKVIIKIGGE----KFKAKGKTLLFDG 167
Query: 424 FLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEI 483
+LKV+ E+ EE+I LP + ++L E + T+PP RY+E+SLIK ME+
Sbjct: 168 WLKVYP-----EEKKEEEIELPTLKKGDELKVEEVEVEEKKTKPPARYTEASLIKLMEKR 222
Query: 484 GIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIV 520
GIGRPSTYA I+ETL R YV EK+K++P G V
Sbjct: 223 GIGRPSTYAEIIETLLDRGYVTKEKKKLIPTELGIAV 259
>gnl|CDD|162177 TIGR01054, rgy, reverse gyrase. Generally, these gyrases are encoded
as a single polypeptide. An exception was found in
Methanopyrus kandleri, where enzyme is split within the
topoisomerase domain, yielding a heterodimer of gene
products designated RgyB and RgyA.
Length = 1171
Score = 267 bits (684), Expect = 9e-72
Identities = 173/629 (27%), Positives = 268/629 (42%), Gaps = 128/629 (20%)
Query: 4 IIVESPAKAKTISKYLGS-------------------NYKVLSSFGHIRDLPAKKG---- 40
++VESP KA+TI+++ G + +S GH+ DL KG
Sbjct: 605 LVVESPNKARTIARFFGKPSVRKIGGSVVYEVPVGDLILMITASGGHVFDLVTDKGFHGV 664
Query: 41 ----------------------------SVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSS 72
P+ E I + S + L+ + H V
Sbjct: 665 LVENGRYVPVYTSIKRCRDCGYQFTEDRESCPKCGSENIED-SKSIIEILRELAHEVDE- 722
Query: 73 TILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINL 132
+ + TDPD EGE I W + +L N ++R F+ +T++ +L A++SPR ++
Sbjct: 723 --VFIGTDPDTEGEKIGWDLALLLSPYN----PNVKRAEFHEVTRRAILEALESPRSVDE 776
Query: 133 DLVNAYLARRALDYLVGFNLSPILWQKL-PGARSAGRVQSVALRLICNRENQIESFVSEE 191
+LV A + RR D +GF LS LW+ SAGRVQ+ L I +R ES
Sbjct: 777 NLVKAQVVRRIEDRWIGFTLSQKLWEAFNKRWLSAGRVQTPVLGWIIDRYR--ESREKRG 834
Query: 192 YWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKATYSVEKIENKP 251
Y + L + R+ N+ EA + + VE I +
Sbjct: 835 YLLIFALE---------------SDFRL-GLEHDNRLEAKEFEKDLTWL--DVEDIAERE 876
Query: 252 IKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHM 311
+RNP P +TT T+ + A+ +LG S TM+IAQ+L+E GLITY RTD +
Sbjct: 877 EERNPLPPYTTDTMLEDANRKLGLSVKETMQIAQELFE--------NGLITYHRTDSTRV 928
Query: 312 SPDALEAVRRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPN---DFDFLPSKMK-- 366
S + + + S G Y PR + AHE IRP D D L +
Sbjct: 929 SDVGMRVAKEYLASRLGGEYF--YPREWGEGG-----AHECIRPTRPLDVDDLQRLILEG 981
Query: 367 --QFLDS--DQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFD 422
+ + +LY+LI++R +ASQM AK + + + A +
Sbjct: 982 VIELEGLTREHLRLYDLIFRRFMASQMRPAKVDTKEITLKADGKEAEEEGIVEIV---ER 1038
Query: 423 GFLKVW--ENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPP--PRYSESSLIK 478
GF V+ + + EK S + + P Y++ +++
Sbjct: 1039 GFELVYPLWRKNELEKGSTFIV-----------------KDKELRSVPKVYPYTQGEIVQ 1081
Query: 479 KMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTA 538
+M+E GIGRPSTYATI+E L +R YV+ K ++P G V +L N + + V D T
Sbjct: 1082 EMKERGIGRPSTYATIVEKLLRRGYVVESKGFLIPTKLGIEVYNYLTNRYPKLVSEDRTR 1141
Query: 539 DLEEKLDEISTGKLNWKEVLHEFWEEFIE 567
+LEE +D+I G+L++ EVL + E
Sbjct: 1142 ELEEAMDKIERGELDYLEVLESVYREIKS 1170
>gnl|CDD|180251 PRK05776, PRK05776, DNA topoisomerase I; Provisional.
Length = 670
Score = 250 bits (641), Expect = 1e-66
Identities = 183/620 (29%), Positives = 282/620 (45%), Gaps = 87/620 (14%)
Query: 3 VIIVESPAKAKTIS--------------------KYLGSNYKVLSSFGHIRDL-PAKKGS 41
++I E P A+ I+ K G V + GH+ L KG
Sbjct: 4 LVIAEKPKAARKIAEALSEKPIRCRIYGVPYWIVKRDGKKIVVAPAAGHLFGLHTKSKGF 63
Query: 42 VLPEKEFEMIWNIDPSSQKHLQNIIHAVKS----STILILATDPDREGEAISWHVLDVLR 97
+ + E++ ++ ID S K+ + + S + I A D D EG I + ++
Sbjct: 64 PVFDYEWKPLYEIDKGS-KYTKKYYELLSSLSKYADEFINACDYDIEGSVIGYLII---- 118
Query: 98 QKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNAYLARRALDYLVGFNLSPIL- 156
K L + K +R+ F+A+TK + A ++ ++ +++NA +AR LD+L G N+S L
Sbjct: 119 -KYLGDPKKAKRMKFSALTKSDIRRAFRNLETLDYEMINAGIARHELDWLWGINVSRALM 177
Query: 157 --WQKLPGAR---SAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAHL 211
+ G R SAGRVQS L+ + RE + FV Y+S+S+++E +FT
Sbjct: 178 SSVRDASGKRVILSAGRVQSPTLKYVVEREIERNLFVPLPYFSVSIIIEK-NGYEFTL-- 234
Query: 212 TDFNGQRIEKKSISNKKEADDLISFVKKATY-SVEKIENKPIKRNPWPAFTTSTLQQVAS 270
+ E K K+EA +++ +KK Y V K+E K P P F LQ A+
Sbjct: 235 ------KYENKKFETKEEAKEILEEIKKTGYLKVTKVEVKIEILEPPPPFNLGDLQVEAA 288
Query: 271 SRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPD-----ALEAVRRSITS 325
GFS T IA+ LY GLI+Y RT+ + P L+ + RS
Sbjct: 289 RIYGFSPYKTQSIAEDLYLD--------GLISYPRTNSQKLPPTLNIRNILKGLSRS--P 338
Query: 326 HYGD--HYLPEKPRIYSSKSKNAQE--AHEAIRPNDFDFLPSKMKQFLDSDQFQLYNLIW 381
Y + L ++ + + ++ AH AI P P L D+F+LY+LI
Sbjct: 339 QYRPLVNLLLKETKGVLKPVQGPKDDPAHPAIYPT--GEPPKN----LSKDEFKLYDLIV 392
Query: 382 KRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEED 441
+R +AS A A T V +G + G+LK Y K EE+
Sbjct: 393 RRFLASFAAPAVLSNTIV--TLRVPGFPLVFSASGQRIEERGWLKY----YPFHKFDEEE 446
Query: 442 ILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKR 501
LP + E++ + + +T+PP RYS++SL+K ME +GIG +T A I+ETL+KR
Sbjct: 447 --LPLLKKGERVKIVDVKVRKSYTKPPSRYSKASLLKWMESVGIGTEATRARIIETLFKR 504
Query: 502 KYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHE- 560
Y+ + + I G V LE +F V + T D EEKL+ I TGK +EV+ E
Sbjct: 505 GYLTSNGKYIEVTPLGFGVAEVLEKYFPDIVSVELTRDFEEKLEMIRTGKATREEVIEEA 564
Query: 561 ------FWEEFIEKIDSIKK 574
EEF + D I +
Sbjct: 565 KETLNKLLEEFKKNKDEIGE 584
>gnl|CDD|181093 PRK07726, PRK07726, DNA topoisomerase III; Provisional.
Length = 658
Score = 239 bits (613), Expect = 2e-63
Identities = 175/703 (24%), Positives = 305/703 (43%), Gaps = 126/703 (17%)
Query: 1 MNVIIVESPAKAKTISKYL-----------GSNYKVLSSFGH------------------ 31
M + I E P+ + I+ L G+ Y V + GH
Sbjct: 1 MRLFIAEKPSVGRDIADVLKPHKKGDGYIEGNGYIVTWAIGHLLELAEPEAYDERYKRWR 60
Query: 32 IRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILATDPDREGEAISWH 91
+ DLP ++PEK + + K + +K +T +++ATD DREGE I+
Sbjct: 61 LEDLP-----IIPEK---WKLVVKKKTAKQFNVVKKLLKQATEIVIATDADREGELIARE 112
Query: 92 VLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNAY---LAR-RALDYL 147
+LD + I+R+ +++T + + A + + + + Y LAR RA D+L
Sbjct: 113 ILDYCGVRK-----PIKRLWISSLTDKAIKRAFANLKP-GKETIPLYYSALARSRA-DWL 165
Query: 148 VGFNLS---PILWQKLP--GARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETP 202
VG N++ +L +K G S GRVQ+ L L+ R+ +IE+FV + YW + L
Sbjct: 166 VGINMTRAYTLLGRKAGYNGVLSVGRVQTPTLALVVRRDEEIENFVPKPYWEVEAHL--T 223
Query: 203 RNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKATYSVEKIENKPIKRNPWPAFTT 262
++FTA + E+ + ++ A+ +++ ++ V ++E K K +
Sbjct: 224 PGERFTAKWQPSEPYQDEEGRLLDRPLAEQVVARIQGQPAKVTEVETKRKKEYAPLLYDL 283
Query: 263 STLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPD---ALEAV 319
S LQ A+ R G SA T+ IAQ LY E LITY RTD ++ D L V
Sbjct: 284 SELQIDANKRFGLSAKETLDIAQSLY-------ETHKLITYPRTDSRYLPEDMVATLPEV 336
Query: 320 RRSITSHYGDHYLPEKPRIYSSKSKNAQ------EAHEAIRPNDFDFLPSKMKQFLDSDQ 373
+I+ D YL P + ++ AH AI P + SK L D+
Sbjct: 337 LNAISKV--DPYLLLAPPVLDPSIRSRAWNDKKVTAHHAIIPTEQPPNLSK----LSEDE 390
Query: 374 FQLYNLIWKRSVASQMASAKFERTTVN-IIATYNDQIGHLRTTGSLLCFDGFLKVWENQY 432
++Y+LI +R +A + A++++TT+ IA G G + G+ +
Sbjct: 391 RKVYDLIARRYLAQFLPPAEYDKTTIELEIAG-----GTFIAKGKQVVEAGWKALLG--- 442
Query: 433 DQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEI--------- 483
+E++ E++ LP ++ ++L + + T+PP R++E +L+ ME I
Sbjct: 443 KKEEDEEKEQPLPVLAKGDELKVEKGEVKEGQTQPPKRFTEGTLLSAMENIARFVQDKEL 502
Query: 484 --------GIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYD 535
G+G +T A I+E L+KR Y+ + + I + G+ ++ + D
Sbjct: 503 KKTLKETDGLGTEATRAGIIEKLFKRGYLEKKGKYIHATDKGK---QLIDALPEELTSPD 559
Query: 536 FTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKI-DSIKKLRISNVLDILNDTLSSVIFP 594
TA E+ LD+IS G+L+ +++F++ + +K+L V +
Sbjct: 560 MTAKWEQALDQISEGQLS--------YQDFMQPLKQWLKQL----VEQAKQSSEKYKF-- 605
Query: 595 PKENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTR 637
+N CP+C LK+ K G + C + K
Sbjct: 606 ---DNLTGPKCPDC--GKPMLKVKGKNGKMLVCQDRECGKRKN 643
>gnl|CDD|162179 TIGR01057, topA_arch, DNA topoisomerase I, archaeal. This model
describes topoisomerase I from archaea. These enzymes
are involved in the control of DNA topology. DNA
topoisomerase I belongs to the type I topoisomerases,
which are ATP-independent.
Length = 618
Score = 231 bits (591), Expect = 5e-61
Identities = 178/628 (28%), Positives = 283/628 (45%), Gaps = 70/628 (11%)
Query: 25 VLSSFGHIRDLPAKKGSVLPEKEFEMIW---NIDPSSQKHLQNIIHAV----KSSTILIL 77
V S+ GH+ L K P + E W + ++ I A+ K + I
Sbjct: 42 VASAVGHLFGLHPKSRGGYPVFDIE--WVPIFEFDKGKGYVSKYIKALSKLAKGADEYIN 99
Query: 78 ATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNA 137
A D D EGE I + L K + +R+ F+ +TKQ + A +P +I+ +V+A
Sbjct: 100 ACDYDIEGEVIGFKAL-----KYFCGVERAKRMKFSTLTKQDIRRAYANPEEIDYGMVDA 154
Query: 138 YLARRALDYLVGFNLSPILWQKLPGAR------SAGRVQSVALRLICNRENQIESFVSEE 191
+AR LD+ G NLS L + + A SAGRVQ L + RE +I FV +
Sbjct: 155 GMARHILDWYWGINLSRALMEAIRAAAGRWVILSAGRVQGPTLAFLVEREREINLFVPKP 214
Query: 192 YWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKATY-SVEKIENK 250
YW + LE F A R EK I +++EA + +KK+ + +VE++ ++
Sbjct: 215 YWVIKATLEK-GGGVFDA--------RPEKWKIWSEEEAKSIKEELKKSPWAAVEEVRSE 265
Query: 251 PIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVH 310
P P F TLQ+ A GFS T IAQ+LYE LI+Y RT
Sbjct: 266 RSILKPPPPFDLGTLQREAYRIFGFSPKKTQSIAQELYEE--------ALISYPRTSSQK 317
Query: 311 MSPD-ALEAVRRSITSH--YGDH--YLPEKPRIYSSKSKNAQEAHEAIRPNDFDFLPSKM 365
+ P A+ ++ Y + L E + + K AH AI P
Sbjct: 318 LPPSINYRAILDNLAKGPLYREAAERLLETGVLKPVEGKKEDPAHPAIHPTG-----EIP 372
Query: 366 KQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFL 425
Q L D+ ++Y+LI +R +A+ A E++ V + R +G + G+L
Sbjct: 373 SQELSKDEKKVYDLIVRRFLAAFSEEAIREKSKVLL----RIGQEKFRLSGLRVVKLGWL 428
Query: 426 KVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGI 485
+ + + E+ LP + +++ + T+PP RY ++SLI++ME G+
Sbjct: 429 EYYH------YSKFEEKELPPLDRGDKIKVVRVDVRVKETQPPARYDKASLIREMESRGL 482
Query: 486 GRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLD 545
G +T A I+ETLYKR Y+ K+ I G V L+ + + + + T E KL+
Sbjct: 483 GTKATRARIIETLYKRGYIEG-KKSIKVTPLGEAVIETLQRYCPEIISEELTRRFESKLE 541
Query: 546 EISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSRTC 605
+I +G++ EV+ E + + ++ KK + DI + S+ + E C
Sbjct: 542 DIMSGRITKDEVIDEAKKRLRKILEEFKK----RLDDIGIELGKSL-----GSVEVVGKC 592
Query: 606 PECHTHSLSLKLSSKYGAFVGCTNYPEC 633
P+C +S +K G FVGC+NYPEC
Sbjct: 593 PKCGGKLVSKY--AKKGRFVGCSNYPEC 618
>gnl|CDD|180892 PRK07220, PRK07220, DNA topoisomerase I; Validated.
Length = 740
Score = 219 bits (560), Expect = 2e-57
Identities = 178/594 (29%), Positives = 274/594 (46%), Gaps = 72/594 (12%)
Query: 70 KSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRD 129
K + + +ATD DREGE I L+++++ N K RV ++AITK+ + A +P +
Sbjct: 96 KEADRVTIATDYDREGELIGVEALNIIKKVN--PDIKFDRVRYSAITKKEIERAFSNPVE 153
Query: 130 INLDLVNAYLARRALDYLVGFNLSPILWQKLPGAR------SAGRVQSVALRLICNRENQ 183
++ +L +A +R+ +D + G L+ + L R S GRVQS L LI +RE +
Sbjct: 154 VDFNLADAGHSRQVIDLVWGAALTR--YISLAAGRLGKMFLSVGRVQSPTLALIVDREKE 211
Query: 184 IESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKATYS 243
E+FV YW + LE F A + + K+EAD + + K T
Sbjct: 212 REAFVPTPYWEIYATLENNGET-FVA--------QHSTRRFWEKEEADRVFEKLGK-TAE 261
Query: 244 VEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITY 303
V ++E P F T+ A+S +GFSA++ MRIA+ LY NG I+Y
Sbjct: 262 VTEVEKGTKTDKPPTPFNTTEFISAANS-IGFSAANAMRIAESLY----TNG----YISY 312
Query: 304 MRTDGVHMSPDALEAVRRSI----TSHYGDH--YLPEKPRIYSSKSKNAQEAHEAIRPND 357
RTD + P++L+ +R I +G++ L EK + ++ K H I P
Sbjct: 313 PRTDNT-VYPESLD-LREQIEIFAEGPFGEYAQKLLEKGELVPTRGKKETTDHPPIYPAS 370
Query: 358 FDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIG--HLRTT 415
K L D++++Y L+ +R A+ A++E + IG R
Sbjct: 371 -----LAKKSELKEDEWKVYELVVRRFFATFAGPAEWETMKLRF------DIGGEEFRAN 419
Query: 416 GSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESS 475
GS L G+ W Y N+ ED LLP +S E+L + T+PP RY +
Sbjct: 420 GSRLTEPGWR--WYYPY----NAPEDRLLPELSEGEELKVKKKEMLDKETQPPGRYGQGR 473
Query: 476 LIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYD 535
LIK ME++G+G +T I+ LY R Y+ I P NT V LE + + D
Sbjct: 474 LIKLMEDLGLGTKATRHEIISKLYSRAYI--HGNPIQPTNTAFAVVDALEKYAPTITKPD 531
Query: 536 FTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPP 595
T+ LEE +D+I+ GK+ VL E E + D + K R + + L + L
Sbjct: 532 MTSRLEEDMDKIAEGKIKEDAVLEESREMLEQVFDELDKNR-EKIRESLREGL------- 583
Query: 596 KENNEDSR--TCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLTSNPQDIP 647
ED CP C + L ++ S + F+GC YPEC ++ L + Q I
Sbjct: 584 ---REDKIIGKCPLCGS-DLMVRRSKRGSRFIGCEGYPECTFSLPLPKSGQIIV 633
>gnl|CDD|184936 PRK14973, PRK14973, DNA topoisomerase I; Provisional.
Length = 936
Score = 214 bits (546), Expect = 9e-56
Identities = 170/595 (28%), Positives = 265/595 (44%), Gaps = 74/595 (12%)
Query: 58 SQKHLQNIIHAV-KSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAIT 116
++K + +I + K + + +ATD D EGE I +++R N K I R F+AIT
Sbjct: 82 TEKKIVGLIQKLAKKADRVTIATDFDTEGELIGKEAYELVRAVN--PKVPIDRARFSAIT 139
Query: 117 KQVVLNAMKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQKLPGAR------SAGRVQ 170
K+ ++ A P D++ L A AR+ +D + G +L+ + L R S GRVQ
Sbjct: 140 KEEIVTAFAEPTDLDFALAAAGEARQIIDLIWGASLTRFI--SLAAHRGGDNILSVGRVQ 197
Query: 171 SVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSI----SN 226
S L +I +RE +IE+FV E+YW LS+ T+ +G+ IE + ++
Sbjct: 198 SPTLAMIVDREKEIEAFVPEKYWMLSLA-------------TEKDGEGIEARHTHGRFTD 244
Query: 227 KKEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQK 286
A+ K+ E E + R P P TT+ + VA+SRLGFSA++ MRIA+
Sbjct: 245 SAAAEAAYDATKEPLVVTEVKEGHKVDRAPTPFDTTTFI--VAASRLGFSAANAMRIAED 302
Query: 287 LYEGIDVNGEIVGLITYMRTDGVHMSP-----DALEAVRRSITSHYGDHYLPEKPRIYSS 341
LY + G I+Y RTD L + + S ++ + R +
Sbjct: 303 LY--------MNGYISYPRTDNTIYPKSLDLNGVLATLAKGAFSKDVA-WVKDNRRPVPT 353
Query: 342 KSKNAQEAHEAIRPNDFDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNI 401
+ K + H I P ++ L D+++LY L+ +R +A+ A++ VN
Sbjct: 354 RGKKSSTDHPPIHPTG-----VATREELGDDRWKLYELVVRRFLATLSPDAEWATMKVNF 408
Query: 402 IATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNAS 461
A TG L G W Y + E +LP + E+L N
Sbjct: 409 DAGGEPYT----ATGGRLLEAG----WRTVYPYSEAKEN--ILPAFALGEKLPILAVNLE 458
Query: 462 QHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVT 521
+ T+PP RYS+S LI++MEE+G+G ST ++ L RKY+ E + P GR VT
Sbjct: 459 EKETQPPARYSQSRLIQRMEELGLGTKSTRHEVIGKLVSRKYI--EGNPLRPTLVGRAVT 516
Query: 522 AFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVL 581
LE E D T LEE + +I K +V+ E + D ++
Sbjct: 517 ESLEEHAGTITEPDMTQTLEEHMQQIKERKRTRDDVVTESRKMLHRAFDELEANEAVIGR 576
Query: 582 DILNDTLSSVIFPPKENNEDSRTCPEC-HTHSLSLKLSSKYGAFVGCTNYPECKY 635
DI+ T + P CP C + SS+ F+GC+ YP+C +
Sbjct: 577 DIMERTAEELTIGP---------CPVCGKDLRIKHIGSSQ---FIGCSGYPDCTF 619
>gnl|CDD|162178 TIGR01056, topB, DNA topoisomerase III, bacteria and conjugative
plasmid. This model describes topoisomerase III from
bacteria and its equivalents encoded on plasmids. The
gene is designated topB if found in the bacterial
chromosome, traE on conjugative plasmid RP4, etc. These
enzymes are involved in the control of DNA topology. DNA
topoisomerase III belongs to the type I topoisomerases,
which are ATP-independent.
Length = 660
Score = 191 bits (487), Expect = 5e-49
Identities = 161/702 (22%), Positives = 288/702 (41%), Gaps = 130/702 (18%)
Query: 1 MNVIIVESPAKAKTISKYL------------GSNYKVLSSFGHIRDL--PAKKGS----- 41
M +++ E P++A+ ++ L G V + GH+ +L P +
Sbjct: 1 MTLVLCEKPSQARDLATVLAKKKKGNGYLEIGVGGFVTWAVGHLVELAEPEEYDEKYKNW 60
Query: 42 ------VLPEKEFEMIWNIDPSSQKHLQNI---IHAVKSSTILILATDPDREGEAISWHV 92
+ PE ++++ + ++K I + K ++I ATDPDREGE I+ +
Sbjct: 61 RTYDLPLEPED-WQLV--VSDKTKKQFNVIKRILKENKVDEVVI-ATDPDREGELIAREI 116
Query: 93 LDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKS--PRDINLDLVNAYLARRALDYLVGF 150
LD L + +K I+R+ +++ + A K+ P+ L + +AR D+LVG
Sbjct: 117 LDYL---KVTDKVTIKRLWISSLVDSSIRKAFKNLRPKSETEGLYKSGVARARADWLVGI 173
Query: 151 NLSPILWQK-----LPGARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRND 205
NL+ + G S GRVQ+ L ++ REN+I++FV + ++ +S +
Sbjct: 174 NLTRAFTKLGREAGNDGVLSVGRVQTPTLAMVVKRENEIKNFVGKPFYEVSATINKD-EQ 232
Query: 206 KFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTL 265
+FT + + E++ ++ A+++++ + + V IE + K + + S L
Sbjct: 233 EFTTEWQPY---KDEEERELHEFLAENVVTDLTQKPALVTDIEKERKKTSAPLFYDLSAL 289
Query: 266 QQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPDALEAVRRSITS 325
Q+ A+ R G SA T+ IAQKLYE LITY RTD ++ D E + +
Sbjct: 290 QEDANKRFGISAKRTLDIAQKLYETHK-------LITYPRTDSRYLPEDEKEMLLEVLD- 341
Query: 326 HYGDHYLPEKPRI-YSSKSKNAQ-----------EAHEAIRPNDFDFLPSKMKQFLDSDQ 373
L K ++ E H AI P DF S + + ++
Sbjct: 342 -----ALKVITPALLPIKKRDELTNNRLWNDKKIEDHHAIIPTGNDFNLSDLSE----EE 392
Query: 374 FQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYD 433
+Y LI + + M ++E TT+ G +L +G W+
Sbjct: 393 RNVYKLIAQNYLMQFMPKEEYETTTI----EIAIGKLMFEAKGKILQDNG----WKALLG 444
Query: 434 QEKNSEED--ILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEI-------- 483
+++ EE LP ++L + T+PP RY+E +L+ M
Sbjct: 445 KQEEDEETEDTTLPAFQKGDELDVETLELLEKQTKPPARYTEGTLLSAMTNPAAFVQDKG 504
Query: 484 ---------GIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEY 534
G+G +T A I+E L+KR ++ +K KI G+++ L ++
Sbjct: 505 LKKTLKETKGLGTEATRADIIENLFKRGFIQKKKNKIYITKNGKLLCLLLPELLTK---P 561
Query: 535 DFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFP 594
D TA E+ L+ IS G+ + ++FI I N+ + I
Sbjct: 562 DLTAQWEQYLNGISAGEKD--------DDDFINTI---------------NEMIKQTINE 598
Query: 595 PKENNEDSR--TCPECHTHSLSLKLSSKYGAFVGCTNYPECK 634
K+N E + ++ + G + C +PEC
Sbjct: 599 EKKNPETIQKVAKEPVSCGGIAKCPAKDNGRLIDCKKFPECT 640
>gnl|CDD|181267 PRK08173, PRK08173, DNA topoisomerase III; Validated.
Length = 862
Score = 150 bits (381), Expect = 1e-36
Identities = 162/643 (25%), Positives = 270/643 (41%), Gaps = 138/643 (21%)
Query: 4 IIVESPAKAKTISKYLG----------SNYKVLSS-FGHIRDLPA------KKGS----- 41
II E P+ A I++ LG S+ VLSS GH+ ++ A K+G
Sbjct: 6 IIAEKPSVANDIARALGGFTKHDEYFESDEYVLSSAVGHLLEIAAPEEYEVKRGKWSFAH 65
Query: 42 --VLPEKEFEMIWNIDPSSQKHLQNIIHAVKSS--TILILATDPDREGEAISWHVLDVLR 97
V+P F++ N ++ L+ + +K T LI A D REGE I +
Sbjct: 66 LPVIPPH-FDL--NPIAKTESRLKVLTKLIKRKDVTRLINACDAGREGELIFRLIA---- 118
Query: 98 QKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDIN--LDLVNAYLARRALDYLVGFNLSPI 155
++ K ++R+ ++T Q + + + R L +A R D+LVG N
Sbjct: 119 -QHAKAKKPVKRLWLQSMTPQAIRDGFANLRSDEDMQPLADAARCRSEADWLVGIN---- 173
Query: 156 LWQKLPGARS---------------AGRVQSVALRLICNRENQIESFVSEEYWSLSVLLE 200
G R+ GRVQ+ L ++ RE +I FV +YW +
Sbjct: 174 ------GTRAMTAFNSKGGGFFLTTVGRVQTPTLSIVVEREEKIRRFVPRDYWEVRAEFV 227
Query: 201 TPR--------NDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKATYSVEKIENKPI 252
+ KF +F+ ++ + + ++ A+ +++ + +V + E+KP
Sbjct: 228 AAAGFYEGRWFDPKFKK--DEFDPEKRASR-LWSEAAAEAIVAACRGKPGTVTE-ESKPS 283
Query: 253 KRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMS 312
+ F ++LQ+ A+ R GFSA +T+ +AQ LYE V +TY RTD +
Sbjct: 284 TQLSPLLFDLTSLQREANGRFGFSAKNTLGLAQALYEKHKV-------LTYPRTDSRALP 336
Query: 313 PDALEAVRRSITSHYGD-HYLPEKPRIYSSKSKNAQEAHEAIRPNDFDFLPSKMKQFLDS 371
D L V++++ +YLP +I ++PN F SK+ S
Sbjct: 337 EDYLGTVKQTLEMLKESNNYLPHAKQILDKG---------WVKPNKRIFDNSKI-----S 382
Query: 372 DQF-----------------QLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRT 414
D F +LY+L+ KR +A +A+F TT I H +T
Sbjct: 383 DHFAIIPTLQAPKSLSEPEQKLYDLVVKRFLAVFFPAAEFLVTTR--ITEVAGH--HFKT 438
Query: 415 TGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSES 474
G +L G+L V Y +E + L+P + E++ + A T+PP RY+E+
Sbjct: 439 EGKVLVNPGWLAV----YGKEAQGADANLVP-VQKGEKVKTDKIEAVALTTKPPARYNEA 493
Query: 475 SLIKKME----------------EIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGR 518
+L+ ME E G+G P+T A I+E L KY++ E R+++P
Sbjct: 494 TLLSAMEGAGKLVEDDELREAMAEKGLGTPATRAAIIEGLLGEKYLVREGRELIPTAKAF 553
Query: 519 IVTAFLENF-FSQYVEYDFTADLEEKLDEISTGKLNWKEVLHE 560
+ L + + T + E KL +I GKL+ + E
Sbjct: 554 QLMTLLRGLGVEELTSPELTGEWEYKLSQIERGKLSRDAFMQE 596
>gnl|CDD|173597 PTZ00407, PTZ00407, DNA topoisomerase IA; Provisional.
Length = 805
Score = 138 bits (348), Expect = 8e-33
Identities = 141/577 (24%), Positives = 239/577 (41%), Gaps = 91/577 (15%)
Query: 47 EFEMIWNIDPSS--QKHLQNIIHA-VKSSTILILATDPDREGEAISWHVLDVLRQKNLIE 103
E+ + W + P Q+ L+ I + T +ILATDPDREGE I+ H L +++
Sbjct: 97 EYTLEWELLPGRRIQETLERYIEEKADNVTEIILATDPDREGELIAVHALQTIKRLYPKL 156
Query: 104 KTKIQRVSFNAITKQVVLNAMK--SPRDINLDLVNAYLARRALDYLVGFNLSPILWQKLP 161
K R ++IT+ + AM+ + DL NA R A+D + GF S ++
Sbjct: 157 KVPFSRAYMHSITEDGIRKAMRERHVEACDYDLANAAETRHAMDRIFGFLGSSVVRAANS 216
Query: 162 GARSAGRVQSVALRLICNRENQIESFVSEEYWSLSV----LLETPRNDKFTAHLTDFNGQ 217
RS GRVQ+ AL LI RE++I++F+ + V +P F+ +T +
Sbjct: 217 QMRSIGRVQTPALILINEREDKIKAFLESNKSTFEVQAMCQFPSPHGTTFSQVVTITPDR 276
Query: 218 RIEKKSISNKKEADDLISFVKKATYSVEKIENKPI----KRNPWPAFTTSTLQQVASSRL 273
+ + + EA + K + + +P P FT +T A+ +L
Sbjct: 277 KGGASHWATEAEARRCLEQWKLNNCTGFSVPLEPKPQPSVVPPPQPFTMATAIAKANRQL 336
Query: 274 GFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPDALEAVRRSITSHYGDHYL- 332
+S+ Q L++ +G ITY RTD + AL + ++ +G +L
Sbjct: 337 KYSSEMVSGCLQDLFQ--------LGHITYPRTDSTRIDESALPDIYAAVKKEFGKEFLY 388
Query: 333 --------------PEKPRIYSSKSK---------NAQEAHEAIRPNDFDF------LPS 363
+K S + N ++AHEAIRP + D L
Sbjct: 389 RLEDRTVSAQEGKGSKKTGKKRSTKQKKGADTPVGNVEDAHEAIRPTNIDTTGESLSLSP 448
Query: 364 KMKQFLDSDQFQLYNLIWKRSVASQMASAKFER--TTVNIIATYNDQI------GHLRTT 415
+ +Y+L+ + ++A M K E+ TV + +++ +
Sbjct: 449 PTR--------AVYDLVRRNTLAVFMIPMKTEKIVATVKFTSGSGEKLEFELQGKRVVEP 500
Query: 416 GSLLCFDGFLK-----VWENQYDQEKNSEEDILLPYISANE----QLIATETNA--SQHF 464
G F K E D E ++P +S E + ++ + + F
Sbjct: 501 GWTRAFHKGDKGTTGPAEETDEDITAVEEGAPVVPSLSQEEFKAIMNLRSQLGSGVQKGF 560
Query: 465 TE------------PPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYV-IAEKRKI 511
E PP +SE +LI++++ G+GRPSTY I++TL R Y+ + K +
Sbjct: 561 FELRSPQVRENRPVPPLPHSEGTLIEELKNNGVGRPSTYPMIVKTLLARGYIAVNPKGRC 620
Query: 512 LPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEIS 548
GR++ ++ F V+ FTA E+KLD I+
Sbjct: 621 ETTPVGRMLVETAKSTFPSIVDIGFTAAFEKKLDRIA 657
>gnl|CDD|184805 PRK14724, PRK14724, DNA topoisomerase III; Provisional.
Length = 987
Score = 130 bits (327), Expect = 2e-30
Identities = 139/591 (23%), Positives = 252/591 (42%), Gaps = 91/591 (15%)
Query: 70 KSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVV---LNAMKS 126
K T L+ A D REGE I + ++R+ ++T Q + + ++S
Sbjct: 98 KDVTELVNACDAGREGELIFRLIEQYAGGAKGGLGKPVKRLWLQSMTPQAIRDGFDNLRS 157
Query: 127 PRDINLDLVNAYLARRALDYLVGFNLSPIL--WQKLPGA---RSAGRVQSVALRLICNRE 181
+ L +A +R D+LVG N + + + G + GRVQ+ L L+ RE
Sbjct: 158 DAQM-QGLASAARSRSEADWLVGINGTRAMTAFNSRDGGFFLTTVGRVQTPTLSLVVERE 216
Query: 182 NQIESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKS------ISNKKEADDLIS 235
+I FVS +YW + + + D ++ + +++EA +
Sbjct: 217 EKIRKFVSRDYWEIHAGFHAEAGE-YLGKWFDPQWKKASDDPEARADRVWSEREARAIAD 275
Query: 236 FVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNG 295
V+ +V + E+KP + F ++LQ+ A+ + GFSA T+ +AQ LYE
Sbjct: 276 AVRGKAATVTE-ESKPTTQASPLLFDLTSLQREANGKFGFSAKTTLALAQSLYERHKA-- 332
Query: 296 EIVGLITYMRTDGVHMSPDALEAVRR-------SITSHYGDH--------YLPEKPRIYS 340
+TY RTD + D L ++ S H Y+ RI+
Sbjct: 333 -----LTYPRTDSRALPEDYLPVAKQTFEMLATSGMRHLAPFAQQALDGNYVRPSKRIFD 387
Query: 341 SKSKNAQEA-HEAIRPNDFDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTT- 398
N++ + H AI P PS + +++Q +LY+L+ +R +A SA+++ TT
Sbjct: 388 ----NSKVSDHFAIIPT--TQAPSGLS---EAEQ-KLYDLVVRRFMAVFFPSAEYQVTTR 437
Query: 399 VNIIATYNDQIGHLRTTGSLLCFDGFLKVW----ENQYDQEKNSEEDILLPYISANEQLI 454
++ + ++ +T G +L G+L ++ N+ + K+ ++ L + E +
Sbjct: 438 ISQVVGHS-----FKTEGKVLVKPGWLAIYGKEAANEVEDAKDGDKGQPLVPVKPGEMVR 492
Query: 455 ATETNASQHFTEPPPRYSESSLIKKME----------------EIGIGRPSTYATILETL 498
A T+PP RYSE++L+ ME E G+G P+T A I+E L
Sbjct: 493 TEFAEAKGLKTKPPARYSEATLLGAMESAGKQIDDDELREAMQEKGLGTPATRAAIIEGL 552
Query: 499 YKRKYVIAEKRKILPQNTGRIVTAFLENF-FSQYVEYDFTADLEEKLDEISTGKLNWKEV 557
KY++ E R+++P + L + + T + E KL ++ G+L+
Sbjct: 553 LTEKYMLREGRELIPTAKAFQLMTLLRGLGVEELSRAELTGEWEYKLAQMEKGQLS---- 608
Query: 558 LHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSRTCPEC 608
E F+++I ++ + + + DT+ P + S CP C
Sbjct: 609 ----REAFMQQIAAMTEKLVKKAKEYDRDTI------PGDYATLSTPCPNC 649
>gnl|CDD|128713 smart00436, TOP1Bc, Bacterial DNA topoisomeraes I ATP-binding
domain. Extension of TOPRIM in Bacterial DNA
topoisomeraes I and III, Eukaryotic DNA topoisomeraes
III, reverse gyrase beta subunit.
Length = 89
Score = 126 bits (320), Expect = 2e-29
Identities = 47/88 (53%), Positives = 65/88 (73%), Gaps = 1/88 (1%)
Query: 107 IQRVSFNAITKQVVLNAMKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQKL-PGARS 165
I+R+ F+ ITK+ + A+K+PR+I+ +LVNA LARR LD L+GFNLS +L +KL G S
Sbjct: 1 IKRIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRKGVLS 60
Query: 166 AGRVQSVALRLICNRENQIESFVSEEYW 193
AGRVQ+ L LI RE +I++FV + YW
Sbjct: 61 AGRVQTPTLGLIVEREREIKNFVPKPYW 88
>gnl|CDD|184796 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 122 bits (308), Expect = 3e-28
Identities = 95/341 (27%), Positives = 150/341 (43%), Gaps = 91/341 (26%)
Query: 3 VIIVESPAKAKTISKYLGS-------------------NYKVLSSFGHIRDLPAKKG--S 41
++IVESP KA+TI+ + G + +S GH+ DL +G
Sbjct: 583 LMIVESPNKARTIANFFGQPSVRKIGDLVAYEVSIGDHMLIITASGGHVFDLVTNEGFHG 642
Query: 42 VLPEKE-FEMIW----------------------------NIDPSSQ--KHLQNIIHAVK 70
VL F I+ N+D + + K ++ + H V
Sbjct: 643 VLINNNLFIPIYDSIKRCRDCGHQFTDWEDKGVCPRCGSKNVDDAKENIKAMRELAHEVD 702
Query: 71 SSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDI 130
+++ TDPD EGE I+W + +VL I+R+ F+ +T++ +L A+K RDI
Sbjct: 703 E---ILIGTDPDTEGEKIAWDIRNVLAPYG----PNIKRIEFHEVTRRAILKAIKEARDI 755
Query: 131 NLDLVNAYLARRALDYLVGFNLSPILWQKLPGAR--SAGRVQSVALRLICNRENQIESFV 188
+ + V A + RR D +GF LS LW+ R SAGRVQ+ L I R + F
Sbjct: 756 DENRVKAQIVRRIEDRWIGFELSQKLWEVF-EDRNLSAGRVQTPVLGWIIQRYKE---FT 811
Query: 189 SEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKATYSVEKIE 248
+ L ++LE N + I + K+ ++ VE +E
Sbjct: 812 ESKVPFLGIILE--------------NDLTVT---IEDSKDEVEV---------EVELVE 845
Query: 249 NKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYE 289
+ +RNP P +TT T+ + AS+ L SA TM++AQ L+E
Sbjct: 846 EEEKERNPLPPYTTDTMLRDASAFLKLSAKETMKLAQDLFE 886
Score = 118 bits (297), Expect = 7e-27
Identities = 82/286 (28%), Positives = 130/286 (45%), Gaps = 35/286 (12%)
Query: 294 NGEIVGLITYMRTDGVHMSPDALEAVRRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAI 353
NG + TY RTD +S + R +T G+ Y KPR + + AHE I
Sbjct: 1374 NGMVSHNCTYHRTDSTRVSNTGIRVAREYLTQENGEDYF--KPRDWFMEG-----AHECI 1426
Query: 354 RPN---DFDFLPSKMKQ------FLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIAT 404
RP D D L +++ L + +LY+LI++R +ASQM AK I
Sbjct: 1427 RPTRPIDTDRLIQLIREGIIQVPGLTRNHLRLYDLIFRRFMASQMKPAKVLYEKALI--- 1483
Query: 405 YNDQIGHLRTTGSL-LCFDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQH 463
+ G + + DG+ +++ LP + + + A
Sbjct: 1484 -RYDGKDVEVEGYVEIEGDGWSRLYSLPLRV---------LPKLEKGKLKV---LEAKIR 1530
Query: 464 FTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEK--RKILPQNTGRIVT 521
P Y++ ++ M+E GIGRPSTYA I++TL R YVI K +K++P G V
Sbjct: 1531 KAPKVPLYTQGDIVALMKERGIGRPSTYAKIVDTLLMRGYVIETKGRKKLIPTKKGIKVY 1590
Query: 522 AFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIE 567
+L + + V + T +LEE +D + G+L++ +VL E +EE
Sbjct: 1591 NYLISNYGDLVSEERTRELEEIMDAVEEGELDYIKVLQELYEEIRR 1636
>gnl|CDD|128769 smart00493, TOPRIM, topoisomerases, DnaG-type primases, OLD family
nucleases and RecR proteins.
Length = 76
Score = 72.7 bits (179), Expect = 4e-13
Identities = 28/98 (28%), Positives = 44/98 (44%), Gaps = 25/98 (25%)
Query: 3 VIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHL 62
+IIVE PA A + K G V++ GH+ ++ +
Sbjct: 3 LIIVEGPADAIALEKAGGFGGNVVALGGHLL------------------------KKEII 38
Query: 63 QNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKN 100
+ + K + ILATDPDREGEAI+W + ++L+
Sbjct: 39 KLLKRLAKKKEV-ILATDPDREGEAIAWKLAELLKPAG 75
>gnl|CDD|151040 pfam10474, DUF2451, Protein of unknown function C-terminus
(DUF2451). This protein is found in eukaryotes but its
function is not known. The C-terminal part of some
members is DUF2450.
Length = 234
Score = 31.5 bits (72), Expect = 0.88
Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 17/63 (26%)
Query: 511 ILPQNTGRIVTAFLENFFSQYVE---------YDFTA----DLEEKLDEISTGKLNWKEV 557
+LP N L+ F+SQ V Y A +LE L+ ++ K + KEV
Sbjct: 31 LLPLNK----RDALDRFYSQTVSIVPDLRKHIYKCVASRLLNLEALLNSMANVKWDIKEV 86
Query: 558 LHE 560
+
Sbjct: 87 PSQ 89
>gnl|CDD|152018 pfam11582, DUF3240, Protein of unknown function (DUF3240). This
family of proteins with unknown function appears to be
restricted to Proteobacteria.
Length = 100
Score = 30.3 bits (69), Expect = 1.9
Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 9/63 (14%)
Query: 127 PRDINLDLVNAYLARRALDYLVGFNLSPILW----QKLPGA--RSAGRVQSVALRLICNR 180
PR++ DLV+ + LD + GF L P L + G +VA+ ++
Sbjct: 11 PRELEDDLVDCLIE---LDAVSGFTLLPAAGHGREHALFDIAEQVRGYRDAVAVEIVLPA 67
Query: 181 ENQ 183
+
Sbjct: 68 ADL 70
>gnl|CDD|182287 PRK10177, PRK10177, putative invasin; Provisional.
Length = 465
Score = 30.1 bits (68), Expect = 2.5
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 7/57 (12%)
Query: 73 TILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRD 129
TI++ A D + EG + W L V+ +E + QRVS N IT +V D
Sbjct: 410 TIIMPAWD-NGEGASNRWR-LSVV-----VEDNQGQRVSSNEITLTLVEPFDALSND 459
>gnl|CDD|152252 pfam11816, DUF3337, Domain of unknown function (DUF3337). This
family of proteins are functionally uncharacterized.
This family is only found in eukaryotes. This presumed
domain is typically between 285 to 342 amino acids in
length.
Length = 318
Score = 29.8 bits (67), Expect = 2.9
Identities = 26/145 (17%), Positives = 45/145 (31%), Gaps = 12/145 (8%)
Query: 458 TNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEK--RKILPQN 515
S E P S IK++E + P+ + T+ K + K + +
Sbjct: 23 DIPSGKKVEDPGEVSFEEEIKELEMVSS--PAWF-TVDTREGKLSSSLFGKEFQCFSSKL 79
Query: 516 TGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKL 575
+ Q D ++ EK +I+ G L L E+W + +
Sbjct: 80 LKKQ-GRTSTEAAPQKQSIDLSSSGAEKDPKINLGGLL-LRALLEYWTKLKCSPRVLVFS 137
Query: 576 RISNVLDILNDTL-----SSVIFPP 595
D N L +S+I
Sbjct: 138 TFLPSPDNENPVLELPPDTSIIISE 162
>gnl|CDD|161960 TIGR00615, recR, recombination protein RecR. This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University).
Length = 195
Score = 29.2 bits (66), Expect = 4.7
Identities = 26/113 (23%), Positives = 48/113 (42%), Gaps = 29/113 (25%)
Query: 5 IVESPAKAKTISK---YLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKH 61
+VE P + K + G Y VL GHI L + PE
Sbjct: 83 VVEDPKDVFALEKTKEFRG-RYHVLG--GHISPLD----GIGPE-------------DLT 122
Query: 62 LQNIIHAVKSSTI--LILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSF 112
+ ++ ++ ++ +ILAT+P EGEA + ++ +L+ + K+ R++
Sbjct: 123 IAALLKRLQEESVKEVILATNPTVEGEATALYIARLLQPFGV----KVTRIAS 171
>gnl|CDD|178985 PRK00357, rpsS, 30S ribosomal protein S19; Reviewed.
Length = 92
Score = 29.0 bits (66), Expect = 5.1
Identities = 17/42 (40%), Positives = 21/42 (50%), Gaps = 12/42 (28%)
Query: 765 KKIEKSSRKNSKNQGHVIGTH-------PE--GGSITVHNGR 797
KK+EK++ K VI T PE G +I VHNGR
Sbjct: 17 KKVEKANESGDKK---VIKTWSRRSTILPEFVGLTIAVHNGR 55
>gnl|CDD|152517 pfam12082, DUF3559, Domain of unknown function (DUF3559). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria and archaea. This domain is
typically between 305 to 348 amino acids in length. This
domain is found associated with pfam04851, pfam00271,
pfam04313.
Length = 307
Score = 28.7 bits (65), Expect = 5.6
Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 9/72 (12%)
Query: 170 QSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKE 229
+ AL+++ NR + + +E L L+ R T+ R K + N+
Sbjct: 158 EIAALQIVYNRPRDLTRAMLKE---LEEKLKLDRP-----GFTEERLWRAYKNA-KNEDI 208
Query: 230 ADDLISFVKKAT 241
D+IS +++A
Sbjct: 209 LADIISLIRRAA 220
>gnl|CDD|130580 TIGR01517, ATPase-IIB_Ca, plasma-membrane calcium-translocating
P-type ATPase. The calcium P-type ATPases have been
characterized as Type IIB based on a phylogenetic
analysis which distinguishes this group from the Type
IIA SERCA calcium pump. A separate analysis divides Type
IIA into sub-types (SERCA and PMR1), which are modelled
by the corresponding TIGR01116 and TIGR01522. This model
is well separated from the two others.
Length = 941
Score = 28.2 bits (63), Expect = 8.0
Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 10/54 (18%)
Query: 286 KLYEGIDVNGEIVGLITYMRTD---GVHMSPDALEAVRRSITSHYGDHYLPEKP 336
+YE + G G+ T ++TD GV +S LE R + YG + LPEKP
Sbjct: 36 PIYEKL---GGAEGIATKLKTDLNEGVRLSSSTLE-RREKV---YGKNELPEKP 82
>gnl|CDD|179809 PRK04286, PRK04286, hypothetical protein; Provisional.
Length = 298
Score = 28.4 bits (64), Expect = 8.3
Identities = 12/44 (27%), Positives = 15/44 (34%), Gaps = 12/44 (27%)
Query: 314 DALEAVRRSIT-----------SHY-GDHYLPEKPRIYSSKSKN 345
+ LE VR I SHY DH+ P Y +
Sbjct: 50 ERLEEVREKILEYAKKADVITISHYHYDHHTPFYEDPYELSDEE 93
>gnl|CDD|182444 PRK10419, nikE, nickel transporter ATP-binding protein NikE;
Provisional.
Length = 268
Score = 28.5 bits (64), Expect = 8.3
Identities = 14/43 (32%), Positives = 19/43 (44%)
Query: 132 LDLVNAYLARRALDYLVGFNLSPILWQKLPGARSAGRVQSVAL 174
L L A RA + L +L + K P S G++Q V L
Sbjct: 120 LSLDKAERLARASEMLRAVDLDDSVLDKRPPQLSGGQLQRVCL 162
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.315 0.132 0.378
Gapped
Lambda K H
0.267 0.0680 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 13,440,029
Number of extensions: 871703
Number of successful extensions: 1977
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1827
Number of HSP's successfully gapped: 66
Length of query: 837
Length of database: 5,994,473
Length adjustment: 102
Effective length of query: 735
Effective length of database: 3,790,457
Effective search space: 2785985895
Effective search space used: 2785985895
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 (21.5 bits)
S2: 61 (27.4 bits)