RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15524
(930 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 = 306 bits (786), Expect = 4e-94
Identities = 130/397 (32%), Positives = 210/397 (52%), Gaps = 27/397 (6%)
Query: 389 PTSYEEFPGIHPFMKKNLNEGMNITQVTTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAI 448
P + G+ P + + L + + + T +Q +I IL G DVL ++QTG+GKT A+ +
Sbjct: 28 PPEFASL-GLSPELLQALKD-LGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLL 85
Query: 449 PIIQKLQEMRPKISRKDGIYAVIILPTRELALQTLEIFTKLCKSFTWIVPSWLTGGEKMK 508
P++QK+ K + + A+I+ PTRELA+Q E KL K+ + + + GG ++
Sbjct: 86 PLLQKIL----KSVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIR 141
Query: 509 SEKARIRKGISILVATPGRLLDHCKHTETLKFSKVEHLVLDEADRILDQGYERDIAEFLE 568
+ +++G+ I+VATPGRLLD L S VE LVLDEADR+LD G+ DI +
Sbjct: 142 KQIEALKRGVDIVVATPGRLLDL-IKRGKLDLSGVETLVLDEADRMLDMGFIDDI---EK 197
Query: 569 ILKKQKPQFQSILLSATLTPAVQRLAGMTLQNPIQIDAADSTDIHNTTDSLVIPDSLKQH 628
ILK P Q++L SAT+ ++ LA L +P++I+ + +KQ
Sbjct: 198 ILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEK-------LERTLKKIKQF 250
Query: 629 FIVTPPKLRLVALASFILGKCQNVNEDEESKMLVFMATQDMADYHTELLSTVLGENIAFF 688
++ + + L +L +++E +++VF+ T+ + + E L
Sbjct: 251 YLEVESEEEKLELLLKLL------KDEDEGRVIVFVRTKRLVEELAESLRK---RGFKVA 301
Query: 689 KLHGSMSQSERTEVFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPSSSTDYVHRV 748
LHG + Q ER + F+ + VL+ TDVAARGLD+P V ++ Y P DYVHR+
Sbjct: 302 ALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRI 361
Query: 749 GRTARVGHEGSSLLFLIPS-EVKLVEELQNRRIRIEE 784
GRT R G +G ++ F+ EVK ++ ++ R R
Sbjct: 362 GRTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLP 398
Score = 180 bits (458), Expect = 2e-48
Identities = 72/180 (40%), Positives = 107/180 (59%), Gaps = 8/180 (4%)
Query: 1 MNITQVTTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYA 60
+ + T +Q +I IL G DVL ++QTG+GKT A+ +P++QK+ K + + A
Sbjct: 47 LGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKIL----KSVERKYVSA 102
Query: 61 VIILPTRELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLL 120
+I+ PTRELA+Q E KL K+ + + + GG ++ + +++G+ I+VATPGRLL
Sbjct: 103 LILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLL 162
Query: 121 DHCKHTETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATLTPA 180
D L S VE LVLDEADR+LD G+ DI +ILK P Q++L SAT+
Sbjct: 163 DL-IKRGKLDLSGVETLVLDEADRMLDMGFIDDI---EKILKALPPDRQTLLFSATMPDD 218
>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 = 210 bits (536), Expect = 1e-62
Identities = 87/208 (41%), Positives = 130/208 (62%), Gaps = 10/208 (4%)
Query: 397 GIHPFMKKNLNEGMNITQVTTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQE 456
G+ P + + + + + T +Q +I P+L G DV+ ++QTGSGKT A+ IPI++KL
Sbjct: 5 GLSPELLRGIYA-LGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDP 63
Query: 457 MRPKISRKDGIYAVIILPTRELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRK 516
+KDG A+I+ PTRELALQ E+ KL K T + + GG + + ++++
Sbjct: 64 SP----KKDGPQALILAPTRELALQIAEVARKLGK-HTNLKVVVIYGGTSIDKQIRKLKR 118
Query: 517 GISILVATPGRLLDHCKHTETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQ 576
G I+VATPGRLLD + L SKV++LVLDEADR+LD G+E I E L++L K +
Sbjct: 119 GPHIVVATPGRLLDLLERG-KLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDR-- 175
Query: 577 FQSILLSATLTPAVQRLAGMTLQNPIQI 604
Q++L SAT+ V+ LA L+NP++I
Sbjct: 176 -QTLLFSATMPKEVRDLARKFLRNPVRI 202
Score = 191 bits (489), Expect = 4e-56
Identities = 78/180 (43%), Positives = 113/180 (62%), Gaps = 9/180 (5%)
Query: 1 MNITQVTTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYA 60
+ + T +Q +I P+L G DV+ ++QTGSGKT A+ IPI++KL +KDG A
Sbjct: 17 LGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSP----KKDGPQA 72
Query: 61 VIILPTRELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLL 120
+I+ PTRELALQ E+ KL K T + + GG + + ++++G I+VATPGRLL
Sbjct: 73 LILAPTRELALQIAEVARKLGK-HTNLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLL 131
Query: 121 DHCKHTETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATLTPA 180
D + L SKV++LVLDEADR+LD G+E I E L++L K + Q++L SAT+
Sbjct: 132 DLLERG-KLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDR---QTLLFSATMPKE 187
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 211 bits (539), Expect = 8e-60
Identities = 126/412 (30%), Positives = 202/412 (49%), Gaps = 55/412 (13%)
Query: 388 APTSYEEFPGIHPFMKKNLNEGMNITQVTTVQQLSIQPILDGGDVLVRSQTGSGKTLAYA 447
+ T++ P + P + NLNE + T++T +Q S+ IL G DV+ +++TGSGKT A+
Sbjct: 2 SMTAFSTLP-LPPALLANLNE-LGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFG 59
Query: 448 IPIIQKLQEMRPKISRKDGIYAVIILPTRELALQ-TLEI-----FTKLCKSFTWIVPSWL 501
+ ++QKL R ++ A+++ PTRELA Q EI F K T L
Sbjct: 60 LGLLQKLDVKRFRVQ------ALVLCPTRELADQVAKEIRRLARFIPNIKVLT------L 107
Query: 502 TGGEKMKSEKARIRKGISILVATPGRLLDHCKHTETLKFSKVEHLVLDEADRILDQGYER 561
GG M + + G I+V TPGR+LDH + TL + LVLDEADR+LD G++
Sbjct: 108 CGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRK-GTLDLDALNTLVLDEADRMLDMGFQD 166
Query: 562 DIAEFLEILKKQKPQFQSILLSATLTPAVQRLAGMTLQNPIQIDAADSTDIHNTTDSLVI 621
I I+++ + Q++L SAT + ++ ++P+++ +S
Sbjct: 167 AID---AIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEV----------KVESTHD 213
Query: 622 PDSLKQHFIVTPPKLRLVALASFILGKCQNVNEDEESKMLVFMAT----QDMADYHTELL 677
+++Q F P RL AL +L Q + +VF T Q++AD
Sbjct: 214 LPAIEQRFYEVSPDERLPALQR-LLLHHQPES------CVVFCNTKKECQEVADALNAQG 266
Query: 678 STVLGENIAFFKLHGSMSQSERTEVFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTA 737
+ L LHG + Q +R +V F + VL+ TDVAARGLD+ ++ ++ Y
Sbjct: 267 FSALA-------LHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYEL 319
Query: 738 PSSSTDYVHRVGRTARVGHEGSSLLFLIPSE---VKLVEELQNRRIRIEEIK 786
+VHR+GRT R G +G +L + P E +E+ R++ E +
Sbjct: 320 ARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAIEDYLGRKLNWEPLP 371
Score = 124 bits (315), Expect = 4e-30
Identities = 67/182 (36%), Positives = 100/182 (54%), Gaps = 22/182 (12%)
Query: 1 MNITQVTTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYA 60
+ T++T +Q S+ IL G DV+ +++TGSGKT A+ + ++QKL R ++ A
Sbjct: 22 LGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQ------A 75
Query: 61 VIILPTRELALQ-TLEI-----FTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVA 114
+++ PTRELA Q EI F K T L GG M + + G I+V
Sbjct: 76 LVLCPTRELADQVAKEIRRLARFIPNIKVLT------LCGGVPMGPQIDSLEHGAHIIVG 129
Query: 115 TPGRLLDHCKHTETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLS 174
TPGR+LDH + TL + LVLDEADR+LD G++ I I+++ + Q++L S
Sbjct: 130 TPGRILDHLRK-GTLDLDALNTLVLDEADRMLDMGFQDAID---AIIRQAPARRQTLLFS 185
Query: 175 AT 176
AT
Sbjct: 186 AT 187
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 204 bits (520), Expect = 2e-57
Identities = 130/368 (35%), Positives = 197/368 (53%), Gaps = 27/368 (7%)
Query: 416 TTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPT 475
T +QQ +I +L+G D++ +QTG+GKT + +P++Q L +P + + A+I+ PT
Sbjct: 25 TPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPT 84
Query: 476 RELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLDHCKHT 535
RELA Q E K + I + GG + + ++R G+ +LVATPGRLLD +H
Sbjct: 85 RELAAQIGENVRDYSK-YLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLD-LEHQ 142
Query: 536 ETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATLTPAVQRLAG 595
+K +VE LVLDEADR+LD G+ DI +L K + Q++L SAT + ++ LA
Sbjct: 143 NAVKLDQVEILVLDEADRMLDMGFIHDIRR---VLAKLPAKRQNLLFSATFSDDIKALAE 199
Query: 596 MTLQNPIQIDAADSTDIHNTTDSLVIPDSLKQHFIVTPPKLRLVALASFILGKCQNVNED 655
L NP++I+ A NT V + HF+ K R L S ++G +
Sbjct: 200 KLLHNPLEIEVAR----RNTASEQV---TQHVHFV---DKKRKRELLSQMIG------KG 243
Query: 656 EESKMLVFMATQDMADYHTELLSTVLGENIAFFKLHGSMSQSERTEVFKTFRSVKSGVLI 715
++LVF T+ A++ E L+ + I +HG+ SQ RT F+S VL+
Sbjct: 244 NWQQVLVFTRTKHGANHLAEQLNK---DGIRSAAIHGNKSQGARTRALADFKSGDIRVLV 300
Query: 716 CTDVAARGLDLPLVDWIVQYTAPSSSTDYVHRVGRTARVGHEGSSLLFLIPSEVKL---V 772
TD+AARGLD+ + +V Y P+ DYVHR+GRT R G +L + E KL +
Sbjct: 301 ATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDI 360
Query: 773 EELQNRRI 780
E+L + I
Sbjct: 361 EKLLKKEI 368
Score = 124 bits (312), Expect = 6e-30
Identities = 67/172 (38%), Positives = 102/172 (59%), Gaps = 5/172 (2%)
Query: 7 TTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPT 66
T +QQ +I +L+G D++ +QTG+GKT + +P++Q L +P + + A+I+ PT
Sbjct: 25 TPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPT 84
Query: 67 RELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLDHCKHT 126
RELA Q E K + I + GG + + ++R G+ +LVATPGRLLD +H
Sbjct: 85 RELAAQIGENVRDYSK-YLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLD-LEHQ 142
Query: 127 ETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATLT 178
+K +VE LVLDEADR+LD G+ DI +L K + Q++L SAT +
Sbjct: 143 NAVKLDQVEILVLDEADRMLDMGFIHDIR---RVLAKLPAKRQNLLFSATFS 191
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 194 bits (494), Expect = 5e-53
Identities = 138/411 (33%), Positives = 211/411 (51%), Gaps = 50/411 (12%)
Query: 373 NVPTRRLKPVSEALFAPTSYEE--FPGIHPFMKKNLNEGMNITQVTTVQQLSIQ--PI-L 427
NVP KPV S+E FP ++ K+L T+ T +Q +Q PI L
Sbjct: 124 NVP----KPV-------VSFEYTSFPD---YILKSLKNA-GFTEPTPIQ---VQGWPIAL 165
Query: 428 DGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELALQTLEIFT 487
G D++ ++TGSGKTLA+ +P I + +P + DG +++ PTRELA Q E
Sbjct: 166 SGRDMIGIAETGSGKTLAFLLPAIVHINA-QPLLRYGDGPIVLVLAPTRELAEQIREQCN 224
Query: 488 KLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLDHCKHTETLKFSKVEHLV 547
K S I + GG + + +R+G+ IL+A PGRL+D + T +V +LV
Sbjct: 225 KFGASSK-IRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVT-NLRRVTYLV 282
Query: 548 LDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATLTPAVQRLA-GMTLQNPIQID- 605
LDEADR+LD G+E I + I+ + +P Q+++ SAT VQ LA + + P+ ++
Sbjct: 283 LDEADRMLDMGFEPQIRK---IVSQIRPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNV 339
Query: 606 -AADSTDIHNTTDSLVIPDSLKQHFIVTPPKLRLVALASFILGKCQNVNEDEESKMLVFM 664
+ D T HN +KQ V + L L + K+L+F+
Sbjct: 340 GSLDLTACHN----------IKQEVFVVEEHEKRGKLKML-LQRIMRDG----DKILIFV 384
Query: 665 ATQDMADYHTELLSTVLGENIAFFKLHGSMSQSERTEVFKTFRSVKSGVLICTDVAARGL 724
T+ AD+ T+ L + +HG Q ERT V F++ KS ++I TDVA+RGL
Sbjct: 385 ETKKGADFLTKELRL---DGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGL 441
Query: 725 DLPLVDWIVQYTAPSSSTDYVHRVGRTARVGHEGSSLLFLIPSEVKLVEEL 775
D+ V +++ + P+ DYVHR+GRT R G +G+S FL P + +L +L
Sbjct: 442 DVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDL 492
Score = 100 bits (251), Expect = 6e-22
Identities = 69/192 (35%), Positives = 106/192 (55%), Gaps = 18/192 (9%)
Query: 2 NITQVTTVQQLSIQ--PI-LDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGI 58
T+ T +Q +Q PI L G D++ ++TGSGKTLA+ +P I + +P + DG
Sbjct: 149 GFTEPTPIQ---VQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINA-QPLLRYGDGP 204
Query: 59 YAVIILPTRELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGR 118
+++ PTRELA Q E K S I + GG + + +R+G+ IL+A PGR
Sbjct: 205 IVLVLAPTRELAEQIREQCNKFGASSK-IRNTVAYGGVPKRGQIYALRRGVEILIACPGR 263
Query: 119 LLDHCKHTETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATLT 178
L+D + T +V +LVLDEADR+LD G+E I +I+ + +P Q+++ SAT
Sbjct: 264 LIDFLESNVT-NLRRVTYLVLDEADRMLDMGFEPQIR---KIVSQIRPDRQTLMWSAT-- 317
Query: 179 PATCWCKHTETL 190
W K ++L
Sbjct: 318 ----WPKEVQSL 325
Score = 55.9 bits (135), Expect = 6e-08
Identities = 42/140 (30%), Positives = 68/140 (48%), Gaps = 21/140 (15%)
Query: 193 SKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSVLLSATLTPAVQRLA-GMTLQ 251
+V +LVLDEADR+LD G+E I +I+ + +P Q+++ SAT VQ LA + +
Sbjct: 276 RRVTYLVLDEADRMLDMGFEPQIR---KIVSQIRPDRQTLMWSATWPKEVQSLARDLCKE 332
Query: 252 NPIQID--AADSTDIHNTTDSLVIPDSLKQHFIVTPPKLRLVALASFILGKCQNVNEDEE 309
P+ ++ + D T HN +KQ V + L L +
Sbjct: 333 EPVHVNVGSLDLTACHN----------IKQEVFVVEEHEKRGKLKML-LQRIMRDG---- 377
Query: 310 SKMLVFMATQDMADYHTELL 329
K+L+F+ T+ AD+ T+ L
Sbjct: 378 DKILIFVETKKGADFLTKEL 397
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 186 bits (474), Expect = 2e-51
Identities = 129/390 (33%), Positives = 197/390 (50%), Gaps = 46/390 (11%)
Query: 390 TSYEEFPGIHPFMKKNLNEGMNITQVTTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIP 449
T++ E + + + L + T+ T +Q +I P LDG DVL + TG+GKT A+ +P
Sbjct: 1 TTFSELE-LDESLLEALQD-KGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLP 58
Query: 450 IIQKLQEMRPKISRKDGIYAVIIL-PTRELALQTLEIFTKLCKSFTWIVPSWLTGGEKMK 508
+Q L + P+ RK G ++IL PTRELA+Q + +L K T + + +TGG
Sbjct: 59 ALQHLLDF-PR--RKSGPPRILILTPTRELAMQVADQARELAK-HTHLDIATITGGVAYM 114
Query: 509 SEKARIRKGISILVATPGRLLDHCKHTETLKFSKVEHLVLDEADRILDQGYERDIAEFLE 568
+ + I+VATPGRLL + K E VE L+LDEADR+LD G+ +DI
Sbjct: 115 NHAEVFSENQDIVVATPGRLLQYIK-EENFDCRAVETLILDEADRMLDMGFAQDIE---T 170
Query: 569 ILKKQKPQFQSILLSATLT-PAVQRLAGMTLQNPIQIDAADST----DIHNTTDSLVIPD 623
I + + + Q++L SATL AVQ A L +P++++A S IH D
Sbjct: 171 IAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQ---WYYRAD 227
Query: 624 SLKQHFIVTPPKLRLVALASFILGKCQNVNEDEESKMLVFMATQDMADYHTELLSTVLGE 683
L+ H K L L + + E ++ +VF+ T++ EL +
Sbjct: 228 DLE-H------KTAL--LCHLL-------KQPEVTRSIVFVRTRERV---HELAGWLRKA 268
Query: 684 NIAFFKLHGSMSQSERTEVFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPSSSTD 743
I L G M Q++R E K + VL+ TDVAARG+D+ V ++ + P S+
Sbjct: 269 GINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADT 328
Query: 744 YVHRVGRTARVGHEGSSLLFLIPSEVKLVE 773
Y+HR+GRT R G +G++ + LVE
Sbjct: 329 YLHRIGRTGRAGRKGTA--------ISLVE 350
Score = 114 bits (288), Expect = 6e-27
Identities = 70/172 (40%), Positives = 100/172 (58%), Gaps = 9/172 (5%)
Query: 7 TTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIIL-P 65
T +Q +I P LDG DVL + TG+GKT A+ +P +Q L + P+ RK G ++IL P
Sbjct: 25 TAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDF-PR--RKSGPPRILILTP 81
Query: 66 TRELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLDHCKH 125
TRELA+Q + +L K T + + +TGG + + I+VATPGRLL + K
Sbjct: 82 TRELAMQVADQARELAK-HTHLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIK- 139
Query: 126 TETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATL 177
E VE L+LDEADR+LD G+ +DI I + + + Q++L SATL
Sbjct: 140 EENFDCRAVETLILDEADRMLDMGFAQDIE---TIAAETRWRKQTLLFSATL 188
>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 = 164 bits (417), Expect = 9e-47
Identities = 76/179 (42%), Positives = 106/179 (59%), Gaps = 11/179 (6%)
Query: 416 TTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPT 475
T +Q +I IL G DVLV++ TGSGKTLA+ +PI+Q L + +K G A+++ PT
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQAL------LPKKGGPQALVLAPT 54
Query: 476 RELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKG-ISILVATPGRLLDHCKH 534
RELA Q E KL K + + LTGG +K + +++KG ILV TPGRLLD +
Sbjct: 55 RELAEQIYEELKKLFK-ILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRR 113
Query: 535 TETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATLTPAVQRL 593
+ ++ LVLDEA R+LD G+ D+ EIL + P Q +LLSATL ++ L
Sbjct: 114 GKLKLLKNLKLLVLDEAHRLLDMGFGDDLE---EILSRLPPDRQILLLSATLPRNLEDL 169
Score = 160 bits (407), Expect = 2e-45
Identities = 75/173 (43%), Positives = 103/173 (59%), Gaps = 11/173 (6%)
Query: 7 TTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPT 66
T +Q +I IL G DVLV++ TGSGKTLA+ +PI+Q L + +K G A+++ PT
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQAL------LPKKGGPQALVLAPT 54
Query: 67 RELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKG-ISILVATPGRLLDHCKH 125
RELA Q E KL K + + LTGG +K + +++KG ILV TPGRLLD +
Sbjct: 55 RELAEQIYEELKKLFK-ILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRR 113
Query: 126 TETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATLT 178
+ ++ LVLDEA R+LD G+ D+ EIL + P Q +LLSATL
Sbjct: 114 GKLKLLKNLKLLVLDEAHRLLDMGFGDDLE---EILSRLPPDRQILLLSATLP 163
Score = 55.7 bits (135), Expect = 8e-09
Identities = 32/95 (33%), Positives = 45/95 (47%), Gaps = 11/95 (11%)
Query: 153 DIAEFLEILKKQKPQFQSILLSATLTPATCW--CKHTETLKFSKVEHLVLDEADRILDQG 210
+ E LKK K IL+ TP + + ++ LVLDEA R+LD G
Sbjct: 84 SLKEQARKLKKGKAD---ILVG---TPGRLLDLLRRGKLKLLKNLKLLVLDEAHRLLDMG 137
Query: 211 YERDIAEFLEILKKQKPQFQSVLLSATLTPAVQRL 245
+ D+ EIL + P Q +LLSATL ++ L
Sbjct: 138 FGDDLE---EILSRLPPDRQILLLSATLPRNLEDL 169
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 166 bits (421), Expect = 5e-44
Identities = 134/457 (29%), Positives = 211/457 (46%), Gaps = 56/457 (12%)
Query: 351 PKKTEVKSGPISSLFQNNPDIPNVPTRRLKPVSEALFAP-----------TSYEEFPGIH 399
+ P ++ + + P R KP +L+ T + +F +
Sbjct: 37 AAPATKAAAPAAAAPRAEKPKKDKPRRERKPKPASLWKLEDFVVEPQEGKTRFHDF-NLA 95
Query: 400 PFMKKNLNEGMNITQVTTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRP 459
P + +++ + T +Q + L G D + R+QTG+GKT A+ I II +L + P
Sbjct: 96 PELMHAIHD-LGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPP 154
Query: 460 KISRKDG-IYAVIILPTRELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGI 518
R G A+II PTREL +Q + L K V +++ G + K K +
Sbjct: 155 PKERYMGEPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFC 214
Query: 519 SILVATPGRLLDHCKHTETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKK--QKPQ 576
ILVATPGRLLD + E + VE +VLDEADR+LD G+ I + +I+++ +K +
Sbjct: 215 DILVATPGRLLDFNQRGE-VHLDMVEVMVLDEADRMLDMGF---IPQVRQIIRQTPRKEE 270
Query: 577 FQSILLSATLTPAVQRLAGMTLQNPIQIDAADSTDIHNTTDSLVIPDSLKQHF--IVTPP 634
Q++L SAT T V LA +P ++ V D+++QH +
Sbjct: 271 RQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPEN---------VASDTVEQHVYAVAGSD 321
Query: 635 KLRLVALASFILGKCQN-VNEDEESKMLVFMATQDMADYHTELLSTVLGENIAFFKLHGS 693
K +L+ N V ++ +++VF +D E L G N A +L G
Sbjct: 322 KYKLL----------YNLVTQNPWERVMVFANRKDEVRRIEERL-VKDGINAA--QLSGD 368
Query: 694 MSQSERTEVFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPSSSTDYVHRVGRTAR 753
+ Q +R + + FR K VL+ TDVA RG+ + + ++ +T P DYVHR+GRT R
Sbjct: 369 VPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGR 428
Query: 754 VGHEGSSLLFL-------IPSEVKLVEELQNRRIRIE 783
G G S+ F +P +EEL R+I E
Sbjct: 429 AGASGVSISFAGEDDAFQLPE----IEELLGRKISCE 461
Score = 103 bits (257), Expect = 6e-23
Identities = 68/178 (38%), Positives = 98/178 (55%), Gaps = 7/178 (3%)
Query: 4 TQVTTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDG-IYAVI 62
T +Q + L G D + R+QTG+GKT A+ I II +L + P R G A+I
Sbjct: 108 PYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALI 167
Query: 63 ILPTRELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLDH 122
I PTREL +Q + L K V +++ G + K K + ILVATPGRLLD
Sbjct: 168 IAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDF 227
Query: 123 CKHTETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKK--QKPQFQSILLSATLT 178
+ E + VE +VLDEADR+LD G+ I + +I+++ +K + Q++L SAT T
Sbjct: 228 NQRGE-VHLDMVEVMVLDEADRMLDMGF---IPQVRQIIRQTPRKEERQTLLFSATFT 281
Score = 44.5 bits (105), Expect = 2e-04
Identities = 25/65 (38%), Positives = 40/65 (61%), Gaps = 5/65 (7%)
Query: 195 VEHLVLDEADRILDQGYERDIAEFLEILKK--QKPQFQSVLLSATLTPAVQRLAGMTLQN 252
VE +VLDEADR+LD G+ I + +I+++ +K + Q++L SAT T V LA +
Sbjct: 238 VEVMVLDEADRMLDMGF---IPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTD 294
Query: 253 PIQID 257
P ++
Sbjct: 295 PAIVE 299
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 166 bits (422), Expect = 4e-43
Identities = 138/416 (33%), Positives = 212/416 (50%), Gaps = 49/416 (11%)
Query: 418 VQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQ-EMR-PKISRKDGIYAVIILPT 475
+Q I +L+G DVL +QTGSGKT A+++P++ L E++ P+I +++ PT
Sbjct: 32 IQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQI--------LVLAPT 83
Query: 476 RELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLDHCKHT 535
RELA+Q E T K + L GG++ + +R+G I+V TPGRLLDH K
Sbjct: 84 RELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRG 143
Query: 536 ETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKP-QFQSILLSATLTPAVQRLA 594
TL SK+ LVLDEAD +L G+ D+ E + Q P Q+ L SAT+ A++R+
Sbjct: 144 -TLDLSKLSGLVLDEADEMLRMGFIEDV----ETIMAQIPEGHQTALFSATMPEAIRRIT 198
Query: 595 GMTLQNPIQIDAADSTDIHNTTDSLVIPDSLKQHFIVTPPKLRLVALASFILGKCQNVNE 654
++ P ++ S TT PD + Q + + AL F+ E
Sbjct: 199 RRFMKEPQEVRIQSSV----TTR----PD-ISQSYWTVWGMRKNEALVRFLEA------E 243
Query: 655 DEESKMLVFMATQDMADYHTELLSTVLGENIAFFKLHGSMSQSERTEVFKTFRSVKSGVL 714
D ++ ++F+ T++ E L G N A L+G M+Q+ R + + + + +L
Sbjct: 244 DFDAA-IIFVRTKNATLEVAEALERN-GYNSA--ALNGDMNQALREQTLERLKDGRLDIL 299
Query: 715 ICTDVAARGLDLPLVDWIVQYTAPSSSTDYVHRVGRTARVGHEGSSLLFLIPSEVKLVEE 774
I TDVAARGLD+ + +V Y P S YVHR+GRT R G G +LLF+ E +L+
Sbjct: 300 IATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRN 359
Query: 775 LQ-NRRIRIEEIKLKDCLQNLLSVKMEGDLSRLADGNVETAATALQMSFESAVLQQ 829
++ ++ I E++L + LL + RL E A +Q ES+ L Q
Sbjct: 360 IERTMKLTIPEVELPNA--ELLGKR------RL-----EKFAAKVQQQLESSDLDQ 402
Score = 105 bits (264), Expect = 2e-23
Identities = 69/175 (39%), Positives = 99/175 (56%), Gaps = 16/175 (9%)
Query: 9 VQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQ-EMR-PKISRKDGIYAVIILPT 66
+Q I +L+G DVL +QTGSGKT A+++P++ L E++ P+I +++ PT
Sbjct: 32 IQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQI--------LVLAPT 83
Query: 67 RELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLDHCKHT 126
RELA+Q E T K + L GG++ + +R+G I+V TPGRLLDH K
Sbjct: 84 RELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRG 143
Query: 127 ETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKP-QFQSILLSATLTPA 180
TL SK+ LVLDEAD +L G+ D+ E + Q P Q+ L SAT+ A
Sbjct: 144 -TLDLSKLSGLVLDEADEMLRMGFIEDV----ETIMAQIPEGHQTALFSATMPEA 193
Score = 42.1 bits (99), Expect = 0.001
Identities = 29/81 (35%), Positives = 41/81 (50%), Gaps = 9/81 (11%)
Query: 189 TLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKP-QFQSVLLSATLTPAVQRLAG 247
TL SK+ LVLDEAD +L G+ D+ E + Q P Q+ L SAT+ A++R+
Sbjct: 144 TLDLSKLSGLVLDEADEMLRMGFIEDV----ETIMAQIPEGHQTALFSATMPEAIRRITR 199
Query: 248 MTLQNP----IQIDAADSTDI 264
++ P IQ DI
Sbjct: 200 RFMKEPQEVRIQSSVTTRPDI 220
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 158 bits (400), Expect = 7e-41
Identities = 111/378 (29%), Positives = 183/378 (48%), Gaps = 57/378 (15%)
Query: 416 TTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPK-ISRKDGIYAVIILP 474
T +Q +I L G +LV + TGSGKT ++ +PII + +R S + A+++ P
Sbjct: 145 TPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTP 204
Query: 475 TRELALQTLEIFTKLCKSF---TWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLD- 530
TREL +Q + L K T +V GG+ M + RI++G+ ++V TPGRL+D
Sbjct: 205 TRELCVQVEDQAKVLGKGLPFKTALV----VGGDAMPQQLYRIQQGVELIVGTPGRLIDL 260
Query: 531 HCKHTETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATLTPAV 590
KH L V LVLDE D +L++G+ + + + L Q Q +L SAT++P V
Sbjct: 261 LSKHDIEL--DNVSVLVLDEVDCMLERGFRDQVMQIFQAL----SQPQVLLFSATVSPEV 314
Query: 591 QRLAGMTLQNPIQIDAADSTDIHNTTDSLVI-----------PDSL--KQHFIVTPPKLR 637
++ A ++ I I + + L I D L KQHF PP
Sbjct: 315 EKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQKLFDILKSKQHF--KPP--- 369
Query: 638 LVALASFILGKCQNVNEDEESKMLVFMATQDMADYHTELLSTVLGENIAFFKLHGSMSQS 697
+VF++++ AD ++ V G + +HG S
Sbjct: 370 ----------------------AVVFVSSRLGADLLANAITVVTG--LKALSIHGEKSMK 405
Query: 698 ERTEVFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPSSSTDYVHRVGRTARVGHE 757
ER EV K+F + V++ T V RG+DL V ++ + P++ +Y+H++GR +R+G +
Sbjct: 406 ERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEK 465
Query: 758 GSSLLFLIPSEVKLVEEL 775
G++++F+ + L EL
Sbjct: 466 GTAIVFVNEEDRNLFPEL 483
Score = 100 bits (251), Expect = 5e-22
Identities = 62/179 (34%), Positives = 96/179 (53%), Gaps = 15/179 (8%)
Query: 7 TTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPK-ISRKDGIYAVIILP 65
T +Q +I L G +LV + TGSGKT ++ +PII + +R S + A+++ P
Sbjct: 145 TPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTP 204
Query: 66 TRELALQTLEIFTKLCKSF---TWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLD- 121
TREL +Q + L K T +V GG+ M + RI++G+ ++V TPGRL+D
Sbjct: 205 TRELCVQVEDQAKVLGKGLPFKTALV----VGGDAMPQQLYRIQQGVELIVGTPGRLIDL 260
Query: 122 HCKHTETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATLTPA 180
KH L V LVLDE D +L++G+ + + + L Q Q +L SAT++P
Sbjct: 261 LSKHDIEL--DNVSVLVLDEVDCMLERGFRDQVMQIFQAL----SQPQVLLFSATVSPE 313
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 157 bits (398), Expect = 3e-40
Identities = 117/402 (29%), Positives = 202/402 (50%), Gaps = 63/402 (15%)
Query: 380 KPVSEALFAPTSYEEFPGIHPFMKKNLNEGMNITQVTTVQQLSIQPILDGGDVLVRSQTG 439
KP+++ F +S++ +HP + L E T+ T +Q L++ L GGDV ++QTG
Sbjct: 4 KPLTDLTF--SSFD----LHPALLAGL-ESAGFTRCTPIQALTLPVALPGGDVAGQAQTG 56
Query: 440 SGKTLAYAIPIIQKLQEMRPKISRK--DGIYAVIILPTRELALQ----TLEIFTKLCKSF 493
+GKTLA+ + ++ +L RP ++ + + A+I+ PTRELA+Q ++ L F
Sbjct: 57 TGKTLAFLVAVMNRLLS-RPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLRF 115
Query: 494 TWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLDHCKHTETLKFSKVEHLVLDEADR 553
+ GG ++ +++G+ +++ATPGRL+D+ K + + E VLDEADR
Sbjct: 116 ALVY-----GGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADR 170
Query: 554 ILDQGYERDIAEFLEILKKQKPQFQSILLSATLTPAVQRLAGMTLQNPIQIDAADSTDIH 613
+ D G+ +DI L + ++ + Q++L SATL+ V LA + P ++ T
Sbjct: 171 MFDLGFIKDIRFLLRRMPERGTR-QTLLFSATLSHRVLELAYEHMNEPEKLVVETET--- 226
Query: 614 NTTDSLVIPDSLKQ--HFIVTPPKLRLVALASFILGKCQNVNEDEESKMLVFMATQ---- 667
+ ++Q +F K L +LG ++ E ++ +VF+ T+
Sbjct: 227 ------ITAARVRQRIYFPADEEKQTL------LLGL---LSRSEGARTMVFVNTKAFVE 271
Query: 668 ------DMADYHTELLSTVLGENIAFFKLHGSMSQSERTEVFKTFRSVKSGVLICTDVAA 721
+ Y +LS G + Q +R + F+ + +L+ TDVAA
Sbjct: 272 RVARTLERHGYRVGVLS-------------GDVPQKKRESLLNRFQKGQLEILVATDVAA 318
Query: 722 RGLDLPLVDWIVQYTAPSSSTDYVHRVGRTARVGHEGSSLLF 763
RGL + V ++ Y P + DYVHR+GRTAR+G EG ++ F
Sbjct: 319 RGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISF 360
Score = 101 bits (254), Expect = 2e-22
Identities = 61/181 (33%), Positives = 106/181 (58%), Gaps = 13/181 (7%)
Query: 4 TQVTTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRK--DGIYAV 61
T+ T +Q L++ L GGDV ++QTG+GKTLA+ + ++ +L RP ++ + + A+
Sbjct: 30 TRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLS-RPALADRKPEDPRAL 88
Query: 62 IILPTRELALQ----TLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPG 117
I+ PTRELA+Q ++ L F + GG ++ +++G+ +++ATPG
Sbjct: 89 ILAPTRELAIQIHKDAVKFGADLGLRFALVY-----GGVDYDKQRELLQQGVDVIIATPG 143
Query: 118 RLLDHCKHTETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATL 177
RL+D+ K + + E VLDEADR+ D G+ +DI L + ++ + Q++L SATL
Sbjct: 144 RLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMPERGTR-QTLLFSATL 202
Query: 178 T 178
+
Sbjct: 203 S 203
Score = 39.9 bits (93), Expect = 0.007
Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 183 WCKHTETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSVLLSATLTPAV 242
+ K + + E VLDEADR+ D G+ +DI L + ++ + Q++L SATL+ V
Sbjct: 148 YVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMPERGTR-QTLLFSATLSHRV 206
Query: 243 QRLAGMTLQNP 253
LA + P
Sbjct: 207 LELAYEHMNEP 217
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 143 bits (361), Expect = 7e-39
Identities = 68/199 (34%), Positives = 104/199 (52%), Gaps = 12/199 (6%)
Query: 408 EGMNITQVTTVQQLSIQPILDG-GDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDG 466
E + Q+ +I+ +L G DV++ + TGSGKTLA +P ++ L+ R G
Sbjct: 2 EKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALK-------RGKG 54
Query: 467 IYAVIILPTRELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPG 526
++++PTRELA Q E KL S V G K + + ILV TPG
Sbjct: 55 GRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPG 114
Query: 527 RLLDHCKHTETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATL 586
RLLD ++ + L S V+ ++LDEA R+LD G+ + + L++L K Q +LLSAT
Sbjct: 115 RLLDLLEN-DKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNV---QLLLLSATP 170
Query: 587 TPAVQRLAGMTLQNPIQID 605
++ L + L +P+ ID
Sbjct: 171 PEEIENLLELFLNDPVFID 189
Score = 131 bits (331), Expect = 8e-35
Identities = 62/181 (34%), Positives = 93/181 (51%), Gaps = 12/181 (6%)
Query: 1 MNITQVTTVQQLSIQPILDG-GDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIY 59
+ Q+ +I+ +L G DV++ + TGSGKTLA +P ++ L+ R G
Sbjct: 4 FGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALK-------RGKGGR 56
Query: 60 AVIILPTRELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRL 119
++++PTRELA Q E KL S V G K + + ILV TPGRL
Sbjct: 57 VLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRL 116
Query: 120 LDHCKHTETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATLTP 179
LD ++ + L S V+ ++LDEA R+LD G+ + + L++L K Q +LLSAT
Sbjct: 117 LDLLEN-DKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNV---QLLLLSATPPE 172
Query: 180 A 180
Sbjct: 173 E 173
Score = 57.9 bits (140), Expect = 2e-09
Identities = 25/68 (36%), Positives = 40/68 (58%), Gaps = 3/68 (4%)
Query: 190 LKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSVLLSATLTPAVQRLAGMT 249
L S V+ ++LDEA R+LD G+ + + L++L K Q +LLSAT ++ L +
Sbjct: 125 LSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNV---QLLLLSATPPEEIENLLELF 181
Query: 250 LQNPIQID 257
L +P+ ID
Sbjct: 182 LNDPVFID 189
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 144 bits (366), Expect = 4e-37
Identities = 110/392 (28%), Positives = 176/392 (44%), Gaps = 72/392 (18%)
Query: 397 GIHPFMKKNLNEGMNITQVTTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAI-------- 448
+HP + + L + T +Q L++ L G DV ++QTG+GKT+A+
Sbjct: 14 ALHPQVVEALEK-KGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLS 72
Query: 449 -PIIQKLQEMRPKISRKDGIYAVIILPTRELALQT---LEIFTKLCKSFTWIVPSWLTGG 504
P + + +P+ A+I+ PTRELA+Q E + + GG
Sbjct: 73 HPAPEDRKVNQPR--------ALIMAPTRELAVQIHADAEPLAQATGLKLGLA----YGG 120
Query: 505 EKMKSEKARIRKGISILVATPGRLLDHCKHTETLKFSKVEHLVLDEADRILDQGYERDIA 564
+ + + G+ IL+ T GRL+D+ K + ++ +VLDEADR+ D G+ +DI
Sbjct: 121 DGYDKQLKVLESGVDILIGTTGRLIDYAKQ-NHINLGAIQVVVLDEADRMFDLGFIKDI- 178
Query: 565 EFLEILKKQKPQFQ--SILLSATLTPAVQRLAGMTLQNP--IQIDAADSTDIHNTTDSLV 620
+L ++ P Q ++L SATL+ V+ LA + NP ++++ T H + L
Sbjct: 179 RWL--FRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTG-HRIKEELF 235
Query: 621 IPDSLKQHFIVTPPKLRLVALASFILGKCQNVNEDEESKMLVFMATQD---------MAD 671
P K+RL L + I E+ + ++F T+ AD
Sbjct: 236 YPS--------NEEKMRL--LQTLI-------EEEWPDRAIIFANTKHRCEEIWGHLAAD 278
Query: 672 YHTELLSTVLGENIAFFKLHGSMSQSERTEVFKTFRSVKSGVLICTDVAARGLDLPLVDW 731
H L L G ++Q +R + + F +L+ TDVAARGL +P V
Sbjct: 279 GHRVGL------------LTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTH 326
Query: 732 IVQYTAPSSSTDYVHRVGRTARVGHEGSSLLF 763
+ Y P DYVHR+GRT R G G S+
Sbjct: 327 VFNYDLPDDCEDYVHRIGRTGRAGASGHSISL 358
Score = 87.7 bits (218), Expect = 3e-18
Identities = 56/186 (30%), Positives = 93/186 (50%), Gaps = 30/186 (16%)
Query: 7 TTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAI---------PIIQKLQEMRPKISRKDG 57
T +Q L++ L G DV ++QTG+GKT+A+ P + + +P+
Sbjct: 32 TPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPR------ 85
Query: 58 IYAVIILPTRELALQT---LEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVA 114
A+I+ PTRELA+Q E + + GG+ + + G+ IL+
Sbjct: 86 --ALIMAPTRELAVQIHADAEPLAQATGLKLGLA----YGGDGYDKQLKVLESGVDILIG 139
Query: 115 TPGRLLDHCKHTETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQ--SIL 172
T GRL+D+ K + ++ +VLDEADR+ D G+ +DI +L ++ P Q ++L
Sbjct: 140 TTGRLIDYAKQ-NHINLGAIQVVVLDEADRMFDLGFIKDI-RWL--FRRMPPANQRLNML 195
Query: 173 LSATLT 178
SATL+
Sbjct: 196 FSATLS 201
Score = 41.1 bits (97), Expect = 0.002
Identities = 28/87 (32%), Positives = 47/87 (54%), Gaps = 8/87 (9%)
Query: 192 FSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQ--SVLLSATLTPAVQRLAGMT 249
++ +VLDEADR+ D G+ +DI +L ++ P Q ++L SATL+ V+ LA
Sbjct: 155 LGAIQVVVLDEADRMFDLGFIKDI-RWL--FRRMPPANQRLNMLFSATLSYRVRELAFEH 211
Query: 250 LQNP--IQIDAADSTDIHNTTDSLVIP 274
+ NP ++++ T H + L P
Sbjct: 212 MNNPEYVEVEPEQKTG-HRIKEELFYP 237
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 143 bits (363), Expect = 5e-37
Identities = 100/374 (26%), Positives = 191/374 (51%), Gaps = 32/374 (8%)
Query: 416 TTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPT 475
+ +QQ I+PILDG D + ++Q+G+GKT + I +Q + + + A+I+ PT
Sbjct: 52 SAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLID---YDL---NACQALILAPT 105
Query: 476 RELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLDHCKHT 535
RELA Q ++ L + + GG ++ + +++ G+ ++V TPGR+ D
Sbjct: 106 RELAQQIQKVVLAL-GDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMID-K 163
Query: 536 ETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATLTPAVQRLAG 595
L+ ++ +LDEAD +L +G++ I ++ KK P Q L SAT+ + L
Sbjct: 164 RHLRVDDLKLFILDEADEMLSRGFKGQIY---DVFKKLPPDVQVALFSATMPNEILELTT 220
Query: 596 MTLQNPIQIDAADSTDIHNTTDSLVIPDSLKQHFI-VTPPKLRLVALASFILGKCQNVNE 654
+++P +I D L + + ++Q ++ V + + L C
Sbjct: 221 KFMRDPKRILV--------KKDELTL-EGIRQFYVAVEKEEWKFDTL-------CDLYET 264
Query: 655 DEESKMLVFMATQDMADYHTELLSTVLGENIAFFKLHGSMSQSERTEVFKTFRSVKSGVL 714
++ +++ T+ DY T+ + + +HG M Q +R + + FRS + VL
Sbjct: 265 LTITQAIIYCNTRRKVDYLTKKMHE---RDFTVSCMHGDMDQKDRDLIMREFRSGSTRVL 321
Query: 715 ICTDVAARGLDLPLVDWIVQYTAPSSSTDYVHRVGRTARVGHEGSSLLFLIPSEVKLVEE 774
I TD+ ARG+D+ V ++ Y P+S +Y+HR+GR+ R G +G ++ F+ P +++ ++E
Sbjct: 322 ITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKE 381
Query: 775 LQNR-RIRIEEIKL 787
++ +IEE+ +
Sbjct: 382 IERHYNTQIEEMPM 395
Score = 83.0 bits (205), Expect = 1e-16
Identities = 52/171 (30%), Positives = 92/171 (53%), Gaps = 11/171 (6%)
Query: 7 TTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPT 66
+ +QQ I+PILDG D + ++Q+G+GKT + I +Q + + + A+I+ PT
Sbjct: 52 SAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLID---YDL---NACQALILAPT 105
Query: 67 RELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLDHCKHT 126
RELA Q ++ L + + GG ++ + +++ G+ ++V TPGR+ D
Sbjct: 106 RELAQQIQKVVLAL-GDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMID-K 163
Query: 127 ETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATL 177
L+ ++ +LDEAD +L +G++ I ++ KK P Q L SAT+
Sbjct: 164 RHLRVDDLKLFILDEADEMLSRGFKGQIY---DVFKKLPPDVQVALFSATM 211
Score = 37.1 bits (86), Expect = 0.042
Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 3/67 (4%)
Query: 190 LKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSVLLSATLTPAVQRLAGMT 249
L+ ++ +LDEAD +L +G++ I ++ KK P Q L SAT+ + L
Sbjct: 166 LRVDDLKLFILDEADEMLSRGFKGQIY---DVFKKLPPDVQVALFSATMPNEILELTTKF 222
Query: 250 LQNPIQI 256
+++P +I
Sbjct: 223 MRDPKRI 229
>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 = 123 bits (311), Expect = 9e-33
Identities = 59/156 (37%), Positives = 82/156 (52%), Gaps = 13/156 (8%)
Query: 22 DVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELALQTLEIFTKLC 81
DVL+ + TGSGKTLA +PI++ L G +++ PTRELA Q E +L
Sbjct: 2 DVLLAAPTGSGKTLAALLPILELLDS-------LKGGQVLVLAPTRELANQVAERLKELF 54
Query: 82 KSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLDHCKHTETLKFSKVEHLVLDE 141
I +L GG +K ++ + I+V TPGRLLD L K++ L+LDE
Sbjct: 55 GEG--IKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDE-LERLKLSLKKLDLLILDE 111
Query: 142 ADRILDQGYERDIAEFLEILKKQKPQFQSILLSATL 177
A R+L+QG+ L+IL K Q +LLSAT
Sbjct: 112 AHRLLNQGFGLLG---LKILLKLPKDRQVLLLSATP 144
Score = 123 bits (311), Expect = 9e-33
Identities = 59/156 (37%), Positives = 82/156 (52%), Gaps = 13/156 (8%)
Query: 431 DVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELALQTLEIFTKLC 490
DVL+ + TGSGKTLA +PI++ L G +++ PTRELA Q E +L
Sbjct: 2 DVLLAAPTGSGKTLAALLPILELLDS-------LKGGQVLVLAPTRELANQVAERLKELF 54
Query: 491 KSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLDHCKHTETLKFSKVEHLVLDE 550
I +L GG +K ++ + I+V TPGRLLD L K++ L+LDE
Sbjct: 55 GEG--IKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDE-LERLKLSLKKLDLLILDE 111
Query: 551 ADRILDQGYERDIAEFLEILKKQKPQFQSILLSATL 586
A R+L+QG+ L+IL K Q +LLSAT
Sbjct: 112 AHRLLNQGFGLLG---LKILLKLPKDRQVLLLSATP 144
Score = 48.5 bits (116), Expect = 1e-06
Identities = 21/54 (38%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 185 KHTETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSVLLSATL 238
L K++ L+LDEA R+L+QG+ L+IL K Q +LLSAT
Sbjct: 94 LERLKLSLKKLDLLILDEAHRLLNQGFGLLG---LKILLKLPKDRQVLLLSATP 144
>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 = 115 bits (290), Expect = 4e-30
Identities = 47/137 (34%), Positives = 71/137 (51%), Gaps = 8/137 (5%)
Query: 627 QHFIVTPPKLRLVALASFILGKCQNVNEDEESKMLVFMATQDMADYHTELLSTVLGENIA 686
+ +++ +L AL + + + K+L+F ++ M D ELL I
Sbjct: 3 KQYVLPVEDEKLEALLELL----KEHLKKGG-KVLIFCPSKKMLDELAELLR---KPGIK 54
Query: 687 FFKLHGSMSQSERTEVFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPSSSTDYVH 746
LHG SQ ER EV K FR + VL+ TDV ARG+DLP V ++ Y P S + Y+
Sbjct: 55 VAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQ 114
Query: 747 RVGRTARVGHEGSSLLF 763
R+GR R G +G+++L
Sbjct: 115 RIGRAGRAGQKGTAILL 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 = 101 bits (254), Expect = 7e-26
Identities = 33/73 (45%), Positives = 46/73 (63%)
Query: 683 ENIAFFKLHGSMSQSERTEVFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPSSST 742
I +LHG +SQ ER E+ + FR+ KS VL+ TDVA RG+DLP V+ ++ Y P +
Sbjct: 6 PGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPWNPA 65
Query: 743 DYVHRVGRTARVG 755
Y+ R+GR R G
Sbjct: 66 SYIQRIGRAGRAG 78
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 94.6 bits (236), Expect = 2e-23
Identities = 38/82 (46%), Positives = 49/82 (59%), Gaps = 1/82 (1%)
Query: 675 ELLSTVLGE-NIAFFKLHGSMSQSERTEVFKTFRSVKSGVLICTDVAARGLDLPLVDWIV 733
E L+ +L E I +LHG +SQ ER E+ F + K VL+ TDVA RGLDLP VD ++
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60
Query: 734 QYTAPSSSTDYVHRVGRTARVG 755
Y P S Y+ R+GR R G
Sbjct: 61 IYDLPWSPASYIQRIGRAGRAG 82
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 97.7 bits (244), Expect = 9e-21
Identities = 102/443 (23%), Positives = 177/443 (39%), Gaps = 69/443 (15%)
Query: 393 EEFPGIHPFMKKNLNEGMNITQVTTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQ 452
E F + P +++ T +T Q+ +I I G +VL+ + TGSGKT A +P+I
Sbjct: 3 EIFNILDPRVREWFKR--KFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVIN 60
Query: 453 KLQEMRPKISRKDGIYAVIILPTRELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKA 512
+L K +DGIYA+ I P + L + + V G+ +SEK
Sbjct: 61 ELLS-LGKGKLEDGIYALYISPLKALNNDIRRRLEEPLRELGIEVAVR--HGDTPQSEKQ 117
Query: 513 RIRKGIS-ILVATPGRLLDHCKHTETL-----------KFSKVEHLVLDEADRILDQGYE 560
++ K IL+ TP E+L V ++++DE + + +
Sbjct: 118 KMLKNPPHILITTP----------ESLAILLNSPKFRELLRDVRYVIVDEIHALAES--K 165
Query: 561 R--DIAEFLEILKKQKPQFQSILLSATLTPA--VQR-LAGMTLQNPIQIDAADSTDIHNT 615
R +A LE L++ FQ I LSAT+ P V + L G
Sbjct: 166 RGVQLALSLERLRELAGDFQRIGLSATVGPPEEVAKFLVG------------------FG 207
Query: 616 TDSLVIPDSLKQH--FIVTPPKLRLVALASFILGKCQNVNE--DEESKMLVFMATQDMAD 671
++ S + V P L+ + + E + L+F T+ A+
Sbjct: 208 DPCEIVDVSAAKKLEIKVISPVEDLIYDEELWAALYERIAELVKKHRTTLIFTNTRSGAE 267
Query: 672 YHTELLSTVLGENIAFFKLHGSMSQSERTEVFKTFRSVKSGVLICTDVAARGLDLPLVDW 731
L + + I HGS+S+ R EV + + + ++ T G+D+ +D
Sbjct: 268 RLAFRLKKLGPDIIEVH--HGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIGDIDL 325
Query: 732 IVQYTAPSSSTDYVHRVGRTARVGHEGSSLLFLIPSEV-KLVEEL----QNRRIRIEEIK 786
++Q +P S ++ R+GR E S +I + L+E L ++E IK
Sbjct: 326 VIQLGSPKSVNRFLQRIGRAGHRLGE-VSKGIIIAEDRDDLLECLVLADLALEGKLERIK 384
Query: 787 L-KDCL----QNLLSVKMEGDLS 804
+ K+ L Q ++ + +E
Sbjct: 385 IPKNPLDVLAQQIVGMALEKVWE 407
Score = 66.9 bits (164), Expect = 3e-11
Identities = 55/192 (28%), Positives = 86/192 (44%), Gaps = 29/192 (15%)
Query: 2 NITQVTTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAV 61
T +T Q+ +I I G +VL+ + TGSGKT A +P+I +L K +DGIYA+
Sbjct: 19 KFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLS-LGKGKLEDGIYAL 77
Query: 62 IILPTRELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGIS-ILVATPGRLL 120
I P + L + + V G+ +SEK ++ K IL+ TP
Sbjct: 78 YISPLKALNNDIRRRLEEPLRELGIEVAVR--HGDTPQSEKQKMLKNPPHILITTP---- 131
Query: 121 DHCKHTETL-----------KFSKVEHLVLDEADRILDQGYER--DIAEFLEILKKQKPQ 167
E+L V ++++DE + + +R +A LE L++
Sbjct: 132 ------ESLAILLNSPKFRELLRDVRYVIVDEIHALAES--KRGVQLALSLERLRELAGD 183
Query: 168 FQSILLSATLTP 179
FQ I LSAT+ P
Sbjct: 184 FQRIGLSATVGP 195
>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 = 75.2 bits (186), Expect = 8e-17
Identities = 29/63 (46%), Positives = 39/63 (61%), Gaps = 2/63 (3%)
Query: 818 LQMSFESAVLQQKILHTSACKGYTSWVRFYASYSKDLRHIFNFKQIHLGHFAKSFALRDA 877
+Q+ E VL+ + L A K + S+VR YAS+S L+ IFN K++ LGH AKSF L
Sbjct: 2 IQLQLEKLVLKDRELKELAQKAFVSYVRAYASHS--LKSIFNVKKLDLGHLAKSFGLLRL 59
Query: 878 PSV 880
P V
Sbjct: 60 PKV 62
>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 = 72.1 bits (177), Expect = 8e-13
Identities = 78/384 (20%), Positives = 138/384 (35%), Gaps = 79/384 (20%)
Query: 422 SIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELALQ 481
+++ I +G +V+V + TGSGKT ++ +PI+ L +R +R A+++ PT LA
Sbjct: 78 ALRLIREGRNVVVTTGTGSGKTESFLLPILDHL--LRDPSAR-----ALLLYPTNALAND 130
Query: 482 TLEIFTKLCKSF-TWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLDHCKHTETLK- 539
E +L + TG + +A IR IL+ P L H L+
Sbjct: 131 QAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDML-----HYLLLRN 185
Query: 540 -------FSKVEHLVLDEA---------------DRILDQGYERDIAEFLEILKKQKPQF 577
+++LV+DE R+ Q
Sbjct: 186 HDAWLWLLRNLKYLVVDELHTYRGVQGSEVALLLRRL------LRRLRRY----GSPLQI 235
Query: 578 QSILLSATL-TP--AVQRLAGMTLQNPIQIDAADSTDIHNTTDSLVIPDSLKQ--HFIVT 632
I SATL P + L G + P+ D + + V + + +
Sbjct: 236 --ICTSATLANPGEFAEELFGRDFEVPVDEDGSPRGLRY-----FVRREPPIRELAESIR 288
Query: 633 PPKLRLVA-LASFILGKCQNVNEDEESKMLVF-----MATQDMADYHTEL--LSTVLGEN 684
L +A LA+ ++ + LVF L L +
Sbjct: 289 RSALAELATLAALLV--------RNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDA 340
Query: 685 IAFFKLHGSMSQSERTEVFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPSSS-TD 743
++ + + + ER + F+ + +I T+ G+D+ +D ++ Y P S
Sbjct: 341 VSTY--RAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLS 398
Query: 744 YVHRVGRTARVGHEGSSLLFLIPS 767
+ R GR R G E SL+ ++
Sbjct: 399 FRQRAGRAGRRGQE--SLVLVVLR 420
Score = 52.8 bits (127), Expect = 7e-07
Identities = 44/189 (23%), Positives = 71/189 (37%), Gaps = 48/189 (25%)
Query: 13 SIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELALQ 72
+++ I +G +V+V + TGSGKT ++ +PI+ L +R +R A+++ PT LA
Sbjct: 78 ALRLIREGRNVVVTTGTGSGKTESFLLPILDHL--LRDPSAR-----ALLLYPTNALAND 130
Query: 73 TLEIFTKLCKSF-TWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLDHCKHTETLK- 130
E +L + TG + +A IR IL+ P L H L+
Sbjct: 131 QAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDML-----HYLLLRN 185
Query: 131 -------FSKVEHLVLDEA---------------DRILDQGYERDIAEFLEILKKQKPQF 168
+++LV+DE R+ Q
Sbjct: 186 HDAWLWLLRNLKYLVVDELHTYRGVQGSEVALLLRRL------LRRLRRY----GSPLQI 235
Query: 169 QSILLSATL 177
I SATL
Sbjct: 236 --ICTSATL 242
>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 = 66.7 bits (163), Expect = 3e-11
Identities = 92/387 (23%), Positives = 155/387 (40%), Gaps = 59/387 (15%)
Query: 417 TVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTR 476
VQ I +L G D V TG GK+L Y +P S DGI ++I P
Sbjct: 14 PVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLP---------ALCS--DGI-TLVISPLI 61
Query: 477 EL---ALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKG-----ISILVATPGRL 528
L + L+ +P+ + K ++ + I +L TP +
Sbjct: 62 SLMEDQVLQLKASG---------IPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKC 112
Query: 529 LDHCKHTETLK-FSKVEHLVLDEADRILDQGYE-RDIAEFLEILKKQKPQFQSILLSATL 586
+ +TL+ + + +DEA I G++ R + L LK++ P + L+AT
Sbjct: 113 SASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGSLKQKFPNVPIMALTATA 172
Query: 587 TPAVQR--LAGMTLQNPIQIDAADSTDIHNTTDSLVIPDSLKQHFIVTPPKLRLVALASF 644
+P+V+ L + L+NP QI S D N L PK+ L L F
Sbjct: 173 SPSVREDILRQLNLKNP-QIFCT-SFDRPN----------LYYEVRRKTPKI-LEDLLRF 219
Query: 645 ILGKCQNVNEDEESKMLVFMATQDMADYHTELLSTVLGENIAFFKLHGSMSQSERTEVFK 704
I E + +++ ++ ++ T L IA H + S R +V
Sbjct: 220 IRK------EFKGKSGIIYCPSRKKSEQVTASLQN---LGIAAGAYHAGLEISARDDVHH 270
Query: 705 TFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPSSSTDYVHRVGRTARVGHEGSSLLFL 764
F+ + V++ T G++ P V +++ Y+ P S Y GR R G LF
Sbjct: 271 KFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFY 330
Query: 765 IPSEV----KLVEELQNRRIRIEEIKL 787
P+++ +L+ E + + R ++KL
Sbjct: 331 APADINRLRRLLMEEPDGQQRTYKLKL 357
Score = 40.5 bits (95), Expect = 0.003
Identities = 44/184 (23%), Positives = 74/184 (40%), Gaps = 31/184 (16%)
Query: 8 TVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTR 67
VQ I +L G D V TG GK+L Y +P S DGI ++I P
Sbjct: 14 PVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLP---------ALCS--DGI-TLVISPLI 61
Query: 68 EL---ALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKG-----ISILVATPGRL 119
L + L+ +P+ + K ++ + I +L TP +
Sbjct: 62 SLMEDQVLQLKASG---------IPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKC 112
Query: 120 LDHCKHTETLK-FSKVEHLVLDEADRILDQGYE-RDIAEFLEILKKQKPQFQSILLSATL 177
+ +TL+ + + +DEA I G++ R + L LK++ P + L+AT
Sbjct: 113 SASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGSLKQKFPNVPIMALTATA 172
Query: 178 TPAT 181
+P+
Sbjct: 173 SPSV 176
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 66.6 bits (163), Expect = 4e-11
Identities = 86/403 (21%), Positives = 147/403 (36%), Gaps = 79/403 (19%)
Query: 419 QQLSIQPILDGGDVLVRSQTGSGKTLAYAIP-IIQKLQEMRPKISRKDGIYAVIILPTRE 477
QQ I +L G D LV TG GK+L Y IP ++ +G+ +++ P
Sbjct: 22 QQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL------------EGL-TLVVSPL-- 66
Query: 478 LAL-----QTLEIF----TKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRL 528
++L LE L + L+ E+ + + +L +P RL
Sbjct: 67 ISLMKDQVDQLEAAGIRAAYLNST--------LSREERQQVLNQLKSGQLKLLYISPERL 118
Query: 529 L-DHCKHTETLKFSKVEHLVLDEADRILDQG------YERDIAEFLEILKKQKPQFQSIL 581
+ E LK + + +DEA I G Y R L L+ P +
Sbjct: 119 MSPRFL--ELLKRLPISLVAIDEAHCISQWGHDFRPDYRR-----LGRLRAGLPNPPVLA 171
Query: 582 LSATLTPAVQR--LAGMTLQNP-IQIDAADSTDIHNTTDSLVIPDSLKQHFIVTPPKLRL 638
L+AT TP V+ + LQ+ I + D ++ P +L
Sbjct: 172 LTATATPRVRDDIREQLGLQDANIFRGSFDRPNLALK------------VVEKGEPSDQL 219
Query: 639 VALASFILGKCQNVNEDEESKMLVFMATQDMADYHTELLSTVLGENIAFFKLHGSMSQSE 698
L V +++ T+ + E L G + + H +S E
Sbjct: 220 AFL--------ATVLPQLSKSGIIYCLTRKKVEELAEWLRKN-GISAGAY--HAGLSNEE 268
Query: 699 RTEVFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPSSSTDYVHRVGRTARVGHEG 758
R V + F + + V++ T+ G+D P V +++ Y P S Y GR R G
Sbjct: 269 RERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPA 328
Query: 759 SSLLFLIPSEVKLVEELQNRRIRIEEIKLKDCLQNLLSVKMEG 801
++L P +++ +R IE+ K + + + K+
Sbjct: 329 EAILLYSPEDIRW------QRYLIEQSKPDEEQKQIELAKLRQ 365
Score = 38.0 bits (89), Expect = 0.021
Identities = 46/189 (24%), Positives = 71/189 (37%), Gaps = 47/189 (24%)
Query: 10 QQLSIQPILDGGDVLVRSQTGSGKTLAYAIP-IIQKLQEMRPKISRKDGIYAVIILPTRE 68
QQ I +L G D LV TG GK+L Y IP ++ +G+ +++ P
Sbjct: 22 QQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL------------EGL-TLVVSPL-- 66
Query: 69 LAL-----QTLEIF----TKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRL 119
++L LE L + L+ E+ + + +L +P RL
Sbjct: 67 ISLMKDQVDQLEAAGIRAAYLNST--------LSREERQQVLNQLKSGQLKLLYISPERL 118
Query: 120 L-DHCKHTETLKFSKVEHLVLDEADRILDQG------YERDIAEFLEILKKQKPQFQSIL 172
+ E LK + + +DEA I G Y R L L+ P +
Sbjct: 119 MSPRFL--ELLKRLPISLVAIDEAHCISQWGHDFRPDYRR-----LGRLRAGLPNPPVLA 171
Query: 173 LSATLTPAT 181
L+AT TP
Sbjct: 172 LTATATPRV 180
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 61.2 bits (149), Expect = 2e-09
Identities = 37/130 (28%), Positives = 55/130 (42%), Gaps = 13/130 (10%)
Query: 631 VTPPKLRLVALASFILGKCQNVNEDE-ESKMLVFMATQDMADYHTELLSTVLGENIAFFK 689
V PKL + + E +S+++VF +D A+ L + + F
Sbjct: 345 VEHPKLEKL------REILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFI 398
Query: 690 LHGS------MSQSERTEVFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPSSSTD 743
S MSQ E+ E+ FR + VL+ T V GLD+P VD ++ Y S
Sbjct: 399 GQASREGDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIR 458
Query: 744 YVHRVGRTAR 753
+ R GRT R
Sbjct: 459 SIQRKGRTGR 468
Score = 34.6 bits (80), Expect = 0.25
Identities = 43/158 (27%), Positives = 59/158 (37%), Gaps = 24/158 (15%)
Query: 399 HPFMKKNLNEGMNITQVTTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMR 458
HP +K N + Q L + LV TG GKT A+ I +L
Sbjct: 6 HPLIKPNT------IEPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRL---- 54
Query: 459 PKISRKDGIYAVIILPTRELALQTLEIFTKLCKSFTWIVPSW---LTGGEKMKSEKARIR 515
R G + + PT+ L LQ E C+ T I LT GE E+ +
Sbjct: 55 ----RWFGGKVLFLAPTKPLVLQHAE----FCRKVTGIPEDEIAALT-GEVRPEEREELW 105
Query: 516 KGISILVATPGRLLDHCKHTETLKFSKVEHLVLDEADR 553
+ VATP + + K + V L+ DEA R
Sbjct: 106 AKKKVFVATPQVVENDLKAG-RIDLDDVSLLIFDEAHR 142
Score = 34.6 bits (80), Expect = 0.28
Identities = 39/138 (28%), Positives = 53/138 (38%), Gaps = 18/138 (13%)
Query: 10 QQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTREL 69
Q L + LV TG GKT A+ I +L R G + + PT+ L
Sbjct: 20 QLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRL--------RWFGGKVLFLAPTKPL 70
Query: 70 ALQTLEIFTKLCKSFTWIVPSW---LTGGEKMKSEKARIRKGISILVATPGRLLDHCKHT 126
LQ E C+ T I LT GE E+ + + VATP + + K
Sbjct: 71 VLQHAE----FCRKVTGIPEDEIAALT-GEVRPEEREELWAKKKVFVATPQVVENDLKAG 125
Query: 127 ETLKFSKVEHLVLDEADR 144
+ V L+ DEA R
Sbjct: 126 -RIDLDDVSLLIFDEAHR 142
>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 = 60.1 bits (146), Expect = 4e-09
Identities = 81/398 (20%), Positives = 151/398 (37%), Gaps = 77/398 (19%)
Query: 419 QQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTREL 478
Q+ I +LDG DVLV TG GK+L Y +P + + + V+I P L
Sbjct: 18 QEEIISHVLDGRDVLVVMPTGGGKSLCYQVPAL-----LLKGL-------TVVISPLISL 65
Query: 479 ------ALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRL---- 528
L+ + + S L+ E+ EKA + + +L P RL
Sbjct: 66 MKDQVDQLRAAGVAAAY-------LNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDY 118
Query: 529 -LDHCKHTETLKFSKVEHLVLDEADRILDQGYE-----RDIAEFLEILKKQKPQFQSILL 582
L+ + + + +DEA + G++ + + E PQ I L
Sbjct: 119 FLNMLQRI------PIALVAVDEAHCVSQWGHDFRPEYQRLGSLAERF----PQVPRIAL 168
Query: 583 SATLTPAVQR--LAGMTLQNPIQIDAADSTDIHNTTDSLVIPDSLKQHFIVTPPKLRLVA 640
+AT ++ + L + + S D N S V+ + KQ F++
Sbjct: 169 TATADAETRQDIRELLRLADANEF--ITSFDRPNLRFS-VVKKNNKQKFLL--------- 216
Query: 641 LASFILGKCQNVNEDEESKMLVFMATQDMADYHTELLSTVLGENIAFFKLHGSMSQSERT 700
++ +S +++ +++ + E L + + I+ H +S R
Sbjct: 217 --DYL------KKHRGQSG-IIYASSRKKVEELAERLES---QGISALAYHAGLSNKVRA 264
Query: 701 EVFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPSSSTDYVHRVGRTARVGHEGSS 760
E + F V++ T+ G+D P V +++ Y P + Y GR R G +
Sbjct: 265 ENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEA 324
Query: 761 LLFLIPSEVKLVEEL------QNRRIRIEEIKLKDCLQ 792
+L P+++ L++ + +IE KL+ +
Sbjct: 325 ILLYSPADIALLKRRIEQSEADDDYKQIEREKLRAMIA 362
Score = 37.7 bits (88), Expect = 0.030
Identities = 52/237 (21%), Positives = 87/237 (36%), Gaps = 56/237 (23%)
Query: 10 QQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTREL 69
Q+ I +LDG DVLV TG GK+L Y +P + + + V+I P L
Sbjct: 18 QEEIISHVLDGRDVLVVMPTGGGKSLCYQVPAL-----LLKGL-------TVVISPLISL 65
Query: 70 ------ALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRL---- 119
L+ + + S L+ E+ EKA + + +L P RL
Sbjct: 66 MKDQVDQLRAAGVAAAY-------LNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDY 118
Query: 120 -LDHCKHTETLKFSKVEHLVLDEADRILDQGYE-----RDIAEFLEILKKQKPQFQSILL 173
L+ + + + +DEA + G++ + + E PQ I L
Sbjct: 119 FLNMLQRI------PIALVAVDEAHCVSQWGHDFRPEYQRLGSLAERF----PQVPRIAL 168
Query: 174 SATLTPATCWCKHTETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQ 230
+AT T + E L L +A+ + ++R ++KK Q
Sbjct: 169 TATADAET---------RQDIRELLRLADANEFIT-SFDRP-NLRFSVVKKNNKQKF 214
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 52.8 bits (127), Expect = 5e-07
Identities = 77/387 (19%), Positives = 129/387 (33%), Gaps = 70/387 (18%)
Query: 429 GGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIIL-PTRELALQTLEIFT 487
++ TG+GKT+ A I +L+ ++L PT+EL Q E
Sbjct: 55 ERRGVIVLPTGAGKTVV-AAEAIAELKRS------------TLVLVPTKELLDQWAEALK 101
Query: 488 KLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLDHCKHTETLKFSKVEH-- 545
K I GGEK + E A++ VAT + + +F E
Sbjct: 102 KFLLLNDEI--GIYGGGEK-ELEPAKV------TVAT---VQTLARRQLLDEFLGNEFGL 149
Query: 546 LVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATLTPAVQRLAGMTLQ------ 599
++ DE + Y R I E L + + L+AT G
Sbjct: 150 IIFDEVHHLPAPSY-RRILELL------SAAYPRLGLTATPEREDGGRIGDLFDLIGPIV 202
Query: 600 -------------------NPIQIDAADSTDIHNTTDSLVIPDSLKQHFIVTPP-KLRLV 639
I++ + + +S + L+ + + R +
Sbjct: 203 YEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKESARFRELLRARGTLRAENEARRI 262
Query: 640 ALAS---FILGKCQNVNEDEESKMLVFMATQDMADYHTELLSTVLGENIAFFKLHGSMSQ 696
A+AS + + K L+F + + A +L + G +
Sbjct: 263 AIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGIVEA----ITGETPK 318
Query: 697 SERTEVFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPSSSTDYVHRVGRTAR--V 754
ER + + FR+ VL+ V G+D+P D ++ S ++ R+GR R
Sbjct: 319 EEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLGRGLRPAE 378
Query: 755 GHEGSSLLFLIPSEVKLVEELQNRRIR 781
G E + L L EE RR R
Sbjct: 379 GKEDTLALDYSLVPDDLGEEDIARRRR 405
Score = 32.8 bits (75), Expect = 0.78
Identities = 38/161 (23%), Positives = 59/161 (36%), Gaps = 35/161 (21%)
Query: 20 GGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIIL-PTRELALQTLEIFT 78
++ TG+GKT+ A I +L+ ++L PT+EL Q E
Sbjct: 55 ERRGVIVLPTGAGKTVV-AAEAIAELKRS------------TLVLVPTKELLDQWAEALK 101
Query: 79 KLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLDHCKHTETLKFSKVEH-- 136
K I GGEK + E A+ + VAT + + +F E
Sbjct: 102 KFLLLNDEI--GIYGGGEK-ELEPAK------VTVAT---VQTLARRQLLDEFLGNEFGL 149
Query: 137 LVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATL 177
++ DE + Y R I E L + + L+AT
Sbjct: 150 IIFDEVHHLPAPSY-RRILELL------SAAYPRLGLTATP 183
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 53.2 bits (128), Expect = 5e-07
Identities = 76/345 (22%), Positives = 127/345 (36%), Gaps = 59/345 (17%)
Query: 419 QQLSIQP-ILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRE 477
QQ +++ +L +VL+ + TGSGKTL + I+ L E K+ +Y V P +
Sbjct: 36 QQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGGGKV-----VYIV---PLKA 87
Query: 478 LALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLDHCKHTET 537
LA + E F++L I TG + R+ ++V TP + LD
Sbjct: 88 LAEEKYEEFSRL--EELGIRVGISTGD--YDLDDERL-ARYDVIVTTPEK-LDSLTRKRP 141
Query: 538 LKFSKVEHLVLDEADRILDQGYERDIAEFLEI----LKKQKPQFQSILLSATL------- 586
+V+ +V+DE + D R LE +++ + + LSATL
Sbjct: 142 SWIEEVDLVVIDEIHLLGD--RTRG--PVLESIVARMRRLNELIRIVGLSATLPNAEEVA 197
Query: 587 --------------------TPAVQRLAGMTLQNPIQIDAADSTDIHNTTDSLVIPDSLK 626
P V G + D+ + +SL
Sbjct: 198 DWLNAKLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNLALELVLESL---AEGG 254
Query: 627 QHFIVTPPKLRLVALASFILGKCQNVNEDEESKMLVFMAT----QDMADYHTELLSTVLG 682
Q + + A + K D+E +L A+ + E L+ ++
Sbjct: 255 QVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVL 314
Query: 683 ENIAFFKLHGSMSQSERTEVFKTFRSVKSGVLICTDVAARGLDLP 727
+AF H + + +R V FR K VL+ T A G++LP
Sbjct: 315 RGVAFH--HAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLP 357
Score = 51.6 bits (124), Expect = 2e-06
Identities = 46/173 (26%), Positives = 76/173 (43%), Gaps = 23/173 (13%)
Query: 10 QQLSIQP-ILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRE 68
QQ +++ +L +VL+ + TGSGKTL + I+ L E K+ +Y V P +
Sbjct: 36 QQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGGGKV-----VYIV---PLKA 87
Query: 69 LALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLDHCKHTET 128
LA + E F++L I TG + R+ ++V TP + LD
Sbjct: 88 LAEEKYEEFSRL--EELGIRVGISTGD--YDLDDERL-ARYDVIVTTPEK-LDSLTRKRP 141
Query: 129 LKFSKVEHLVLDEADRILDQGYERDIAEFLEI----LKKQKPQFQSILLSATL 177
+V+ +V+DE + D R LE +++ + + LSATL
Sbjct: 142 SWIEEVDLVVIDEIHLLGD--RTRG--PVLESIVARMRRLNELIRIVGLSATL 190
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 51.8 bits (125), Expect = 1e-06
Identities = 54/197 (27%), Positives = 90/197 (45%), Gaps = 35/197 (17%)
Query: 7 TTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPT 66
T Q+ +I I +G +VL+ S TGSGKTLA + II +L + + +D +Y + + P
Sbjct: 34 TPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPL 93
Query: 67 RELA-------LQTL----EIFTKLCKSFTWIVPSWLTGGEKMKSEKAR-IRKGISILVA 114
R L + L EI + + I + T G+ EK + ++K IL+
Sbjct: 94 RALNNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRT-GDTSSYEKQKMLKKPPHILIT 152
Query: 115 TPGRLLDHCKHTETL-------KFSK----VEHLVLDEADRILDQGYERDIAEFLEILKK 163
TP E+L KF + V+ +++DE + + ++ LE L++
Sbjct: 153 TP----------ESLAILLNSPKFREKLRTVKWVIVDEIHSLAENKRGVHLSLSLERLEE 202
Query: 164 -QKPQFQSILLSATLTP 179
+F I LSAT+ P
Sbjct: 203 LAGGEFVRIGLSATIEP 219
Score = 51.8 bits (125), Expect = 1e-06
Identities = 54/197 (27%), Positives = 90/197 (45%), Gaps = 35/197 (17%)
Query: 416 TTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPT 475
T Q+ +I I +G +VL+ S TGSGKTLA + II +L + + +D +Y + + P
Sbjct: 34 TPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPL 93
Query: 476 RELA-------LQTL----EIFTKLCKSFTWIVPSWLTGGEKMKSEKAR-IRKGISILVA 523
R L + L EI + + I + T G+ EK + ++K IL+
Sbjct: 94 RALNNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRT-GDTSSYEKQKMLKKPPHILIT 152
Query: 524 TPGRLLDHCKHTETL-------KFSK----VEHLVLDEADRILDQGYERDIAEFLEILKK 572
TP E+L KF + V+ +++DE + + ++ LE L++
Sbjct: 153 TP----------ESLAILLNSPKFREKLRTVKWVIVDEIHSLAENKRGVHLSLSLERLEE 202
Query: 573 -QKPQFQSILLSATLTP 588
+F I LSAT+ P
Sbjct: 203 LAGGEFVRIGLSATIEP 219
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 50.6 bits (122), Expect = 3e-06
Identities = 44/134 (32%), Positives = 64/134 (47%), Gaps = 19/134 (14%)
Query: 634 PKL-RLVALASFILGKCQNVNEDEESKMLVFMATQDMADYHTELLSTVLGENIAFFKLHG 692
PKL +L + LGK + +S+++VF +D A+ +LL E I + G
Sbjct: 347 PKLEKLREIVKEQLGK------NPDSRIIVFTQYRDTAEKIVDLLE---KEGIKAVRFVG 397
Query: 693 S--------MSQSERTEVFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPSSSTDY 744
MSQ E+ E+ FR+ + VL+ T VA GLD+P VD ++ Y S
Sbjct: 398 QASKDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRS 457
Query: 745 VHRVGRTARVGHEG 758
+ R GRT R EG
Sbjct: 458 IQRKGRTGR-QEEG 470
Score = 33.7 bits (78), Expect = 0.60
Identities = 43/175 (24%), Positives = 63/175 (36%), Gaps = 58/175 (33%)
Query: 399 HPFMKKNLNEGMNITQVTTVQQLSIQPILDG----GDVLVRSQTGSGKTLAYAIPIIQKL 454
HP +K N T++ Q +L + LV TG GKT + I ++L
Sbjct: 6 HPLIKPN-----------TIEARLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIAERL 54
Query: 455 QEMRPKISRKDGIYAVIILPTRELALQTLEIFTKL-------CKSFTWIVPSWLTGGEKM 507
+K G +I+ PT+ L Q E F K FT GE
Sbjct: 55 H-------KKGG-KVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFT---------GEVS 97
Query: 508 KSEKARIRKGISILVATP---------GRLLDHCKHTETLKFSKVEHLVLDEADR 553
++A + + ++VATP GR + V L+ DEA R
Sbjct: 98 PEKRAELWEKAKVIVATPQVIENDLIAGR----------ISLEDVSLLIFDEAHR 142
Score = 32.9 bits (76), Expect = 0.87
Identities = 34/132 (25%), Positives = 49/132 (37%), Gaps = 43/132 (32%)
Query: 29 TGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELALQTLEIFTKL-------C 81
TG GKT + I ++L +K G +I+ PT+ L Q E F K
Sbjct: 38 TGLGKTAIALLVIAERLH-------KKGG-KVLILAPTKPLVEQHAEFFRKFLNIPEEKI 89
Query: 82 KSFTWIVPSWLTGGEKMKSEKARIRKGISILVATP---------GRLLDHCKHTETLKFS 132
FT GE ++A + + ++VATP GR +
Sbjct: 90 VVFT---------GEVSPEKRAELWEKAKVIVATPQVIENDLIAGR----------ISLE 130
Query: 133 KVEHLVLDEADR 144
V L+ DEA R
Sbjct: 131 DVSLLIFDEAHR 142
>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 = 49.5 bits (119), Expect = 7e-06
Identities = 94/373 (25%), Positives = 150/373 (40%), Gaps = 59/373 (15%)
Query: 419 QQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTREL 478
Q L+G L+ + TGSGKTLA +P L ++ K G++ + I P R L
Sbjct: 18 QLEMWAAALEGRSGLLIAPTGSGKTLAGFLPS---LIDLAGPEKPKKGLHTLYITPLRAL 74
Query: 479 ALQTLEIFTKLCKSFTWIVPSWLTG---GEKMKSEKARIRKGI-SILVATPGRL---LDH 531
A ++I L + G+ SE+AR RK IL+ TP L L +
Sbjct: 75 A---VDIARNLQAPIEELGLPIRVETRTGDTSSSERARQRKKPPDILLTTPESLALLLSY 131
Query: 532 CKHTETLKFSKVEHLVLDEADRILDQGYER-DIAEF-LEILKKQKPQFQSILLSAT---L 586
L F + +V+DE + G +R D E L L++ P + LSAT L
Sbjct: 132 -PDAARL-FKDLRCVVVDEWHELA--GSKRGDQLELALARLRRLAPGLRRWGLSATIGNL 187
Query: 587 TPAVQRLAGMTLQNPIQIDAADSTDIHNTTDSLVIPDSLKQHFIVTPP-----KLRLVAL 641
A + L G+ + + I + ++P+S + P LR +
Sbjct: 188 EEARRVLLGVGGAPAVLVRGKLPKAIPVIS---LLPESEE-----RFPWAGHLGLRALP- 238
Query: 642 ASFILGKCQNVNEDEESKM-LVFMATQDMADYHTELLSTVLGEN---IAFFKLHGSMSQS 697
+ E ++++ LVF T+ A+ + L E IA HGS+ +
Sbjct: 239 --------EVYAEIDQARTTLVFTNTRSQAELWFQALWEANPEFALPIALH--HGSLDRE 288
Query: 698 ERTEVFKTFRSVKSGVL---ICTDVAARGLDLPLVDWIVQYTAPSSSTDYVHRVGRTA-R 753
+R ++ +G L +CT G+D VD ++Q +P + R GR+ R
Sbjct: 289 QR---RWVEAAMAAGRLRAVVCTSSLDLGVDFGPVDLVIQIGSPKGVARLLQRAGRSNHR 345
Query: 754 VGHEGSSLLFLIP 766
G S L+P
Sbjct: 346 PG--EPSRALLVP 356
Score = 37.1 bits (87), Expect = 0.053
Identities = 52/177 (29%), Positives = 77/177 (43%), Gaps = 19/177 (10%)
Query: 10 QQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTREL 69
Q L+G L+ + TGSGKTLA +P L ++ K G++ + I P R L
Sbjct: 18 QLEMWAAALEGRSGLLIAPTGSGKTLAGFLPS---LIDLAGPEKPKKGLHTLYITPLRAL 74
Query: 70 ALQTLEIFTKLCKSFTWIVPSWLTG---GEKMKSEKARIRKGI-SILVATPGRL---LDH 122
A ++I L + G+ SE+AR RK IL+ TP L L +
Sbjct: 75 A---VDIARNLQAPIEELGLPIRVETRTGDTSSSERARQRKKPPDILLTTPESLALLLSY 131
Query: 123 CKHTETLKFSKVEHLVLDEADRILDQGYER-DIAEF-LEILKKQKPQFQSILLSATL 177
L F + +V+DE + G +R D E L L++ P + LSAT+
Sbjct: 132 -PDAARL-FKDLRCVVVDEWHELA--GSKRGDQLELALARLRRLAPGLRRWGLSATI 184
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 46.5 bits (110), Expect = 7e-05
Identities = 32/100 (32%), Positives = 49/100 (49%), Gaps = 14/100 (14%)
Query: 691 HGSMSQSERTEVFKTFRSVKSGVLIC---TDVAARGLDLPLVDWIVQYTAPSSSTDYVHR 747
HGS+S+ +R T +++KSG L C T G+D+ VD ++Q P S + R
Sbjct: 308 HGSVSKEQRAI---TEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQR 364
Query: 748 VGRTA-RVGHEGSSLLF------LIPSEVKLVEELQNRRI 780
+GR +VG L F L+ S V +VE + R+
Sbjct: 365 IGRAGHQVGGVSKGLFFPRTRRDLVDSAV-IVECMFAGRL 403
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 42.7 bits (101), Expect = 8e-04
Identities = 82/355 (23%), Positives = 135/355 (38%), Gaps = 78/355 (21%)
Query: 430 GDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELALQTLEIFTKL 489
GDV GSGKTL A+ ++ ++ G ++ PT LA Q L
Sbjct: 263 GDV------GSGKTLVAALAMLAAIEA---------GYQVALMAPTEILAEQHYNSLRNL 307
Query: 490 CKSFTWIVPSWLTGGEKMKSEK---ARIRKG-ISILVATPGRLLDHCKHTETLKFSKVEH 545
V + LTG K K K I G I ++V T H E ++F ++
Sbjct: 308 LAPLGIEV-ALLTGSLKGKRRKELLETIASGQIHLVVGT------HALIQEKVEFKRLAL 360
Query: 546 LVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATLTPAVQRLAGMTLQNPIQID 605
+++DE R G E+ ++ +K + F +L + TP + LA +T+ +
Sbjct: 361 VIIDEQHRF---GVEQR----KKLREKGQGGFTPHVLVMSATPIPRTLA-LTVYGDLDTS 412
Query: 606 AADS---------TDIHNTTD-----SLVIPDSLK--QHFIVTPPKLRLVALASFILGKC 649
D T + + + + K Q ++V P L+
Sbjct: 413 IIDELPPGRKPITTVLIKHDEKDIVYEFIEEEIAKGRQAYVVYP----LI---------- 458
Query: 650 QNVNEDEESKMLVFMATQDMADYHTELLSTVLGE-NIAFFKLHGSMSQSERTEVFKTFRS 708
EES+ L A + + + L + N+ LHG M E+ V + FR
Sbjct: 459 ------EESEKLDLKAAEALYER----LKKAFPKYNVGL--LHGRMKSDEKEAVMEEFRE 506
Query: 709 VKSGVLICTDVAARGLDLPLVDWIVQYTAPSSSTDYVHRV-GRTARVGHEGSSLL 762
+ +L+ T V G+D+P +V A +H++ GR R H+ LL
Sbjct: 507 GEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLL 561
>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 = 40.0 bits (94), Expect = 0.007
Identities = 28/99 (28%), Positives = 46/99 (46%), Gaps = 8/99 (8%)
Query: 690 LHGSMSQSERTEVFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPSSSTDYVH--- 746
HG M+++E EV F + VL+CT + G+D+P + I+ A ++
Sbjct: 692 AHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLR 751
Query: 747 -RVGRTARVGHEGSSLLFLIPSEVKLVEELQNRRIRIEE 784
RVGR+ + + L P + L E+ Q R I+E
Sbjct: 752 GRVGRSKKKAYA----YLLYPHQKALTEDAQKRLEAIQE 786
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 39.4 bits (92), Expect = 0.009
Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 9/86 (10%)
Query: 404 KNLNEGMNITQVTTVQQLSIQP-ILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKIS 462
K + + I ++ VQ L+++ +L+G ++LV S T SGKTL + I +L K+
Sbjct: 206 KRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSGGKKM- 264
Query: 463 RKDGIYAVIILPTRELALQTLEIFTK 488
++ V P LA Q E F +
Sbjct: 265 ----LFLV---PLVALANQKYEDFKE 283
Score = 37.5 bits (87), Expect = 0.036
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 9/80 (11%)
Query: 1 MNITQVTTVQQLSIQP-ILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIY 59
I ++ VQ L+++ +L+G ++LV S T SGKTL + I +L K+ ++
Sbjct: 212 EGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSGGKKM-----LF 266
Query: 60 AVIILPTRELALQTLEIFTK 79
V P LA Q E F +
Sbjct: 267 LV---PLVALANQKYEDFKE 283
>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 = 38.6 bits (90), Expect = 0.012
Identities = 69/358 (19%), Positives = 117/358 (32%), Gaps = 71/358 (19%)
Query: 431 DVLVRSQTGSGKT-LAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELALQTLEIFTKL 489
+++ + TG GKT A + + ++ +I LPTR +L
Sbjct: 1 LLVIEAPTGYGKTEAALLWALHSIKSQKADRV--------IIALPTRATINAMYRRAKEL 52
Query: 490 CKSFT-WIVPSWLTGGEKMKS-----EKARIRKGIS--------ILVATPGRLL---DHC 532
S + S K E S I V T ++L
Sbjct: 53 FGSNLGLLHSSSSFKRIKEMGDSEEFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGE 112
Query: 533 -KHTETLKFS-KVEHLVLDEADRILDQGYERDIAEF-LEILKKQKPQFQSILLSATLTPA 589
H E S L+ DE + Y + LE+LK +L+SATL
Sbjct: 113 FGHYEFTLASIANSLLIFDEVHFYDE--YTLALILAVLEVLKDNDVPI--LLMSATLPKF 168
Query: 590 VQRLAGMTLQNPIQIDAADSTDIHNTTDSLVIPDSLKQHFIVTPPKLRLVALASFILGKC 649
++ A N L ++H R + + S +G+
Sbjct: 169 LKEYAEKIG-----------YVEFNEPLDLKEERRFERH--------RFIKIESDKVGEI 209
Query: 650 QNVNE-----DEESKMLVFMATQDMADYHTELLSTVLGENIAFFK---LHGSMSQSER-- 699
++ + K+ + + T D A L EN + LH ++ +R
Sbjct: 210 SSLERLLEFIKKGGKIAIIVNTVDRAQE----FYQQLKENAPEEEIMLLHSRFTEKDRAK 265
Query: 700 --TEVFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPSSSTDYVHRVGRTARVG 755
E+ + + + V++ T V LD+ D ++ AP S + R+GR R G
Sbjct: 266 KEAELLEEMKKNEKFVIVATQVIEASLDIS-ADVMITELAPIDS--LIQRLGRLHRYG 320
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 38.3 bits (90), Expect = 0.020
Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 7/73 (9%)
Query: 656 EESKMLVFMATQDMADYHTELLSTVLGE-NIAFFKLHGSMSQSERTEVFKTFRSVKSGVL 714
EES+ L A +++ + L + L E + +HG M +E+ V + F+ + +L
Sbjct: 484 EESEKLELQAAEELYEE----LKSFLPELKVGL--VHGRMKPAEKDAVMEAFKEGEIDIL 537
Query: 715 ICTDVAARGLDLP 727
+ T V G+D+P
Sbjct: 538 VATTVIEVGVDVP 550
>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 = 37.8 bits (88), Expect = 0.021
Identities = 67/354 (18%), Positives = 115/354 (32%), Gaps = 67/354 (18%)
Query: 431 DVLVRSQTGSGKT---LAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELALQTLEIFT 487
+++ + TG GKT L +A+ ++ + R +I LPTR
Sbjct: 1 LLVIEAPTGYGKTEAALLWALHSLKSQKADR----------VIIALPTRATINAMYRRAK 50
Query: 488 KLCKSFTWIVPSWLTGGEKMKS-----EKARIRKGIS--------ILVATPGRLL---DH 531
+ S L+ K E S I V T ++L
Sbjct: 51 EAFGETGLYHSSILSSRIKEMGDSEEFEHLFPLYIHSNDTLFLDPITVCTIDQVLKSVFG 110
Query: 532 C-KHTETLKFS-KVEHLVLDEADRILDQGYERDIAEF-LEILKKQKPQFQSILLSATLTP 588
H E S L+ DE + Y + LE+LK +L+SATL
Sbjct: 111 EFGHYEFTLASIANSLLIFDEVHFYDE--YTLALILAVLEVLKDNDVPI--LLMSATLPK 166
Query: 589 AVQRLAGMTLQNPIQIDAADSTDIHNTTDSLVIPDSLKQHFIVTPPKLRLVALASFILGK 648
++ A + + D + D + + + RL+
Sbjct: 167 FLKEYAEKIG-YVEENEPLDLKPNERAPFIKIESDKVGEISSLE----RLLEFI------ 215
Query: 649 CQNVNEDEESKMLVFMATQDMADYHTELLSTVLGENIAFFK---LHGSMSQSER----TE 701
+ + + + T D A L E + +H ++ +R E
Sbjct: 216 ------KKGGSVAIIVNTVDRAQE----FYQQLKEKGPEEEIMLIHSRFTEKDRAKKEAE 265
Query: 702 VFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPSSSTDYVHRVGRTARVG 755
+ F+ + V++ T V LD+ VD ++ AP S + R+GR R G
Sbjct: 266 LLLEFKKSEKFVIVATQVIEASLDIS-VDVMITELAPIDS--LIQRLGRLHRYG 316
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 37.9 bits (88), Expect = 0.023
Identities = 74/382 (19%), Positives = 149/382 (39%), Gaps = 58/382 (15%)
Query: 405 NLNEGMNITQVTTVQQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRK 464
NL G N ++ Q+++I+ + G +V+V T +GKTL I + +
Sbjct: 14 NLFTG-NDFELYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFL------AGL 66
Query: 465 DGIYAVIILPTRELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVAT 524
IY I+P R LA++ E ++L +S V ++ G+ R + IL +
Sbjct: 67 KSIY---IVPLRSLAMEKYEELSRL-RSLGMRVK--ISIGDYDDPPDFIKRYDVVILTSE 120
Query: 525 PGRLLDHCKHTETLKFSKVEHLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSA 584
D H + + V +V DE I D+ + L + P + + LSA
Sbjct: 121 KA---DSLIHHDPYIINDVGLIVADEIHIIGDEDRGPTLETVLSSARYVNPDARILALSA 177
Query: 585 TLTPA------------------VQRLAGMTLQNPIQIDAADSTDIHNTTDSLVIPDSLK 626
T++ A V G+ + + +D + + + + +I +++
Sbjct: 178 TVSNANELAQWLNASLIKSNFRPVPLKLGILYRKRLILDGYERSQV---DINSLIKETVN 234
Query: 627 ---QHFIVTPPKLRLVALASFILGKCQNVNEDEESKMLVFMATQDMADYHTELLSTVLGE 683
Q + + A ++ Q+ E + F + + + + + L+ +L
Sbjct: 235 DGGQVLVFVSSRKNAEDYAEMLI---QHFPEFND-----FKVSSENNNVYDDSLNEMLPH 286
Query: 684 NIAFFKLHGSMSQSERTEVFKTFRSVKSGVLICTDVAARGLDLP--------LVDWIVQY 735
+AF H +S +R + + FR+ V++ T A G++LP + +
Sbjct: 287 GVAFH--HAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIVRDITRYGNGG 344
Query: 736 TAPSSSTDYVHRVGRTARVGHE 757
S+ + +GR R G++
Sbjct: 345 IRYLSNMEIKQMIGRAGRPGYD 366
Score = 29.9 bits (67), Expect = 9.0
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 9/71 (12%)
Query: 10 QQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTREL 69
Q+++I+ + G +V+V T +GKTL I + + IY I+P R L
Sbjct: 27 QRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFL------AGLKSIY---IVPLRSL 77
Query: 70 ALQTLEIFTKL 80
A++ E ++L
Sbjct: 78 AMEKYEELSRL 88
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 37.6 bits (87), Expect = 0.041
Identities = 89/367 (24%), Positives = 145/367 (39%), Gaps = 70/367 (19%)
Query: 419 QQLSIQPILDGGDVLVRSQTGSGKTLAYAIP---------IIQKLQEM-RPKISR--KDG 466
Q+ I + G DV V TG GK+L Y +P +I L + + +I +
Sbjct: 465 QREIINATMSGYDVFVLMPTGGGKSLTYQLPALICPGITLVISPLVSLIQDQIMNLLQAN 524
Query: 467 IYAVIILPTRELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPG 526
I A + E A Q LEI +L SE ++ + +L TP
Sbjct: 525 IPAASLSAGMEWAEQ-LEILQELS------------------SEYSKYK----LLYVTPE 561
Query: 527 RLLDH---CKHTETLKF-SKVEHLVLDEADRILDQGYE-RDIAEFLEILKKQKPQFQSIL 581
++ +H E L + V+DEA + G++ R + L ILK++ P +
Sbjct: 562 KVAKSDSLLRHLENLNSRGLLARFVIDEAHCVSQWGHDFRPDYQGLGILKQKFPNIPVLA 621
Query: 582 LSATLTPAVQRLAGMTLQNPIQIDAADSTDIHNTTDSLVIPDSLKQ----HFIVTPPKLR 637
L+AT T +V+ D + +V S + + +V K
Sbjct: 622 LTATATASVKE---------------DVVQALGLVNCVVFRQSFNRPNLWYSVVPKTKKC 666
Query: 638 LVALASFILGKCQNVNEDEESKMLVFMATQDMADYHTELLSTVLGENIAFFKLHGSMSQS 697
L + FI N +E ++ ++ D + E L G AF+ HGSM +
Sbjct: 667 LEDIDKFI-----KENHFDECGIIYCLSRMD-CEKVAERLQ-EFGHKAAFY--HGSMDPA 717
Query: 698 ERTEVFKTFRSVKSGVLICTDVA-ARGLDLPLVDWIVQYTAPSSSTDYVHRVGRTARVGH 756
+R V K + S +IC VA G++ P V +++ ++ P S Y GR R G
Sbjct: 718 QRAFVQKQW-SKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQ 776
Query: 757 EGSSLLF 763
S +L+
Sbjct: 777 RSSCVLY 783
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 37.0 bits (86), Expect = 0.050
Identities = 90/385 (23%), Positives = 144/385 (37%), Gaps = 89/385 (23%)
Query: 419 QQLSIQPILDGGDVLVRSQTGSGKTLAYAIP--IIQKLQ-EMRPKIS---------RKDG 466
QQ I +L G D LV TG GK+L Y IP ++ L + P IS +G
Sbjct: 30 QQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVLDGLTLVVSPLISLMKDQVDQLLANG 89
Query: 467 IYAVIILPT--RELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKG-ISILVA 523
+ A + T RE Q LE+ A R G I +L
Sbjct: 90 VAAACLNSTQTRE---QQLEVM-------------------------AGCRTGQIKLLYI 121
Query: 524 TPGRL-----LDHCKHTETLKFSKVEHLVLDEADRILDQGYE-RDIAEFLEILKKQKPQF 577
P RL L+H H L +DEA I G++ R L L+++ P
Sbjct: 122 APERLMMDNFLEHLAHWNPAL------LAVDEAHCISQWGHDFRPEYAALGQLRQRFPTL 175
Query: 578 QSILLSATLTPAVQR--LAGMTLQNP-IQIDAADSTDIHNTTDSLVIPDSLKQHFIVTPP 634
+ L+AT ++ + + L +P IQI + D +I T L + F
Sbjct: 176 PFMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYT---------LVEKFKPLDQ 226
Query: 635 KLRLVALASFILGKCQNVNEDEESKMLVFMATQDMADYHTELLSTVLGEN-IAFFKLHGS 693
+R V GK + + +K+ E + L I+ H
Sbjct: 227 LMRYVQEQR---GKSGIIYCNSRAKV--------------EDTAARLQSRGISAAAYHAG 269
Query: 694 MSQSERTEVFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPSSSTDYVHRVGRTAR 753
+ R +V + F+ +++ T G++ P V ++V + P + Y GR R
Sbjct: 270 LDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGR 329
Query: 754 VGHEGSSLLFLIPSEV----KLVEE 774
G ++LF P+++ + +EE
Sbjct: 330 DGLPAEAMLFYDPADMAWLRRCLEE 354
Score = 36.2 bits (84), Expect = 0.093
Identities = 16/31 (51%), Positives = 18/31 (58%)
Query: 10 QQLSIQPILDGGDVLVRSQTGSGKTLAYAIP 40
QQ I +L G D LV TG GK+L Y IP
Sbjct: 30 QQEIIDAVLSGRDCLVVMPTGGGKSLCYQIP 60
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 36.7 bits (85), Expect = 0.069
Identities = 34/173 (19%), Positives = 64/173 (36%), Gaps = 22/173 (12%)
Query: 561 RDIAEFL--EILKKQKPQFQSILLSATLTP--AVQRLAGM-TLQNPIQIDAADSTDIHNT 615
+ L E+ K +L SATL+P + L G+ L+ ++ + S +
Sbjct: 389 LLVPSKLLEELFSKVAS---VVLTSATLSPLDSFSSLLGLLGLEEKLRFLSLPSPFNYEE 445
Query: 616 TDSLVIPDSLKQHFIVTPPKLRLVALASFILGKCQNVNEDEESKMLVFMATQDMADYHTE 675
L +P L P+L L LA+++ + + +LV + + E
Sbjct: 446 QGQLYVPTDL---PEPREPEL-LAKLAAYLR----EILKASPGGVLVLFPSYEYLKRVAE 497
Query: 676 LLSTVLGENIAFFKLHGSMSQSERTEVFKTFR-SVKSGVLICTDVAARGLDLP 727
L + + ER E+ + F+ S + +L+ G+D P
Sbjct: 498 RLKDER-----STLPVLTQGEDEREELLEKFKASGEGLILVGGGSFWEGVDFP 545
Score = 34.8 bits (80), Expect = 0.26
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 17 ILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTREL 69
+ G +L+ + TG+GKTLAY +P + +E K+ +I T+ L
Sbjct: 31 LKGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKKV--------IISTRTKAL 75
Score = 34.8 bits (80), Expect = 0.26
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 426 ILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTREL 478
+ G +L+ + TG+GKTLAY +P + +E K+ +I T+ L
Sbjct: 31 LKGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKKV--------IISTRTKAL 75
>gnl|CDD|182031 PRK09694, PRK09694, helicase Cas3; Provisional.
Length = 878
Score = 35.9 bits (83), Expect = 0.12
Identities = 60/241 (24%), Positives = 90/241 (37%), Gaps = 78/241 (32%)
Query: 416 TTVQQLSIQPILDGGDVLVRSQTGSGKT---LAYAIPIIQKLQEMRPKISRKDGIYAVII 472
T V L +QP G ++ + TGSGKT LAYA +I + D I +
Sbjct: 292 TLVDALPLQP----GLTIIEAPTGSGKTEAALAYAWRLIDQGL--------ADSI--IFA 337
Query: 473 LPTRELA---LQTLE-----IFT-----------KLCKSFTWIVP----------SWLTG 503
LPT+ A L LE +F + F + +W+
Sbjct: 338 LPTQATANAMLSRLEALASKLFPSPNLILAHGNSRFNHLFQSLKSRAATEQGQEEAWVQC 397
Query: 504 GEKMKSEKARIRKGISILVATPGRLLDHCKHTETLKFSKVEH------------LVLDEA 551
E + R+ G I V T ++L + V+H L++DE
Sbjct: 398 CEWLSQSNKRVFLG-QIGVCTIDQVL--------ISVLPVKHRFIRGFGLGRSVLIVDEV 448
Query: 552 DRILDQGYERDIAEFLE-ILKKQKPQFQS-ILLSATLTPAVQR---LAGMTLQNPIQIDA 606
Y+ + LE +LK Q S ILLSATL PA + L +P+++ +
Sbjct: 449 -----HAYDAYMYGLLEAVLKAQAQAGGSVILLSATL-PATLKQKLLDTYGGHDPVELSS 502
Query: 607 A 607
A
Sbjct: 503 A 503
Score = 34.0 bits (78), Expect = 0.41
Identities = 58/221 (26%), Positives = 82/221 (37%), Gaps = 75/221 (33%)
Query: 7 TTVQQLSIQPILDGGDVLVRSQTGSGKT---LAYAIPIIQKLQEMRPKISRKDGIYAVII 63
T V L +QP G ++ + TGSGKT LAYA +I + D I +
Sbjct: 292 TLVDALPLQP----GLTIIEAPTGSGKTEAALAYAWRLIDQGL--------ADSI--IFA 337
Query: 64 LPTRELA---LQTLE-----IFT-----------KLCKSFTWIVP----------SWLTG 94
LPT+ A L LE +F + F + +W+
Sbjct: 338 LPTQATANAMLSRLEALASKLFPSPNLILAHGNSRFNHLFQSLKSRAATEQGQEEAWVQC 397
Query: 95 GEKMKSEKARIRKGISILVATPGRLLDHCKHTETLKFSKVEH------------LVLDEA 142
E + R+ G I V T ++L + V+H L++DE
Sbjct: 398 CEWLSQSNKRVFLG-QIGVCTIDQVL--------ISVLPVKHRFIRGFGLGRSVLIVDEV 448
Query: 143 DRILDQGYERDIAEFLE-ILKKQKPQFQS-ILLSATLTPAT 181
Y+ + LE +LK Q S ILLSATL PAT
Sbjct: 449 -----HAYDAYMYGLLEAVLKAQAQAGGSVILLSATL-PAT 483
Score = 30.2 bits (68), Expect = 6.5
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 5/44 (11%)
Query: 220 EILKKQKPQFQSV-LLSATLTPAVQR---LAGMTLQNPIQIDAA 259
+LK Q SV LLSATL PA + L +P+++ +A
Sbjct: 461 AVLKAQAQAGGSVILLSATL-PATLKQKLLDTYGGHDPVELSSA 503
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 35.7 bits (83), Expect = 0.14
Identities = 32/126 (25%), Positives = 49/126 (38%), Gaps = 23/126 (18%)
Query: 29 TGSGKT---LAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELALQTLEIFTKLCKSFT 85
TG GKT L ++ + +K +K + II PTR L Q +E K +
Sbjct: 104 TGVGKTTFGLVMSLYLAKK--------GKK----SYIIFPTRLLVEQVVEKLEKFGEKVG 151
Query: 86 WIVPSWLTGGEKMKSEKARIRKGI-----SILVATPGRLLDHCKHTETLKFSKVEHLVLD 140
V K EK + + ILV T L K+ + L K + + +D
Sbjct: 152 CGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLS---KNFDELPKKKFDFVFVD 208
Query: 141 EADRIL 146
+ D +L
Sbjct: 209 DVDAVL 214
Score = 35.7 bits (83), Expect = 0.14
Identities = 32/126 (25%), Positives = 49/126 (38%), Gaps = 23/126 (18%)
Query: 438 TGSGKT---LAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELALQTLEIFTKLCKSFT 494
TG GKT L ++ + +K +K + II PTR L Q +E K +
Sbjct: 104 TGVGKTTFGLVMSLYLAKK--------GKK----SYIIFPTRLLVEQVVEKLEKFGEKVG 151
Query: 495 WIVPSWLTGGEKMKSEKARIRKGI-----SILVATPGRLLDHCKHTETLKFSKVEHLVLD 549
V K EK + + ILV T L K+ + L K + + +D
Sbjct: 152 CGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLS---KNFDELPKKKFDFVFVD 208
Query: 550 EADRIL 555
+ D +L
Sbjct: 209 DVDAVL 214
>gnl|CDD|143600 cd07576, R-amidase_like, Pseudomonas sp. MCI3434 R-amidase and
related proteins (putative class 13 nitrilases).
Pseudomonas sp. MCI3434 R-amidase hydrolyzes
(R,S)-piperazine-2-tert-butylcarboxamide to form
(R)-piperazine-2-carboxylic acid. It does so with strict
R-stereoselectively. Its preferred substrates are
carboxamide compounds which have the amino or imino
group connected to their beta- or gamma-carbon. This
subgroup belongs to a larger nitrilase superfamily
comprised of nitrile- or amide-hydrolyzing enzymes and
amide-condensing enzymes, which depend on a Glu-Lys-Cys
catalytic triad. This superfamily has been classified in
the literature based on global and structure based
sequence analysis into thirteen different enzyme classes
(referred to as 1-13), class 13 represents proteins that
at the time were difficult to place in a distinct
similarity group. It has been suggested that this
subgroup represents a new class. Members of the
nitrilase superfamily generally form homomeric
complexes, the basic building block of which is a
homodimer. Native R-amidase however appears to be a
monomer.
Length = 254
Score = 34.5 bits (80), Expect = 0.19
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 5/55 (9%)
Query: 698 ERTEVFKTFRSVKSGVLICTDV----AARGLDLPLVDWIVQYTAPSSSTDYVHRV 748
+R V + R ++ G+LIC DV R L L D ++ TA +V R
Sbjct: 125 DRFPVVE-LRGLRVGLLICYDVEFPELVRALALAGADLVLVPTALMEPYGFVART 178
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 35.2 bits (81), Expect = 0.20
Identities = 76/335 (22%), Positives = 128/335 (38%), Gaps = 47/335 (14%)
Query: 426 ILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELALQTLEI 485
+L+G ++++ T SGKTL I ++ KL ++G AV ++P + LA +
Sbjct: 36 VLEGKNLVLAIPTASGKTLVAEIVMVNKLL--------REGGKAVYLVPLKALAEEKYRE 87
Query: 486 FTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGISILVATPGRLLDHCKHTETLKFSKVEH 545
F K + + TG E I++AT + +H + V+
Sbjct: 88 FKDWEKLGLRVAMT--TGDYDSTDEWL---GKYDIIIATAEKFDSLLRHGSSW-IKDVKL 141
Query: 546 LVLDEADRILDQGYERDIAEFLE-ILKKQKPQFQSILLSATLTPA--------------- 589
+V DE I D LE IL + Q + LSAT+ A
Sbjct: 142 VVADEIHLI----GSYDRGATLEMILTHMLGRAQILGLSATVGNAEELAEWLNAELVVSD 197
Query: 590 ---VQRLAGMTLQNPIQIDAADSTDIHNTTDSLVIPDSLKQH-----FIVTPPKLRLVAL 641
V+ G+ Q + + N+ +SLV D++K+ F+ T AL
Sbjct: 198 WRPVKLRKGVFYQGFLFWEDGKIERFPNSWESLVY-DAVKKGKGALVFVNTRRSAEKEAL 256
Query: 642 ASFILGKCQNVNEDEESKMLVFMATQDMADYHTELLSTVLGENIAFFKLHGSMSQSERTE 701
+ K + E + L +A + E L L +AF H + ++ER
Sbjct: 257 E--LAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFH--HAGLGRTERVL 312
Query: 702 VFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYT 736
+ FR V+ T + G++LP I++ T
Sbjct: 313 IEDAFREGLIKVITATPTLSAGINLPAFRVIIRDT 347
Score = 30.2 bits (68), Expect = 6.7
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 8/54 (14%)
Query: 17 ILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELA 70
+L+G ++++ T SGKTL I ++ KL ++G AV ++P + LA
Sbjct: 36 VLEGKNLVLAIPTASGKTLVAEIVMVNKLL--------REGGKAVYLVPLKALA 81
>gnl|CDD|222037 pfam13307, Helicase_C_2, Helicase C-terminal domain. This domain
is the second of two tandem AAA domains found in a wide
variety of helicase enzymes.
Length = 165
Score = 33.7 bits (78), Expect = 0.21
Identities = 13/70 (18%), Positives = 25/70 (35%), Gaps = 5/70 (7%)
Query: 659 KMLVFMATQD-MADYHTELLSTVLGENIAFFKLHGSMSQSERTEVFKTFRSVKSGVLICT 717
+LV + + L S +L + I + R ++ + F+ K +L
Sbjct: 11 GVLVLFPSYSLLEQVAELLASELLEKGIELL----VQGEGSREKLLERFKKGKGAILFGV 66
Query: 718 DVAARGLDLP 727
G+D P
Sbjct: 67 GSFWEGIDFP 76
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 34.7 bits (80), Expect = 0.23
Identities = 70/343 (20%), Positives = 113/343 (32%), Gaps = 48/343 (13%)
Query: 438 TGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTR-------ELALQTLEIFTKLC 490
TG GKT A I + L E SR IY +LP R A + +F+ +
Sbjct: 223 TGYGKTEASLILALALLDEKIKLKSR--VIY---VLPFRTIIEDMYRRAKEIFGLFSVIG 277
Query: 491 KSFTW-IVPSWLTGGEKMKSEKARIR-KGISILVATPG-RLLDHCKHTETLKFSKVE--- 544
KS L ++ +L+A + ++K K E
Sbjct: 278 KSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQI--LIFSVKGFKFEFLA 335
Query: 545 -----HLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATLTPAVQRLAGMTLQ 599
++LDE D+ + LE L + +L+SATL P ++ L
Sbjct: 336 LLLTSLVILDEVHLYADETMLAALLALLEALAEAGVPV--LLMSATLPPFLKEKLKKALG 393
Query: 600 NPIQIDAADSTDIHNTTDSLVIPDSLKQHFIVTPPKLRLVALASFILGKCQNVNEDEESK 659
++ D + + L I E K
Sbjct: 394 KGREVVENAKFCPKE--DEPGLKRKERVDVE----DGPQEELIELIS-----EEVKEGKK 442
Query: 660 MLVFMATQDMADYHTELLSTVLGENIAFFKLHGSMSQSERTE----VFKTFRSVKSGVLI 715
+LV + T D A E L G + LH + +R E + K F+ + +++
Sbjct: 443 VLVIVNTVDRAIELYEKLK-EKGPKVLL--LHSRFTLKDREEKERELKKLFKQNEGFIVV 499
Query: 716 CTDVAARGLDLPLVDWIVQYTAPSSSTDYVHRVGRTARVGHEG 758
T V G+D+ D + T + + R GR R G +
Sbjct: 500 ATQVIEAGVDID-FDVL--ITELAPIDSLIQRAGRVNRHGKKE 539
Score = 31.7 bits (72), Expect = 2.3
Identities = 39/170 (22%), Positives = 59/170 (34%), Gaps = 27/170 (15%)
Query: 29 TGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTR-------ELALQTLEIFTKLC 81
TG GKT A I + L E SR IY +LP R A + +F+ +
Sbjct: 223 TGYGKTEASLILALALLDEKIKLKSR--VIY---VLPFRTIIEDMYRRAKEIFGLFSVIG 277
Query: 82 KSFTW-IVPSWLTGGEKMKSEKARIR-KGISILVATPG-RLLDHCKHTETLKFSKVE--- 135
KS L ++ +L+A + ++K K E
Sbjct: 278 KSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQI--LIFSVKGFKFEFLA 335
Query: 136 -----HLVLDEADRILDQGYERDIAEFLEILKKQKPQFQSILLSATLTPA 180
++LDE D+ + LE L + +L+SATL P
Sbjct: 336 LLLTSLVILDEVHLYADETMLAALLALLEALAEAGVPV--LLMSATLPPF 383
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 34.6 bits (80), Expect = 0.31
Identities = 48/235 (20%), Positives = 92/235 (39%), Gaps = 47/235 (20%)
Query: 504 GEKMKSEKARIRKGISILVATPGRLLDHCKHTETLKFSKVEHLVLDEADRILDQGYER-- 561
E S + RI+ V T G LL ++ L S +++DEA +ER
Sbjct: 132 FESKVSPRTRIK------VMTDGILLREIQNDPLL--SGYSVVIIDEA-------HERSL 176
Query: 562 --DI--AEFLEILKKQKPQFQSILLSATLTPAVQRLAGMTLQNP-IQIDAADSTDIHNTT 616
DI ++L +++ + I++SATL +R + P I+I+
Sbjct: 177 NTDILLGLLKDLLARRRDDLKLIIMSATLD--AERFSAYFGNAPVIEIEG---------- 224
Query: 617 DSLVIPDSLKQHFIVTPPKLRLVALASFILGKCQNVNE---DEESKMLVFM-ATQDMADY 672
+ + + A + V+ + +LVF+ +++
Sbjct: 225 ---------RTYPVEIRYLPEAEADYILLDAIVAAVDIHLREGSGSILVFLPGQREIERT 275
Query: 673 HTELLSTVLGENIAFFKLHGSMSQSERTEVFKTFRSVKSGVLICTDVAARGLDLP 727
L LG+++ L+G++S E+ VF+ K V++ T++A L +P
Sbjct: 276 AEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIP 330
>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 = 34.3 bits (79), Expect = 0.36
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 7/52 (13%)
Query: 19 DGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELA 70
G V+V + T SGK+LAY +P++ L + A+ + PT+ LA
Sbjct: 50 AGRHVVVATGTASGKSLAYQLPVLSAL-------ADDPRATALYLAPTKALA 94
Score = 34.3 bits (79), Expect = 0.36
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 7/52 (13%)
Query: 428 DGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELA 479
G V+V + T SGK+LAY +P++ L + A+ + PT+ LA
Sbjct: 50 AGRHVVVATGTASGKSLAYQLPVLSAL-------ADDPRATALYLAPTKALA 94
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 33.6 bits (76), Expect = 0.65
Identities = 40/228 (17%), Positives = 76/228 (33%), Gaps = 23/228 (10%)
Query: 541 SKVEHLVLDEADRILDQGYERDIAEFLEILKKQKP-QFQSILLSATLTPAVQRLAGMTL- 598
K+E ++ E + YE + + + + + + + LA +T
Sbjct: 589 PKIEKVLECELSEEQRELYEALLEGAEKNQQLLEDLEKADSDENRIGDSELNILALLTRL 648
Query: 599 ----QNPIQIDAADSTDIHNTTDSLVIPDSL---KQHFIVTPPKLRLVALASFILGKCQN 651
+P +D + L+ D + ++ K +L AL +L K
Sbjct: 649 RQICNHPALVDE-GLEATFDRIVLLLREDKDFDYLKKPLIQLSKGKLQALDELLLDK--L 705
Query: 652 VNEDEESKMLVFMATQDMADYHTELLSTVLGENIAFFKLHGSMSQSERTEVFKTFRSVKS 711
+ E K+L+F + D + L I + +L GS R E+ F + +
Sbjct: 706 LEEGHYHKVLIFSQFTPVLDLLEDYLKA---LGIKYVRLDGSTPAKRRQELIDRFNADEE 762
Query: 712 GVLICTDVAARGLDLPLVDW--------IVQYTAPSSSTDYVHRVGRT 751
+ + A GL L L + D HR+G+
Sbjct: 763 EKVFLLSLKAGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQK 810
>gnl|CDD|236632 PRK09918, PRK09918, putative fimbrial chaperone protein;
Provisional.
Length = 230
Score = 32.3 bits (74), Expect = 0.75
Identities = 18/87 (20%), Positives = 34/87 (39%), Gaps = 18/87 (20%)
Query: 579 SILLSATLTPAVQRLAGMTLQNPIQI-DAAD---STDIHNTTDSLV--------IPDSLK 626
L + + AGM + + I + +D S ++ NT + + +P+
Sbjct: 9 FTALVLLSSSSAVHAAGMVPETSVVIVEESDGEGSINVKNTDSNPILLYTTLVDLPEDKS 68
Query: 627 QHFIVTPPKLRLVALASFILGKCQNVN 653
+ +VTPP R+ G+ Q V
Sbjct: 69 KLLLVTPPVARVEP------GQSQQVR 89
Score = 31.5 bits (72), Expect = 1.4
Identities = 19/94 (20%), Positives = 36/94 (38%), Gaps = 19/94 (20%)
Query: 225 QKPQFQSVLLSATLTPAVQRLA-GMTLQNPIQI-DAAD---STDIHNTTDSLV------- 272
+ F L+ + A GM + + I + +D S ++ NT + +
Sbjct: 2 RFNLFFLFTALVLLSSSSAVHAAGMVPETSVVIVEESDGEGSINVKNTDSNPILLYTTLV 61
Query: 273 -IPDSLKQHFIVTPPKLRLVALASFILGKCQNVN 305
+P+ + +VTPP R+ G+ Q V
Sbjct: 62 DLPEDKSKLLLVTPPVARVEP------GQSQQVR 89
>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor;
Provisional.
Length = 1147
Score = 33.2 bits (76), Expect = 0.77
Identities = 25/89 (28%), Positives = 40/89 (44%), Gaps = 2/89 (2%)
Query: 691 HGSMSQSERTEVFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPSSSTDYVHRV-G 749
HG M + E V F + VL+CT + G+D+P + I+ A +H++ G
Sbjct: 842 HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRG 901
Query: 750 RTARVGHEGSSLLFLIPSEVKLVEELQNR 778
R R H+ + L L P + + Q R
Sbjct: 902 RVGRSHHQAYAWL-LTPHPKAMTTDAQKR 929
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 32.9 bits (75), Expect = 1.1
Identities = 91/447 (20%), Positives = 148/447 (33%), Gaps = 102/447 (22%)
Query: 417 TVQQLSIQPILDGGDVLVRSQTGSGK-TLAYAIPIIQKLQEMRPKISRKDGIYAVIILPT 475
++Q+ + IL G + + TG GK T I + L+ G IILPT
Sbjct: 82 SIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLALK----------GKKCYIILPT 131
Query: 476 RELALQTLEIFTKLCKSFTWIVPSWLTGGEKMKSEKARIRKGI-----SILVATPGRLLD 530
L QT+E C+ V K EK + I ILV T L
Sbjct: 132 TLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLAR 191
Query: 531 HCKHTETLKFSKVEHLVLDEADRIL------------------------------DQGYE 560
+ + LKF + + +D+ D L QG
Sbjct: 192 NFPEMKHLKF---DFIFVDDVDAFLKASKNIDRSLQLLGFYEEIIEKAWKIIYLKKQGNI 248
Query: 561 RDIAEFLEILKKQKPQFQS-----ILLSATLTPAVQRLAGMTLQNPIQIDAADSTD-IHN 614
D E EIL K+ + + I+ SAT R+ + + + + N
Sbjct: 249 EDAMEKREILNKEIEKIGNKIGCLIVASATGKAKGDRVK--LYRELLGFEVGSGRSALRN 306
Query: 615 TTDSLVIPDSLKQHFIVTPPKLRLVALASFILGKCQNVNEDEESKMLVFMATQDMADYHT 674
D + P+ + + + K LGK L+F+ + A+
Sbjct: 307 IVDVYLNPEKIIKEHVRELLKK---------LGK----------GGLIFVPIDEGAEKAE 347
Query: 675 ELLSTVLGENIAFFKLHGSMSQSERTEVFKTFRSVKSGVLICT----DVAARGLDLP-LV 729
E+ +L + FK+ + ++ + F F + LI RGLDLP +
Sbjct: 348 EIEKYLLEDG---FKI--ELVSAKNKKGFDLFEEGEIDYLIGVATYYGTLVRGLDLPERI 402
Query: 730 DWIVQYTAPS---SSTDYVHRVGRTARVGH----------EGSSLLFLIPSEVKLVEELQ 776
+ V Y P + R + EG + ++ + VE L
Sbjct: 403 RFAVFYGVPKFRFRVDLEDPTIYRILGLLSEILKIEEELKEGIPIEGVLDVFPEDVEFL- 461
Query: 777 NRRIRIEEIKLKDCLQN-LLSVKMEGD 802
R I +E +K + +S+K E
Sbjct: 462 -RSILKDEEVIKKVAERPFVSLKKEEG 487
>gnl|CDD|153233 cd03139, GATase1_PfpI_2, Type 1 glutamine amidotransferase
(GATase1)-like domain found in a subgroup of proteins
similar to PfpI from Pyrococcus furiosus. Type 1
glutamine amidotransferase (GATase1)-like domain found
in a subgroup of proteins similar to PfpI from
Pyrococcus furiosus. PfpI is an ATP-independent
intracellular proteases which may hydrolyze small
peptides to provide a nutritional source. Only Cys of
the catalytic triad typical of GATase1 domains is
conserved in this group. This Cys residue is found in
the sharp turn between a beta strand and an alpha helix
termed the nucleophile elbow.
Length = 183
Score = 31.0 bits (71), Expect = 1.6
Identities = 12/58 (20%), Positives = 21/58 (36%), Gaps = 7/58 (12%)
Query: 217 EFLEILKKQKPQFQSVLLSATLTPAVQRLAGMTLQNPIQIDAADSTDIHNTTDSLVIP 274
E + F+ L+S T P R +G+T+ D+ L++P
Sbjct: 19 EVFGRAPRLAAPFEVFLVSETGGPVSSR-SGLTVLPDTSFADPPDLDV------LLVP 69
Score = 29.8 bits (68), Expect = 4.1
Identities = 12/58 (20%), Positives = 21/58 (36%), Gaps = 7/58 (12%)
Query: 565 EFLEILKKQKPQFQSILLSATLTPAVQRLAGMTLQNPIQIDAADSTDIHNTTDSLVIP 622
E + F+ L+S T P R +G+T+ D+ L++P
Sbjct: 19 EVFGRAPRLAAPFEVFLVSETGGPVSSR-SGLTVLPDTSFADPPDLDV------LLVP 69
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 29.9 bits (68), Expect = 1.7
Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 9/68 (13%)
Query: 10 QQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTREL 69
Q+ +I+ +L+ L+ TGSGKTL A +I +L + + K+ + ++P ++L
Sbjct: 8 QEEAIERLLEKKRGLIVMATGSGKTLTAAA-LIARLAKGKKKV--------LFVVPRKDL 58
Query: 70 ALQTLEIF 77
Q L I
Sbjct: 59 LEQALVII 66
Score = 29.9 bits (68), Expect = 1.7
Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 9/68 (13%)
Query: 419 QQLSIQPILDGGDVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTREL 478
Q+ +I+ +L+ L+ TGSGKTL A +I +L + + K+ + ++P ++L
Sbjct: 8 QEEAIERLLEKKRGLIVMATGSGKTLTAAA-LIARLAKGKKKV--------LFVVPRKDL 58
Query: 479 ALQTLEIF 486
Q L I
Sbjct: 59 LEQALVII 66
>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 = 32.1 bits (73), Expect = 1.7
Identities = 72/395 (18%), Positives = 127/395 (32%), Gaps = 102/395 (25%)
Query: 438 TGSGKT-LAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELALQTLEIFTKLCKSFTWI 496
TG GKT A+ + + R IILPT L +Q E + L +
Sbjct: 102 TGVGKTTFGLAMSLFLAKKGKR----------CYIILPTTLLVIQVAEKISSLAEKAGVG 151
Query: 497 VPSWLTGGEKM-----KSEKARIRKG-ISILVATPGRLLDHCKHTETLKFSKVEHLVLDE 550
+ ++ K RI G IL+ T L K+ + L K + + +D+
Sbjct: 152 TVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFL---SKNYDELG-PKFDFIFVDD 207
Query: 551 ADRILDQG------------YERDIAEFLEILKKQKPQFQS------------------- 579
D +L E I + ++++ + +++
Sbjct: 208 VDALLKASKNVDKLLKLLGFSEELIEKAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRG 267
Query: 580 --ILLSATLTPAVQR------LAGMTLQNPIQIDAADSTDIHNTTDSLVIPDSLKQHFIV 631
I+ SAT P +R L G + S + N D V + LK+
Sbjct: 268 CLIVSSATGRPRGKRAKLFRELLGFEVGGG-------SDTLRNVVDVYVEDEDLKE---- 316
Query: 632 TPPKLRLVALASFILGKCQNVNEDEESKMLVFMATQDMADYHTELLSTVLGENIAFFKLH 691
L+ + LG +V+++ + E+ + + H
Sbjct: 317 -----TLLEIVK-KLGT----------GGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYH 360
Query: 692 GSMSQSERTEVFKTFRSVKSGVLICT----DVAARGLDLP-LVDWIVQYTAPSSSTDYVH 746
+ + E ++ F + VLI RGLDLP V + V P
Sbjct: 361 ATKPK----EDYEKFAEGEIDVLIGVASYYGTLVRGLDLPERVRYAVFLGVPK------F 410
Query: 747 RVGRTARVGHEGSSLLFLIPSEVKLVEELQNRRIR 781
+V + LL L + + +E L + +
Sbjct: 411 KVPLKEALSSPRRLLLLLSILQEERIESLSEKARK 445
>gnl|CDD|227226 COG4889, COG4889, Predicted helicase [General function prediction
only].
Length = 1518
Score = 31.7 bits (72), Expect = 2.5
Identities = 34/134 (25%), Positives = 53/134 (39%), Gaps = 13/134 (9%)
Query: 623 DSLKQHFIVTPPKLRLVALASFILGKCQNVNEDEESKMLVFMATQDMADYHTELLSTVLG 682
+ LK T P R +A A I + SK + + Y EL
Sbjct: 448 NDLKNIKADTAPMQRAIAFAKDI----------KTSKQIAESFETVVEAYDEELKKDFKN 497
Query: 683 ENIAFFKLHGSMSQSER---TEVFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPS 739
I+ + G+M+ ER E+ TF + +L + G+D+P +D ++ + S
Sbjct: 498 LKISIDHVDGTMNALERLDLLELKNTFEPNECKILSNARCLSEGVDVPALDSVIFFDPRS 557
Query: 740 SSTDYVHRVGRTAR 753
S D V VGR R
Sbjct: 558 SMVDIVQAVGRVMR 571
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 31.5 bits (72), Expect = 2.5
Identities = 26/92 (28%), Positives = 43/92 (46%), Gaps = 8/92 (8%)
Query: 691 HGSMSQSERTEVFKTFRSVKSGVLICTDVAARGLDLPLVDWIVQYTAPSSSTDYVH---- 746
HG M + E EV F + + VL+CT + G+D+P + I+ A ++
Sbjct: 836 HGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRG 895
Query: 747 RVGRTARVGHEGSSLLFLIPSEVKLVEELQNR 778
RVGR+ + + FL P + L E+ + R
Sbjct: 896 RVGRSNKQAYA----YFLYPPQKALTEDAEKR 923
>gnl|CDD|233063 TIGR00631, uvrb, excinuclease ABC, B subunit. All proteins in this
family for wich functions are known are DNA helicases
that function in the nucleotide excision repair and are
endonucleases that make the 3' incision next to DNA
damage. They are part of a pathway requiring UvrA, UvrB,
UvrC, and UvrD homologs. 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 = 655
Score = 31.1 bits (71), Expect = 3.0
Identities = 35/124 (28%), Positives = 54/124 (43%), Gaps = 17/124 (13%)
Query: 664 MATQDMADYHTELLSTVLGENIAFFKLHGSMSQSERTEVFKTFRSVKSGVLICTDVAARG 723
MA +D+ DY EL I LH + ER E+ + R + VL+ ++ G
Sbjct: 454 MA-EDLTDYLKEL-------GIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREG 505
Query: 724 LDLPLVDWIVQYTA-----PSSSTDYVHRVGRTARVGHEGSSLLF---LIPSEVKLVEEL 775
LDLP V + A S + +GR AR + G +++ + S K +EE
Sbjct: 506 LDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVN-GKVIMYADKITDSMQKAIEET 564
Query: 776 QNRR 779
+ RR
Sbjct: 565 ERRR 568
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6
family in eukaryotes. Several members may be found in
genome and interact with each other [DNA metabolism,
DNA replication, recombination, and repair].
Length = 365
Score = 30.3 bits (69), Expect = 5.3
Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 12/69 (17%)
Query: 14 IQPILDGG---DVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVI-----ILP 65
++PIL G +V + +TG+GKT ++++L+E +D + IL
Sbjct: 31 LRPILRGSRPSNVFIYGKTGTGKTAV-TKYVMKELEE---AAEDRDVRVVTVYVNCQILD 86
Query: 66 TRELALQTL 74
T L L
Sbjct: 87 TLYQVLVEL 95
Score = 30.3 bits (69), Expect = 5.3
Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 12/69 (17%)
Query: 423 IQPILDGG---DVLVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVI-----ILP 474
++PIL G +V + +TG+GKT ++++L+E +D + IL
Sbjct: 31 LRPILRGSRPSNVFIYGKTGTGKTAV-TKYVMKELEE---AAEDRDVRVVTVYVNCQILD 86
Query: 475 TRELALQTL 483
T L L
Sbjct: 87 TLYQVLVEL 95
>gnl|CDD|234113 TIGR03117, cas_csf4, CRISPR type AFERR-associated DEAD/DEAH-box
helicase Csf4. Members of this family show up near
CRISPR repeats in Acidithiobacillus ferrooxidans ATCC
23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens
DSM 15236. In the latter two species, the CRISPR/cas
locus is found on a plasmid. This family is one of
several characteristic of a type of CRISPR-associated
(cas) gene cluster we designate Aferr after A.
ferrooxidans, where it is both chromosomal and the only
type of cas gene cluster found. The gene is designated
csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein
1), as it lies farthest (fourth closest) from the
repeats in the A. ferrooxidans genome [Mobile and
extrachromosomal element functions, Other].
Length = 636
Score = 30.3 bits (68), Expect = 6.0
Identities = 19/70 (27%), Positives = 29/70 (41%), Gaps = 8/70 (11%)
Query: 12 LSIQPILDGGDV-LVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELA 70
L+ L + ++ + TG GKTLA + + L+E R D I +PT L
Sbjct: 7 LNCLTSLRQKRIGMLEASTGVGKTLAMIMAALTMLKE------RPDQ-KIAIAVPTLALM 59
Query: 71 LQTLEIFTKL 80
Q +L
Sbjct: 60 GQLWSELERL 69
Score = 30.3 bits (68), Expect = 6.0
Identities = 19/70 (27%), Positives = 29/70 (41%), Gaps = 8/70 (11%)
Query: 421 LSIQPILDGGDV-LVRSQTGSGKTLAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELA 479
L+ L + ++ + TG GKTLA + + L+E R D I +PT L
Sbjct: 7 LNCLTSLRQKRIGMLEASTGVGKTLAMIMAALTMLKE------RPDQ-KIAIAVPTLALM 59
Query: 480 LQTLEIFTKL 489
Q +L
Sbjct: 60 GQLWSELERL 69
>gnl|CDD|132756 cd07071, NR_LBD_Nurr1, The ligand binding domain of Nurr1, a
member of conserved family of nuclear receptors. The
ligand binding domain of nuclear receptor Nurr1: Nurr1
belongs to the conserved family of nuclear receptors. It
is a transcription factor that is expressed in the
embryonic ventral midbrain and is critical for the
development of dopamine (DA) neurons. Structural studies
have shown that the ligand binding pocket of Nurr1 is
filled by bulky hydrophobic residues, making it unable
to bind to ligands. Therefore, it belongs to the class
of orphan receptors. However, Nurr1 forms heterodimers
with RXR and can promote signaling via its partner, RXR.
Like other members of the nuclear receptor (NR)
superfamily of ligand-activated transcription factors,
Nurr1 has a central well conserved DNA binding domain
(DBD), a variable N-terminal domain, a flexible hinge
and a C-terminal ligand binding domain (LBD).
Length = 238
Score = 29.6 bits (66), Expect = 6.3
Identities = 28/118 (23%), Positives = 54/118 (45%), Gaps = 13/118 (11%)
Query: 818 LQMSFESAVLQQK-------ILHTSAC-KGYTSWVRFYASYSKDLRHIFNFKQIHLGHFA 869
L++++ S ++ K +LH C +G+ W+ +S +L+++ I + F+
Sbjct: 89 LRLAYRSNPVEGKLIFCNGVVLHRLQCVRGFGEWIDSIVEFSSNLQNM----NIDISAFS 144
Query: 870 KSFALRDAPSVISGIGKPKNKEELKNKKMAINKEKSFKQRGNFSKKQMLSEFDSGLPQ 927
AL G+ +PK EEL+NK + K+ G ++ LS+ LP+
Sbjct: 145 CIAALAMVTER-HGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPE 201
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 30.4 bits (69), Expect = 6.4
Identities = 33/127 (25%), Positives = 47/127 (37%), Gaps = 25/127 (19%)
Query: 29 TGSGKT---LAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELALQTLEIFTKL----- 80
TG GKT L ++ + + R II+PT L Q E K
Sbjct: 106 TGVGKTTFGLLMSLYL--AKKGKR----------VYIIVPTTTLVRQVYERLKKFAEDAG 153
Query: 81 CKSFTWIVPSWLTGGEKMKSEKARIRKG-ISILVATPGRLLDHCKHTETLKFSKVEHLVL 139
+ S L EK ++ + RI G IL+ T L + LKF + +
Sbjct: 154 SLDVLVVYHSALPTKEKEEALE-RIESGDFDILITTSQFLSKRFEELSKLKFDFI---FV 209
Query: 140 DEADRIL 146
D+ D IL
Sbjct: 210 DDVDAIL 216
Score = 30.4 bits (69), Expect = 6.4
Identities = 33/127 (25%), Positives = 47/127 (37%), Gaps = 25/127 (19%)
Query: 438 TGSGKT---LAYAIPIIQKLQEMRPKISRKDGIYAVIILPTRELALQTLEIFTKL----- 489
TG GKT L ++ + + R II+PT L Q E K
Sbjct: 106 TGVGKTTFGLLMSLYL--AKKGKR----------VYIIVPTTTLVRQVYERLKKFAEDAG 153
Query: 490 CKSFTWIVPSWLTGGEKMKSEKARIRKG-ISILVATPGRLLDHCKHTETLKFSKVEHLVL 548
+ S L EK ++ + RI G IL+ T L + LKF + +
Sbjct: 154 SLDVLVVYHSALPTKEKEEALE-RIESGDFDILITTSQFLSKRFEELSKLKFDFI---FV 209
Query: 549 DEADRIL 555
D+ D IL
Sbjct: 210 DDVDAIL 216
>gnl|CDD|217743 pfam03810, IBN_N, Importin-beta N-terminal domain.
Length = 71
Score = 27.2 bits (61), Expect = 7.5
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 565 EFLEILKKQKPQF----QSILLSATLTPAVQRLAGMTLQNPIQ 603
+ LE +KQ P F IL + V++LA + L+N I
Sbjct: 3 KQLEQFEKQDPGFWSKLLQILSDTSSDLQVRQLAALYLKNLIT 45
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 30.1 bits (68), Expect = 8.1
Identities = 47/182 (25%), Positives = 69/182 (37%), Gaps = 49/182 (26%)
Query: 10 QQLSIQPILDGGDVLVRSQTGSGKTLA--YAIPIIQKLQEMRPKISRKDGIYAVIILPTR 67
QQ +I + G VLV + T SGKT+ YAI ++ +DG + P +
Sbjct: 124 QQEAIAILERGESVLVCAPTSSGKTVVAEYAI-----------ALALRDGQRVIYTSPIK 172
Query: 68 ELALQTLEIFTKLCKSFTWIVPSW--LTGGEKMKSEKARIRKGISILVATPGRLLDHCKH 125
L+ Q + L F + +TG I LV T
Sbjct: 173 ALSNQ---KYRDLLAKFGDVADMVGLMTG-------DVSINPDAPCLVMT---------- 212
Query: 126 TETLK---------FSKVEHLVLDEADRILDQGYERDIA-EFLEILKKQKPQFQSILLSA 175
TE L+ +E +V DE I D+ ER + E + IL +F + LSA
Sbjct: 213 TEILRNMLYRGSESLRDIEWVVFDEVHYIGDR--ERGVVWEEVIILLPDHVRF--VFLSA 268
Query: 176 TL 177
T+
Sbjct: 269 TV 270
Score = 30.1 bits (68), Expect = 8.1
Identities = 47/182 (25%), Positives = 69/182 (37%), Gaps = 49/182 (26%)
Query: 419 QQLSIQPILDGGDVLVRSQTGSGKTLA--YAIPIIQKLQEMRPKISRKDGIYAVIILPTR 476
QQ +I + G VLV + T SGKT+ YAI ++ +DG + P +
Sbjct: 124 QQEAIAILERGESVLVCAPTSSGKTVVAEYAI-----------ALALRDGQRVIYTSPIK 172
Query: 477 ELALQTLEIFTKLCKSFTWIVPSW--LTGGEKMKSEKARIRKGISILVATPGRLLDHCKH 534
L+ Q + L F + +TG I LV T
Sbjct: 173 ALSNQ---KYRDLLAKFGDVADMVGLMTG-------DVSINPDAPCLVMT---------- 212
Query: 535 TETLK---------FSKVEHLVLDEADRILDQGYERDIA-EFLEILKKQKPQFQSILLSA 584
TE L+ +E +V DE I D+ ER + E + IL +F + LSA
Sbjct: 213 TEILRNMLYRGSESLRDIEWVVFDEVHYIGDR--ERGVVWEEVIILLPDHVRF--VFLSA 268
Query: 585 TL 586
T+
Sbjct: 269 TV 270
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
0.318 0.134 0.379
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: 47,099,693
Number of extensions: 4687575
Number of successful extensions: 5193
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5041
Number of HSP's successfully gapped: 191
Length of query: 930
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 824
Effective length of database: 6,236,078
Effective search space: 5138528272
Effective search space used: 5138528272
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 64 (28.3 bits)