RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13360
(1161 letters)
>gnl|CDD|237860 PRK14939, gyrB, DNA gyrase subunit B; Provisional.
Length = 756
Score = 1226 bits (3174), Expect = 0.0
Identities = 424/821 (51%), Positives = 576/821 (70%), Gaps = 65/821 (7%)
Query: 341 DTQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTK 400
+SY ASSI++L+GL+AVRKRP MYIGDT DGTGLHH V+E++DNAIDE+LAG+C
Sbjct: 1 SMMSNSYGASSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVYEVVDNAIDEALAGHCDD 60
Query: 401 INVTIYSDNSISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGG 460
I VTI++D S+S+SDNGRGIP DI + SAAE++MT LHAGGKF++NSYK+SGG
Sbjct: 61 ITVTIHADGSVSVSDNGRGIPTDIH----PEEGVSAAEVIMTVLHAGGKFDQNSYKVSGG 116
Query: 461 LHGIGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNK 520
LHG+G+S VN LS +L+LTI R+ KIH EF +G+ V+P+K++G+T+K
Sbjct: 117 LHGVGVSVVNALSEWLELTIRRDGKIHEQEFE------------HGVPVAPLKVVGETDK 164
Query: 521 QGTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKGGTS 580
GT++ FW +IF N EF Y+IL KR+REL+FLN+GV I L DER K+E F ++GG
Sbjct: 165 TGTEVRFWPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRLKDERDGKEEEFHYEGGIK 224
Query: 581 GFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQVDG 640
FV Y+N++K +HP IF S +K+ I ++V++QWN+SY EN+LCFTNNI Q DG
Sbjct: 225 AFVEYLNRNKTPLHPNIFY-----FSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDG 279
Query: 641 GTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKN 700
GTHL G R+ +TR IN YIE+ KK+K+ + G+D REGLT VLS+K+PDPKF+SQTK+
Sbjct: 280 GTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKD 339
Query: 701 KLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTRKKNLI 760
KLVSSEVR VE ++ + L +FL+ENP E+K+I KII+AAR+REAARK RELTR+K +
Sbjct: 340 KLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGAL 399
Query: 761 DDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARF 820
D L KLADCQEK+P L ELY+VEGDSAGGS KQGRDR+FQA+LPL+GK+LN+EKARF
Sbjct: 400 DIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARF 459
Query: 821 EKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKM 880
+K++ S++I TLI+ LG GI +DEFN +KLRYH+IIIMTDAD+DG+HIR LLLTFFYR+M
Sbjct: 460 DKMLSSQEIGTLITALGCGIGRDEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQM 519
Query: 881 PKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKNVKLISIENGDIIKEN 940
P+LIE G++YIAQPPLYK+K G E YL+DD + Y++++A + L + +G I
Sbjct: 520 PELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDYLIELALEGATLH-LADGPAISGE 578
Query: 941 YFFKLIDKYNKTIEIVHRLKQIIDISILSAIMSDVILNLDTRENAEQFAKKIIKKLNDSN 1000
KL+ +Y +I+ RL++ ++L A++ L+LD + A
Sbjct: 579 ALEKLVKEYRAVRKIIDRLERRYPRAVLEALIYAPALDLDDLADEAAVAA---------- 628
Query: 1001 IEIIVEFDQLNNKYLLNIKKKFLKKKNYIIDINFINNKDYKKLVSIISTFKKIIGKGVII 1060
+D +F+ + +Y++LV + + +I +G +
Sbjct: 629 -----------------------------LDADFLTSAEYRRLVELAEKLRGLIEEGAYL 659
Query: 1061 QKSIGEKIKKYTANNFYKIINYLRNEAENMVIKQRYKGLGEMNPGQLWETTMNPMIRCLL 1120
++ GE +K ++F + +++L EA + QRYKGLGEMNP QLWETTM+P R LL
Sbjct: 660 ER--GE--RKQPVSSFEEALDWLLAEARKGLSIQRYKGLGEMNPEQLWETTMDPENRRLL 715
Query: 1121 KVKIKDAISADKIFMTLMGDNVELRRKFIELNALHAKNIDI 1161
+V I+DAI+AD+IF TLMGD VE RR+FIE NAL+ N+D+
Sbjct: 716 QVTIEDAIAADEIFTTLMGDEVEPRREFIEENALNVANLDV 756
>gnl|CDD|235542 PRK05644, gyrB, DNA gyrase subunit B; Validated.
Length = 638
Score = 860 bits (2225), Expect = 0.0
Identities = 312/593 (52%), Positives = 412/593 (69%), Gaps = 28/593 (4%)
Query: 342 TQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKI 401
+ Y AS IQ+LEGLEAVRKRP MYIG T + GLHH V+EI+DN+IDE+LAGYC I
Sbjct: 3 EKAQEYDASQIQVLEGLEAVRKRPGMYIGSTGE-RGLHHLVYEIVDNSIDEALAGYCDHI 61
Query: 402 NVTIYSDNSISISDNGRGIPIDIKIDDKH-KPKRSAAEIVMTELHAGGKFNKNSYKISGG 460
VTI D SI+++DNGRGIP+DI H K + A E+V+T LHAGGKF YK+SGG
Sbjct: 62 EVTINEDGSITVTDNGRGIPVDI-----HPKTGKPAVEVVLTVLHAGGKFGGGGYKVSGG 116
Query: 461 LHGIGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNK 520
LHG+G+S VN LS +L++ + R+ KI+Y E+ G+ V+P+++IG+T++
Sbjct: 117 LHGVGVSVVNALSTWLEVEVKRDGKIYYQEYE------------RGVPVTPLEVIGETDE 164
Query: 521 QGTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDER--IKKKEIFEFKGG 578
GT + F D +IF EF Y+ L R+REL+FLN G+ ITL DER +K+E F ++GG
Sbjct: 165 TGTTVTFKPDPEIFETTEFDYDTLATRLRELAFLNKGLKITLTDEREGEEKEETFHYEGG 224
Query: 579 TSGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQV 638
+V Y+N++K +H +K+ I ++V+MQ+N+ Y+ENIL F NNI
Sbjct: 225 IKEYVEYLNRNKEPLHEEPIY-----FEGEKDGIEVEVAMQYNDGYSENILSFANNINTH 279
Query: 639 DGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQT 698
+GGTH G ++ +TR IN Y +N+ LK+ + GED+REGLT V+S+K P+P+F QT
Sbjct: 280 EGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVREGLTAVISVKHPEPQFEGQT 339
Query: 699 KNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTRKKN 758
K KL +SEVR V+ ++ + L +FL+ENP +K I EK I AAR+REAARK RELTR+K+
Sbjct: 340 KTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKS 399
Query: 759 LIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKA 818
++ L KLADC K+PE ELYIVEGDSAGGS KQGRDRRFQA+LPLRGK+LN+EKA
Sbjct: 400 ALESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKA 459
Query: 819 RFEKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYR 878
R +KI+ +E+I LI+ LG GI D+F++ KLRYH+IIIMTDAD+DGAHIR LLLTFFYR
Sbjct: 460 RLDKILKNEEIRALITALGTGIG-DDFDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYR 518
Query: 879 KMPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKNVKLISI 931
M LIE GY+YIAQPPLYKIK G E Y D E + + ++ K I
Sbjct: 519 YMRPLIEAGYVYIAQPPLYKIKKGGKE-YAYSDEELDEILAELKLKGNPKYGI 570
Score = 131 bits (333), Expect = 2e-31
Identities = 48/84 (57%), Positives = 61/84 (72%)
Query: 1078 KIINYLRNEAENMVIKQRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTL 1137
+I+ L+ + QRYKGLGEMNP QLWETTM+P R LL+V I+DA AD+IF L
Sbjct: 555 EILAELKLKGNPKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSIL 614
Query: 1138 MGDNVELRRKFIELNALHAKNIDI 1161
MGD+VE RR+FIE NA + +N+DI
Sbjct: 615 MGDDVEPRREFIEENAKYVRNLDI 638
>gnl|CDD|223265 COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), B subunit [DNA replication,
recombination, and repair].
Length = 635
Score = 828 bits (2141), Expect = 0.0
Identities = 325/588 (55%), Positives = 427/588 (72%), Gaps = 29/588 (4%)
Query: 342 TQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKI 401
++ ++Y ASSIQ+LEGLEAVRKRP MYIG T DG GLHH V+E++DN+IDE+LAGY +I
Sbjct: 1 SKTNNYDASSIQVLEGLEAVRKRPGMYIGSTGDGRGLHHLVWEVVDNSIDEALAGYADRI 60
Query: 402 NVTIYSDNSISISDNGRGIPIDIKIDDKH-KPKRSAAEIVMTELHAGGKFNKNSYKISGG 460
+VT++ D SIS+ DNGRGIP+DI H K K SA E++ T LHAGGKF+ +SYK+SGG
Sbjct: 61 DVTLHEDGSISVEDNGRGIPVDI-----HPKEKVSAVEVIFTVLHAGGKFDNDSYKVSGG 115
Query: 461 LHGIGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTN- 519
LHG+G+S VN LS +L++ + R+ KI+ F G+ V+P+++IG T+
Sbjct: 116 LHGVGVSVVNALSTWLEVEVKRDGKIYRQRFE------------RGVPVTPLEVIGSTDT 163
Query: 520 -KQGTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERI-KKKEIFEFKG 577
K GTK+ F D +IF EF YEILK+R+REL+FLN GV ITL DER ++K+ F ++G
Sbjct: 164 KKTGTKVRFKPDPEIFGETEFDYEILKRRLRELAFLNKGVKITLTDERTGEEKKEFHYEG 223
Query: 578 GTSGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQ 637
G +V Y+NK K +H IF G +K+ I ++V++QWN+ Y+ENIL F NNI
Sbjct: 224 GLKDYVEYLNKGKTPLHEEIFYFNG-----EKDGIAVEVALQWNDGYSENILSFVNNIPT 278
Query: 638 VDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQ 697
+GGTH G RS +TRAIN+Y ++ LK+ + G+DIREGLT V+S+KIPDP+F Q
Sbjct: 279 REGGTHEAGFRSALTRAINEYAKKKNLLKEGDLT--GDDIREGLTAVISVKIPDPQFEGQ 336
Query: 698 TKNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTRKK 757
TK KL +SEVR VE+++ + FL+ENP E+K I EK I AA++REAARK RELTR+K
Sbjct: 337 TKEKLGNSEVRSIVEKLVSEAFSLFLEENPQEAKKIVEKAIAAAKAREAARKARELTRRK 396
Query: 758 NLIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEK 817
+ +D L KLADC K+PE EL++VEGDSAGGS KQGRDR FQA+LPLRGK+LN+EK
Sbjct: 397 SALDIPGLPGKLADCTSKDPEKSELFLVEGDSAGGSAKQGRDREFQAILPLRGKILNVEK 456
Query: 818 ARFEKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFY 877
AR +KI+ +E+I T+I+ LG GI +F+LEKLRYH+IIIMTDAD+DGAHIR LLLTFFY
Sbjct: 457 ARLDKILKNEEIQTIITALGTGI-GKDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFY 515
Query: 878 RKMPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKN 925
R MP LIE G++YIAQPPLYK+K G Y DD E E+ + ++ K
Sbjct: 516 RYMPPLIENGHVYIAQPPLYKVKKGKKTFYAYDDEELEKLLERLGKKK 563
Score = 123 bits (310), Expect = 1e-28
Identities = 48/68 (70%), Positives = 54/68 (79%)
Query: 1094 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNA 1153
QRYKGLGEMNP QLWETTM+P R LL+V I+DA AD+IF TLMGD VE RR FIE NA
Sbjct: 568 QRYKGLGEMNPDQLWETTMDPETRRLLQVTIEDADEADEIFSTLMGDKVEPRRNFIEENA 627
Query: 1154 LHAKNIDI 1161
L +N+DI
Sbjct: 628 LFVENLDI 635
>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 = 811 bits (2096), Expect = 0.0
Identities = 322/572 (56%), Positives = 420/572 (73%), Gaps = 27/572 (4%)
Query: 347 YSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTIY 406
Y ASSI++LEGLEAVRKRP MYIG T + TGLHH V+E++DN+IDE++AGYC INVTI
Sbjct: 1 YDASSIKVLEGLEAVRKRPGMYIGSTGE-TGLHHLVYEVVDNSIDEAMAGYCDTINVTIN 59
Query: 407 SDNSISISDNGRGIPIDIKIDDKH-KPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIG 465
D S+++ DNGRGIP+DI H + SA E+V+T LHAGGKF+K+SYK+SGGLHG+G
Sbjct: 60 DDGSVTVEDNGRGIPVDI-----HPEEGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVG 114
Query: 466 LSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKI 525
+S VN LS +L++T+ R+ KI+ EF GI + P++++G+T K GT +
Sbjct: 115 VSVVNALSEWLEVTVFRDGKIYRQEFE------------RGIPLGPLEVVGETKKTGTTV 162
Query: 526 HFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIK--KKEIFEFKGGTSGFV 583
FW D +IF EF ++IL KR+REL+FLN+GV I+L DER K F ++GG FV
Sbjct: 163 RFWPDPEIFETTEFDFDILAKRLRELAFLNSGVKISLEDERDGKGKSVTFHYEGGIKSFV 222
Query: 584 SYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQVDGGTH 643
Y+N++K +H I I +K I ++V++QWN+ Y+ENIL F NNI +GGTH
Sbjct: 223 KYLNRNKEPLHEEIIY-----IKGEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTH 277
Query: 644 LTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKNKLV 703
L G RS +TR IN Y + N+ LK+SK + GEDIREGLT V+S+K+PDP+F QTK KL
Sbjct: 278 LEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLG 337
Query: 704 SSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTRKKNLIDDI 763
+SEVR VE ++ + L +F +ENP E+K I EK I AA++REAARK RELTR+K+ +D
Sbjct: 338 NSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSG 397
Query: 764 ELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKI 823
L KLADC K+P ELYIVEGDSAGGS KQGRDR+FQA+LPLRGK+LN+EKAR +KI
Sbjct: 398 GLPGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRKFQAILPLRGKILNVEKARLDKI 457
Query: 824 ILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKL 883
+ +++I +I+ LG GI +D F+LEKLRYH+IIIMTDAD+DG+HIR LLLTFFYR M L
Sbjct: 458 LSNQEIGAIITALGCGIGKD-FDLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPL 516
Query: 884 IEYGYIYIAQPPLYKIKYGNNECYLRDDIEEE 915
IE GY+YIAQPPLYK+K G E Y++DD E+E
Sbjct: 517 IENGYVYIAQPPLYKVKKGKKERYIKDDKEKE 548
Score = 124 bits (312), Expect = 5e-29
Identities = 48/68 (70%), Positives = 55/68 (80%)
Query: 1094 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNA 1153
QRYKGLGEMN QLWETTM+P R LLKV I+DA+ AD+IF TLMGD VE RR+FIE NA
Sbjct: 587 QRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEPRREFIEANA 646
Query: 1154 LHAKNIDI 1161
L KN+D+
Sbjct: 647 LDVKNLDV 654
>gnl|CDD|235501 PRK05559, PRK05559, DNA topoisomerase IV subunit B; Reviewed.
Length = 631
Score = 705 bits (1823), Expect = 0.0
Identities = 254/589 (43%), Positives = 369/589 (62%), Gaps = 32/589 (5%)
Query: 342 TQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKI 401
++Y+A SI++LEGLE VRKRP MYIG T D GLHH V E++DN++DE+LAG+ +I
Sbjct: 3 MMTNNYNADSIEVLEGLEPVRKRPGMYIGST-DTRGLHHLVQEVIDNSVDEALAGHGKRI 61
Query: 402 NVTIYSDNSISISDNGRGIPIDIKIDDKH-KPKRSAAEIVMTELHAGGKFNKNSYKISGG 460
VT+++D S+S+ DNGRGIP+ I H + +S E+++T+LHAGGKF+ +YK SGG
Sbjct: 62 EVTLHADGSVSVRDNGRGIPVGI-----HPEEGKSGVEVILTKLHAGGKFSNKAYKFSGG 116
Query: 461 LHGIGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDT-- 518
LHG+G+S VN LS L++ + R+ K++ F G V P++++G
Sbjct: 117 LHGVGVSVVNALSSRLEVEVKRDGKVYRQRFE------------GGDPVGPLEVVGTAGK 164
Query: 519 NKQGTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKGG 578
K GT++ FW D KIF + +F E LK+R+R +FL G+ ITL DER +++ F ++ G
Sbjct: 165 RKTGTRVRFWPDPKIFDSPKFSPERLKERLRSKAFLLPGLTITLNDER--ERQTFHYENG 222
Query: 579 TSGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQV 638
+++ +N+ K + + ++ ++QW + ENI + N I
Sbjct: 223 LKDYLAELNEGKETLPEEFVG----SFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTP 278
Query: 639 DGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQT 698
GGTH G R G+ +A+ ++ E+ L K K ++ GED+REGL VLS+KIP+P+F QT
Sbjct: 279 QGGTHENGFREGLLKAVREFAEKRNLLPKGK-KLEGEDVREGLAAVLSVKIPEPQFEGQT 337
Query: 699 KNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTRKKN 758
K KL S E R+ V ++ +L +NP ++ + EK I+AA++R A K + RKK
Sbjct: 338 KEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEKAIKAAQARLRAAKKVK--RKKK 395
Query: 759 LIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKA 818
L KLADC ++PE EL++VEGDSAGGS KQ RDR FQA+LPLRGK+LN +A
Sbjct: 396 T-SGPALPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEA 454
Query: 819 RFEKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYR 878
+ ++ +E+I +I +GIG D F+LE LRY +IIIMTDAD+DGAHI LLLTFFYR
Sbjct: 455 SLDDVLANEEIHDIIVAIGIGP-GDSFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYR 513
Query: 879 KMPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKNVK 927
P L+E G++YIA PPLY++ G + Y D+ E+E + K+ K K
Sbjct: 514 HFPPLVEAGHVYIALPPLYRVDKGKKKIYALDEEEKEELLKKLGKKGGK 562
Score = 102 bits (258), Expect = 2e-22
Identities = 34/60 (56%), Positives = 42/60 (70%)
Query: 1094 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNA 1153
QR+KGLGEMNP QLWETTM+P R L++V I DA +K+ LMG E RR++IE N
Sbjct: 566 QRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEETEKLVDMLMGKKAEPRREWIEENG 625
>gnl|CDD|214659 smart00433, TOP2c, TopoisomeraseII. Eukaryotic DNA topoisomerase
II, GyrB, ParE.
Length = 594
Score = 629 bits (1624), Expect = 0.0
Identities = 276/554 (49%), Positives = 372/554 (67%), Gaps = 27/554 (4%)
Query: 377 GLHHFVFEILDNAIDESLAGYCTKINVTIYSDNSISISDNGRGIPIDIKIDDKHKPKRSA 436
GLHH V EI+DNA DE+LAGY I VTI DNSIS+ DNGRGIP++I K K+ A
Sbjct: 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHP----KEKKYA 56
Query: 437 AEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVL 496
E++ T LHAGGKF+ ++YK+SGGLHG+G S VN LS ++ + R+ K + F
Sbjct: 57 PEVIFTVLHAGGKFDDDAYKVSGGLHGVGASVVNALSTEFEVEVARDGKEYKQSFSN--- 113
Query: 497 QNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVDEKIFSNI-EFHYEILKKRIRELSFLN 555
NG +S KIIGDT K GTK+ F D +IF + +E+LK+R+REL+FLN
Sbjct: 114 --------NGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGMTTDDDFELLKRRLRELAFLN 165
Query: 556 NGVCITLIDERIKKKEIFEFKGGTSGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINID 615
GV ITL DER +++ F F+GG +V +NK+K ++ P I +K+NI ++
Sbjct: 166 KGVKITLNDERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPT-----YIEGEKDNIRVE 220
Query: 616 VSMQWNNSYNENILCFTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGE 675
V+ Q+ + Y+ENI+ F NNI +GGTH G + +TR IN+Y ++ + LK+ I+ GE
Sbjct: 221 VAFQYTDGYSENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKKKLKEKNIK--GE 278
Query: 676 DIREGLTCVLSIKIPDPKFNSQTKNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICE 735
D+REGLT +S+KIP+P+F QTK KL +SEVR VE+I+ + L FL+ENP E+ I E
Sbjct: 279 DVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIVSECLLSFLEENPVEASKIVE 338
Query: 736 KIIEAARSREAARKTRELTRKKNLIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVK 795
K++ AA++R AA+K RELTRKK L I L KLAD P+ CEL++VEGDSAGGS K
Sbjct: 339 KVLLAAKARAAAKKARELTRKKKL-SSISLPGKLADASSAGPKKCELFLVEGDSAGGSAK 397
Query: 796 QGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRI 855
GRDR FQA+LPLRGK+LN+EKA +KI+ +E+I LI+ LG+GI +F++EKLRY +I
Sbjct: 398 SGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIG-KDFDIEKLRYGKI 456
Query: 856 IIMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQPPLYKIKYGNNECYLRD--DIE 913
IIMTDAD+DG+HI+ LLLTFFYR MP LIE G++YIA PPLYK+ G + E
Sbjct: 457 IIMTDADVDGSHIKGLLLTFFYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVYSFYSLDE 516
Query: 914 EERYMLKIAFKNVK 927
E+++ K K
Sbjct: 517 YEKWLEKTEGNKSK 530
Score = 97.2 bits (243), Expect = 1e-20
Identities = 39/60 (65%), Positives = 44/60 (73%)
Query: 1094 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNA 1153
QRYKGLGEMN QLWETTM+P R LL V + DA AD IF LMGD VE R+++IE NA
Sbjct: 534 QRYKGLGEMNADQLWETTMDPERRTLLFVTLDDADEADLIFSALMGDKVEPRKEWIEENA 593
>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 = 562 bits (1451), Expect = 0.0
Identities = 273/590 (46%), Positives = 375/590 (63%), Gaps = 31/590 (5%)
Query: 345 SSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVT 404
S Y+A +I+ILEGL+AVRKRP MYIG T D GLHH V+EI+DN++DE LAGY I VT
Sbjct: 3 SKYNADAIKILEGLDAVRKRPGMYIGST-DSKGLHHLVWEIVDNSVDEVLAGYADNITVT 61
Query: 405 IYSDNSISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGI 464
++ DNSI++ D+GRGIP I D S E V T LHAGGKF++ YK +GGLHG+
Sbjct: 62 LHKDNSITVQDDGRGIPTGIHQDGN----ISTVETVFTVLHAGGKFDQGGYKTAGGLHGV 117
Query: 465 GLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTK 524
G S VN LS +L++T+ R+ +I+ F G G V +K IG T K GT
Sbjct: 118 GASVVNALSSWLEVTVKRDGQIYQQRFENG-----------GKIVQSLKKIGTTKKTGTL 166
Query: 525 IHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKGGTSGFVS 584
+HF D IF +F+ I+K+R++E +FL + +T D+R K +F ++ G FV
Sbjct: 167 VHFHPDPTIFKTTQFNSNIIKERLKESAFLLKKLKLTFTDKRTNKTTVFFYENGLVDFVD 226
Query: 585 YINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQVDGGTHL 644
YIN++K + + +KN I ++V+ Q+N+ +ENIL F N++ +GGTH
Sbjct: 227 YINETKETLSQVTY------FEGEKNGIEVEVAFQFNDGDSENILSFANSVKTKEGGTHE 280
Query: 645 TGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDP--KFNSQTKNKL 702
G + IT IN Y + LK+ + G DIREGL+ ++S++IP+ +F QTK+KL
Sbjct: 281 NGFKLAITDVINSYARKYNLLKEKDKNLEGSDIREGLSAIISVRIPEELIQFEGQTKSKL 340
Query: 703 VSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTR--KKNLI 760
S E R V+EI+ LF FL+EN ++KL+ +K I+A ++EAA+K RE + KK
Sbjct: 341 FSPEARNVVDEIVQDHLFFFLEENNNDAKLLIDKAIKARDAKEAAKKAREEKKSGKKPKK 400
Query: 761 DDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARF 820
+ LS KL Q KNP EL++VEGDSAGGS KQGRDR+FQA+LPLRGKVLN+EKA+
Sbjct: 401 EKGILSGKLTPAQSKNPAKNELFLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKAKL 460
Query: 821 EKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKM 880
I+ +E+I T+I +G GI D F+++ L+Y +IIIMTDAD DGAHI+ LLLTFFYR M
Sbjct: 461 ADILKNEEINTIIFCIGTGIGAD-FSIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYM 519
Query: 881 PKLIEYGYIYIAQPPLYKIKYGNNE--CYLRDDIEEERYMLKIAFKNVKL 928
LIE G++YIA PPLYK+ + + Y D+E E +K KN L
Sbjct: 520 RPLIELGHVYIALPPLYKLSKKDGKKVKYAWSDLELES--VKKKLKNYTL 567
Score = 87.2 bits (216), Expect = 2e-17
Identities = 39/70 (55%), Positives = 50/70 (71%), Gaps = 1/70 (1%)
Query: 1083 LRNEAENMVIKQRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNV 1142
++ + +N + QRYKGLGEMN QLWETTMNP R L++VKI D A++ TLMGD V
Sbjct: 558 VKKKLKNYTL-QRYKGLGEMNADQLWETTMNPETRTLVRVKIDDLARAERQINTLMGDKV 616
Query: 1143 ELRRKFIELN 1152
E R+K+IE N
Sbjct: 617 EPRKKWIEAN 626
>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 = 423 bits (1088), Expect = e-134
Identities = 216/587 (36%), Positives = 334/587 (56%), Gaps = 36/587 (6%)
Query: 345 SSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVT 404
++YSA I++L+GLE VRKRP MY D T +H V E++DN++DE+LAG+ + I V
Sbjct: 2 TNYSAKDIEVLDGLEPVRKRPGMYT----DTTRPNHLVQEVIDNSVDEALAGFASIIMVI 57
Query: 405 IYSDNSISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGI 464
++ D SI + DNGRG+P+DI K SA E+++T LHAGGKF+ +Y SGGLHG+
Sbjct: 58 LHQDQSIEVFDNGRGMPVDIH----PKEGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGV 113
Query: 465 GLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQ--G 522
G+S VN LS+ +++ + R K++ + F NG V+ + G K+ G
Sbjct: 114 GISVVNALSKRVKIKVYRQGKLYSIAFE------------NGAKVTDLISAGTCGKRLTG 161
Query: 523 TKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKGGTSGF 582
T +HF D +IF ++ F L +R + L GV I DE K ++ + G +
Sbjct: 162 TSVHFTPDPEIFDSLHFSVSRLYHILRAKAVLCRGVEIEFEDEVNNTKALWNYPDGLKDY 221
Query: 583 VS-YINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENIL-CFTNNILQVDG 640
+S +N + P F GN + ++ ++ ++ W E + + N I G
Sbjct: 222 LSEAVNGDNTLP-PKPF--SGNF---EGDDEAVEWALLWLPEGGELFMESYVNLIPTPQG 275
Query: 641 GTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKN 700
GTH+ GLR G+ A+ ++ E L + +++ EDI + + VLSIK+ DP+F QTK
Sbjct: 276 GTHVNGLRQGLLDALREFCEMRNNLPRG-VKLTAEDIWDRCSYVLSIKMQDPQFAGQTKE 334
Query: 701 KLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTRKKNLI 760
+L S +V K V +I +L +N ++ + E I +A+ R+ R +++ RKK L
Sbjct: 335 RLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAEHAISSAQRRK--RAAKKVVRKK-LT 391
Query: 761 DDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARF 820
L KLADC ++ E EL++VEGDSAGGS KQ RDR +QA+LPL GK+LN +
Sbjct: 392 SGPALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSL 451
Query: 821 EKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKM 880
+K++ S++I + + +GI+ D +L +LRY +I I+ DAD DG HI LL F+
Sbjct: 452 DKVLNSQEIHDI--EVALGIDPDSNDLSQLRYGKICILADADSDGLHIATLLCALFFLHF 509
Query: 881 PKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKNVK 927
PKL+E G++Y+A+PPLY+I Y D+ E+E+ + K+ K K
Sbjct: 510 PKLVEEGHVYVAKPPLYRIDLSKEVYYALDEEEKEKLLYKLKKKKGK 556
Score = 55.7 bits (134), Expect = 1e-07
Identities = 26/60 (43%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 1094 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDA--ISADKIFMTLMGDNV-ELRRKFIE 1150
QR+KGLGEMNP QL ETTM+P R L+++ + D DKI L+ E R +++
Sbjct: 560 QRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDDVQDQRVDKIMDMLLAKKRSEDRFNWLQ 619
>gnl|CDD|240272 PTZ00109, PTZ00109, DNA gyrase subunit b; Provisional.
Length = 903
Score = 424 bits (1092), Expect = e-132
Identities = 240/668 (35%), Positives = 349/668 (52%), Gaps = 121/668 (18%)
Query: 331 LKNKNSYDIQDTQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAI 390
+ + +Q E Y A I +LEGLEAVRKRP MYIG+T D GLH +FEILDN++
Sbjct: 86 QQKERVPQLQRCSE--YDADDIVVLEGLEAVRKRPGMYIGNT-DEKGLHQLLFEILDNSV 142
Query: 391 DESLAGYCTKINVTIYSDNSISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKF 450
DE LAG C KI V ++ D S+ ISDNGRGIP D+ K +S E V+T LH+GGKF
Sbjct: 143 DEYLAGECNKITVVLHKDGSVEISDNGRGIPCDVS----EKTGKSGLETVLTVLHSGGKF 198
Query: 451 N----------------------------------------KNSYKISGGLHGIGLSCVN 470
Y+ S GLHG+GLS VN
Sbjct: 199 QDTFPKNSRSDKSEDKNDTKSSKKGKSSHVKGPKEAKEKESSQMYEYSSGLHGVGLSVVN 258
Query: 471 GLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVD 530
LS FL++ + + KI+ +E G ++ K ++ + P+K K+GT IHF D
Sbjct: 259 ALSSFLKVDVFKGGKIYSIELSKG----KVTKPLS-VFSCPLK------KRGTTIHFLPD 307
Query: 531 EK-IFSN--------------IEFHYEILKKRIRELSFLNNGVCITLIDERIKKK----- 570
K IF F+ +++K RI ELS+LN G+ L+DERI +
Sbjct: 308 YKHIFKTHHQHTETEEEEGCKNGFNLDLIKNRIHELSYLNPGLTFYLVDERIANENNFYP 367
Query: 571 -EIFEFKGGTSGFVSYINKSKLVVHPTIFQAIGN-KISEKKNNINIDVSMQWN-NSYNEN 627
E + +GGT F+ + K K +++ I I N+N++VS+ W+ SY
Sbjct: 368 YETIKHEGGTREFLEELIKDKT----PLYKDINIISIRGVIKNVNVEVSLSWSLESYTAL 423
Query: 628 ILCFTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSI 687
I F NN+ GTH+ G + ITR +N I++N + K + + I GE IREG+T ++S+
Sbjct: 424 IKSFANNV-STTAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISV 482
Query: 688 KIPDPKFNSQTKNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAA 747
K+ +F+ QTK KL + ++ +E I+ + L + L+ P I K + A ++ E A
Sbjct: 483 KLNGAEFDGQTKTKLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEA 542
Query: 748 RKTRELTRKKN--LIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAV 805
+ ++L R+KN I L KL DC + E EL+IVEG+SA G+ KQ R+R FQAV
Sbjct: 543 KAAKDLIRQKNNQYYSTI-LPGKLVDCISDDIERNELFIVEGESAAGNAKQARNREFQAV 601
Query: 806 LPLRGKVLNIEKARFEKIIL-SEQITTLISTLGIGI------------------------ 840
LPL+GK+LNIEK + K + + +I LI+++G+ +
Sbjct: 602 LPLKGKILNIEKIKNNKKVFENSEIKLLITSIGLSVNPVTWRQYDLSHGTKASKDESVQN 661
Query: 841 -------EQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQ 893
+++ LRY +II++TDAD+DG H+R LLLT YR P L E+G +Y+A
Sbjct: 662 NNSTLTKKKNSLFDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVAC 721
Query: 894 PPLYKIKY 901
PPLY+I
Sbjct: 722 PPLYRITN 729
Score = 70.3 bits (172), Expect = 5e-12
Identities = 29/60 (48%), Positives = 44/60 (73%)
Query: 1094 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNA 1153
QR+KGLGEM QLWETTM+P R L+++ + DA+ A ++ LMG++V+ R++FI N+
Sbjct: 840 QRFKGLGEMMADQLWETTMDPKKRILIRITVSDAMRASELIFLLMGEDVQSRKQFIFENS 899
>gnl|CDD|235541 PRK05643, PRK05643, DNA polymerase III subunit beta; Validated.
Length = 367
Score = 315 bits (811), Expect = 4e-98
Identities = 130/319 (40%), Positives = 207/319 (64%), Gaps = 5/319 (1%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
M+ ++ +NA+L LQ+V VE++N +PILSN+L+ K+S +TD E+ I T
Sbjct: 1 MKFTIS--RNALLKALQLVQGAVERRNTIPILSNVLIEAEGGKLSLTATDLEISIETTIP 58
Query: 61 VGYGNSSINIIVAARKFIDILRSLPETEKVTIYI-ENKHMFIKSGKSKFTLQTLDAKEYP 119
+I V A+K +DI+R LP+ ++T+ + EN + IKSGKS+F L TL A+++P
Sbjct: 59 AEVEVEEGSITVPAKKLLDIVRKLPDGAEITLELEENNRLTIKSGKSRFNLPTLPAEDFP 118
Query: 120 IMTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHR 179
+ + + FTL QKTLK ++ F+++ Q+ RYYLNG+LL + + AV++DGHR
Sbjct: 119 NLP-EIEEEVSFTLPQKTLKRLIEKTQFAMSTQETRYYLNGVLLEIEGNELRAVATDGHR 177
Query: 180 LTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISK 239
L ++ +++ +IIPRKT+ LQ+LL++ E PVE+ IS+NQI F N SK
Sbjct: 178 LAVRKLELEEGSLGDFSVIIPRKTLLELQKLLDD-EEPVEIFISDNQILFEFGNTIFTSK 236
Query: 240 LIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVS 299
LIDGKF DY+ VI +++K V+R +LL++L+R SI+SN+K +GV+L + LKI+ +
Sbjct: 237 LIDGKFPDYRRVIPKEFDKKLTVDRKELLQALERASILSNEKSRGVKLSLSEGQLKISAN 296
Query: 300 SSNREKASEELEINYNGKD 318
+ + +A EELE+ Y+G++
Sbjct: 297 NPEQGEAEEELEVEYSGEE 315
>gnl|CDD|238082 cd00140, beta_clamp, Beta clamp domain. The beta subunit
(processivity factor) of DNA polymerase III holoenzyme,
refered to as the beta clamp, forms a ring shaped dimer
that encircles dsDNA (sliding clamp) in bacteria. The
beta-clamp is structurally similar to the trimeric ring
formed by PCNA (found in eukaryotes and archaea) and the
processivity factor (found in bacteriophages T4 and
RB69). This structural correspondence further
substantiates the mechanistic connection between
eukaryotic and prokaryotic DNA replication that has been
suggested on biochemical grounds. .
Length = 365
Score = 284 bits (730), Expect = 1e-86
Identities = 122/352 (34%), Positives = 206/352 (58%), Gaps = 9/352 (2%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
M+ +N + A+L LQ V +E +N +PILSN+L+ + ++ +TD E+ I T
Sbjct: 1 MKFTIN--REALLEALQKVSRAIESRNTIPILSNVLIEASDGGLTLTATDLEISIKTTIP 58
Query: 61 VGYGNSSINIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPI 120
++ V A+K +DI+R LP+ E+VT+ E + IKSGKS+F+L TL A+E+P
Sbjct: 59 AEEVEEEGSVTVPAKKLLDIVRKLPD-EEVTLETEENRLTIKSGKSRFSLNTLPAEEFPE 117
Query: 121 MTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRL 180
+ + FT+ LK ++ F+++ + R LNG+LL + + AV++DGHRL
Sbjct: 118 LP-EIENGSSFTIPASELKELIKKTAFAVSTDETRPILNGVLLEIEDNKLRAVATDGHRL 176
Query: 181 TYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKL 240
++ ++ ++I+PRKT+ L +LLE+ + VE+ IS NQI N S+L
Sbjct: 177 ALREIELESGAEEDFNVIVPRKTLNELLKLLEDDDEEVEISISENQILFKLGNTTFTSRL 236
Query: 241 IDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSS 300
I+G+F DY+ VI ++EKS V+R +LL +L+R+S++SN+K +GV+L I LK++ ++
Sbjct: 237 IEGEFPDYERVIPKEFEKSLTVDREELLEALKRVSLLSNEKNRGVKLEISEGQLKLSANN 296
Query: 301 SNREKASEELEINYNGKDKNF---IKFLIKIMLLKNKNSYDIQDTQESSYSA 349
+A EELE+ Y G++ K+L+ LK +S +++ + S S
Sbjct: 297 PEIGEAEEELEVEYEGEELEIGFNPKYLLDA--LKAIDSEEVRLSFTDSNSP 346
>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 = 231 bits (591), Expect = 4e-70
Identities = 87/177 (49%), Positives = 122/177 (68%), Gaps = 5/177 (2%)
Query: 577 GGTSGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNIL 636
GG FV +NK K +H I +K+ + ++V++QW +SY+ENIL F NNI
Sbjct: 1 GGLKDFVEELNKDKEPLHEEPI-----YIEGEKDGVEVEVALQWTDSYSENILSFVNNIP 55
Query: 637 QVDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNS 696
+GGTH TG R+ +TRAIN Y ++N LKK +++ G+DIREGLT V+S+K+P+P+F
Sbjct: 56 TPEGGTHETGFRAALTRAINDYAKKNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEG 115
Query: 697 QTKNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTREL 753
QTK+KL +SEVR VE + + L ++L+ENP E+K I EK I AA++REAARK REL
Sbjct: 116 QTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAILAAKAREAARKAREL 172
>gnl|CDD|214686 smart00480, POL3Bc, DNA polymerase III beta subunit.
Length = 345
Score = 234 bits (599), Expect = 9e-69
Identities = 111/324 (34%), Positives = 191/324 (58%), Gaps = 6/324 (1%)
Query: 19 VISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSSINIIVAARKFI 78
V ++ +N +PILSNIL+ + ++ +TD E+ I + + + ++ V A+KF+
Sbjct: 1 VSRVISNRNTIPILSNILLEAKDDGLTLTATDLEISIKSSISAEVEDEEGSVTVPAKKFL 60
Query: 79 DILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKYDFEFTLSQKTL 138
DI+R LP+ +++T+ +E + I SGKS+F L TLDA+E+P + + F L K L
Sbjct: 61 DIVRKLPD-KEITLSVEEDKLVITSGKSRFNLPTLDAEEFPELPFIEE-GVTFELPTKLL 118
Query: 139 KCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDKKFSSCSDII 198
K + F+++ + R LNG+ L + V++DGHRL ++ ++ + +I
Sbjct: 119 KEGIEKTAFAVSTDETRPVLNGVNLEISNGELRLVATDGHRLAVREIKLESEEDD-FSVI 177
Query: 199 IPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKLIDGKFLDYKYVISNKYEK 258
IPRK++ L +LL + E VE+ IS+NQI N+ S+LIDG+F DYK VI ++E
Sbjct: 178 IPRKSLLELNKLLTDNEELVEIFISSNQILFETGNVIFTSRLIDGEFPDYKRVIPKEFET 237
Query: 259 SFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKASEELEINYNGKD 318
VNR +L +L+R+++++N+K + V+L ++ LK+T +S +A EE++++Y G+D
Sbjct: 238 KLTVNRKELKEALKRVALLANEKNRSVKLTLEEGQLKLTANSPEVGEAEEEVDVDYEGED 297
Query: 319 KNFIKFLIKIML--LKNKNSYDIQ 340
I F K +L LK S +I+
Sbjct: 298 LE-IAFNPKYLLDALKALKSEEIE 320
>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 = 214 bits (546), Expect = 6e-65
Identities = 84/115 (73%), Positives = 100/115 (86%), Gaps = 1/115 (0%)
Query: 780 CELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIG 839
ELYIVEGDSAGGS KQGRDRRFQA+LPLRGK+LN+EKAR +KI+ +E+I LI+ LG G
Sbjct: 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTG 60
Query: 840 IEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQP 894
I ++F+LEKLRYH+IIIMTDAD+DGAHIR LLLTFF+R M LIE G++YIAQP
Sbjct: 61 I-GEDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
>gnl|CDD|223665 COG0592, DnaN, DNA polymerase sliding clamp subunit (PCNA homolog)
[DNA replication, recombination, and repair].
Length = 364
Score = 208 bits (532), Expect = 1e-59
Identities = 96/328 (29%), Positives = 178/328 (54%), Gaps = 9/328 (2%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
M+ + + +L LQ+V IVE + +PILSN+L+ ++ TD E+ +
Sbjct: 1 MKFSIE--RENLLKALQLVSRIVESRPTIPILSNVLIEAKENGLTLTGTDLEISLEARIP 58
Query: 61 VGYGNSSINIIVAARKFIDILRSLPETEKVTIYIE-NKHMFIKSGKSKFTLQTLDAKEYP 119
+ + V A+K +DI+ LP+ + + + + SGKS F L TL A+++P
Sbjct: 59 AEV-EAEGEVAVPAKKLLDIISKLPDEAVFLVTEDGISLLAVDSGKSAFVLLTLPAEDFP 117
Query: 120 IMTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHR 179
++ + + EF L + LK I+ F+ + + RY LNG+LL + + V++DGHR
Sbjct: 118 EYPVDEE-EVEFGLPTELLKKIIKRTKFADSLLETRYELNGVLLEIEGTKLRLVATDGHR 176
Query: 180 LTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISK 239
L ++ I + + +IIP KT+ L +LL++ + VE+ + ++QI+ + SK
Sbjct: 177 LAVEELEIPE-LEEDASVIIPAKTLKELIKLLKDAD--VEIFLVSDQIRFKAGETILFSK 233
Query: 240 LIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVS 299
LI+G+F DY+ VI ++EK ++R +L +L+R+ +S K +G +L + +K+++
Sbjct: 234 LIEGEFPDYERVIPKEFEKELTLDRLELKEALKRVYSLSYLKDRGKKLSLADGEVKLSLG 293
Query: 300 SSNREKASEELEINYNGKDKNFIKFLIK 327
+ KA EE+++ Y G++ I F +
Sbjct: 294 NDEPGKAEEEIDVGYTGEELK-IGFNLA 320
>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 = 198 bits (507), Expect = 2e-59
Identities = 77/115 (66%), Positives = 96/115 (83%)
Query: 780 CELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIG 839
CEL +VEGDSAGGS KQGRDR FQAV PLRGK+LN+EKA +KI+ +E+I +I LG+G
Sbjct: 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLG 60
Query: 840 IEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQP 894
I +D+F+L+KLRY +IIIMTDAD+DG+HIR LLLTFFYR P L+E G++YIAQ
Sbjct: 61 IGKDDFDLDKLRYGKIIIMTDADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
>gnl|CDD|215785 pfam00204, DNA_gyraseB, DNA gyrase B. This family represents the
second domain of DNA gyrase B which has a ribosomal S5
domain 2-like fold. This family is structurally related
to PF01119.
Length = 173
Score = 197 bits (503), Expect = 4e-58
Identities = 83/176 (47%), Positives = 119/176 (67%), Gaps = 3/176 (1%)
Query: 578 GTSGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQ 637
G +V +NK K +HP + G + + I ++V++QWN+SY+ENI+ F NNI
Sbjct: 1 GLKDYVKELNKDKTPLHPEVIYFEGEE--AFDDRIEVEVALQWNDSYSENIVSFVNNIPT 58
Query: 638 VDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQ 697
DGGTH+ G R+ +TRA+N+Y ++ LKK K +I G+DIREGLT V+S+KIP+P+F Q
Sbjct: 59 PDGGTHVDGFRAALTRALNEYAKKKGLLKK-KDKITGDDIREGLTAVVSVKIPNPQFEGQ 117
Query: 698 TKNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTREL 753
TK KL +SEVR VE ++ + FL++NP +K I EK + AA++R AARK REL
Sbjct: 118 TKEKLGNSEVRSAVESVVSEKFAKFLEKNPEIAKKILEKALAAAKARLAARKAREL 173
>gnl|CDD|233078 TIGR00663, dnan, DNA polymerase III, beta subunit. All proteins in
this family for which functions are known are components
of the DNA polymerase III complex (beta subunit). 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 = 367
Score = 201 bits (514), Expect = 4e-57
Identities = 102/339 (30%), Positives = 182/339 (53%), Gaps = 6/339 (1%)
Query: 5 VNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYG 64
E++ +L L V ++ + +PILSNIL+ +K++ +TD ++ + +
Sbjct: 3 FIIERDDLLKELSKVQRVLSNRPTIPILSNILLEVKDDKLTITATDLDISLESQIFTINS 62
Query: 65 NSSINIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLN 124
++ + A+KF+DI+R+LP K+T+ ++N + I S KS+F L TL A+E+P +
Sbjct: 63 EQEGSVTINAKKFLDIVRALP-DSKITLEVKNDKLAITSEKSRFKLPTLSAEEFPNLP-T 120
Query: 125 SKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQ 184
+ + LK +N F+ + + R LNG+L+ + K ++ V++DGHRL +
Sbjct: 121 IEEGVSIEIPSDVLKEAINQTAFAAGEDETRPVLNGVLIEQKGKTLLLVATDGHRLAVCK 180
Query: 185 VNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKLIDGK 244
+ + +IIP K + L +LL + V +++ + I N + SKLI+G
Sbjct: 181 LKSEVSDEEDFSVIIPAKALNELLKLLSENGSVVLKSLNDQLVYIELGNYKFTSKLIEGN 240
Query: 245 FLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVR-LVIKPNYLKITVSSSNR 303
+ DYK VI + + SF VNR +L +++R+S+++++K V L LK + +
Sbjct: 241 YPDYKSVIPKEQKNSFTVNREELKEAIKRVSLLADEKRNLVLTLSENGKKLKESSDTQEI 300
Query: 304 EKASEELEINYNGKDKNFIKFLIKIML--LKNKNSYDIQ 340
+A EE+E+ Y+G+D I F IK +L LK S +IQ
Sbjct: 301 GEAEEEIEVAYDGEDLV-IAFNIKYLLDALKALKSKEIQ 338
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 179 bits (457), Expect = 1e-45
Identities = 158/617 (25%), Positives = 261/617 (42%), Gaps = 109/617 (17%)
Query: 342 TQESSYSASSIQILEGLEAVRKRPEMYIG------------DTSDGT----------GLH 379
T E Y Q +E + RP+ YIG D GL+
Sbjct: 5 TVEERY-----QKKTQIEHILLRPDTYIGSIETQTEDMWVYDEEKNRMVYKTITYVPGLY 59
Query: 380 HFVFEILDNAID----ESLAGYCTKINVTI-YSDNSISISDNGRGIPIDIKIDDKHK--- 431
EIL NA D + T I VTI + IS+ ++G GIP+ I +HK
Sbjct: 60 KIFDEILVNAADNKARDKGGHRMTYIKVTIDEENGEISVYNDGEGIPVQI--HKEHKIYV 117
Query: 432 PKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLS-RF-LQLTINRNKKIHYM 489
P E++ L ++ +++GG +G G N S +F ++ +++ K M
Sbjct: 118 P-----EMIFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECVDSKSGKKFKM 172
Query: 490 EFRYGVLQNR--IIKTINGISVSPIKIIGDTNKQGTKIHFWVDEKIFSNIEF---HYEIL 544
+ + + I + +G K TK+ F+ D F EF +L
Sbjct: 173 TWTDNMSKKSEPRITSYDG------------KKDYTKVTFYPDYAKFGMTEFDDDMLRLL 220
Query: 545 KKRIRELSFLNNGVCITLIDERIKKKEIFEFKGGTSGFVSYINKSKLVVHPTIFQAIGNK 604
KKR+ +L+ + + L ERI K F Y++ L +
Sbjct: 221 KKRVYDLAGCFGKLKVYLNGERIAIKS----------FKDYVD---LYLPD-----GEEG 262
Query: 605 ISEKKNNINIDVSMQWN--NSYNE---NILCFTNNILQVDGGTHLTGLRSGITRAINKYI 659
+ V+ +W S ++ + F N+I GGTH+ + + + +
Sbjct: 263 KKPPYPFVYTSVNGRWEVVVSLSDGQFQQVSFVNSICTTKGGTHVNYILDQLISKLQEKA 322
Query: 660 EENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKNKLVSSEVRKPVEEIIIKTL 719
++ KK EI I+ L ++ I +P F+SQTK L + + + + L
Sbjct: 323 KK---KKKKGKEIKPNQIKNHLWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKL 379
Query: 720 FDFLQENPGESKLICEKIIEAARSREAARKTREL-TRKKNLIDDIELSTKLADCQE---K 775
++ ++P I E I+E A+++ AA +++ KK+ I I KL D + K
Sbjct: 380 IKYVLKSP-----ILENIVEWAQAKLAAELNKKMKAGKKSRILGI---PKLDDANDAGGK 431
Query: 776 NPELCELYIVEGDSA------GGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQI 829
N E C L + EGDSA G SV GRD V PLRGK+LN+ A ++++ +++I
Sbjct: 432 NSEECTLILTEGDSAKALALAGLSVV-GRDY--YGVFPLRGKLLNVRDASLKQLMNNKEI 488
Query: 830 TTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEY-GY 888
L LG+ I + + + LRY ++IMTD D DG+HI+ LL+ + P L++ G+
Sbjct: 489 QNLFKILGLDIGKKYEDPKGLRYGSLMIMTDQDHDGSHIKGLLINMIHHFWPSLLKNPGF 548
Query: 889 IYIAQPPLYKIKYGNNE 905
+ P+ K N+
Sbjct: 549 LKEFITPIVKATKKGNQ 565
>gnl|CDD|177398 PHA02569, 39, DNA topoisomerase II large subunit; Provisional.
Length = 602
Score = 166 bits (422), Expect = 6e-43
Identities = 164/606 (27%), Positives = 266/606 (43%), Gaps = 101/606 (16%)
Query: 352 IQILEGLEAVRKRPEMYIGDTSDGT----------------GLHHFVFEILDNAIDESLA 395
++L E + KRP MYIG + GL + EI+DN++DE++
Sbjct: 4 FKVLSDREHILKRPGMYIGSVAYEAHERFLFGKFTQVEYVPGLVKIIDEIIDNSVDEAIR 63
Query: 396 G---YCTKINVTIYSDNSISISDNGRGIPIDIKIDDKHK--PKRSAAEIVMTELHAGGKF 450
+ KI+VTI +N +++SDNGRGIP + + + P AA T AG F
Sbjct: 64 TNFKFANKIDVTI-KNNQVTVSDNGRGIPQAMVTTPEGEEIPGPVAA---WTRTKAGSNF 119
Query: 451 NKNSYKISGGLHGIGLSCVNGLSR-FLQLTINRNKKIHYMEFRYGVLQNRIIKTING--- 506
+ ++ +++GG++G+G S N S F+ T + ++ + NG
Sbjct: 120 D-DTNRVTGGMNGVGSSLTNFFSVLFIGETCDGKNEV-------------TVNCSNGAEN 165
Query: 507 ISVSPIKIIGDTNKQGTKIHFWVDEKIFS--NIEFHY-EILKKRIRELSFLNNGVCITLI 563
IS S +GT + F D F ++ Y +I+ R++ L+ ++
Sbjct: 166 ISWSTKP----GKGKGTSVTFIPDFSHFEVNGLDQQYLDIILDRLQTLA---------VV 212
Query: 564 DERIKKKEIFEFKGGT--SGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWN 621
IK F F G F Y +K TI Q E N VS+
Sbjct: 213 FPDIK----FTFNGKKVSGKFKKY---AKQFGDDTIVQ-------ENDN-----VSIALA 253
Query: 622 NSYNE-NILCFTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREG 680
S + L F N + +GG H+ + I + I+ KK KIE+ ++E
Sbjct: 254 PSPDGFRQLSFVNGLHTKNGGHHVDCVMDDICEELIPMIK-----KKHKIEVTKARVKEC 308
Query: 681 LTCVLSIK-IPDPKFNSQTKNKLVSS--EVRKPVEEIIIKTLFDFLQENPGESKLICEKI 737
LT VL ++ + +P+F+SQTK +L S E+R ++ + K + + + I I
Sbjct: 309 LTIVLFVRNMSNPRFDSQTKERLTSPFGEIRNHID-LDYKKIAKQILKTEA----IIMPI 363
Query: 738 IEAARSREAARKTRELTRKKNLIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQG 797
IEAA +R+ A + T+ +++ + L++ EGDSA G + +
Sbjct: 364 IEAALARKLAAEKAAETKAAKKAKKAKVAKHIKANLIGKDAETTLFLTEGDSAIGYLIEV 423
Query: 798 RDRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIII 857
RD PLRGKVLN + I+ ++++ + + G+ + + N + Y I I
Sbjct: 424 RDEELHGGYPLRGKVLNTWGMSYADILKNKELFDICAITGLVLGEKAEN---MNYKNIAI 480
Query: 858 MTDADIDG-AHIRALLLTFFYRKMPKLIEYGYIYIAQPPLYKIKYGNNE--CYLRDDIEE 914
MTDAD+DG I LLL FF R P+L E G I + P+ + G Y D+ E+
Sbjct: 481 MTDADVDGKGSIYPLLLAFFSR-WPELFEQGRIRFVKTPVIIAQVGKETKWFYSLDEFEK 539
Query: 915 ERYMLK 920
+ LK
Sbjct: 540 AKDSLK 545
>gnl|CDD|184904 PRK14940, PRK14940, DNA polymerase III subunit beta; Provisional.
Length = 367
Score = 147 bits (372), Expect = 2e-38
Identities = 94/319 (29%), Positives = 162/319 (50%), Gaps = 18/319 (5%)
Query: 8 EKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSS 67
EK A+L + + I+ K L ILSN+L+ ++ +TDT+V T V
Sbjct: 6 EKEALLKEISIAQEIISTKKALSILSNVLLAAQDGSLTIKATDTKVSFETSIPV------ 59
Query: 68 INII------VAARKFIDILRSLPETEKVTIYIENKHMFIKS--GKSKFTLQTLDAKEYP 119
NI+ V KF+ IL SLP E + + + ++ + I K F L+T+ + +P
Sbjct: 60 -NILAEGSTTVFCDKFVGILSSLPTGE-IELELCDEQLVITPPNKKISFQLKTISHESFP 117
Query: 120 IMTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHR 179
N F + K L+ ++N F+++ + RY++NG+ + FQ NII V++DG R
Sbjct: 118 CFPENEG-GVSFAIPTKDLREMINQTIFAVSDDETRYFMNGVYVEFQYGNIICVATDGRR 176
Query: 180 LTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISK 239
L Y + + S +I+P K + + + L + N V L I++ I F + S
Sbjct: 177 LAYIKKKGESSPQEFSGVIVPPKILGIINKKLSPEGN-VTLCITSQNIFFFFGGYKFSSV 235
Query: 240 LIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVS 299
LI+G+F +YK VI + E+SF V R +L+ +L+R+S++ K + + L I+ L ++
Sbjct: 236 LIEGQFPNYKRVIPDHQERSFCVGRVELMEALKRVSLLVEQKSRRIFLTIQQGLLTLSSQ 295
Query: 300 SSNREKASEELEINYNGKD 318
+ A EE+ Y G++
Sbjct: 296 ENEIGDAQEEIACAYTGEE 314
>gnl|CDD|184907 PRK14943, PRK14943, DNA polymerase III subunit beta; Provisional.
Length = 374
Score = 141 bits (357), Expect = 2e-36
Identities = 94/334 (28%), Positives = 167/334 (50%), Gaps = 27/334 (8%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
M+ +N K+ L+ L+ V+++V K +PILSN+L+ + +IS +T+ ++ I
Sbjct: 1 MKFKIN--KDHFLNGLRQVLNVVSSKTTMPILSNVLIEAENGQISLTTTNLDLGIRCVIK 58
Query: 61 VGYGNSSINIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPI 120
+ + +K I+R LPE E +N ++SG S+F + + A+E+P
Sbjct: 59 ANVLREG-TVTLPVKKLATIVRELPEAEVQVDANQNNQAKVESGGSQFKIMGIPAEEFPP 117
Query: 121 MTLNSKYDFE----FTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSD 176
+ FE F L Q L+ +L V ++ + + RY LNG+ +F+ + V++D
Sbjct: 118 LP-----SFEQATVFQLEQSELRDMLKSVEYAQSTDETRYILNGVYFNFRDGKLTLVATD 172
Query: 177 GHRLTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIF----- 231
G RL + ++ D I+P KTV L+RLL+ +LKI N + F
Sbjct: 173 GRRLALAETELEFPEDQAGDAILPAKTVGELRRLLDKGG---KLKIRFNDRQAAFEISIG 229
Query: 232 -------SNIEIISKLIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKG 284
++ +ISKL++G + +Y+ VI + ++ + R LL + R +++S+DK
Sbjct: 230 EDSSGLANDTYLISKLVEGNYPNYRQVIPKETKERIKLERELLLECVHRAALVSSDKSNS 289
Query: 285 VRLVIKPNYLKITVSSSNREKASEELEINYNGKD 318
V+L N L+I SS +A E + I Y+G +
Sbjct: 290 VKLKFSENLLEIASSSEGVGEAHESMAITYSGPE 323
>gnl|CDD|215593 PLN03128, PLN03128, DNA topoisomerase 2; Provisional.
Length = 1135
Score = 147 bits (373), Expect = 8e-36
Identities = 155/578 (26%), Positives = 252/578 (43%), Gaps = 104/578 (17%)
Query: 358 LEAVRKRPEMYIGDTSDGT--------------------GLHHFVFEILDNAIDESLAG- 396
LE + RP+ YIG T T GL+ EIL NA D
Sbjct: 13 LEHILLRPDTYIGSTEKHTQTLWVYEGGEMVNREVTYVPGLYKIFDEILVNAADNKQRDP 72
Query: 397 YCTKINVTIYSD-NSISISDNGRGIPIDIKIDDKHKPKRS-AAEIVMTELHAGGKFNKNS 454
+ V I + N+IS+ +NG+GIP++I HK + E++ L F+ N
Sbjct: 73 SMDSLKVDIDVEQNTISVYNNGKGIPVEI-----HKEEGVYVPELIFGHLLTSSNFDDNE 127
Query: 455 YKISGGLHGIGLSCVNGLS-RFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIK 513
K +GG +G G N S F T + N+ Y + + T N S K
Sbjct: 128 KKTTGGRNGYGAKLANIFSTEFTVETADGNRGKKY----------KQVFTNNMSVKSEPK 177
Query: 514 IIG-DTNKQGTKIHFWVDEKIFSNIEFH---YEILKKRIRELS-FLNNGVCITLIDERIK 568
I ++ TKI F D F+ ++ KR+ +++ L + + L +++
Sbjct: 178 ITSCKASENWTKITFKPDLAKFNMTRLDEDVVALMSKRVYDIAGCLGKKLKVELNGKKLP 237
Query: 569 KKEIFEFKGGTSGFVSYINKSKLVVHPTIFQAIGNKISEKKNN---INIDVSMQWNNSYN 625
K F Y+ L + P + +I EK N+ + + +S + S+
Sbjct: 238 VK----------SFQDYVG---LYLGPNSREDPLPRIYEKVNDRWEVCVSLS---DGSFQ 281
Query: 626 ENILCFTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLKKSK--IEIIGEDIREGLTC 683
+ + F N+I + GGTH+ + I + I + ++ KK+K + I+ L
Sbjct: 282 Q--VSFVNSIATIKGGTHVDYVADQIVKHIQEKVK-----KKNKNATHVKPFQIKNHLWV 334
Query: 684 VLSIKIPDPKFNSQTKNKLVSSEVR-----KPVEEIIIKTLFDFLQENPGESKLICEKII 738
++ I +P F+SQTK L + + EE + K E G + E I+
Sbjct: 335 FVNCLIENPTFDSQTKETLTTRPSSFGSKCELSEEFLKKV------EKCG----VVENIL 384
Query: 739 EAARSREAARKTRELTRKKNLIDDIELSTKLADCQE---KNPELCELYIVEGDSA----- 790
A+ ++ ++ K+ + I KL D + K + C L + EGDSA
Sbjct: 385 SWAQFKQQKELKKKDGAKRQRLTGIP---KLDDANDAGGKKSKDCTLILTEGDSAKALAM 441
Query: 791 -GGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGI--GIEQDEFNL 847
G SV GRD V PLRGK+LN+ +A ++I+ + +IT + LG+ G DE N
Sbjct: 442 SGLSV-VGRD--HYGVFPLRGKLLNVREASHKQIMKNAEITNIKQILGLQFGKTYDEENT 498
Query: 848 EKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIE 885
+ LRY ++IMTD D DG+HI+ L++ FF+ P L++
Sbjct: 499 KSLRYGHLMIMTDQDHDGSHIKGLIINFFHSFWPSLLK 536
>gnl|CDD|201537 pfam00986, DNA_gyraseB_C, DNA gyrase B subunit, carboxyl terminus.
The amino terminus of eukaryotic and prokaryotic DNA
topoisomerase II are similar, but they have a different
carboxyl terminus. The amino-terminal portion of the DNA
gyrase B protein is thought to catalyze the ATP-dependent
super-coiling of DNA. See pfam00204. The
carboxyl-terminal end supports the complexation with the
DNA gyrase A protein and the ATP-independent relaxation.
This family also contains Topoisomerase IV. This is a
bacterial enzyme that is closely related to DNA gyrase.
Length = 65
Score = 108 bits (272), Expect = 2e-28
Identities = 39/57 (68%), Positives = 47/57 (82%)
Query: 1094 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIE 1150
QR+KGLGEMNP QLWETTM+P R LL+V I+DA AD++F TLMG +VE RR+FIE
Sbjct: 9 QRFKGLGEMNPEQLWETTMDPETRRLLQVTIEDAEEADEMFSTLMGKDVEPRREFIE 65
>gnl|CDD|184905 PRK14941, PRK14941, DNA polymerase III subunit beta; Provisional.
Length = 374
Score = 108 bits (271), Expect = 5e-25
Identities = 78/308 (25%), Positives = 149/308 (48%), Gaps = 15/308 (4%)
Query: 19 VISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSSINIIVAARKFI 78
V + K+I P NI + + K++ +TD E+ IT T V +S NI + AR
Sbjct: 17 VAQAIPAKSIDPRFENIHLTLENGKLTLFATDGELSITAKTEVESSDSG-NIGIRARTLQ 75
Query: 79 DILRSLPETEKVTIYIENKHM------FIKSGKSKFTLQ-TLDAKEYPIMTLNSKYDFEF 131
D LRS+ +TE VT IE + + I + K ++ + ++K +D
Sbjct: 76 DFLRSMYDTE-VTFSIERQEISDHGTVHIATDKGRYKIPCLFESKP---EKQEKNFDISL 131
Query: 132 TLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDKKF 191
L L ++ F+ + +R + G+L + I AVS+DGHRL + N
Sbjct: 132 DLETSELLDLIQKTIFACSVDGMRPAMMGVLFELEGNTITAVSTDGHRLVRCRKNSSVGV 191
Query: 192 SSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKLIDGKFLDYKYV 251
I++P + + LQ+L +++ + + ++ I N+ + + LI + +Y+ V
Sbjct: 192 EEKQKIVVPARVLSILQKLAQHETVTMSIDSERRFVRFICGNVVLDAALIVEPYPNYEAV 251
Query: 252 ISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNR-EKASEEL 310
I + +K ++NR+ + S++R+ S+ + +++ ++ + LK+ ++N E A EEL
Sbjct: 252 IPVENDKKLVINRSNIYDSVKRVGRFSS--IGDIKISVEGSVLKVMAENTNEGESAQEEL 309
Query: 311 EINYNGKD 318
+Y G+D
Sbjct: 310 PCSYTGED 317
>gnl|CDD|202381 pfam02767, DNA_pol3_beta_2, DNA polymerase III beta subunit,
central domain. A dimer of the beta subunit of DNA
polymerase beta forms a ring which encircles duplex DNA.
Each monomer contains three domains of identical
topology and DNA clamp fold.
Length = 116
Score = 99.3 bits (248), Expect = 1e-24
Identities = 42/116 (36%), Positives = 67/116 (57%)
Query: 132 TLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDKKF 191
TL QK LK ++ F++ + + RY LNG+ L + + V++DGHRL ++ + +
Sbjct: 1 TLPQKVLKELIEQTAFAMGRDETRYVLNGVNLETEGNELRLVATDGHRLAVRKLELSVEN 60
Query: 192 SSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKLIDGKFLD 247
+I+PRKT+ L +LL + V+L+I QI+ F N+ S+LIDGKF D
Sbjct: 61 PDIFSVIVPRKTLLELAKLLTDNGELVKLQIGEGQIRFEFGNVIFTSRLIDGKFPD 116
Score = 30.7 bits (70), Expect = 1.2
Identities = 16/104 (15%), Positives = 41/104 (39%), Gaps = 17/104 (16%)
Query: 25 KKNILPILSNILVCKNSEKISFLSTD--------TEVQITTYTAVGYGNSSINIIVAARK 76
+ +L+ + + ++ ++TD E+ + ++IV +
Sbjct: 20 RDETRYVLNGVNLETEGNELRLVATDGHRLAVRKLELSVEN-------PDIFSVIVPRKT 72
Query: 77 FIDILRSLPET-EKVTIYIENKHMFIKSGKSKFTLQTLDAKEYP 119
+++ + L + E V + I + + G FT + +D K +P
Sbjct: 73 LLELAKLLTDNGELVKLQIGEGQIRFEFGNVIFTSRLIDGK-FP 115
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 108 bits (272), Expect = 8e-24
Identities = 147/578 (25%), Positives = 242/578 (41%), Gaps = 105/578 (18%)
Query: 358 LEAVRKRPEMYIGDTSDGT--------------------GLHHFVFEILDNAIDE----- 392
LE + RP+ YIG T GL+ EIL NA D
Sbjct: 38 LEHILLRPDTYIGSIEKHTQTLWVYETDKMVQRSVTYVPGLYKIFDEILVNAADNKQRDP 97
Query: 393 SLAGYCTKINVTIYSDNSISISDNGRGIPIDIKIDDKHKPKR-SAAEIVMTELHAGGKFN 451
+ I+V N IS+ +NG G+P++I H+ + E++ L ++
Sbjct: 98 KMDSLRVVIDV---EQNLISVYNNGDGVPVEI-----HQEEGVYVPEMIFGHLLTSSNYD 149
Query: 452 KNSYKISGGLHGIGLSCVNGLS-RFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVS 510
N K +GG +G G N S F+ T + ++ Y + V N + G
Sbjct: 150 DNEKKTTGGRNGYGAKLTNIFSTEFVIETADGKRQKKYKQ----VFSNNM-----GKKSE 200
Query: 511 PIKIIGDTNKQGTKIHFWVDEKIFSNIEFHYEI---LKKRIRELS-FLNNGVCITLIDER 566
P+ ++ TK+ F D F+ ++ +KKR+ +++ L V + L +R
Sbjct: 201 PVITKCKKSENWTKVTFKPDLAKFNMTHLEDDVVALMKKRVVDIAGCLGKTVKVELNGKR 260
Query: 567 IKKKEIFEFKGGTSGFVSYIN---KSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNS 623
I K F Y++ +S P I K++++ + VS+
Sbjct: 261 IPVK----------SFSDYVDLYLESANKSRPENLPRIYEKVNDR---WEVCVSLSEGQF 307
Query: 624 YNENILCFTNNILQVDGGTHLTGLRSGIT----RAINKYIEENEFLKKSKIEIIGEDIRE 679
+ F N+I + GGTH+ + + I A+NK K I +++
Sbjct: 308 QQ---VSFVNSIATIKGGTHVDYVTNQIANHVMEAVNK--------KNKNANIKAHNVKN 356
Query: 680 GLTCVLSIKIPDPKFNSQTKNKLV--SSEVRKPVEEIIIKTLFDFLQENPGESKLICEKI 737
L ++ I +P F+SQTK L S E DFL+ K++ I
Sbjct: 357 HLWVFVNALIDNPAFDSQTKETLTLRQSSFGSKCELSE-----DFLK------KVMKSGI 405
Query: 738 IEAARSREAARKTRELTR----KKNLIDDIELSTKLADCQE---KNPELCELYIVEGDSA 790
+E S ++++EL + K + I KL D E KN E C L + EGDSA
Sbjct: 406 VENLLSWADFKQSKELKKTDGAKTTRVTGIP---KLEDANEAGGKNSEKCTLILTEGDSA 462
Query: 791 GGSVKQGR---DRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIGIEQDEFNL 847
G R + V PLRGK+LN+ +A ++I+ + +I + LG+ + ++
Sbjct: 463 KALAVAGLSVVGRNYYGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYESV 522
Query: 848 EKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIE 885
+ LRY ++IMTD D DG+HI+ LL+ F + P L++
Sbjct: 523 KSLRYGHLMIMTDQDHDGSHIKGLLINFIHSFWPSLLK 560
>gnl|CDD|216076 pfam00712, DNA_pol3_beta, DNA polymerase III beta subunit,
N-terminal domain. A dimer of the beta subunit of DNA
polymerase beta forms a ring which encircles duplex DNA.
Each monomer contains three domains of identical
topology and DNA clamp fold.
Length = 120
Score = 86.5 bits (215), Expect = 4e-20
Identities = 38/122 (31%), Positives = 72/122 (59%), Gaps = 2/122 (1%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
M+ + E++ +L LQ V ++ + +PILS IL+ +++S TD E+ I + +
Sbjct: 1 MKFTI--ERDQLLKALQKVARVLSNRPTIPILSGILLEVKDDQLSLTGTDLEISIESTIS 58
Query: 61 VGYGNSSINIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPI 120
+ ++++ ARKF+DI+R+LP+ + V + + + I SG S+F+L TL A++YP
Sbjct: 59 AEIESEPGSVLIPARKFLDIVRALPDDKDVKLSVNEDRLLIISGNSRFSLPTLPAEDYPN 118
Query: 121 MT 122
+
Sbjct: 119 LP 120
>gnl|CDD|173785 cd03365, TOPRIM_TopoIIA, TOPRIM_TopoIIA: topoisomerase-primase
(TOPRIM) nucleotidyl transferase/hydrolase domain of the
type found in proteins of the type IIA family of DNA
topoisomerases similar to Saccharomyces cerevisiae
Topoisomerase II. TopoIIA enzymes cut both strands of
the duplex DNA to remove (relax) both positive and
negative supercoils in DNA. These enzymes covalently
attach to the 5' ends of the cut DNA, separate the free
ends of the cleaved strands, pass another region of the
duplex through this gap, then rejoin the ends. These
proteins also catenate/ decatenate duplex rings. The
TOPRIM domain has two conserved motifs, one of which
centers at a conserved glutamate and the other one at
two conserved aspartates (DxD). This glutamate and two
aspartates, cluster together to form a highly acid
surface patch. The conserved glutamate may act as a
general base in strand joining and as a general acid in
strand cleavage by topisomerases. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 120
Score = 86.6 bits (215), Expect = 5e-20
Identities = 40/109 (36%), Positives = 64/109 (58%), Gaps = 4/109 (3%)
Query: 780 CELYIVEGDSAGGSVKQGR---DRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTL 836
C L + EGDSA G R + V PLRGK+LN+ +A ++I+ + +I + L
Sbjct: 1 CTLILTEGDSAKALAVAGLSVVGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKIL 60
Query: 837 GIGIEQDEF-NLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLI 884
G+ + ++ + + LRY R++IMTD D DG+HI+ LL+ F + P L+
Sbjct: 61 GLQHGKSDYESTKSLRYGRLMIMTDQDHDGSHIKGLLINFIHSFWPSLL 109
>gnl|CDD|184909 PRK14945, PRK14945, DNA polymerase III subunit beta; Provisional.
Length = 362
Score = 91.3 bits (227), Expect = 1e-19
Identities = 59/252 (23%), Positives = 122/252 (48%), Gaps = 10/252 (3%)
Query: 69 NIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKYD 128
++V A F I+R+LP E V + + + ++SG S+ LQT + YP ++ S
Sbjct: 66 RVVVPAHLFFQIVRNLP-GELVELEFQGGELEVRSGSSRTKLQTAPPEGYPELSFPS--Q 122
Query: 129 FEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNID 188
+ LS L L V ++ + ++ + G+ L + + AV+SDG+RL Y +
Sbjct: 123 GDVRLSAGELAKALTHVRYAASNEEFQAIFRGVKLEHSPQGLRAVASDGYRLAIYDLPAS 182
Query: 189 KKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKLIDGKFLDY 248
+ ++IP ++ L R+L++ + L + + + + + KL++G+F DY
Sbjct: 183 QGQGR--KLVIPARSADELVRVLKDGDE-ASLALGEGVLTLTTGGVRMNLKLMEGEFPDY 239
Query: 249 KYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKG--VRLVIKPNYLKITVSSSNREKA 306
+ VI ++ + L ++ R++++S D+ V L++ L++T + + +
Sbjct: 240 ERVIPQDFKLQVTLPAEALREAVNRVAVLS-DRNANNRVELLVAEGRLRLT-AEGDYGRG 297
Query: 307 SEELEINYNGKD 318
EEL + G +
Sbjct: 298 QEELAVTQEGSE 309
>gnl|CDD|135998 PRK06673, PRK06673, DNA polymerase III subunit beta; Validated.
Length = 376
Score = 89.3 bits (221), Expect = 1e-18
Identities = 78/341 (22%), Positives = 162/341 (47%), Gaps = 18/341 (5%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
M+ +VN + L V + K I+PILS I + + I+ +++++ + I +
Sbjct: 1 MEFIVNHKH--FTQALSEVSKAISTKAIIPILSGIKITADQSGITLIASNSNIFIEKFIP 58
Query: 61 VGYGNSSI-------NIIVAARKFIDILRSLPETEKVTIYIENKHMF-IKSGKSKFTLQT 112
+ I I+V A+ FI+I++ +P + I +N+ I+SG+ L
Sbjct: 59 SAIDDEQITTILQAGTIVVPAKYFIEIIKKMPS--DIVIKSKNEQTITIQSGEITLNLNG 116
Query: 113 LDAKEYPIMTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIA 172
A E+P + + E + K L F++A+ + R L G+ + +I
Sbjct: 117 FPANEFPNVPQIDDHT-EIQIETKQLIDAFKQTVFAVAKNESRPVLTGVHIELDHNKLIC 175
Query: 173 VSSDGHRLTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFS 232
++D HRL + I + + I+P T+ L +L+ + V + +S + I F
Sbjct: 176 AATDSHRLAIRETLISTNMKA--NCIVPSATINELLKLMNSNLEFVSIYLSESHIIFTFG 233
Query: 233 NIEIISKLIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISND-KLKGVRL-VIK 290
+ S+LI+GK+ + +I N+++ ++R ++L+ + R S+++++ V L ++
Sbjct: 234 TTTLYSRLIEGKYPNISTLIPNEFQTVINIDRQRMLQGVDRSSLLASEWANNNVNLEIVN 293
Query: 291 PNYLKITVSSSNREKASEELEIN-YNGKDKNFIKFLIKIML 330
+ ++I+ ++S K SE +I+ G+ + I F + ML
Sbjct: 294 ESTIQISSNASQIGKISETQQIDAIQGEKQLNISFDGRFML 334
>gnl|CDD|184906 PRK14942, PRK14942, DNA polymerase III subunit beta; Provisional.
Length = 373
Score = 88.5 bits (219), Expect = 2e-18
Identities = 96/335 (28%), Positives = 165/335 (49%), Gaps = 31/335 (9%)
Query: 1 MQLVVNT-EKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLS-TDTEVQITTY 58
M++ VNT E +H ++ VIS+ E K+IL SN+ + + EK FLS TD E+ I T
Sbjct: 1 MKIKVNTSEFLKAIHAVEGVISVREIKSIL---SNLKI-EAEEKEVFLSATDLEISIKTS 56
Query: 59 ---TAVGYGNSSI-----NIIVAARKFIDILRSLPET--EKVTIYIENKHMFIKSGKS-- 106
T G +S+ + F L SL E+ E +YI + SGK+
Sbjct: 57 VPATVGQKGTASLPAKQLSSFFKTIHFETTLLSLEESDSESSIVYITDA-----SGKNDY 111
Query: 107 KFTLQTLDAKEYPIMTLNSKYDFEFTLSQKTLKCILNMV---YFSIAQQDIRYYLNGLLL 163
K + +DA+E I T+ SK D E +S + I +M+ ++IA +D R+ NGL +
Sbjct: 112 KSKISGMDAEE--IKTI-SKVD-ESQVSSFPSQLINDMIRKTSYAIAHEDQRFIFNGLYM 167
Query: 164 SFQKKNIIAVSSDGHRLTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKIS 223
+I V +DG RL + + II+P K V + +++ E + +
Sbjct: 168 IPDGTKLIFVGTDGRRLCKIERTLPSPLQFKDSIIVPAKAVREISKMIATSETG-NIGLI 226
Query: 224 NNQIKIIFSNIEIISKLIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLK 283
+ QI + +NIE++ KLI+G F +Y+ VI + + S +++ + SL+++ + + +
Sbjct: 227 DEQIYVSANNIELLCKLIEGNFPNYEQVIPKQTKFSVRISKEEFQVSLRQVLTAAEEPSR 286
Query: 284 GVRLVIKPNYLKITVSSSNREKASEELEINYNGKD 318
VRL N L + + +A + I Y+G++
Sbjct: 287 QVRLTFSKNNLNLFAQTLGASEADINMPIEYSGEE 321
>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 = 66.9 bits (164), Expect = 2e-13
Identities = 25/114 (21%), Positives = 39/114 (34%), Gaps = 28/114 (24%)
Query: 781 ELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIGI 840
EL IVEG S ++++ AV+ G L++E + L L
Sbjct: 1 ELIIVEGPSDAIALEKAGGVLGGAVVATSGHALDLEHIK-----------ELKKALK--- 46
Query: 841 EQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQP 894
+I+ TD D +G I LL P G + I++
Sbjct: 47 ----------GAKEVILATDPDREGEAIALKLLELLKPLGP----IGRVEISEL 86
>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 = 66.5 bits (163), Expect = 4e-13
Identities = 24/104 (23%), Positives = 43/104 (41%), Gaps = 23/104 (22%)
Query: 605 ISEKKNNINIDVSMQWNN---SYNENILCFTNNILQVDGGTHLTGLRSGITRAINKYIEE 661
+ + + ++ ++ + + S + F N +GGTH+ +R TRA+N
Sbjct: 20 VEGESDGFRVEGAISYPDSGRSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN----- 74
Query: 662 NEFLKKSKIEIIGEDIREGLTCVLSIKIPD--PKFN-SQTKNKL 702
G+D+R VLS+KIP N TK ++
Sbjct: 75 ------------GDDVRRYPVAVLSLKIPPSLVDVNVHPTKEEV 106
>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 = 63.5 bits (155), Expect = 4e-12
Identities = 32/113 (28%), Positives = 45/113 (39%), Gaps = 22/113 (19%)
Query: 374 DGTGLHHFVFEILDNAIDESLAGYCTKINVTIYSD---NSISISDNGRGIPIDIKIDDKH 430
D L + +LDNAI + AG +I VT+ D I++ DNG GIP
Sbjct: 2 DEDRLRQVLSNLLDNAIKHAPAG--GEIEVTLERDGGRLRITVEDNGIGIP--------- 50
Query: 431 KPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFLQLTINRN 483
E + + + +S K+ G G+GLS V L TI
Sbjct: 51 ------PEDLPKIFEPFFRTDSSSRKVGG--TGLGLSIVRKLVELHGGTITVE 95
>gnl|CDD|214643 smart00387, HATPase_c, Histidine kinase-like ATPases. Histidine
kinase-, DNA gyrase B-, phytochrome-like ATPases.
Length = 111
Score = 61.9 bits (151), Expect = 2e-11
Identities = 32/113 (28%), Positives = 44/113 (38%), Gaps = 22/113 (19%)
Query: 374 DGTGLHHFVFEILDNAIDESLAGYCTKINVTIYSDN---SISISDNGRGIPIDIKIDDKH 430
D L + +LDNAI + G +I VT+ D I++ DNG GIP
Sbjct: 2 DPDRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGDHVEITVEDNGPGIP--------- 50
Query: 431 KPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFLQLTINRN 483
E + + +K S KI G G+GLS V L I+
Sbjct: 51 ------PEDLEKIFEPFFRTDKRSRKIGG--TGLGLSIVKKLVELHGGEISVE 95
>gnl|CDD|236089 PRK07761, PRK07761, DNA polymerase III subunit beta; Validated.
Length = 376
Score = 66.8 bits (164), Expect = 2e-11
Identities = 62/311 (19%), Positives = 136/311 (43%), Gaps = 42/311 (13%)
Query: 29 LPILSNILVCKNSEKISFLSTDTEV--QITTYTAVGYGNSSINIIVAARKFIDILRSLPE 86
+P+L+ +L+ + ++ D EV ++T V ++V+ R DI RSLP
Sbjct: 27 VPVLAGVLLEADDGGLTLSGFDYEVSARVTIEAEVDEPGR---VLVSGRLLADITRSLPN 83
Query: 87 TEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIM--------TLNSKYDFEFTLSQKTL 138
+ V I ++ + + G ++FTL T+ ++YP + T+++ F +SQ
Sbjct: 84 -KPVDISVDGSRVTLTCGSARFTLPTMPVEDYPTLPELPEATGTVDAD-AFAEAVSQ--- 138
Query: 139 KCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRL-------TYYQVNIDKKF 191
V + + D L G+ + + + ++D +RL +I
Sbjct: 139 ------VAVAAGRDDTLPMLTGVRVEIEGDTVTLAATDRYRLAVRELTWKPASPDIS--- 189
Query: 192 SSCSDIIIPRKTVFTLQRLLENKEN-PVELKISNNQIKII-FSN--IEIISKLIDGKFLD 247
+ ++P +T+ + L + N + L +I F ++L+DG+F
Sbjct: 190 ---AAALVPARTLSDTAKSLGSGGNVSIALSTGVGGEGLIGFEGGGRRTTTRLLDGEFPK 246
Query: 248 YKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKAS 307
+ + +++ +V L+ +++R+++++ ++ VRL L ++ + +AS
Sbjct: 247 VRRLFPDEHPAVAVVETAPLIEAIKRVALVA-ERNAPVRLEFSDGQLTLSAGGGDDAQAS 305
Query: 308 EELEINYNGKD 318
E LE + G+D
Sbjct: 306 EALEADLTGED 316
>gnl|CDD|184908 PRK14944, PRK14944, DNA polymerase III subunit beta; Provisional.
Length = 375
Score = 64.9 bits (158), Expect = 1e-10
Identities = 57/279 (20%), Positives = 139/279 (49%), Gaps = 21/279 (7%)
Query: 70 IIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKYDF 129
I R FI+I++ + ++ +EN + IK+ ++ L+ +D + + +
Sbjct: 70 IACLGRYFIEIIKKINDSLIKMTVMENNFLVIKTEFCEYKLKLMDLCNFLELDFFFEKKE 129
Query: 130 EFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDK 189
F + K I+ + S ++ + R L GL L +QK + A+++D R++ ++ +D
Sbjct: 130 FFEIKTHFFKKIIKEINISTSKNEKRPILTGLNLIYQKNLLKALATDSFRMSQKKIKLDF 189
Query: 190 KFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIF--SNIEIISKLIDGKFLD 247
+ + +I+IP K++ L ++LE ++ LKI ++ KI N+ + L++G +
Sbjct: 190 NYHN-FNIVIPNKSLEELSKILEYYQSK-NLKIYSDSKKIFLKIDNLWFQTSLLEGNYPQ 247
Query: 248 YKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVI----KPNYLKITVSSSN- 302
+ + + S +N++ L+++L+R+S++ + + +V K ++I+ S+ +
Sbjct: 248 IQEIKLTNFPFSIHLNKDDLMKALERVSLLFSKEQNNTNVVKFILTKEKSIEISSSNESL 307
Query: 303 ---------REKASEELEINYNGKDKNFIKFLIKIMLLK 332
+ ++ EI +N K +++ ++K++ +K
Sbjct: 308 GTALEKIIPLKVSANSFEIAFNAK---YLEDILKVLSVK 343
>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 = 58.8 bits (143), Expect = 1e-10
Identities = 26/106 (24%), Positives = 38/106 (35%), Gaps = 22/106 (20%)
Query: 378 LHHFVFEILDNAIDESLAGYCTKINVTIYSDN---SISISDNGRGIPIDIKIDDKHKPKR 434
L + +L NAI + G +I +++ D I + DNG GIP +
Sbjct: 1 LQQVLLNLLSNAIKHTPEG-GGRITISVERDGDHLEIRVEDNGPGIPEEDL--------- 50
Query: 435 SAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFLQLTI 480
+F+ S GG G+GLS V L I
Sbjct: 51 ---------ERIFERFSDGSRSRKGGGTGLGLSIVKKLVELHGGRI 87
>gnl|CDD|111641 pfam02768, DNA_pol3_beta_3, DNA polymerase III beta subunit,
C-terminal domain. A dimer of the beta subunit of DNA
polymerase beta forms a ring which encircles duplex DNA.
Each monomer contains three domains of identical
topology and DNA clamp fold.
Length = 121
Score = 57.3 bits (139), Expect = 8e-10
Identities = 27/94 (28%), Positives = 56/94 (59%), Gaps = 3/94 (3%)
Query: 249 KYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKASE 308
+ V+ ++E V+ +L ++L R+++++N+K +GVRL + LK+T ++ +A E
Sbjct: 1 RRVLPKEFETKITVDNKELKKALARVALLANEKNRGVRLSFEEGQLKLTANNPEIGRAEE 60
Query: 309 ELEINYNGKDKNFIKFLIKIML--LKNKNSYDIQ 340
E++++Y G+ I F + +L LK S +I+
Sbjct: 61 EVDVDYIGEPLE-IAFNVSYLLDALKALKSEEIE 93
>gnl|CDD|237861 PRK14947, PRK14947, DNA polymerase III subunit beta; Provisional.
Length = 384
Score = 61.3 bits (149), Expect = 1e-09
Identities = 87/353 (24%), Positives = 148/353 (41%), Gaps = 42/353 (11%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQIT-TYT 59
M L VN K ++ LQ +I+ K L I + +S +STD+ ++ TY
Sbjct: 1 MYLKVN--KEDVIDGLQKAANIIPAKTGAAYLRTIWLKAEDGTLSIMSTDSNIEFRGTYP 58
Query: 60 AVGYGNSSINIIVAARKFIDILRSLPETEKVTIYI--ENKHMFIKSGKSKFTLQTLDA-- 115
A V R F+D++R LP E +T+ + + ++ I+ G+ K+ L D
Sbjct: 59 AEVTEPGLAG--VQGRAFVDLVRKLPPGE-ITLKLDASSGNLLIEQGRRKYKLPVNDPSW 115
Query: 116 ----KEYPIMTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNII 171
+P + S L+ +++ + F I+ +D + L + N I
Sbjct: 116 FQNFSAFP-------AEGAVVWSGDFLQELIDRIAFCISDEDAMEAIACLKIKPVADNAI 168
Query: 172 AVSS-DGH---RLTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQI 227
V +GH L + +I K I+I +K + L++ L E +EL IS
Sbjct: 169 EVCGLNGHQFALLRFLNDDIHAKLPQ-EGILIQKKYLLELKKWLGADE--IELSISEK-- 223
Query: 228 KIIFSNI---EIIS-KLIDGKFLDYKYVISNKYEK--SFL-VNRNKLLRSLQRISIISND 280
++ F E S L ++ DY +S S L V+R + + +L RI I + D
Sbjct: 224 RLFFRTGDGKETFSLPLSYYQYPDYMNFLSKLQGDDVSNLEVDRKECMDALDRILIFNTD 283
Query: 281 KLKGVRLVIKPNYLKITVSSSNREKASEELEINYNGKDKNFIKF----LIKIM 329
+ P L ++ + A+E LE+ Y+G D I F LI+I+
Sbjct: 284 NNRCTYFDFGPGELSLSAQGQDVGSATESLEVTYSG-DIKKIAFPTKNLIEIL 335
>gnl|CDD|173773 cd00188, TOPRIM, Topoisomerase-primase domain. This is a
nucleotidyl transferase/hydrolase domain found in type
IA, type IIA and type IIB topoisomerases, bacterial
DnaG-type primases, small primase-like proteins from
bacteria and archaea, OLD family nucleases from
bacterial and archaea, and bacterial DNA repair proteins
of the RecR/M family. This domain has two conserved
motifs, one of which centers at a conserved glutamate
and the other one at two conserved aspartates (DxD).
This glutamate and two aspartates, cluster together to
form a highly acid surface patch. The conserved
glutamate may act as a general base in nucleotide
polymerization by primases and in strand joining in
topoisomerases and, as a general acid in strand cleavage
by topisomerases and nucleases. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 83
Score = 39.3 bits (92), Expect = 6e-04
Identities = 24/105 (22%), Positives = 35/105 (33%), Gaps = 26/105 (24%)
Query: 780 CELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIG 839
+L IVEG S ++ Q AV+ L G LN + +++
Sbjct: 1 KKLIIVEGPSDALALAQAGGYG-GAVVALGGHALNKTRELLKRL---------------- 43
Query: 840 IEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLI 884
+II TDAD +G I LL K+
Sbjct: 44 ---------LGEAKEVIIATDADREGEAIALRLLELLKSLGKKVR 79
>gnl|CDD|239563 cd03481, TopoIIA_Trans_ScTopoIIA, TopoIIA_Trans_ScTopoIIA:
Transducer domain, having a ribosomal S5 domain 2-like
fold, of the type found in proteins of the type IIA
family of DNA topoisomerases similar to Saccharomyces
cerevisiae Topo IIA. S. cerevisiae Topo IIA is a
homodimer encoded by a single gene. The type IIA enzymes
are the predominant form of topoisomerase and are found
in some bacteriophages, viruses and archaea, and in all
bacteria and eukaryotes. All type IIA topoisomerases
are related to each other at amino acid sequence level,
though their oligomeric organization sometimes differs.
TopoIIA enzymes cut both strands of the duplex DNA to
remove (relax) both positive and negative supercoils in
DNA. These enzymes covalently attach to the 5' ends of
the cut DNA, separate the free ends of the cleaved
strands, pass another region of the duplex through this
gap, then rejoin the ends. TopoIIA enzymes also
catenate/ decatenate duplex rings. This transducer
domain is homologous to the second domain of the DNA
gyrase B subunit, which is known to be important in
nucleotide hydrolysis and the transduction of structural
signals from ATP-binding site to the DNA
breakage/reunion regions of the enzymes.
Length = 153
Score = 39.6 bits (93), Expect = 0.002
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 631 FTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIP 690
F N+I GGTH+ + I + +++ +++ K I + ++ L ++ I
Sbjct: 49 FVNSIATTKGGTHVDYVADQIVKKLDEVVKK---KNKGGINVKPFQVKNHLWIFVNCLIE 105
Query: 691 DPKFNSQTKNKLVS 704
+P F+SQTK L +
Sbjct: 106 NPSFDSQTKETLTT 119
>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated.
Length = 1437
Score = 41.4 bits (98), Expect = 0.003
Identities = 27/176 (15%), Positives = 59/176 (33%), Gaps = 13/176 (7%)
Query: 907 YLRDDIEEERYMLKIAFKNVKLISIENGDIIKENYFFKLIDKYNKTIEIVHRLKQIIDIS 966
+ K+ + KLI N +I ++ L K+ + + +
Sbjct: 105 KNSPLFKSLLKKQKVEVEGNKLIIKVNNEIERD----HLKKKHLPKLIKQYEKFGFGILK 160
Query: 967 ILSAIMSDVILNLDTRENAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKK 1026
I D++E E+F + ++ E + +L + K K+
Sbjct: 161 I-------DFEIDDSKEELEKFEAQKEEEDEKLAKEALEAMKKLEAEKKKQSKNFDPKEG 213
Query: 1027 NYIIDINFINNKDYKKLVSIISTFKKIIGKGVIIQKSIGEKIKKYTANNFYKIINY 1082
I I+ ++ + I ++++ +G + + I E F KI +Y
Sbjct: 214 PVQIGKK-IDKEEITPMKEINEEERRVVVEGYVFKVEIKELKSGRHILTF-KITDY 267
>gnl|CDD|184910 PRK14946, PRK14946, DNA polymerase III subunit beta; Provisional.
Length = 366
Score = 37.5 bits (87), Expect = 0.035
Identities = 50/301 (16%), Positives = 113/301 (37%), Gaps = 26/301 (8%)
Query: 32 LSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSSINIIVAARKFID------ILRSLP 85
LS + + +ST++E+ ++ I I ID I++
Sbjct: 29 LSGFFLKLTRSGLFIISTNSELSYKSFIN---KKDLIEINDVGSCLIDGVFLKNIIKKS- 84
Query: 86 ETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKYDFEFTLSQKTLKCILNMV 145
+++ + + + ++F+ D+ +P + K + T++ K LK +
Sbjct: 85 -DNQISFELIGSELKVFWEDAQFSKTLRDSSFFPEINFEQK-GIKLTVNAKNLKRAIKNT 142
Query: 146 YFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDKKFSSCSDIIIPRKTVF 205
F+ + L+ + L + + ++D R ++ I S I I
Sbjct: 143 AFATTNNPNQPILSAINLKSEDNFLHFSATDTIRFASEKIEISNP----SRIDISISAKN 198
Query: 206 TLQRLLENKENPVELKISNNQIKIIFSNIEIISKLIDGKFLDYKYVISNKYE--KSFLVN 263
+ + +EL I +++I + N+ I S++ ++ D V+ E S +
Sbjct: 199 LKDFIPPELDKDIELFIESSKISYTYDNLTIQSRIFTIEYKDISNVLPKDSEILYSLTIE 258
Query: 264 RNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKASEELEINYNGKDKNFIK 323
+ ++L + + +II+ K + + N ++ S E N K KN ++
Sbjct: 259 KKEILDLIDKATIITPGKDNVINFSLSKN--ELKGYISQYESG------QSNVKTKNVLR 310
Query: 324 F 324
F
Sbjct: 311 F 311
>gnl|CDD|223400 COG0323, MutL, DNA mismatch repair enzyme (predicted ATPase) [DNA
replication, recombination, and repair].
Length = 638
Score = 36.9 bits (86), Expect = 0.065
Identities = 13/42 (30%), Positives = 24/42 (57%), Gaps = 6/42 (14%)
Query: 384 EILDNAIDESLAGYCTKINVTI--YSDNSISISDNGRGIPID 423
E+++N++D AG T+I++ + I + DNG GI +
Sbjct: 30 ELVENSLD---AG-ATRIDIEVEGGGLKLIRVRDNGSGIDKE 67
>gnl|CDD|234630 PRK00095, mutL, DNA mismatch repair protein; Reviewed.
Length = 617
Score = 35.6 bits (83), Expect = 0.20
Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 6/40 (15%)
Query: 384 EILDNAIDESLAGYCTKINVTIYSD--NSISISDNGRGIP 421
E+++NA+D AG T+I++ I I + DNG GI
Sbjct: 29 ELVENALD---AG-ATRIDIEIEEGGLKLIRVRDNGCGIS 64
>gnl|CDD|225115 COG2205, KdpD, Osmosensitive K+ channel histidine kinase [Signal
transduction mechanisms].
Length = 890
Score = 35.0 bits (81), Expect = 0.27
Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 7/61 (11%)
Query: 374 DGTGLHHFVFEILDNAIDESLAGYCTKINVTIYSDNS---ISISDNGRGIPIDI--KIDD 428
D + + +L+NA+ A ++I + + S+ D G GIP +I D
Sbjct: 772 DSPLIEQVLINLLENAL--KYAPPGSEIRINAGVERENVVFSVIDEGPGIPEGELERIFD 829
Query: 429 K 429
K
Sbjct: 830 K 830
>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 = 32.6 bits (75), Expect = 0.38
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 7/45 (15%)
Query: 382 VFEILDNAIDESLAGYCTKINVTIYSDN---SISISDNGRGIPID 423
+ E++DN+ID T + ++I D ISI DNG G+ +
Sbjct: 7 IAELIDNSID----ADATNVKISIDPDRGEDGISIEDNGGGMSYE 47
>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 = 33.8 bits (78), Expect = 0.47
Identities = 17/44 (38%), Positives = 26/44 (59%), Gaps = 6/44 (13%)
Query: 382 VFEILDNAIDESLAGYCTKINVTI--YSDNSISISDNGRGIPID 423
V E+++N++D AG T+I+V I I +SDNG GI +
Sbjct: 27 VKELVENSLD---AG-ATRIDVEIEEGGLKLIEVSDNGSGIDKE 66
>gnl|CDD|236673 PRK10340, ebgA, cryptic beta-D-galactosidase subunit alpha;
Reviewed.
Length = 1021
Score = 33.9 bits (78), Expect = 0.57
Identities = 25/123 (20%), Positives = 44/123 (35%), Gaps = 20/123 (16%)
Query: 156 YYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKE 215
+LN ++ K + S GH + YQ + + + TL+ E
Sbjct: 671 AFLN---ITVTKDSRTRYSEAGHSIATYQFPLKENTAQPVPFAPNNARPLTLE------E 721
Query: 216 NPVELKISNNQIKIIFSNI--EIISKLIDG--------KFLDYKYVISN-KYEKSFLVNR 264
+ + + I FS + ++ S ++G K +K +I N K E L
Sbjct: 722 DRLSCTVRGYNFAITFSKVSGKLTSWQVNGESLLTREPKINFFKPMIDNHKQEYEGLWQP 781
Query: 265 NKL 267
N L
Sbjct: 782 NHL 784
>gnl|CDD|224307 COG1389, COG1389, DNA topoisomerase VI, subunit B [DNA replication,
recombination, and repair].
Length = 538
Score = 33.5 bits (77), Expect = 0.74
Identities = 52/226 (23%), Positives = 85/226 (37%), Gaps = 58/226 (25%)
Query: 359 EAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDES-LAGYCTKINVTIYSDN----SISI 413
E RK EM +G L V E++ N++D AG I V I + +
Sbjct: 19 EFFRKNKEM-LGFDGPIRSLTTTVHELVTNSLDACEEAGILPDIKVEIERIGKDHYKVIV 77
Query: 414 SDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLS 473
DNG GIP ++ PK V ++ G KF++N S G GIG+S
Sbjct: 78 EDNGPGIP------EEQIPK------VFGKMLYGSKFHRN--IQSRGQQGIGIS---AAV 120
Query: 474 RFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVDEKI 533
+ Q+T + P+++I T GT + + +
Sbjct: 121 LYSQMTTGK----------------------------PVRVISSTGDSGTAYEYELKIDV 152
Query: 534 FSNIEFHYEILKKRIRELSFLNNGVCITL-IDE---RIKKKEIFEF 575
N EI+++ E +G + L + R K++ I+E+
Sbjct: 153 QKN---EPEIVERGEVENPGGWHGTRVELELKGVWYRAKRQGIYEY 195
>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A'';
Validated.
Length = 383
Score = 32.9 bits (76), Expect = 1.0
Identities = 30/112 (26%), Positives = 49/112 (43%), Gaps = 28/112 (25%)
Query: 982 RENAEQFAKKIIK-KLND---------SNIEIIVEFDQ--LNNKYLL--NIKKKFLKKK- 1026
RE AE+ A+KI L + +N+ II+E D+ L ++ L ++K+ KKK
Sbjct: 126 REKAEEVARKIEATTLENLAKDISVDLANMTIIIELDEEMLEDRGLTVDDVKEAIEKKKG 185
Query: 1027 ------NYIIDINFINNKDYKKLVSIISTFKKIIGKG------VIIQKSIGE 1066
+ I+ Y++L + + I KG VII+K E
Sbjct: 186 GEVEIEGNTLIIS-PKEPSYRELRKLAEKIRNIKIKGIKGIKRVIIRKEGDE 236
>gnl|CDD|238394 cd00771, ThrRS_core, Threonyl-tRNA synthetase (ThrRS) class II core
catalytic domain. ThrRS is a homodimer. It is
responsible for the attachment of threonine to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. Class II assignment is
based upon its structure and the presence of three
characteristic sequence motifs in the core domain.
Length = 298
Score = 32.5 bits (75), Expect = 1.3
Identities = 17/66 (25%), Positives = 22/66 (33%), Gaps = 15/66 (22%)
Query: 865 GAHIRALLLTFFYRKMPKLIEYGYIYIAQPPLYKI----------KYGNNECYLRDDIEE 914
GA IR L F + GY + P +Y Y N + E+
Sbjct: 29 GAIIRNELEDFLRELQ---RKRGYQEVETPIIYNKELWETSGHWDHYRENM--FPFEEED 83
Query: 915 ERYMLK 920
E Y LK
Sbjct: 84 EEYGLK 89
>gnl|CDD|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366). This
family of proteins is found in bacteria and eukaryotes.
Proteins in this family are typically between 227 and
387 amino acids in length.
Length = 213
Score = 31.5 bits (72), Expect = 1.7
Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 13/68 (19%)
Query: 907 YLRDDIEEERYMLKIAFKNVKLISIENGDIIKENYFFKLIDKYNKTIEIVHRLKQIIDIS 966
L DD + + I++ N F+ +ID E VH L Q +D +
Sbjct: 62 TLVDDATDA--------SGKQFITVTTKS---GNTFYIVID-RAAEGENVHFLNQ-VDEA 108
Query: 967 ILSAIMSD 974
L A+M +
Sbjct: 109 DLLALMEE 116
>gnl|CDD|221957 pfam13175, AAA_15, AAA ATPase domain. This family of domains contain
a P-loop motif that is characteristic of the AAA
superfamily.
Length = 320
Score = 31.6 bits (72), Expect = 2.5
Identities = 25/180 (13%), Positives = 53/180 (29%), Gaps = 9/180 (5%)
Query: 873 LTFFYRKMPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKNVKLISIE 932
Y + KIK ++I+ + + + +
Sbjct: 48 KKKIYISISDNKADIDKENLNKKSKKIKISIIIELSSNEIKSFSIKFYLNYYLEIINNDV 107
Query: 933 NGDIIKENYFFKLIDKYNKTIEIVHRLKQIIDISILSAIMSDVILNLDTRENAEQFAKKI 992
+I + L K ++ + + +I S I +D I
Sbjct: 108 EDEIELLLFSKNLEYILKKILDKIEKFDEIKGAKKKDFFKSINIYEID---------NFI 158
Query: 993 IKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYIIDINFINNKDYKKLVSIISTFKK 1052
K L+ + IV D L + F +K + + + N+ K +++ I+ K
Sbjct: 159 DKTLSKILDDNIVFQDNLEKNIDDKLSNIFNEKLSNLKNEKISINEKIKSILNEINPDSK 218
>gnl|CDD|176642 cd00457, PEBP, PhosphatidylEthanolamine-Binding Protein (PEBP)
domain. PhosphatidylEthanolamine-Binding Proteins
(PEBPs) are represented in all three major phylogenetic
divisions (eukaryotes, bacteria, archaea). A number of
biological roles for members of the PEBP family include
serine protease inhibition, membrane biogenesis,
regulation of flowering plant stem architecture, and
Raf-1 kinase inhibition. Although their overall
structures are similar, the members of the PEBP family
bind very different substrates including phospholipids,
opioids, and hydrophobic odorant molecules as well as
having different oligomerization states
(monomer/dimer/tetramer).
Length = 159
Score = 30.4 bits (69), Expect = 2.8
Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 2/27 (7%)
Query: 375 GTGLHHFVFEI--LDNAIDESLAGYCT 399
G G H + F++ LD +D S G
Sbjct: 109 GHGPHRYFFQVYALDEPLDRSKLGDGR 135
>gnl|CDD|223127 COG0049, RpsG, Ribosomal protein S7 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 30.2 bits (69), Expect = 2.9
Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 4/68 (5%)
Query: 688 KIPDPKFNSQTKNKLVSSEVR---KPVEEIIIKTLFDFLQENPGESKL-ICEKIIEAARS 743
+PDPK+NS +L++ +R K + E I+ FD +++ G++ L + EK IE +
Sbjct: 11 VLPDPKYNSVIVERLINKIMRDGKKSLAEKIVYGAFDIIEKKTGQNPLQVFEKAIENVKP 70
Query: 744 REAARKTR 751
RE + R
Sbjct: 71 REEVKSRR 78
>gnl|CDD|223715 COG0642, BaeS, Signal transduction histidine kinase [Signal
transduction mechanisms].
Length = 336
Score = 30.9 bits (69), Expect = 4.3
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 6/44 (13%)
Query: 385 ILDNAIDESLAGYCTKINVTIYSDNS---ISISDNGRGIPIDIK 425
+L NAI + G +I +++ D+ IS+ D G GIP +
Sbjct: 236 LLSNAIKYTPGG---EITISVRQDDEQVTISVEDTGPGIPEEEL 276
>gnl|CDD|139929 PRK13869, PRK13869, plasmid-partitioning protein RepA; Provisional.
Length = 405
Score = 30.8 bits (69), Expect = 4.5
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 706 EVRKPVEEIIIKTLFDFLQENPGESKLI-CEKIIEAARSREAARKTRELTRKKNLIDDI 763
+ R+P+ ++I T FD L PG +L+ E A S + R TR D++
Sbjct: 190 DTRRPLRDVIRPTYFDGLHLVPGNLELMEFEHTTPKALSDKGTRDGLFFTRVAQAFDEV 248
>gnl|CDD|235947 PRK07152, nadD, putative nicotinate-nucleotide adenylyltransferase;
Validated.
Length = 342
Score = 30.7 bits (70), Expect = 4.6
Identities = 41/190 (21%), Positives = 72/190 (37%), Gaps = 43/190 (22%)
Query: 911 DIEEERY-MLKIAFKNVKLISIENGDIIKENYFFKLIDKYNKTIEIVHRLKQIIDISILS 969
E R MLK+A KN+ + + + +I ++N + TI+ + K+ +
Sbjct: 50 SNGEHRLNMLKLALKNLPKMEVSDFEIKRQNVSY--------TIDTIKYFKKKYPNDEIY 101
Query: 970 AIM-SDVILNLDTRENAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKK-KFLKKKN 1027
I+ SD + +N E+ KK+ IV F + N N+KK L KN
Sbjct: 102 FIIGSDNLEKFKKWKNIEEILKKV----------QIVVFKRKKNINKKNLKKYNVLLLKN 151
Query: 1028 YIIDINFINNKDYKKLVSIISTFKKIIGKGVIIQKSIGEKIKKYTANNFYKIINYLRNEA 1087
I++ +K + + K+ Y NF YL +
Sbjct: 152 ---KNLNISSTKIRKG---------------NLLGKLDPKVNDYINENFL----YLEDIL 189
Query: 1088 ENMVIKQRYK 1097
++ + + RYK
Sbjct: 190 KSFLDEYRYK 199
>gnl|CDD|233238 TIGR01029, rpsG_bact, ribosomal protein S7, bacterial/organelle.
This model describes the bacterial and organellar branch
of the ribosomal protein S7 family (includes prokaroytic
S7 and eukaryotic S5). The eukaryotic and archaeal
branch is described by model TIGR01028 [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 154
Score = 29.6 bits (67), Expect = 5.5
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 690 PDPKFNSQTKNKLVS---SEVRKPVEEIIIKTLFDFLQENPGESKLIC-EKIIEAAR 742
PDP + S NK ++ + +K + E I+ F+ + + GE L E+ +E +
Sbjct: 12 PDPVYGSVLLNKFINRVMKDGKKSLAESIVYKAFERIAKKTGEDPLEVFEQALENVK 68
>gnl|CDD|214359 CHL00085, ycf24, putative ABC transporter.
Length = 485
Score = 30.8 bits (70), Expect = 5.5
Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 12/82 (14%)
Query: 990 KKIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYIIDINFINNKDYKKLVSIIST 1049
KK + L++ + E++ F++L LN +K+ N +D F + VSI +T
Sbjct: 96 KKKLNSLDEVDPELLDTFEKLGIS--LNEQKRL---ANVAVDAVFDS-------VSIGTT 143
Query: 1050 FKKIIGKGVIIQKSIGEKIKKY 1071
FK+ + K +I SI E I+KY
Sbjct: 144 FKEELAKAGVIFCSISEAIQKY 165
>gnl|CDD|223074 PHA03396, lef-9, late expression factor 9; Provisional.
Length = 493
Score = 30.3 bits (69), Expect = 6.9
Identities = 23/103 (22%), Positives = 45/103 (43%), Gaps = 20/103 (19%)
Query: 999 SNIEIIVEFDQLNNKYLLNIK--KKFLKKKNYIIDINFINNKDYKKLVSII--------- 1047
++ +++ + ++L+N + +NI+ KKFL +N I D+ I + L+ +
Sbjct: 13 TSFDLLTDPNKLDNVFFINIEEFKKFL--RNLISDLKKIKINYFNSLIEQLISVYQECEL 70
Query: 1048 -----STFKKIIGKGVIIQKSIGEKI--KKYTANNFYKIINYL 1083
KII ++ + + KK N F I+YL
Sbjct: 71 RNEHTDLLSKIILATNVVVTDLPSNVFLKKLKTNKFTDNIDYL 113
>gnl|CDD|216028 pfam00621, RhoGEF, RhoGEF domain. Guanine nucleotide exchange
factor for Rho/Rac/Cdc42-like GTPases Also called
Dbl-homologous (DH) domain. It appears that pfam00169
domains invariably occur C-terminal to RhoGEF/DH
domains.
Length = 179
Score = 29.5 bits (67), Expect = 7.1
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 204 VFTLQRLLENKENPVELK--ISNNQIKIIFSNIEIISKL 240
V L+ L+E P+ +S +IK IFSNIE I +L
Sbjct: 13 VRDLKILVEVFLKPLRESPILSEEEIKTIFSNIEEILEL 51
>gnl|CDD|226475 COG3966, DltD, Protein involved in D-alanine esterification of
lipoteichoic acid and wall teichoic acid (D-alanine
transfer protein) [Cell envelope biogenesis, outer
membrane].
Length = 415
Score = 30.1 bits (68), Expect = 7.1
Identities = 27/117 (23%), Positives = 48/117 (41%), Gaps = 21/117 (17%)
Query: 937 IKENYFFKLIDKYNKTIEIVHRLKQIIDISILSAIMSDVILNLDTRENAEQFAKKIIKKL 996
+++ F K I LK + D + + E+ A +I KK
Sbjct: 210 ERKDLLFSATSKSGPLKHIKKALKDLPDQF--------------SYKELEKLAVEIGKKS 255
Query: 997 NDSNIEIIVEFDQLNNK-YLLNIKKKFLKKKNYIIDINFINNKDYKKLVSIISTFKK 1052
+N F + NK Y+ IK K+ K K+ + ++ + +Y+ L ++ TFKK
Sbjct: 256 TTNN-----PF-GIKNKYYIKKIKPKYKKLKDSQKNFTYLESPEYQDLQLLLDTFKK 306
>gnl|CDD|173015 PRK14550, rnhB, ribonuclease HII; Provisional.
Length = 204
Score = 29.5 bits (66), Expect = 7.2
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 517 DTNKQGTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERI 567
D+ K K F++++KI ++ E + ++KK E+ L G C+ L + I
Sbjct: 39 DSKKLSPKKRFFLEDKIKTHGEVGFFVVKKSANEIDSLGLGACLKLAIQEI 89
>gnl|CDD|202547 pfam03129, HGTP_anticodon, Anticodon binding domain. This domain is
found in histidyl, glycyl, threonyl and prolyl tRNA
synthetases it is probably the anticodon binding domain.
Length = 93
Score = 27.9 bits (63), Expect = 7.5
Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 10/60 (16%)
Query: 975 VILNLDTRENAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKF----LKKKNYII 1030
V++ L ++ E +A+K+ ++L ++ I VE D N + KKF L + +
Sbjct: 3 VVIPLGEKDELEDYAQKLAEELREAGIR--VELDDRNES----LGKKFRDADLIGIPFRL 56
>gnl|CDD|219694 pfam08008, Viral_cys_rich, Viral cysteine rich. Members of this
family are polydna viral proteins that contain a cysteine
rich motif. Some members of this family have multiple
copies of this domain.
Length = 86
Score = 28.1 bits (63), Expect = 7.6
Identities = 10/37 (27%), Positives = 23/37 (62%), Gaps = 7/37 (18%)
Query: 984 NAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKK 1020
N + + ++K+LND+N F++L+N+Y +++
Sbjct: 54 NLTLYLE-LVKQLNDTN------FEELSNQYWKDLQP 83
>gnl|CDD|236359 PRK08974, PRK08974, long-chain-fatty-acid--CoA ligase; Validated.
Length = 560
Score = 30.0 bits (68), Expect = 7.7
Identities = 11/41 (26%), Positives = 25/41 (60%), Gaps = 2/41 (4%)
Query: 1035 INNKDYKKLVSIISTFKKIIGKGVIIQKSIGEKIKKYTANN 1075
+NN+++++L S+ K +G G+ +Q+++ E+ K T
Sbjct: 314 LNNEEFQELD--FSSLKLSVGGGMAVQQAVAERWVKLTGQY 352
>gnl|CDD|223138 COG0060, IleS, Isoleucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 933
Score = 30.3 bits (69), Expect = 7.8
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 779 LCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLN-IEKARFEKIILSE 827
L + E D V+ R++A+L LR V +E AR EK+I S
Sbjct: 789 LEDWP--EVDEELIDVEAALAARWEALLKLRDPVNKALEAARLEKVIGSS 836
>gnl|CDD|236846 PRK11100, PRK11100, sensory histidine kinase CreC; Provisional.
Length = 475
Score = 30.2 bits (69), Expect = 8.2
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 5/40 (12%)
Query: 385 ILDNAIDESLAGYCTKINVTIYSDNS---ISISDNGRGIP 421
+LDNAID S G I ++ D +S+ D G GIP
Sbjct: 376 LLDNAIDFSPEGGT--ITLSAEVDGEQVALSVEDQGPGIP 413
>gnl|CDD|235319 PRK04914, PRK04914, ATP-dependent helicase HepA; Validated.
Length = 956
Score = 30.2 bits (69), Expect = 8.6
Identities = 22/94 (23%), Positives = 42/94 (44%), Gaps = 22/94 (23%)
Query: 685 LSIKIPDPKFNSQ-------TKNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKI 737
LS ++ N Q T +KLV + V++ + +++ K E E++ ++
Sbjct: 842 LSAQVEFESLNRQLSAVNRHTASKLVKA-VQQDIHKLLQKA------EAQAEAQA--REL 892
Query: 738 IEAARSREAARKTRELTRKKNL------IDDIEL 765
IE A+ + + EL+R + L I D E+
Sbjct: 893 IEQAKQEADEKLSAELSRLEALKAVNPNIRDDEI 926
>gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP).
Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a
large multi-subunit complex responsible for the synthesis
of all RNAs in the cell. The relative positioning of the
RNAP core is highly conserved between archaeal RNAP and
the three classes of eukaryotic RNAPs. In archaea, the
largest subunit is split into two polypeptides, A' and
A'', which are encoded by separate genes in an operon.
Sequence alignments reveal that the archaeal A'' subunit
corresponds to the C-terminal one-third of the RNAPII
largest subunit (Rpb1). In subunit A'', several loops in
the jaw domain are shorter. The RNAPII Rpb1 interacts
with the second-largest subunit (Rpb2) to form the DNA
entry and RNA exit channels in addition to the catalytic
center of RNA synthesis.
Length = 363
Score = 29.9 bits (68), Expect = 8.8
Identities = 25/113 (22%), Positives = 43/113 (38%), Gaps = 28/113 (24%)
Query: 982 RENAEQFAKKIIK-KLND---------SNIEIIVEFDQ--LNNKYL-----LN-IKKKFL 1023
RE AE+ A+KI + L + N+ I +E D+ L ++ + L I+K
Sbjct: 107 REKAEEVARKIEETTLENLAEDISIDLFNMRITIELDEEMLEDRGITVDDVLKAIEKLKK 166
Query: 1024 KKK----NYIIDINFINNKDYKKLVSIISTFKKIIGKG------VIIQKSIGE 1066
K + + + K+L + KG VI++K E
Sbjct: 167 GKVGEEGDVTLIVLKAEEPSIKELRKLAEKILNTKIKGIKGIKRVIVRKEEDE 219
>gnl|CDD|221018 pfam11186, DUF2972, Protein of unknown function (DUF2972). Some
members in this family of proteins with unknown function
are annotated as sugar transferase proteins, however this
cannot be confirmed.
Length = 197
Score = 29.2 bits (66), Expect = 9.2
Identities = 20/99 (20%), Positives = 41/99 (41%), Gaps = 6/99 (6%)
Query: 991 KIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYIID--INFINNKDYKKLVSIIS 1048
K + + F ++ Y+ +I K+ K N I+D I I +D++ L
Sbjct: 57 KENNISITKTNRVFIIFLEIKENYI-DITKELFNK-NDILDNIIICIKKEDFEILKQDEK 114
Query: 1049 TFKKIIGKGVIIQKSIGEKIKKYTANNFY--KIINYLRN 1085
FKKI +++ +++K + ++ YL+
Sbjct: 115 LFKKIKKYLKKFIEALEKQVKIEESKKLKEKDVLEYLKE 153
>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
Length = 1364
Score = 29.9 bits (68), Expect = 9.7
Identities = 30/155 (19%), Positives = 60/155 (38%), Gaps = 13/155 (8%)
Query: 189 KKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKLIDGKFLDY 248
K S S I+IP T + + +N + ++ K F + + + + D
Sbjct: 729 DKISRHSGILIPPGTGKKNSKESKKIKNWIYVQRITPTKKKYFVLVRPV---VTYEIADG 785
Query: 249 KYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKG------VRLVIKPNYLKITVSSSN 302
+ + + N LR + I + ++G VR + N+ + SSS
Sbjct: 786 INLATLFPQDLLQEKDNLQLRVVNYILYGNGKPIRGISSIQLVRTCLVLNWDQDKKSSSI 845
Query: 303 REKASEELEINYNGKDKNFIKFLIKIMLLKNKNSY 337
E + +E+ + I+ ++I L+K+ SY
Sbjct: 846 EEARASFVEV----RTNGLIRDFLRINLVKSPISY 876
>gnl|CDD|220920 pfam10977, DUF2797, Protein of unknown function (DUF2797). This
family of proteins has no known function.
Length = 233
Score = 29.2 bits (66), Expect = 9.8
Identities = 25/85 (29%), Positives = 40/85 (47%), Gaps = 4/85 (4%)
Query: 737 IIEAARSREAARKTRELTRKKNLIDDIELSTKLADCQEKNP-ELCELYIVEGDSAGGSVK 795
I+E A A KT K L++D++L+ + A E+ EL EL + G+ A +
Sbjct: 117 IVEVALKAHVADKTNWRKMLKGLVEDVDLAAERARLLEEIAEELKELRLEYGEDAIEEDE 176
Query: 796 QGRDRRFQAVL--PLRGKVLNIEKA 818
+ VL P + K LN++K
Sbjct: 177 AVFSINY-PVLEYPTKVKSLNLDKT 200
>gnl|CDD|144538 pfam00981, Rota_NS53, Rotavirus RNA-binding Protein 53 (NS53).
This protein is also known as NSP1. NS53 is encoded by
gene 5. It is made in low levels in the infected cells
and is a component of early replication. The protein is
known to accumulate on the cytoskeleton of the infected
cell. NS53 is an RNA binding protein that contains a
characteristic cysteine rich region.
Length = 488
Score = 29.6 bits (67), Expect = 10.0
Identities = 24/105 (22%), Positives = 47/105 (44%), Gaps = 16/105 (15%)
Query: 205 FTLQRLLENKENPVELK-ISNNQIKIIFSNIEIISKLIDGKFLDYKYVISNKYEKSFLVN 263
F+ LEN NP + ++ N ++ F+ E ++D Y + Y + + V+
Sbjct: 228 FSKN-TLENLHNPTSKRQVTRNCTEMDFNWNEECKLIVDKN--KYLEALKTSYTEHYSVS 284
Query: 264 RNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKASE 308
L + ++ +S +IKPNY ++S++ + ASE
Sbjct: 285 DRCLGFTKYKLFELSK--------LIKPNY----IASNHWQPASE 317
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
0.319 0.138 0.382
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 59,833,866
Number of extensions: 6300607
Number of successful extensions: 7465
Number of sequences better than 10.0: 1
Number of HSP's gapped: 7158
Number of HSP's successfully gapped: 398
Length of query: 1161
Length of database: 10,937,602
Length adjustment: 108
Effective length of query: 1053
Effective length of database: 6,147,370
Effective search space: 6473180610
Effective search space used: 6473180610
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 65 (28.8 bits)