RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8714
(562 letters)
>gnl|CDD|223624 COG0550, TopA, Topoisomerase IA [DNA replication, recombination,
and repair].
Length = 570
Score = 379 bits (976), Expect = e-125
Identities = 148/518 (28%), Positives = 220/518 (42%), Gaps = 32/518 (6%)
Query: 51 FKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLP--AFLANEAKDCE 108
+ +T+ GH+ L F +Y W VD K P K L AK +
Sbjct: 23 YVVTASVGHLRDLPFPEEYKGWVDVDLPIFE----PKYIIKPGKKKKVVKKLKKLAKKAD 78
Query: 109 FLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNI 168
+ L D D+EGE I + ++E + + +P V R FS IT K I +A N + ++
Sbjct: 79 EVYLATDPDREGEAIGWHILE----VLKLKNPSKVKRVVFSEITKKAILSAFKNPREIDM 134
Query: 169 FEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKI 228
+ AR+ LD +G +R K + ++S G Q+P L VER +I
Sbjct: 135 NLVDAQLARRILDRLVGYNLSRLLWKKLKRG-------VLSAGRVQSPALRLVVEREREI 187
Query: 229 RTFKPEPYWLLDLTLNLNGVAVSVTWSR---GHIFDKSTCNVFFKAVEKEKH--VTVVDV 283
F PE YW + G S + + + V K K VV V
Sbjct: 188 EAFVPEEYWEIKAIFEKGGGEFSARLTEIEGKKEGRLKDKDEAEEIVNKLKGKPAKVVSV 247
Query: 284 QSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLY-TQGYVSYPRTETTQYPEN 342
+ K ++ P T L + AS LG M IA++LY G ++YPRT++T+ E
Sbjct: 248 EKKPKKRSPPPPFTTSTLQQEASRKLGFSAKKTMDIAQKLYEGHGLITYPRTDSTRLSEE 307
Query: 343 FDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGK-DVGDHPPITPTKLATRTQL-DGDA 400
A L + +G + P KGK H I PT T L D
Sbjct: 308 ALAEARLYILAIA--YGKEYLPLKPR--RYPSKGKKAQEAHEAIRPTDFETPESLKAYDE 363
Query: 401 WRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNES 460
+LYD I R F+ + D +Y + VA E F K L G+ V + E
Sbjct: 364 LKLYDLIWRRFLASQMPDAIYEKTTVTLEVAGEKFKASGKVLKFDGWLKVYGEDKDEEED 423
Query: 461 I--PDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQR 518
P+ K GD + ++ +++ E T PP TE+ L+ MEK GIGT ++ I + +R
Sbjct: 424 KELPELKEGDELKVEKLEVEEHFTKPPPRYTEASLVKAMEKLGIGTPSTYASIIETLQKR 483
Query: 519 NYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRS 556
YV G+RLVPT LG ++ ++ ELV+P +
Sbjct: 484 GYVEK-KGKRLVPTELGEAVIELLEEYFPELVDPDFTA 520
>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated.
Length = 822
Score = 382 bits (984), Expect = e-123
Identities = 167/532 (31%), Positives = 263/532 (49%), Gaps = 21/532 (3%)
Query: 30 RMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKRE 89
R+NG +E+ + + + GHI+ +DF +Y +W VDP EL K+
Sbjct: 28 RVNGV-PYYEFER----KGEKWIVIGLSGHIVTVDFPEEYGDWRDVDPAELIDADPVKKI 82
Query: 90 ATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFS 149
K L AKD + +++ D D+EGE I E +R + V RARFS
Sbjct: 83 T--KQNYINALKKLAKDADEIIIATDYDREGELIGKEAYHILREVCQVP----VKRARFS 136
Query: 150 AITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLIS 209
++T K+I+ A N + + A + +ARQ +DL G A TR+ + + G D +S
Sbjct: 137 SLTKKEIRKAFENPDEIDFNLADAGEARQIIDLYWGAALTRFLS-LSVRQLGRWD--FLS 193
Query: 210 YGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGH----IFDKSTC 265
G QTPTL F V+R +IR F PE YW ++ L+ GH +D+
Sbjct: 194 VGRVQTPTLAFIVDREREIRAFDPEDYWKIEALLDKEAQYFYRDLIGGHEAEKFWDEEEA 253
Query: 266 NVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYT 325
++ ++ K TV V+ ++ + P NT E +R AS G+ P AM+IAE+LYT
Sbjct: 254 EEIYEKLKGAKEATVSSVKKRERTISPPAPFNTTEFLREASKIFGISPKRAMEIAEKLYT 313
Query: 326 QGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKG-KDVGDHPP 384
GY+SYPRT+ T YP++ D +L++ ++G + +L KP +G K+ DHPP
Sbjct: 314 AGYISYPRTDNTVYPDDLDPKELLKKLSKKKEYGPYAESILEQENIKPTEGKKETTDHPP 373
Query: 385 ITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLH 444
I P + R +L D W++Y+ IVR F+ TL + + V E+F L+
Sbjct: 374 IHPVDVPKREELSDDEWKVYELIVRRFLATLADPAEWEYLKVELDVNGEIFKASGSRLVE 433
Query: 445 PGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGT 504
G+ V + + +PD + G+ + + +++ ++T PP T+S LI MEK G+GT
Sbjct: 434 EGWHEVYPYEKFDEKELPDLEEGEKLKVNKIEIEAKETQPPKRYTQSSLIKEMEKRGLGT 493
Query: 505 DASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRS 556
A+ I + +R Y V G PT LGI ++ +K E+V M +
Sbjct: 494 KATRHDIIEKLYKRGY--VIEGDPPRPTDLGIAVIEALEKYAPEIVSEEMTA 543
>gnl|CDD|238110 cd00186, TOP1Ac, DNA Topoisomerase, subtype IA; DNA-binding,
ATP-binding and catalytic domain of bacterial DNA
topoisomerases I and III, and eukaryotic DNA
topoisomerase III and eubacterial and archael reverse
gyrases. Topoisomerases clevage single or double
stranded DNA and then rejoin the broken phosphodiester
backbone. Proposed catalytic mechanism of single
stranded DNA cleavage is by phosphoryl transfer through
a tyrosine nucleophile using acid/base catalysis. Tyr is
activated by a nearby group (not yet identified) acting
as a general base for nucleophilic attack on the 5'
phosphate of the scissile bond. Arg and Lys stabilize
the pentavalent transition state. Glu then acts as a
proton donor for the leaving 3'-oxygen, upon cleavage of
the scissile strand.
Length = 381
Score = 362 bits (932), Expect = e-121
Identities = 116/391 (29%), Positives = 167/391 (42%), Gaps = 49/391 (12%)
Query: 171 ARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRT 230
+ AR+ LD +G +R TK + K +S G Q+PTLG VER +I+
Sbjct: 4 VNAQLARRILDRLVGFNLSRLLTKKLRRKGV------LSAGRVQSPTLGLIVEREREIKA 57
Query: 231 FKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSK 290
F PE YW + K VV V+ K K
Sbjct: 58 FVPEDYWEI------------------------------------KEAVVVSVEKKEKKK 81
Query: 291 TKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLR 350
P T L + ASS LG MQIA++LY G ++YPRT++T+ E L A
Sbjct: 82 NPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGLITYPRTDSTRLSEEAILEAREY 141
Query: 351 QQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLA----TRTQLDGDAWRLYDY 406
Q + +L + R K+ G H I PTK+A L D ++LY+
Sbjct: 142 IQAIYGKEYLYPAPLLGR-RNPKRGKKEQGAHEAIRPTKVAPTPELEANLSEDEFKLYEL 200
Query: 407 IVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESI-PDFK 465
I R F+ + D Y + + E F K LL G+ V E P K
Sbjct: 201 IWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLK 260
Query: 466 PGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTS 525
GD + ++ V++ E++T PP TE+ LI LMEK GIG ++ I + R YV
Sbjct: 261 EGDELKLEEVELEEKETQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKE- 319
Query: 526 GRRLVPTSLGIVLVHGYQKIDRELVEPTMRS 556
++L+PT LG ++ +K ELV+P +
Sbjct: 320 KKKLIPTELGFAVIELLEKHFPELVDPEFTA 350
>gnl|CDD|216317 pfam01131, Topoisom_bac, DNA topoisomerase. This subfamily of
topoisomerase is divided on the basis that these enzymes
preferentially relax negatively supercoiled DNA, from a
5' phospho- tyrosine linkage in the enzyme-DNA covalent
intermediate and has high affinity for single stranded
DNA.
Length = 365
Score = 321 bits (824), Expect = e-105
Identities = 120/396 (30%), Positives = 173/396 (43%), Gaps = 56/396 (14%)
Query: 165 KPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVER 224
+ + + +AR+ LD IG +R T F K ++S G QTPTLG VER
Sbjct: 1 EEDENLVDAQEARRILDRLIGFNLSRALTLKFNNK-------VLSAGRVQTPTLGLIVER 53
Query: 225 HDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQ 284
+I F PEPYW TV V+
Sbjct: 54 EKEIENFVPEPYW-----------------------------------------TVKSVE 72
Query: 285 SSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFD 344
K + P NT L + AS LG M IA++LY G ++YPRT++T E+ +
Sbjct: 73 KKEKKEPPPLPFNTSTLQKEASRKLGFSAKKTMDIAQKLYEGGLITYPRTDSTYLSEDAE 132
Query: 345 LVAVLRQQES--SPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLATRTQ-LDGDAW 401
L A+L D+ + ++ K VG H I PT R L D
Sbjct: 133 LAAILEYLAKRFGEDYLPYAPLLVK---GKSWGNAKVGAHEAIRPTGPIPRLPELSDDER 189
Query: 402 RLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNE-S 460
+LYD IVR F+ + VY + + V E F K LL PG+ V ++E
Sbjct: 190 KLYDLIVRRFLASQMPPAVYEETKVELEVGGEEFKASGKVLLEPGWKKVYPDEKDEDEEP 249
Query: 461 IPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNY 520
+P+ K G+ + ++ V++ E+KT PP TE+ LI MEK GIGT A+ I + +R Y
Sbjct: 250 LPELKEGEELDVKDVELEEKKTKPPPRYTEASLIKAMEKRGIGTPATRASIIETLLERGY 309
Query: 521 VTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRS 556
V ++LVPT LG L+ + +LV P + +
Sbjct: 310 VERKKKKKLVPTDLGRALIDALPRFP-DLVSPELTA 344
>gnl|CDD|180892 PRK07220, PRK07220, DNA topoisomerase I; Validated.
Length = 740
Score = 305 bits (783), Expect = 6e-95
Identities = 161/505 (31%), Positives = 254/505 (50%), Gaps = 27/505 (5%)
Query: 58 GHIMGLDFTSKYNNWDKVDPLELF-----SCPTEKREATPKLKLPAFLANEAKDCEFLVL 112
GHI+ +DF +YNNW KVD +L + PT+K+ T KL K+ + + +
Sbjct: 51 GHIVNIDFPKEYNNWQKVDARDLIDAEIITTPTQKKIVTALKKL-------GKEADRVTI 103
Query: 113 WLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEAR 172
D D+EGE I E + ++ +N R R+SAIT K+I+ A N V+ + A
Sbjct: 104 ATDYDREGELIGVEALNIIK---KVNPDIKFDRVRYSAITKKEIERAFSNPVEVDFNLAD 160
Query: 173 SVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFK 232
+ +RQ +DL G A TRY G+ G +S G Q+PTL V+R + F
Sbjct: 161 AGHSRQVIDLVWGAALTRY-ISLAAGRLGK---MFLSVGRVQSPTLALIVDREKEREAFV 216
Query: 233 PEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTK 292
P PYW + TL NG S ++K + F+ + K V +V+ TK+
Sbjct: 217 PTPYWEIYATLENNGETFVAQHSTRRFWEKEEADRVFEKLGKT--AEVTEVEKGTKTDKP 274
Query: 293 PQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQ 352
P NT E + A+S +G +AM+IAE LYT GY+SYPRT+ T YPE+ DL +
Sbjct: 275 PTPFNTTEFISAANS-IGFSAANAMRIAESLYTNGYISYPRTDNTVYPESLDLREQIEIF 333
Query: 353 ESSPDWGDHVREVLSNGISKPRKGK-DVGDHPPITPTKLATRTQLDGDAWRLYDYIVRHF 411
P +G++ +++L G P +GK + DHPPI P LA +++L D W++Y+ +VR F
Sbjct: 334 AEGP-FGEYAQKLLEKGELVPTRGKKETTDHPPIYPASLAKKSELKEDEWKVYELVVRRF 392
Query: 412 IGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIP 471
T G + +F + E F L PG+ ++A ++ +P+ G+ +
Sbjct: 393 FATFAGPAEWETMKLRFDIGGEEFRANGSRLTEPGWRWYYPYNAPEDRLLPELSEGEELK 452
Query: 472 IQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVP 531
++ +M++++T PP + LI LME G+GT A+ I+ + R Y+ G + P
Sbjct: 453 VKKKEMLDKETQPPGRYGQGRLIKLMEDLGLGTKATRHEIISKLYSRAYI---HGNPIQP 509
Query: 532 TSLGIVLVHGYQKIDRELVEPTMRS 556
T+ +V +K + +P M S
Sbjct: 510 TNTAFAVVDALEKYAPTITKPDMTS 534
>gnl|CDD|214663 smart00437, TOP1Ac, Bacterial DNA topoisomerase I DNA-binding
domain. Bacterial DNA topoisomerase I and III,
Eukaryotic DNA topoisomeraes III, reverse gyrase alpha
subunit.
Length = 259
Score = 256 bits (656), Expect = 6e-82
Identities = 86/258 (33%), Positives = 126/258 (48%), Gaps = 10/258 (3%)
Query: 288 KSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVA 347
K K P T L + AS LG MQIA++LY +G ++YPRT++T+ E L A
Sbjct: 5 KKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEA 64
Query: 348 VLR-QQESSPDWGDHVREVLSNGISKPRKGKD-VGDHPPITPTKLATRTQ----LDGDAW 401
Q+ ++ D +L KPRKGK G H I PTK + L D +
Sbjct: 65 RNYIQKLYGKEYLDLAVVLLKPR--KPRKGKKAQGAHEAIRPTKPIFTPELEKELSEDEF 122
Query: 402 RLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTW-SAMKNES 460
+LY+ I R F+ + D Y + + E F + K LL G+ V +
Sbjct: 123 KLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAKGKTLLFDGWLKVYPEEKKEEEIE 182
Query: 461 IPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNY 520
+P K GD + ++ V++ E++T PP TE+ LI LMEK GIG ++ I + R Y
Sbjct: 183 LPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGIGRPSTYASIIETLLDRGY 242
Query: 521 VTVTSGRRLVPTSLGIVL 538
VT ++L+PT LGI +
Sbjct: 243 VTKK-KKKLIPTELGIAV 259
>gnl|CDD|184936 PRK14973, PRK14973, DNA topoisomerase I; Provisional.
Length = 936
Score = 265 bits (680), Expect = 1e-78
Identities = 169/518 (32%), Positives = 247/518 (47%), Gaps = 32/518 (6%)
Query: 45 FGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVD--PLELFSC-----PTEKREATPKLKLP 97
F D V+ + GH++ +DF Y NW + P L PTEK+ KL
Sbjct: 38 FDDTVVVGLR---GHVVEVDFEPGYTNWRSEEHTPRSLIDADTIKKPTEKKIVGLIQKL- 93
Query: 98 AFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIK 157
AK + + + D D EGE I E E VR +N P + RARFSAIT ++I
Sbjct: 94 ------AKKADRVTIATDFDTEGELIGKEAYELVR-AVNPKVP--IDRARFSAITKEEIV 144
Query: 158 AAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPT 217
A + A + +ARQ +DL G + TR+ + G +++S G Q+PT
Sbjct: 145 TAFAEPTDLDFALAAAGEARQIIDLIWGASLTRFIS--LAAHRGG--DNILSVGRVQSPT 200
Query: 218 LGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKH 277
L V+R +I F PE YW+L L +G + + G D + + A ++
Sbjct: 201 LAMIVDREKEIEAFVPEKYWMLSLATEKDGEGIEARHTHGRFTDSAAAEAAYDATKEPLV 260
Query: 278 VTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETT 337
VT +V+ K P +T + VA+S LG +AM+IAE LY GY+SYPRT+ T
Sbjct: 261 VT--EVKEGHKVDRAPTPFDTTTFI-VAASRLGFSAANAMRIAEDLYMNGYISYPRTDNT 317
Query: 338 QYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGK-DVGDHPPITPTKLATRTQL 396
YP++ DL VL + V V N P +GK DHPPI PT +ATR +L
Sbjct: 318 IYPKSLDLNGVLATLAKGA-FSKDVAWVKDNRRPVPTRGKKSSTDHPPIHPTGVATREEL 376
Query: 397 DGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAM 456
D W+LY+ +VR F+ TL D + F E +T LL G+ V +S
Sbjct: 377 GDDRWKLYELVVRRFLATLSPDAEWATMKVNFDAGGEPYTATGGRLLEAGWRTVYPYSEA 436
Query: 457 KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNIC 516
K +P F G+ +PI +V + E++T PP ++S LI ME+ G+GT ++ I +
Sbjct: 437 KENILPAFALGEKLPILAVNLEEKETQPPARYSQSRLIQRMEELGLGTKSTRHEVIGKLV 496
Query: 517 QRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTM 554
R Y+ G L PT +G + ++ + EP M
Sbjct: 497 SRKYI---EGNPLRPTLVGRAVTESLEEHAGTITEPDM 531
>gnl|CDD|235602 PRK05776, PRK05776, DNA topoisomerase I; Provisional.
Length = 670
Score = 206 bits (526), Expect = 1e-58
Identities = 121/449 (26%), Positives = 197/449 (43%), Gaps = 23/449 (5%)
Query: 115 DCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSV 174
D D EG I + +++ + PK R +FSA+T DI+ A NL + +
Sbjct: 105 DYDIEGSVIGYLIIK------YLGDPKKAKRMKFSALTKSDIRRAFRNLETLDYEMINAG 158
Query: 175 DARQELDLRIGCAFTRYQTKFFQGKYGDLDAS----LISYGPCQTPTLGFCVERHDKIRT 230
AR ELD G +R + DAS ++S G Q+PTL + VER +
Sbjct: 159 IARHELDWLWGINVSRALMSSVR------DASGKRVILSAGRVQSPTLKYVVEREIERNL 212
Query: 231 FKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSK 290
F P PY+ + + + NG ++ + K + ++K ++ V V+ +
Sbjct: 213 FVPLPYFSVSIIIEKNGYEFTLKYENKKFETKEEAKEILEEIKKTGYLKVTKVEVKIEIL 272
Query: 291 TKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLR 350
P N +L A+ G P+ IAE LY G +SYPRT + + P ++ +L+
Sbjct: 273 EPPPPFNLGDLQVEAARIYGFSPYKTQSIAEDLYLDGLISYPRTNSQKLPPTLNIRNILK 332
Query: 351 QQESSPDWGDHVREVLS--NGISKPRKG-KDVGDHPPITPTKLATRTQLDGDAWRLYDYI 407
SP + V +L G+ KP +G KD HP I PT L D ++LYD I
Sbjct: 333 GLSRSPQYRPLVNLLLKETKGVLKPVQGPKDDPAHPAIYPTGEPP-KNLSKDEFKLYDLI 391
Query: 408 VRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYL--LHPGFTGVMTWSAMKNESIPDFK 465
VR F+ + V + + V A G+ + E +P K
Sbjct: 392 VRRFLASFAAPAVLSNTIVTLRVPGFPLVFSASGQRIEERGWLKYYPFHKFDEEELPLLK 451
Query: 466 PGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTS 525
G+ + I VK+ + T PP +++ L+ ME GIGT+A+ I + +R Y+T ++
Sbjct: 452 KGERVKIVDVKVRKSYTKPPSRYSKASLLKWMESVGIGTEATRARIIETLFKRGYLT-SN 510
Query: 526 GRRLVPTSLGIVLVHGYQKIDRELVEPTM 554
G+ + T LG + +K ++V +
Sbjct: 511 GKYIEVTPLGFGVAEVLEKYFPDIVSVEL 539
>gnl|CDD|233253 TIGR01057, topA_arch, DNA topoisomerase I, archaeal. This model
describes topoisomerase I from archaea. These enzymes
are involved in the control of DNA topology. DNA
topoisomerase I belongs to the type I topoisomerases,
which are ATP-independent [DNA metabolism, DNA
replication, recombination, and repair].
Length = 618
Score = 203 bits (518), Expect = 7e-58
Identities = 115/452 (25%), Positives = 194/452 (42%), Gaps = 11/452 (2%)
Query: 104 AKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNL 163
AK + + D D EGE I F+ ++ + K R +FS +T +DI+ A N
Sbjct: 91 AKGADEYINACDYDIEGEVIGFKALKYF---CGVERAK---RMKFSTLTKQDIRRAYANP 144
Query: 164 VKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVE 223
+ + + AR LD G +R + + G ++S G Q PTL F VE
Sbjct: 145 EEIDYGMVDAGMARHILDWYWGINLSRALMEAIRAAAGRW--VILSAGRVQGPTLAFLVE 202
Query: 224 RHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDV 283
R +I F P+PYW++ TL G + I+ + + ++K V +V
Sbjct: 203 REREINLFVPKPYWVIKATLEKGGGVFDARPEKWKIWSEEEAKSIKEELKKSPWAAVEEV 262
Query: 284 QSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENF 343
+S P + L R A G P IA+ LY + +SYPRT + + P +
Sbjct: 263 RSERSILKPPPPFDLGTLQREAYRIFGFSPKKTQSIAQELYEEALISYPRTSSQKLPPSI 322
Query: 344 DLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGD-HPPITPTKLATRTQLDGDAWR 402
+ A+L P + + +L G+ KP +GK HP I PT +L D +
Sbjct: 323 NYRAILDNLAKGPLYREAAERLLETGVLKPVEGKKEDPAHPAIHPTGEIPSQELSKDEKK 382
Query: 403 LYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIP 462
+YD IVR F+ + + + + E F + ++ G+ +S + + +P
Sbjct: 383 VYDLIVRRFLAAFSEEAIREKSKVLLRIGQEKFRLSGLRVVKLGWLEYYHYSKFEEKELP 442
Query: 463 DFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVT 522
GD I + V + ++T PP ++ LI ME G+GT A+ I + +R Y
Sbjct: 443 PLDRGDKIKVVRVDVRVKETQPPARYDKASLIREMESRGLGTKATRARIIETLYKRGY-- 500
Query: 523 VTSGRRLVPTSLGIVLVHGYQKIDRELVEPTM 554
+ + + T LG ++ Q+ E++ +
Sbjct: 501 IEGKKSIKVTPLGEAVIETLQRYCPEIISEEL 532
>gnl|CDD|236078 PRK07726, PRK07726, DNA topoisomerase III; Provisional.
Length = 658
Score = 169 bits (432), Expect = 2e-45
Identities = 121/473 (25%), Positives = 191/473 (40%), Gaps = 71/473 (15%)
Query: 115 DCDKEGENICFEVME--AVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNI-FE- 170
D D+EGE I E+++ VR I K +W S++TDK IK A NL KP
Sbjct: 101 DADREGELIAREILDYCGVRKPI-----KRLW---ISSLTDKAIKRAFANL-KPGKETIP 151
Query: 171 -ARSVDARQELDLRIGCAFTR-YQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKI 228
S AR D +G TR Y + Y + +S G QTPTL V R ++I
Sbjct: 152 LYYSALARSRADWLVGINMTRAYTLLGRKAGYNGV----LSVGRVQTPTLALVVRRDEEI 207
Query: 229 RTFKPEPYWLLDLTLNLNGVAVSVTW--------SRGHIFDKSTCNVFFKAVEK--EKHV 278
F P+PYW ++ L G + W G + D+ + V + +
Sbjct: 208 ENFVPKPYWEVEAHL-TPGERFTAKWQPSEPYQDEEGRLLDRPLAE---QVVARIQGQPA 263
Query: 279 TVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLY-TQGYVSYPRTETT 337
V +V++ K + P + EL A+ G+ + IA+ LY T ++YPRT++
Sbjct: 264 KVTEVETKRKKEYAPLLYDLSELQIDANKRFGLSAKETLDIAQSLYETHKLITYPRTDSR 323
Query: 338 QYPEN-FDLV-AVLRQQESSPDWGDHVREVLSNGISKPRKG----KDVGDHPPITPT-KL 390
PE+ + VL + VL I R K V H I PT +
Sbjct: 324 YLPEDMVATLPEVLNAISKVDPYLLLAPPVLDPSI---RSRAWNDKKVTAHHAIIPTEQP 380
Query: 391 ATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGV 450
++L D ++YD I R ++ Y + + +A F + K ++ G+ +
Sbjct: 381 PNLSKLSEDERKVYDLIARRYLAQFLPPAEYDKTTIELEIAGGTFIAKGKQVVEAGWKAL 440
Query: 451 MTWSAMKNE---SIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLM---------- 497
+ E +P GD + ++ ++ E +T PP TE L+S M
Sbjct: 441 LGKKEEDEEKEQPLPVLAKGDELKVEKGEVKEGQTQPPKRFTEGTLLSAMENIARFVQDK 500
Query: 498 -------EKHGIGTDA---SIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVH 540
E G+GT+A I I + +R Y+ G+ + T G L+
Sbjct: 501 ELKKTLKETDGLGTEATRAGI---IEKLFKRGYLEKK-GKYIHATDKGKQLID 549
>gnl|CDD|233252 TIGR01056, topB, DNA topoisomerase III, bacteria and conjugative
plasmid. This model describes topoisomerase III from
bacteria and its equivalents encoded on plasmids. The
gene is designated topB if found in the bacterial
chromosome, traE on conjugative plasmid RP4, etc. These
enzymes are involved in the control of DNA topology. DNA
topoisomerase III belongs to the type I topoisomerases,
which are ATP-independent [DNA metabolism, DNA
replication, recombination, and repair].
Length = 660
Score = 156 bits (397), Expect = 6e-41
Identities = 119/529 (22%), Positives = 222/529 (41%), Gaps = 64/529 (12%)
Query: 58 GHIMGL----DFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLAN-----EAKDCE 108
GH++ L ++ KY NW + L L E + K + +
Sbjct: 42 GHLVELAEPEEYDEKYKNW-RTYDLPLEP---EDWQLVVSDKTKKQFNVIKRILKENKVD 97
Query: 109 FLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNI 168
+V+ D D+EGE I E+++ + + T+ R S++ D I+ A NL +
Sbjct: 98 EVVIATDPDREGELIAREILD----YLKVTDKVTIKRLWISSLVDSSIRKAFKNLRPKSE 153
Query: 169 FEA--RSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHD 226
E +S AR D +G TR TK G+ D ++S G QTPTL V+R +
Sbjct: 154 TEGLYKSGVARARADWLVGINLTRAFTKL--GREAGNDG-VLSVGRVQTPTLAMVVKREN 210
Query: 227 KIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTC---NVFFKAVE--KEKHVTVV 281
+I+ F +P++ + T+N + + W + + ++ + V +K V
Sbjct: 211 EIKNFVGKPFYEVSATINKDEQEFTTEW-QPYKDEEERELHEFLAENVVTDLTQKPALVT 269
Query: 282 DVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLY-TQGYVSYPRTETTQYP 340
D++ K + P + L A+ G+ + IA++LY T ++YPRT++ P
Sbjct: 270 DIEKERKKTSAPLFYDLSALQEDANKRFGISAKRTLDIAQKLYETHKLITYPRTDSRYLP 329
Query: 341 ENFDLVAVLRQ-----QESSPDW--GDHVREVLSNGISKPRKGKDVGDHPPITPTK-LAT 392
E D +L + + +P E+ +N + +K + DH I PT
Sbjct: 330 E--DEKEMLLEVLDALKVITPALLPIKKRDELTNNRLWNDKK---IEDHHAIIPTGNDFN 384
Query: 393 RTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMT 452
+ L + +Y I ++++ Y + ++ MF + K L G+ ++
Sbjct: 385 LSDLSEEERNVYKLIAQNYLMQFMPKEEYETTTIEIAIGKLMFEAKGKILQDNGWKALLG 444
Query: 453 WSAMKNE----SIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLM----------- 497
E ++P F+ GD + +++++++E++T PP TE L+S M
Sbjct: 445 KQEEDEETEDTTLPAFQKGDELDVETLELLEKQTKPPARYTEGTLLSAMTNPAAFVQDKG 504
Query: 498 ------EKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVH 540
E G+GT+A+ I N+ +R ++ ++ T G +L
Sbjct: 505 LKKTLKETKGLGTEATRADIIENLFKRGFIQK-KKNKIYITKNGKLLCL 552
>gnl|CDD|233249 TIGR01051, topA_bact, DNA topoisomerase I, bacterial. This model
describes DNA topoisomerase I among the members of
bacteria. DNA topoisomerase I transiently cleaves one
DNA strand and thus relaxes negatively supercoiled DNA
during replication, transcription and recombination
events [DNA metabolism, DNA replication, recombination,
and repair].
Length = 610
Score = 151 bits (383), Expect = 3e-39
Identities = 135/538 (25%), Positives = 222/538 (41%), Gaps = 72/538 (13%)
Query: 51 FKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFL 110
+++ + GHI L + + +K D + K++ +LK AK + +
Sbjct: 21 YEVEASMGHIRDLPKSRLGVDIEK-DFEPEYVVSKGKKKVVKELK------TLAKKADEV 73
Query: 111 VLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFE 170
L D D+EGE I + + E ++ + + R F+ IT K I+AA+ N + ++
Sbjct: 74 YLATDPDREGEAIAWHLAEVLKPKDPVYK-----RIVFNEITKKAIRAALKNPREIDMNL 128
Query: 171 ARSVDARQELDLRIGCAFTR-YQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIR 229
+ AR+ LD +G + K +G S G Q+ L V+R +I+
Sbjct: 129 VNAQQARRILDRLVGYTLSPLLWKKVAKGL---------SAGRVQSVALRLIVDREREIK 179
Query: 230 TFKPEPYWLLDLTLNLNGVAVSVTWSR--------GHIFDKSTCNVFFKAVEKEKHVTVV 281
F PE YW +D T + G D++ + ++ E+ V
Sbjct: 180 RFVPEEYWTIDATFQKGEETFEALLTEVNGKKLKAGSDLDEAEATALKEQLKGEELVVEE 239
Query: 282 DVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLY--------TQGYVSYPR 333
+ KS+ P T L + AS LG M IA+RLY T G ++Y R
Sbjct: 240 IEKKPKKSRPPP-PFTTSTLQQEASRKLGFSAKKTMMIAQRLYEGVSTGDGTIGLITYMR 298
Query: 334 TETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPR----KGKDVGD-HPPITPT 388
T++T+ V R ++G E L KP+ K K+ + H I PT
Sbjct: 299 TDSTRLSNQA--VNEARNLIDK-NYGK---EYLG---PKPKRYKSKEKNAQEAHEAIRPT 349
Query: 389 KL-----ATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEA--KY 441
+ + L D +RLY+ I + F+ + D Y + + D + +A +
Sbjct: 350 SVFRTPEELKDYLKRDEFRLYELIWKRFVASQMADARYDSTSVRLTNEDGEYVFKATGRK 409
Query: 442 LLHPGFTGVM-----TWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISL 496
L+ G+ V K+ +P K GD + + VK + T PP TE+ L+
Sbjct: 410 LIFDGYYKVYVEGSDDPLEEKDRILPPLKEGDAVKLVEVKPNQHFTQPPARYTEASLVKE 469
Query: 497 MEKHGIG---TDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVE 551
+E+ GIG T ASI I+ I R YV +RL PT LG + +K ++V+
Sbjct: 470 LEELGIGRPSTYASI---ISTIQDRGYVKKE-NKRLYPTELGFAVTDLLEKHFGDVVD 523
>gnl|CDD|173782 cd03362, TOPRIM_TopoIA_TopoIII, TOPRIM_TopoIA_TopoIII: The
topoisomerase-primase (TORPIM) domain found in members
of the type IA family of DNA topoisomerases (Topo IA)
similar to topoisomerase III. Type IA DNA
topoisomerases remove (relax) negative supercoils in the
DNA by: cleaving one strand of the DNA duplex,
covalently linking to the 5' phosphoryl end of the DNA
break and, allowing the other strand of the duplex to
pass through the gap. The TOPRIM domain has two
conserved motifs, one of which centers at a conserved
glutamate and the other one at two conserved aspartates
(DxD). For topoisomerases the conserved glutamate is
believed to act as a general base in strand joining and,
as a general acid in strand cleavage. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 151
Score = 131 bits (333), Expect = 3e-36
Identities = 43/115 (37%), Positives = 61/115 (53%), Gaps = 6/115 (5%)
Query: 51 FKMTSVCGHIMGLDFTSKYNNWDKVDPLE--LFSCPTEKREATPKLKLPAFLANEAKDCE 108
+ +T GH++ LDF +Y+ WDKV PLE LF P + + K K L AK +
Sbjct: 41 YVVTWASGHLLELDFPEEYDPWDKVWPLEDPLFPAPFKLKVDKGKKKQFKVLKKLAKRAD 100
Query: 109 FLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNL 163
+V+ D D+EGE I E++E + K V RA FS++T K I+ A NL
Sbjct: 101 EIVIATDADREGELIGREILEYAKCVKR----KPVKRAWFSSLTPKAIRRAFKNL 151
>gnl|CDD|235516 PRK05582, PRK05582, DNA topoisomerase I; Validated.
Length = 650
Score = 136 bits (344), Expect = 8e-34
Identities = 124/536 (23%), Positives = 200/536 (37%), Gaps = 103/536 (19%)
Query: 51 FKMTSVCGHI-------MGLDFTSKYNNWD---KVDPLELFSCPTEKREATPKLKLPAFL 100
+K+ + GHI +G+D NN++ K +LK
Sbjct: 25 YKVVASMGHIRDLPKSQLGIDIE---NNFEPKYITIR--------GKGPVIKELK----- 68
Query: 101 ANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAM 160
AK + + L D D+EGE I + + + ++ R F+ IT IK A
Sbjct: 69 -KAAKKAKKVYLATDPDREGEAIAWHLAHIL--GLDEKEKN---RIVFNEITKDAIKNAF 122
Query: 161 WNLVKPNIFEARSVDA---RQELDLRIGCAFTRY------QTKFFQGKYGDLDASLISYG 211
N K ++ VDA R+ LD +G Y K +G S G
Sbjct: 123 KNPRKIDMN---LVDAQQARRILDRLVG-----YKLSPLLWKKVKKGL---------SAG 165
Query: 212 PCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLN-----LNGVAVSVTWSRGHIFDKSTCN 266
Q+ L ++R +IR F PE YW +D + + ++
Sbjct: 166 RVQSVALKLIIDREKEIRAFVPEEYWTIDAEFKKGKKKFEASFYGYKGKKIELKNEEDVK 225
Query: 267 VFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLY-- 324
++K+ V V+ + + P T L + A+ L M IA++LY
Sbjct: 226 EILAELKKKDFK-VSKVKKKERKRNPPPPFTTSTLQQEAARKLNFSTKKTMMIAQQLYEG 284
Query: 325 -------TQGYVSYPRTETTQYPENFDLVAVLRQQESSP----DWGDHVREVLSNGISKP 373
T G ++Y RT++T+ + Q+E+ +G E L
Sbjct: 285 IDLGKQGTVGLITYMRTDSTRISDTA-------QEEAREFIEEKYGK---EYLPKKPKVY 334
Query: 374 RKGKDVGD-HPPITPTKLATRT------QLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVA 426
+K D H I PT + T L D +LY I F+ + V+
Sbjct: 335 KKKSGAQDAHEAIRPTSV-FLTPESAKKYLTKDQLKLYKLIWNRFVASQMAPAVFDTVSV 393
Query: 427 KFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPD 486
F + GF V K++ +P+ + G+ + ++ ++ + T PP
Sbjct: 394 DLENNGVKFRASGSKVKFDGFMKVYVGDEEKDKMLPELEEGEKVKLKKIEPEQHFTQPPA 453
Query: 487 YLTESELISLMEKHGIG---TDASIPVHINNICQRNYVTVTSGRRLVPTSLG-IVL 538
TE+ LI +E+ GIG T A I+ I +R YV + +RLVPT LG IV
Sbjct: 454 RYTEASLIKTLEELGIGRPSTYAPT---ISTIQKRGYVKLEK-KRLVPTELGEIVN 505
>gnl|CDD|173778 cd01028, TOPRIM_TopoIA, TOPRIM_TopoIA: topoisomerase-primase
(TOPRIM) nucleotidyl transferase/hydrolase domain of the
type found in the type IA family of DNA topoisomerases
(TopoIA). This subgroup contains proteins similar to
the Type I DNA topoisomerases: E. coli topisomerases I
and III, eukaryotic topoisomerase III and, ATP-dependent
reverse gyrase found in archaea and thermophilic
bacteria. Type IA DNA topoisomerases remove (relax)
negative supercoils in the DNA. These enzymes cleave one
strand of the DNA duplex, covalently link to the 5'
phosphoryl end of the DNA break and allow the other
strand of the duplex to pass through the gap. Reverse
gyrase is also able to insert positive supercoils in the
presence of ATP and negative supercoils in the presence
of AMPPNP. The TOPRIM domain has two conserved motifs,
one of which centers at a conserved glutamate and the
other one at two conserved aspartates (DxD). For
topoisomerases the conserved glutamate is believed to
act as a general base in strand joining and, as a
general acid in strand cleavage. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 142
Score = 123 bits (310), Expect = 4e-33
Identities = 42/113 (37%), Positives = 59/113 (52%), Gaps = 5/113 (4%)
Query: 51 FKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFL 110
+ +T+ GH++ L F +Y +WDK PLELF + K K L AK + +
Sbjct: 35 YVVTASVGHLLELPFPEEYVDWDKDWPLELFPFEPKYVVIPDKKKQLKALKKLAKKADEI 94
Query: 111 VLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNL 163
VL D D+EGE I +E++E ++ K V RA FS IT K I+ A NL
Sbjct: 95 VLATDPDREGELIAWEILEVLK-----CDNKPVKRAWFSEITPKAIREAFKNL 142
>gnl|CDD|214662 smart00436, TOP1Bc, Bacterial DNA topoisomeraes I ATP-binding
domain. Extension of TOPRIM in Bacterial DNA
topoisomeraes I and III, Eukaryotic DNA topoisomeraes
III, reverse gyrase beta subunit.
Length = 89
Score = 110 bits (277), Expect = 3e-29
Identities = 35/93 (37%), Positives = 48/93 (51%), Gaps = 7/93 (7%)
Query: 145 RARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLD 204
R FS IT K I+ A+ N + + + AR+ LD IG +R TK +
Sbjct: 3 RIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLR------- 55
Query: 205 ASLISYGPCQTPTLGFCVERHDKIRTFKPEPYW 237
++S G QTPTLG VER +I+ F P+PYW
Sbjct: 56 NGVLSAGRVQTPTLGLIVEREREIKNFVPKPYW 88
>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase. This model describes reverse gyrase,
found in both archaeal and bacterial thermophiles. This
enzyme, a fusion of a type I topoisomerase domain and a
helicase domain, introduces positive supercoiling to
increase the melting temperature of DNA double strands.
Generally, these gyrases are encoded as a single
polypeptide. An exception was found in Methanopyrus
kandleri, where enzyme is split within the topoisomerase
domain, yielding a heterodimer of gene products
designated RgyB and RgyA [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1171
Score = 120 bits (302), Expect = 2e-28
Identities = 99/452 (21%), Positives = 180/452 (39%), Gaps = 66/452 (14%)
Query: 104 AKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNL 163
A + + + + D D EGE I +++ + N N V RA F +T + I A+ +
Sbjct: 717 AHEVDEVFIGTDPDTEGEKIGWDLALLLS-PYNPN----VKRAEFHEVTRRAILEALESP 771
Query: 164 --VKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFC 221
V N+ +A+ V R+ D IG ++ + F ++ +S G QTP LG+
Sbjct: 772 RSVDENLVKAQVV--RRIEDRWIGFTLSQKLWEAFNKRW-------LSAGRVQTPVLGWI 822
Query: 222 VERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVV 281
++R+ + R + L + + + + ++ F K + V
Sbjct: 823 IDRYRESREKRGY----LLIFALESDFRLGLEHD-----NRLEAKEFEK---DLTWLDVE 870
Query: 282 DVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPE 341
D+ + + T ++ A+ LG+ MQIA+ L+ G ++Y RT++T+ +
Sbjct: 871 DIAEREEERNPLPPYTTDTMLEDANRKLGLSVKETMQIAQELFENGLITYHRTDSTRVSD 930
Query: 342 NFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTK-----------L 390
VA +++ L PR+ + G H I PT+ L
Sbjct: 931 VGMRVAK-----------EYLASRLGGEYFYPREWGEGGAHECIRPTRPLDVDDLQRLIL 979
Query: 391 ATRTQLDGDAW---RLYDYIVRHFIGTLC--GDLVYTQKVAKFSVADEMFTMEAKYLLHP 445
+L+G RLYD I R F+ + + + K + + +
Sbjct: 980 EGVIELEGLTREHLRLYDLIFRRFMASQMRPAKVDTKEITLKADGKEAEEEGIVEIVER- 1038
Query: 446 GFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYL-TESELISLMEKHGIGT 504
GF V + + + VK E ++ P Y T+ E++ M++ GIG
Sbjct: 1039 GFELV--YPLWRKNELEKGSTFI------VKDKELRSVPKVYPYTQGEIVQEMKERGIGR 1090
Query: 505 DASIPVHINNICQRNYVTVTSGRRLVPTSLGI 536
++ + + +R YV V S L+PT LGI
Sbjct: 1091 PSTYATIVEKLLRRGYV-VESKGFLIPTKLGI 1121
>gnl|CDD|236172 PRK08173, PRK08173, DNA topoisomerase III; Validated.
Length = 862
Score = 119 bits (299), Expect = 4e-28
Identities = 135/541 (24%), Positives = 213/541 (39%), Gaps = 90/541 (16%)
Query: 53 MTSVCGHIMGL----DFTSKYNNWD----KVDPLELFSCPTEKREATPKLKLPAFLANEA 104
++S GH++ + ++ K W V P P K E+ +LK+ L
Sbjct: 38 LSSAVGHLLEIAAPEEYEVKRGKWSFAHLPVIPPHFDLNPIAKTES--RLKVLTKLIKR- 94
Query: 105 KDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNL- 163
KD L+ D +EGE I F ++ +H + K V R ++T + I+ NL
Sbjct: 95 KDVTRLINACDAGREGELI-FRLI--AQH---AKAKKPVKRLWLQSMTPQAIRDGFANLR 148
Query: 164 ----VKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLG 219
++P AR R E D +G TR T F K G L + G QTPTL
Sbjct: 149 SDEDMQPLADAARC---RSEADWLVGINGTRAMTAF-NSKGGGF--FLTTVGRVQTPTLS 202
Query: 220 FCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVT 279
VER +KIR F P YW + W FD FK E +
Sbjct: 203 IVVEREEKIRRFVPRDYWEVRAEFVAAAGFYEGRW-----FDPK-----FKKDEFDPEKR 252
Query: 280 ----------------------VVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAM 317
V +S ++ P + L R A+ G + +
Sbjct: 253 ASRLWSEAAAEAIVAACRGKPGTVTEESKPSTQLSPLLFDLTSLQREANGRFGFSAKNTL 312
Query: 318 QIAERLYTQGYV-SYPRTETTQYPENFDLVAVLRQ----QESSPDWGDHVREVLSNGISK 372
+A+ LY + V +YPRT++ PE D + ++Q + S ++ H +++L G K
Sbjct: 313 GLAQALYEKHKVLTYPRTDSRALPE--DYLGTVKQTLEMLKESNNYLPHAKQILDKGWVK 370
Query: 373 PRK----GKDVGDHPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKF 428
P K + DH I PT A ++ + + +LYD +V+ F+ +
Sbjct: 371 PNKRIFDNSKISDHFAIIPTLQAPKSLSEPEQ-KLYDLVVKRFLAVFFPAAEFLVTTRIT 429
Query: 429 SVADEMFTMEAKYLLHPGFTGVMTWSAM-KNESIPDFKPGDLIPIQSVKMVERKTTPPDY 487
VA F E K L++PG+ V A + ++ + G+ + ++ V T PP
Sbjct: 430 EVAGHHFKTEGKVLVNPGWLAVYGKEAQGADANLVPVQKGEKVKTDKIEAVALTTKPPAR 489
Query: 488 LTESELISLME----------------KHGIGTDASIPVHINNICQRNYVTVTSGRRLVP 531
E+ L+S ME + G+GT A+ I + Y+ V GR L+P
Sbjct: 490 YNEATLLSAMEGAGKLVEDDELREAMAEKGLGTPATRAAIIEGLLGEKYL-VREGRELIP 548
Query: 532 T 532
T
Sbjct: 549 T 549
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination, and
repair].
Length = 1187
Score = 117 bits (295), Expect = 2e-27
Identities = 119/484 (24%), Positives = 193/484 (39%), Gaps = 86/484 (17%)
Query: 82 SCPTEKRE----ATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQINI 137
CP T ++ LA E + +++ D D EGE I ++V +R
Sbjct: 710 KCPRCGSRNVEDKTETVEALRELALEV---DEILIGTDPDTEGEKIAWDVFNYLR----- 761
Query: 138 NSPKT--VWRARFSAITDKDIKAAMWNL--VKPNIFEARSVDARQELDLRIGCAFTRYQT 193
P V R F +T + I A+ N V N+ +A+ V R+ D IG ++
Sbjct: 762 --PYNPNVKRIEFHEVTRRAILEALKNPRDVDENLVKAQIV--RRIEDRWIGFELSQKLW 817
Query: 194 KFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVT 253
F K +S G QTP LG+ V R+++ + + LDL L
Sbjct: 818 DVFNNKN-------LSAGRVQTPVLGWIVNRYEEYKEKRGYLVIQLDLDLPSG------- 863
Query: 254 WSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGP 313
+R + + K K V VVDV + K T ++R AS L +
Sbjct: 864 -NREEVEN-------VKRKLKLIVVEVVDVVEREEEKNPLPPYTTDTMLRDASRRLRLSA 915
Query: 314 HHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKP 373
MQIA+ L+ G ++Y RT++T+ + VA +++R+ +P
Sbjct: 916 DETMQIAQDLFEGGLITYHRTDSTRVSDVGIRVAR-----------EYLRKEFGEEYFRP 964
Query: 374 RKGKDVGDHPPITPTK---------------LATRTQLDGDAWRLYDYIVRHFIGTLCGD 418
R + G H I PT+ + +L + R+YD I R F+ +
Sbjct: 965 RSWGEEGAHEAIRPTRPIDVEELITLIEEGVIQLPIRLTKNHLRVYDLIFRRFMASQMRP 1024
Query: 419 LVYTQKVAKFSV-ADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKM 477
++ A+ ++ +L GF V +P+ + G L V
Sbjct: 1025 AKVLKEKAEVKADGKDVELEALVEILEDGFALV-----YPTRVLPELEKGTL----KVTE 1075
Query: 478 VERKTTPPDYL-TESELISLMEKHGIG---TDASIPVHINNICQRNYVTVTSGRR-LVPT 532
VE + YL T+ E++ M++ GIG T A I + + +R YV + GR+ L+PT
Sbjct: 1076 VEIRKVSKVYLYTQGEVVEEMKERGIGRPSTYAKI---VETLLRRGYVIESKGRKKLIPT 1132
Query: 533 SLGI 536
LGI
Sbjct: 1133 KLGI 1136
>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated.
Length = 859
Score = 114 bits (289), Expect = 1e-26
Identities = 125/490 (25%), Positives = 194/490 (39%), Gaps = 104/490 (21%)
Query: 100 LANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKT-VWRARFSAITDKDIKA 158
L AKD + L L D D+EGE I + ++E + V R F+ IT I+
Sbjct: 80 LKKAAKDADELYLATDPDREGEAIAWHLLEV------LGGDDVPVKRVVFNEITKNAIQE 133
Query: 159 AMWNLVKP-NIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLD------------- 204
A N P + V+A Q + F LD
Sbjct: 134 AFEN---PRELDINL-VNA--------------QQARRF------LDRLVGYMVSPLLWK 169
Query: 205 --ASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLN-------------LNGVA 249
A +S G Q+ + VER +I F PE YW + L L+G
Sbjct: 170 KIARGLSAGRVQSVAVRLIVEREREIEAFVPEEYWDIHADLTTPRGDAFEARLTHLDGKK 229
Query: 250 VSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTK-SKTKPQA-LNTVELMRVASS 307
+ + +++ A+E ++ +V V+ K + KP A T L + AS
Sbjct: 230 FA----PVDLLNEAQAEAAVAALEGARY-SVASVE--DKPTTRKPSAPFTTSTLQQEASR 282
Query: 308 GLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLS 367
LG M+IA+RLY GY++Y RT++T + + + R ++G + L
Sbjct: 283 KLGFSVKKTMRIAQRLYEAGYITYMRTDSTNLSQ--EAINAARGYIGD-NYGK---KYLP 336
Query: 368 NGISKPR----KGKDVGD-HPPITPTKLATR----TQLDGDAWRLYDYIVRHFIGTLCGD 418
KPR K K+ + H I P+ + L+GDA RLY+ I + F+ +
Sbjct: 337 ---EKPRQYSSKAKNAQEAHEAIRPSDVFRTPDQLKGLEGDAQRLYELIWKRFVASQMAP 393
Query: 419 LVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESI-------PDFKPGDLIP 471
Y + D + L GF V +++++ P K GD +
Sbjct: 394 ARYDSTTVTIAAGDAELRATGRVLRFDGFLKVYV--EGRDDALDDEDRRLPALKVGDALT 451
Query: 472 IQSVKMVERKTTPPDYLTESELISLMEKHGIG---TDASIPVHINNICQRNYVTVTSGRR 528
++ + + T PP +E+ L+ +EK GIG T ASI I+ I R YV + RR
Sbjct: 452 LEKLDPTQHFTKPPARYSEASLVKELEKLGIGRPSTYASI---ISTIQDRGYVRL-ENRR 507
Query: 529 LVPTSLG-IV 537
P +G IV
Sbjct: 508 FYPEKMGRIV 517
>gnl|CDD|235840 PRK06599, PRK06599, DNA topoisomerase I; Validated.
Length = 675
Score = 113 bits (286), Expect = 2e-26
Identities = 125/503 (24%), Positives = 202/503 (40%), Gaps = 97/503 (19%)
Query: 100 LANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAA 159
L AK + + L D D+EGE I + + E ++ K V R F+ IT K ++ A
Sbjct: 67 LKKAAKKADAVYLATDPDREGEAIAWHIAEVLK--EAKLKDKNVKRVVFNEITKKAVQEA 124
Query: 160 MWNLVKPNIFEARSVD---ARQELDLRIGCAFTRYQ------TKFFQGKYGDLDASLISY 210
+ N P + VD AR+ LD +G ++ K +G S
Sbjct: 125 IEN---PRDIDMDLVDAQQARRALDYLVG-----FKLSPLLWKKVRRGL---------SA 167
Query: 211 GPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTL-NLNGVAVSVTWS--------RGHIFD 261
G Q+ L ER D+I F P+ YW ++ L NG + + I +
Sbjct: 168 GRVQSVALRLICEREDEIEAFIPQEYWTIEADLATSNGEPFTAKLVEVNGKKLEKFSITN 227
Query: 262 KSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAE 321
+ KA+E + TV ++ + + P T L + AS LG M+IA+
Sbjct: 228 EEQAKALVKALEG-QAYTVDKIEKKERKRNPPPPFITSTLQQEASRKLGFSAKKTMRIAQ 286
Query: 322 RLY--------TQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGI--- 370
+LY T G ++Y RT D V + S + D R+ ++
Sbjct: 287 KLYEGIDLGEGTVGLITYMRT---------DSVRL------SNEALDEARKYITKKYGKE 331
Query: 371 ---SKPR----KGKDVGD-HPPITPTKLATRT------QLDGDAWRLYDYIVRHFIGTLC 416
+KPR K K+ + H I PT + RT L D ++LY+ I + + +
Sbjct: 332 YLPAKPRVYKKKSKNAQEAHEAIRPTSI-NRTPESLKPYLTPDQFKLYELIWKRTVASQM 390
Query: 417 GDLVYTQKVAKFSVADEMFTMEAK--YLLHPGF-----TGVMTWSAMKNESIPDFKPGDL 469
+ Q + + + A +L PGF + +P K G+
Sbjct: 391 APAILDQTSVDIASENGKYVFRATGSVILFPGFLKVYGESKDDEEEDDEKLLPPLKEGEK 450
Query: 470 IPIQSVKMVERKTTPPDYLTESELISLMEKHGIG---TDASIPVHINNICQRNYVTVTSG 526
+ + + + T PP +E+ L+ +E++GIG T ASI I+ + R YV +
Sbjct: 451 LKLDELLPEQHFTEPPPRYSEASLVKKLEEYGIGRPSTYASI---ISTLQDREYVEL-EK 506
Query: 527 RRLVPTSLG-IV---LVHGYQKI 545
+R +PT LG IV LV + K
Sbjct: 507 KRFIPTDLGRIVNDFLVEHFPKY 529
>gnl|CDD|181555 PRK08780, PRK08780, DNA topoisomerase I; Provisional.
Length = 780
Score = 105 bits (263), Expect = 1e-23
Identities = 124/488 (25%), Positives = 194/488 (39%), Gaps = 85/488 (17%)
Query: 100 LANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAA 159
+A AK + L L D D+EGE I + + E ++ + + K + R F+ IT + IK A
Sbjct: 67 IAKAAKSADDLYLATDPDREGEAISWHLAEILKERGLLKD-KPMQRVVFTEITPRAIKEA 125
Query: 160 MWNLVKPNIFEARSVDARQE---LDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTP 216
M KP + VDA+Q LD +G + + Q +S G Q+P
Sbjct: 126 M---AKPRDIASDLVDAQQARRALDYLVGFNLSPLLWRKIQ--------RGLSAGRVQSP 174
Query: 217 TLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSR--GHIFDKSTCNVFFKAVEK 274
L VER ++I F YW ++ + + G F++ T A
Sbjct: 175 ALRMIVEREEEIEAFIAREYWSIEADCAHPSQPFNAKLIKLDGQKFEQFTITDGDTAEAA 234
Query: 275 EKHVT--------VVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLY-- 324
+ V DV+S + + T L + AS LG MQ+A++LY
Sbjct: 235 RLRIQQAAQGTLHVTDVESKERKRNPAPPFTTSTLQQEASRKLGFTTRRTMQVAQKLYEG 294
Query: 325 -------TQGYVSYPRTETTQYPENFDLVAVLRQ-------QESSPDWGDHVREVLSNGI 370
+ G ++Y RT++ + D +A +R S PD
Sbjct: 295 VDLGDEGSVGLITYMRTDSVNLSQ--DALAEIRDVIARDYGTASLPD------------- 339
Query: 371 SKPR----KGKDVGD-HPPITPTKLATRT------QLDGDAWRLYDYIVRHFIGTLCGDL 419
+P K K+ + H + PT A RT L D RLY+ I + +
Sbjct: 340 -QPNTYKTKSKNAQEAHEAVRPTS-ALRTPAQVARFLSDDQRRLYELIWKRAVACQMIPA 397
Query: 420 VYTQKVAKFSVADE-MFTMEAKYLLHPGFTGVM-----TWSAMKNES---IPDFKPGDLI 470
+ E +F ++ PGF V SA + +P K GD +
Sbjct: 398 TLNTVSVDLAAGSEHVFRATGSTVVVPGFLAVYEEGKDDKSAEDEDEGRKLPPMKEGDNV 457
Query: 471 PIQSVKMVERKTTPPDYLTESELISLMEKHGIG---TDASIPVHINNICQRNYVTVTSGR 527
P++ ++ + T PP TE+ L+ +E++GIG T ASI I+ + R YV GR
Sbjct: 458 PLERIRAEQHFTEPPPRYTEASLVKALEEYGIGRPSTYASI---ISTLQFRKYV-EMEGR 513
Query: 528 RLVPTSLG 535
R PT +G
Sbjct: 514 RFRPTDVG 521
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 103 bits (260), Expect = 4e-23
Identities = 110/452 (24%), Positives = 179/452 (39%), Gaps = 87/452 (19%)
Query: 115 DCDKEGENICFEVMEAVRHQININSP--KTVWRARFSAITDKDIKAAMWNL--VKPNIFE 170
D D EGE I +++ + P + R F +T K I A+ N V N+ +
Sbjct: 728 DPDTEGEKIAWDLYLLLS-------PYNSNIKRIEFHEVTRKAILEALRNPRDVNENLVK 780
Query: 171 ARSVDARQELDLRIGCAFTRY-QTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIR 229
A+ V R+ D IG ++ Q KF GK +S G QTP LG+ VER+ + +
Sbjct: 781 AQIV--RRIEDRWIGFELSQKLQKKF--GKRN------LSAGRVQTPVLGWIVERYKEYK 830
Query: 230 TFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKS 289
K + Y L+ N G+ + +K F+ + + V V+ +
Sbjct: 831 --KSKGYVLVIKLENGGGLELEGE-----FSEKEEAEKFYNNLIE-----VEKVEEKEEE 878
Query: 290 KTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVL 349
T L+ AS L + M+IA+ L+ G ++Y RT++T+ V+
Sbjct: 879 LNPLPPYTTDTLLSDASRKLRLSAQETMRIAQDLFELGLITYHRTDSTR-------VS-- 929
Query: 350 RQQESSPDWGDHV-----REVLSNGISKPRKGKDVGDHPPITPTKLATRTQL-----DG- 398
D G V + PR + G H I PT+ +L +G
Sbjct: 930 -------DVGISVAKEYLEKRGGEEYFVPRSWGEGGAHEAIRPTRPLDAEELRQMIEEGI 982
Query: 399 ---------DAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEA-KYLLHPGFT 448
+ RLYD I R F+ + + + +E +L GF
Sbjct: 983 LKLSEGLTKNHLRLYDLIFRRFMASQMKPAKVRYQKVLIKADGKELELELVVEILEDGFN 1042
Query: 449 GVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIG---TD 505
V+ + P + + ++ K ++ P T+ +LIS M++ GIG T
Sbjct: 1043 KVLPL-----KLYPLLEGK--VKVKEKKTYKKSKVPL--YTQGDLISEMKERGIGRPSTY 1093
Query: 506 ASIPVHINNICQRNYVTVTSG-RRLVPTSLGI 536
A I + + +R YV + G +RL+PT LGI
Sbjct: 1094 AKI---VETLLRRGYVIESKGKKRLIPTKLGI 1122
>gnl|CDD|237803 PRK14724, PRK14724, DNA topoisomerase III; Provisional.
Length = 987
Score = 99.6 bits (248), Expect = 8e-22
Identities = 124/491 (25%), Positives = 194/491 (39%), Gaps = 81/491 (16%)
Query: 105 KDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNL- 163
KD LV D +EGE I F ++E K V R ++T + I+ NL
Sbjct: 98 KDVTELVNACDAGREGELI-FRLIEQYAGGAKGGLGKPVKRLWLQSMTPQAIRDGFDNLR 156
Query: 164 ----VKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLG 219
++ ARS R E D +G TR T F G L + G QTPTL
Sbjct: 157 SDAQMQGLASAARS---RSEADWLVGINGTRAMTAFNSRDGGFF---LTTVGRVQTPTLS 210
Query: 220 FCVERHDKIRTFKPEPYWLLDLTLNLN-----GVAVSVTWSRG---------HIFDKSTC 265
VER +KIR F YW + + G W + ++ +
Sbjct: 211 LVVEREEKIRKFVSRDYWEIHAGFHAEAGEYLGKWFDPQWKKASDDPEARADRVWSEREA 270
Query: 266 NVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYT 325
AV + K TV + +S ++ P + L R A+ G + +A+ LY
Sbjct: 271 RAIADAV-RGKAATVTE-ESKPTTQASPLLFDLTSLQREANGKFGFSAKTTLALAQSLYE 328
Query: 326 Q-GYVSYPRTETTQYPEN--------FDLVAVLRQQESSPDWGDHVREVLSNGISKPRK- 375
+ ++YPRT++ PE+ F+++A + +P ++ L +P K
Sbjct: 329 RHKALTYPRTDSRALPEDYLPVAKQTFEMLATSGMRHLAP----FAQQALDGNYVRPSKR 384
Query: 376 ---GKDVGDHPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVY--TQKVAKFSV 430
V DH I PT A + L +LYD +VR F+ Y T ++++ V
Sbjct: 385 IFDNSKVSDHFAIIPTTQAP-SGLSEAEQKLYDLVVRRFMAVFFPSAEYQVTTRISQ--V 441
Query: 431 ADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGD----LIPIQSVKMVER------ 480
F E K L+ PG+ + + + D K GD L+P++ +MV
Sbjct: 442 VGHSFKTEGKVLVKPGWLAI--YGKEAANEVEDAKDGDKGQPLVPVKPGEMVRTEFAEAK 499
Query: 481 --KTTPPDYLTESELISLME----------------KHGIGTDASIPVHINNICQRNYVT 522
KT PP +E+ L+ ME + G+GT A+ I + Y+
Sbjct: 500 GLKTKPPARYSEATLLGAMESAGKQIDDDELREAMQEKGLGTPATRAAIIEGLLTEKYM- 558
Query: 523 VTSGRRLVPTS 533
+ GR L+PT+
Sbjct: 559 LREGRELIPTA 569
>gnl|CDD|235778 PRK06319, PRK06319, DNA topoisomerase I/SWI domain fusion protein;
Validated.
Length = 860
Score = 83.3 bits (206), Expect = 1e-16
Identities = 109/492 (22%), Positives = 183/492 (37%), Gaps = 83/492 (16%)
Query: 100 LANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAA 159
+ AK C+ + L D D+EGE I + + + I R F+AIT + A
Sbjct: 67 ICKLAKKCDVVYLSPDPDREGEAIAWHIANQLPKNTKIQ------RISFNAITKGAVTEA 120
Query: 160 MWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLG 219
+ + + ++ + AR+ LD +G + ++ Q + G +S G Q+ L
Sbjct: 121 LKHPREIDMALVNAQQARRLLDRIVGYKISPILSRKLQRRSG------VSAGRVQSVALK 174
Query: 220 FCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVT------------WSRGHIFDKSTCNV 267
V+R I F P YW ++ ++L T W + K+ V
Sbjct: 175 LVVDREKAIEAFVPVEYW--NIRVHLKDPKTQKTFWAHLYSVDGKKWEKEIPEGKTEDEV 232
Query: 268 FF-KAVEKEKHV---------TVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAM 317
+ EK H+ TV V+S K + T L + AS M
Sbjct: 233 LLINSKEKADHIVELLESATYTVTRVESKEKRRNAYPPFITSTLQQEASRHFRFSSSRTM 292
Query: 318 QIAERLY---------TQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSN 368
IA+ LY G ++Y RT++ + + P+ VR+ +
Sbjct: 293 NIAQTLYEGVDLDSEGATGLITYMRTDSVR---------------TDPEALKQVRKYIEG 337
Query: 369 GISK---PRKG------KDVGD-HPPITPTKLA-----TRTQLDGDAWRLYDYIVRHFIG 413
K P K D H I PT + R++L D ++LY I + F+
Sbjct: 338 TFGKEFLPSSPNVYTTKKMAQDAHEAIRPTDITLTPEKLRSKLTEDQYKLYSLIWKRFVA 397
Query: 414 TLCGDLVYTQKVAKFSVADEMFTMEAKYLLH-PGFTGVM------TWSAMKNESIPDFKP 466
+ +Y + + + LL GF V +N +P
Sbjct: 398 SQMIPAIYDTLAIRITTNKGIDLRATGSLLKFKGFLAVYEEKRDDEGDEEENIHLPKLHE 457
Query: 467 GDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSG 526
D++ + + + T P TE+ L+ +EK GIG ++ +N I R Y T+
Sbjct: 458 QDVLTKEELSAEQAFTKPLPRFTEASLVKELEKSGIGRPSTYATIMNKIQSREY-TLKEN 516
Query: 527 RRLVPTSLGIVL 538
+RL PT LG ++
Sbjct: 517 QRLRPTELGKII 528
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 61.4 bits (149), Expect = 9e-10
Identities = 62/254 (24%), Positives = 98/254 (38%), Gaps = 46/254 (18%)
Query: 319 IAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQ---------ESSPDWGDHVREVLSNG 369
+ ER YT GYV Y T TT ENF ++ S RE L+
Sbjct: 1352 VEERYYT-GYV-YDFTTTT---ENFISNGMVSHNCTYHRTDSTRVSNTGIRVAREYLTQE 1406
Query: 370 IS----KPRKGKDVGDHPPITPTK--------------LATRTQLDGDAWRLYDYIVRHF 411
KPR G H I PT+ + L + RLYD I R F
Sbjct: 1407 NGEDYFKPRDWFMEGAHECIRPTRPIDTDRLIQLIREGIIQVPGLTRNHLRLYDLIFRRF 1466
Query: 412 IGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKN---ESIPDFKPGD 468
+ + K + + +E + + G WS + + +P + G
Sbjct: 1467 MASQMKP--AKVLYEKALIRYDGKDVEVEGYVEIEGDG---WSRLYSLPLRVLPKLEKGK 1521
Query: 469 LIPIQSVKMVERKTTPPDYL-TESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGR 527
L V + + P L T+ ++++LM++ GIG ++ ++ + R YV T GR
Sbjct: 1522 L----KVLEAKIRKAPKVPLYTQGDIVALMKERGIGRPSTYAKIVDTLLMRGYVIETKGR 1577
Query: 528 -RLVPTSLGIVLVH 540
+L+PT GI + +
Sbjct: 1578 KKLIPTKKGIKVYN 1591
Score = 48.7 bits (116), Expect = 8e-06
Identities = 52/235 (22%), Positives = 96/235 (40%), Gaps = 41/235 (17%)
Query: 104 AKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSP--KTVWRARFSAITDKDIKAAMW 161
A + + +++ D D EGE I +++ N+ +P + R F +T + I A+
Sbjct: 698 AHEVDEILIGTDPDTEGEKIAWDIR-------NVLAPYGPNIKRIEFHEVTRRAILKAIK 750
Query: 162 NL--VKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLG 219
+ N +A+ V R+ D IG ++ + F+ + +S G QTP LG
Sbjct: 751 EARDIDENRVKAQIV--RRIEDRWIGFELSQKLWEVFEDRN-------LSAGRVQTPVLG 801
Query: 220 FCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVT 279
+ ++R+ + F L + L N + V++ S+ E V
Sbjct: 802 WIIQRYKE---FTESKVPFLGIILE-NDLTVTIEDSKD-----------------EVEVE 840
Query: 280 VVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRT 334
V V+ K + T ++R AS+ L + M++A+ L+ G P T
Sbjct: 841 VELVEEEEKERNPLPPYTTDTMLRDASAFLKLSAKETMKLAQDLFEAGLCVTPDT 895
>gnl|CDD|173597 PTZ00407, PTZ00407, DNA topoisomerase IA; Provisional.
Length = 805
Score = 58.8 bits (142), Expect = 6e-09
Identities = 103/519 (19%), Positives = 189/519 (36%), Gaps = 105/519 (20%)
Query: 110 LVLWLDCDKEGENICFEVMEAVRHQI-NINSPKTVWRARFSAITDKDIKAAMWNLVKPNI 168
++L D D+EGE I ++ ++ + P + RA +IT+ I+ AM
Sbjct: 128 IILATDPDREGELIAVHALQTIKRLYPKLKVPFS--RAYMHSITEDGIRKAMRER-HVEA 184
Query: 169 FE---ARSVDARQELDLRI----GCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFC 221
+ A + + R +D RI G + R ++ + S G QTP L
Sbjct: 185 CDYDLANAAETRHAMD-RIFGFLGSSVVRAA-----------NSQMRSIGRVQTPALILI 232
Query: 222 VERHDKIRTF--KPEPYWLLDLTLNLNG-------VAVSVTWSR----GHIFDKSTCNVF 268
ER DKI+ F + + + V++T R H ++
Sbjct: 233 NEREDKIKAFLESNKSTFEVQAMCQFPSPHGTTFSQVVTITPDRKGGASHWATEAEARRC 292
Query: 269 FK--AVEKEKHVTVVDVQSSTKSKTKP-QALNTVELMRVASSGLGMGPHHAMQIAERLYT 325
+ + +V S P Q + A+ L + L+
Sbjct: 293 LEQWKLNNCTGFSVPLEPKPQPSVVPPPQPFTMATAIAKANRQLKYSSEMVSGCLQDLFQ 352
Query: 326 QGYVSYPRTETTQYPENF--DLVAVLRQQ-------------ESSPDWGDHVREVLSNGI 370
G+++YPRT++T+ E+ D+ A ++++ S+ + G ++
Sbjct: 353 LGHITYPRTDSTRIDESALPDIYAAVKKEFGKEFLYRLEDRTVSAQE-GKGSKKTGKKRS 411
Query: 371 SKPRKGKD--VGD----HPPITPTKLATRTQ---LDGDAWRLYDYIVR-----HFIGTLC 416
+K +KG D VG+ H I PT + T + L +YD + R I
Sbjct: 412 TKQKKGADTPVGNVEDAHEAIRPTNIDTTGESLSLSPPTRAVYDLVRRNTLAVFMIPMKT 471
Query: 417 GDLVYTQKVAKFSVADEMFTMEAKYLLHPGFT--------GVMTWSAMKNESIPDFKPGD 468
+V T K S F ++ K ++ PG+T G + +E I + G
Sbjct: 472 EKIVATVKFTSGSGEKLEFELQGKRVVEPGWTRAFHKGDKGTTGPAEETDEDITAVEEGA 531
Query: 469 LI----------------------------PIQSVKMVERKTTPPDYLTESELISLMEKH 500
+ ++S ++ E + PP +E LI ++ +
Sbjct: 532 PVVPSLSQEEFKAIMNLRSQLGSGVQKGFFELRSPQVRENRPVPPLPHSEGTLIEELKNN 591
Query: 501 GIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLV 539
G+G ++ P+ + + R Y+ V R T +G +LV
Sbjct: 592 GVGRPSTYPMIVKTLLARGYIAVNPKGRCETTPVGRMLV 630
>gnl|CDD|173783 cd03363, TOPRIM_TopoIA_TopoI, TOPRIM_TopoIA_TopoI: The
topoisomerase-primase (TORPIM) domain found in members
of the type IA family of DNA topoisomerases (Topo IA)
similar to Escherichia coli DNA topoisomerase I. Type
IA DNA topoisomerases remove (relax) negative supercoils
in the DNA by: cleaving one strand of the DNA duplex,
covalently linking to the 5' phosphoryl end of the DNA
break and, allowing the other strand of the duplex to
pass through the gap. The TOPRIM domain has two
conserved motifs, one of which centers at a conserved
glutamate and the other one at two conserved aspartates
(DxD). For topoisomerases the conserved glutamate is
believed to act as a general base in strand joining and,
as a general acid in strand cleavage. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 123
Score = 42.5 bits (101), Expect = 6e-05
Identities = 30/106 (28%), Positives = 41/106 (38%), Gaps = 12/106 (11%)
Query: 57 CGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDC 116
GHI L VD + P K K+ L AK + + L D
Sbjct: 29 VGHIRDLPKKGLG-----VDGEDDGFEPKYVVIPG-KKKVVKELKKLAKKADEIYLATDP 82
Query: 117 DKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWN 162
D+EGE I + + E + K V R F+ IT + IK A+ N
Sbjct: 83 DREGEAIAWHLAEV------LKLKKNVKRVVFNEITKEAIKEALKN 122
>gnl|CDD|214695 smart00493, TOPRIM, topoisomerases, DnaG-type primases, OLD family
nucleases and RecR proteins.
Length = 75
Score = 38.8 bits (91), Expect = 4e-04
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 93 KLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRH 133
+ L AK E ++L D D+EGE I +E+ E ++
Sbjct: 34 SKEQIKLLKKLAKKAE-VILATDPDREGEAIAWELAELLKP 73
>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 = 36.9 bits (86), Expect = 0.003
Identities = 18/107 (16%), Positives = 34/107 (31%), Gaps = 37/107 (34%)
Query: 45 FGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEA 104
G ++ + + GH + L +K L
Sbjct: 17 AGGVLGGAVVATSGHALDL----------------------------EHIKE---LKKAL 45
Query: 105 KDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAI 151
K + ++L D D+EGE I +++E ++ I R S +
Sbjct: 46 KGAKEVILATDPDREGEAIALKLLELLKPLGPIG------RVEISEL 86
>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 = 35.1 bits (81), Expect = 0.009
Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 5/58 (8%)
Query: 91 TPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARF 148
K L + + +++ D D+EGE I ++E ++ K V R
Sbjct: 31 HALNKTRELLKRLLGEAKEVIIATDADREGEAIALRLLELLKSL-----GKKVRRLLL 83
>gnl|CDD|238590 cd01185, INT_Tn4399, Tn4399 and related integrases, DNA
breaking-rejoining enzymes, integrase/recombinases, N-
and C-terminal domains. This CD includes various
bacterial integrases, including cLV25, a Bacteroides
fragilis chromosomal transfer factor integrase similar
to the Bacteroides mobilizable transposon, Tn4399,
integrase.
Length = 299
Score = 34.2 bits (79), Expect = 0.17
Identities = 10/31 (32%), Positives = 13/31 (41%)
Query: 470 IPIQSVKMVERKTTPPDYLTESELISLMEKH 500
P K + + T +YLT EL L E
Sbjct: 112 NPFAKFKCKKEEETDREYLTPDELQKLAETP 142
>gnl|CDD|204620 pfam11267, DUF3067, Protein of unknown function (DUF3067). This
family of proteins has no known function.
Length = 99
Score = 28.8 bits (65), Expect = 2.1
Identities = 24/70 (34%), Positives = 31/70 (44%), Gaps = 14/70 (20%)
Query: 318 QIAERLYTQ---GYV---SYPRTETTQYPENFDLVAVLRQQESSPDWG--DHVREVLSNG 369
+ R+Y Q Y+ S+P +E Y E+ D VA WG + VRE L
Sbjct: 22 RRRGRIYLQVMWKYLEQASFPLSEEE-YREHLDAVAEYLN-----RWGQAEAVREWLETT 75
Query: 370 ISKPRKGKDV 379
KPR GK V
Sbjct: 76 REKPRLGKAV 85
>gnl|CDD|130262 TIGR01194, cyc_pep_trnsptr, cyclic peptide transporter. This model
describes cyclic peptide transporter in bacteria.
Bacteria have elaborate pathways for the production of
toxins and secondary metabolites. Many such compounds,
including syringomycin and pyoverdine are synthesized on
non-ribosomal templates consisting of a multienzyme
complex. On several occasions the proteins of the
complex and transporter protein are present on the same
operon. Often times these compounds cross the biological
membrane by specific transporters. Syringomycin is an
amphipathic, cylclic lipodepsipeptide when inserted into
host causes formation of channels, permeable to variety
of cations. On the other hand, pyoverdine is a cyclic
octa-peptidyl dihydroxyquinoline, which is efficient in
sequestering iron for uptake [Transport and binding
proteins, Amino acids, peptides and amines, Transport
and binding proteins, Other].
Length = 555
Score = 30.7 bits (69), Expect = 2.7
Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 134 QININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFT 189
++ I+ + + A AI + A ++++ IF A + L IGCA
Sbjct: 203 ELKIHGIRRLSFAH-GAIQESANNIADLHIIEILIFIAAENFGQLLFFLLIGCALF 257
>gnl|CDD|107343 cd06348, PBP1_ABC_ligand_binding_like_13, Type I periplasmic
ligand-binding domain of uncharacterized ABC (Atpase
Binding Cassette)-type active transport systems that are
predicted to be involved in uptake of amino acids,
peptides, or inorganic ions. This subgroup includes the
type I periplasmic ligand-binding domain of
uncharacterized ABC (Atpase Binding Cassette)-type
active transport systems that are predicted to be
involved in uptake of amino acids, peptides, or
inorganic ions. This subgroup has high sequence
similarity to members of the family of hydrophobic amino
acid transporters (HAAT), such as
leucine/isoleucine/valine binding protein (LIVBP);
however its ligand specificity has not been determined
experimentally.
Length = 344
Score = 30.1 bits (68), Expect = 2.8
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 239 LDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNT 298
L L + VAV +++ F S +F KA+ + + +V VQ+ T QA T
Sbjct: 130 LKLNPGIKRVAV--FYAQDDAFSVSETEIFQKALRDQG-LNLVTVQTFQTGDTDFQAQIT 186
>gnl|CDD|172536 PRK14042, PRK14042, pyruvate carboxylase subunit B; Provisional.
Length = 596
Score = 30.1 bits (67), Expect = 3.4
Identities = 36/144 (25%), Positives = 58/144 (40%), Gaps = 32/144 (22%)
Query: 332 PRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTK 389
PR + Q P +L L++Q ++ D D V + + PR KD+G P +TPT
Sbjct: 289 PRVQLYQVPGGMISNLYNQLKEQ-NALDKMDAVHKEI------PRVRKDLGYPPLVTPTS 341
Query: 390 LATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEM-FTMEAKYLLHPG-F 447
TQ I L G+ T + +E+ + KY PG
Sbjct: 342 QVVGTQA--------------VINVLTGERYKT-------ITNEVKLYCQGKYGTPPGKI 380
Query: 448 TGVMTWSAMKNESIPDFKPGDLIP 471
+ + A+ + + +PGDL+P
Sbjct: 381 SSALRKKAIGRTEVIEVRPGDLLP 404
>gnl|CDD|237634 PRK14179, PRK14179, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 284
Score = 29.3 bits (66), Expect = 5.2
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 7/36 (19%)
Query: 485 PDYLTESELISLMEK-------HGIGTDASIPVHIN 513
P+ +++ EL+ L+E+ HGI +P HIN
Sbjct: 70 PETISQEELLDLIERYNQDPTWHGILVQLPLPKHIN 105
>gnl|CDD|133427 cd05291, HicDH_like, L-2-hydroxyisocapronate dehydrogenases and
some bacterial L-lactate dehydrogenases.
L-2-hydroxyisocapronate dehydrogenase (HicDH) catalyzes
the conversion of a variety of 2-oxo carboxylic acids
with medium-sized aliphatic or aromatic side chains.
This subfamily is composed of HicDHs and some bacterial
L-lactate dehydrogenases (LDH). LDHs catalyze the last
step of glycolysis in which pyruvate is converted to
L-lactate. Bacterial LDHs can be non-allosteric or may
be activated by an allosteric effector such as
fructose-1,6-bisphosphate. Members of this subfamily
with known structures such as the HicDH of Lactobacillus
confusus, the non-allosteric LDH of Lactobacillus
pentosus, and the allosteric LDH of Bacillus
stearothermophilus, show that they exist as
homotetramers. The HicDH-like subfamily is part of the
NAD(P)-binding Rossmann fold superfamily, which includes
a wide variety of protein families including the
NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 306
Score = 29.0 bits (66), Expect = 6.6
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 7/54 (12%)
Query: 167 NIFEARSV-DARQELDLRIGCAFTRYQTKFFQGKYGDL-DASL--ISYGPCQTP 216
+I E ++ +A LDL AF K G Y D DA + I+ G Q P
Sbjct: 32 DINEEKAEGEA---LDLEDALAFLPSPVKIKAGDYSDCKDADIVVITAGAPQKP 82
>gnl|CDD|182633 PRK10669, PRK10669, putative cation:proton antiport protein;
Provisional.
Length = 558
Score = 28.9 bits (65), Expect = 9.1
Identities = 10/40 (25%), Positives = 18/40 (45%)
Query: 145 RARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRI 184
R R + ++ I+A + N I + +D + L L I
Sbjct: 450 RTRVDELRERGIRAVLGNAANEEIMQLAHLDCARWLLLTI 489
>gnl|CDD|173781 cd03361, TOPRIM_TopoIA_RevGyr, TopoIA_RevGyr : The
topoisomerase-primase (TORPIM) domain found in members
of the type IA family of DNA topoisomerases (Topo IA)
similar to the ATP-dependent reverse gyrase found in
archaea and thermophilic bacteria. Type IA DNA
topoisomerases remove (relax) negative supercoils in the
DNA by: cleaving one strand of the DNA duplex,
covalently linking to the 5' phosphoryl end of the DNA
break and, allowing the other strand of the duplex to
pass through the gap. Reverse gyrase is also able to
insert positive supercoils in the presence of ATP and
negative supercoils in the presence of AMPPNP. The
TOPRIM domain has two conserved motifs, one of which
centers at a conserved glutamate and the other one at
two conserved aspartates (DxD). For topoisomerases the
conserved glutamate is believed to act as a general base
in strand joining and, as a general acid in strand
cleavage. The DXD motif may co-ordinate Mg2+, a cofactor
required for full catalytic function.
Length = 170
Score = 28.0 bits (63), Expect = 9.6
Identities = 24/84 (28%), Positives = 36/84 (42%), Gaps = 12/84 (14%)
Query: 83 CPTEKRE----ATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININ 138
CP E L+ LA E + +++ D D EGE I ++V A+R
Sbjct: 94 CPRCGSENIDDKLETLEALRELALEV---DEVLIATDPDTEGEKIAWDVYLALR-----P 145
Query: 139 SPKTVWRARFSAITDKDIKAAMWN 162
K + RA F +T + I A+ N
Sbjct: 146 YNKNIKRAEFHEVTRRAILEALRN 169
>gnl|CDD|224425 COG1508, RpoN, DNA-directed RNA polymerase specialized sigma
subunit, sigma54 homolog [Transcription].
Length = 444
Score = 28.5 bits (64), Expect = 9.8
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 8/44 (18%)
Query: 156 IKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGK 199
++ A W L+K S++ R+E L++ YQ FF+G
Sbjct: 289 LQEAKW-LIK-------SLEQREETLLKVAEEIVEYQKAFFEGG 324
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
0.320 0.136 0.416
Gapped
Lambda K H
0.267 0.0755 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 28,474,526
Number of extensions: 2714131
Number of successful extensions: 2175
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2067
Number of HSP's successfully gapped: 55
Length of query: 562
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 460
Effective length of database: 6,413,494
Effective search space: 2950207240
Effective search space used: 2950207240
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 (21.8 bits)
S2: 62 (27.6 bits)