RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9399
(453 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 = 417 bits (1074), Expect = e-142
Identities = 172/411 (41%), Positives = 247/411 (60%), Gaps = 30/411 (7%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
F S+GL +L+AL +G+ +PT +Q AIP ++GRD++ +QTG+GKTAAF+LP L
Sbjct: 29 PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLL 88
Query: 61 HKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERY 120
K S + L+L PTRELA+Q+ +
Sbjct: 89 QKILKSV--------------------------ERKYVSALILAPTRELAVQIAEELRKL 122
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
G + ++ + GG+ +Q++ L R +I++ATPGRL+D + GK++ S ++ LVLDE
Sbjct: 123 GKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDE 182
Query: 181 ADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNS--IEK 238
ADRMLDMGFI+DIEKI+ A P RQT+LFSAT+ + +A DP+ ++V+ +E+
Sbjct: 183 ADRMLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLER 242
Query: 239 KQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAP 298
K I Q L V+ K LL LL+D+ G+ +VF TKR + +A+ L GF A
Sbjct: 243 TLKKIKQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAA 302
Query: 299 LHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIG 358
LHGDL Q R+R LE + G +++LVATDVAARG+D+P ++HV NYDLP PEDYVHRIG
Sbjct: 303 LHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIG 362
Query: 359 RTGRAGRNGFAVSLVNH-AERMNIKKIERFTKQQIPIEV-INGFEPKKRIR 407
RTGRAGR G A+S V E +K+IE+ ++++P V + EP+
Sbjct: 363 RTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLPSAVLLPLDEPEDAKL 413
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 361 bits (929), Expect = e-122
Identities = 162/407 (39%), Positives = 237/407 (58%), Gaps = 28/407 (6%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
F + L E +L+AL GYT+PT +Q +AIP A+ GRD++ S+ TG+GKTAAF+LPAL
Sbjct: 1 TTFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPAL 60
Query: 61 HKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERY 120
P R K PR+L+LTPTRELA+QV
Sbjct: 61 QHLLD----FP--------------------RRKSGPPRILILTPTRELAMQVADQAREL 96
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
+ + +I GG+ Y+ ++ S N +I++ATPGRL+ ++ + ++ L+LDE
Sbjct: 97 AKHTH-LDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDE 155
Query: 181 ADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDG-IVGNMAENITKDPLILKVNSIEKK 239
ADRMLDMGF DIE I T +QT+LFSATL+G V + AE + DP+ ++ ++
Sbjct: 156 ADRMLDMGFAQDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRE 215
Query: 240 QKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPL 299
+K I Q DD+ HK LL +LL+ V +++VF T+ +A L +G L
Sbjct: 216 RKKIHQWYYRADDLEHKTALLCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYL 275
Query: 300 HGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGR 359
G++ Q RN ++ L GR+ +LVATDVAARGID+ ++HV N+D+P+ + Y+HRIGR
Sbjct: 276 EGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGR 335
Query: 360 TGRAGRNGFAVSLV-NHAERMNIKKIERFTKQQIPIEVINGFEPKKR 405
TGRAGR G A+SLV H + + KIER+ ++ + VI+ PK +
Sbjct: 336 TGRAGRKGTAISLVEAHDHLL-LGKIERYIEEPLKARVIDELRPKTK 381
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 337 bits (867), Expect = e-112
Identities = 169/411 (41%), Positives = 241/411 (58%), Gaps = 32/411 (7%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
M+F S+GL +L+A+ + GY +PT +Q+QAIPA + GRDL+ S+QTG+GKTA F LP L
Sbjct: 1 MSFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLL 60
Query: 61 HKFASS----KNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAA 116
+ K + PV R L+LTPTRELA Q+
Sbjct: 61 QHLITRQPHAKGRRPV--------------------------RALILTPTRELAAQIGEN 94
Query: 117 TERYGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQIL 176
Y Y+ I+++ + GG+ QM L ++L+ATPGRL+D + + ++IL
Sbjct: 95 VRDYSKYLN-IRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEIL 153
Query: 177 VLDEADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSI 236
VLDEADRMLDMGFI+DI +++ P RQ +LFSAT + +AE + +PL ++V
Sbjct: 154 VLDEADRMLDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARR 213
Query: 237 EKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLA 296
+ +TQ + FVD K LL ++ Q +VFT TK A+ +A++LN G +
Sbjct: 214 NTASEQVTQHVHFVDK-KRKRELLSQMIGKGNWQQVLVFTRTKHGANHLAEQLNKDGIRS 272
Query: 297 APLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHR 356
A +HG+ Q AR R L + + G I++LVATD+AARG+D+ + HV NY+LP PEDYVHR
Sbjct: 273 AAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHR 332
Query: 357 IGRTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEVINGFEPKKRIR 407
IGRTGRA G A+SLV E ++ IE+ K++IP I G+EP I+
Sbjct: 333 IGRTGRAAATGEALSLVCVDEHKLLRDIEKLLKKEIPRIAIPGYEPDPSIK 383
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 330 bits (849), Expect = e-109
Identities = 154/402 (38%), Positives = 216/402 (53%), Gaps = 32/402 (7%)
Query: 3 FKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHK 62
F ++ L +L L ++GYT+ T +Q Q++PA ++G+D+I ++TGSGKTAAF L L K
Sbjct: 6 FSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQK 65
Query: 63 FASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGL 122
RF + + LVL PTRELA QV R
Sbjct: 66 LDVK-------------------------RF---RVQALVLCPTRELADQVAKEIRRLAR 97
Query: 123 YMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEAD 182
++ IK +++ GG+P Q+ L I++ TPGR++DH+ G ++ L LVLDEAD
Sbjct: 98 FIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEAD 157
Query: 183 RMLDMGFINDIEKIVDATPVTRQTMLFSATL-DGIVGNMAENITKDPLILKVNSIEKKQK 241
RMLDMGF + I+ I+ P RQT+LFSAT +GI +++ +DP+ +KV S
Sbjct: 158 RMLDMGFQDAIDAIIRQAPARRQTLLFSATYPEGIA-AISQRFQRDPVEVKVESTHDLPA 216
Query: 242 NITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHG 301
I Q V + L LL + VVF TK++ +AD LN GF A LHG
Sbjct: 217 -IEQRFYEVSP-DERLPALQRLLLHHQPESCVVFCNTKKECQEVADALNAQGFSALALHG 274
Query: 302 DLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTG 361
DL Q R++ L +LVATDVAARG+D+ A+ V NY+L + PE +VHRIGRTG
Sbjct: 275 DLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTG 334
Query: 362 RAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEVINGFEPK 403
RAG G A+SLV E IE + +++ E + P
Sbjct: 335 RAGSKGLALSLVAPEEMQRANAIEDYLGRKLNWEPLPSLSPL 376
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 302 bits (774), Expect = 3e-96
Identities = 161/393 (40%), Positives = 229/393 (58%), Gaps = 29/393 (7%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
F +GL +L+AL +GY KP+ +Q + IP ++GRD++ +QTGSGKTAAF LP L
Sbjct: 6 TTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLL 65
Query: 61 HKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERY 120
H N P +K P++LVL PTRELA+QV A +
Sbjct: 66 H------NLDPELKA----------------------PQILVLAPTRELAVQVAEAMTDF 97
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDE 180
+M+ + +++ GG Y Q++ L + P+I++ TPGRL+DH+ G ++ S L LVLDE
Sbjct: 98 SKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDE 157
Query: 181 ADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQ 240
AD ML MGFI D+E I+ P QT LFSAT+ + + K+P +++ S +
Sbjct: 158 ADEMLRMGFIEDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTR 217
Query: 241 KNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLH 300
+I+QS V + KN L L + A++F TK +A+ L +G+ +A L+
Sbjct: 218 PDISQSYWTVWG-MRKNEALVRFLEAEDFDAAIIFVRTKNATLEVAEALERNGYNSAALN 276
Query: 301 GDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRT 360
GD++Q R +TLE L+ GR+ IL+ATDVAARG+DV I+ V NYD+P E YVHRIGRT
Sbjct: 277 GDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRT 336
Query: 361 GRAGRNGFAVSLVNHAERMNIKKIERFTKQQIP 393
GRAGR G A+ V + ER ++ IER K IP
Sbjct: 337 GRAGRAGRALLFVENRERRLLRNIERTMKLTIP 369
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 279 bits (716), Expect = 6e-90
Identities = 160/439 (36%), Positives = 220/439 (50%), Gaps = 35/439 (7%)
Query: 3 FKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHK 62
F LH V++AL K G+ T +Q A+P ++GRD+ +QTG+GKT AF+ H
Sbjct: 10 FSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHY 69
Query: 63 FASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGL 122
S ++R K QPR L++ PTRELA+Q+ A E
Sbjct: 70 LLSHP------------------APEDR---KVNQPRALIMAPTRELAVQIHADAEPL-A 107
Query: 123 YMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEAD 182
+K GG Y +Q+++L +IL+ T GRLID+ IN +Q++VLDEAD
Sbjct: 108 QATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEAD 167
Query: 183 RMLDMGFINDIEKIVDATPVT--RQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQ 240
RM D+GFI DI + P R MLFSATL V +A +P ++V +K
Sbjct: 168 RMFDLGFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTG 227
Query: 241 KNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLH 300
I + LF K RLL L+ ++ +A++F TK + I L G L
Sbjct: 228 HRIKEE-LFYPSNEEKMRLLQTLIEEEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLT 286
Query: 301 GDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRT 360
GD+ Q R R LE RG + ILVATDVAARG+ +PA+THVFNYDLP EDYVHRIGRT
Sbjct: 287 GDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRT 346
Query: 361 GRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIE------VINGFEPKKRIRTYYSRYR 414
GRAG +G ++SL +N+ IE + IP+ ++ R+ R R
Sbjct: 347 GRAGASGHSISLACEEYALNLPAIETYIGHSIPVSKYDSDALLTDLPKPLRLT----RPR 402
Query: 415 FNNNNWKTHNINKSNITKR 433
N ++ KR
Sbjct: 403 TGNGPRRSGAPRNRRRRKR 421
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 276 bits (708), Expect = 2e-87
Identities = 161/429 (37%), Positives = 230/429 (53%), Gaps = 37/429 (8%)
Query: 3 FKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL-H 61
F+ + +LK+L G+T+PT +Q Q P A+SGRD+I ++TGSGKT AF+LPA+ H
Sbjct: 132 FEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVH 191
Query: 62 KFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYG 121
A + LR+ P +LVL PTRELA Q+ ++G
Sbjct: 192 INA-----------------------QPLLRYGDG-PIVLVLAPTRELAEQIREQCNKFG 227
Query: 122 LYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEA 181
KI+ GG+P Q+ L R EIL+A PGRLID + S N + LVLDEA
Sbjct: 228 A-SSKIRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEA 286
Query: 182 DRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKD-PLILKVNSIE-KK 239
DRMLDMGF I KIV RQT+++SAT V ++A ++ K+ P+ + V S++
Sbjct: 287 DRMLDMGFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTA 346
Query: 240 QKNITQSILFVDDILHKNRLLDYLLRDKRVGQAV-VFTATKRDADIIADRLNISGFLAAP 298
NI Q + V++ + +L L R R G + +F TK+ AD + L + G+ A
Sbjct: 347 CHNIKQEVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALC 406
Query: 299 LHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIG 358
+HGD Q R L + G+ I++ATDVA+RG+DV + +V N+D P EDYVHRIG
Sbjct: 407 IHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIG 466
Query: 359 RTGRAGRNGFAVS-LVNHAERM--NIKKIERFTKQQIPIEVI-----NGFEPKKRIRTYY 410
RTGRAG G + + L R+ ++ K+ R KQ +P E+ ++R Y
Sbjct: 467 RTGRAGAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEKLSNERSNGTERRRWGGY 526
Query: 411 SRYRFNNNN 419
R+ N NN
Sbjct: 527 GRFSNNVNN 535
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 267 bits (683), Expect = 2e-84
Identities = 146/400 (36%), Positives = 224/400 (56%), Gaps = 32/400 (8%)
Query: 3 FKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHK 62
F L ++ A+ +G+ T +Q Q + ++G D I +QTG+GKTAAF++ +++
Sbjct: 89 FHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQ 148
Query: 63 FASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQV---TAATER 119
+ P KER +PR L++ PTREL +Q+ AA +
Sbjct: 149 LL--QTPPP----------------KERYM---GEPRALIIAPTRELVVQIAKDAAALTK 187
Query: 120 YGLYMKKIKAISILGGMPYLRQM-QLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVL 178
Y + ++ +GGM + +Q+ QL +R +IL+ATPGRL+D G+++ ++++VL
Sbjct: 188 Y----TGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVL 243
Query: 179 DEADRMLDMGFINDIEKIVDATPVT--RQTMLFSATLDGIVGNMAENITKDPLILKVNSI 236
DEADRMLDMGFI + +I+ TP RQT+LFSAT V N+A+ T DP I+++
Sbjct: 244 DEADRMLDMGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPE 303
Query: 237 EKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLA 296
+ Q + V K +LL L+ + +VF K + I +RL G A
Sbjct: 304 NVASDTVEQHVYAVAG-SDKYKLLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGINA 362
Query: 297 APLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHR 356
A L GD+ Q+ R +TLE R G+I++LVATDVA RGI + I+HV N+ LP+ P+DYVHR
Sbjct: 363 AQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHR 422
Query: 357 IGRTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEV 396
IGRTGRAG +G ++S + + +IE ++I E+
Sbjct: 423 IGRTGRAGASGVSISFAGEDDAFQLPEIEELLGRKISCEM 462
>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 = 249 bits (639), Expect = 2e-81
Identities = 90/230 (39%), Positives = 134/230 (58%), Gaps = 27/230 (11%)
Query: 3 FKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHK 62
F+ +GL +L+ + +G+ KPT +Q +AIP +SGRD+I +QTGSGKTAAF++P L K
Sbjct: 1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60
Query: 63 FASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGL 122
+ K P+ L+L PTRELALQ+ + G
Sbjct: 61 ---------------------LDPSP-----KKDGPQALILAPTRELALQIAEVARKLGK 94
Query: 123 YMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEAD 182
+ +K + I GG +Q++ L R P I++ATPGRL+D + GK++ S ++ LVLDEAD
Sbjct: 95 HTN-LKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEAD 153
Query: 183 RMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILK 232
RMLDMGF + I +I+ P RQT+LFSAT+ V ++A ++P+ +
Sbjct: 154 RMLDMGFEDQIREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRIL 203
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 246 bits (629), Expect = 2e-75
Identities = 149/400 (37%), Positives = 216/400 (54%), Gaps = 26/400 (6%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
+ F S LH +L L G+T+ T +Q +P A+ G D+ +QTG+GKT AF+
Sbjct: 9 LTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFL---- 64
Query: 61 HKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERY 120
+ VM N++ + KP PR L+L PTRELA+Q+ ++
Sbjct: 65 ---------VAVM--------NRLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKF 107
Query: 121 GLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHL-QILVLD 179
G + A+ + GG+ Y +Q +LL + ++++ATPGRLID++ K+ H +I VLD
Sbjct: 108 GADLGLRFAL-VYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLD 166
Query: 180 EADRMLDMGFINDIEKIVDATP--VTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIE 237
EADRM D+GFI DI ++ P TRQT+LFSATL V +A +P L V +
Sbjct: 167 EADRMFDLGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETET 226
Query: 238 KKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAA 297
+ Q I F D K LL LL + +VF TK + +A L G+
Sbjct: 227 ITAARVRQRIYFPADE-EKQTLLLGLLSRSEGARTMVFVNTKAFVERVARTLERHGYRVG 285
Query: 298 PLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRI 357
L GD+ Q R L ++G+++ILVATDVAARG+ + + +V+NYDLP EDYVHRI
Sbjct: 286 VLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRI 345
Query: 358 GRTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEVI 397
GRT R G G A+S M++ IE + +Q+IP+E +
Sbjct: 346 GRTARLGEEGDAISFACERYAMSLPDIEAYIEQKIPVEPV 385
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 217 bits (555), Expect = 2e-66
Identities = 122/397 (30%), Positives = 195/397 (49%), Gaps = 32/397 (8%)
Query: 3 FKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHK 62
F ++ L+E +L+ + G+ KP+ +Q++ I + G D I +Q+G+GKTA F++ AL
Sbjct: 30 FDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQL 89
Query: 63 FASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGL 122
N L+L PTRELA Q+ G
Sbjct: 90 IDYDLNACQA----------------------------LILAPTRELAQQIQKVVLALGD 121
Query: 123 YMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEAD 182
Y+K ++ + +GG + L +++ TPGR+ D ++ + L++ +LDEAD
Sbjct: 122 YLK-VRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEAD 180
Query: 183 RMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQKN 242
ML GF I + P Q LFSAT+ + + +DP + V E +
Sbjct: 181 EMLSRGFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEG 240
Query: 243 ITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGD 302
I Q + V+ K L L + QA+++ T+R D + +++ F + +HGD
Sbjct: 241 IRQFYVAVEKEEWKFDTLCDLYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGD 300
Query: 303 LHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGR 362
+ Q R+ + R G ++L+ TD+ ARGIDV ++ V NYDLP PE+Y+HRIGR+GR
Sbjct: 301 MDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGR 360
Query: 363 AGRNGFAVSLVNHAERMNIKKIERFTKQQI---PIEV 396
GR G A++ V + +K+IER QI P+EV
Sbjct: 361 FGRKGVAINFVTPDDIEQLKEIERHYNTQIEEMPMEV 397
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 219 bits (560), Expect = 7e-66
Identities = 132/422 (31%), Positives = 220/422 (52%), Gaps = 33/422 (7%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
++F S GL +L L GY PT +Q QAIPAA+SGR L+VS+ TGSGKTA+F++P +
Sbjct: 121 LSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPII 180
Query: 61 HKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERY 120
+ + ++ P ++N P +VLTPTREL +QV ++
Sbjct: 181 SRCCTIRSGHPSEQRN---------------------PLAMVLTPTRELCVQV---EDQA 216
Query: 121 GLYMKKI--KAISILGGMPYLRQMQLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVL 178
+ K + K ++GG +Q+ + + E+++ TPGRLID ++ I ++ +LVL
Sbjct: 217 KVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVL 276
Query: 179 DEADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEK 238
DE D ML+ GF + + +I A Q +LFSAT+ V A ++ KD +++ + + +
Sbjct: 277 DEVDCMLERGFRDQVMQIFQALS-QPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNR 335
Query: 239 KQKNITQSILFVDDILHKNRLLDYLLRDKRVG-QAVVFTATKRDADIIADRLNI-SGFLA 296
K + Q ++V+ K +L D L + AVVF +++ AD++A+ + + +G A
Sbjct: 336 PNKAVKQLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKA 395
Query: 297 APLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHR 356
+HG+ R +++ G + ++VAT V RG+D+ + V +D+P ++Y+H+
Sbjct: 396 LSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQ 455
Query: 357 IGRTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQ---IPIEVINGFE-PKKRIRTYYSR 412
IGR R G G A+ VN +R ++ K IP E+ N R R R
Sbjct: 456 IGRASRMGEKGTAIVFVNEEDRNLFPELVALLKSSGAAIPRELANSRYLGSGRKRKKKRR 515
Query: 413 YR 414
Y
Sbjct: 516 YG 517
>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 = 163 bits (415), Expect = 1e-48
Identities = 72/191 (37%), Positives = 102/191 (53%), Gaps = 31/191 (16%)
Query: 25 TGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKI 84
T +Q QAIPA +SG+D++V + TGSGKT AF+LP L K
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGG--------------- 45
Query: 85 YTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQL 144
P+ LVL PTRELA Q+ ++ + ++ + GG Q +
Sbjct: 46 -------------PQALVLAPTRELAEQIYEELKKLFKILG-LRVALLTGGTSLKEQARK 91
Query: 145 LSRN-PEILLATPGRLIDHMNSGKINFSH-LQILVLDEADRMLDMGFINDIEKIVDATPV 202
L + +IL+ TPGRL+D + GK+ L++LVLDEA R+LDMGF +D+E+I+ P
Sbjct: 92 LKKGKADILVGTPGRLLDLLRRGKLKLLKNLKLLVLDEAHRLLDMGFGDDLEEILSRLPP 151
Query: 203 TRQTMLFSATL 213
RQ +L SATL
Sbjct: 152 DRQILLLSATL 162
Score = 33.0 bits (76), Expect = 0.16
Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 7/72 (9%)
Query: 259 LLDYLLRDKRVGQAVVFTATK---RD-ADIIADRLNISGFLAAPLHGDLHQNARNRTLEN 314
+L LL K QA+V T+ + + I G A L G +
Sbjct: 35 ILQALLPKKGGPQALVLAPTRELAEQIYEELKKLFKILGLRVALLTGGT---SLKEQARK 91
Query: 315 LRRGRIKILVAT 326
L++G+ ILV T
Sbjct: 92 LKKGKADILVGT 103
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 141 bits (356), Expect = 1e-39
Identities = 74/228 (32%), Positives = 115/228 (50%), Gaps = 34/228 (14%)
Query: 20 GYTKPTGVQEQAIPAAISG-RDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLN 78
G+ Q++AI A +SG RD+I+++ TGSGKT A +LPAL K
Sbjct: 5 GFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKG---------- 54
Query: 79 QNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPY 138
R+LVL PTRELA Q ++ G + +K + + GG
Sbjct: 55 -------------------GRVLVLVPTRELAEQWAEELKKLGPSLG-LKVVGLYGGDSK 94
Query: 139 LRQM-QLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEADRMLDMGFINDIEKIV 197
Q+ +L S +IL+ TPGRL+D + + K++ S++ +++LDEA R+LD GF + +EK++
Sbjct: 95 REQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLL 154
Query: 198 DATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIEKKQKNITQ 245
P Q +L SAT + N+ E DP+ + V + I Q
Sbjct: 155 KLLPKNVQLLLLSATPPEEIENLLELFLNDPVFIDV--GFTPLEPIEQ 200
>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 = 136 bits (346), Expect = 6e-39
Identities = 59/133 (44%), Positives = 80/133 (60%), Gaps = 4/133 (3%)
Query: 242 NITQSILFVDDILHKNRLLDYLLRD--KRVGQAVVFTATKRDADIIADRLNISGFLAAPL 299
I Q +L V+D K L LL++ K+ G+ ++F +K+ D +A+ L G A L
Sbjct: 1 PIKQYVLPVED--EKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAAL 58
Query: 300 HGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGR 359
HGD Q R L++ R G I +LVATDV ARGID+P ++ V NYDLP P Y+ RIGR
Sbjct: 59 HGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGR 118
Query: 360 TGRAGRNGFAVSL 372
GRAG+ G A+ L
Sbjct: 119 AGRAGQKGTAILL 131
>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 = 119 bits (301), Expect = 2e-32
Identities = 60/175 (34%), Positives = 86/175 (49%), Gaps = 31/175 (17%)
Query: 39 RDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQP 98
RD+++++ TGSGKT A +LP L S K
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKGG----------------------------- 31
Query: 99 RMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQLLSRNPEILLATPGR 158
++LVL PTRELA QV + IK ++GG +Q +LLS +I++ TPGR
Sbjct: 32 QVLVLAPTRELANQVAERLKELFGE--GIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGR 89
Query: 159 LIDHMNSGKINFSHLQILVLDEADRMLDMGFINDIEKIVDATPVTRQTMLFSATL 213
L+D + K++ L +L+LDEA R+L+ GF KI+ P RQ +L SAT
Sbjct: 90 LLDELERLKLSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP 144
>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 = 108 bits (272), Expect = 5e-29
Identities = 42/78 (53%), Positives = 48/78 (61%)
Query: 287 DRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDL 346
L G A LHG L Q R LE+ R G+ K+LVATDVA RGID+P + V NYDL
Sbjct: 1 KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60
Query: 347 PKFPEDYVHRIGRTGRAG 364
P P Y+ RIGR GRAG
Sbjct: 61 PWNPASYIQRIGRAGRAG 78
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 105 bits (264), Expect = 8e-28
Identities = 40/82 (48%), Positives = 50/82 (60%)
Query: 283 DIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVF 342
+ +A+ L G A LHG L Q R L+ G+IK+LVATDVA RG+D+P + V
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60
Query: 343 NYDLPKFPEDYVHRIGRTGRAG 364
YDLP P Y+ RIGR GRAG
Sbjct: 61 IYDLPWSPASYIQRIGRAGRAG 82
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 97.8 bits (244), Expect = 1e-21
Identities = 87/388 (22%), Positives = 138/388 (35%), Gaps = 99/388 (25%)
Query: 10 ELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNK 69
+ VLK GY Q++ I A +SG+D +V TG GK+ + +PAL
Sbjct: 6 QQVLKQ--VFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPAL--------- 54
Query: 70 IPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELAL---QVTAATERYGLYMKK 126
L LV++P ++L QV E G
Sbjct: 55 ---------------------LLEGLT----LVVSPL--ISLMKDQV-DQLEAAG----- 81
Query: 127 IKAISILGGM----PYLRQMQLLSRNPEILLATPGRLIDHMNSGKINF-SHLQI--LVLD 179
I+A + + QL S ++L +P RL M+ + L I + +D
Sbjct: 82 IRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERL---MSPRFLELLKRLPISLVAID 138
Query: 180 EADRMLDMG--FINDIEKIVD----------------ATPVTRQ---TMLFSATLDGIVG 218
EA + G F D ++ ATP R L + G
Sbjct: 139 EAHCISQWGHDFRPDYRRLGRLRAGLPNPPVLALTATATPRVRDDIREQLGLQDANIFRG 198
Query: 219 NMA-ENITKDPLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTA 277
+ N+ + +K + Q + F+ +L + +++
Sbjct: 199 SFDRPNLA--------LKVVEKGEPSDQ-LAFLATVLPQ-----------LSKSGIIYCL 238
Query: 278 TKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPA 337
T++ + +A+ L +G A H L R R + IK++VAT+ GID P
Sbjct: 239 TRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPD 298
Query: 338 ITHVFNYDLPKFPEDYVHRIGRTGRAGR 365
+ V +YDLP E Y GR GR G
Sbjct: 299 VRFVIHYDLPGSIESYYQETGRAGRDGL 326
>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 = 89.0 bits (221), Expect = 8e-19
Identities = 80/404 (19%), Positives = 136/404 (33%), Gaps = 81/404 (20%)
Query: 10 ELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNK 69
E + ALVK G + Q A+ GR+++V++ TGSGKT +F+LP L
Sbjct: 57 ESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLL----- 111
Query: 70 IPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELAL-QVTA-ATERYGLYMKKI 127
+ R L+L PT LA Q L K+
Sbjct: 112 ------------------------RDPSARALLLYPTNALANDQAERLRELISDLP-GKV 146
Query: 128 KAISILGGMPYLRQMQLLSRNPEILLATPGRL-IDHMNSG---KINFSHLQILVLDEA-- 181
G P + ++ P+ILL P L + + +L+ LV+DE
Sbjct: 147 TFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHT 206
Query: 182 -------------DRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVG--------NM 220
R+L + Q + SATL +
Sbjct: 207 YRGVQGSEVALLLRRLLRR---------LRRYGSPLQIICTSATLANPGEFAEELFGRDF 257
Query: 221 AENITKDPLI--LKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTAT 278
+ +D L+ + + + L L+R+ Q +VF +
Sbjct: 258 EVPVDEDGSPRGLRYFVRREPPIRELAESIRRSALAELATLAALLVRNGI--QTLVFFRS 315
Query: 279 KRDADII-------ADRLNISGFLAAPLH-GDLHQNARNRTLENLRRGRIKILVATDVAA 330
++ +++ R A + LH+ R R + G + ++AT+
Sbjct: 316 RKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIATNALE 375
Query: 331 RGIDVPAITHVFNYDLPKFPE-DYVHRIGRTGRAGRNGFAVSLV 373
GID+ ++ V Y P + R GR GR G+ + ++
Sbjct: 376 LGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVL 419
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 87.3 bits (217), Expect = 3e-18
Identities = 89/375 (23%), Positives = 150/375 (40%), Gaps = 55/375 (14%)
Query: 8 LHELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSK 67
L V + K +T T Q AIP SG ++++ + TGSGKT A LP +++ S
Sbjct: 8 LDPRVREWF-KRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLG 66
Query: 68 NKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKI 127
+ IY L ++P + L + E + I
Sbjct: 67 KGKLE---------DGIYA--------------LYISPLKALNNDIRRRLEEPLREL-GI 102
Query: 128 KAISILGGMP-YLRQMQLLSRNPEILLATPGRLIDHMNSGKI--NFSHLQILVLDEADRM 184
+ G P +Q ++L P IL+ TP L +NS K ++ +++DE +
Sbjct: 103 EVAVRHGDTPQSEKQ-KMLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEIHAL 161
Query: 185 LDMGFIND--------IEKIVD-ATPVTRQTMLFSATLD--GIVGNMAENITKDPLILKV 233
+ + +E++ + A Q + SAT+ V I+ V
Sbjct: 162 AE----SKRGVQLALSLERLRELAGDF--QRIGLSATVGPPEEVAKFLVGFGDPCEIVDV 215
Query: 234 NSIEKKQKNITQSILFVDDILHKNRLLDYLLRD-----KRVGQAVVFTATKRDADIIADR 288
++ +K + + I V+D+++ L L K+ ++FT T+ A+ +A R
Sbjct: 216 SAAKKLEIKV---ISPVEDLIYDEELWAALYERIAELVKKHRTTLIFTNTRSGAERLAFR 272
Query: 289 LN-ISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLP 347
L + + HG L + R E L+ G +K +VAT GID+ I V P
Sbjct: 273 LKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIGDIDLVIQLGSP 332
Query: 348 KFPEDYVHRIGRTGR 362
K ++ RIGR G
Sbjct: 333 KSVNRFLQRIGRAGH 347
>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 = 66.2 bits (162), Expect = 1e-11
Identities = 43/147 (29%), Positives = 72/147 (48%), Gaps = 6/147 (4%)
Query: 259 LLDYLLRDKRVGQA-VVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRR 317
LLDYL + + GQ+ +++ ++++ + +A+RL G A H L R E+
Sbjct: 215 LLDYLKKHR--GQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLY 272
Query: 318 GRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGRAGRNGFAVSLVNHAE 377
+K++VAT+ GID P + V +YD+P E Y GR GR G A+ L + A+
Sbjct: 273 DDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPAD 332
Query: 378 RMNIKKIERFTKQQIPIEVINGFEPKK 404
+ + K R +Q + E +K
Sbjct: 333 -IALLK--RRIEQSEADDDYKQIEREK 356
Score = 32.4 bits (74), Expect = 0.56
Identities = 16/41 (39%), Positives = 23/41 (56%)
Query: 20 GYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
GY QE+ I + GRD++V TG GK+ + +PAL
Sbjct: 10 GYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPAL 50
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 64.0 bits (156), Expect = 8e-11
Identities = 89/393 (22%), Positives = 144/393 (36%), Gaps = 76/393 (19%)
Query: 1 MNFKSIGLHELVLKALVKVGYTKPTGVQEQAIPAA-ISGRDLIVSSQTGSGKTAAFMLPA 59
+ + + E + L + G + VQ A+ A + G +L+V S T SGKT L
Sbjct: 194 VPVDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAG 253
Query: 60 LHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTRELALQ-VTAATE 118
+ + S K ML L P LA Q E
Sbjct: 254 IPRLLSGGKK------------------------------MLFLVPLVALANQKYEDFKE 283
Query: 119 RYG-LYMKKIKAISILGGMPYLRQMQLL-----SRNPEILLAT-PGRLIDHM-------- 163
RY L +K ++I GM ++ + S + +I++ T G ID++
Sbjct: 284 RYSKLGLK----VAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEG--IDYLLRTGKDLG 337
Query: 164 NSGKINFSHLQILVLDEADRMLDMGFINDIEKIVDATPVTRQTMLFSATLDGIVGNMAEN 223
+ G + + L +E LD G I + + Q + SAT VGN E
Sbjct: 338 DIGTVVIDEIHTLEDEERGPRLD-GLIGRLRYLFPGA----QFIYLSAT----VGNPEEL 388
Query: 224 ITKDPLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYLLRD--------KRVGQAVVF 275
K L K+ +++ + + ++F + K ++ L++ GQ +VF
Sbjct: 389 AKK--LGAKLVLYDERPVPLERHLVFARNESEKWDIIARLVKREFSTESSKGYRGQTIVF 446
Query: 276 TATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDV 335
T ++R +AD L G AAP H L R + +V T A G+D
Sbjct: 447 TYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDF 506
Query: 336 PAITHVFNYDLPKF----PEDYVHRIGRTGRAG 364
PA +F ++ +GR GR
Sbjct: 507 PASQVIFESLAMGIEWLSVREFQQMLGRAGRPD 539
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 63.2 bits (154), Expect = 8e-11
Identities = 78/430 (18%), Positives = 127/430 (29%), Gaps = 122/430 (28%)
Query: 3 FKSIGLHELV---------LKALVKVGYTKPTGVQEQAIPAAIS----GRDLIVSSQTGS 49
S G EL LK +V + + QE+A+ A + R ++ TG+
Sbjct: 8 LSSKGAEELADYVLDEGLPLKLIVAFEF-ELRPYQEEALDALVKNRRTERRGVIVLPTGA 66
Query: 50 GKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPTREL 109
GKT + + + LVL PT+EL
Sbjct: 67 GKTVVAAE--------------AIAE--------------------LKRSTLVLVPTKEL 92
Query: 110 ALQVTAATERYGLYMKKIKAISILGGM--------------------------------- 136
Q A +++ L I I GG
Sbjct: 93 LDQWAEALKKFLL---LNDEIGIYGGGEKELEPAKVTVATVQTLARRQLLDEFLGNEFGL 149
Query: 137 -----------PYLRQMQLLSRNPEILL---ATPGRLIDHMNSGKINFSHLQILVLDE-A 181
P R++ L L ATP R D G + F + +V +
Sbjct: 150 IIFDEVHHLPAPSYRRILELLSAAYPRLGLTATPER-EDGGRIGDL-FDLIGPIVYEVSL 207
Query: 182 DRMLDMGFINDIE----KIVDATPVTRQTMLFSATLDGIVGNMAENITKDPLILKVNSIE 237
++D G++ + K+ R+ SA ++ ++ + E
Sbjct: 208 KELIDEGYLAPYKYVEIKVTLTEDEEREYAKESARFRELLRARGTLRAENEARRIAIASE 267
Query: 238 KKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAA 297
+K I LL R + ++F + A IA G
Sbjct: 268 RK-------------IAAVRGLLLKHARGDKT---LIFASDVEHAYEIAKLFLAPGI-VE 310
Query: 298 PLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRI 357
+ G+ + R LE R G IK+LV V G+D+P + ++ R+
Sbjct: 311 AITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRL 370
Query: 358 GRTGRAGRNG 367
GR R
Sbjct: 371 GRGLRPAEGK 380
>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 = 59.0 bits (143), Expect = 2e-09
Identities = 29/106 (27%), Positives = 52/106 (49%)
Query: 259 LLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRG 318
LL ++ ++ + +++ +++ ++ + L G A H L +AR+ +R
Sbjct: 216 LLRFIRKEFKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRD 275
Query: 319 RIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGRAG 364
I+++VAT GI+ P + V +Y LPK E Y GR GR G
Sbjct: 276 EIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDG 321
Score = 37.1 bits (86), Expect = 0.020
Identities = 17/41 (41%), Positives = 22/41 (53%)
Query: 20 GYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
G + VQ + I A + GRD V TG GK+ + LPAL
Sbjct: 8 GLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPAL 48
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 59.0 bits (143), Expect = 2e-09
Identities = 92/361 (25%), Positives = 148/361 (40%), Gaps = 80/361 (22%)
Query: 28 QEQAIPAAISGRDLIVSSQTGSGKT-----AAFMLPALHKFASSKNKIPVMKKNLNQNNN 82
Q++ I A +SGRD +V TG GK+ A +L L S I +MK ++Q
Sbjct: 30 QQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVLDGLTLVVSPL--ISLMKDQVDQ--- 84
Query: 83 KIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQM 142
L L T TRE L+V A R G Q+
Sbjct: 85 --------LLANGVAAACLNSTQTREQQLEVMAGC-RTG-------------------QI 116
Query: 143 QLLSRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEA--------DRMLDMGFINDIE 194
+LL PE L+ ++H+ + +L +DEA D + + +
Sbjct: 117 KLLYIAPERLMMD--NFLEHLAH-----WNPALLAVDEAHCISQWGHDFRPEYAALGQLR 169
Query: 195 KIVDATPVTRQTMLFSATLDGIVGNMAENITK-----DPLILKVNSIEKKQKNITQSILF 249
+ P M +AT D +I + DPLI +++S ++ NI +++
Sbjct: 170 QRFPTLPF----MALTATADDTTRQ---DIVRLLGLNDPLI-QISSFDRP--NIRYTLV- 218
Query: 250 VDDILHKNRLLDYLLR---DKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQN 306
K + LD L+R ++R +++ ++ + A RL G AA H L +
Sbjct: 219 -----EKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDND 273
Query: 307 ARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGRAGRN 366
R E +R ++I+VAT GI+ P + V ++D+P+ E Y TGRAGR+
Sbjct: 274 VRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQ---ETGRAGRD 330
Query: 367 G 367
G
Sbjct: 331 G 331
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 53.9 bits (130), Expect = 1e-07
Identities = 36/116 (31%), Positives = 51/116 (43%), Gaps = 10/116 (8%)
Query: 272 AVVFTATKRDADIIADRLNISGFLA-------APLHGD--LHQNARNRTLENLRRGRIKI 322
+VFT + A+ I + L G A A GD + Q + ++ R+G +
Sbjct: 369 VIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNV 428
Query: 323 LVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGRAGRNGFAVSLVNHAER 378
LVAT V G+D+P + V Y+ + R GRTGR R G V LV R
Sbjct: 429 LVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGR-KRKGRVVVLVTEGTR 483
>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 = 52.3 bits (126), Expect = 4e-07
Identities = 46/168 (27%), Positives = 74/168 (44%), Gaps = 15/168 (8%)
Query: 250 VDDILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARN 309
VDD+L + R R R + +V T TK+ A+ + D L G LH ++ R
Sbjct: 428 VDDLLSEIRQ-----RVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERV 482
Query: 310 RTLENLRRGRIKILVATDVAARGIDVPAITHV--FNYDLPKFPEDYVHRIGRTGRAGRN- 366
+ +LR G +LV ++ G+D+P ++ V + D F I GRA RN
Sbjct: 483 EIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNV 542
Query: 367 -GFAVSLVNH---AERMNIKKIERFTKQQIPIEVINGFEPK---KRIR 407
G + + + + I++ ER K Q+ +G P+ K IR
Sbjct: 543 NGKVIMYADKITDSMQKAIEETERRRKIQMAYNEEHGITPQTIRKPIR 590
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 49.9 bits (120), Expect = 2e-06
Identities = 39/123 (31%), Positives = 53/123 (43%), Gaps = 26/123 (21%)
Query: 266 DKRVGQAVVFTATKRD-ADIIADRLNISGFLAAPLHGD--------LHQNARNRTLENLR 316
D R+ +VFT RD A+ I D L G A G + Q + L+ R
Sbjct: 365 DSRI---IVFT-QYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFR 420
Query: 317 RGRIKILVATDVAARGIDVPAITHVFNYDLPKFPED------YVHRIGRTGRAGRNGFAV 370
G +LV+T VA G+D+P++ DL F E + R GRTGR G V
Sbjct: 421 AGEFNVLVSTSVAEEGLDIPSV------DLVIFYEPVPSEIRSIQRKGRTGR-QEEGRVV 473
Query: 371 SLV 373
L+
Sbjct: 474 VLI 476
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 48.5 bits (116), Expect = 5e-06
Identities = 78/411 (18%), Positives = 135/411 (32%), Gaps = 127/411 (30%)
Query: 28 QEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYTH 87
QE +S ++++S+ TGSGKT +L L K+ +Y
Sbjct: 37 QEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGGGKV-------------VY-- 81
Query: 88 KERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQMQLLSR 147
+ P + LA + R ++ IS G + L+R
Sbjct: 82 ---------------IVPLKALAEEKYEEFSRLEELGIRV-GIST-GDYDLDDER--LAR 122
Query: 148 NPEILLATPGRLIDHMNSGKINFSHLQI----LVLDEADRMLDMGFIND------IEKIV 197
++++ TP +L +S +V+DE + D +E IV
Sbjct: 123 Y-DVIVTTPEKL----DSLTRKRPSWIEEVDLVVIDEIH------LLGDRTRGPVLESIV 171
Query: 198 DATPVTRQTMLF---SATLDGIVGNM--------AENITKD----PL---ILKVNSIEKK 239
+ + SAT + N A+ + D PL + V +
Sbjct: 172 ARMRRLNELIRIVGLSAT----LPNAEEVADWLNAKLVESDWRPVPLRRGVPYVGAFLGA 227
Query: 240 QKNITQSILFVDDILHKNRLLDYLLRDKRVGQAVVFTATKRDA------------DIIAD 287
L +D++ +L+ L GQ +VF ++++A ++D
Sbjct: 228 DGKKKTWPLLIDNLA-LELVLESL---AEGGQVLVFVHSRKEAEKTAKKLRIKMSATLSD 283
Query: 288 RLNI-SGFLAAPLHGDLHQNARNRTLENL------------------------RRGRIKI 322
I A+P+ + + L L R+G+IK+
Sbjct: 284 DEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPREDRQLVEDAFRKGKIKV 343
Query: 323 LVATDVAARGIDVPA----ITHVFNYDLPKFPE-----DYVHRIGRTGRAG 364
LV+T A G+++PA I YD D + GR GR G
Sbjct: 344 LVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPG 394
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 44.9 bits (107), Expect = 7e-05
Identities = 48/176 (27%), Positives = 74/176 (42%), Gaps = 28/176 (15%)
Query: 203 TRQTMLFSAT-----LDGIVGNMAENITK-----DPLILKVNSIEKKQKNITQSILFVDD 252
QT+ SAT L+ GN+ E I + DP I + + Q VDD
Sbjct: 386 IPQTIYVSATPGDYELEQSGGNVVEQIIRPTGLLDPEI----EVRPTK---GQ----VDD 434
Query: 253 ILHKNRLLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTL 312
+L + R R + + +V T TK+ A+ + + L G LH D+ R +
Sbjct: 435 LLSEIRK-----RVAKNERVLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEII 489
Query: 313 ENLRRGRIKILVATDVAARGIDVPAITHV--FNYDLPKFPEDYVHRIGRTGRAGRN 366
+LR G +LV ++ G+D+P ++ V + D F I GRA RN
Sbjct: 490 RDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN 545
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 44.9 bits (106), Expect = 9e-05
Identities = 30/110 (27%), Positives = 53/110 (48%)
Query: 273 VVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARG 332
+++ ++ D + +A+RL G AA HG + R + + I I+ AT G
Sbjct: 684 IIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMG 743
Query: 333 IDVPAITHVFNYDLPKFPEDYVHRIGRTGRAGRNGFAVSLVNHAERMNIK 382
I+ P + V ++ LPK E Y GR GR G+ V ++++ + +K
Sbjct: 744 INKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSDYIRVK 793
Score = 32.9 bits (75), Expect = 0.41
Identities = 15/33 (45%), Positives = 20/33 (60%)
Query: 28 QEQAIPAAISGRDLIVSSQTGSGKTAAFMLPAL 60
Q + I A +SG D+ V TG GK+ + LPAL
Sbjct: 465 QREIINATMSGYDVFVLMPTGGGKSLTYQLPAL 497
>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 = 42.8 bits (101), Expect = 3e-04
Identities = 21/58 (36%), Positives = 31/58 (53%)
Query: 9 HELVLKALVKVGYTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASS 66
H V+ AL G +P Q +A A +GR ++V++ T SGK+ A+ LP L A
Sbjct: 22 HPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADD 79
Score = 35.9 bits (83), Expect = 0.052
Identities = 31/136 (22%), Positives = 56/136 (41%), Gaps = 22/136 (16%)
Query: 271 QAVVFTATKRDADIIA----DRL-----NISGFLAAPLHGDLHQNARNRTLEN-LRRGRI 320
+ + F ++R A+++A L +++ +AA G L ++ R LE LR G +
Sbjct: 273 RTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPED--RRELERALRDGEL 330
Query: 321 KILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGRAGRNGFAV---------- 370
+ T+ G+D+ + V P + GR GR G+ V
Sbjct: 331 LGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARDDPLDT 390
Query: 371 SLVNHAERMNIKKIER 386
LV+H E + + +E
Sbjct: 391 YLVHHPEALFDRPVEA 406
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 40.8 bits (96), Expect = 0.001
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 299 LHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRI- 357
LHG + + + +E R G + ILVAT V G+DVP T + D +F +H++
Sbjct: 488 LHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLR 547
Query: 358 GRTGRAGRNGFAV 370
GR GR + +
Sbjct: 548 GRVGRGDHQSYCL 560
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 40.6 bits (96), Expect = 0.001
Identities = 87/385 (22%), Positives = 156/385 (40%), Gaps = 76/385 (19%)
Query: 21 YTKPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQN 80
+ T Q AIP G+++++SS TGSGKT L F + +++ + + +
Sbjct: 30 FGTFTPPQRYAIPLIHEGKNVLISSPTGSGKT-------LAAFLAIIDELFRLGRE-GEL 81
Query: 81 NNKIYTHKERLRFKPAQPRMLVLTPTRELA----------LQ-VTAATERYGLYMKKIKA 129
+K+Y L ++P R L L + + G + +I+
Sbjct: 82 EDKVYC--------------LYVSPLRALNNDIHRNLEEPLTEIREIAKERGEELPEIR- 126
Query: 130 ISILGG--MPYLRQMQLLSRNPEILLATPGRLIDHMNSGKIN--FSHLQILVLDEADRML 185
++I G Y +Q ++L + P IL+ TP L +NS K ++ +++DE +
Sbjct: 127 VAIRTGDTSSYEKQ-KMLKKPPHILITTPESLAILLNSPKFREKLRTVKWVIVDEIHSLA 185
Query: 186 D-------MGFINDIEKIVDATPVTRQTMLFSAT---LDGI----VGNMAENITKDPLIL 231
+ + +E++ R + SAT L+ + VG + +D I+
Sbjct: 186 ENKRGVHLSLSLERLEELAG-GEFVR--IGLSATIEPLEEVAKFLVGYEDDGEPRDCEIV 242
Query: 232 KVNSIEKKQKNITQSILFVDDILHKN---------RLLDYLLRDKRVGQAVVFTATKRDA 282
+ K +I + I VDD++H L L+++ R ++FT T+ A
Sbjct: 243 DARFV--KPFDI-KVISPVDDLIHTPAEEISEALYETLHELIKEHR--TTLIFTNTRSGA 297
Query: 283 DIIADRL------NISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVP 336
+ + L H L + R E L+RG +K++V++ GID+
Sbjct: 298 ERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIG 357
Query: 337 AITHVFNYDLPKFPEDYVHRIGRTG 361
I V PK + RIGR G
Sbjct: 358 YIDLVVLLGSPKSVSRLLQRIGRAG 382
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 39.7 bits (92), Expect = 0.003
Identities = 23/110 (20%), Positives = 39/110 (35%), Gaps = 8/110 (7%)
Query: 259 LLDYLLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRG 318
LLD LL + + ++F+ D++ D L G L G R ++
Sbjct: 701 LLDKLLEEGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNAD 760
Query: 319 RIKILVATDVAARGIDVPAIT--HVFNYDLPKFP------EDYVHRIGRT 360
+ + + A G+ + V +D P D HRIG+
Sbjct: 761 EEEKVFLLSLKAGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQK 810
>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 = 39.6 bits (93), Expect = 0.003
Identities = 24/104 (23%), Positives = 44/104 (42%), Gaps = 8/104 (7%)
Query: 299 LHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRI- 357
HG + +N + +G ++LV T + GID+P + KF ++++
Sbjct: 692 AHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLR 751
Query: 358 GRTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEVINGFE 401
GR GR+ + +A L H + + +R +E I F
Sbjct: 752 GRVGRSKKKAYAYLLYPHQKALTEDAQKR-------LEAIQEFS 788
>gnl|CDD|233660 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB. This model
represents HrpB, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria,
but also in a few species of other lineages. The member
from Rhizobium meliloti has been designated HelO. HrpB
is typically about 800 residues in length, while its
paralog HrpA (TIGR01967), also uncharacterized, is about
1300 amino acids long. Related characterized eukarotic
proteins are RNA helicases associated with pre-mRNA
processing [Unknown function, Enzymes of unknown
specificity].
Length = 819
Score = 39.4 bits (92), Expect = 0.004
Identities = 32/115 (27%), Positives = 57/115 (49%), Gaps = 18/115 (15%)
Query: 280 RDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAIT 339
R + +A+RL+ S L PL+G+L A++R ++ +GR K+++AT++A + + I
Sbjct: 224 RVQEQLAERLD-SDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIR 282
Query: 340 HVFNYDL---PKF-PEDYVHRIG-----------RTGRAGR--NGFAVSLVNHAE 377
V + L +F P+ + R+ R GRAGR G L + +
Sbjct: 283 VVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRLEPGVCYRLWSEEQ 337
>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 = 39.1 bits (92), Expect = 0.005
Identities = 40/163 (24%), Positives = 65/163 (39%), Gaps = 32/163 (19%)
Query: 23 KPTGVQEQAIPAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNN 82
P Q + AA+ GR ++ + TGSGKT A LP+L A +
Sbjct: 13 TPRPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPE--------------- 57
Query: 83 KIYTHKERLRFKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGG--MPYLR 140
K+ L L +TP R LA+ + + + + G R
Sbjct: 58 ---KPKKGL-------HTLYITPLRALAVDIARNLQAPIEELGLPIRVETRTGDTSSSER 107
Query: 141 QMQLLSRNPEILLATPGRL---IDHMNSGKINFSHLQILVLDE 180
Q + P+ILL TP L + + ++ ++ F L+ +V+DE
Sbjct: 108 ARQ-RKKPPDILLTTPESLALLLSYPDAARL-FKDLRCVVVDE 148
Score = 36.4 bits (85), Expect = 0.032
Identities = 16/62 (25%), Positives = 25/62 (40%)
Query: 300 HGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGR 359
HG L + R + GR++ +V T G+D + V PK + R GR
Sbjct: 282 HGSLDREQRRWVEAAMAAGRLRAVVCTSSLDLGVDFGPVDLVIQIGSPKGVARLLQRAGR 341
Query: 360 TG 361
+
Sbjct: 342 SN 343
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 36.9 bits (86), Expect = 0.023
Identities = 27/103 (26%), Positives = 42/103 (40%), Gaps = 17/103 (16%)
Query: 279 KRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAI 338
+R A+ + PL+G L + R E G+ K+++AT++A + +P I
Sbjct: 273 ERTAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGI 332
Query: 339 THVFNYDLPKFPEDYVHRIG----------------RTGRAGR 365
+V + L K Y R G R GRAGR
Sbjct: 333 RYVIDSGLAKEK-RYDPRTGLTRLETEPISKASADQRAGRAGR 374
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 36.4 bits (85), Expect = 0.032
Identities = 16/41 (39%), Positives = 23/41 (56%)
Query: 299 LHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAIT 339
+HG + ++ +E + G I ILVAT V G+DVP T
Sbjct: 513 VHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPNAT 553
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 36.1 bits (84), Expect = 0.045
Identities = 73/385 (18%), Positives = 128/385 (33%), Gaps = 99/385 (25%)
Query: 99 RMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQ-------MQLLSRNPEI 151
+ ++ PTR L QV E++G K + IL L++ +L + +I
Sbjct: 125 KSYIIFPTRLLVEQVVEKLEKFG--EKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDI 182
Query: 152 LLATPGRLI---DHMNSGKINFSHLQILVLD---------EADRMLDM-GFINDI----- 193
L+ T L D + K +F + V D D++L + GF +
Sbjct: 183 LVTTSQFLSKNFDELPKKKFDF----VFVDDVDAVLKSSKNIDKLLYLLGFSEEDIEKAM 238
Query: 194 --------------------EKIVDATPVTRQTMLFSATLD--GIVGNMAENITKDPLIL 231
EKI + ++ SAT G +
Sbjct: 239 ELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGN----------RVKLF 288
Query: 232 K------VNSIEKKQKNITQSILFVDDILHKNRLLDYLLRDKRVGQ-AVVFTAT---KRD 281
+ V S +NI S + +D +L++ + KR+G ++F + K
Sbjct: 289 RELLGFEVGSPVFYLRNIVDSYIVDEDS--VEKLVELV---KRLGDGGLIFVPSDKGKEY 343
Query: 282 ADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRRGRIKILV--AT--DVAARGIDVPA 337
A+ +A+ L G A R E G + +LV A+ V RGID+P
Sbjct: 344 AEELAEYLEDLGINAELAISGF-----ERKFEKFEEGEVDVLVGVASYYGVLVRGIDLPE 398
Query: 338 ITH--VFNYDLPKF-----PEDYV-HRIGR--TGRAGRNGFAVSLVNHAE-RMNIKKIER 386
+F Y +PKF E + R + + R ++ +
Sbjct: 399 RIRYAIF-YGVPKFKFSLEEELAPPFLLLRLLSLLPLIKNDKEIRELVSYLRRRLRNLSP 457
Query: 387 FTKQQIPIEVINGFEPKKRIRTYYS 411
+ Q + + G + + S
Sbjct: 458 YELQMLAFAIREGELLEGVLEELRS 482
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 35.6 bits (82), Expect = 0.053
Identities = 27/101 (26%), Positives = 43/101 (42%), Gaps = 8/101 (7%)
Query: 275 FTATKRDADIIADRLN-ISGFLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGI 333
F + + ++ D LN + A H L R E R IK++VAT A G+
Sbjct: 266 FKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGV 325
Query: 334 DVPAITHVFNYDLPKFPEDYVHRIGRT------GRAGRNGF 368
++PA V D+ ++ + + GRAGR G+
Sbjct: 326 NLPA-RLVIVRDITRYGNGGIRYLSNMEIKQMIGRAGRPGY 365
>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 = 34.7 bits (80), Expect = 0.074
Identities = 74/352 (21%), Positives = 120/352 (34%), Gaps = 57/352 (16%)
Query: 40 DLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPR 99
L++ + TG GKT A +L ALH S K ++ N +Y R K
Sbjct: 1 LLVIEAPTGYGKTEAALLWALHSIKSQKADRVIIALPTRATINAMYR-----RAKELFGS 55
Query: 100 MLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPYLRQM-QLLSRNPEILLATPGR 158
L L K I +G + L + + L P
Sbjct: 56 NLGLL-----------------HSSSSFKRIKEMGDSEEFEHLFPLYIHSNDKLFLDPIT 98
Query: 159 L--IDH-MNSGKINFSHLQI---------LVLDEADRMLD--MGFINDIEKIVDATPVTR 204
+ ID + S F H + L+ DE + + I +++
Sbjct: 99 VCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYTLALI---LAVLEVLKDND 155
Query: 205 QT-MLFSATLDGIVGNMAENITKDPLILKVNSIEKKQKNITQSILFVDDILHKNRLLDYL 263
+L SATL + AE I ++ E+++ + I D + + L+ L
Sbjct: 156 VPILLMSATLPKFLKEYAEKIGYVEFNEPLDLKEERRFERHRFIKIESDKVGEISSLERL 215
Query: 264 LRD-KRVGQAVVFTATKRDADIIADRL--NISGFLAAPLHGDLHQNAR----NRTLENLR 316
L K+ G+ + T A +L N LH + R LE ++
Sbjct: 216 LEFIKKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMK 275
Query: 317 RGRIKILVATDVAARGIDVPA---ITHVFNYDLPKFPEDYVHRIGRTGRAGR 365
+ ++VAT V +D+ A IT + D + R+GR R GR
Sbjct: 276 KNEKFVIVATQVIEASLDISADVMITELAPIDS------LIQRLGRLHRYGR 321
>gnl|CDD|233040 TIGR00595, priA, primosomal protein N'. All proteins in this
family for which functions are known are components of
the primosome which is involved in replication, repair,
and recombination.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 = 505
Score = 35.1 bits (81), Expect = 0.087
Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 12/75 (16%)
Query: 305 QNARNRTLENLRRGRIKILVATDVAARGIDVPAIT--HVFNYDLPKFPEDY--------- 353
+ A L G+ IL+ T + A+G P +T V + D D+
Sbjct: 298 KGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQL 357
Query: 354 VHRI-GRTGRAGRNG 367
+ ++ GR GRA G
Sbjct: 358 LTQVAGRAGRAEDPG 372
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 34.9 bits (80), Expect = 0.096
Identities = 22/68 (32%), Positives = 33/68 (48%)
Query: 294 FLAAPLHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDY 353
F+A HG + + R T + L+ G ++ +VAT GID+ A+ V P
Sbjct: 302 FIARSHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASG 361
Query: 354 VHRIGRTG 361
+ RIGR G
Sbjct: 362 LQRIGRAG 369
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 34.3 bits (79), Expect = 0.15
Identities = 24/86 (27%), Positives = 37/86 (43%), Gaps = 17/86 (19%)
Query: 317 RGRIKILVATDVAARGIDVPAITHVFNYDLPKF---------PEDYVHRIGRTGRAGRNG 367
G +K++ AT+ A GI++PA T VF L KF P +Y ++ +GRAGR G
Sbjct: 468 EGLVKVVFATETFAIGINMPARTVVF-TSLSKFDGNGHRWLSPGEY-TQM--SGRAGRRG 523
Query: 368 F----AVSLVNHAERMNIKKIERFTK 389
V ++ +
Sbjct: 524 LDVLGTVIVIEPPFESEPSEAAGLAS 549
>gnl|CDD|226583 COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA
uptake (late competence protein) [DNA replication,
recombination, and repair].
Length = 441
Score = 34.0 bits (78), Expect = 0.15
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 308 RNRTLENLRRGRIKILVATDVAARGIDVPAI-THVFNYDLPKFPEDYVHRIGRTGRAGR 365
R +E R G+I +L+ T + RG+ P + V + F E + +I GR GR
Sbjct: 344 RKEKVEAFRDGKITLLITTTILERGVTFPNVDVFVLGAEHRVFTESALVQIA--GRVGR 400
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 33.6 bits (77), Expect = 0.23
Identities = 42/192 (21%), Positives = 65/192 (33%), Gaps = 24/192 (12%)
Query: 204 RQTMLFSATLDGIVGNMAENITK-DPLILKVNSIEKKQKN--ITQSILFVDDILHKNR-- 258
+L SATL + ++ L K+ + Q L+V L + R
Sbjct: 404 ASVVLTSATLS--PLDSFSSLLGLLGLEEKLRFLSLPSPFNYEEQGQLYVPTDLPEPREP 461
Query: 259 -----LLDYLLR--DKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRT 311
L YL G +V + +A+RL + ++ R
Sbjct: 462 ELLAKLAAYLREILKASPGGVLVLFPSYEYLKRVAERL--KDERSTLPVLTQGEDEREEL 519
Query: 312 LENLR-RGRIKILVATDVAARGIDVP--AITHVFNYDLPKFP--EDYV--HRIGRTGRAG 364
LE + G ILV G+D P A+ V LP FP +D + R+ R G
Sbjct: 520 LEKFKASGEGLILVGGGSFWEGVDFPGDALRLVVIVGLP-FPNPDDPLLKARLEFLKRLG 578
Query: 365 RNGFAVSLVNHA 376
+ F + A
Sbjct: 579 GDPFEEFYLPPA 590
Score = 31.3 bits (71), Expect = 1.3
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 28 QEQAI----PAAISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKI 70
Q + A G L++ + TG+GKT A++LPAL K+
Sbjct: 20 QREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKKV 66
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 33.6 bits (77), Expect = 0.24
Identities = 35/139 (25%), Positives = 51/139 (36%), Gaps = 42/139 (30%)
Query: 267 KRVGQAVVFTATKRDADIIADRLN--ISGFLAAP-------LHGDLHQNARNRTL----- 312
K+ A+VF T+R A+ A L I FL P L L +N N L
Sbjct: 236 KKGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALR 295
Query: 313 -------------------ENLRRGRIKILVATDVAARGIDVPAITHVF-------NYDL 346
+ R G IK++ AT + GI++PA + N+
Sbjct: 296 GGVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGW 355
Query: 347 PKFPEDYVHRIGRTGRAGR 365
P + ++ GRAGR
Sbjct: 356 EDIPVLEIQQM--MGRAGR 372
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 32.8 bits (76), Expect = 0.36
Identities = 15/38 (39%), Positives = 21/38 (55%)
Query: 299 LHGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVP 336
LHG + ++ + + G I ILVAT V G+DVP
Sbjct: 511 LHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVP 548
>gnl|CDD|145959 pfam03085, RAP-1, Rhoptry-associated protein 1 (RAP-1). Members of
this family are found in Babesia species. Though not in
this Pfam family, rhoptry-associated proteins are also
found in Plasmodium falciparum. Indeed, animal infection
with Babesia may produce a pattern similar to human
malaria. Rhoptry organelles form part of the apical
complex in apicomplexan parasites. Rhoptry-associated
proteins are antigenic, and generate partially
protective immune responses in infected mammals. Thus
RAPs are among the targeted vaccine antigens for
babesial (and malarial) parasites. However, RAP-1
proteins are encoded by by a multigene family; thus
RAP-1 proteins are polymorphic, with B and T cell
epitopes that are conserved among strains, but not
across species. Antibodies to Babesia RAP-1 may also be
helpful in the serological detection of Babesia
infections.
Length = 251
Score = 31.2 bits (71), Expect = 0.91
Identities = 9/35 (25%), Positives = 14/35 (40%), Gaps = 2/35 (5%)
Query: 408 TYYSRYRFNNNNWKTHNINKSNITKRFY-RQIKKT 441
YY Y N + NK T+ + + IK+
Sbjct: 159 IYYKTY-LNLDKMNAKLQNKIAFTRHIFGKGIKRA 192
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 31.3 bits (71), Expect = 1.3
Identities = 56/323 (17%), Positives = 101/323 (31%), Gaps = 69/323 (21%)
Query: 47 TGSGKTAAFMLPALHKFASSKNKIPVMKKNLNQNNNKIYTHKERLRFKPAQPRMLVLTPT 106
TG GKT A ++ AL + R++ + P
Sbjct: 223 TGYGKTEASLILALALLDE---------------------------KIKLKSRVIYVLPF 255
Query: 107 REL-ALQVTAATERYGLYMKKIKAISILGGMPYLRQMQ--------LLSRNPEILLATPG 157
R + A E +GL+ K++ P L + ++LLA
Sbjct: 256 RTIIEDMYRRAKEIFGLFSVIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIV 315
Query: 158 -RLIDHMNSGKINFSHLQI-------LVLDEADRMLDMGFINDIEKIVDATPVTRQTMLF 209
I + F + ++LDE D + + +++A +L
Sbjct: 316 VTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLYADETMLAALLALLEALAEAGVPVLL 375
Query: 210 -SATLD-----------GIVGNMAENITKDPLILKVNSIEKKQKNITQSILFVDDILHKN 257
SATL G + EN P + K++ ++
Sbjct: 376 MSATLPPFLKEKLKKALGKGREVVENAKFCPKEDEPGLKRKERVDVEDGP-----QEELI 430
Query: 258 RLLDYLLRD-KRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNAR----NRTL 312
L+ +++ K+V V+ T A + ++L G LH R
Sbjct: 431 ELISEEVKEGKKV--LVIVN-TVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELK 487
Query: 313 ENLRRGRIKILVATDVAARGIDV 335
+ ++ I+VAT V G+D+
Sbjct: 488 KLFKQNEGFIVVATQVIEAGVDI 510
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 31.1 bits (71), Expect = 1.7
Identities = 22/103 (21%), Positives = 41/103 (39%), Gaps = 8/103 (7%)
Query: 300 HGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRI-G 358
HG + + + + G +LV T + GID+P + KF ++++ G
Sbjct: 836 HGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRG 895
Query: 359 RTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEVINGFE 401
R GR+ + +A L + + +R +E I F
Sbjct: 896 RVGRSNKQAYAYFLYPPQKALTEDAEKR-------LEAIASFT 931
>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor;
Provisional.
Length = 1147
Score = 30.9 bits (70), Expect = 1.9
Identities = 21/81 (25%), Positives = 35/81 (43%), Gaps = 1/81 (1%)
Query: 300 HGDLHQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRI-G 358
HG + + R + + R +LV T + GID+P + F +H++ G
Sbjct: 842 HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRG 901
Query: 359 RTGRAGRNGFAVSLVNHAERM 379
R GR+ +A L H + M
Sbjct: 902 RVGRSHHQAYAWLLTPHPKAM 922
>gnl|CDD|234013 TIGR02785, addA_Gpos, helicase-exonuclease AddAB, AddA subunit,
Firmicutes type. AddAB, also called RexAB, substitutes
for RecBCD in several bacterial lineages. These DNA
recombination proteins act before synapse and are
particularly important for DNA repair of
double-stranded breaks by homologous recombination. The
term AddAB is used broadly, with AddA homologous
between the Firmicutes (as modeled here) and the
alphaproteobacteria, while the partner AddB proteins
show no strong homology across the two groups of
species [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1230
Score = 30.4 bits (69), Expect = 2.2
Identities = 15/29 (51%), Positives = 19/29 (65%), Gaps = 2/29 (6%)
Query: 25 TGVQEQAIPAAISGRDLIVSSQTGSGKTA 53
T Q QAI G+D++VS+ GSGKTA
Sbjct: 3 TDEQWQAIYT--RGQDILVSASAGSGKTA 29
>gnl|CDD|222931 PHA02798, PHA02798, ankyrin-like protein; Provisional.
Length = 489
Score = 30.2 bits (68), Expect = 2.4
Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 11/69 (15%)
Query: 387 FTKQQIPIEVINGFEPKKRIRTYYSRYRFNNNNWKTHNINKSNITKRFYRQIKKTS--IS 444
F K+ IPI+ IN + KK Y++ + N K I KS K+ Y I K S I+
Sbjct: 404 FNKKYIPIKYINNKKLKK-----YTKLFYYGNIIKK-IIEKS---KKRYENIYKVSCYIT 454
Query: 445 ASSKNSINY 453
N ++Y
Sbjct: 455 KICSNELSY 463
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 30.4 bits (69), Expect = 2.4
Identities = 23/76 (30%), Positives = 32/76 (42%), Gaps = 12/76 (15%)
Query: 304 HQNARNRTLENLRRGRIKILVATDVAARGIDVPAITHV--FNYD----LPKF--PEDYVH 355
+ A L+ G IL+ T + A+G D P +T V + D P F E
Sbjct: 519 RKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRASERTFQ 578
Query: 356 RI----GRTGRAGRNG 367
+ GR GRAG+ G
Sbjct: 579 LLMQVAGRAGRAGKPG 594
>gnl|CDD|176070 cd08688, C2_KIAA0528-like, C2 domain found in the Human KIAA0528
cDNA clone. The members of this CD are named after the
Human KIAA0528 cDNA clone. All members here contain a
single C2 repeat. No other information on this protein
is currently known. The C2 domain was first identified
in PKC. C2 domains fold into an 8-standed
beta-sandwich that can adopt 2 structural arrangements:
Type I and Type II, distinguished by a circular
permutation involving their N- and C-terminal beta
strands. Many C2 domains are Ca2+-dependent
membrane-targeting modules that bind a wide variety of
substances including bind phospholipids, inositol
polyphosphates, and intracellular proteins. Most C2
domain proteins are either signal transduction enzymes
that contain a single C2 domain, such as protein kinase
C, or membrane trafficking proteins which contain at
least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of
piccolo/aczonin and intersectin which only have a
single C2 domain. C2 domains with a calcium binding
region have negatively charged residues, primarily
aspartates, that serve as ligands for calcium ions.
Length = 110
Score = 28.0 bits (63), Expect = 4.1
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 4/43 (9%)
Query: 36 ISGRDLIVSSQTGSGKTAAFMLPALHKFASSKNKIPVMKKNLN 78
++ RDL V ++ S T AF KF S+ K V+KK+LN
Sbjct: 6 VAARDLPVMDRS-SDLTDAF---VEVKFGSTTYKTDVVKKSLN 44
>gnl|CDD|218251 pfam04762, IKI3, IKI3 family. Members of this family are
components of the elongator multi-subunit component of a
novel RNA polymerase II holoenzyme for transcriptional
elongation. This region contains WD40 like repeats.
Length = 903
Score = 29.6 bits (67), Expect = 4.8
Identities = 26/130 (20%), Positives = 47/130 (36%), Gaps = 16/130 (12%)
Query: 93 FKPAQPRMLVLTPTRELALQVTAATERYGLYMKKIKAISILGGMPY-------LRQMQLL 145
F + + VLT ++++ + +R K+ + L + QL
Sbjct: 419 FSKSNSCVAVLTSDGDISIYELSLKKRKPGSPPKLTSKFSLDKVENSDSEVALGSLRQLA 478
Query: 146 SRNPEILLATPGRLIDHMNSGKINFSHLQILVLDEADRMLDMGFINDIEKIVDATPVTRQ 205
N LL L D N +I ++ +D+ + L + I +IE IV
Sbjct: 479 FLNDSELLV----LSDSDNITEI-----VLVDVDDTENPLSVSVITEIEGIVLILSSNDY 529
Query: 206 TMLFSATLDG 215
++ T DG
Sbjct: 530 KHVYIETRDG 539
>gnl|CDD|213255 cd03288, ABCC_SUR2, ATP-binding cassette domain 2 of the
sulfonylurea receptor SUR. The SUR domain 2. The
sulfonylurea receptor SUR is an ATP binding cassette
(ABC) protein of the ABCC/MRP family. Unlike other ABC
proteins, it has no intrinsic transport function,
neither active nor passive, but associates with the
potassium channel proteins Kir6.1 or Kir6.2 to form the
ATP-sensitive potassium (K(ATP)) channel. Within the
channel complex, SUR serves as a regulatory subunit that
fine-tunes the gating of Kir6.x in response to
alterations in cellular metabolism. It constitutes a
major pharmaceutical target as it binds numerous drugs,
K(ATP) channel openers and blockers, capable of up- or
down-regulating channel activity.
Length = 257
Score = 28.7 bits (64), Expect = 5.3
Identities = 29/108 (26%), Positives = 47/108 (43%), Gaps = 25/108 (23%)
Query: 154 ATPGRLIDHMNSGKINFSHLQ---------------ILVLDEADRMLDMGFINDIEKIV- 197
+ PG L + G NFS Q IL++DEA +DM N ++K+V
Sbjct: 141 SLPGGLDAVVTEGGENFSVGQRQLFCLARAFVRKSSILIMDEATASIDMATENILQKVVM 200
Query: 198 ----DATPVT---RQTMLFSATLDGIV--GNMAENITKDPLILKVNSI 236
D T VT R + + A L ++ G + E T + L+ + + +
Sbjct: 201 TAFADRTVVTIAHRVSTILDADLVLVLSRGILVECDTPENLLAQEDGV 248
>gnl|CDD|236912 PRK11448, hsdR, type I restriction enzyme EcoKI subunit R;
Provisional.
Length = 1123
Score = 29.1 bits (66), Expect = 6.2
Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 15/85 (17%)
Query: 270 GQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNA-------RNRTLENLRRGR--- 319
G+ ++F AT AD++ L F +G + +A ++ + +RR +
Sbjct: 699 GKTLIFAATDAHADMVVRLL-KEAFKKK--YGQVEDDAVIKITGSIDKPDQLIRRFKNER 755
Query: 320 -IKILVATDVAARGIDVPAITH-VF 342
I+V D+ GIDVP+I + VF
Sbjct: 756 LPNIVVTVDLLTTGIDVPSICNLVF 780
>gnl|CDD|215594 PLN03129, PLN03129, NADP-dependent malic enzyme; Provisional.
Length = 581
Score = 28.7 bits (65), Expect = 8.3
Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 8/55 (14%)
Query: 263 LLRDKRVGQAVVFTATKRDADIIADRLNISGFLAAPLHGDLHQNARNRTLENLRR 317
LLRD R + + FT T+R DRL + G L + Q R +ENLR
Sbjct: 45 LLRDPRYNKGLAFTETER------DRLGLRGLLPPAVLSQELQVK--RFMENLRA 91
>gnl|CDD|234468 TIGR04095, dnd_restrict_1, DNA phosphorothioation system
restriction enzyme. The DNA phosphorothioate
modification system dnd (DNA instability during
electrophoresis) recently has been shown to provide a
modification essential to a restriction system. This
protein family was detected by Partial Phylogenetic
Profiling as linked to dnd, and its members usually are
clustered with the dndABCDE genes.
Length = 451
Score = 28.5 bits (64), Expect = 8.6
Identities = 15/55 (27%), Positives = 22/55 (40%)
Query: 308 RNRTLENLRRGRIKILVATDVAARGIDVPAITHVFNYDLPKFPEDYVHRIGRTGR 362
R L G ++ LVA G+D+PA + P ++ R GR R
Sbjct: 328 REELLRQFESGLLQGLVAIRCLDEGVDIPATRTAYILASSSNPRQFIQRRGRVLR 382
>gnl|CDD|225463 COG2911, COG2911, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 1278
Score = 28.5 bits (64), Expect = 8.8
Identities = 17/45 (37%), Positives = 20/45 (44%), Gaps = 6/45 (13%)
Query: 285 IADRLNISGF-LAAPLHGDLH-----QNARNRTLENLRRGRIKIL 323
D + + GF L A L GDLH N NLRRGR +
Sbjct: 1056 AGDDIFVRGFGLDAELGGDLHVRQPKGNLGLNGQINLRRGRYRAY 1100
>gnl|CDD|223518 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 589
Score = 28.4 bits (64), Expect = 9.5
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 351 EDYVHRIGRTGRAGRNGFAVSLVNHAERMNIKKIERFTKQQIPIEVING 399
DY + R G V + + E++ KKI Q+IP ++ G
Sbjct: 500 LDYAKEVAEKLRK--AGIRVDIDDRNEKLG-KKIREAGTQKIPYVIVVG 545
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
0.321 0.136 0.382
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: 23,602,131
Number of extensions: 2399310
Number of successful extensions: 2619
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2557
Number of HSP's successfully gapped: 110
Length of query: 453
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 353
Effective length of database: 6,502,202
Effective search space: 2295277306
Effective search space used: 2295277306
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 61 (27.2 bits)