RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13286
(351 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 = 289 bits (742), Expect = 3e-94
Identities = 110/298 (36%), Positives = 174/298 (58%), Gaps = 6/298 (2%)
Query: 27 TLIIVPTRELALQTSQICIELAKHL-NVKVMVTTGGTNLRDDIMRIYQKVHLIIATPGRI 85
LI+ PTRELA+Q ++ +L K+L ++V V GG ++R I + + V +++ATPGR+
Sbjct: 102 ALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRL 161
Query: 86 LDLMDKQVANMDHCKILVLDEADKLLSQDFKGMLDHVISILPHERQILLYSATFPLTVKN 145
LDL+ + ++ + LVLDEAD++L F ++ ++ LP +RQ LL+SAT P ++
Sbjct: 162 LDLIKRGKLDLSGVETLVLDEADRMLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIRE 221
Query: 146 FMEKHLKDPYEINL---MEELTLKGVTQYYAFV-QERQKVHCLNTLFSKLQINQSIIFCN 201
++L DP EI + E TLK + Q+Y V E +K+ L L + I+F
Sbjct: 222 LARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVR 281
Query: 202 STQRVELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQA 261
+ + VE LA+ + + G+ +H + Q R+R F+ G R LV +D+ RG+D+
Sbjct: 282 TKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPD 341
Query: 262 VNVVINFDFPKMAETYLHRIGRSGRYGHLGIAINLITY-EDRYALHRIEKELGTEIKS 318
V+ VIN+D P E Y+HRIGR+GR G G+AI+ +T E+ L RIEK L ++ S
Sbjct: 342 VSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLPS 399
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 264 bits (677), Expect = 6e-86
Identities = 124/302 (41%), Positives = 188/302 (62%), Gaps = 2/302 (0%)
Query: 21 KITSKATLIIVPTRELALQTSQICIELAKHLNVKVMVTTGGTNLRDDIMRIYQKVHLIIA 80
+ + LI+ PTRELA Q ++ + L +L V+ GGT +RDDI ++ VH+++
Sbjct: 93 DLNACQALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVG 152
Query: 81 TPGRILDLMDKQVANMDHCKILVLDEADKLLSQDFKGMLDHVISILPHERQILLYSATFP 140
TPGR+ D++DK+ +D K+ +LDEAD++LS+ FKG + V LP + Q+ L+SAT P
Sbjct: 153 TPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQIYDVFKKLPPDVQVALFSATMP 212
Query: 141 LTVKNFMEKHLKDPYEINL-MEELTLKGVTQYYAFVQ-ERQKVHCLNTLFSKLQINQSII 198
+ K ++DP I + +ELTL+G+ Q+Y V+ E K L L+ L I Q+II
Sbjct: 213 NEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLCDLYETLTITQAII 272
Query: 199 FCNSTQRVELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGID 258
+CN+ ++V+ L KK+ E + +H M Q R+ + +FRSG R L+ +DL RGID
Sbjct: 273 YCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGID 332
Query: 259 VQAVNVVINFDFPKMAETYLHRIGRSGRYGHLGIAINLITYEDRYALHRIEKELGTEIKS 318
VQ V++VIN+D P E Y+HRIGRSGR+G G+AIN +T +D L IE+ T+I+
Sbjct: 333 VQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIERHYNTQIEE 392
Query: 319 IP 320
+P
Sbjct: 393 MP 394
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 205 bits (524), Expect = 3e-62
Identities = 99/308 (32%), Positives = 167/308 (54%), Gaps = 2/308 (0%)
Query: 14 LNKLTPAKITSKATLIIVPTRELALQTSQICIELAKHL-NVKVMVTTGGTNLRDDIMRIY 72
L KL + +A L++ PTRELA Q ++ LA+ + N+KV+ GG + I +
Sbjct: 63 LQKLDVKRFRVQA-LVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLE 121
Query: 73 QKVHLIIATPGRILDLMDKQVANMDHCKILVLDEADKLLSQDFKGMLDHVISILPHERQI 132
H+I+ TPGRILD + K ++D LVLDEAD++L F+ +D +I P RQ
Sbjct: 122 HGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAPARRQT 181
Query: 133 LLYSATFPLTVKNFMEKHLKDPYEINLMEELTLKGVTQYYAFVQERQKVHCLNTLFSKLQ 192
LL+SAT+P + ++ +DP E+ + L + Q + V +++ L L Q
Sbjct: 182 LLFSATYPEGIAAISQRFQRDPVEVKVESTHDLPAIEQRFYEVSPDERLPALQRLLLHHQ 241
Query: 193 INQSIIFCNSTQRVELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDL 252
++FCN+ + + +A + G+ +H + Q R++V F + C LV +D+
Sbjct: 242 PESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDV 301
Query: 253 FTRGIDVQAVNVVINFDFPKMAETYLHRIGRSGRYGHLGIAINLITYEDRYALHRIEKEL 312
RG+D++A+ VIN++ + E ++HRIGR+GR G G+A++L+ E+ + IE L
Sbjct: 302 AARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAIEDYL 361
Query: 313 GTEIKSIP 320
G ++ P
Sbjct: 362 GRKLNWEP 369
>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 = 189 bits (482), Expect = 4e-59
Identities = 59/146 (40%), Positives = 94/146 (64%), Gaps = 1/146 (0%)
Query: 14 LNKLTPAKITSKA-TLIIVPTRELALQTSQICIELAKHLNVKVMVTTGGTNLRDDIMRIY 72
L KL P+ LI+ PTRELALQ +++ +L KH N+KV+V GGT++ I ++
Sbjct: 58 LEKLDPSPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLK 117
Query: 73 QKVHLIIATPGRILDLMDKQVANMDHCKILVLDEADKLLSQDFKGMLDHVISILPHERQI 132
+ H+++ATPGR+LDL+++ ++ K LVLDEAD++L F+ + ++ +LP +RQ
Sbjct: 118 RGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDRQT 177
Query: 133 LLYSATFPLTVKNFMEKHLKDPYEIN 158
LL+SAT P V++ K L++P I
Sbjct: 178 LLFSATMPKEVRDLARKFLRNPVRIL 203
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 192 bits (489), Expect = 2e-57
Identities = 107/293 (36%), Positives = 170/293 (58%), Gaps = 1/293 (0%)
Query: 28 LIIVPTRELALQTSQICIELAKHLNVKVMVTTGGTNLRDDIMRIYQKVHLIIATPGRILD 87
LI+ PTRELA Q + + +K+LN++ +V GG ++ +M++ V +++ATPGR+LD
Sbjct: 79 LILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLD 138
Query: 88 LMDKQVANMDHCKILVLDEADKLLSQDFKGMLDHVISILPHERQILLYSATFPLTVKNFM 147
L + +D +ILVLDEAD++L F + V++ LP +RQ LL+SATF +K
Sbjct: 139 LEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALA 198
Query: 148 EKHLKDPYEINLMEELTL-KGVTQYYAFVQERQKVHCLNTLFSKLQINQSIIFCNSTQRV 206
EK L +P EI + T + VTQ+ FV +++K L+ + K Q ++F +
Sbjct: 199 EKLLHNPLEIEVARRNTASEQVTQHVHFVDKKRKRELLSQMIGKGNWQQVLVFTRTKHGA 258
Query: 207 ELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVI 266
LA+++ + G IH +Q R R DF+SG R LV +D+ RG+D++ + V+
Sbjct: 259 NHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVV 318
Query: 267 NFDFPKMAETYLHRIGRSGRYGHLGIAINLITYEDRYALHRIEKELGTEIKSI 319
N++ P + E Y+HRIGR+GR G A++L+ ++ L IEK L EI I
Sbjct: 319 NYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDIEKLLKKEIPRI 371
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 179 bits (455), Expect = 1e-51
Identities = 93/286 (32%), Positives = 153/286 (53%), Gaps = 8/286 (2%)
Query: 28 LIIVPTRELALQTSQICIELAKHLNVKVMVTTGGTNLRDDIMRIYQKVHLIIATPGRILD 87
L++ PTRELA Q + C + ++ V GG R I + + V ++IA PGR++D
Sbjct: 207 LVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALRRGVEILIACPGRLID 266
Query: 88 LMDKQVANMDHCKILVLDEADKLLSQDFKGMLDHVISILPHERQILLYSATFPLTVKNFM 147
++ V N+ LVLDEAD++L F+ + ++S + +RQ L++SAT+P V++
Sbjct: 267 FLESNVTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSLA 326
Query: 148 EKHLKD-PYEINLMEELTLKG---VTQYYAFVQERQKVHCLNTLFSKLQINQS--IIFCN 201
K+ P +N+ L L + Q V+E +K L L ++ + +IF
Sbjct: 327 RDLCKEEPVHVNV-GSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVE 385
Query: 202 STQRVELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQA 261
+ + + L K++ G+ IH Q R V ++F++G ++ +D+ +RG+DV+
Sbjct: 386 TKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKD 445
Query: 262 VNVVINFDFPKMAETYLHRIGRSGRYGHLGIAINLITYEDRYALHR 307
V VINFDFP E Y+HRIGR+GR G G + +T D+Y L R
Sbjct: 446 VKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLT-PDKYRLAR 490
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 175 bits (447), Expect = 2e-51
Identities = 108/315 (34%), Positives = 167/315 (53%), Gaps = 16/315 (5%)
Query: 16 KLTPAKITSKATLIIVPTRELALQTSQICIELAKHLNVKVMVTTGGTNLRDDIMRIYQKV 75
K P +I LI+ PTRELA+Q + ELAKH ++ + TGG + +
Sbjct: 70 KSGPPRI-----LILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSENQ 124
Query: 76 HLIIATPGRILDLMDKQVANMDHCKILVLDEADKLLSQDFKGMLDHVISILPHERQILLY 135
+++ATPGR+L + ++ + + L+LDEAD++L F ++ + + +Q LL+
Sbjct: 125 DIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIETIAAETRWRKQTLLF 184
Query: 136 SATFP-LTVKNFMEKHLKDPYEIN----LMEELTLKGVTQYYAFVQERQ-KVHCLNTLFS 189
SAT V++F E+ L DP E+ E K + Q+Y + + K L L
Sbjct: 185 SATLEGDAVQDFAERLLNDPVEVEAEPSRRER---KKIHQWYYRADDLEHKTALLCHLLK 241
Query: 190 KLQINQSIIFCNSTQRVELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVC 249
+ ++ +SI+F + +RV LA + + G C Y+ M QA RN G LV
Sbjct: 242 QPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVA 301
Query: 250 SDLFTRGIDVQAVNVVINFDFPKMAETYLHRIGRSGRYGHLGIAINLITYEDRYALHRIE 309
+D+ RGID+ V+ VINFD P+ A+TYLHRIGR+GR G G AI+L+ D L +IE
Sbjct: 302 TDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLLGKIE 361
Query: 310 KELGTEIKSIPKVID 324
+ + +K +VID
Sbjct: 362 RYIEEPLK--ARVID 374
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 171 bits (435), Expect = 3e-49
Identities = 92/294 (31%), Positives = 152/294 (51%), Gaps = 4/294 (1%)
Query: 28 LIIVPTRELALQTSQICIELAKHLNVKVMVTTGGTNLRDDIMRIYQK-VHLIIATPGRIL 86
LII PTREL +Q ++ L K+ + VM GG + + ++ + +++ATPGR+L
Sbjct: 166 LIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLL 225
Query: 87 DLMDKQVANMDHCKILVLDEADKLLSQDFKGMLDHVISILPH--ERQILLYSATFPLTVK 144
D + ++D +++VLDEAD++L F + +I P ERQ LL+SATF V
Sbjct: 226 DFNQRGEVHLDMVEVMVLDEADRMLDMGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVM 285
Query: 145 NFMEKHLKDPYEINL-MEELTLKGVTQYYAFVQERQKVHCLNTLFSKLQINQSIIFCNST 203
N ++ DP + + E + V Q+ V K L L ++ + ++F N
Sbjct: 286 NLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAGSDKYKLLYNLVTQNPWERVMVFANRK 345
Query: 204 QRVELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVN 263
V + +++ + G + + Q R + FR G R LV +D+ RGI + ++
Sbjct: 346 DEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGIS 405
Query: 264 VVINFDFPKMAETYLHRIGRSGRYGHLGIAINLITYEDRYALHRIEKELGTEIK 317
VINF P+ + Y+HRIGR+GR G G++I+ +D + L IE+ LG +I
Sbjct: 406 HVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPEIEELLGRKIS 459
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 158 bits (400), Expect = 2e-43
Identities = 90/311 (28%), Positives = 164/311 (52%), Gaps = 6/311 (1%)
Query: 14 LNKLTPAKITSKATLIIVPTRELALQTSQICIELAKHLN-VKVMVTTGGTNLRDDIMRIY 72
L+ L P ++ + L++ PTRELA+Q ++ + +KH+ V V+ GG + +
Sbjct: 65 LHNLDP-ELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALR 123
Query: 73 QKVHLIIATPGRILDLMDKQVANMDHCKILVLDEADKLLSQDFKGMLDHVISILPHERQI 132
Q +++ TPGR+LD + + ++ LVLDEAD++L F ++ +++ +P Q
Sbjct: 124 QGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGHQT 183
Query: 133 LLYSATFPLTVKNFMEKHLKDPYEINLMEELTLK-GVTQYYAFVQERQKVHCLNTLFSKL 191
L+SAT P ++ + +K+P E+ + +T + ++Q Y V +K L
Sbjct: 184 ALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMRKNEALVRFLEAE 243
Query: 192 QINQSIIFCNSTQRVELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSD 251
+ +IIF + +A+ + GY ++ M QA R + + G L+ +D
Sbjct: 244 DFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATD 303
Query: 252 LFTRGIDVQAVNVVINFDFPKMAETYLHRIGRSGRYGHLGIAINLITYEDRYALHRIEKE 311
+ RG+DV+ +++V+N+D P +E+Y+HRIGR+GR G G A+ + +R L IE+
Sbjct: 304 VAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNIER- 362
Query: 312 LGTEIKSIPKV 322
T +IP+V
Sbjct: 363 --TMKLTIPEV 371
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 148 bits (376), Expect = 2e-40
Identities = 99/329 (30%), Positives = 165/329 (50%), Gaps = 9/329 (2%)
Query: 28 LIIVPTRELALQTSQICIELAKHLNVKVMVTTGGTNLRDDIMRIYQKVHLIIATPGRILD 87
LI+ PTRELA+Q + ++ L ++ + GG + + Q V +IIATPGR++D
Sbjct: 88 LILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLID 147
Query: 88 LMDK-QVANMDHCKILVLDEADKLLSQDFKGMLDHVISILPHE--RQILLYSATFPLTVK 144
+ + +V ++ C+I VLDEAD++ F + ++ +P RQ LL+SAT V
Sbjct: 148 YVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVL 207
Query: 145 NFMEKHLKDPYEINL-MEELTLKGVTQYYAFVQERQKVHCLNTLFSKLQINQSIIFCNST 203
+H+ +P ++ + E +T V Q F + +K L L S+ + ++++F N+
Sbjct: 208 ELAYEHMNEPEKLVVETETITAARVRQRIYFPADEEKQTLLLGLLSRSEGARTMVFVNTK 267
Query: 204 QRVELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVN 263
VE +A+ + GY + + Q R + + F+ G LV +D+ RG+ + V
Sbjct: 268 AFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVK 327
Query: 264 VVINFDFPKMAETYLHRIGRSGRYGHLGIAINLITYEDRYA--LHRIEKELGTEIKSIPK 321
V N+D P AE Y+HRIGR+ R G G AI+ +RYA L IE + +I P
Sbjct: 328 YVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFAC--ERYAMSLPDIEAYIEQKIPVEPV 385
Query: 322 VIDPALYVARPEDMDRDNSTGASEENNVS 350
+ + RP + + A +E S
Sbjct: 386 TAELLTPLPRPPRVPVE-GEEADDEAGDS 413
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 146 bits (371), Expect = 7e-40
Identities = 100/321 (31%), Positives = 153/321 (47%), Gaps = 19/321 (5%)
Query: 28 LIIVPTRELALQTSQICIELAKHLNVKVMVTTGGTNLRDDIMRIYQKVHLIIATPGRILD 87
+++ PTREL +Q L K L K + GG + + RI Q V LI+ TPGR++D
Sbjct: 200 MVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLID 259
Query: 88 LMDKQVANMDHCKILVLDEADKLLSQDFKGMLDHVISILPHERQILLYSATFPLTVKNFM 147
L+ K +D+ +LVLDE D +L + F+ + + L + Q+LL+SAT V+ F
Sbjct: 260 LLSKHDIELDNVSVLVLDEVDCMLERGFRDQVMQIFQALS-QPQVLLFSATVSPEVEKFA 318
Query: 148 EKHLKDPYEINL-MEELTLKGVTQYYAFVQERQKVHCLNTLFSKLQINQ-----SIIFCN 201
KD I++ K V Q +V+ +QK LF L+ Q +++F +
Sbjct: 319 SSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQ---KLFDILKSKQHFKPPAVVFVS 375
Query: 202 STQRVELLAKKITEL-GYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQ 260
S +LLA IT + G IH + R V F G +V + + RG+D+
Sbjct: 376 SRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLL 435
Query: 261 AVNVVINFDFPKMAETYLHRIGRSGRYGHLGIAINLITYEDRYALHRIEKELGTEIKS-- 318
V VI FD P + Y+H+IGR+ R G G AI + EDR + EL +KS
Sbjct: 436 RVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDR----NLFPELVALLKSSG 491
Query: 319 --IPKVIDPALYVARPEDMDR 337
IP+ + + Y+ +
Sbjct: 492 AAIPRELANSRYLGSGRKRKK 512
>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 = 123 bits (311), Expect = 1e-34
Identities = 49/131 (37%), Positives = 70/131 (53%), Gaps = 3/131 (2%)
Query: 168 VTQYYAFVQERQKVHCLNTLFSKLQIN--QSIIFCNSTQRVELLAKKITELGYCCYYIHA 225
+ QY V E +K+ L L + + +IFC S + ++ LA+ + + G +H
Sbjct: 2 IKQYVLPV-EDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHG 60
Query: 226 RMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVINFDFPKMAETYLHRIGRSG 285
+Q R V DFR G LV +D+ RGID+ V+VVIN+D P +YL RIGR+G
Sbjct: 61 DGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAG 120
Query: 286 RYGHLGIAINL 296
R G G AI L
Sbjct: 121 RAGQKGTAILL 131
>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 = 119 bits (300), Expect = 1e-32
Identities = 53/135 (39%), Positives = 84/135 (62%), Gaps = 3/135 (2%)
Query: 14 LNKLTPAKITSKATLIIVPTRELALQTSQICIELAKHLNVKVMVTTGGTNLRDDIMRIYQ 73
L L P K +A L++ PTRELA Q + +L K L ++V + TGGT+L++ ++ +
Sbjct: 36 LQALLPKKGGPQA-LVLAPTRELAEQIYEELKKLFKILGLRVALLTGGTSLKEQARKLKK 94
Query: 74 -KVHLIIATPGRILDLMDKQVANM-DHCKILVLDEADKLLSQDFKGMLDHVISILPHERQ 131
K +++ TPGR+LDL+ + + + K+LVLDEA +LL F L+ ++S LP +RQ
Sbjct: 95 GKADILVGTPGRLLDLLRRGKLKLLKNLKLLVLDEAHRLLDMGFGDDLEEILSRLPPDRQ 154
Query: 132 ILLYSATFPLTVKNF 146
ILL SAT P +++
Sbjct: 155 ILLLSATLPRNLEDL 169
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 120 bits (303), Expect = 1e-30
Identities = 89/302 (29%), Positives = 148/302 (49%), Gaps = 18/302 (5%)
Query: 28 LIIVPTRELALQTSQICIELAKHLNVKVMVTTGGTNLRDDIMRIYQKVHLIIATPGRILD 87
LI+ PTRELA+Q LA+ +K+ + GG + + V ++I T GR++D
Sbjct: 87 LIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLID 146
Query: 88 LMDKQVANMDHCKILVLDEADKLLS----QD----FKGMLDHVISILPHERQILLYSATF 139
+ N+ +++VLDEAD++ +D F+ M ++R +L+SAT
Sbjct: 147 YAKQNHINLGAIQVVVLDEADRMFDLGFIKDIRWLFRRMPP------ANQRLNMLFSATL 200
Query: 140 PLTVKNFMEKHLKDPYEINLM-EELTLKGVTQYYAFVQERQKVHCLNTLFSKLQINQSII 198
V+ +H+ +P + + E+ T + + + +K+ L TL + +++II
Sbjct: 201 SYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYPSNEEKMRLLQTLIEEEWPDRAII 260
Query: 199 FCNSTQRVELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGID 258
F N+ R E + + G+ + +AQ R R+ +F G LV +D+ RG+
Sbjct: 261 FANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLH 320
Query: 259 VQAVNVVINFDFPKMAETYLHRIGRSGRYGHLGIAINLITYEDRYALHRIEKELGTEIKS 318
+ AV V N+D P E Y+HRIGR+GR G G +I+L E L IE +G S
Sbjct: 321 IPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACEEYALNLPAIETYIG---HS 377
Query: 319 IP 320
IP
Sbjct: 378 IP 379
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 115 bits (289), Expect = 1e-30
Identities = 48/146 (32%), Positives = 86/146 (58%), Gaps = 2/146 (1%)
Query: 27 TLIIVPTRELALQTSQICIELAKHLNVKVMVTTGGTNLRDDIMRIYQKV-HLIIATPGRI 85
L++VPTRELA Q ++ +L L +KV+ GG + R+ + ++ +++ TPGR+
Sbjct: 57 VLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRL 116
Query: 86 LDLMDKQVANMDHCKILVLDEADKLLSQDFKGMLDHVISILPHERQILLYSATFPLTVKN 145
LDL++ ++ + +++LDEA +LL F L+ ++ +LP Q+LL SAT P ++N
Sbjct: 117 LDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIEN 176
Query: 146 FMEKHLKDPYEINLMEELTLKGVTQY 171
+E L DP I++ L+ + Q+
Sbjct: 177 LLELFLNDPVFIDV-GFTPLEPIEQF 201
>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 = 95.7 bits (239), Expect = 7e-25
Identities = 31/78 (39%), Positives = 47/78 (60%)
Query: 211 KKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVINFDF 270
K + + G +H ++Q R + DFR+G + LV +D+ RGID+ VN+VIN+D
Sbjct: 1 KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60
Query: 271 PKMAETYLHRIGRSGRYG 288
P +Y+ RIGR+GR G
Sbjct: 61 PWNPASYIQRIGRAGRAG 78
>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 = 96.3 bits (240), Expect = 3e-24
Identities = 40/113 (35%), Positives = 67/113 (59%), Gaps = 1/113 (0%)
Query: 27 TLIIVPTRELALQTSQICIELAKHLNVKVMVTTGGTNLRDDIMRIYQKVHLIIATPGRIL 86
L++ PTRELA Q ++ EL +KV GGT+++ + K +++ TPGR+L
Sbjct: 33 VLVLAPTRELANQVAERLKELFGE-GIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLL 91
Query: 87 DLMDKQVANMDHCKILVLDEADKLLSQDFKGMLDHVISILPHERQILLYSATF 139
D +++ ++ +L+LDEA +LL+Q F + ++ LP +RQ+LL SAT
Sbjct: 92 DELERLKLSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP 144
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 93.8 bits (234), Expect = 5e-24
Identities = 30/82 (36%), Positives = 48/82 (58%)
Query: 207 ELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVI 266
E LA+ + ELG +H ++Q R + F +G + LV +D+ RG+D+ V++VI
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60
Query: 267 NFDFPKMAETYLHRIGRSGRYG 288
+D P +Y+ RIGR+GR G
Sbjct: 61 IYDLPWSPASYIQRIGRAGRAG 82
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 67.7 bits (166), Expect = 2e-12
Identities = 40/121 (33%), Positives = 62/121 (51%), Gaps = 1/121 (0%)
Query: 196 SIIFCNSTQRVELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTR 255
II+C + ++VE LA+ + + G HA ++ R RV F + + +V ++ F
Sbjct: 233 GIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGM 292
Query: 256 GIDVQAVNVVINFDFPKMAETYLHRIGRSGRYGHLGIAINLITYED-RYALHRIEKELGT 314
GID V VI++D P E+Y GR+GR G AI L + ED R+ + IE+
Sbjct: 293 GIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQRYLIEQSKPD 352
Query: 315 E 315
E
Sbjct: 353 E 353
>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 = 65.2 bits (159), Expect = 1e-11
Identities = 75/323 (23%), Positives = 121/323 (37%), Gaps = 60/323 (18%)
Query: 19 PAKITSKATLIIVPTREL------ALQTSQI---CIELAKHLNVKVMVTTGGTNLRDDIM 69
PA + TL+I P L L+ S I + ++ + V T L+D +
Sbjct: 46 PALCSDGITLVISPLISLMEDQVLQLKASGIPATFLNSSQSKEQQKNVLTD---LKDGKI 102
Query: 70 RIYQKVHLIIATPGRI---LDLMDKQVANMDHCKILVLDEADKLLSQ---DFK------G 117
+ L+ TP + L+ I V DEA +SQ DF+ G
Sbjct: 103 K------LLYVTPEKCSASNRLLQTLEERKGITLIAV-DEA-HCISQWGHDFRPDYKALG 154
Query: 118 MLDHVISILPHERQILLYSATFPLTVKNFMEKHL--KDPYEI-------NL---MEELTL 165
L +P I+ +AT +V+ + + L K+P NL + T
Sbjct: 155 SLKQKFPNVP----IMALTATASPSVREDILRQLNLKNPQIFCTSFDRPNLYYEVRRKTP 210
Query: 166 KGVTQYYAFVQERQKVHCLNTLFSKLQINQSIIFCNSTQRVELLAKKITELGYCCYYIHA 225
K + F+++ K II+C S ++ E + + LG HA
Sbjct: 211 KILEDLLRFIRKEFKG------------KSGIIYCPSRKKSEQVTASLQNLGIAAGAYHA 258
Query: 226 RMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVINFDFPKMAETYLHRIGRSG 285
+ + R+ V H F+ + +V + F GI+ V VI++ PK E+Y GR+G
Sbjct: 259 GLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAG 318
Query: 286 RYGHLGIAINLITYEDRYALHRI 308
R G D L R+
Sbjct: 319 RDGLPSECHLFYAPADINRLRRL 341
>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 = 59.3 bits (144), Expect = 1e-09
Identities = 55/210 (26%), Positives = 87/210 (41%), Gaps = 30/210 (14%)
Query: 96 MDHCKI--LVLDEADKLLSQ---DFK---GMLDHVISILPHERQILLYSATFPLTVKNFM 147
+ I + +DEA +SQ DF+ L + P +I L + T ++
Sbjct: 123 LQRIPIALVAVDEA-HCVSQWGHDFRPEYQRLGSLAERFPQVPRIALTATADAETRQDIR 181
Query: 148 EK-HLKDPYEI-------NLMEELTLKGVTQYYAFVQERQKVHCLNTLFSKLQINQS-II 198
E L D E NL ++ V++ K L + K QS II
Sbjct: 182 ELLRLADANEFITSFDRPNL-----------RFSVVKKNNKQKFL-LDYLKKHRGQSGII 229
Query: 199 FCNSTQRVELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGID 258
+ +S ++VE LA+++ G HA ++ R DF + +V ++ F GID
Sbjct: 230 YASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGID 289
Query: 259 VQAVNVVINFDFPKMAETYLHRIGRSGRYG 288
V VI++D P E+Y GR+GR G
Sbjct: 290 KPNVRFVIHYDMPGNLESYYQEAGRAGRDG 319
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 58.6 bits (142), Expect = 2e-09
Identities = 64/256 (25%), Positives = 102/256 (39%), Gaps = 51/256 (19%)
Query: 62 TNLRDDIMRIYQKVH-----LIIATPGRILDLMDKQVANMDHCK--ILVLDEADKLLSQ- 113
T R+ + + L+ P R++ MD + ++ H +L +DEA +SQ
Sbjct: 98 TQTREQQLEVMAGCRTGQIKLLYIAPERLM--MDNFLEHLAHWNPALLAVDEA-HCISQW 154
Query: 114 --DFK------GMLDHVISILPHERQILLYSATFPLTVKNFMEK--HLKDPYE------- 156
DF+ G L LP + +AT T + + + L DP
Sbjct: 155 GHDFRPEYAALGQLRQRFPTLP----FMALTATADDTTRQDIVRLLGLNDPLIQISSFDR 210
Query: 157 ----INLMEELTLKGVTQYYAFVQERQKVHCLNTLFSKLQINQSIIFCNSTQRVELLAKK 212
L+E+ K + Q +VQE Q+ II+CNS +VE A +
Sbjct: 211 PNIRYTLVEKF--KPLDQLMRYVQE-QRGKS------------GIIYCNSRAKVEDTAAR 255
Query: 213 ITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVINFDFPK 272
+ G HA + R V F+ + +V + F GI+ V V++FD P+
Sbjct: 256 LQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPR 315
Query: 273 MAETYLHRIGRSGRYG 288
E+Y GR+GR G
Sbjct: 316 NIESYYQETGRAGRDG 331
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 53.4 bits (129), Expect = 1e-07
Identities = 26/95 (27%), Positives = 46/95 (48%), Gaps = 1/95 (1%)
Query: 196 SIIFCNSTQRVELLAKKITELGYCCYYIH-ARMAQAHRNRVFHDFRSGLCRNLVCSDLFT 254
++IF N+ E LA ++ +LG +H +++ R V + G + +V +
Sbjct: 256 TLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLE 315
Query: 255 RGIDVQAVNVVINFDFPKMAETYLHRIGRSGRYGH 289
GID+ +++VI PK +L RIGR+G
Sbjct: 316 LGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGHRLG 350
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 49.4 bits (118), Expect = 2e-06
Identities = 55/312 (17%), Positives = 106/312 (33%), Gaps = 63/312 (20%)
Query: 20 AKITSKATLIIVPTRELALQTSQICIELAKHLNVKVMVTTGGTNLRDDIMRIYQKVHLII 79
++TL++VPT+EL Q ++ L K L + + G ++ + + +
Sbjct: 76 IAELKRSTLVLVPTKELLDQWAE---ALKKFLLLNDEIGIYGGGEKE-----LEPAKVTV 127
Query: 80 AT--PGRILDLMDKQVANMDHCKILVLDEADKLLSQDFKGMLDHVISILPHERQILLYSA 137
AT L+D+ + N +++ DE L + ++ +L+ L L +A
Sbjct: 128 ATVQTLARRQLLDEFLGN--EFGLIIFDEVHHLPAPSYRRILEL----LSAAYPRLGLTA 181
Query: 138 TFPLTVKNFMEKHL----KDPYEINLME-----------------ELTLKGVTQYY---- 172
T + YE++L E LT +Y
Sbjct: 182 TPEREDGGRIGDLFDLIGPIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKESA 241
Query: 173 ---------------------AFVQERQKVHCLNTLFSKLQINQSIIFCNSTQRVELLAK 211
A ER+ L + ++++IF + + +AK
Sbjct: 242 RFRELLRARGTLRAENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAK 301
Query: 212 KITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVINFDFP 271
G I + R + FR+G + LV + G+D+ +V+I
Sbjct: 302 LFLAPGIVEA-ITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPT 360
Query: 272 KMAETYLHRIGR 283
++ R+GR
Sbjct: 361 GSRRLFIQRLGR 372
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 43.3 bits (102), Expect = 1e-04
Identities = 78/354 (22%), Positives = 134/354 (37%), Gaps = 90/354 (25%)
Query: 27 TLIIVPTRELALQTSQICIELAKHLNVKVMVTTGGTNLRDDIMRIYQKVHLIIATPGRIL 86
+ +VP + LA + + + K L ++V +TTG + D+ + Y +IIAT +
Sbjct: 71 AVYLVPLKALAEEKYREFKDWEK-LGLRVAMTTGDYDSTDEWLGKYD---IIIATAEKFD 126
Query: 87 DLMDKQVANMDHCKILVLDEADKLLSQDFKGMLDHVISILPHERQILLYSATFPLTVKNF 146
L+ + + K++V DE + S D L+ +++ + QIL SAT
Sbjct: 127 SLLRHGSSWIKDVKLVVADEIHLIGSYDRGATLEMILTHMLGRAQILGLSAT-------- 178
Query: 147 MEKHLKDPYEINLMEELTLKGVTQYYAFVQERQKVHCLNTLF-------------SKLQI 193
+ + E L E L + V + V+ R+ V LF L
Sbjct: 179 ----VGNAEE--LAEWLNAELVVSDWRPVKLRKGVFYQGFLFWEDGKIERFPNSWESLVY 232
Query: 194 N------QSIIFCNSTQRVE----LLAKKITEL--------------------------- 216
+ +++F N+ + E LAKKI
Sbjct: 233 DAVKKGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKK 292
Query: 217 ---GYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVINFDFPKM 273
G ++ HA + + R + FR GL + + + + GI++ A V+I D +
Sbjct: 293 ALRGGVAFH-HAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIR-DTKRY 350
Query: 274 AETYLHRI---------GRSGR--YGHLGIAINLITYED------RYALHRIEK 310
+ I GR+GR Y +G AI + T E+ RY + EK
Sbjct: 351 SNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEEPSKLMERYIFGKPEK 404
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 42.6 bits (100), Expect = 3e-04
Identities = 33/106 (31%), Positives = 50/106 (47%), Gaps = 2/106 (1%)
Query: 197 IIFCNSTQRVELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDL-FTR 255
II+C S E +A+++ E G+ + H M A R V + S N++C+ + F
Sbjct: 684 IIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQW-SKDEINIICATVAFGM 742
Query: 256 GIDVQAVNVVINFDFPKMAETYLHRIGRSGRYGHLGIAINLITYED 301
GI+ V VI+ PK E Y GR+GR G + +Y D
Sbjct: 743 GINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSD 788
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 41.7 bits (98), Expect = 5e-04
Identities = 26/101 (25%), Positives = 41/101 (40%), Gaps = 8/101 (7%)
Query: 195 QSIIFCNSTQRVELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFT 254
Q+I+F S +R LA +T G HA + R V F + +V +
Sbjct: 442 QTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALA 501
Query: 255 RGIDVQAVNVVINFDFPKMAETYL------HRIGRSGRYGH 289
G+D A V+ F+ M +L +GR+GR +
Sbjct: 502 AGVDFPASQVI--FESLAMGIEWLSVREFQQMLGRAGRPDY 540
>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 = 40.2 bits (95), Expect = 0.001
Identities = 23/69 (33%), Positives = 31/69 (44%), Gaps = 7/69 (10%)
Query: 224 HARMAQAHRNRVFHDFRSGLCRNLVCS---DLFTRGIDVQAVNVVINFDFPKMAETYLHR 280
H + + R V +G R +VC+ DL G+D V++VI PK L R
Sbjct: 282 HGSLDREQRRWVEAAMAAGRLRAVVCTSSLDL---GVDFGPVDLVIQIGSPKGVARLLQR 338
Query: 281 IGRSG-RYG 288
GRS R G
Sbjct: 339 AGRSNHRPG 347
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 40.4 bits (95), Expect = 0.001
Identities = 42/202 (20%), Positives = 85/202 (42%), Gaps = 28/202 (13%)
Query: 30 IVPTRELALQTSQICIELAKH--LNVKVMVTTGGTNLRDDIMRIYQKVHLIIATPGRILD 87
IVP + LA + E ++ L ++V ++TG +L D+ + Y +I+ TP ++
Sbjct: 82 IVPLKALA---EEKYEEFSRLEELGIRVGISTGDYDLDDERLARYD---VIVTTPEKLDS 135
Query: 88 LMDKQVANMDHCKILVLDEADKLLSQDFKGMLDHVISILPHER---QILLYSATFPLTVK 144
L K+ + ++ ++V+DE L + +L+ +++ + +I+ SAT P
Sbjct: 136 LTRKRPSWIEEVDLVVIDEIHLLGDRTRGPVLESIVARMRRLNELIRIVGLSATLP---- 191
Query: 145 NFME--KHLK-DPYEIN-----LMEELTLKGVTQYYAFVQERQKVHCLNTLFSKLQIN-- 194
N E L E + L + G ++ + N + +
Sbjct: 192 NAEEVADWLNAKLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNLALELVLESLA 251
Query: 195 ---QSIIFCNSTQRVELLAKKI 213
Q ++F +S + E AKK+
Sbjct: 252 EGGQVLVFVHSRKEAEKTAKKL 273
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 40.0 bits (94), Expect = 0.001
Identities = 25/113 (22%), Positives = 45/113 (39%), Gaps = 19/113 (16%)
Query: 188 FSKLQINQSIIFCNSTQRVELLAKKITELGYCCYYIHAR--------------MAQAHRN 233
K ++ I+F E + + ++G I AR M+Q +
Sbjct: 361 LEKNGDSRVIVFTEYRDTAEEIVNFLKKIG-----IKARVRFIGQASREGDKGMSQKEQK 415
Query: 234 RVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVINFDFPKMAETYLHRIGRSGR 286
+ FR G LV + + G+D+ V++VI ++ + R GR+GR
Sbjct: 416 EIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGR 468
Score = 30.0 bits (68), Expect = 2.2
Identities = 18/83 (21%), Positives = 39/83 (46%), Gaps = 1/83 (1%)
Query: 25 KATLIIVPTRELALQTSQICIELAKHLNVKVMVTTGGTNLRDDIMRIYQKVHLIIATPGR 84
L + PT+ L LQ ++ C ++ ++ TG ++ ++ K + +ATP
Sbjct: 59 GKVLFLAPTKPLVLQHAEFCRKVTGIPEDEIAALTGEVR-PEEREELWAKKKVFVATPQV 117
Query: 85 ILDLMDKQVANMDHCKILVLDEA 107
+ + + ++D +L+ DEA
Sbjct: 118 VENDLKAGRIDLDDVSLLIFDEA 140
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 38.8 bits (90), Expect = 0.005
Identities = 20/62 (32%), Positives = 31/62 (50%)
Query: 224 HARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVINFDFPKMAETYLHRIGR 283
H +++ R +SG R +V + GID+ AV++VI P + L RIGR
Sbjct: 308 HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGR 367
Query: 284 SG 285
+G
Sbjct: 368 AG 369
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 38.2 bits (89), Expect = 0.006
Identities = 45/252 (17%), Positives = 91/252 (36%), Gaps = 44/252 (17%)
Query: 101 ILVLDEADKLLSQDFKGMLDHVISILPHERQ------ILLYSATFPLTVKNFMEKHLKDP 154
+++LDE + ML ++++L E +LL SAT P +K ++K L
Sbjct: 341 LVILDEVHLY---ADETMLAALLALL--EALAEAGVPVLLMSATLPPFLKEKLKKALGKG 395
Query: 155 YEINLMEELTLK----GVTQYYAFVQERQKVHCLNTLFSKLQINQSI---IFCNSTQRVE 207
E+ + K G+ + V ++ + + N+ R
Sbjct: 396 REVVENAKFCPKEDEPGLKRKE-RVDVEDGPQEELIELISEEVKEGKKVLVIVNTVDRAI 454
Query: 208 LLAKKITELGYCCYYIHARMAQAHR----NRVFHDFRSGLCRNLVCSDLFTRGIDVQAVN 263
L +K+ E G +H+R R + F+ +V + Q +
Sbjct: 455 ELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVAT---------QVIE 505
Query: 264 VVINFDFPKM------AETYLHRIGRSGRYGHLG----IAINLITYE--DRYALHRIEKE 311
++ DF + ++ + R GR R+G N +Y+ ++EK+
Sbjct: 506 AGVDIDFDVLITELAPIDSLIQRAGRVNRHGKKENGKIYVYNDEERGPYLKYSYEKLEKK 565
Query: 312 LGTEIKSIPKVI 323
L + + ++I
Sbjct: 566 LKSLEELPLEII 577
>gnl|CDD|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3. CRISPR
(Clustered Regularly Interspaced Short Palindromic
Repeats) and associated Cas proteins comprise a system
for heritable host defense by prokaryotic cells against
phage and other foreign DNA; DEAD/DEAH box helicase DNA
helicase cas3'; Often but not always is fused to HD
nuclease domain; signature gene for Type I.
Length = 353
Score = 37.4 bits (87), Expect = 0.008
Identities = 35/209 (16%), Positives = 69/209 (33%), Gaps = 41/209 (19%)
Query: 102 LVLDEADKLLSQDFKGMLDHVISILPHERQ-ILLYSATFPLTVKNFMEKHLKDPYEINLM 160
L+ DE + ++ V+ +L ILL SAT P +K + EK E N
Sbjct: 127 LIFDEVH-FYDEYTLALILAVLEVLKDNDVPILLMSATLPKFLKEYAEKI--GYVEENEP 183
Query: 161 EELTLKGVTQYYAFVQERQKVHCLNTLFSKLQI-----------NQSIIFCNSTQRVELL 209
+ + + + ++ I N+ R +
Sbjct: 184 LD---------LKPNERAPFIKIESDKVGEISSLERLLEFIKKGGSVAIIVNTVDRAQEF 234
Query: 210 AKKITELGYCCYY--IHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDV--QAVNVV 265
+++ E G IH+R + R + + ++ + + V Q +
Sbjct: 235 YQQLKEKGPEEEIMLIHSRFTEKDRAKKEAELLLEFKKS-------EKFVIVATQVIEAS 287
Query: 266 INFDFPKM------AETYLHRIGRSGRYG 288
++ M ++ + R+GR RYG
Sbjct: 288 LDISVDVMITELAPIDSLIQRLGRLHRYG 316
>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 = 37.7 bits (88), Expect = 0.009
Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 6/87 (6%)
Query: 207 ELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVI 266
L + + E H +M + V +F G + LVC+ + GID+ N +I
Sbjct: 678 TQLRELVPEARIA--IAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTII 735
Query: 267 NFDFPKMAETYLH----RIGRSGRYGH 289
K L+ R+GRS + +
Sbjct: 736 IERADKFGLAQLYQLRGRVGRSKKKAY 762
>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 = 37.0 bits (86), Expect = 0.010
Identities = 39/205 (19%), Positives = 76/205 (37%), Gaps = 30/205 (14%)
Query: 102 LVLDEADKLLSQDFKGMLDHVISILPHERQ-ILLYSATFPLTVKNFMEKHLKDPYEINLM 160
L+ DE + ++ V+ +L ILL SAT P +K + EK E N
Sbjct: 128 LIFDEVH-FYDEYTLALILAVLEVLKDNDVPILLMSATLPKFLKEYAEKI--GYVEFNEP 184
Query: 161 EELT-LKGVTQYYAFVQERQKVHCLNTLFSKLQI----NQSIIFCNSTQRVELLAKKITE 215
+L + ++ E KV +++L L+ + I N+ R + +++ E
Sbjct: 185 LDLKEERRFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAIIVNTVDRAQEFYQQLKE 244
Query: 216 LG--YCCYYIHARMAQAHR----NRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVINFD 269
+H+R + R + + + +V + Q + ++
Sbjct: 245 NAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVAT---------QVIEASLDIS 295
Query: 270 FPKM------AETYLHRIGRSGRYG 288
M ++ + R+GR RYG
Sbjct: 296 ADVMITELAPIDSLIQRLGRLHRYG 320
>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 = 36.2 bits (84), Expect = 0.026
Identities = 24/111 (21%), Positives = 45/111 (40%), Gaps = 10/111 (9%)
Query: 232 RNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVINFDFPKMAETYLHRIGRSGRYGHLG 291
R + R G + ++ G+D+ ++ V+ FP + + GR+GR G
Sbjct: 318 RRELERALRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGA 377
Query: 292 IAINLITYE---DRYALHRIEKELGTEIKSI------PKVIDPALYVARPE 333
+ + L+ + D Y +H E +++ P V+ P L A E
Sbjct: 378 LVV-LVARDDPLDTYLVHHPEALFDRPVEATVFDPDNPYVLGPHLCCAAAE 427
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 34.5 bits (79), Expect = 0.082
Identities = 62/315 (19%), Positives = 119/315 (37%), Gaps = 49/315 (15%)
Query: 25 KATLIIVPTRELALQTSQICIELAKHLNVKVMVTTGGTNLRDDIMRIYQKVHLIIATPGR 84
++ IVP R LA++ + L + L ++V ++ G + D ++ Y ++I T +
Sbjct: 66 LKSIYIVPLRSLAMEKYEELSRL-RSLGMRVKISIGDYDDPPDFIKRYD---VVILTSEK 121
Query: 85 ILDLMDKQVANMDHCKILVLDEADKLLSQDFKGMLDHVISILPH---ERQILLYSATFP- 140
L+ ++ ++V DE + +D L+ V+S + + +IL SAT
Sbjct: 122 ADSLIHHDPYIINDVGLIVADEIHIIGDEDRGPTLETVLSSARYVNPDARILALSATVSN 181
Query: 141 -----------LTVKNFMEKHLK-----------DPYE-----INLMEELTLKGVTQYYA 173
L NF LK D YE IN + + T+ Q
Sbjct: 182 ANELAQWLNASLIKSNFRPVPLKLGILYRKRLILDGYERSQVDINSLIKETVNDGGQVLV 241
Query: 174 FVQERQKVHCLNTLFSKL--QINQSIIFCNSTQRVELLAKKITELGYCCYYIHARMAQAH 231
FV R+ + + + N + + + ++ G + HA ++
Sbjct: 242 FVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVA--FHHAGLSNEQ 299
Query: 232 RNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVINFDFPKMAETYL---------HRIG 282
R + FR+ + +V + G+++ A V++ D + + IG
Sbjct: 300 RRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIVR-DITRYGNGGIRYLSNMEIKQMIG 358
Query: 283 RSGRYGHLGIAINLI 297
R+GR G+ I I
Sbjct: 359 RAGRPGYDQYGIGYI 373
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 33.9 bits (78), Expect = 0.12
Identities = 64/303 (21%), Positives = 116/303 (38%), Gaps = 74/303 (24%)
Query: 27 TLIIVPTRELALQTSQICIELAKHLNVKVMVTTGGT------NLRDDIMRIYQKVHLIIA 80
++ PT LA Q L L ++V + TG L + I ++HL++
Sbjct: 287 VALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIAS--GQIHLVVG 344
Query: 81 TPGRILDLMD-KQVANMDHCKILVLDEA--------DKLLSQDFKGMLDHVISILPHERQ 131
T I + ++ K++A ++++DE KL + G HV
Sbjct: 345 THALIQEKVEFKRLA------LVIIDEQHRFGVEQRKKLREKGQGGFTPHV--------- 389
Query: 132 ILLYSAT-----FPLTVKNFMEKHLKDPYEINLMEELTL--KGVTQYYAFVQERQKVH-- 182
L+ SAT LTV ++ ++++EL K +T E+ V+
Sbjct: 390 -LVMSATPIPRTLALTVYGDLD--------TSIIDELPPGRKPITTVLIKHDEKDIVYEF 440
Query: 183 ---CLNTLFSKLQINQSIIFC---NSTQRVEL---------LAKKITELGYCCYYIHARM 227
+ + Q+ + +++++L L K + Y +H RM
Sbjct: 441 IEEEIA------KGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPK--YNVGLLHGRM 492
Query: 228 AQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVINFDFPKMAETYLHRI-GRSGR 286
+ V +FR G LV + + G+DV V++ D + + LH++ GR GR
Sbjct: 493 KSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGR 552
Query: 287 YGH 289
H
Sbjct: 553 GDH 555
>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor;
Provisional.
Length = 1147
Score = 32.4 bits (74), Expect = 0.40
Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 224 HARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVI--NFDFPKMAETYLHRI 281
H +M + RV +DF LVC+ + GID+ N +I D +A+ LH++
Sbjct: 842 HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQ--LHQL 899
Query: 282 -GRSGRYGH 289
GR GR H
Sbjct: 900 RGRVGRSHH 908
>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 = 32.0 bits (73), Expect = 0.51
Identities = 67/307 (21%), Positives = 120/307 (39%), Gaps = 47/307 (15%)
Query: 28 LIIVPTRELALQTSQI--CIELAKHL--NVKVMVTTGGTNLRDDIMRIYQKVHLIIATPG 83
L++ PT AL Q EL L V TG T + I +++ P
Sbjct: 119 LLLYPTN--ALANDQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNP- 175
Query: 84 RILDLM-----DKQVANMDHCKILVLDEA---DKLLSQDFKGMLD---HVISILPHERQI 132
+L + D + + + K LV+DE + + +L + QI
Sbjct: 176 DMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGSEVALLLRRLLRRLRRYGSPLQI 235
Query: 133 LLYSATFPLTVKN---FMEKHLKDPYEINLMEEL---TLKGVTQYYAFVQE------RQK 180
+ SAT + N F E+ +E+ + E+ L+ + ++E R
Sbjct: 236 ICTSAT----LANPGEFAEELFGRDFEVPVDEDGSPRGLRYFVRREPPIRELAESIRRSA 291
Query: 181 VHCLNTLFSKLQIN--QSIIFCNSTQRVELLAKKITEL-----GYCCYYIHARMAQAH-- 231
+ L TL + L N Q+++F S ++VELL G + A H
Sbjct: 292 LAELATLAALLVRNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHRE 351
Query: 232 -RNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVINFDFP--KMAETYLHRIGRSGRYG 288
R R+ +F+ G ++ ++ GID+ +++ VI + +P + + R GR+GR G
Sbjct: 352 ERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLS-FRQRAGRAGRRG 410
Query: 289 HLGIAIN 295
+ +
Sbjct: 411 QESLVLV 417
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 31.4 bits (72), Expect = 0.73
Identities = 24/85 (28%), Positives = 39/85 (45%), Gaps = 5/85 (5%)
Query: 207 ELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVI 266
E L + + ELG Y+H+ + R + D R G LV +L G+D+ V++V
Sbjct: 460 EDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVA 519
Query: 267 NFD-----FPKMAETYLHRIGRSGR 286
D F + + + IGR+ R
Sbjct: 520 ILDADKEGFLRSERSLIQTIGRAAR 544
>gnl|CDD|233063 TIGR00631, uvrb, excinuclease ABC, B subunit. All proteins in this
family for wich functions are known are DNA helicases
that function in the nucleotide excision repair and are
endonucleases that make the 3' incision next to DNA
damage. They are part of a pathway requiring UvrA, UvrB,
UvrC, and UvrD homologs. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 655
Score = 31.1 bits (71), Expect = 1.1
Identities = 28/101 (27%), Positives = 44/101 (43%), Gaps = 9/101 (8%)
Query: 207 ELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVI 266
E L + ELG Y+H+ + R + D R G LV +L G+D+ V++V
Sbjct: 456 EDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVA 515
Query: 267 NFD-----FPKMAETYLHRIGRSGRYGHLGIAINLITYEDR 302
D F + + + IGR+ R + G I Y D+
Sbjct: 516 ILDADKEGFLRSERSLIQTIGRAARNVN-GKV---IMYADK 552
>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 = 1.1
Identities = 23/90 (25%), Positives = 38/90 (42%), Gaps = 6/90 (6%)
Query: 204 QRVELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVN 263
++ E L + + E H +M + V DF +G LVC+ + GID+ N
Sbjct: 818 KKAERLRELVPEARIA--VAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNAN 875
Query: 264 VVINFDFPKMAETYLH----RIGRSGRYGH 289
+I K L+ R+GRS + +
Sbjct: 876 TIIIERADKFGLAQLYQLRGRVGRSNKQAY 905
>gnl|CDD|225625 COG3083, COG3083, Predicted hydrolase of alkaline phosphatase
superfamily [General function prediction only].
Length = 600
Score = 30.9 bits (70), Expect = 1.1
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 4/25 (16%)
Query: 130 RQILLYSATFPL----TVKNFMEKH 150
R I + A FPL T ++F+EKH
Sbjct: 197 RPITMQRANFPLSYPMTARSFLEKH 221
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 31.0 bits (71), Expect = 1.2
Identities = 39/178 (21%), Positives = 69/178 (38%), Gaps = 29/178 (16%)
Query: 191 LQINQS---IIFCNSTQRVELLAKKITELGYCCYYIHAR-------------MAQAHRNR 234
L N I+F E + + + G I A M+Q +
Sbjct: 360 LGKNPDSRIIVFTQYRDTAEKIVDLLEKEG-----IKAVRFVGQASKDGDKGMSQKEQIE 414
Query: 235 VFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVINFDFPKMAET-YLHRIGRSGRYGHLGIA 293
+ FR+G LV + + G+D+ +V++VI F P +E + R GR+GR G
Sbjct: 415 ILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVI-FYEPVPSEIRSIQRKGRTGR-QEEGRV 472
Query: 294 INLITYEDR-----YALHRIEKELGTEIKSIPKVIDPALYVARPEDMDRDNSTGASEE 346
+ LI R ++ R EK++ E+K++ +++ L E +
Sbjct: 473 VVLIAKGTRDEAYYWSSRRKEKKMKEELKNLKGILNKKLQELDEEQKGEEEEKDEQLS 530
>gnl|CDD|239660 cd03689, RF3_II, RF3_II: this subfamily represents the domain II of
bacterial Release Factor 3 (RF3). Termination of protein
synthesis by the ribosome requires two release factor
(RF) classes. The class II RF3 is a GTPase that removes
class I RFs (RF1 or RF2) from the ribosome after release
of the nascent polypeptide. RF3 in the GDP state binds
to the ribosomal class I RF complex, followed by an
exchange of GDP for GTP and release of the class I RF.
Sequence comparison of class II release factors with
elongation factors shows that prokaryotic RF3 is more
similar to EF-G whereas eukaryotic eRF3 is more similar
to eEF1A, implying that their precise function may
differ.
Length = 85
Score = 27.6 bits (62), Expect = 2.5
Identities = 17/41 (41%), Positives = 21/41 (51%), Gaps = 10/41 (24%)
Query: 223 IHARMAQAHRNRV-FHDFRSGLCRNLVCSDLFTRGIDVQAV 262
I A M AHR+R+ F R VCS F RG+ V+ V
Sbjct: 6 IQANMDPAHRDRIAF--VR-------VCSGKFERGMKVKHV 37
>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 28.3 bits (64), Expect = 2.6
Identities = 13/80 (16%), Positives = 29/80 (36%), Gaps = 12/80 (15%)
Query: 47 LAKHLNVKVMVTTGGTNLRDDIMRIYQKVHLIIATPGRILDLMDKQVANMDHCKILVLDE 106
+AK L + +G +++ Y + + R+ +L + A ++ +DE
Sbjct: 18 VAKELGAPFIEISGS-----ELVSKY-----VGESEKRLRELFEA--AKKLAPCVIFIDE 65
Query: 107 ADKLLSQDFKGMLDHVISIL 126
D L G ++
Sbjct: 66 IDALAGSRGSGGDSESRRVV 85
>gnl|CDD|216822 pfam01976, DUF116, Protein of unknown function DUF116. This
archaebacterial protein has no known function. The
protein contains seven conserved cysteines and may also
be an integral membrane protein.
Length = 158
Score = 27.9 bits (63), Expect = 5.7
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 45 IELAKHLNVKVMVTTGGTNLRDDIMR 70
ELA+ KV + GGT + I
Sbjct: 79 KELAEEYGYKVYIVPGGTFAKKIIKE 104
>gnl|CDD|225042 COG2131, ComEB, Deoxycytidylate deaminase [Nucleotide transport and
metabolism].
Length = 164
Score = 27.7 bits (62), Expect = 6.1
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 3/39 (7%)
Query: 200 CNSTQRVELLAKKITELGYCCYYIHARM---AQAHRNRV 235
C + +T G+CC +HA QA R+ V
Sbjct: 55 CIDRGCLRDKVVFVTTCGHCCRTLHAEQNAILQAARHGV 93
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 28.3 bits (64), Expect = 7.5
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 256 GIDVQAVNVVINFDFPKMAETYLHRIGRSG 285
GID+ +++V+ PK L RIGR+G
Sbjct: 353 GIDIGYIDLVVLLGSPKSVSRLLQRIGRAG 382
>gnl|CDD|232826 TIGR00106, TIGR00106, uncharacterized protein, MTH1187 family.
This protein has been crystallized in both
Methanobacterium thermoautotrophicum and yeast, but its
function remains unknown. Both crystal structures
showed sulfate ions bound at the interface of two
dimers to form a tetramer [Unknown function, General].
Length = 97
Score = 26.6 bits (59), Expect = 7.5
Identities = 8/36 (22%), Positives = 16/36 (44%), Gaps = 3/36 (8%)
Query: 44 CIELAKHLNVKVMVTTGGTNLR---DDIMRIYQKVH 76
IE+ K +K + GT + D++ + +H
Sbjct: 24 AIEVLKESGLKYELHPMGTLIEGDLDELFEAIKAIH 59
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 28.3 bits (64), Expect = 7.8
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 223 IHARMAQAHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVINFDFPKMAETY----L 278
+H RM A ++ V F+ G LV + + G+DV V++ + AE + L
Sbjct: 513 VHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPNATVMVIEN----AERFGLAQL 568
Query: 279 HRI-GRSGRYGH 289
H++ GR GR
Sbjct: 569 HQLRGRVGRGDL 580
>gnl|CDD|131210 TIGR02155, PA_CoA_ligase, phenylacetate-CoA ligase.
Phenylacetate-CoA ligase (PA-CoA ligase) catalyzes the
first step in aromatic catabolism of phenylacetic acid
(PA) into phenylacetyl-CoA (PA-CoA). Often located in a
conserved gene cluster with enzymes involved in
phenylacetic acid activation (paaG/H/I/J),
phenylacetate-CoA ligase has been found among the
proteobacteria as well as in gram positive prokaryotes.
In the B-subclass proteobacterium Azoarcus evansii,
phenylacetate-CoA ligase has been shown to be induced
under aerobic and anaerobic growth conditions. It
remains unclear however, whether this induction is due
to the same enzyme or to another isoenzyme restricted to
specific anaerobic growth conditions [Energy metabolism,
Other].
Length = 422
Score = 27.9 bits (62), Expect = 8.6
Identities = 21/72 (29%), Positives = 26/72 (36%), Gaps = 17/72 (23%)
Query: 102 LVLDEADKLLSQDFKGMLDHVISILPHER-------------QILLYSATFPLTVKNFME 148
LDE L +Q K + H +PH R Q L A FP T K+
Sbjct: 3 ASLDELRALQTQRLKWTVKHAYENVPHYRKAFDAAGVHPDDLQSLSDLAKFPFTQKH--- 59
Query: 149 KHLKDPYEINLM 160
L+D Y L
Sbjct: 60 -DLRDNYPFGLF 70
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
0.324 0.138 0.399
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: 17,733,301
Number of extensions: 1726914
Number of successful extensions: 2170
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2125
Number of HSP's successfully gapped: 78
Length of query: 351
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 253
Effective length of database: 6,590,910
Effective search space: 1667500230
Effective search space used: 1667500230
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 59 (26.4 bits)