RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12983
(838 letters)
>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA
replication, recombination, and repair / Transcription /
Translation, ribosomal structure and biogenesis].
Length = 513
Score = 376 bits (968), Expect = e-121
Identities = 149/457 (32%), Positives = 236/457 (51%), Gaps = 19/457 (4%)
Query: 375 VGTVISADVSLSIPSILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGR 434
V + +V+LS + +F +L L+A+ D+GF + T IQ IP +L GR
Sbjct: 10 VKLKSAHNVALSRGEEKTPPEFASLGLS--PELLQALKDLGFEEPTPIQLAAIPLILAGR 67
Query: 435 DLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTRELSMQTFGVLKELMKY 494
D++G A+TG+GKT AFL+P ++ I R +I++PTREL++Q L++L K
Sbjct: 68 DVLGQAQTGTGKTAAFLLPLLQKILKSV--ERKYVSALILAPTRELAVQIAEELRKLGKN 125
Query: 495 HHHTY-GLIMGGASRQAEAQKLAKGINIIVATPGRLLDHLQNTPEFLYKNLQCLIIDEAD 553
++ GG S + + + L +G++I+VATPGRLLD ++ + ++ L++DEAD
Sbjct: 126 LGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRG-KLDLSGVETLVLDEAD 184
Query: 554 RILDIGFEEDMKQIVNLLPKRRQTMLFSATTTAKTETLTKLALKKEPVYIGVDDTKEEAT 613
R+LD+GF +D+++I+ LP RQT+LFSAT L + L PV I V K E T
Sbjct: 185 RMLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLND-PVEIEVSVEKLERT 243
Query: 614 VAGLEQGYVVCPSEK-RFLLLFTFLKKNRKKKVMVFFSSCMSVKFHHELLNYIDLPVMCI 672
+ ++Q Y+ SE+ + LL LK + +V+VF + V+ E L V +
Sbjct: 244 LKKIKQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAAL 303
Query: 673 HGKQKQMKRTTTFFQFCNAETGILLCTDVAARGLDIPAVDWIVQYDPPDDPKEYIHRVGR 732
HG Q +R +F + E +L+ TDVAARGLDIP V ++ YD P DP++Y+HR+GR
Sbjct: 304 HGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGR 363
Query: 733 TARGEGSSGHALLILRP-EELGFLRYLKQAKIPLNEFEFSWSKISDIQLQLEKLISKNYF 791
T R G G A+ + EE+ L+ +++ L S + + + KL+
Sbjct: 364 TGRA-GRKGVAISFVTEEEEVKKLKRIEKR---LERKLPSAVLLPLDEPEDAKLLKTT-- 417
Query: 792 LNMSGKEAFKAYVRAYDSHHLKQIFDIDTMDLGKDSK 828
+ + + LK LG
Sbjct: 418 ----RPGLEEESDISDEIKKLKSSKKALLRGLGVRFT 450
Score = 54.4 bits (131), Expect = 2e-07
Identities = 26/75 (34%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 175 ERRQTMLFSATTTAKTETLTKLALKKEPVYIGVDDTKEEATVAGLEQGYVVCPSEK-RFL 233
RQT+LFSAT L + L PV I V K E T+ ++Q Y+ SE+ +
Sbjct: 204 PDRQTLLFSATMPDDIRELARRYLND-PVEIEVSVEKLERTLKKIKQFYLEVESEEEKLE 262
Query: 234 LLFTFLKKNHIGEIV 248
LL LK G ++
Sbjct: 263 LLLKLLKDEDEGRVI 277
>gnl|CDD|238167 cd00268, DEADc, DEAD-box helicases. A diverse family of proteins
involved in ATP-dependent RNA unwinding, needed in a
variety of cellular processes including splicing,
ribosome biogenesis and RNA degradation. The name
derives from the sequence of the Walker B motif (motif
II). This domain contains the ATP- binding region.
Length = 203
Score = 251 bits (643), Expect = 2e-78
Identities = 92/208 (44%), Positives = 135/208 (64%), Gaps = 6/208 (2%)
Query: 396 FEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAV 455
FE L + L+ I +GF K T IQAR IPPLL GRD++G A+TGSGKT AFL+P +
Sbjct: 1 FEELG--LSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPIL 58
Query: 456 ELIYNLKFMPRNGTGIIIISPTRELSMQTFGVLKELMKYHHHTYGLIMGGASRQAEAQKL 515
E + ++G +I++PTREL++Q V ++L K+ + +I GG S + +KL
Sbjct: 59 EKLDPSP--KKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKL 116
Query: 516 AKGINIIVATPGRLLDHLQNTPEFLYKNLQCLIIDEADRILDIGFEEDMKQIVNLLPKRR 575
+G +I+VATPGRLLD L+ + ++ L++DEADR+LD+GFE+ +++I+ LLPK R
Sbjct: 117 KRGPHIVVATPGRLLDLLERG-KLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDR 175
Query: 576 QTMLFSATTTAKTETLTKLALKKEPVYI 603
QT+LFSAT + L + L+ PV I
Sbjct: 176 QTLLFSATMPKEVRDLARKFLRN-PVRI 202
Score = 34.8 bits (81), Expect = 0.10
Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 175 ERRQTMLFSATTTAKTETLTKLALKKEPVYI 205
+ RQT+LFSAT + L + L+ PV I
Sbjct: 173 KDRQTLLFSATMPKEVRDLARKFLRN-PVRI 202
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 241 bits (617), Expect = 2e-71
Identities = 135/380 (35%), Positives = 211/380 (55%), Gaps = 27/380 (7%)
Query: 394 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVP 453
T F L+ + E+ L+A+ D G+T+ T IQA IPP L+GRD++GSA TG+GKT AFL+P
Sbjct: 1 TTFSELE--LDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLP 58
Query: 454 AVELIYNLKFMPRNGTG---IIIISPTRELSMQTFGVLKELMKYHHHTYGLIMGGASRQA 510
A L + L F PR +G I+I++PTREL+MQ +EL K+ H I GG +
Sbjct: 59 A--LQHLLDF-PRRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMN 115
Query: 511 EAQKLAKGINIIVATPGRLLDHLQNTPEFLYKNLQCLIIDEADRILDIGFEEDMKQIVNL 570
A+ ++ +I+VATPGRLL +++ F + ++ LI+DEADR+LD+GF +D++ I
Sbjct: 116 HAEVFSENQDIVVATPGRLLQYIKEE-NFDCRAVETLILDEADRMLDMGFAQDIETIAAE 174
Query: 571 LPKRRQTMLFSATTTAKTETLTKLA--LKKEPVYIGVDDTKEEATVAGLEQGYVVCPS-E 627
R+QT+LFSAT + + + A L +PV + + ++ E + Q Y E
Sbjct: 175 TRWRKQTLLFSATL--EGDAVQDFAERLLNDPVEVEAEPSRRER--KKIHQWYYRADDLE 230
Query: 628 KRFLLLFTFLKKNRKKKVMVFFSSCMSVKFHHELLNYI---DLPVMCIHGKQKQMKRTTT 684
+ LL LK+ + +VF + V HEL ++ + + G+ Q KR
Sbjct: 231 HKTALLCHLLKQPEVTRSIVFVRTRERV---HELAGWLRKAGINCCYLEGEMVQAKRNEA 287
Query: 685 FFQFCNAETGILLCTDVAARGLDIPAVDWIVQYDPPDDPKEYIHRVGRTARGEGSSGHAL 744
+ + +L+ TDVAARG+DI V ++ +D P Y+HR+GRT R G G A+
Sbjct: 288 IKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRA-GRKGTAI 346
Query: 745 LILRPEELGFL----RYLKQ 760
++ + L RY+++
Sbjct: 347 SLVEAHDHLLLGKIERYIEE 366
Score = 31.5 bits (72), Expect = 1.8
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 4/40 (10%)
Query: 176 RRQTMLFSATTTAKTETLTKLA--LKKEPVYIGVDDTKEE 213
R+QT+LFSAT + + + A L +PV + + ++ E
Sbjct: 178 RKQTLLFSATL--EGDAVQDFAERLLNDPVEVEAEPSRRE 215
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 237 bits (606), Expect = 1e-69
Identities = 121/350 (34%), Positives = 197/350 (56%), Gaps = 17/350 (4%)
Query: 408 LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRN 467
L + ++G+T+MT IQA+++P +L G+D++ AKTGSGKT AF + L+ L + R
Sbjct: 16 LANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAF---GLGLLQKLD-VKRF 71
Query: 468 GTGIIIISPTRELSMQTFGVLKELMKYHHHTYGLIM-GGASRQAEAQKLAKGINIIVATP 526
+++ PTREL+ Q ++ L ++ + L + GG + L G +IIV TP
Sbjct: 72 RVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTP 131
Query: 527 GRLLDHLQNTPEFLYKNLQCLIIDEADRILDIGFEEDMKQIVNLLPKRRQTMLFSATTTA 586
GR+LDHL+ L L L++DEADR+LD+GF++ + I+ P RRQT+LFSAT
Sbjct: 132 GRILDHLRKGTLDL-DALNTLVLDEADRMLDMGFQDAIDAIIRQAPARRQTLLFSATYPE 190
Query: 587 KTETLTKLALKKEPVYIGVDDTKEEATVAGLEQGYVVCPSEKRFLLLFTFLKKNRKKKVM 646
+++ +++PV + V+ T + + EQ + ++R L L ++ + +
Sbjct: 191 GIAAISQ-RFQRDPVEVKVESTHDLPAI---EQRFYEVSPDERLPALQRLLLHHQPESCV 246
Query: 647 VFFSS---CMSVKFHHELLNYIDLPVMCIHGKQKQMKRTTTFFQFCNAETGILLCTDVAA 703
VF ++ C V + LN + +HG +Q R +F N +L+ TDVAA
Sbjct: 247 VFCNTKKECQEVA---DALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAA 303
Query: 704 RGLDIPAVDWIVQYDPPDDPKEYIHRVGRTARGEGSSGHALLILRPEELG 753
RGLDI A++ ++ Y+ DP+ ++HR+GRT R GS G AL ++ PEE+
Sbjct: 304 RGLDIKALEAVINYELARDPEVHVHRIGRTGRA-GSKGLALSLVAPEEMQ 352
Score = 35.5 bits (83), Expect = 0.12
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 175 ERRQTMLFSATTTAKTETLTKLALKKEPVYIGVDDTKEEATVAGLEQGYVVCPSEKRFLL 234
RRQT+LFSAT +++ +++PV + V+ T + + EQ + ++R
Sbjct: 177 ARRQTLLFSATYPEGIAAISQ-RFQRDPVEVKVESTHDLPAI---EQRFYEVSPDERLPA 232
Query: 235 LFTFLKK 241
L L
Sbjct: 233 LQRLLLH 239
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 217 bits (555), Expect = 1e-61
Identities = 134/404 (33%), Positives = 225/404 (55%), Gaps = 43/404 (10%)
Query: 408 LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRN 467
LK++ + GFT+ T IQ + P L GRD++G A+TGSGKTLAFL+PA+ I N + + R
Sbjct: 142 LKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHI-NAQPLLRY 200
Query: 468 GTGII--IISPTRELSMQ------TFGVLKELMKYHHHTYGLIMGGASRQAEAQKLAKGI 519
G G I +++PTREL+ Q FG ++ +T + GG ++ + L +G+
Sbjct: 201 GDGPIVLVLAPTRELAEQIREQCNKFGASSKI----RNT--VAYGGVPKRGQIYALRRGV 254
Query: 520 NIIVATPGRLLDHLQNTPEFLYKNLQ---CLIIDEADRILDIGFEEDMKQIVNLLPKRRQ 576
I++A PGRL+D L++ NL+ L++DEADR+LD+GFE +++IV+ + RQ
Sbjct: 255 EILIACPGRLIDFLESN----VTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQIRPDRQ 310
Query: 577 TMLFSATTTAKTETLTKLALKKEPVYIGVDDTKEEATVAGLEQGYVVCPSEKRFLLLFTF 636
T+++SAT + ++L + K+EPV++ V A ++ +VV EKR L
Sbjct: 311 TLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEHEKR-GKLKML 369
Query: 637 LKK--NRKKKVMVFFSSCMSVKFHHELLNYIDLPVMCIHGKQKQMKRTTTFFQFCNAETG 694
L++ K+++F + F + L P +CIHG +KQ +RT +F ++
Sbjct: 370 LQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSP 429
Query: 695 ILLCTDVAARGLDIPAVDWIVQYDPPDDPKEYIHRVGRTARGEGSSGHALLILRPEEL-- 752
I++ TDVA+RGLD+ V +++ +D P+ ++Y+HR+GRT R G+ G + L P++
Sbjct: 430 IMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRA-GAKGASYTFLTPDKYRL 488
Query: 753 --GFLRYLKQAKIPLNEFEFSWSKISDIQLQLEKLISKNYFLNM 794
++ L++AK P + +LEKL ++
Sbjct: 489 ARDLVKVLREAKQP-------------VPPELEKLSNERSNGTE 519
Score = 32.4 bits (74), Expect = 1.0
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 177 RQTMLFSATTTAKTETLTKLALKKEPVYIGVDDTKEEATVAGLEQGYVVCPSEKRFLLLF 236
RQT+++SAT + ++L + K+EPV++ V A ++ +VV EKR L
Sbjct: 309 RQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEHEKR-GKLK 367
Query: 237 TFLKK 241
L++
Sbjct: 368 MLLQR 372
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 208 bits (530), Expect = 4e-59
Identities = 124/355 (34%), Positives = 200/355 (56%), Gaps = 15/355 (4%)
Query: 408 LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMP-- 465
L+A+A+ G+ + T IQ + IP +LEGRDL+ SA+TG+GKT F +P ++ + +
Sbjct: 13 LRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKG 72
Query: 466 RNGTGIIIISPTRELSMQTFGVLKELMKYHHHTYGLIMGGASRQAEAQKLAKGINIIVAT 525
R +I++PTREL+ Q +++ KY + ++ GG S + KL G++++VAT
Sbjct: 73 RRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGGVDVLVAT 132
Query: 526 PGRLLD--HLQNTPEFLYKNLQCLIIDEADRILDIGFEEDMKQIVNLLPKRRQTMLFSAT 583
PGRLLD H QN + ++ L++DEADR+LD+GF D+++++ LP +RQ +LFSAT
Sbjct: 133 PGRLLDLEH-QNAVKL--DQVEILVLDEADRMLDMGFIHDIRRVLAKLPAKRQNLLFSAT 189
Query: 584 TTAKTETLT-KLALKKEPVYIGVDDTKEEATVAGLEQG-YVVCPSEKRFLLLFTFLKKNR 641
+ + L KL + + +T E + Q + V KR LL + K
Sbjct: 190 FSDDIKALAEKLLHNPLEIEVARRNTASEQ----VTQHVHFVDKKRKRELLSQ-MIGKGN 244
Query: 642 KKKVMVFFSSCMSVKFHHELLNYIDLPVMCIHGKQKQMKRTTTFFQFCNAETGILLCTDV 701
++V+VF + E LN + IHG + Q RT F + + +L+ TD+
Sbjct: 245 WQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDI 304
Query: 702 AARGLDIPAVDWIVQYDPPDDPKEYIHRVGRTARGEGSSGHALLILRPEELGFLR 756
AARGLDI + +V Y+ P+ P++Y+HR+GRT R ++G AL ++ +E LR
Sbjct: 305 AARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAA-ATGEALSLVCVDEHKLLR 358
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 194 bits (495), Expect = 9e-58
Identities = 77/173 (44%), Positives = 113/173 (65%), Gaps = 5/173 (2%)
Query: 420 TEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTRE 479
T IQA+ IP +L G+D++ A TGSGKTLAFL+P ++ + K P+ ++++PTRE
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQ----ALVLAPTRE 56
Query: 480 LSMQTFGVLKELMKYHHHTYGLIMGGASRQAEAQKLAKG-INIIVATPGRLLDHLQNTPE 538
L+ Q + LK+L K L+ GG S + +A+KL KG +I+V TPGRLLD L+
Sbjct: 57 LAEQIYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKL 116
Query: 539 FLYKNLQCLIIDEADRILDIGFEEDMKQIVNLLPKRRQTMLFSATTTAKTETL 591
L KNL+ L++DEA R+LD+GF +D+++I++ LP RQ +L SAT E L
Sbjct: 117 KLLKNLKLLVLDEAHRLLDMGFGDDLEEILSRLPPDRQILLLSATLPRNLEDL 169
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 193 bits (493), Expect = 3e-54
Identities = 125/374 (33%), Positives = 193/374 (51%), Gaps = 42/374 (11%)
Query: 391 LSSTQFE--ALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTL 448
L+ +F AL +V ++A+ GF T IQA +P L GRD+ G A+TG+GKT+
Sbjct: 5 LTEQKFSDFALHPQV----VEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTM 60
Query: 449 AFLV---------PAVELIYNLKFMPRNGTGIIIISPTRELSMQTFGVLKELMKYHHHTY 499
AFL PA E PR +I++PTREL++Q + L +
Sbjct: 61 AFLTATFHYLLSHPAPED--RKVNQPR----ALIMAPTRELAVQIHADAEPLAQATGLKL 114
Query: 500 GLIMGGASRQAEAQKLAKGINIIVATPGRLLDHL-QNTPEFLYKNLQCLIIDEADRILDI 558
GL GG + + L G++I++ T GRL+D+ QN +Q +++DEADR+ D+
Sbjct: 115 GLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNH--INLGAIQVVVLDEADRMFDL 172
Query: 559 GFEEDMKQIVNLLP--KRRQTMLFSATTTAKTETLTKLALK--KEPVYIGVDDTKEEATV 614
GF +D++ + +P +R MLFSAT + + +LA + P Y+ V+ ++
Sbjct: 173 GFIKDIRWLFRRMPPANQRLNMLFSATLSYRVR---ELAFEHMNNPEYVEVEPEQKTGHR 229
Query: 615 AGLEQGYVVCPS-EKRFLLLFTFLKKNRKKKVMVFFS---SCMSVKFHHELLNYIDLPVM 670
E Y PS E++ LL T +++ + ++F + C + H L V
Sbjct: 230 IKEELFY---PSNEEKMRLLQTLIEEEWPDRAIIFANTKHRCEEIWGH---LAADGHRVG 283
Query: 671 CIHGKQKQMKRTTTFFQFCNAETGILLCTDVAARGLDIPAVDWIVQYDPPDDPKEYIHRV 730
+ G Q KR +F + IL+ TDVAARGL IPAV + YD PDD ++Y+HR+
Sbjct: 284 LLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRI 343
Query: 731 GRTARGEGSSGHAL 744
GRT R G+SGH++
Sbjct: 344 GRTGRA-GASGHSI 356
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 189 bits (482), Expect = 2e-52
Identities = 122/359 (33%), Positives = 188/359 (52%), Gaps = 23/359 (6%)
Query: 394 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVP 453
T+F + + AI D+GF T IQA+ + L G D +G A+TG+GKT AFL+
Sbjct: 87 TRFHDFN--LAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLIS 144
Query: 454 AVELIYNL-----KFM--PRNGTGIIIISPTRELSMQTFGVLKELMKYHHHTYGLIMGGA 506
+ + ++M PR +II+PTREL +Q L KY +GG
Sbjct: 145 IINQLLQTPPPKERYMGEPR----ALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGM 200
Query: 507 SRQAEAQKL-AKGINIIVATPGRLLDHLQNTPEFLYKNLQCLIIDEADRILDIGFEEDMK 565
+ ++L A+ +I+VATPGRLLD Q E ++ +++DEADR+LD+GF ++
Sbjct: 201 DFDKQLKQLEARFCDILVATPGRLLDFNQRG-EVHLDMVEVMVLDEADRMLDMGFIPQVR 259
Query: 566 QIVNLLPKR--RQTMLFSATTTAKTETLTKLALKKEPVYIGVDDTKEEATVAGLEQG-YV 622
QI+ P++ RQT+LFSAT T L K +P + ++ E +EQ Y
Sbjct: 260 QIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTT-DPAIVEIE--PENVASDTVEQHVYA 316
Query: 623 VCPSEKRFLLLFTFLKKNRKKKVMVFFSSCMSVKFHHELLNYIDLPVMCIHGKQKQMKRT 682
V S+K + LL+ + +N ++VMVF + V+ E L + + G Q KR
Sbjct: 317 VAGSDK-YKLLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRI 375
Query: 683 TTFFQFCNAETGILLCTDVAARGLDIPAVDWIVQYDPPDDPKEYIHRVGRTARGEGSSG 741
T F + +L+ TDVA RG+ I + ++ + P+DP +Y+HR+GRT R G+SG
Sbjct: 376 KTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRA-GASG 433
Score = 30.3 bits (68), Expect = 4.9
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 5/75 (6%)
Query: 175 ERRQTMLFSATTTAKTETLTKLALKKEPVYIGVDDTKEEATVAGLEQG-YVVCPSEKRFL 233
E RQT+LFSAT T L K +P + ++ E +EQ Y V S+K +
Sbjct: 269 EERQTLLFSATFTDDVMNLAKQWT-TDPAIVEIE--PENVASDTVEQHVYAVAGSDK-YK 324
Query: 234 LLFTFLKKNHIGEIV 248
LL+ + +N ++
Sbjct: 325 LLYNLVTQNPWERVM 339
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 190 bits (485), Expect = 7e-52
Identities = 117/342 (34%), Positives = 187/342 (54%), Gaps = 23/342 (6%)
Query: 415 GFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFM-------PRN 467
GFT+ T IQA T+P L G D+ G A+TG+GKTLAFLV + + + + PR
Sbjct: 28 GFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPR- 86
Query: 468 GTGIIIISPTRELSMQTFGVLKELMKYHHH---TYGLIMGGASRQAEAQKLAKGINIIVA 524
+I++PTREL++Q + K+ +K+ + L+ GG + + L +G+++I+A
Sbjct: 87 ---ALILAPTRELAIQ---IHKDAVKFGADLGLRFALVYGGVDYDKQRELLQQGVDVIIA 140
Query: 525 TPGRLLDHLQNTPEFLYKNLQCLIIDEADRILDIGFEEDMKQIVNLLPKR--RQTMLFSA 582
TPGRL+D+++ + ++DEADR+ D+GF +D++ ++ +P+R RQT+LFSA
Sbjct: 141 TPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMPERGTRQTLLFSA 200
Query: 583 TTTAKTETLTKLALKKEPVYIGVDDTKEEATVAGLEQGYVVCPSEKRFLLLFTFLKKNRK 642
T + + L + EP + V+ E T A + Q E++ LL L ++
Sbjct: 201 TLSHRVLELAYEHMN-EPEKLVVE--TETITAARVRQRIYFPADEEKQTLLLGLLSRSEG 257
Query: 643 KKVMVFFSSCMSVKFHHELLNYIDLPVMCIHGKQKQMKRTTTFFQFCNAETGILLCTDVA 702
+ MVF ++ V+ L V + G Q KR + +F + IL+ TDVA
Sbjct: 258 ARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVA 317
Query: 703 ARGLDIPAVDWIVQYDPPDDPKEYIHRVGRTARGEGSSGHAL 744
ARGL I V ++ YD P D ++Y+HR+GRTAR G G A+
Sbjct: 318 ARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTAR-LGEEGDAI 358
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 185 bits (472), Expect = 1e-51
Identities = 118/363 (32%), Positives = 194/363 (53%), Gaps = 14/363 (3%)
Query: 396 FEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAV 455
F+ALK + E+ L+ I GF K + IQ R I P+L+G D +G A++G+GKT F++ A+
Sbjct: 30 FDALK--LNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAAL 87
Query: 456 ELI-YNLKFMPRNGTGIIIISPTRELSMQTFGVLKELMKYHHHTYGLIMGGASRQAEAQK 514
+LI Y+L N +I++PTREL+ Q V+ L Y +GG + + K
Sbjct: 88 QLIDYDL-----NACQALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINK 142
Query: 515 LAKGINIIVATPGRLLDHLQNTPEFLYKNLQCLIIDEADRILDIGFEEDMKQIVNLLPKR 574
L G++++V TPGR+ D + + +L+ I+DEAD +L GF+ + + LP
Sbjct: 143 LKAGVHMVVGTPGRVYDMI-DKRHLRVDDLKLFILDEADEMLSRGFKGQIYDVFKKLPPD 201
Query: 575 RQTMLFSATTTAKTETLTKLALKKEPVYIGVDDTKEEATVAGLEQGYVVCPSEK-RFLLL 633
Q LFSAT + LT ++P I V K+E T+ G+ Q YV E+ +F L
Sbjct: 202 VQVALFSATMPNEILELTT-KFMRDPKRILV--KKDELTLEGIRQFYVAVEKEEWKFDTL 258
Query: 634 FTFLKKNRKKKVMVFFSSCMSVKFHHELLNYIDLPVMCIHGKQKQMKRTTTFFQFCNAET 693
+ + +++ ++ V + + ++ D V C+HG Q R +F + T
Sbjct: 259 CDLYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGST 318
Query: 694 GILLCTDVAARGLDIPAVDWIVQYDPPDDPKEYIHRVGRTARGEGSSGHALLILRPEELG 753
+L+ TD+ ARG+D+ V ++ YD P P+ YIHR+GR+ R G G A+ + P+++
Sbjct: 319 RVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRF-GRKGVAINFVTPDDIE 377
Query: 754 FLR 756
L+
Sbjct: 378 QLK 380
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 189 bits (482), Expect = 3e-51
Identities = 135/420 (32%), Positives = 217/420 (51%), Gaps = 19/420 (4%)
Query: 408 LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRN 467
L+A+ D+G+ K + IQA IP LL GRD++G A+TGSGKT AF +P L++NL +
Sbjct: 18 LEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLP---LLHNLDPELK- 73
Query: 468 GTGIIIISPTRELSMQTFGVLKELMKYHHHTYGL----IMGGASRQAEAQKLAKGINIIV 523
I++++PTREL++Q V + + + H G+ + GG + + L +G I+V
Sbjct: 74 APQILVLAPTRELAVQ---VAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVV 130
Query: 524 ATPGRLLDHLQNTPEFLYKNLQCLIIDEADRILDIGFEEDMKQIVNLLPKRRQTMLFSAT 583
TPGRLLDHL+ L L L++DEAD +L +GF ED++ I+ +P+ QT LFSAT
Sbjct: 131 GTPGRLLDHLKRGTLDL-SKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGHQTALFSAT 189
Query: 584 TTAKTETLTKLALKKEPVYIGVDDTKEEATVAGLEQGYVVCPSEKRFLLLFTFLKKNRKK 643
+T+ KEP + + + T + Q Y ++ L FL+
Sbjct: 190 MPEAIRRITR-RFMKEPQEVRIQSSV--TTRPDISQSYWTVWGMRKNEALVRFLEAEDFD 246
Query: 644 KVMVFFSSCMSVKFHHELLNYIDLPVMCIHGKQKQMKRTTTFFQFCNAETGILLCTDVAA 703
++F + + E L ++G Q R T + + IL+ TDVAA
Sbjct: 247 AAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAA 306
Query: 704 RGLDIPAVDWIVQYDPPDDPKEYIHRVGRTARGEGSSGHALLILRPEELGFLRYLKQA-K 762
RGLD+ + +V YD P D + Y+HR+GRT R G +G ALL + E LR +++ K
Sbjct: 307 RGLDVERISLVVNYDIPMDSESYVHRIGRTGRA-GRAGRALLFVENRERRLLRNIERTMK 365
Query: 763 IPLNEFEFSWSKISDIQLQLEKLISK-NYFLNMSGKEAFKAYVRAYDSHHLKQIFDIDTM 821
+ + E E +++ + +LEK +K L S + ++A + + D++T+
Sbjct: 366 LTIPEVELPNAELLG-KRRLEKFAAKVQQQLESSDLDQYRALLAKIQPTAEGEELDLETL 424
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 158 bits (402), Expect = 2e-44
Identities = 80/203 (39%), Positives = 116/203 (57%), Gaps = 9/203 (4%)
Query: 411 IADMGFTKMTEIQARTIPPLLEG-RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGT 469
I GF + Q I LL G RD++ +A TGSGKTLA L+PA+E + G
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKR-----GKGG 55
Query: 470 GIIIISPTRELSMQTFGVLKELMKYHHHTYGLIMGGASRQAEAQKLAKG-INIIVATPGR 528
++++ PTREL+ Q LK+L + GG S++ + +KL G +I+V TPGR
Sbjct: 56 RVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGR 115
Query: 529 LLDHLQNTPEFLYKNLQCLIIDEADRILDIGFEEDMKQIVNLLPKRRQTMLFSATTTAKT 588
LLD L+N L N+ +I+DEA R+LD GF + +++++ LLPK Q +L SAT +
Sbjct: 116 LLDLLENDKLSL-SNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEI 174
Query: 589 ETLTKLALKKEPVYIGVDDTKEE 611
E L +L L +PV+I V T E
Sbjct: 175 ENLLELFL-NDPVFIDVGFTPLE 196
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 138 bits (349), Expect = 6e-38
Identities = 64/150 (42%), Positives = 92/150 (61%), Gaps = 7/150 (4%)
Query: 434 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTRELSMQTFGVLKELMK 493
RD++ +A TGSGKTLA L+P +EL+ +LK +++++PTREL+ Q LKEL
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQ-----VLVLAPTRELANQVAERLKELFG 55
Query: 494 YHHHTYGLIMGGASRQAEAQKLAKGINIIVATPGRLLDHLQNTPEFLYKNLQCLIIDEAD 553
G ++GG S + + + L+ +I+V TPGRLLD L+ L K L LI+DEA
Sbjct: 56 EGIKV-GYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSL-KKLDLLILDEAH 113
Query: 554 RILDIGFEEDMKQIVNLLPKRRQTMLFSAT 583
R+L+ GF +I+ LPK RQ +L SAT
Sbjct: 114 RLLNQGFGLLGLKILLKLPKDRQVLLLSAT 143
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 143 bits (363), Expect = 4e-36
Identities = 117/393 (29%), Positives = 187/393 (47%), Gaps = 35/393 (8%)
Query: 386 SIPSILSSTQFEALKGKV------------------C---ENTLKAIADMGFTKMTEIQA 424
S LSS+Q E L+ K+ C L + G+ T IQ
Sbjct: 90 GSTSGLSSSQAELLRRKLEIHVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQM 149
Query: 425 RTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVE---LIYNLKFMPRNGTGIIIISPTRELS 481
+ IP L GR L+ SA TGSGKT +FLVP + I + + ++++PTREL
Sbjct: 150 QAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELC 209
Query: 482 MQTFGVLKELMKYHHHTYGLIMGGASRQAEAQKLAKGINIIVATPGRLLDHLQNTPEFLY 541
+Q K L K L++GG + + ++ +G+ +IV TPGRL+D L +
Sbjct: 210 VQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKH-DIEL 268
Query: 542 KNLQCLIIDEADRILDIGFEEDMKQIVNLLPKRRQTMLFSATTTAKTETLTKLALKKEPV 601
N+ L++DE D +L+ GF + + QI L + Q +LFSAT + + E +L K+ +
Sbjct: 269 DNVSVLVLDEVDCMLERGFRDQVMQIFQALSQ-PQVLLFSATVSPEVEKFAS-SLAKDII 326
Query: 602 YIGVDDTKEEATVAGLEQGYVVCPSEKRFLLLFTFLK-KNR-KKKVMVFFSSCMSVKFHH 659
I + ++Q + ++++ LF LK K K +VF SS +
Sbjct: 327 LISIG--NPNRPNKAVKQLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLA 384
Query: 660 ELLNYID-LPVMCIHGKQKQMK-RTTTFFQFCNAETGILLCTDVAARGLDIPAVDWIVQY 717
+ + L + IHG +K MK R F E +++ T V RG+D+ V ++ +
Sbjct: 385 NAITVVTGLKALSIHG-EKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIF 443
Query: 718 DPPDDPKEYIHRVGRTARGEGSSGHALLILRPE 750
D P+ KEYIH++GR +R G G A++ + E
Sbjct: 444 DMPNTIKEYIHQIGRASR-MGEKGTAIVFVNEE 475
>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
with DEXDc-, DEAD-, and DEAH-box proteins, yeast
initiation factor 4A, Ski2p, and Hepatitis C virus NS3
helicases; this domain is found in a wide variety of
helicases and helicase related proteins; may not be an
autonomously folding unit, but an integral part of the
helicase; 4 helicase superfamilies at present according
to the organization of their signature motifs; all
helicases share the ability to unwind nucleic acid
duplexes with a distinct directional polarity; they
utilize the free energy from nucleoside triphosphate
hydrolysis to fuel their translocation along DNA,
unwinding the duplex in the process.
Length = 131
Score = 114 bits (287), Expect = 1e-29
Identities = 43/132 (32%), Positives = 64/132 (48%), Gaps = 4/132 (3%)
Query: 617 LEQGYVVCPSEKRFLLLFTFLKK--NRKKKVMVFFSSCMSVKFHHELLNYIDLPVMCIHG 674
++Q + EK L LK+ + KV++F S + ELL + V +HG
Sbjct: 2 IKQYVLPVEDEK-LEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHG 60
Query: 675 KQKQMKRTTTFFQFCNAETGILLCTDVAARGLDIPAVDWIVQYDPPDDPKEYIHRVGRTA 734
Q +R F E +L+ TDV ARG+D+P V ++ YD P P Y+ R+GR
Sbjct: 61 DGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAG 120
Query: 735 RGEGSSGHALLI 746
R G G A+L+
Sbjct: 121 RA-GQKGTAILL 131
>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain. The
Prosite family is restricted to DEAD/H helicases,
whereas this domain family is found in a wide variety of
helicases and helicase related proteins. It may be that
this is not an autonomously folding unit, but an
integral part of the helicase.
Length = 78
Score = 99 bits (250), Expect = 2e-25
Identities = 29/76 (38%), Positives = 44/76 (57%)
Query: 660 ELLNYIDLPVMCIHGKQKQMKRTTTFFQFCNAETGILLCTDVAARGLDIPAVDWIVQYDP 719
+LL + V +HG Q +R F N ++ +L+ TDVA RG+D+P V+ ++ YD
Sbjct: 1 KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60
Query: 720 PDDPKEYIHRVGRTAR 735
P +P YI R+GR R
Sbjct: 61 PWNPASYIQRIGRAGR 76
>gnl|CDD|220074 pfam08925, DUF1907, Domain of Unknown Function (DUF1907). The
structure of this domain displays an
alpha-beta-beta-alpha four layer topology, with an
HxHxxxxxxxxxH motif that coordinates a zinc ion, and an
acetate anion at a site that likely supports the
enzymatic activity of an ester hydrolase.
Length = 283
Score = 103 bits (260), Expect = 2e-24
Identities = 39/127 (30%), Positives = 62/127 (48%), Gaps = 39/127 (30%)
Query: 256 QVIKIKVQTRIGKEDFVTSVRNVLAAHYKDQPVGLGGVILIENAPAKHHVMPDFSTTPLE 315
+V+K+ + R G+++FV+ +R L HY D+PVGLGGV LI+ AK HVMP+F
Sbjct: 150 KVLKVTAKKRTGEKNFVSCIRKGLEEHYGDKPVGLGGVFLIKKGKAKQHVMPEF------ 203
Query: 316 TKDQLNVRSNYIGLGGVILIENAPAKHHVMPDFSTTPLETKDQLNEWLVFKDLTPPLISV 375
S P+ T +++N WL F +++ PL+ +
Sbjct: 204 ---------------------------------SKCPINTDEEVNNWLKFYEMSAPLVCL 230
Query: 376 GTVISAD 382
G ++S D
Sbjct: 231 GVLVSKD 237
Score = 43.4 bits (103), Expect = 3e-04
Identities = 15/32 (46%), Positives = 18/32 (56%)
Query: 142 VLNQGLGKYFKEVSVSFTECPNLTSHPFNLTS 173
VL GL F+ VSVS +CP+L PF L
Sbjct: 1 VLQSGLKANFETVSVSVVDCPDLRKPPFGLAV 32
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 94.2 bits (235), Expect = 2e-23
Identities = 32/80 (40%), Positives = 45/80 (56%)
Query: 656 KFHHELLNYIDLPVMCIHGKQKQMKRTTTFFQFCNAETGILLCTDVAARGLDIPAVDWIV 715
+ ELL + + V +HG Q +R +F N + +L+ TDVA RGLD+P VD ++
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60
Query: 716 QYDPPDDPKEYIHRVGRTAR 735
YD P P YI R+GR R
Sbjct: 61 IYDLPWSPASYIQRIGRAGR 80
>gnl|CDD|222474 pfam13959, DUF4217, Domain of unknown function (DUF4217). This
short domain is found at the C-terminus of many helicase
proteins.
Length = 64
Score = 73.6 bits (182), Expect = 2e-16
Identities = 26/49 (53%), Positives = 35/49 (71%)
Query: 777 DIQLQLEKLISKNYFLNMSGKEAFKAYVRAYDSHHLKQIFDIDTMDLGK 825
+IQLQLEKL+ K+ L ++AF +YVRAY SH LK IF++ +DLG
Sbjct: 1 NIQLQLEKLVLKDRELKELAQKAFVSYVRAYASHSLKSIFNVKKLDLGH 49
>gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ. The
ATP-dependent DNA helicase RecQ of E. coli is about 600
residues long. This model represents bacterial proteins
with a high degree of similarity in domain architecture
and in primary sequence to E. coli RecQ. The model
excludes eukaryotic and archaeal proteins with RecQ-like
regions, as well as more distantly related bacterial
helicases related to RecQ [DNA metabolism, DNA
replication, recombination, and repair].
Length = 591
Score = 67.8 bits (166), Expect = 1e-11
Identities = 87/409 (21%), Positives = 154/409 (37%), Gaps = 73/409 (17%)
Query: 423 QARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTRELSM 482
Q I +L+GRD++ TG GK+L + VPA L+ G ++ISP
Sbjct: 18 QEEIISHVLDGRDVLVVMPTGGGKSLCYQVPA--LL-------LKGLT-VVISP------ 61
Query: 483 QTFGVLKELMKYHHHTYGLIMGGASR------QAEAQKLAKG-----INIIVATPGRL-- 529
L LMK A+ E Q + K + ++ P RL
Sbjct: 62 -----LISLMKDQVDQLRAAGVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQ 116
Query: 530 ---LDHLQNTPEFLYKNLQCLIIDEADRILDIG--FEEDMKQI---VNLLPKRRQTMLFS 581
L+ LQ P L + +DEA + G F + +++ P+ + +
Sbjct: 117 DYFLNMLQRIPIAL------VAVDEAHCVSQWGHDFRPEYQRLGSLAERFPQ-VPRIALT 169
Query: 582 ATTTAKT--ETLTKLALKKEPVYIGVDDTKEEATVAGLEQGYVVCPSEKRFLLLFTFLKK 639
AT A+T + L L +I D + V + L +LKK
Sbjct: 170 ATADAETRQDIRELLRLADANEFITSFDRPNLR--------FSVVKKNNKQKFLLDYLKK 221
Query: 640 NRKKKVMVFFSSCMSVKFHHELLNYIDLPVMCIHGKQKQMKRTTTFFQFCNAETGILLCT 699
+R + +++ SS V+ E L + + H R F + +++ T
Sbjct: 222 HRGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVAT 281
Query: 700 DVAARGLDIPAVDWIVQYDPPDDPKEYIHRVGRTARGEGSSGHALLILRPEELGFLRYLK 759
+ G+D P V +++ YD P + + Y GR R +G A+L+ P ++ L+
Sbjct: 282 NAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGR-DGLPAEAILLYSPADIALLKRRI 340
Query: 760 QAKIPLNEFEFSWSKISDIQLQLEKLISKNYFLNMS-GKEAFKAYVRAY 807
+ ++++ Q++ EKL + + +AY+ Y
Sbjct: 341 EQSEADDDYK---------QIEREKL---RAMIAYCETQTCRRAYILRY 377
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 64.2 bits (157), Expect = 2e-10
Identities = 77/362 (21%), Positives = 138/362 (38%), Gaps = 69/362 (19%)
Query: 416 FTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPA-VELIYNLKFMPRNGTGIIII 474
FT +T Q IP + G +++ A TGSGKT A +P EL+ K +G + I
Sbjct: 20 FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYI 79
Query: 475 SPTRELSMQTFGVLKELMK------YHHHTYGLIMGGASRQAEAQKLAKGI-NIIVATPG 527
SP + L+ L+E ++ H G + Q+E QK+ K +I++ TP
Sbjct: 80 SPLKALNNDIRRRLEEPLRELGIEVAVRH-------GDTPQSEKQKMLKNPPHILITTPE 132
Query: 528 RLLDHLQNTPEF--LYKNLQCLIIDEADRI--------LDIGFEEDMKQIVNLLPKRRQT 577
L L N+P+F L ++++ +I+DE + L + E + L Q
Sbjct: 133 SLAILL-NSPKFRELLRDVRYVIVDEIHALAESKRGVQLALSLER-----LRELAGDFQR 186
Query: 578 MLFSATTTAKTE------------TLTKLALKKEP----VYIGVDDTKEEATVAGLEQGY 621
+ SAT E + ++ K+ + D +E A L +
Sbjct: 187 IGLSATVGPPEEVAKFLVGFGDPCEIVDVSAAKKLEIKVISPVEDLIYDEELWAALYERI 246
Query: 622 VVCPSEKRFLLLFTFLKKNRKKKVMVFFSSCMSVKFHHELLNYI-DLPVMCIHGKQKQMK 680
L+ + + ++F ++ + L + + HG +
Sbjct: 247 -------AELV-------KKHRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSREL 292
Query: 681 RTTTFFQFCNAETGILLCTDVAARGLDIPAVDWIVQYDPPDDPKEYIHRVGRTARGEGSS 740
R + E ++ T G+DI +D ++Q P ++ R+GR +
Sbjct: 293 RLEVEERLKEGELKAVVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGR-------A 345
Query: 741 GH 742
GH
Sbjct: 346 GH 347
>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 62.0 bits (151), Expect = 1e-09
Identities = 81/416 (19%), Positives = 152/416 (36%), Gaps = 58/416 (13%)
Query: 393 STQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLV 452
S E + +KA G ++ Q + + EGR++V + TGSGKT +FL+
Sbjct: 49 SEFPELRDESLKSALVKA----GIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLL 104
Query: 453 PAVELIYNLKFMPRNGTG-IIIISPTRELSM-QTFGVLKELMKYHHHTYGLI----MGGA 506
P ++ + R+ + +++ PT L+ Q + L + G + G
Sbjct: 105 PILDHLL------RDPSARALLLYPTNALANDQ----AERLRELISDLPGKVTFGRYTGD 154
Query: 507 SRQAEAQKLAKG-INIIVATPGRLLDHL----QNTPEFLYKNLQCLIIDEADRILDIGFE 561
+ E + + + +I++ P +L +L + +L +NL+ L++DE
Sbjct: 155 TPPEERRAIIRNPPDILLTNP-DMLHYLLLRNHDAWLWLLRNLKYLVVDEL-HTYRGVQG 212
Query: 562 EDM-------KQIVNLLPKRRQTMLFSATTTAKTETLTKLALKKEPVYIGVDDTKEEA-- 612
++ + + Q + SAT E +L + V + D +
Sbjct: 213 SEVALLLRRLLRRLRRYGSPLQIICTSATLANPGEFAEELFGRDFEVPVDEDGSPRGLRY 272
Query: 613 TVAGLEQGYVVCPSEKR-----FLLLFTFLKKNRKKKVMVFFSSCMSVK----FHHELLN 663
V + S +R L L +N + +VFF S V+ L
Sbjct: 273 FVRREPPIRELAESIRRSALAELATLAALLVRN-GIQTLVFFRSRKQVELLYLSPRRRLV 331
Query: 664 YIDLP----VMCIHG--KQKQMKRTTTFFQFCNAETGILLCTDVAARGLDIPAVDWIVQY 717
V +++ +R +F E ++ T+ G+DI ++D ++ Y
Sbjct: 332 REGGKLLDAVSTYRAGLHREERRRIEA--EFKEGELLGVIATNALELGIDIGSLDAVIAY 389
Query: 718 DPPDDP-KEYIHRVGRTARGEGSSGHALLILRPEELGFLRYLKQAKIPLNEFEFSW 772
P + R GR R S L++LR + Y + L E F
Sbjct: 390 GYPGVSVLSFRQRAGRAGRRGQES-LVLVVLRSD--PLDSYYLRHPEELLETGFGP 442
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 58.5 bits (142), Expect = 1e-08
Identities = 37/125 (29%), Positives = 50/125 (40%), Gaps = 13/125 (10%)
Query: 632 LLFTFLKKNRKKKVMVFFSSCMSVKFHHELL--NYIDLPVMCI------HGK---QKQMK 680
+L L+KN +V+VF + + L I V I K QK+ K
Sbjct: 356 ILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQK 415
Query: 681 RTTTFFQFCNAETGILLCTDVAARGLDIPAVDWIVQYDPPDDPKEYIHRVGRTARGEGSS 740
QF E +L+ T V GLDIP VD ++ Y+P I R GRT R
Sbjct: 416 EIID--QFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRKRKGR 473
Query: 741 GHALL 745
L+
Sbjct: 474 VVVLV 478
Score = 33.1 bits (76), Expect = 0.74
Identities = 28/118 (23%), Positives = 45/118 (38%), Gaps = 18/118 (15%)
Query: 442 TGSGKTL-AFLVPAVELIYNLKFMPRNGTGIIIISPTRELSMQTFGVLKELMKYHHHTYG 500
TG GKT A +V A + G ++ ++PT+ L +Q +++
Sbjct: 38 TGLGKTFIAAMVIA-------NRLRWFGGKVLFLAPTKPLVLQHAEFCRKVTGI-PEDEI 89
Query: 501 LIMGGASRQAEAQKLAKGINIIVATP----GRLLDHLQNTPEFLYKNLQCLIIDEADR 554
+ G R E ++L + VATP L + + LI DEA R
Sbjct: 90 AALTGEVRPEEREELWAKKKVFVATPQVVENDLKAGRIDLDDVS-----LLIFDEAHR 142
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 57.8 bits (140), Expect = 1e-08
Identities = 70/352 (19%), Positives = 111/352 (31%), Gaps = 74/352 (21%)
Query: 442 TGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTRELSMQTFGVLKELMKYHHHTYGL 501
TG+GKT+ E I LK +++ PT+EL Q LK+ +
Sbjct: 64 TGAGKTVVAA----EAIAELK------RSTLVLVPTKELLDQWAEALKK--FLLLNDEIG 111
Query: 502 IMGGASRQAEAQKLAKGINIIVAT----PGRLLDHLQNTPEFLYKNLQCLIIDEADRILD 557
I GG +K + + VAT R L EF +I DE +
Sbjct: 112 IYGGG------EKELEPAKVTVATVQTLARRQLLDEFLGNEFGL-----IIFDEVHHLPA 160
Query: 558 IGFEEDMKQIVNLLPKRRQTMLFSATT--------------------TAKTETLTKLALK 597
+ ++I+ LL + +AT + L
Sbjct: 161 PSY----RRILELLSAAYPRLGLTATPEREDGGRIGDLFDLIGPIVYEVSLKELIDEGYL 216
Query: 598 KEPVYIGVDDT----------KEEATVAGLEQGYVVCPSE------------KRFLLLFT 635
Y+ + T KE A L + +E K +
Sbjct: 217 APYKYVEIKVTLTEDEEREYAKESARFRELLRARGTLRAENEARRIAIASERKIAAVRGL 276
Query: 636 FLKKNRKKKVMVFFSSCMSVKFHHELLNYIDLPVMCIHGKQKQMKRTTTFFQFCNAETGI 695
LK R K ++F S +L V I G+ + +R +F +
Sbjct: 277 LLKHARGDKTLIFASDVEHAYEIAKLFL-APGIVEAITGETPKEEREAILERFRTGGIKV 335
Query: 696 LLCTDVAARGLDIPAVDWIVQYDPPDDPKEYIHRVGRTARGEGSSGHALLIL 747
L+ V G+DIP D ++ P + +I R+GR R L +
Sbjct: 336 LVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLGRGLRPAEGKEDTLALD 387
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 55.4 bits (134), Expect = 8e-08
Identities = 87/403 (21%), Positives = 151/403 (37%), Gaps = 94/403 (23%)
Query: 405 ENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFM 464
+ LK + G+ Q I LL G+D + TG GK+L + +PA L+
Sbjct: 6 QQVLKQV--FGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPA--LL------ 55
Query: 465 PRNGTGIIIISPTRELSMQTFGVLKELMK---YHHHTYGL----IMGGASRQAEAQ---K 514
G +++SP L LMK G+ + SR+ Q +
Sbjct: 56 -LEGLT-LVVSP-----------LISLMKDQVDQLEAAGIRAAYLNSTLSREERQQVLNQ 102
Query: 515 LAKG-INIIVATPGRLLDHLQNTPEFLYKNLQCLI----IDEADRILDIG--FEEDMKQI 567
L G + ++ +P RL +P FL + I IDEA I G F D +++
Sbjct: 103 LKSGQLKLLYISPERL-----MSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPDYRRL 157
Query: 568 VNLLPKRRQT--MLFSATTTAKTE--TLTKLALKKEPVYIG-------------VDDTKE 610
L + +AT T + +L L+ ++ G + +
Sbjct: 158 GRLRAGLPNPPVLALTATATPRVRDDIREQLGLQDANIFRGSFDRPNLALKVVEKGEPSD 217
Query: 611 EATV------AGLEQGYVVCPSEKRFLLLFTFLKKNRKKKVMVFFSSCMSVKFHHELLNY 664
+ + G + C + K+ L +L+KN + +H L N
Sbjct: 218 QLAFLATVLPQLSKSGIIYCLTRKKVEELAEWLRKNGIS----------AGAYHAGLSN- 266
Query: 665 IDLPVMCIHGKQKQMKRTTTFFQFCNAETGILLCTDVAARGLDIPAVDWIVQYDPPDDPK 724
++++ + F N E +++ T+ G+D P V +++ YD P +
Sbjct: 267 ----------EERERVQQ----AFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIE 312
Query: 725 EYIHRVGRTARGEGSSGHALLILRPEELGFLRYLKQAKIPLNE 767
Y GR A +G A+L+ PE++ + RYL + P E
Sbjct: 313 SYYQETGR-AGRDGLPAEAILLYSPEDIRWQRYLIEQSKPDEE 354
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 49.9 bits (120), Expect = 5e-06
Identities = 34/114 (29%), Positives = 51/114 (44%), Gaps = 16/114 (14%)
Query: 637 LKKNRKKKVMVFFSSCMSVKFHHELLNYIDLPVMCIHGK----------QKQMKRTTTFF 686
L KN +++VF + + +LL + + G+ QK+
Sbjct: 360 LGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILD-- 417
Query: 687 QFCNAETGILLCTDVAARGLDIPAVDWIVQYDPPDDPKE--YIHRVGRTARGEG 738
+F E +L+ T VA GLDIP+VD ++ Y+P P E I R GRT R E
Sbjct: 418 KFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPV--PSEIRSIQRKGRTGRQEE 469
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 48.9 bits (117), Expect = 1e-05
Identities = 31/130 (23%), Positives = 58/130 (44%), Gaps = 11/130 (8%)
Query: 428 PPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTRELSMQTFGV 487
LL +++ SA TGSGKTL L+ L + G ++ I P + L+ + +
Sbjct: 42 KGLLSDENVLISAPTGSGKTLIALLAI------LSTLLEGGGKVVYIVPLKALAEEKYEE 95
Query: 488 LKELMKYHHHTYGLIMGGASRQAEAQKLAKGINIIVATPGRLLDHLQNTPEFLYKNLQCL 547
L + G+ G + ++L ++IV TP +L + P ++ + + +
Sbjct: 96 FSRLEEL-GIRVGISTG--DYDLDDERL-ARYDVIVTTPEKLDSLTRKRPSWI-EEVDLV 150
Query: 548 IIDEADRILD 557
+IDE + D
Sbjct: 151 VIDEIHLLGD 160
>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA
ligase-associated. Members of this protein family are
DEAD/DEAH box helicases found associated with a
bacterial ATP-dependent DNA ligase, part of a four-gene
system that occurs in about 12 % of prokaryotic
reference genomes. The actual motif in this family is
DE[VILW]H.
Length = 803
Score = 46.4 bits (111), Expect = 7e-05
Identities = 42/144 (29%), Positives = 64/144 (44%), Gaps = 28/144 (19%)
Query: 423 QARTIPPLLEGRDLVGSAKTGSGKTLA-FLVPAVELIYNLKFMPRNGTGIIIISPTRELS 481
Q LEGR + A TGSGKTLA FL ++L K P+ G + I+P R L+
Sbjct: 18 QLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEK--PKKGLHTLYITPLRALA 75
Query: 482 MQTFGVLK----ELMKYHHHTYGLIMGGASR-----QAEAQK-LAKGINIIVATPGRLLD 531
+ L+ EL GL + +R +E + K +I++ TP L
Sbjct: 76 VDIARNLQAPIEEL--------GLPIRVETRTGDTSSSERARQRKKPPDILLTTPESL-- 125
Query: 532 HL----QNTPEFLYKNLQCLIIDE 551
L + K+L+C+++DE
Sbjct: 126 ALLLSYPDAARLF-KDLRCVVVDE 148
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 46.2 bits (110), Expect = 7e-05
Identities = 104/403 (25%), Positives = 156/403 (38%), Gaps = 95/403 (23%)
Query: 395 QFEALKGKVCENTL-KAIADMGFTKMTEIQARTIPPLLE--------GRDLVGSAKTGSG 445
QF A E L K +A + F K+T Q R + +L+ R L G GSG
Sbjct: 212 QFSAPPANPSEELLTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGD--VGSG 268
Query: 446 KTL-AFL--VPAVELIYNLKFMPRNGTGIIIISPTRELSMQTFGVLKELMKYHHHTYGLI 502
KTL A L + A+E Y + M +PT L+ Q + L+ L+ L+
Sbjct: 269 KTLVAALAMLAAIEAGYQVALM----------APTEILAEQHYNSLRNLLAPLGIEVALL 318
Query: 503 MG---GASRQAEAQKLAKG-INIIVATPGRLLDH--LQNTPEFLYKNLQCLIIDEADRIL 556
G G R+ + +A G I+++V T H +Q EF K L +IIDE R
Sbjct: 319 TGSLKGKRRKELLETIASGQIHLVVGT------HALIQEKVEF--KRLALVIIDEQHRF- 369
Query: 557 DIGFEEDMKQIVNLLPKRRQTM-----LFSAT----TTA-------KTETLTKLALKKEP 600
++Q L K + + SAT T A T + +L ++P
Sbjct: 370 ------GVEQRKKLREKGQGGFTPHVLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKP 423
Query: 601 V--YIGVDDTKE------EATVAGLEQGYVVCP----SEKRFLLLFTFLKKNRKKKVMVF 648
+ + D K+ E +A Q YVV P SEK L L
Sbjct: 424 ITTVLIKHDEKDIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEAL----------- 472
Query: 649 FSSCMSVKFHHELLNYIDLPVMCIHGKQKQMKRTTTFFQFCNAETGILLCTDVAARGLDI 708
+K N V +HG+ K ++ +F E IL+ T V G+D+
Sbjct: 473 ---YERLKKAFPKYN-----VGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDV 524
Query: 709 PAVDWIVQYDPPDDPKEYIHRV-GRTARGEGSSGHALLILRPE 750
P +V D +H++ GR RG+ S + LL+ +
Sbjct: 525 PNATVMVIEDAERFGLSQLHQLRGRVGRGDHQS-YCLLVYKNP 566
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 45.5 bits (108), Expect = 1e-04
Identities = 65/330 (19%), Positives = 111/330 (33%), Gaps = 50/330 (15%)
Query: 440 AKTGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTRELSMQTFGVLKELMKYHHHTY 499
A TG GKT A L+ A+ L+ + + +I + P R + + KE+
Sbjct: 221 APTGYGKTEASLILALALLDEKI---KLKSRVIYVLPFRTIIEDMYRRAKEIFGLFSVIG 277
Query: 500 GLIMGGASRQA-EAQKLAKGINI----------IVATPGRLLDHLQNTPEFLYKNLQC-- 546
+ + + + + + L +K
Sbjct: 278 KSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQIL-IFSVKGFKFEFLAL 336
Query: 547 -----LIIDEADRILDIGFEEDMKQI----VNLLPKRRQTMLF-SATTTAKTETLTKLAL 596
+I+DE D E M + L + +L SAT + K AL
Sbjct: 337 LLTSLVILDEVHLYAD----ETMLAALLALLEALAEAGVPVLLMSATLPPFLKEKLKKAL 392
Query: 597 --KKEPVYIGVDDTKEEATVAGLEQGYVVCPSEKRFLLLFTFLKKNRK--KKVMVFFSSC 652
+E V KE+ GL++ V + L + + K KKV+V ++
Sbjct: 393 GKGREVVENAKFCPKEDEP--GLKRKERVDVEDGPQEELIELISEEVKEGKKVLVIVNTV 450
Query: 653 MSVKFHHELLNYIDLPVMCIHG------KQKQMKRTTTFFQFCNAETGILLCTDVAARGL 706
+E L V+ +H ++++ + F+ E I++ T V G+
Sbjct: 451 DRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFK--QNEGFIVVATQVIEAGV 508
Query: 707 DIPAVDW-IVQYDPPDDPKEYIHRVGRTAR 735
DI D I + P D I R GR R
Sbjct: 509 DI-DFDVLITELAPID---SLIQRAGRVNR 534
>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family. All
proteins in this family for which functions are known
are 3'-5' DNA-DNA helicases. These proteins are used for
recombination, recombinational repair, and possibly
maintenance of chromosome stability. 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 = 470
Score = 42.4 bits (100), Expect = 7e-04
Identities = 81/367 (22%), Positives = 132/367 (35%), Gaps = 56/367 (15%)
Query: 415 GFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGTGIIII 474
G + +Q I +L GRD TG GK+L + +PA+ +G ++I
Sbjct: 8 GLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCS---------DGIT-LVI 57
Query: 475 SPTRELSMQTFGVLKELMKYHHHTYGLIMGGASRQAEAQ------KLAKGINIIVATP-- 526
SP L LK + + + + + K K I ++ TP
Sbjct: 58 SPLISLMEDQVLQLKAS-----GIPATFLNSSQSKEQQKNVLTDLKDGK-IKLLYVTPEK 111
Query: 527 ----GRLLDHLQNTPEFLYKNLQCLIIDEADRILDIG--FEEDMKQIVNLLPKRR----Q 576
RLL L+ K + + +DEA I G F D K + +L K++
Sbjct: 112 CSASNRLLQTLEE-----RKGITLIAVDEAHCISQWGHDFRPDYKALGSL--KQKFPNVP 164
Query: 577 TMLFSATTTAKTET--LTKLALKKEPVYIGVDDTKEEATVAGLEQGYVVCPSEKRFLL-L 633
M +AT + L +L LK ++ D Y V + L L
Sbjct: 165 IMALTATASPSVREDILRQLNLKNPQIFCTSFDRPNLY--------YEVRRKTPKILEDL 216
Query: 634 FTFLKKNRKKKVMVF--FSSCMSVKFHHELLNYIDLPVMCIHGKQKQMKRTTTFFQFCNA 691
F++K K K + S S + L N + + H + R +F
Sbjct: 217 LRFIRKEFKGKSGIIYCPSRKKSEQVTASLQN-LGIAAGAYHAGLEISARDDVHHKFQRD 275
Query: 692 ETGILLCTDVAARGLDIPAVDWIVQYDPPDDPKEYIHRVGRTARGEGSSGHALLILRPEE 751
E +++ T G++ P V +++ Y P + Y GR R +G L P +
Sbjct: 276 EIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGR-DGLPSECHLFYAPAD 334
Query: 752 LGFLRYL 758
+ LR L
Sbjct: 335 INRLRRL 341
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 42.4 bits (100), Expect = 0.001
Identities = 44/185 (23%), Positives = 69/185 (37%), Gaps = 38/185 (20%)
Query: 411 IADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGTG 470
+ F ++ Q I L G ++ A T SGKT V Y + R+G
Sbjct: 113 AREYPF-ELDPFQQEAIAILERGESVLVCAPTSSGKT-------VVAEYAIALALRDGQR 164
Query: 471 IIIISPTRELSMQTFGVLKELMKYHHHTYGLIMGGASRQAEAQKLAKGINIIVATPGRLL 530
+I SP + LS Q + L GL+ G S +A +V T
Sbjct: 165 VIYTSPIKALSNQKYRDLLAKFGDVADMVGLMTGDVSINPDA-------PCLVMTT---- 213
Query: 531 DHLQNTPEFLYKNLQCLIIDEADRILDIGFEE-----DM------KQIVNLLPKRRQTML 579
+ L+N LY+ + L E + F+E D ++++ LLP + +
Sbjct: 214 EILRN---MLYRGSESLRDIEW-----VVFDEVHYIGDRERGVVWEEVIILLPDHVRFVF 265
Query: 580 FSATT 584
SAT
Sbjct: 266 LSATV 270
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 40.7 bits (96), Expect = 0.003
Identities = 78/317 (24%), Positives = 124/317 (39%), Gaps = 89/317 (28%)
Query: 443 GSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTRELSMQTFGVLKELMKYHHHTYGLI 502
GSGKT+ L+ + I G +++PT L+ Q + L++ ++ L+
Sbjct: 293 GSGKTVVALLAMLAAI-------EAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALL 345
Query: 503 MG---GASRQAEAQKLAKG-INIIVATPGRLLDH--LQNTPEFLYKNLQCLIIDEADRIL 556
G G +R+ ++LA G I+I+V T H +Q+ EF NL +IIDE R
Sbjct: 346 TGSLKGKARKEILEQLASGEIDIVVGT------HALIQDKVEF--HNLGLVIIDEQHR-- 395
Query: 557 DIGFEEDMKQIVNLLPKRRQT--ML-FSAT----TTA-------KTETLTKLALKKEPV- 601
F + Q + L K Q +L +AT T A + +L ++P+
Sbjct: 396 ---F--GVHQRLALREKGEQNPHVLVMTATPIPRTLALTAFGDLDVSIIDELPPGRKPIT 450
Query: 602 --YIGVDDTKE-----EATVAGLEQGYVVCP----SEKRFLLLFTFLKKNRKKKVMVFFS 650
I + E +A Q YVVCP SEK L
Sbjct: 451 TVVIPHERRPEVYERIREEIAKGRQAYVVCPLIEESEKLEL------------------- 491
Query: 651 SCMSVKFHHELLNYI--DLPVMCIHGK----QKQ--MKRTTTFFQFCNAETGILLCTDVA 702
+ + +E L +L V +HG+ +K M+ F E IL+ T V
Sbjct: 492 --QAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEA------FKEGEIDILVATTVI 543
Query: 703 ARGLDIPAVDWIVQYDP 719
G+D+P +V +
Sbjct: 544 EVGVDVPNATVMVIENA 560
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 40.3 bits (95), Expect = 0.004
Identities = 43/174 (24%), Positives = 70/174 (40%), Gaps = 44/174 (25%)
Query: 430 LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTRELSMQTFGVLK 489
LL G A TG GKT F L+ +L ++ + G II PTR L Q L+
Sbjct: 92 LLLGESFAIIAPTGVGKT-TFG-----LVMSL-YLAKKGKKSYIIFPTRLLVEQVVEKLE 144
Query: 490 ELM-KYHHHTYGLIMGGASRQAEAQKLAKGI-----NIIVATPGRLLDHLQNTPEFLYKN 543
+ K L + ++ E ++ + + +I+V T FL KN
Sbjct: 145 KFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQ-----------FLSKN 193
Query: 544 LQCL--------IIDEADRIL------D-----IGF-EEDMKQIVNLLPKRRQT 577
L +D+ D +L D +GF EED+++ + L+ +R+
Sbjct: 194 FDELPKKKFDFVFVDDVDAVLKSSKNIDKLLYLLGFSEEDIEKAMELIRLKRKY 247
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 38.2 bits (89), Expect = 0.018
Identities = 74/364 (20%), Positives = 137/364 (37%), Gaps = 74/364 (20%)
Query: 411 IADMGFTKMTEIQARTIPP-LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGT 469
+ G ++ +Q + LLEG +L+ + T SGKTL + + + + G
Sbjct: 209 LKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTL------IGELAGIPRLLSGGK 262
Query: 470 GIIIISPTRELSMQTFGVLKELMKYHHHTYGL-IMGGASRQAEAQKLAKG-----INIIV 523
++ + P L+ Q + KE +Y + I G SR ++ +IIV
Sbjct: 263 KMLFLVPLVALANQKYEDFKE--RYSKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIV 320
Query: 524 AT-PGRLLDHLQNTPEFLYKNLQCLIIDEADRILDIGFEEDMKQIVNLLPKRR------Q 576
T G +D+L T + L ++ ++IDE + D EE ++ L+ + R Q
Sbjct: 321 GTYEG--IDYLLRTGKDL-GDIGTVVIDEIHTLED---EERGPRLDGLIGRLRYLFPGAQ 374
Query: 577 TMLFSATTTAKTETLTKLALK-----KEPV------YIGVDDTKEEATVAGLEQGYVVCP 625
+ SAT E KL K + PV +++++ +A L +
Sbjct: 375 FIYLSATVGNPEELAKKLGAKLVLYDERPVPLERHLVFARNESEKWDIIARLVKREFSTE 434
Query: 626 SEKRF---LLLFTFLKKNRKKKVMVFFSSCMSVKFHHELLNYIDLPVMCIHGKQKQMKRT 682
S K + ++FT+ ++ + + +H L Y +R
Sbjct: 435 SSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYK--------------ERK 480
Query: 683 TTFFQFCNAETGILLCTDVAARGLDIPA-----------VDWIVQYDPPDDPKEYIHRVG 731
+ F E ++ T A G+D PA ++W+ +E+ +G
Sbjct: 481 SVERAFAAQELAAVVTTAALAAGVDFPASQVIFESLAMGIEWL-------SVREFQQMLG 533
Query: 732 RTAR 735
R R
Sbjct: 534 RAGR 537
>gnl|CDD|223683 COG0610, COG0610, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 962
Score = 36.2 bits (84), Expect = 0.074
Identities = 28/116 (24%), Positives = 45/116 (38%), Gaps = 13/116 (11%)
Query: 442 TGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTRELSMQTFGVLKELMKYHHHTYGL 501
GSGKTL + L+ L P+ ++ + ++L QT + K
Sbjct: 282 QGSGKTLT-MFKLARLLLELPKNPK----VLFVVDRKDLDDQTSDEFQSFGKVAF----- 331
Query: 502 IMGGASRQAEAQKLAKGIN--IIVATPGRLLDHLQNTPEFLYKNLQCL-IIDEADR 554
A +E ++L + IIV T + ++ L K + IIDEA R
Sbjct: 332 NDPKAESTSELKELLEDGKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHR 387
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 36.4 bits (85), Expect = 0.077
Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 2/67 (2%)
Query: 416 FTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTL-AFLVPAVELI-YNLKFMPRNGTGIII 473
F T Q IP + EG++++ S+ TGSGKTL AFL EL + + +
Sbjct: 30 FGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLY 89
Query: 474 ISPTREL 480
+SP R L
Sbjct: 90 VSPLRAL 96
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 36.4 bits (84), Expect = 0.086
Identities = 39/170 (22%), Positives = 66/170 (38%), Gaps = 30/170 (17%)
Query: 440 AKTGSGKTLAFLVPAVELIY------NLKFMPRNGTGIIIISPT--------RELSMQTF 485
A TGSGKTLA + A++ ++ + R + I+ ISP R L +
Sbjct: 3 APTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIPLK 62
Query: 486 GVLKELMKYHHH----TYGLIMGGASRQAEAQKLAKGINIIVATPGRLLDHLQNTPEFLY 541
G+ E + G+ G Q ++ +I++ TP L L +
Sbjct: 63 GIADERRRRGETEVNLRVGIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARETL 122
Query: 542 KNLQCLIIDEADRI--------LDIGFEEDMKQIVNLLPKRRQTMLFSAT 583
+ ++ +IIDE + L + E ++ LL Q + SAT
Sbjct: 123 RGVETVIIDEVHAVAGSKRGAHLALSLE----RLDALLHTSAQRIGLSAT 168
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 34.3 bits (78), Expect = 0.088
Identities = 30/136 (22%), Positives = 42/136 (30%), Gaps = 36/136 (26%)
Query: 436 LVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTRELSMQTFGVLKELMKYH 495
+VG GSGKT A L L G G+I I L +L ++
Sbjct: 7 IVGP--PGSGKTTL----ARALARELG---PPGGGVIYIDGEDILEEVLDQLLLIIVGGK 57
Query: 496 HHTYGLIMGGASRQAEAQKLAKGINIIVATPGRLLDHLQNTPEFLYKNLQCLIIDEADRI 555
+ G R A LA+ + V LI+DE +
Sbjct: 58 KASGS----GELRLRLALALARKLKPDV-----------------------LILDEITSL 90
Query: 556 LDIGFEEDMKQIVNLL 571
LD E + + L
Sbjct: 91 LDAEQEALLLLLEELR 106
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 35.6 bits (82), Expect = 0.11
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 9/78 (11%)
Query: 430 LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTREL---SMQTFG 486
L G L+ A TG+GKTLA+L+PA L + G +II + T+ L ++
Sbjct: 31 LKGGEGLLIEAPTGTGKTLAYLLPA------LAYAREEGKKVIISTRTKALQEQLLEEDL 84
Query: 487 VLKELMKYHHHTYGLIMG 504
+ +L+K + L+ G
Sbjct: 85 PIHKLLKKLGGKFALLKG 102
Score = 32.5 bits (74), Expect = 1.0
Identities = 27/125 (21%), Positives = 46/125 (36%), Gaps = 20/125 (16%)
Query: 639 KNRKKKVMVFFSSCMSVKFHHELLN----YIDLPVMCIHGKQKQMKRTTTFFQFCNAETG 694
K V+V F S +K E L + + +++ +++ F E
Sbjct: 476 KASPGGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGEDEREELLEK---FKASG--EGL 530
Query: 695 ILLCTDVAARGLDIP------AVDWIVQYDPPDDP-----KEYIHRVGRTARGEGSSGHA 743
IL+ G+D P V + + PDDP E++ R+G E A
Sbjct: 531 ILVGGGSFWEGVDFPGDALRLVVIVGLPFPNPDDPLLKARLEFLKRLGGDPFEEFYLPPA 590
Query: 744 LLILR 748
++ LR
Sbjct: 591 VIKLR 595
>gnl|CDD|233032 TIGR00580, mfd, transcription-repair coupling factor (mfd). All
proteins in this family for which functions are known
are DNA-dependent ATPases that function in the process
of transcription-coupled DNA repair in which the repair
of the transcribed strand of actively transcribed genes
is repaired at a higher rate than the repair of
non-transcribed regions of the genome and than the
non-transcribed strand of the same gene. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). This family is
closely related to the RecG and UvrB families [DNA
metabolism, DNA replication, recombination, and repair].
Length = 926
Score = 34.6 bits (80), Expect = 0.24
Identities = 28/96 (29%), Positives = 44/96 (45%), Gaps = 18/96 (18%)
Query: 467 NGTGIIIISPTRELSMQTFGVLKELMKYHHHTYGLIMGGASR--QAEAQK-----LAKG- 518
+G + ++ PT L+ Q F KE + + + SR A+ Q LA G
Sbjct: 499 DGKQVAVLVPTTLLAQQHFETFKERFA----NFPVTIELLSRFRSAKEQNEILKELASGK 554
Query: 519 INIIVATPGRLLDHLQNTPEFLYKNLQCLIIDEADR 554
I+I++ T +LL + +K+L LIIDE R
Sbjct: 555 IDILIGT-HKLL-----QKDVKFKDLGLLIIDEEQR 584
Score = 32.3 bits (74), Expect = 1.3
Identities = 12/44 (27%), Positives = 22/44 (50%)
Query: 672 IHGKQKQMKRTTTFFQFCNAETGILLCTDVAARGLDIPAVDWIV 715
HG+ + + +F E +L+CT + G+DIP + I+
Sbjct: 692 AHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTII 735
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 33.5 bits (77), Expect = 0.56
Identities = 80/359 (22%), Positives = 130/359 (36%), Gaps = 64/359 (17%)
Query: 423 QARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTREL-- 480
Q I +L GRD + TG GK+L + +PA + +G +++SP L
Sbjct: 30 QQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPA---------LVLDGL-TLVVSPLISLMK 79
Query: 481 ----SMQTFGVLKELMKYHHHTYGLIMGGASRQAEAQKLA------KG-INIIVATPGRL 529
+ GV + S Q Q+L G I ++ P RL
Sbjct: 80 DQVDQLLANGVAAACLN-------------STQTREQQLEVMAGCRTGQIKLLYIAPERL 126
Query: 530 -----LDHLQNTPEFLYKNLQCLIIDEADRILDIG--FEEDMKQIVNLLPKRRQTMLFSA 582
L+HL + L +DEA I G F + + L +R T+ F A
Sbjct: 127 MMDNFLEHLAHWN------PALLAVDEAHCISQWGHDFRPEYAAL-GQLRQRFPTLPFMA 179
Query: 583 -TTTAKTET----LTKLALKKEPVYIGVDDTKEEATVAGLEQGYVVCPSEKRFLLLFTFL 637
T TA T + L L + I D Y + K L ++
Sbjct: 180 LTATADDTTRQDIVRLLGLNDPLIQISSFDRPNIR--------YTLVEKFKPLDQLMRYV 231
Query: 638 KKNRKKKVMVFFSSCMSVKFHHELLNYIDLPVMCIHGKQKQMKRTTTFFQFCNAETGILL 697
++ R K +++ +S V+ L + H R F + I++
Sbjct: 232 QEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVV 291
Query: 698 CTDVAARGLDIPAVDWIVQYDPPDDPKEYIHRVGRTARGEGSSGHALLILRPEELGFLR 756
T G++ P V ++V +D P + + Y GR R +G A+L P ++ +LR
Sbjct: 292 ATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGR-DGLPAEAMLFYDPADMAWLR 349
>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative
DEAH-box helicase. A conserved gene neighborhood widely
spread in the Actinobacteria contains this
uncharacterized DEAH-box family helicase encoded
convergently towards an operon of genes for protein
homologous to type II secretion and pilus formation
proteins. The context suggests that this helicase may
play a role in conjugal transfer of DNA.
Length = 742
Score = 33.2 bits (76), Expect = 0.65
Identities = 47/203 (23%), Positives = 80/203 (39%), Gaps = 30/203 (14%)
Query: 408 LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRN 467
+ A+ G + + QAR GR +V + T SGK+LA+ +P + L PR
Sbjct: 26 VAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLS---ALADDPRA 82
Query: 468 GTGIIIISPTRELSMQTFGVLKELM--KYHHHTYGLIMGGASRQAEAQKLAKGINIIVAT 525
+ ++PT+ L+ ++EL TY G + E + + ++
Sbjct: 83 TA--LYLAPTKALAADQLRAVRELTLRGVRPATY----DGDTPTEERRWAREHARYVLTN 136
Query: 526 P-----GRLLDHLQNTPEFLYKNLQCLIIDEADRILDIGFEEDMKQIVNLLPKRRQT--- 577
P G L H FL + L+ ++IDE + F + ++ L RR
Sbjct: 137 PDMLHRGILPSH-ARWARFL-RRLRYVVIDECHSYRGV-FGSHVALVLRRL--RRLCARY 191
Query: 578 ------MLFSATTTAKTETLTKL 594
+L SATT ++L
Sbjct: 192 GASPVFVLASATTADPAAAASRL 214
>gnl|CDD|146712 pfam04219, DUF413, Protein of unknown function, DUF.
Length = 94
Score = 30.7 bits (70), Expect = 0.70
Identities = 17/64 (26%), Positives = 23/64 (35%), Gaps = 14/64 (21%)
Query: 741 GHALLILR--------PEELGFLRYLKQAKIPLNEFEFSWSKISDIQLQLEKLISKNYFL 792
G A+L L EE F+ K + P E E W K L+ + K F
Sbjct: 30 GCAMLALESGEREPETEEEEQFVAVCKGEQAPSTEIEKVWLKY------LKLIRGKKRFY 83
Query: 793 NMSG 796
+ G
Sbjct: 84 TLCG 87
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 33.4 bits (77), Expect = 0.70
Identities = 26/96 (27%), Positives = 45/96 (46%), Gaps = 18/96 (18%)
Query: 467 NGTGIIIISPTRELSMQTFGVLKELMKYHHHTYGLIMGGASR---QAEA----QKLAKG- 518
+G + ++ PT L+ Q + KE + + + SR E + LA+G
Sbjct: 642 DGKQVAVLVPTTLLAQQHYETFKERFA----GFPVRIEVLSRFRSAKEQKEILKGLAEGK 697
Query: 519 INIIVATPGRLLDHLQNTPEFLYKNLQCLIIDEADR 554
++I++ T RLL + + +K+L LIIDE R
Sbjct: 698 VDIVIGT-HRLL-----SKDVKFKDLGLLIIDEEQR 727
>gnl|CDD|226583 COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA
uptake (late competence protein) [DNA replication,
recombination, and repair].
Length = 441
Score = 32.8 bits (75), Expect = 0.74
Identities = 66/306 (21%), Positives = 108/306 (35%), Gaps = 80/306 (26%)
Query: 440 AKTGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTRELSMQTFGVLKELMKYHHHTY 499
A TG+GKT + +E N G + I SP ++ ++ + LK+ +
Sbjct: 123 AVTGAGKT-EMIFQGIEQALN------QGGRVCIASPRVDVCLELYPRLKQAFS--NCDI 173
Query: 500 GLIMGGASRQAEAQKLAKGINIIVATPGRLLDHLQNTPEFLYKNLQCLIIDEADR---IL 556
L+ G + A ++VAT +LL + LIIDE D
Sbjct: 174 DLLYGDSDSYFRAP-------LVVATTHQLLR--------FKQAFDLLIIDEVDAFPFSD 218
Query: 557 DIGFEEDMKQIVNLLPKRRQTMLFSATTT------AKTETLTKLALKK----------EP 600
D + +K+ K T+ +AT T L L L +
Sbjct: 219 DQSLQYAVKKARK---KEGATIYLTATPTKKLERKILKGNLRILKLPARFHGKPLPVPKF 275
Query: 601 VYIGVDDTKEEATVAGLEQGYVVCPSEKRFLLLFTFLKKNRKKK--VMVFFSS------- 651
V+IG + K L++ K L L +L+K RK V++FF
Sbjct: 276 VWIGNWNKK-------LQRN-------KLPLKLKRWLEKQRKTGRPVLIFFPEIETMEQV 321
Query: 652 --CMSVKFHHELLNYIDLPVMCIHGKQKQMKRTTTFFQFCNAETGILLCTDVAARGLDIP 709
+ K E + +H + + K F + + +L+ T + RG+ P
Sbjct: 322 AAALKKKLPKE-------TIASVHSEDQHRKEKVE--AFRDGKITLLITTTILERGVTFP 372
Query: 710 AVDWIV 715
VD V
Sbjct: 373 NVDVFV 378
>gnl|CDD|233483 TIGR01587, cas3_core, CRISPR-associated helicase Cas3. This model
represents the highly conserved core region of an
alignment of Cas3, a protein found in association with
CRISPR repeat elements in a broad range of bacteria and
archaea. Cas3 appears to be a helicase, with regions
found by pfam00270 (DEAD/DEAH box helicase) and
pfam00271 (Helicase conserved C-terminal domain). Some
but not all members have an N-terminal HD domain region
(pfam01966) that is not included within this model
[Mobile and extrachromosomal element functions, Other].
Length = 358
Score = 31.3 bits (71), Expect = 1.9
Identities = 65/340 (19%), Positives = 115/340 (33%), Gaps = 61/340 (17%)
Query: 435 DLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTRELSMQTFGVLKELMKY 494
LV A TG GKT A L+ A+ I + K +II PTR + KEL
Sbjct: 1 LLVIEAPTGYGKTEAALLWALHSIKSQKA-----DRVIIALPTRATINAMYRRAKELFG- 54
Query: 495 HHHTYGLIMGGASRQAEAQKLAKG------------------INIIVATPGRLLDHLQNT 536
GL+ +S + + I V T ++L +
Sbjct: 55 --SNLGLLHSSSSFKRIKEMGDSEEFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGE 112
Query: 537 PEFLYKNL-----QCLIIDEADRILDIGFEEDMKQIVNLLP----KRRQTMLFSATTTAK 587
L LI DE + + I+ +L +L SAT
Sbjct: 113 FGHYEFTLASIANSLLIFDEVHFYDE----YTLALILAVLEVLKDNDVPILLMSATLP-- 166
Query: 588 TETLTKLALKKEPVYIGVDDTKEEATVAGLEQGYVVCPSEKRFLLLFTFLKK-----NRK 642
+ L + A K V + + + + E + + L++ +
Sbjct: 167 -KFLKEYAEKIGYV---EFNEPLDLKEERRFERHRFIKIESDKVGEISSLERLLEFIKKG 222
Query: 643 KKVMVFFSSC-MSVKFHHELLNYI-DLPVMCIHGKQKQM----KRTTTFFQFCNAETGIL 696
K+ + ++ + +F+ +L + +M +H + + K + E ++
Sbjct: 223 GKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVI 282
Query: 697 LCTDVAARGLDIPAVDWIV-QYDPPDDPKEYIHRVGRTAR 735
+ T V LDI + D ++ + P D I R+GR R
Sbjct: 283 VATQVIEASLDI-SADVMITELAPID---SLIQRLGRLHR 318
>gnl|CDD|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3. CRISPR
(Clustered Regularly Interspaced Short Palindromic
Repeats) and associated Cas proteins comprise a system
for heritable host defense by prokaryotic cells against
phage and other foreign DNA; DEAD/DEAH box helicase DNA
helicase cas3'; Often but not always is fused to HD
nuclease domain; signature gene for Type I.
Length = 353
Score = 31.2 bits (71), Expect = 2.2
Identities = 64/340 (18%), Positives = 107/340 (31%), Gaps = 65/340 (19%)
Query: 435 DLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTRELSMQTFGVLKELMKY 494
LV A TG GKT A L+ A+ + + K +II PTR + KE
Sbjct: 1 LLVIEAPTGYGKTEAALLWALHSLKSQKA-----DRVIIALPTRATINAMYRRAKEAFGE 55
Query: 495 HHHTYGLIMGGASR----------------QAEAQKLAKGINIIVATPGRLLDHLQNTPE 538
+ I+ + + I V T ++L +
Sbjct: 56 TGLYHSSILSSRIKEMGDSEEFEHLFPLYIHSNDTLFLDPIT--VCTIDQVLKSVFGEFG 113
Query: 539 FLYKNL-----QCLIIDEADRI-----------LDIGFEEDMKQIV--NLLPKRRQTMLF 580
L LI DE L++ + D+ ++ LPK +
Sbjct: 114 HYEFTLASIANSLLIFDEVHFYDEYTLALILAVLEVLKDNDVPILLMSATLPKFLKEYAE 173
Query: 581 SATTTAKTETLTKLALKKEPVYIGVDDTKEEATVAGLEQGYVVCPSEKRFLLLFTFLKKN 640
+ E L ++ P D E + LE+ ++ + +
Sbjct: 174 KIGYVEENEPLDLKPNERAPFIKIESDKVGEISS--LERLLEFIKKGGSVAIIVNTVDR- 230
Query: 641 RKKKVMVFFSSCMSVKFHHELLNYIDLPVMCIHGKQKQMKRTTTFFQ----FCNAETGIL 696
F + K E +M IH + + R + F +E ++
Sbjct: 231 -----AQEFYQQLKEKGPEE-------EIMLIHSRFTEKDRAKKEAELLLEFKKSEKFVI 278
Query: 697 LCTDVAARGLDIPAVDWIV-QYDPPDDPKEYIHRVGRTAR 735
+ T V LDI +VD ++ + P D I R+GR R
Sbjct: 279 VATQVIEASLDI-SVDVMITELAPID---SLIQRLGRLHR 314
>gnl|CDD|236148 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 928
Score = 31.5 bits (72), Expect = 2.6
Identities = 10/16 (62%), Positives = 14/16 (87%)
Query: 440 AKTGSGKTLAFLVPAV 455
A TG+GK+LA+L+PA
Sbjct: 283 AGTGTGKSLAYLLPAA 298
>gnl|CDD|236966 PRK11747, dinG, ATP-dependent DNA helicase DinG; Provisional.
Length = 697
Score = 31.0 bits (71), Expect = 3.1
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 432 EGRDLVGSAKTGSGKTLAFLVPAV 455
+GR LV A TG GKTL++L+ +
Sbjct: 48 DGRILVIEAGTGVGKTLSYLLAGI 71
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 30.8 bits (70), Expect = 3.6
Identities = 30/133 (22%), Positives = 55/133 (41%), Gaps = 16/133 (12%)
Query: 430 LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTRELSMQTFGVLK 489
L+ G+ A TG GKT F L+ +L ++ + G + II PT L Q + LK
Sbjct: 94 LVRGKSFAIIAPTGVGKT-TFG-----LLMSL-YLAKKGKRVYIIVPTTTLVRQVYERLK 146
Query: 490 ELMKYHHHTYGLIMGGASRQAEAQKLAK------GINIIVATPGRLLDHLQNTPEFLYKN 543
+ + L++ ++ + ++ A +I++ T L + E
Sbjct: 147 KFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFL---SKRFEELSKLK 203
Query: 544 LQCLIIDEADRIL 556
+ +D+ D IL
Sbjct: 204 FDFIFVDDVDAIL 216
>gnl|CDD|204097 pfam08926, DUF1908, Domain of unknown function (DUF1908). This
domain is found in a set of hypothetical/structural
eukaryotic proteins.
Length = 282
Score = 30.2 bits (68), Expect = 4.0
Identities = 15/36 (41%), Positives = 21/36 (58%)
Query: 510 AEAQKLAKGINIIVATPGRLLDHLQNTPEFLYKNLQ 545
AE L K + II++ P RLL+ L+ PE Y L+
Sbjct: 213 AEITGLVKKLLIIISRPARLLECLEFDPEEFYHLLE 248
>gnl|CDD|235032 PRK02362, PRK02362, ski2-like helicase; Provisional.
Length = 737
Score = 30.7 bits (70), Expect = 4.1
Identities = 36/123 (29%), Positives = 64/123 (52%), Gaps = 14/123 (11%)
Query: 430 LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTRELSMQTFGVLK 489
LL+G++L+ + T SGKTL EL LK + R G + I+ P R L+ + F +
Sbjct: 36 LLDGKNLLAAIPTASGKTL-----IAELAM-LKAIARGGKALYIV-PLRALASEKFEEFE 88
Query: 490 ELMKYHHHTYGLIMGGASRQAEAQKLAKGIN-IIVATPGRLLDHLQNTPEFLYKNLQCLI 548
+ G+ +G ++ +++ G N IIVAT ++ L+N +L ++ C++
Sbjct: 89 RFEE-----LGVRVGISTGDYDSRDEWLGDNDIIVATSEKVDSLLRNGAPWL-DDITCVV 142
Query: 549 IDE 551
+DE
Sbjct: 143 VDE 145
>gnl|CDD|165711 PLN00143, PLN00143, tyrosine/nicotianamine aminotransferase;
Provisional.
Length = 409
Score = 30.4 bits (68), Expect = 4.6
Identities = 19/80 (23%), Positives = 27/80 (33%), Gaps = 12/80 (15%)
Query: 354 ETKDQLNEWLVFKDLTPPLISVGTVISADVSLSIPSILSSTQFEALKGKVCENTLKAIAD 413
E D + + L P I +IP IL T + + N L+A
Sbjct: 267 EIADSIKKALNPAPFPPTFIQA----------AIPEILEKTTEDFFSKTI--NILRAALA 314
Query: 414 MGFTKMTEIQARTIPPLLEG 433
+ K+ EI P EG
Sbjct: 315 FCYDKLKEIPCIMCPQKAEG 334
>gnl|CDD|187804 cd09673, Cas3_Cas2_I-F, CRISPR/Cas system-associated protein
Cas3/Cas2. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas3/Cas2 fusion; This protein includes both DEAH and HD
motifs for helicase and N-terminal domain corresponding
to Cas2 RNAse; signature gene for Type I and subtype
I-F.
Length = 1106
Score = 30.2 bits (68), Expect = 5.3
Identities = 22/78 (28%), Positives = 31/78 (39%), Gaps = 15/78 (19%)
Query: 437 VGSAKTGSGKTLAFLVPAVELIYNLKFM-----PRNGTGIIIISPTRELSMQTFGVLKEL 491
V A TG GKTLA N + M + G I R L++QT LK
Sbjct: 431 VNMASTGCGKTLA----------NARAMYALRDDKQGARFAIALGLRSLTLQTGHALKTR 480
Query: 492 MKYHHHTYGLIMGGASRQ 509
+ +++GG + Q
Sbjct: 481 LNLSDDDLAVLIGGTAVQ 498
>gnl|CDD|233928 TIGR02562, cas3_yersinia, CRISPR-associated helicase Cas3, subtype
I-F/YPEST. The helicase in many CRISPR-associated (cas)
gene clusters is designated Cas3, and most Cas3 proteins
are described by model TIGR01587. Members of this family
are considerably larger, show a number of motifs in
common with TIGR01587 sequences, and replace Cas3 in
some CRISPR/cas loci in a number of Proteobacteria,
including Yersinia pestis, Chromobacterium violaceum,
Erwinia carotovora subsp. atroseptica SCRI1043,
Photorhabdus luminescens subsp. laumondii TTO1,
Legionella pneumophila, etc [Mobile and extrachromosomal
element functions, Other].
Length = 1110
Score = 30.2 bits (68), Expect = 5.4
Identities = 22/78 (28%), Positives = 31/78 (39%), Gaps = 15/78 (19%)
Query: 437 VGSAKTGSGKTLAFLVPAVELIYNLKFM-----PRNGTGIIIISPTRELSMQTFGVLKEL 491
V A TG GKTLA N + M + G I R L++QT LK
Sbjct: 435 VNMASTGCGKTLA----------NARAMYALRDDKQGARFAIALGLRSLTLQTGHALKTR 484
Query: 492 MKYHHHTYGLIMGGASRQ 509
+ +++GG + Q
Sbjct: 485 LNLSDDDLAVLIGGTAVQ 502
>gnl|CDD|233398 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
putative. This model represents a family of proteins in
Gram-positive bacteria. The N-terminal region of about
200 amino acids resembles the epsilon subunit of E. coli
DNA polymerase III and the homologous region of the
Gram-positive type DNA polymerase III alpha subunit. The
epsilon subunit contains an exonuclease domain. The
remainder of this protein family resembles a predicted
ATP-dependent helicase, the DNA damage-inducible protein
DinG of E. coli [DNA metabolism, DNA replication,
recombination, and repair].
Length = 850
Score = 30.2 bits (68), Expect = 6.0
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 7/44 (15%)
Query: 440 AKTGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTRELSMQ 483
A TG+GKTL +L+PA L Y ++I + T+ L Q
Sbjct: 271 APTGTGKTLGYLLPA--LYYA-----ITEKPVVISTNTKVLQSQ 307
>gnl|CDD|225398 COG2842, COG2842, Uncharacterized ATPase, putative transposase
[General function prediction only].
Length = 297
Score = 29.3 bits (66), Expect = 7.2
Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 8/55 (14%)
Query: 508 RQAEAQKLAKGINIIVATPGRLLDHLQNTPEFLYKNLQCLIIDEADRILDIGFEE 562
A A I T RL+ L++T + I+DEADR+ EE
Sbjct: 138 IICAAAFGATDGTINDLT-ERLMIRLRDTVRLI-------IVDEADRLPYRALEE 184
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 28.0 bits (63), Expect = 7.8
Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 7/43 (16%)
Query: 442 TGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTRELSMQT 484
TGSGKTL A LI L + ++ + P ++L Q
Sbjct: 27 TGSGKTLT----AAALIARLAKGKKK---VLFVVPRKDLLEQA 62
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 29.7 bits (68), Expect = 7.9
Identities = 35/118 (29%), Positives = 56/118 (47%), Gaps = 27/118 (22%)
Query: 443 GSGKTL-AFL--VPAVELIYNLKFMPRNGTGIIIISPTRELSMQTFGVLKELMKYHHHTY 499
GSGKT+ A L + A+E G +++PT L+ Q + LK+L++
Sbjct: 292 GSGKTVVAALAALAAIE----------AGYQAALMAPTEILAEQHYENLKKLLEPLGIRV 341
Query: 500 GLIMG---GASRQAEAQKLAKG-INIIVATPGRLLDH--LQNTPEFLYKNLQCLIIDE 551
L+ G G R+ + +A G +I++ T H +Q+ EF NL +IIDE
Sbjct: 342 ALLTGSLKGKERREILEAIASGEADIVIGT------HALIQDDVEF--HNLGLVIIDE 391
>gnl|CDD|184921 PRK14957, PRK14957, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 546
Score = 29.3 bits (65), Expect = 9.9
Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 23/86 (26%)
Query: 404 CENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKF 463
CEN + AI + F + EI A +++TG +T E++ N+++
Sbjct: 76 CENCV-AINNNSFIDLIEIDA--------------ASRTGVEET-------KEILDNIQY 113
Query: 464 MPRNGT-GIIIISPTRELSMQTFGVL 488
MP G + +I LS Q+F L
Sbjct: 114 MPSQGRYKVYLIDEVHMLSKQSFNAL 139
>gnl|CDD|232933 TIGR00348, hsdR, type I site-specific deoxyribonuclease, HsdR
family. This gene is part of the type I restriction and
modification system which is composed of three
polypeptides R (restriction endonuclease), M
(modification) and S (specificity). This group of
enzymes recognize specific short DNA sequences and have
an absolute requirement for ATP (or dATP) and
S-adenosyl-L-methionine. They also catalyse the
reactions of EC 2.1.1.72 and EC 2.1.1.73, with similar
site specificity.(J. Mol. Biol. 271 (3), 342-348
(1997)). Members of this family are assumed to differ
from each other in DNA site specificity [DNA metabolism,
Restriction/modification].
Length = 667
Score = 29.3 bits (66), Expect = 9.9
Identities = 15/50 (30%), Positives = 19/50 (38%), Gaps = 5/50 (10%)
Query: 442 TGSGKTLAFLVPAVELIYNLKFMPRNGTGIIIISPTRELSMQTFGVLKEL 491
GSGKTL L A L P+ + + REL Q + L
Sbjct: 272 QGSGKTLTMLFAA-RKALELLKNPK----VFFVVDRRELDYQLMKEFQSL 316
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 0.400
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 42,831,530
Number of extensions: 4298396
Number of successful extensions: 3590
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3506
Number of HSP's successfully gapped: 91
Length of query: 838
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 733
Effective length of database: 6,280,432
Effective search space: 4603556656
Effective search space used: 4603556656
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: 63 (27.9 bits)