RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16633
(540 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 = 283 bits (725), Expect = 4e-89
Identities = 132/373 (35%), Positives = 201/373 (53%), Gaps = 35/373 (9%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQV 89
LQA+ LG+ EPT IQ AIPLIL +DVL +A+TG+GKT AF +P++QKI+ + V
Sbjct: 41 LQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYV 100
Query: 90 QETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVA 149
AL+L+P++EL Q+ + +++L K ++ + V + Q L DIVVA
Sbjct: 101 S---ALILAPTRELAVQIAEELRKLG-KNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVA 156
Query: 150 TPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATL 209
TP R L +K LDL S +E +++DEAD + G+ DD++ +LK LP Q +L SAT+
Sbjct: 157 TPGRLLDLIKRGKLDL-SGVETLVLDEADRMLDMGFIDDIEKILKALPPDRQTLLFSATM 215
Query: 210 SEDVLSLKHLILRNPVILKLE----EPAIAPVSQLAHYHILAQEDEKATILYTLLKLNLV 265
+D+ L L +PV +++ E + + Q Y + E+EK +L LLK
Sbjct: 216 PDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQ--FYLEVESEEEKLELLLKLLKDEDE 273
Query: 266 QGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDVIIASDE 325
G+ I+FV T +L L + L+ +LP + R A+ +F G V++A+D
Sbjct: 274 -GRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDV 332
Query: 326 KALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQCYIHRAGRTARGKN 385
+RG+D VS+VIN+D PLD + Y+HR GRT R
Sbjct: 333 -----------------------AARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGR 369
Query: 386 QGTALSFVSLREQ 398
+G A+SFV+ E+
Sbjct: 370 KGVAISFVTEEEE 382
>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 = 190 bits (484), Expect = 2e-57
Identities = 80/199 (40%), Positives = 121/199 (60%), Gaps = 6/199 (3%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQV 89
L+ I LG+ +PT IQ RAIP +L +DV+ +A+TGSGKT AF IP+++K+ +
Sbjct: 11 LRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGP 70
Query: 90 QETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVA 149
Q AL+L+P++EL Q+ + ++L K + ++K V I + Q L P IVVA
Sbjct: 71 Q---ALILAPTRELALQIAEVARKLG-KHT-NLKVVVIYGGTSIDKQIRKLKRGPHIVVA 125
Query: 150 TPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATL 209
TP R L L+ LDL S ++ +++DEAD + G+ED ++ +LK LPK Q +L SAT+
Sbjct: 126 TPGRLLDLLERGKLDL-SKVKYLVLDEADRMLDMGFEDQIREILKLLPKDRQTLLFSATM 184
Query: 210 SEDVLSLKHLILRNPVILK 228
++V L LRNPV +
Sbjct: 185 PKEVRDLARKFLRNPVRIL 203
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 196 bits (500), Expect = 1e-56
Identities = 117/380 (30%), Positives = 190/380 (50%), Gaps = 57/380 (15%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQV 89
L + +LG+ E T IQ +++P IL KDV+ +A+TGSGKT AF + ++QK +++K+ V
Sbjct: 16 LANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQK-LDVKRFR-V 73
Query: 90 QETKALVLSPSKELCNQLHK----------NIQELTMKCSRDVKC--VDISEQVDVSVQE 137
Q ALVL P++EL +Q+ K NI+ LT+ C V + Q+D
Sbjct: 74 Q---ALVLCPTRELADQVAKEIRRLARFIPNIKVLTL-------CGGVPMGPQIDS---- 119
Query: 138 PLLVERPDIVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLP 197
L I+V TP R L HL+ TLDL +L +++DEAD + G++D + A+++ P
Sbjct: 120 --LEHGAHIIVGTPGRILDHLRKGTLDL-DALNTLVLDEADRMLDMGFQDAIDAIIRQAP 176
Query: 198 KLYQAILASATLSEDVLSLKHLILRNPVILKLEEPAIAPVSQLAHYHILAQEDEKATILY 257
Q +L SAT E + ++ R+PV +K+E P + Y + DE+ L
Sbjct: 177 ARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTHDLPAIEQRFYEV--SPDERLPALQ 234
Query: 258 TLLKLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLY 317
LL + + ++F NT +C ++ L S L+ +L + R + +F
Sbjct: 235 RLLLHHQPE-SCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSC 293
Query: 318 DVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQCYIHRA 377
V++A+D A RG+D + + VIN++ D + ++HR
Sbjct: 294 SVLVATDVAA-----------------------RGLDIKALEAVINYELARDPEVHVHRI 330
Query: 378 GRTARGKNQGTALSFVSLRE 397
GRT R ++G ALS V+ E
Sbjct: 331 GRTGRAGSKGLALSLVAPEE 350
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 188 bits (479), Expect = 5e-54
Identities = 114/369 (30%), Positives = 181/369 (49%), Gaps = 37/369 (10%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINL--KQTA 87
L+A+ G+ PT IQ AIP L +DVL A TG+GKT AF +P +Q +++ +++
Sbjct: 13 LEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSG 72
Query: 88 QVQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIV 147
+ L+L+P++EL Q+ +EL + I+ V + E DIV
Sbjct: 73 P---PRILILTPTRELAMQVADQARELAKHT--HLDIATITGGVAYMNHAEVFSENQDIV 127
Query: 148 VATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASA 207
VATP R L ++K + D + ++E +I+DEAD + G+ D++ + Q +L SA
Sbjct: 128 VATPGRLLQYIKEENFDCR-AVETLILDEADRMLDMGFAQDIETIAAETRWRKQTLLFSA 186
Query: 208 TL-SEDVLSLKHLILRNPVILKLEEP--AIAPVSQLAHYHILAQEDEKATILYTLLKLNL 264
TL + V +L +PV ++ E + Q Y+ + K +L LLK
Sbjct: 187 TLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQW--YYRADDLEHKTALLCHLLKQPE 244
Query: 265 VQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDVIIASD 324
V ++I+FV T ++ ++L +L + I+ C L E+ R A+ + G +V++A+D
Sbjct: 245 VT-RSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATD 303
Query: 325 EKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQCYIHRAGRTARGK 384
A RGID VS+VINFD P Y+HR GRT R
Sbjct: 304 VAA-----------------------RGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAG 340
Query: 385 NQGTALSFV 393
+GTA+S V
Sbjct: 341 RKGTAISLV 349
>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 = 160 bits (406), Expect = 1e-46
Identities = 62/173 (35%), Positives = 101/173 (58%), Gaps = 8/173 (4%)
Query: 42 TLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSK 101
T IQ +AIP IL KDVLV+A TGSGKT AF +P++Q ++ K +ALVL+P++
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKG-----GPQALVLAPTR 55
Query: 102 ELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVER-PDIVVATPARALAHLKA 160
EL Q+++ +++L ++ ++ + Q L + DI+V TP R L L+
Sbjct: 56 ELAEQIYEELKKL--FKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRR 113
Query: 161 KTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATLSEDV 213
L L +L+++++DEA + G+ DD++ +L LP Q +L SATL ++
Sbjct: 114 GKLKLLKNLKLLVLDEAHRLLDMGFGDDLEEILSRLPPDRQILLLSATLPRNL 166
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 165 bits (420), Expect = 2e-45
Identities = 111/380 (29%), Positives = 195/380 (51%), Gaps = 39/380 (10%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQV 89
L+A+A+ G+ EPT IQ++AIP +L+ +D++ A+TG+GKT F +P++Q +I + A+
Sbjct: 13 LRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKG 72
Query: 90 QE-TKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQV---DVSVQEPLLVERP- 144
+ +AL+L+P++EL Q+ +N+++ + K ++I V VS+ ++ R
Sbjct: 73 RRPVRALILTPTRELAAQIGENVRDYS-------KYLNIRSLVVFGGVSINPQMMKLRGG 125
Query: 145 -DIVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAI 203
D++VATP R L + L +EI+++DEAD + G+ D++ VL LP Q +
Sbjct: 126 VDVLVATPGRLLDLEHQNAVKL-DQVEILVLDEADRMLDMGFIHDIRRVLAKLPAKRQNL 184
Query: 204 LASATLSEDVLSLKHLILRNPVILKLEEPAIAPVSQLAHYHILAQEDEKATILYTLLKLN 263
L SAT S+D+ +L +L NP+ +++ A H H + ++ ++ + + K N
Sbjct: 185 LFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDKKRKRELLSQMIGKGN 244
Query: 264 LVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDVIIAS 323
Q ++F T L L + I + ++ AR A+ F G V++A+
Sbjct: 245 WQQ--VLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVAT 302
Query: 324 DEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQCYIHRAGRTARG 383
D A RG+D + + +V+N++ P + Y+HR GRT R
Sbjct: 303 DIAA-----------------------RGLDIEELPHVVNYELPNVPEDYVHRIGRTGRA 339
Query: 384 KNQGTALSFVSLREQDLMND 403
G ALS V + E L+ D
Sbjct: 340 AATGEALSLVCVDEHKLLRD 359
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 161 bits (409), Expect = 8e-43
Identities = 111/372 (29%), Positives = 189/372 (50%), Gaps = 32/372 (8%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQV 89
L+A+ LG+ +P+ IQ IP +L +DVL A+TGSGKT AF++P++ + ++
Sbjct: 18 LEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNL-----DPEL 72
Query: 90 QETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVA 149
+ + LVL+P++EL Q+ + + + + K R V V + VQ L + P IVV
Sbjct: 73 KAPQILVLAPTRELAVQVAEAMTDFS-KHMRGVNVVALYGGQRYDVQLRALRQGPQIVVG 131
Query: 150 TPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATL 209
TP R L HLK TLDL S L +++DEAD + G+ +D++ ++ +P+ +Q L SAT+
Sbjct: 132 TPGRLLDHLKRGTLDL-SKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGHQTALFSATM 190
Query: 210 SEDVLSLKHLILRNPVILKLEEPAIAPVSQLAHYHILAQEDEKATILYTLLKLNLVQGKT 269
E + + ++ P ++++ ++ ++ + K L L+
Sbjct: 191 PEAIRRITRRFMKEPQEVRIQS-SVTTRPDISQSYWTVWGMRKNEALVRFLEAEDFDA-A 248
Query: 270 IIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDVIIASDEKALE 329
IIFV T + ++ LE+ ++ LN ++ R + + G D++IA+D A
Sbjct: 249 IIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAA-- 306
Query: 330 TPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQCYIHRAGRTARGKNQGTA 389
RG+D + +S V+N+D P+D + Y+HR GRT R G A
Sbjct: 307 ---------------------RGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRA 345
Query: 390 LSFVSLREQDLM 401
L FV RE+ L+
Sbjct: 346 LLFVENRERRLL 357
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 154 bits (390), Expect = 3e-41
Identities = 104/370 (28%), Positives = 182/370 (49%), Gaps = 33/370 (8%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQ- 88
+ AI LG+ T IQ + + L D + RA+TG+GKT AF I +I +++ +
Sbjct: 99 MHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKER 158
Query: 89 -VQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVER-PDI 146
+ E +AL+++P++EL Q+ K+ LT +V + +D Q L R DI
Sbjct: 159 YMGEPRALIIAPTRELVVQIAKDAAALTKYTGLNV--MTFVGGMDFDKQLKQLEARFCDI 216
Query: 147 VVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKL--YQAIL 204
+VATP R L + + L +E++++DEAD + G+ ++ +++ P+ Q +L
Sbjct: 217 LVATPGRLLDFNQRGEVHL-DMVEVMVLDEADRMLDMGFIPQVRQIIRQTPRKEERQTLL 275
Query: 205 ASATLSEDVLSLKHLILRNPVILKLEEPAIAPVSQLAHYHILAQEDEKATILYTLLKLNL 264
SAT ++DV++L +P I+++E +A + H + +A D K +LY L+ N
Sbjct: 276 FSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAGSD-KYKLLYNLVTQNP 334
Query: 265 VQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDVIIASD 324
+ + ++F N D+ +++ L + I+ L+ ++P R + F +G V++A+D
Sbjct: 335 WE-RVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATD 393
Query: 325 EKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQCYIHRAGRTARGK 384
RGI +S+VINF P D Y+HR GRT R
Sbjct: 394 V-----------------------AGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAG 430
Query: 385 NQGTALSFVS 394
G ++SF
Sbjct: 431 ASGVSISFAG 440
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 150 bits (380), Expect = 3e-39
Identities = 113/376 (30%), Positives = 194/376 (51%), Gaps = 41/376 (10%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTA-- 87
L + G+ T IQ +P+ L DV +A+TG+GKT AF + ++ ++++ A
Sbjct: 21 LAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADR 80
Query: 88 QVQETKALVLSPSKELCNQLHKNIQELTMKCSRDV--KCVDISEQVDVSVQEPLLVERPD 145
+ ++ +AL+L+P++EL Q+HK+ +K D+ + + VD Q LL + D
Sbjct: 81 KPEDPRALILAPTRELAIQIHKD----AVKFGADLGLRFALVYGGVDYDKQRELLQQGVD 136
Query: 146 IVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPK--LYQAI 203
+++ATP R + ++K + + EI ++DEAD +F G+ D++ +L+ +P+ Q +
Sbjct: 137 VIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMPERGTRQTL 196
Query: 204 LASATLSEDVLSLKHLILRNPVILKLEEPAI--APVSQLAHYHILAQEDEKATILYTLLK 261
L SATLS VL L + + P L +E I A V Q ++ ++EK T+L LL
Sbjct: 197 LFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYF---PADEEKQTLLLGLLS 253
Query: 262 LNLVQG-KTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDVI 320
+ +G +T++FVNT ++ LE+ VL+ ++P K R + +F +G +++
Sbjct: 254 RS--EGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEIL 311
Query: 321 IASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQCYIHRAGRT 380
+A+D A RG+ V V N+D P D + Y+HR GRT
Sbjct: 312 VATDVAA-----------------------RGLHIDGVKYVYNYDLPFDAEDYVHRIGRT 348
Query: 381 ARGKNQGTALSFVSLR 396
AR +G A+SF R
Sbjct: 349 ARLGEEGDAISFACER 364
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 144 bits (366), Expect = 2e-38
Identities = 107/377 (28%), Positives = 176/377 (46%), Gaps = 38/377 (10%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQV 89
L+ I G+ +P+ IQ+R I IL D + +A++G+GKT F I +Q I +
Sbjct: 40 LRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLI-----DYDL 94
Query: 90 QETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVA 149
+AL+L+P++EL Q+ K + L V+C V L +VV
Sbjct: 95 NACQALILAPTRELAQQIQKVVLALGDYL--KVRCHACVGGTVVRDDINKLKAGVHMVVG 152
Query: 150 TPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATL 209
TP R + + L L++ I+DEAD + S G++ + V K LP Q L SAT+
Sbjct: 153 TPGRVYDMIDKRHL-RVDDLKLFILDEADEMLSRGFKGQIYDVFKKLPPDVQVALFSATM 211
Query: 210 SEDVLSLKHLILRNP--VILKLEEPAIAPVSQLAHYHILAQEDEKATILYTLLK-LNLVQ 266
++L L +R+P +++K +E + + Q Y + +E+ K L L + L + Q
Sbjct: 212 PNEILELTTKFMRDPKRILVKKDELTLEGIRQF--YVAVEKEEWKFDTLCDLYETLTITQ 269
Query: 267 GKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDVIIASDEK 326
II+ NT K L + + + ++ ++ K R + +F G V+I +D
Sbjct: 270 --AIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLL 327
Query: 327 ALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQCYIHRAGRTARGKNQ 386
A RGID Q VS VIN+D P + YIHR GR+ R +
Sbjct: 328 A-----------------------RGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRK 364
Query: 387 GTALSFVSLREQDLMND 403
G A++FV+ + + + +
Sbjct: 365 GVAINFVTPDDIEQLKE 381
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 132 bits (334), Expect = 5e-36
Identities = 61/202 (30%), Positives = 98/202 (48%), Gaps = 9/202 (4%)
Query: 33 IAKLGWLEPTLIQERAIPLILQN-KDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQE 91
I K G+ Q+ AI +L +DV++ A TGSGKT A +P ++ + K
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGG----- 55
Query: 92 TKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATP 151
+ LVL P++EL Q + +++L L + DI+V TP
Sbjct: 56 -RVLVLVPTRELAEQWAEELKKL-GPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTP 113
Query: 152 ARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATLSE 211
R L L+ L L + +++VI+DEA + G+ D ++ +LK LPK Q +L SAT E
Sbjct: 114 GRLLDLLENDKLSLSN-VDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPE 172
Query: 212 DVLSLKHLILRNPVILKLEEPA 233
++ +L L L +PV + +
Sbjct: 173 EIENLLELFLNDPVFIDVGFTP 194
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 129 bits (326), Expect = 1e-32
Identities = 100/374 (26%), Positives = 177/374 (47%), Gaps = 46/374 (12%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTA-- 87
++A+ K G+ T IQ A+PL L +DV +A+TG+GKT AF +++
Sbjct: 20 VEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDR 79
Query: 88 QVQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIV 147
+V + +AL+++P++EL Q+H + + L + + D Q +L DI+
Sbjct: 80 KVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDK--QLKVLESGVDIL 137
Query: 148 VATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQ--AILA 205
+ T R + + K ++L ++++V++DEAD +F G+ D++ + + +P Q +L
Sbjct: 138 IGTTGRLIDYAKQNHINL-GAIQVVVLDEADRMFDLGFIKDIRWLFRRMPPANQRLNMLF 196
Query: 206 SATLSEDVLSLKHLILRNPVILKLEEPAIAPVSQLAHYHILAQE-------DEKATILYT 258
SATLS V L + NP E + P + H +E +EK +L T
Sbjct: 197 SATLSYRVRELAFEHMNNP-----EYVEVEPEQKTGH---RIKEELFYPSNEEKMRLLQT 248
Query: 259 LLKLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYD 318
L++ + IIF NT +C ++ +L +L ++ K R + +F +G D
Sbjct: 249 LIEEEWPD-RAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLD 307
Query: 319 VIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQCYIHRAG 378
+++A+D A RG+ V++V N+D P D + Y+HR G
Sbjct: 308 ILVATDVAA-----------------------RGLHIPAVTHVFNYDLPDDCEDYVHRIG 344
Query: 379 RTARGKNQGTALSF 392
RT R G ++S
Sbjct: 345 RTGRAGASGHSISL 358
>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 = 109 bits (274), Expect = 3e-28
Identities = 56/154 (36%), Positives = 86/154 (55%), Gaps = 10/154 (6%)
Query: 56 KDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKELCNQLHKNIQELT 115
+DVL+ A TGSGKT A +P+++ + +LK + LVL+P++EL NQ+ + ++EL
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKG------GQVLVLAPTRELANQVAERLKELF 54
Query: 116 MKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPARALAHLKAKTLDLKSSLEIVIID 175
+K + + QE LL + DIVV TP R L L+ L LK L+++I+D
Sbjct: 55 ---GEGIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLK-KLDLLILD 110
Query: 176 EADLVFSFGYEDDMKAVLKFLPKLYQAILASATL 209
EA + + G+ +L LPK Q +L SAT
Sbjct: 111 EAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP 144
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 111 bits (279), Expect = 6e-26
Identities = 99/372 (26%), Positives = 167/372 (44%), Gaps = 38/372 (10%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQV 89
L+++ G+ EPT IQ + P+ L +D++ A TGSGKT AF +P I I AQ
Sbjct: 142 LKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHI-----NAQP 196
Query: 90 QETKA-----LVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERP 144
LVL+P++EL Q+ + Q S ++ V Q L
Sbjct: 197 LLRYGDGPIVLVLAPTRELAEQIRE--QCNKFGASSKIRNTVAYGGVPKRGQIYALRRGV 254
Query: 145 DIVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAIL 204
+I++A P R + L++ +L + +++DEAD + G+E ++ ++ + Q ++
Sbjct: 255 EILIACPGRLIDFLESNVTNL-RRVTYLVLDEADRMLDMGFEPQIRKIVSQIRPDRQTLM 313
Query: 205 ASATLSEDVLSLKHLILRN-PVILKLEEPAIAPVSQLAHYHILAQEDEKATILYTLLKLN 263
SAT ++V SL + + PV + + + + + +E EK L LL+
Sbjct: 314 WSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRI 373
Query: 264 LVQG-KTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDVIIA 322
+ G K +IFV T L L ++ + + R + +F G ++IA
Sbjct: 374 MRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIA 433
Query: 323 SDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQCYIHRAGRTAR 382
+D SRG+D + V VINFDFP I+ Y+HR GRT R
Sbjct: 434 TDV-----------------------ASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGR 470
Query: 383 GKNQGTALSFVS 394
+G + +F++
Sbjct: 471 AGAKGASYTFLT 482
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 111 bits (278), Expect = 6e-26
Identities = 105/396 (26%), Positives = 186/396 (46%), Gaps = 58/396 (14%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQK--IINLKQTA 87
L + G+ PT IQ +AIP L + +LV A TGSGKT +F +P+I + I +
Sbjct: 133 LLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPS 192
Query: 88 QVQETKALVLSPSKELCNQLHKNI----QELTMKCSRDVKCVDISEQVDVSVQEPLLVER 143
+ + A+VL+P++ELC Q+ + L K + V + +Q+ +Q+ +
Sbjct: 193 EQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQL-YRIQQGV---- 247
Query: 144 PDIVVATPARALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAI 203
+++V TP R + L ++L ++ ++++DE D + G+ D + + + L + Q +
Sbjct: 248 -ELIVGTPGRLIDLLSKHDIEL-DNVSVLVLDEVDCMLERGFRDQVMQIFQALSQP-QVL 304
Query: 204 LASATLSEDVLSLKHLILRNPVILKLEEPAIAP---VSQLAHYHILAQEDEKATILYTLL 260
L SAT+S +V + ++ +++ + P P V QLA I + +K L+ +L
Sbjct: 305 LFSATVSPEVEKFASSLAKDIILISIGNPN-RPNKAVKQLA---IWVETKQKKQKLFDIL 360
Query: 261 K-LNLVQGKTIIFVNTVDKCYKL--KLYLEQFKISTCV----LNSELPAKARCHAVYQFN 313
K + ++FV++ +L L + T + ++ E K R + F
Sbjct: 361 KSKQHFKPPAVVFVSS-----RLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFL 415
Query: 314 QGLYDVIIASDEKALETPQINSTNNRKRKRDKESGV-SRGIDFQFVSNVINFDFPLDIQC 372
G VI+A +GV RG+D V VI FD P I+
Sbjct: 416 VGEVPVIVA------------------------TGVLGRGVDLLRVRQVIIFDMPNTIKE 451
Query: 373 YIHRAGRTARGKNQGTALSFVSLREQDLMNDGTALS 408
YIH+ GR +R +GTA+ FV+ +++L + AL
Sbjct: 452 YIHQIGRASRMGEKGTAIVFVNEEDRNLFPELVALL 487
>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 = 94.2 bits (235), Expect = 5e-23
Identities = 43/152 (28%), Positives = 65/152 (42%), Gaps = 24/152 (15%)
Query: 242 HYHILAQEDEKATILYTLLKLNLVQG-KTIIFVNTVDKCYKLKLYLEQFKISTCVLNSEL 300
++L EDEK L LLK +L +G K +IF + +L L + I L+ +
Sbjct: 3 KQYVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDG 62
Query: 301 PAKARCHAVYQFNQGLYDVIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSN 360
+ R + F +G V++A+D ++RGID VS
Sbjct: 63 SQEEREEVLKDFREGEIVVLVATD-----------------------VIARGIDLPNVSV 99
Query: 361 VINFDFPLDIQCYIHRAGRTARGKNQGTALSF 392
VIN+D P Y+ R GR R +GTA+
Sbjct: 100 VINYDLPWSPSSYLQRIGRAGRAGQKGTAILL 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 = 69.5 bits (171), Expect = 7e-15
Identities = 26/101 (25%), Positives = 36/101 (35%), Gaps = 23/101 (22%)
Query: 284 LYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDVIIASDEKALETPQINSTNNRKRKR 343
L + I L+ L + R + F G V++A+D
Sbjct: 1 KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATD--VAG-------------- 44
Query: 344 DKESGVSRGIDFQFVSNVINFDFPLDIQCYIHRAGRTARGK 384
RGID V+ VIN+D P + YI R GR R
Sbjct: 45 -------RGIDLPDVNLVINYDLPWNPASYIQRIGRAGRAG 78
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 67.6 bits (166), Expect = 3e-14
Identities = 27/102 (26%), Positives = 39/102 (38%), Gaps = 23/102 (22%)
Query: 281 KLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDVIIASDEKALETPQINSTNNRK 340
+L L++ I L+ L + R + +FN G V++A+D E
Sbjct: 2 ELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATD--VAE----------- 48
Query: 341 RKRDKESGVSRGIDFQFVSNVINFDFPLDIQCYIHRAGRTAR 382
RG+D V VI +D P YI R GR R
Sbjct: 49 ----------RGLDLPGVDLVIIYDLPWSPASYIQRIGRAGR 80
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 71.9 bits (177), Expect = 4e-13
Identities = 44/160 (27%), Positives = 73/160 (45%), Gaps = 13/160 (8%)
Query: 23 FTLFCIPLQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIIN 82
F + ++ K + T Q AIP I ++VL+ A TGSGKT A +P+I ++++
Sbjct: 5 FNILDPRVREWFKRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLS 64
Query: 83 LKQTAQVQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQV---DVSVQE-- 137
L + AL +SP K L N + + ++E ++ + I V D E
Sbjct: 65 LGKGKLEDGIYALYISPLKALNNDIRRRLEEP-------LRELGIEVAVRHGDTPQSEKQ 117
Query: 138 PLLVERPDIVVATPARALAHLKAKTL-DLKSSLEIVIIDE 176
+L P I++ TP L + +L + VI+DE
Sbjct: 118 KMLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDE 157
>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 62.0 bits (151), Expect = 4e-10
Identities = 43/179 (24%), Positives = 75/179 (41%), Gaps = 19/179 (10%)
Query: 45 QERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKELC 104
Q A+ LI + ++V+V TGSGKT +F +P++ + + +AL+L P+ L
Sbjct: 75 QVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHL------LRDPSARALLLYPTNALA 128
Query: 105 N-QLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPA---RALAHLKA 160
N Q + ++EL V + + ++ PDI++ P L
Sbjct: 129 NDQAER-LRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHD 187
Query: 161 KTLDLKSSLEIVIIDEADLVF--SFGYE-----DDMKAVLKFLPKLYQAILASATLSED 212
L L +L+ +++DE + G E + L+ Q I SATL+
Sbjct: 188 AWLWLLRNLKYLVVDELH-TYRGVQGSEVALLLRRLLRRLRRYGSPLQIICTSATLANP 245
>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 = 49.4 bits (118), Expect = 2e-06
Identities = 51/253 (20%), Positives = 87/253 (34%), Gaps = 43/253 (16%)
Query: 57 DVLVRARTGSGKTGA------------------FAIPMIQKIINLKQTAQVQETKALVLS 98
+++ A TG GKT A A+P + IN + L
Sbjct: 1 LLVIEAPTGYGKTEAALLWALHSLKSQKADRVIIALPT-RATINAMYRRAKEAFGETGLY 59
Query: 99 PSKELCNQLHKNIQELTMKCSRDVKCVDI-SEQVDVSVQEPLLVERPDIVVATPARALAH 157
S L +++ + + D +P+ V D V+ + H
Sbjct: 60 HSSILSSRIKEMGDSEEF-----EHLFPLYIHSNDTLFLDPITVCTIDQVLKSVFGEFGH 114
Query: 158 LKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMK----AVLKFLPKLYQ-AILASATLSED 212
+ + +SL +I DE Y++ AVL+ L +L SATL +
Sbjct: 115 YEFTLASIANSL--LIFDEVHF-----YDEYTLALILAVLEVLKDNDVPILLMSATLPK- 166
Query: 213 VLSLKHLILRNPVILKLEEPAIAPVSQLAHYHILAQEDEKATILYTLLKLNLVQGKTIIF 272
LK + + + E + P + I + + + + L LL+ G I
Sbjct: 167 --FLKEYAEKIGYVEENEPLDLKPNERAPFIKIESDKVGEISSLERLLEFIKKGGSVAII 224
Query: 273 VNTVDK---CYKL 282
VNTVD+ Y+
Sbjct: 225 VNTVDRAQEFYQQ 237
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 47.6 bits (114), Expect = 1e-05
Identities = 26/70 (37%), Positives = 45/70 (64%), Gaps = 1/70 (1%)
Query: 45 QERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQET-KALVLSPSKEL 103
Q AIPLI + K+VL+ + TGSGKT A + +I ++ L + ++++ L +SP + L
Sbjct: 37 QRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRAL 96
Query: 104 CNQLHKNIQE 113
N +H+N++E
Sbjct: 97 NNDIHRNLEE 106
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 45.5 bits (108), Expect = 5e-05
Identities = 54/311 (17%), Positives = 106/311 (34%), Gaps = 64/311 (20%)
Query: 54 QNKDVLVRARTGSGKT--GAFAIPMIQKIINLKQTAQVQETKALVLSPSKELCNQLHKNI 111
+ ++ TG+GKT A AI +++ LVL P+KEL +Q + +
Sbjct: 54 TERRGVIVLPTGAGKTVVAAEAIAELKR-------------STLVLVPTKELLDQWAEAL 100
Query: 112 QELTMK---------CSRDVKCVDISEQVDVSVQ--------EPLLVERPDIVV------ 148
++ + ++++ + +VQ + L +++
Sbjct: 101 KKFLLLNDEIGIYGGGEKELEPAKV---TVATVQTLARRQLLDEFLGNEFGLIIFDEVHH 157
Query: 149 --ATPARA-LAHLKAK--------TLDLKSSLEIVIIDE--ADLVFSFGYEDDMKAVLKF 195
A R L L A T + + I + + +V+ ++ + +
Sbjct: 158 LPAPSYRRILELLSAAYPRLGLTATPEREDGGRIGDLFDLIGPIVYEVSLKELIDE--GY 215
Query: 196 L-PKLYQAILASATLSEDVLSLKHLILRNPVILKLEEPAIAPVSQLAHYHILAQEDEKAT 254
L P Y I + T E+ K R +L+ A I + K
Sbjct: 216 LAPYKYVEIKVTLTEDEEREYAKE-SARFRELLRARGTLRAENEARR---IAIASERKIA 271
Query: 255 ILYTLLKLNLVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQ-FN 313
+ LL + KT+IF + V+ Y++ + E P + R A+ + F
Sbjct: 272 AVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLA-PGIVEAITGETPKEER-EAILERFR 329
Query: 314 QGLYDVIIASD 324
G V++
Sbjct: 330 TGGIKVLVTVK 340
>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 = 44.4 bits (105), Expect = 9e-05
Identities = 49/251 (19%), Positives = 87/251 (34%), Gaps = 35/251 (13%)
Query: 57 DVLVRARTGSGKTGA---FAIPMIQKIINLK--------QTAQVQETKALVLSPSKELCN 105
+++ A TG GKT A +A+ I+ + T +A L S
Sbjct: 1 LLVIEAPTGYGKTEAALLWALHSIKSQKADRVIIALPTRATINAMYRRAKELFGSNLGLL 60
Query: 106 QLHKNIQELTMKCSRD--VKCVDI-SEQVDVSVQEPLLVERPDIVVATPARALAHLKAKT 162
+ + + + + D +P+ V D V+ + H +
Sbjct: 61 HSSSSFKRIKEMGDSEEFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTL 120
Query: 163 LDLKSSLEIVIIDEADLVFSFGYEDDMK----AVLKFLPKLYQ-AILASATLSEDVLSLK 217
+ +SL +I DE Y++ AVL+ L +L SATL + LK
Sbjct: 121 ASIANSL--LIFDEVHF-----YDEYTLALILAVLEVLKDNDVPILLMSATLPK---FLK 170
Query: 218 HLILRNPVILKLEEPAIAPVSQLAHYHI---LAQEDEKATILYTLLKLNLVQGKTIIFVN 274
+ + E + + + + + + + L LL+ GK I VN
Sbjct: 171 EYAEKIGYVEFNEPLDLKEERRFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAIIVN 230
Query: 275 TVDK---CYKL 282
TVD+ Y+
Sbjct: 231 TVDRAQEFYQQ 241
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 44.6 bits (106), Expect = 1e-04
Identities = 76/359 (21%), Positives = 126/359 (35%), Gaps = 81/359 (22%)
Query: 45 QERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKEL- 103
Q+ I +L KD LV TG GK+ + IP A + E LV+SP L
Sbjct: 22 QQEIIDALLSGKDTLVVMPTGGGKSLCYQIP-----------ALLLEGLTLVVSPLISLM 70
Query: 104 ---CNQLH-KNIQ------ELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPAR 153
+QL I+ L+ + E+ V Q + ++ +P R
Sbjct: 71 KDQVDQLEAAGIRAAYLNSTLSRE-----------ERQQVLNQLKS--GQLKLLYISPER 117
Query: 154 -ALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYE-----DDMKAVLKFLPK----LYQAI 203
L SL V IDEA + +G++ + + LP A
Sbjct: 118 LMSPRFLELLKRLPISL--VAIDEAHCISQWGHDFRPDYRRLGRLRAGLPNPPVLALTA- 174
Query: 204 LASATLSEDVLSLKHLILRNPVILKLEEPAIAPVSQLAHYHILAQEDEKATILYTLLKLN 263
A+ + +D+ L L++ I + + ++ + + + + L
Sbjct: 175 TATPRVRDDIRE--QLGLQDANIFR-----GSFDRPNLALKVVEKGEPSDQLAFLATVLP 227
Query: 264 LVQGKTIIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDVIIAS 323
+ II+ T K +L +L + IS ++ L + R F V++A+
Sbjct: 228 QLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVAT 287
Query: 324 DEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQCY---IHRAGR 379
A G+ GID V VI++D P I+ Y RAGR
Sbjct: 288 --NAF-------------------GM--GIDKPDVRFVIHYDLPGSIESYYQETGRAGR 323
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 43.6 bits (103), Expect = 2e-04
Identities = 68/290 (23%), Positives = 116/290 (40%), Gaps = 43/290 (14%)
Query: 52 ILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKELCNQLHKNI 111
+L+ +++LV + T SGKT + I ++++ + K L L P L NQ +++
Sbjct: 229 LLEGENLLVVSATASGKTLIGELAGIPRLLSGGK-------KMLFLVPLVALANQKYEDF 281
Query: 112 QE----LTMKCSRDVKCVDISEQVDVSVQEPLLVERP---DIVVATPARALAHLKAKTLD 164
+E L +K + V I + +EP++V+ DI+V T + +L D
Sbjct: 282 KERYSKLGLKVAIRVGMSRIKTR-----EEPVVVDTSPDADIIVGT-YEGIDYLLRTGKD 335
Query: 165 LKSSLEIVIIDEADLVFSFGYE------DDMKAVLKFLPKLYQAILASATLSEDVLSLKH 218
L + V+IDE + + E D + L++L Q I SAT+ K
Sbjct: 336 LGD-IGTVVIDE---IHTLEDEERGPRLDGLIGRLRYLFPGAQFIYLSATVGNPEELAKK 391
Query: 219 LILRNPVILKLEEPAIAPVSQLAHYHILAQEDEKATILYTLLKLNLVQ-------GKTII 271
L + L PV H E EK I+ L+K G+TI+
Sbjct: 392 LGAK------LVLYDERPVPLERHLVFARNESEKWDIIARLVKREFSTESSKGYRGQTIV 445
Query: 272 FVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYDVII 321
F + +C++L L + ++ LP K R F ++
Sbjct: 446 FTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVV 495
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 43.1 bits (102), Expect = 3e-04
Identities = 41/179 (22%), Positives = 70/179 (39%), Gaps = 42/179 (23%)
Query: 44 IQERAIPLILQNKDVLVRARTGSGKT--GAFAIPMIQKIINLKQTAQVQETKALVLSPSK 101
Q+ AI ++ + + VLV A T SGKT +AI + A + + SP K
Sbjct: 123 FQQEAIAILERGESVLVCAPTSSGKTVVAEYAIAL----------ALRDGQRVIYTSPIK 172
Query: 102 ELCNQLHKNIQELTMKCSRDVKCVDISEQV-----DVSVQEPLLVERPDIVVATPARALA 156
L NQ ++++ K D+++ V DVS+ +V T L
Sbjct: 173 ALSNQKYRDLLA---------KFGDVADMVGLMTGDVSINPD-----APCLVMT-TEILR 217
Query: 157 HLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAV-----LKFLPKLYQAILASATLS 210
++ + + +E V+ DE D + V + LP + + SAT+
Sbjct: 218 NMLYRGSESLRDIEWVVFDEVHY-----IGDRERGVVWEEVIILLPDHVRFVFLSATVP 271
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 42.8 bits (101), Expect = 5e-04
Identities = 42/182 (23%), Positives = 70/182 (38%), Gaps = 41/182 (22%)
Query: 44 IQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKEL 103
QE +L +++VL+ A TGSGKT A+ I T K + + P K L
Sbjct: 36 QQEAVEKGLLSDENVLISAPTGSGKT-LIALLAILS------TLLEGGGKVVYIVPLKAL 88
Query: 104 CNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQE--------PLLVERPDIVVATPARAL 155
+ ++ L E++ + V + R D++V TP + L
Sbjct: 89 AEEKYEEFSRL--------------EELGIRVGISTGDYDLDDERLARYDVIVTTPEK-L 133
Query: 156 AHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPK-------LYQAILASAT 208
L K +++V+IDE L+ + VL+ + L + + SAT
Sbjct: 134 DSLTRKRPSWIEEVDLVVIDEIHLL----GDRTRGPVLESIVARMRRLNELIRIVGLSAT 189
Query: 209 LS 210
L
Sbjct: 190 LP 191
>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 = 41.3 bits (97), Expect = 0.001
Identities = 66/292 (22%), Positives = 119/292 (40%), Gaps = 46/292 (15%)
Query: 44 IQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKEL 103
+ + I Q +D LV A TG+GKT I++ +N Q + + SP ++
Sbjct: 105 ASNQLVQYIKQKEDTLVWAVTGAGKT-EMIFQGIEQALN-------QGGRVCIASPRVDV 156
Query: 104 CNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPARALAHLKAKTL 163
C +L+ ++ + DI D+ + R +VVAT H + L
Sbjct: 157 CLELYPRLK-------QAFSNCDI----DLLYGDSDSYFRAPLVVAT-----TH---QLL 197
Query: 164 DLKSSLEIVIIDEADLVFSFGYEDDMK---AVLKFLPKLYQAILASATLSEDVLSLKHLI 220
K + +++IIDE D +F + DD AV K K I +AT L + ++
Sbjct: 198 RFKQAFDLLIIDEVD---AFPFSDDQSLQYAVKKARKKEGATIYLTAT-PTKKL-ERKIL 252
Query: 221 LRNPVILKL-----EEPAIAP-VSQLAHYHILAQEDEKATILYTLLKLNLVQGK-TIIFV 273
N ILKL +P P + +++ Q ++ L L+ G+ +IF
Sbjct: 253 KGNLRILKLPARFHGKPLPVPKFVWIGNWNKKLQRNKLPLKLKRWLEKQRKTGRPVLIFF 312
Query: 274 NTVDKCYKL-KLYLEQF-KISTCVLNSELPAKARCHAVYQFNQGLYDVIIAS 323
++ ++ ++ K + ++SE + R V F G ++I +
Sbjct: 313 PEIETMEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGKITLLITT 362
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 36.4 bits (85), Expect = 0.004
Identities = 23/69 (33%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 39 LEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLS 98
LE QE AI +L+ K L+ TGSGKT + I L + + K L +
Sbjct: 2 LELRPYQEEAIERLLEKKRGLIVMATGSGKT----LTAAALIARLAK----GKKKVLFVV 53
Query: 99 PSKELCNQL 107
P K+L Q
Sbjct: 54 PRKDLLEQA 62
>gnl|CDD|177443 PHA02653, PHA02653, RNA helicase NPH-II; Provisional.
Length = 675
Score = 38.4 bits (90), Expect = 0.009
Identities = 38/129 (29%), Positives = 59/129 (45%), Gaps = 16/129 (12%)
Query: 171 IVIIDEADLVFSFGYEDDMKAVL-KFLPKLYQAILASATLSEDVLSLKHLILRNPVILKL 229
VIIDE G D + AV K + K+ L +ATL +D +K NP + +
Sbjct: 294 TVIIDEVHEHDQIG--DIIIAVARKHIDKIRSLFLMTATLEDDRDRIKEF-FPNPAFVHI 350
Query: 230 EEPAIAPVSQLAHYHILAQ---------EDEKATILYTLLKLNLVQGKT-IIFVNTVDKC 279
+ P+S++ Y E+EK I+ L K +G + I+FV +V +C
Sbjct: 351 PGGTLFPISEV--YVKNKYNPKNKRAYIEEEKKNIVTALKKYTPPKGSSGIVFVASVSQC 408
Query: 280 YKLKLYLEQ 288
+ K YLE+
Sbjct: 409 EEYKKYLEK 417
>gnl|CDD|187841 cd09710, Cas3_I-D, CRISPR/Cas system-associated protein Cas3;
Distinct diverged subfamily of Cas3 helicase domain.
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;
Diverged DNA helicase Cas3'; signature gene for Type I
and subtype I-D.
Length = 353
Score = 37.2 bits (86), Expect = 0.019
Identities = 35/152 (23%), Positives = 52/152 (34%), Gaps = 39/152 (25%)
Query: 53 LQNKD---VLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKELCNQLHK 109
LQ+KD + A TG+GKT A+ P++ E KA+ L P+ L +
Sbjct: 9 LQSKDADIIFNTAPTGAGKTLAWLTPLLH-----------GENKAIALYPTNALIEDQTE 57
Query: 110 NIQEL--TMKCSRDVKCVDISE----------------------QVDVSVQEP-LLVERP 144
I+E VK + S+ + D+ P +L+ P
Sbjct: 58 AIKEFVDDANPRHQVKSLSASDITLWPNDKNVGSSKGEKLYNLLRNDIGTSTPIILLTNP 117
Query: 145 DIVVATPARALAHLKAKTLDLKSSLEIVIIDE 176
DI V A + VI DE
Sbjct: 118 DIFVYLTRFAYIDRGDIAAGFYTKFSTVIFDE 149
>gnl|CDD|234127 TIGR03158, cas3_cyano, CRISPR-associated helicase Cas3, subtype
CYANO. CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) is a widespread family of
prokaryotic direct repeats with spacers of unique
sequence between consecutive repeats. This protein
family is a CRISPR-associated (Cas) family strictly
associated with the Cyano subtype of CRISPR/Cas locus,
found in several species of Cyanobacteria and several
archaeal species. It contains helicase motifs and
appears to represent the Cas3 protein of the Cyano
subtype of CRISPR/Cas system [Mobile and
extrachromosomal element functions, Other].
Length = 357
Score = 36.4 bits (84), Expect = 0.031
Identities = 23/81 (28%), Positives = 35/81 (43%), Gaps = 16/81 (19%)
Query: 53 LQNKD---VLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKELCNQLHK 109
LQ+KD + A TG+GKT A+ P++ E + L P+ L +
Sbjct: 9 LQSKDADIIFNTAPTGAGKTLAWLTPLLH-----------GENDTIALYPTNALIEDQTE 57
Query: 110 NIQEL--TMKCSRDVKCVDIS 128
I+E K RDV + +S
Sbjct: 58 AIKEFVDVFKPERDVNLLHVS 78
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 36.2 bits (84), Expect = 0.046
Identities = 43/163 (26%), Positives = 71/163 (43%), Gaps = 16/163 (9%)
Query: 38 WLEPTLIQERAIPLILQNK----DVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETK 93
++P I+ R L + K + LV TG GKT A +I L+ K
Sbjct: 8 LIKPNTIEPRLYQLNIAAKALFKNTLVVLPTGLGKT-FIAAMVIANR--LRWFGG----K 60
Query: 94 ALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPAR 153
L L+P+K L Q + +++T ++ ++ +V +E L + + VATP
Sbjct: 61 VLFLAPTKPLVLQHAEFCRKVTGIPEDEI--AALTGEVRPEERE-ELWAKKKVFVATPQV 117
Query: 154 ALAHLKAKTLDLKSSLEIVIIDEAD-LVFSFGYEDDMKAVLKF 195
LKA +DL + ++I DEA V ++ Y K L+
Sbjct: 118 VENDLKAGRIDLD-DVSLLIFDEAHRAVGNYAYVFVAKEYLRS 159
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 35.7 bits (82), Expect = 0.068
Identities = 35/138 (25%), Positives = 60/138 (43%), Gaps = 19/138 (13%)
Query: 60 VRARTGSGKTGAFAIPMIQKIINLKQTAQVQE------TKALVLSPSKELCNQLHKNIQE 113
V A TGSGKT A + + ++ + +E ++ L +SP K L + +N+Q
Sbjct: 1 VIAPTGSGKTLAAFLYALDRLFR-EGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQ- 58
Query: 114 LTMKCSRDVKCVDISEQVDVSV-----------QEPLLVERPDIVVATPARALAHLKAKT 162
+ +K D + +V++ V + L PDI++ TP L ++
Sbjct: 59 IPLKGIADERRRRGETEVNLRVGIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRA 118
Query: 163 LDLKSSLEIVIIDEADLV 180
+ +E VIIDE V
Sbjct: 119 RETLRGVETVIIDEVHAV 136
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 33.1 bits (76), Expect = 0.41
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 14/81 (17%)
Query: 40 EPTLIQERAIPLILQ--NKDV----LVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETK 93
+ T Q+R + ILQ DV L++ GSGKT A+ M+ I Q A
Sbjct: 235 KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVA------ 288
Query: 94 ALVLSPSKELCNQLHKNIQEL 114
+++P++ L Q + +++ L
Sbjct: 289 --LMAPTEILAEQHYNSLRNL 307
>gnl|CDD|235564 PRK05691, PRK05691, peptide synthase; Validated.
Length = 4334
Score = 33.2 bits (76), Expect = 0.48
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 482 RIQSHL-ADVPDYIVPPALKKLAR--IEDDGDEDVRAEPITDEEYNKQYEEYKKRSKENE 538
+++HL +PDY+VP L L + +G D RA P D E N+Q Y+ E E
Sbjct: 2654 ALKAHLKQQLPDYMVPAHLILLDSLPLTANGKLDRRALPAPDPELNRQ--AYQAPRSELE 2711
Query: 539 R 539
+
Sbjct: 2712 Q 2712
>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 = 32.0 bits (73), Expect = 0.91
Identities = 28/94 (29%), Positives = 43/94 (45%), Gaps = 9/94 (9%)
Query: 30 LQAIAKLGWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQV 89
+ A+ G P Q RA L + V+V T SGK+ A+ +P+ L A
Sbjct: 26 VAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPV------LSALADD 79
Query: 90 QETKALVLSPSKELCNQLHKNIQELTMKCSRDVK 123
AL L+P+K L + ++ELT+ R V+
Sbjct: 80 PRATALYLAPTKALAADQLRAVRELTL---RGVR 110
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 31.7 bits (72), Expect = 1.2
Identities = 34/161 (21%), Positives = 77/161 (47%), Gaps = 20/161 (12%)
Query: 52 ILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKELCNQLHKNI 111
+L+ K++++ T SGKT I M+ K++ + KA+ L P K L + ++
Sbjct: 36 VLEGKNLVLAIPTASGKTLVAEIVMVNKLLR-------EGGKAVYLVPLKALAEEKYREF 88
Query: 112 QE---LTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPARALAHLKAKTLDLKSS 168
++ L ++ + D +++ + + DI++AT + + L+ + +K
Sbjct: 89 KDWEKLGLRVAMTTGDYDSTDE---------WLGKYDIIIATAEKFDSLLRHGSSWIK-D 138
Query: 169 LEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATL 209
+++V+ DE L+ S+ ++ +L + Q + SAT+
Sbjct: 139 VKLVVADEIHLIGSYDRGATLEMILTHMLGRAQILGLSATV 179
>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 = 31.0 bits (71), Expect = 2.0
Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 3/77 (3%)
Query: 37 GWLEPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALV 96
GW P Q L+ + L+ A TGSGKT A +P + + + L
Sbjct: 11 GW-TPRPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDL--AGPEKPKKGLHTLY 67
Query: 97 LSPSKELCNQLHKNIQE 113
++P + L + +N+Q
Sbjct: 68 ITPLRALAVDIARNLQA 84
>gnl|CDD|147120 pfam04803, Cor1, Cor1/Xlr/Xmr conserved region. Cor1 is a
component of the chromosome core in the meiotic prophase
chromosomes. Xlr is a lymphoid cell specific protein.
Xlm is abundantly transcribed in testis in a
tissue-specific and developmentally regulated manner.
The protein is located in the nuclei of spermatocytes,
early in the prophase of the first meiotic division, and
later becomes concentrated in the XY nuclear subregion
where it is in particular associated with the axes of
sex chromosomes.
Length = 130
Score = 29.3 bits (66), Expect = 2.2
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 7/53 (13%)
Query: 78 QKIINLKQTAQVQETKALVLSPSKELCNQLHKNIQELTMKCSRDVKCVDISEQ 130
QK+ + Q Q K + KEL Q KN++E ++ S D E+
Sbjct: 77 QKLFQQARIVQNQRLKTI-----KELHEQFLKNLEE--LEKSHDNFLQGAQEE 122
>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 = 30.1 bits (68), Expect = 4.1
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 54 QNKDVLVRARTGSGKTGAFAIPMIQKIIN 82
+ +D+LV A GSGKT +I+KI
Sbjct: 13 RGQDILVSASAGSGKTAVLVERIIRKITR 41
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 29.7 bits (66), Expect = 4.5
Identities = 26/83 (31%), Positives = 37/83 (44%), Gaps = 11/83 (13%)
Query: 466 PTDLETLRHDKALYTVRIQSHL-------ADVPDYIVPPALKKLARIEDDGDEDVR--AE 516
PT + T H A + R HL A Y P A KLA+ ++ E + AE
Sbjct: 536 PTVVNTPSH--ASQSARFYKHLDRGYNSCARTDLYFTPLASSKLAKKREEAVEKAKREAE 593
Query: 517 PITDEEYNKQYEEYKKRSKENER 539
EE ++ E+ K+R +E ER
Sbjct: 594 QKAREEREREKEKEKERERERER 616
>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 = 29.7 bits (67), Expect = 4.6
Identities = 81/365 (22%), Positives = 132/365 (36%), Gaps = 92/365 (25%)
Query: 45 QERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKELC 104
QE I +L +DVLV TG GK+ + +P A + + +V+SP L
Sbjct: 18 QEEIISHVLDGRDVLVVMPTGGGKSLCYQVP-----------ALLLKGLTVVISPLISLM 66
Query: 105 NQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPARA-----LAHLK 159
++ + + + EQ D+ ++ L+ ++ P R L L+
Sbjct: 67 KDQVDQLRAAGVAAAYLNSTLSAKEQQDI--EKALVNGELKLLYVAPERLEQDYFLNMLQ 124
Query: 160 AKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLKFLPKLYQAILASATLSEDVLSLKHL 219
+ L V +DEA V +G++ F P+ YQ L
Sbjct: 125 RIPIAL------VAVDEAHCVSQWGHD--------FRPE-YQR-----------LGSLAE 158
Query: 220 ILRNPVILKLEEPAIAPVSQ-LAHYHILAQEDEKAT------ILYTLLK----------- 261
+ L A A Q + LA +E T + ++++K
Sbjct: 159 RFPQVPRIALTATADAETRQDIRELLRLADANEFITSFDRPNLRFSVVKKNNKQKFLLDY 218
Query: 262 LNLVQGKT-IIFVNTVDKCYKLKLYLEQFKISTCVLNSELPAKARCHAVYQFNQGLYD-- 318
L +G++ II+ ++ K +L LE IS ++ L K R F LYD
Sbjct: 219 LKKHRGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDF---LYDDV 275
Query: 319 -VIIASDEKALETPQINSTNNRKRKRDKESGVSRGIDFQFVSNVINFDFPLDIQCYIHRA 377
V++A TN GID V VI++D P +++ Y A
Sbjct: 276 KVMVA-------------TN----------AFGMGIDKPNVRFVIHYDMPGNLESYYQEA 312
Query: 378 GRTAR 382
GR R
Sbjct: 313 GRAGR 317
>gnl|CDD|233398 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
putative. This model represents a family of proteins in
Gram-positive bacteria. The N-terminal region of about
200 amino acids resembles the epsilon subunit of E. coli
DNA polymerase III and the homologous region of the
Gram-positive type DNA polymerase III alpha subunit. The
epsilon subunit contains an exonuclease domain. The
remainder of this protein family resembles a predicted
ATP-dependent helicase, the DNA damage-inducible protein
DinG of E. coli [DNA metabolism, DNA replication,
recombination, and repair].
Length = 850
Score = 29.8 bits (67), Expect = 5.3
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 10/54 (18%)
Query: 55 NKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLS-PSKELCNQL 107
++ L+ A TG+GKT + +P + K +V+S +K L +QL
Sbjct: 264 SEKSLIEAPTGTGKTLGYLLPAL---------YYAITEKPVVISTNTKVLQSQL 308
>gnl|CDD|151320 pfam10871, DUF2748, Protein of unknown function (DUF2748). This is
a bacterial family of proteins with unknown function.
Length = 452
Score = 29.6 bits (66), Expect = 5.3
Identities = 31/114 (27%), Positives = 45/114 (39%), Gaps = 9/114 (7%)
Query: 243 YHIL----AQEDEKATILYTLLKLNLVQ-GKTIIFVNTVDKCYKLKLYLEQFKISTCVLN 297
YHIL A E E I Y L + L++ GK + ++ D C + I+ + N
Sbjct: 5 YHILDKLPAIEHEDMEIEYEHLAMQLIKSGK--LRIDADDCCNFARFSEPALNINIAISN 62
Query: 298 SELPAKARCHAVYQFNQGLYDVIIASDEKALETPQINSTNNRKRKRDKESGVSR 351
EL H Q +Y I D+ + QI N K+K K V +
Sbjct: 63 EELNDPHLIHETKALFQNIYKKIAEDDKVIHKIKQIFD--NLKKKIAKLLAVEK 114
>gnl|CDD|188912 cd09513, SAM_BAR, SAM domain of BAR subfamily. SAM (sterile alpha
motif) domain of BAR (Bifunctional Apoptosis Regulator)
subfamily is a protein-protein interaction domain. In
addition to the SAM domain, this type of regulator has a
RING finger domain. Proteins of this subfamily are
involved in the apoptosis signal network. Their
overexpression in human neuronal cells significantly
protects cells from a broad range of cell death stimuli.
SAM domain can interact with Caspase8, Bcl-2 and Bcl-X
resulting in suppression of Bax-induced cell death.
Length = 71
Score = 27.1 bits (60), Expect = 5.5
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 413 REQDLMNDVNEYLMTNLHEDDFIIKPYQFN 442
RE+ L +VN L+ L E++ P+
Sbjct: 24 RERFLSENVNGRLLLTLTEEELSKPPFNIE 53
>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 = 29.2 bits (66), Expect = 6.2
Identities = 22/75 (29%), Positives = 31/75 (41%), Gaps = 11/75 (14%)
Query: 40 EPTLIQERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSP 99
+P I + L K + TGSGKT A +I AQV LV++
Sbjct: 14 QPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMA-----NVI-----AQVNR-PTLVIAH 62
Query: 100 SKELCNQLHKNIQEL 114
+K L QL+ +E
Sbjct: 63 NKTLAAQLYNEFKEF 77
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 29.3 bits (66), Expect = 6.4
Identities = 22/70 (31%), Positives = 31/70 (44%), Gaps = 15/70 (21%)
Query: 45 QERAIPLILQNKDVLVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSP----S 100
Q+ I +L +D LV TG GK+ + IP A V + LV+SP
Sbjct: 30 QQEIIDAVLSGRDCLVVMPTGGGKSLCYQIP-----------ALVLDGLTLVVSPLISLM 78
Query: 101 KELCNQLHKN 110
K+ +QL N
Sbjct: 79 KDQVDQLLAN 88
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 29.1 bits (66), Expect = 6.6
Identities = 18/44 (40%), Positives = 22/44 (50%), Gaps = 11/44 (25%)
Query: 64 TGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKELCNQL 107
TGSGKT A +I A+VQ LVL+ +K L QL
Sbjct: 41 TGSGKTFTMA-----NVI-----AKVQRP-TLVLAHNKTLAAQL 73
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 29.1 bits (65), Expect = 7.0
Identities = 43/161 (26%), Positives = 65/161 (40%), Gaps = 31/161 (19%)
Query: 40 EPTLIQERAIPLILQNKDVLVRARTGSGKT--GAFAIPMIQKIINLKQTAQVQETKALVL 97
E IQ+ IL+ K + A TG GK+ GAF I + LK K ++
Sbjct: 79 EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAF----IALFLALKG------KKCYII 128
Query: 98 SPSKELCNQLHKNIQELTMKCSRDVKCV----DISEQVDVSVQEPLLVERPDIVVATPAR 153
P+ L Q + I+ K + DV+ V ++ ++ E + DI+V T A+
Sbjct: 129 LPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILV-TTAQ 187
Query: 154 ALAHLKAKTLDLKSSLEIVIIDEADLVFSFGYEDDMKAVLK 194
LA + LK F F + DD+ A LK
Sbjct: 188 FLARNFPEMKHLK--------------FDFIFVDDVDAFLK 214
>gnl|CDD|224160 COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
Length = 423
Score = 28.9 bits (65), Expect = 7.2
Identities = 18/86 (20%), Positives = 39/86 (45%), Gaps = 8/86 (9%)
Query: 126 DISEQVDVSVQEPLLVERPDIVVATPARALAHLKAKTLDLKSSL-EIVIIDE-----ADL 179
D+ E+V++ + P+ + A A L+A+ + +S L E+ + D+ A+L
Sbjct: 220 DLEERVEIIRRRLAFEAVPEAFLEKYADAQRALRARIIAARSLLSEVELDDDAETKIAEL 279
Query: 180 VFSFGYEDDMKAVLKFLPKLYQAILA 205
D +A + + + +A+ A
Sbjct: 280 CARLAV-DGHRADIVVV-RAAKALAA 303
>gnl|CDD|180137 PRK05572, PRK05572, sporulation sigma factor SigF; Validated.
Length = 252
Score = 28.8 bits (65), Expect = 7.3
Identities = 14/59 (23%), Positives = 30/59 (50%), Gaps = 9/59 (15%)
Query: 101 KELCNQLHKNIQELTMKCSRDVKCVDISEQVDVSVQEPLLVERPDIVVATPA-RALAHL 158
KE N++ K+ EL+ + R+ +++E + V+ +E +V+A A R+ +
Sbjct: 114 KETANKIRKDKDELSKELGREPTIEELAEYLGVTPEE--------VVLAQEASRSPQSI 164
>gnl|CDD|220428 pfam09826, Beta_propel, Beta propeller domain. Members of this
family comprise secreted bacterial proteins containing
C-terminal beta-propeller domain distantly related to
WD-40 repeats.
Length = 521
Score = 28.8 bits (65), Expect = 7.7
Identities = 14/43 (32%), Positives = 18/43 (41%)
Query: 439 YQFNLDEVKGFEYRAKDAWRSNYFEDNPTDLETLRHDKALYTV 481
Y F +D GF K + +P L +L D LYTV
Sbjct: 465 YVFRVDPENGFTLVGKITHPDDGEPWSPYVLRSLYIDDTLYTV 507
>gnl|CDD|235267 PRK04266, PRK04266, fibrillarin; Provisional.
Length = 226
Score = 28.3 bits (64), Expect = 9.0
Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 21/66 (31%)
Query: 439 YQFNLDEVKGFEYRAKDAWRS-------NYFEDNPTDLETLRHDKALY-------TVRIQ 484
Y L + +G EYR + RS ++ P + K LY TV
Sbjct: 35 YGERLIKWEGVEYREWNPRRSKLAAAILKGLKNFPIK----KGSKVLYLGAASGTTV--- 87
Query: 485 SHLADV 490
SH++D+
Sbjct: 88 SHVSDI 93
>gnl|CDD|235395 PRK05298, PRK05298, excinuclease ABC subunit B; Provisional.
Length = 652
Score = 28.9 bits (66), Expect = 9.0
Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 11/44 (25%)
Query: 64 TGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKELCNQL 107
TGSGKT F + +I A++Q LVL+ +K L QL
Sbjct: 41 TGSGKT--FTM---ANVI-----ARLQR-PTLVLAHNKTLAAQL 73
>gnl|CDD|180905 PRK07246, PRK07246, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 820
Score = 28.9 bits (65), Expect = 9.2
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 13/60 (21%)
Query: 59 LVRARTGSGKTGAFAIPMIQKIINLKQTAQVQETKALVLSPSKELCNQLHKN----IQEL 114
+ A+TG GKT + +P++ AQ + + +V P+K L +Q+ IQE+
Sbjct: 268 FIEAQTGIGKTYGYLLPLL---------AQSDQRQIIVSVPTKILQDQIMAEEVKAIQEV 318
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.136 0.386
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: 27,713,067
Number of extensions: 2790753
Number of successful extensions: 2788
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2710
Number of HSP's successfully gapped: 85
Length of query: 540
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 438
Effective length of database: 6,413,494
Effective search space: 2809110372
Effective search space used: 2809110372
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)