|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
28-616 |
0e+00 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 741.97 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 28 EIKPLTQVLVDLKSKKnLKAIVLKECQKPDFKTIEIKEITK-----YFLTPLQLELANFIVYYYASKLGFVL-------- 94
Cdd:PRK05580 26 EVQPGDRVRVPFGNRK-LIGVVVGVEEGSEVPADKLKPILEvldlePLLPPELLRLLDWAADYYLSPLGEVLrlallael 104
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 95 ---------------GFFETSPK----YECQKMFFKDTPKLSNQQQNALSFLQKE---NNSLLFADTGSGKTEIYISLIK 152
Cdd:PRK05580 105 alaassavlkglvkkGLIELEEVevlrLRPPPDPAFEPPTLNPEQAAAVEAIRAAagfSPFLLDGVTGSGKTEVYLQAIA 184
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 153 ECLEQGKQALLLMPEIALTPQMQKRLEVYFKDNFFLWHSKISKKKKQEYLECFCKGEVLLVAGARSALFLPFRNLGLIVV 232
Cdd:PRK05580 185 EVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALFLPFKNLGLIIV 264
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 233 DEEHDNSYKASNQPFINARDLALFLGQKNNIKVVLGSATPSLTSFYKQKS-----FRLKGTFFESK---------KHFLY 298
Cdd:PRK05580 265 DEEHDSSYKQQEGPRYHARDLAVVRAKLENIPVVLGSATPSLESLANAQQgryrlLRLTKRAGGARlpeveiidmRELLR 344
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 299 DENELGITPMLLSELEKSLKHQKQAIVFLPTRANFRQIICKDCGETIKCPFCSIAMSMHKKKNILKCHYCNYTSLIEQNC 378
Cdd:PRK05580 345 GENGSFLSPPLLEAIKQRLERGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKAC 424
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 379 PSCKGEMLEARKIGTAELLELLQNALPLAKIAKFDSDEITSVKKLNTILKNFNENKIDILIGTSMLAKGHDYHSVDLSVI 458
Cdd:PRK05580 425 PECGSTDLVPVGPGTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGV 504
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 459 LGLDEYLLRPSFRASEETLALAMQVAGRAGR-KGKARVLLQT---KNRAFFERYIENYDAFLKDELENRKDL-YPPFKRL 533
Cdd:PRK05580 505 LDADLGLFSPDFRASERTFQLLTQVAGRAGRaEKPGEVLIQTyhpEHPVIQALLAQDYDAFAEQELEERRAAgYPPFGRL 584
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 534 LRVLIEDKDQKSAQKLCEKFASQFRNI---KQVELVGYGICGVEMLYGKYRFYLLLRSENHKALVAIENYILQ------- 603
Cdd:PRK05580 585 ALLRASAKDEEKAEKFAQQLAALLPNLlplLDVEVLGPAPAPIAKIAGRYRYQLLLKSPSRADLQKLLRAWLAllqklpq 664
|
650
....*....|....*
gi 1160598055 604 --FKNASADIDPIDF 616
Cdd:PRK05580 665 arKVRWSIDVDPQSF 679
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
114-615 |
8.81e-168 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 495.79 E-value: 8.81e-168
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 114 PKLSNQQQNALSFLQKENNS----LLFADTGSGKTEIYISLIKECLEQGKQALLLMPEIALTPQMQKRLEVYFKDNFFLW 189
Cdd:COG1198 194 PTLNEEQQAAVEAIRAAAGGfsvfLLHGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQTVERFRARFGARVAVL 273
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 190 HSKISKKKK-QEYLECFcKGEVLLVAGARSALFLPFRNLGLIVVDEEHDNSYKASNQPFINARDLALFLGQKNNIKVVLG 268
Cdd:COG1198 274 HSGLSDGERlDEWRRAR-RGEARIVIGTRSALFAPFPNLGLIIVDEEHDSSYKQEDGPRYHARDVAVVRAKLEGAPVVLG 352
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 269 SATPSLTSFYKQKS-----FRLKGTFFESK---------KHFLYDENELgITPMLLSELEKSLKHQKQAIVFLPTR--AN 332
Cdd:COG1198 353 SATPSLESLYNAQKgryrlLELPERAGGAPlpevelvdmREEPLEGGRI-LSPPLLEAIEETLERGEQVLLFLNRRgyAP 431
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 333 FrqIICKDCGETIKCPFCSIAMSMHKKKNILKCHYCNYTSLIEQNCPSCKGEMLEARKIGTAELLELLQNALPLAKIAKF 412
Cdd:COG1198 432 F--LLCRDCGWVAKCPNCDVSLTYHRSRRRLRCHYCGYEEPVPKQCPECGSDSLRPFGPGTERVEEELAELFPDARVLRM 509
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 413 DSDEITSVKKLNTILKNFNENKIDILIGTSMLAKGHDYHSVDLSVILGLDEYLLRPSFRASEETLALAMQVAGRAGRKGK 492
Cdd:COG1198 510 DRDTTRRKGALEKLLEAFARGEADILVGTQMLAKGHDFPNVTLVGVLDADLGLNSPDFRAAERTFQLLTQVAGRAGRAEK 589
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 493 A-RVLLQT---KNRAFfeRYI--ENYDAFLKDELENRKDL-YPPFKRLLRVLIEDKDQKSAQKLCEKFASQFRNI---KQ 562
Cdd:COG1198 590 PgEVLIQTynpEHPVI--QALlnHDYEAFYEEELAERKAAgYPPFGRLALLRASGKDEEAAEEFAQALARALRALlsaDG 667
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1160598055 563 VELVGYGICGVEMLYGKYRFYLLLRSENHKALVAIENYIL-QFKNASA-------DIDPID 615
Cdd:COG1198 668 VEVLGPAPAPIARLRGRYRWQLLLKAPSRAALQQLLRALLaLLEKPLPrkvrwsiDVDPQS 728
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
134-614 |
3.41e-162 |
|
primosomal protein N'; All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273162 [Multi-domain] Cd Length: 505 Bit Score: 473.79 E-value: 3.41e-162
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 134 LLFADTGSGKTEIYISLIKECLEQGKQALLLMPEIALTPQMQKRLEVYFKDNFFLWHSKISKKKKQEYLECFCKGEVLLV 213
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 214 AGARSALFLPFRNLGLIVVDEEHDNSYKASNQPFINARDLALFLGQKNNIKVVLGSATPSLTSFY--KQKSFR---LKGT 288
Cdd:TIGR00595 81 IGTRSALFLPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKKFNCPVVLGSATPSLESYHnaKQKAYRllvLTRR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 289 FFESK--KHFLYD----ENELGITPMLLSELEKSLKHQKQAIVFLPTRANFRQIICKDCGETIKCPFCSIAMSMHKKKNI 362
Cdd:TIGR00595 161 VSGRKppEVKLIDmrkePRQSFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLTYHKKEGK 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 363 LKCHYCNYTSLIEQNCPSCKGEMLEARKIGTAELLELLQNALPLAKIAKFDSDEITSVKKLNTILKNFNENKIDILIGTS 442
Cdd:TIGR00595 241 LRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQ 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 443 MLAKGHDYHSVDLSVILGLDEYLLRPSFRASEETLALAMQVAGRAGRKGK-ARVLLQTKNR---AFFERYIENYDAFLKD 518
Cdd:TIGR00595 321 MIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDpGQVIIQTYNPnhpAIQAALTGDYEAFYEQ 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 519 ELENRKDL-YPPFKRLLRVLIEDKDQKSAQKLCEKFASQFRNI--KQVELVGYGICGVEMLYGKYRFYLLLRSENHKALV 595
Cdd:TIGR00595 401 ELAQRRALnYPPFTRLIRLIFRGKNEEKAQQTAQAAHELLKQNldEKLEVLGPSPAPIAKIAGRYRYQILLKSKSFLVLQ 480
|
490 500
....*....|....*....|....*
gi 1160598055 596 AIENYIL--QFKNASA----DIDPI 614
Cdd:TIGR00595 481 KLVNKTLlkEIPSSSVycevDVDPI 505
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
120-285 |
7.43e-72 |
|
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350687 [Multi-domain] Cd Length: 178 Bit Score: 229.02 E-value: 7.43e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 120 QQNALSFLQKENNS----LLFADTGSGKTEIYISLIKECLEQGKQALLLMPEIALTPQMQKRLEVYFKDNFFLWHSKISK 195
Cdd:cd17929 1 QRKAYEAIVSSLGGfktfLLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGDKVAVLHSKLSD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 196 KKKQEYLECFCKGEVLLVAGARSALFLPFRNLGLIVVDEEHDNSYKASNQPFINARDLALFLGQKNNIKVVLGSATPSLT 275
Cdd:cd17929 81 KERADEWRKIKRGEAKVVIGARSALFAPFKNLGLIIVDEEHDSSYKQDSGPRYHARDVAIYRAKLENAPVVLGSATPSLE 160
|
170
....*....|..
gi 1160598055 276 SFY--KQKSFRL 285
Cdd:cd17929 161 SYYnaQQGKYRL 172
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
120-273 |
4.23e-15 |
|
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.
Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 73.43 E-value: 4.23e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 120 QQNALSFLQKENNSLLFADTGSGKTEIY----ISLIKECLEqGKQALLLMPEIALTPQMQKRLEVYFKDNFFLWHSKISK 195
Cdd:pfam00270 4 QAEAIPAILEGRDVLVQAPTGSGKTLAFllpaLEALDKLDN-GPQALVLAPTRELAEQIYEELKKLGKGLGLKVASLLGG 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 196 KKKQEYLECFCKGEVLLVAGARSALFL----PFRNLGLIVVDEEH---DNSYKAsnqpfinarDLALFLGQ-KNNIKVVL 267
Cdd:pfam00270 83 DSRKEQLEKLKGPDILVGTPGRLLDLLqerkLLKNLKLLVLDEAHrllDMGFGP---------DLEEILRRlPKKRQILL 153
|
....*.
gi 1160598055 268 GSATPS 273
Cdd:pfam00270 154 LSATLP 159
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
114-273 |
8.64e-15 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 73.30 E-value: 8.64e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 114 PKLSNQQQNALSF-LQKENNSLLFADTGSGKTEIYISLIKECL--EQGKQALLLMPEIALTPQMQKRLEVYFKDNFFLWH 190
Cdd:smart00487 7 EPLRPYQKEAIEAlLSGLRDVILAAPTGSGKTLAALLPALEALkrGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKVV 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 191 SKISKKKKQEYLECFCKGEV-LLVAGARSAL------FLPFRNLGLIVVDEEHDNSYKASNQPFINARDLAlflgqKNNI 263
Cdd:smart00487 87 GLYGGDSKREQLRKLESGKTdILVTTPGRLLdllendKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLL-----PKNV 161
|
170
....*....|
gi 1160598055 264 KVVLGSATPS 273
Cdd:smart00487 162 QLLLLSATPP 171
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
28-616 |
0e+00 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 741.97 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 28 EIKPLTQVLVDLKSKKnLKAIVLKECQKPDFKTIEIKEITK-----YFLTPLQLELANFIVYYYASKLGFVL-------- 94
Cdd:PRK05580 26 EVQPGDRVRVPFGNRK-LIGVVVGVEEGSEVPADKLKPILEvldlePLLPPELLRLLDWAADYYLSPLGEVLrlallael 104
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 95 ---------------GFFETSPK----YECQKMFFKDTPKLSNQQQNALSFLQKE---NNSLLFADTGSGKTEIYISLIK 152
Cdd:PRK05580 105 alaassavlkglvkkGLIELEEVevlrLRPPPDPAFEPPTLNPEQAAAVEAIRAAagfSPFLLDGVTGSGKTEVYLQAIA 184
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 153 ECLEQGKQALLLMPEIALTPQMQKRLEVYFKDNFFLWHSKISKKKKQEYLECFCKGEVLLVAGARSALFLPFRNLGLIVV 232
Cdd:PRK05580 185 EVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALFLPFKNLGLIIV 264
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 233 DEEHDNSYKASNQPFINARDLALFLGQKNNIKVVLGSATPSLTSFYKQKS-----FRLKGTFFESK---------KHFLY 298
Cdd:PRK05580 265 DEEHDSSYKQQEGPRYHARDLAVVRAKLENIPVVLGSATPSLESLANAQQgryrlLRLTKRAGGARlpeveiidmRELLR 344
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 299 DENELGITPMLLSELEKSLKHQKQAIVFLPTRANFRQIICKDCGETIKCPFCSIAMSMHKKKNILKCHYCNYTSLIEQNC 378
Cdd:PRK05580 345 GENGSFLSPPLLEAIKQRLERGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKAC 424
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 379 PSCKGEMLEARKIGTAELLELLQNALPLAKIAKFDSDEITSVKKLNTILKNFNENKIDILIGTSMLAKGHDYHSVDLSVI 458
Cdd:PRK05580 425 PECGSTDLVPVGPGTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGV 504
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 459 LGLDEYLLRPSFRASEETLALAMQVAGRAGR-KGKARVLLQT---KNRAFFERYIENYDAFLKDELENRKDL-YPPFKRL 533
Cdd:PRK05580 505 LDADLGLFSPDFRASERTFQLLTQVAGRAGRaEKPGEVLIQTyhpEHPVIQALLAQDYDAFAEQELEERRAAgYPPFGRL 584
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 534 LRVLIEDKDQKSAQKLCEKFASQFRNI---KQVELVGYGICGVEMLYGKYRFYLLLRSENHKALVAIENYILQ------- 603
Cdd:PRK05580 585 ALLRASAKDEEKAEKFAQQLAALLPNLlplLDVEVLGPAPAPIAKIAGRYRYQLLLKSPSRADLQKLLRAWLAllqklpq 664
|
650
....*....|....*
gi 1160598055 604 --FKNASADIDPIDF 616
Cdd:PRK05580 665 arKVRWSIDVDPQSF 679
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
114-615 |
8.81e-168 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 495.79 E-value: 8.81e-168
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 114 PKLSNQQQNALSFLQKENNS----LLFADTGSGKTEIYISLIKECLEQGKQALLLMPEIALTPQMQKRLEVYFKDNFFLW 189
Cdd:COG1198 194 PTLNEEQQAAVEAIRAAAGGfsvfLLHGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQTVERFRARFGARVAVL 273
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 190 HSKISKKKK-QEYLECFcKGEVLLVAGARSALFLPFRNLGLIVVDEEHDNSYKASNQPFINARDLALFLGQKNNIKVVLG 268
Cdd:COG1198 274 HSGLSDGERlDEWRRAR-RGEARIVIGTRSALFAPFPNLGLIIVDEEHDSSYKQEDGPRYHARDVAVVRAKLEGAPVVLG 352
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 269 SATPSLTSFYKQKS-----FRLKGTFFESK---------KHFLYDENELgITPMLLSELEKSLKHQKQAIVFLPTR--AN 332
Cdd:COG1198 353 SATPSLESLYNAQKgryrlLELPERAGGAPlpevelvdmREEPLEGGRI-LSPPLLEAIEETLERGEQVLLFLNRRgyAP 431
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 333 FrqIICKDCGETIKCPFCSIAMSMHKKKNILKCHYCNYTSLIEQNCPSCKGEMLEARKIGTAELLELLQNALPLAKIAKF 412
Cdd:COG1198 432 F--LLCRDCGWVAKCPNCDVSLTYHRSRRRLRCHYCGYEEPVPKQCPECGSDSLRPFGPGTERVEEELAELFPDARVLRM 509
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 413 DSDEITSVKKLNTILKNFNENKIDILIGTSMLAKGHDYHSVDLSVILGLDEYLLRPSFRASEETLALAMQVAGRAGRKGK 492
Cdd:COG1198 510 DRDTTRRKGALEKLLEAFARGEADILVGTQMLAKGHDFPNVTLVGVLDADLGLNSPDFRAAERTFQLLTQVAGRAGRAEK 589
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 493 A-RVLLQT---KNRAFfeRYI--ENYDAFLKDELENRKDL-YPPFKRLLRVLIEDKDQKSAQKLCEKFASQFRNI---KQ 562
Cdd:COG1198 590 PgEVLIQTynpEHPVI--QALlnHDYEAFYEEELAERKAAgYPPFGRLALLRASGKDEEAAEEFAQALARALRALlsaDG 667
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1160598055 563 VELVGYGICGVEMLYGKYRFYLLLRSENHKALVAIENYIL-QFKNASA-------DIDPID 615
Cdd:COG1198 668 VEVLGPAPAPIARLRGRYRWQLLLKAPSRAALQQLLRALLaLLEKPLPrkvrwsiDVDPQS 728
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
134-614 |
3.41e-162 |
|
primosomal protein N'; All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273162 [Multi-domain] Cd Length: 505 Bit Score: 473.79 E-value: 3.41e-162
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 134 LLFADTGSGKTEIYISLIKECLEQGKQALLLMPEIALTPQMQKRLEVYFKDNFFLWHSKISKKKKQEYLECFCKGEVLLV 213
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 214 AGARSALFLPFRNLGLIVVDEEHDNSYKASNQPFINARDLALFLGQKNNIKVVLGSATPSLTSFY--KQKSFR---LKGT 288
Cdd:TIGR00595 81 IGTRSALFLPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKKFNCPVVLGSATPSLESYHnaKQKAYRllvLTRR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 289 FFESK--KHFLYD----ENELGITPMLLSELEKSLKHQKQAIVFLPTRANFRQIICKDCGETIKCPFCSIAMSMHKKKNI 362
Cdd:TIGR00595 161 VSGRKppEVKLIDmrkePRQSFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLTYHKKEGK 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 363 LKCHYCNYTSLIEQNCPSCKGEMLEARKIGTAELLELLQNALPLAKIAKFDSDEITSVKKLNTILKNFNENKIDILIGTS 442
Cdd:TIGR00595 241 LRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQ 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 443 MLAKGHDYHSVDLSVILGLDEYLLRPSFRASEETLALAMQVAGRAGRKGK-ARVLLQTKNR---AFFERYIENYDAFLKD 518
Cdd:TIGR00595 321 MIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDpGQVIIQTYNPnhpAIQAALTGDYEAFYEQ 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 519 ELENRKDL-YPPFKRLLRVLIEDKDQKSAQKLCEKFASQFRNI--KQVELVGYGICGVEMLYGKYRFYLLLRSENHKALV 595
Cdd:TIGR00595 401 ELAQRRALnYPPFTRLIRLIFRGKNEEKAQQTAQAAHELLKQNldEKLEVLGPSPAPIAKIAGRYRYQILLKSKSFLVLQ 480
|
490 500
....*....|....*....|....*
gi 1160598055 596 AIENYIL--QFKNASA----DIDPI 614
Cdd:TIGR00595 481 KLVNKTLlkEIPSSSVycevDVDPI 505
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
120-285 |
7.43e-72 |
|
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350687 [Multi-domain] Cd Length: 178 Bit Score: 229.02 E-value: 7.43e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 120 QQNALSFLQKENNS----LLFADTGSGKTEIYISLIKECLEQGKQALLLMPEIALTPQMQKRLEVYFKDNFFLWHSKISK 195
Cdd:cd17929 1 QRKAYEAIVSSLGGfktfLLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGDKVAVLHSKLSD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 196 KKKQEYLECFCKGEVLLVAGARSALFLPFRNLGLIVVDEEHDNSYKASNQPFINARDLALFLGQKNNIKVVLGSATPSLT 275
Cdd:cd17929 81 KERADEWRKIKRGEAKVVIGARSALFAPFKNLGLIIVDEEHDSSYKQDSGPRYHARDVAIYRAKLENAPVVLGSATPSLE 160
|
170
....*....|..
gi 1160598055 276 SFY--KQKSFRL 285
Cdd:cd17929 161 SYYnaQQGKYRL 172
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
300-524 |
1.37e-70 |
|
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350191 [Multi-domain] Cd Length: 238 Bit Score: 227.90 E-value: 1.37e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 300 ENELGITPMLLSELEKSLKHQKQAIVFLPTRANFRQIICKDCGETIKCPFCSIAMSMHKKKNILKCHYCNYTSLIEQNCP 379
Cdd:cd18804 10 ELKSGFSPKLLDAIKETLEKGEQVILFLNRRGYSPSVLCRDCGYVPECPNCDVSMTYHKSTNKLKCHYCGYQEPIPKQCP 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 380 SCKGEMLEARKIGTAELLELLQNALPLAKIAKFDSDEITSVKKLNTILKNFNENKIDILIGTSMLAKGHDYHSVDLSVIL 459
Cdd:cd18804 90 ECGSEDLVFKGIGTERVEEELKTLFPEARIARIDRDTTRKKGALEKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVGIL 169
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1160598055 460 GLDEYLLRPSFRASEETLALAMQVAGRAGRKGK-ARVLLQTKNRA--FFERYIEN-YDAFLKDELENRK 524
Cdd:cd18804 170 NADSGLNSPDFRASERAFQLLTQVSGRAGRGDKpGKVIIQTYNPEhpLIQAAKEEdYEAFYEEELAERK 238
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
120-273 |
4.23e-15 |
|
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.
Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 73.43 E-value: 4.23e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 120 QQNALSFLQKENNSLLFADTGSGKTEIY----ISLIKECLEqGKQALLLMPEIALTPQMQKRLEVYFKDNFFLWHSKISK 195
Cdd:pfam00270 4 QAEAIPAILEGRDVLVQAPTGSGKTLAFllpaLEALDKLDN-GPQALVLAPTRELAEQIYEELKKLGKGLGLKVASLLGG 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 196 KKKQEYLECFCKGEVLLVAGARSALFL----PFRNLGLIVVDEEH---DNSYKAsnqpfinarDLALFLGQ-KNNIKVVL 267
Cdd:pfam00270 83 DSRKEQLEKLKGPDILVGTPGRLLDLLqerkLLKNLKLLVLDEAHrllDMGFGP---------DLEEILRRlPKKRQILL 153
|
....*.
gi 1160598055 268 GSATPS 273
Cdd:pfam00270 154 LSATLP 159
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
114-273 |
8.64e-15 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 73.30 E-value: 8.64e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 114 PKLSNQQQNALSF-LQKENNSLLFADTGSGKTEIYISLIKECL--EQGKQALLLMPEIALTPQMQKRLEVYFKDNFFLWH 190
Cdd:smart00487 7 EPLRPYQKEAIEAlLSGLRDVILAAPTGSGKTLAALLPALEALkrGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKVV 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 191 SKISKKKKQEYLECFCKGEV-LLVAGARSAL------FLPFRNLGLIVVDEEHDNSYKASNQPFINARDLAlflgqKNNI 263
Cdd:smart00487 87 GLYGGDSKREQLRKLESGKTdILVTTPGRLLdllendKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLL-----PKNV 161
|
170
....*....|
gi 1160598055 264 KVVLGSATPS 273
Cdd:smart00487 162 QLLLLSATPP 171
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
130-271 |
2.43e-13 |
|
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.
Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 67.81 E-value: 2.43e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 130 ENNSLLFADTGSGKTEIY-ISLIKECLEQGKQALLLMPEIALTPQMQKRLEVYFKdnfflWHSKIS------------KK 196
Cdd:cd00046 1 GENVLITAPTGSGKTLAAlLAALLLLLKKGKKVLVLVPTKALALQTAERLRELFG-----PGIRVAvlvggssaeereKN 75
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1160598055 197 KKQEYLECFCKGEVLLVAGARSALFLpFRNLGLIVVDEEHDNSYkasNQPFINARDLALFLGQKNNIKVVLGSAT 271
Cdd:cd00046 76 KLGDADIIIATPDMLLNLLLREDRLF-LKDLKLIIVDEAHALLI---DSRGALILDLAVRKAGLKNAQVILLSAT 146
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
408-491 |
5.75e-10 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 56.07 E-value: 5.75e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 408 KIAKFDSDeiTSVKKLNTILKNFNENKIDILIGTSMLAKGHDYHSVDLSVILGLDeyllrpsfraseETLALAMQVAGRA 487
Cdd:smart00490 13 KVARLHGG--LSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP------------WSPASYIQRIGRA 78
|
....
gi 1160598055 488 GRKG 491
Cdd:smart00490 79 GRAG 82
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
134-236 |
7.63e-10 |
|
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350749 [Multi-domain] Cd Length: 193 Bit Score: 58.74 E-value: 7.63e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 134 LLFADTGSGKTEIYISLIKECLEQGKQALLLMPEIALTPQ----MQKRLEVyFKDNFFLWHSKISKKKKQEYLECFCKGE 209
Cdd:cd17991 40 LICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQhyetFKERFAN-FPVNVELLSRFTTAAEQREILEGLKEGK 118
|
90 100
....*....|....*....|....*....
gi 1160598055 210 VLLVAGARSALF--LPFRNLGLIVVDEEH 236
Cdd:cd17991 119 VDIVIGTHRLLSkdVEFKNLGLLIIDEEQ 147
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
119-297 |
2.11e-09 |
|
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350769 [Multi-domain] Cd Length: 207 Bit Score: 57.68 E-value: 2.11e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 119 QQQNALSFLQKENNSLLFAD-TGSGKTeiyIS---LIKECLEQG--KQALLLMPEiALTPQMQKRLEVYFKDNFFLWHSK 192
Cdd:cd18011 5 QIDAVLRALRKPPVRLLLADeVGLGKT---IEaglIIKELLLRGdaKRVLILCPA-SLVEQWQDELQDKFGLPFLILDRE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 193 ISKKKKQEYLECFCKGEVLLV-------AGARSALFLPfRNLGLIVVDEEHdnsyKASNQPFINARDLALFLGQ--KNNI 263
Cdd:cd18011 81 TAAQLRRLIGNPFEEFPIVIVsldllkrSEERRGLLLS-EEWDLVVVDEAH----KLRNSGGGKETKRYKLGRLlaKRAR 155
|
170 180 190
....*....|....*....|....*....|....*....
gi 1160598055 264 KVVLGSATPSLTsfyKQKSFR-----LKGTFFESKKHFL 297
Cdd:cd18011 156 HVLLLTATPHNG---KEEDFRallslLDPGRFAVLGRFL 191
|
|
| PriA_C |
pfam18074 |
Primosomal protein N C-terminal domain; This is the C-terminal domain found in PriA DNA ... |
529-613 |
2.31e-09 |
|
Primosomal protein N C-terminal domain; This is the C-terminal domain found in PriA DNA helicase, a multifunctional enzyme that mediates the process of restarting prematurely terminated DNA replication reactions in bacteria. The C-terminal domain (CTD) bears similarity to the S10 subunit which binds branched rRNA within the bacterial ribosome. The C-terminal domain is part of the helicase domain of PriA proteins. It acts together with the 3' DNA-binding domain to form a site for binding ssDNA-binding protein (SSB).
Pssm-ID: 465633 [Multi-domain] Cd Length: 96 Bit Score: 54.53 E-value: 2.31e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 529 PFKRLLRVLIEDKDQKSAQKLCEKFASQFRN---IKQVELVGYGICGVEMLYGKYRFYLLLRSENHKALVAIENYILQFK 605
Cdd:pfam18074 1 PFSRLALIRVSGKDEEKAEKFAEELAELLKEllkLQGVEILGPAPAPIAKIKGRYRYQLLLKSKSRKALHQLLRELLEEL 80
|
90
....*....|....*.
gi 1160598055 606 NA--------SADIDP 613
Cdd:pfam18074 81 QKlpkrkvriSIDVDP 96
|
|
| PriA_CRR |
pfam18319 |
PriA DNA helicase Cys-rich region (CRR) domain; This is a cys-rich region (CRR) domain found ... |
347-371 |
2.99e-09 |
|
PriA DNA helicase Cys-rich region (CRR) domain; This is a cys-rich region (CRR) domain found in PriA DNA helicases. In bacteria, the replication restart process is orchestrated by the PriA DNA helicase, which identifies replication forks via structure-specific DNA binding and interactions with fork-associated ssDNA-binding proteins (SSBs). The CRR region which is embedded within the C-terminal helicase lobe has been identified to bind two Zn2+ ions. This 50-residue insertion forms a structure on the surface of the helicase core in which two Zn2+ ions are coordinated by invariant Cys residues. Biochemical experiments have shown that sequence changes to Zn2+-binding Cys residues in the PriA CRR can eliminate helicase, but not ATPase, activity and can block assembly of PriB onto DNA-bound PriA, implicating the CRR in multiple functions in PriA.
Pssm-ID: 465708 [Multi-domain] Cd Length: 27 Bit Score: 52.53 E-value: 2.99e-09
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
120-272 |
5.55e-09 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 55.37 E-value: 5.55e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 120 QQNAL-----SFLQKENNSLLFADTGSGKTEIYISLIKECLEQG--KQALLLMPEIALTPQMQKRLEVYFKDNFFlwHSK 192
Cdd:pfam04851 8 QIEAIenlleSIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGpiKKVLFLVPRKDLLEQALEEFKKFLPNYVE--IGE 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 193 ISK--KKKQEYLECFckgevlLVAGARSALFLPFRNL---------GLIVVDEEH---DNSYKASNQPFINARDLALflg 258
Cdd:pfam04851 86 IISgdKKDESVDDNK------IVVTTIQSLYKALELAslellpdffDVIIIDEAHrsgASSYRNILEYFKPAFLLGL--- 156
|
170
....*....|....
gi 1160598055 259 qknnikvvlgSATP 272
Cdd:pfam04851 157 ----------TATP 160
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
129-236 |
2.31e-08 |
|
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350792 [Multi-domain] Cd Length: 200 Bit Score: 54.58 E-value: 2.31e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 129 KENNSLLFADTGSGKTEIYISLIKECLEQ-------GKQALLLMPEIALTPQMQKRLEVYFKDNFFLWHSK--ISKKKKQ 199
Cdd:cd18034 15 LKRNTIVVLPTGSGKTLIAVMLIKEMGELnrkeknpKKRAVFLVPTVPLVAQQAEAIRSHTDLKVGEYSGEmgVDKWTKE 94
|
90 100 110 120
....*....|....*....|....*....|....*....|...
gi 1160598055 200 EYLECFCKGEVlLVAGARSAL------FLPFRNLGLIVVDEEH 236
Cdd:cd18034 95 RWKEELEKYDV-LVMTAQILLdalrhgFLSLSDINLLIFDECH 136
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
115-236 |
2.21e-07 |
|
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. It is a member of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350750 [Multi-domain] Cd Length: 225 Bit Score: 52.15 E-value: 2.21e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 115 KLSNQQQNALS------FLQKENNSLLFADTGSGKTEIYISLIKECLEQGKQALLLMP-EIaLTPQMQKRLEVYFKD--- 184
Cdd:cd17992 45 ELTGAQKRVIDeilrdlASEKPMNRLLQGDVGSGKTVVAALAMLAAVENGYQVALMAPtEI-LAEQHYDSLKKLLEPlgi 123
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*
gi 1160598055 185 NFFLWHSKISKKKKQEYLECFCKGEVLLVAGARsALF---LPFRNLGLIVVDEEH 236
Cdd:cd17992 124 RVALLTGSTKAKEKREILEKIASGEIDIVIGTH-ALIqedVEFHNLGLVIIDEQH 177
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
109-236 |
3.83e-07 |
|
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase RecG family is part of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350676 [Multi-domain] Cd Length: 180 Bit Score: 50.49 E-value: 3.83e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 109 FFKDTP-KLSNQQQNALSFLQKENNS------LLFADTGSGKTEIYISLIKECLEQGKQALLLMPEIALTPQMQKRLEVY 181
Cdd:cd17918 8 LCKSLPfSLTKDQAQAIKDIEKDLHSpepmdrLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEARKF 87
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 1160598055 182 FKD-NFFLwhskISKKKKQEYLEcfckgEVLLVAGARSALFL--PFRNLGLIVVDEEH 236
Cdd:cd17918 88 LPFiNVEL----VTGGTKAQILS-----GISLLVGTHALLHLdvKFKNLDLVIVDEQH 136
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
408-491 |
9.16e-07 |
|
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.
Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 47.59 E-value: 9.16e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 408 KIAKFDSDeiTSVKKLNTILKNFNENKIDILIGTSMLAKGHDYHSVDLSVILGLDeyllrpsfraseETLALAMQVAGRA 487
Cdd:pfam00271 40 KVARLHGD--LSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLP------------WNPASYIQRIGRA 105
|
....
gi 1160598055 488 GRKG 491
Cdd:pfam00271 106 GRAG 109
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
87-236 |
2.75e-06 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 50.51 E-value: 2.75e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 87 ASKLGFvlGFFETSPKYE--CQKMFFKDTPklsNQQQ--NA-LSFLQK--ENNSLLFADTGSGKTEIYISLIKECLEQGK 159
Cdd:PRK10689 576 AAKEGF--AFKHDREQYQlfCDSFPFETTP---DQAQaiNAvLSDMCQplAMDRLVCGDVGFGKTEVAMRAAFLAVENHK 650
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 160 QALLLMPEIALTPQMQKRlevyFKDNFFLWHSKI-------SKKKKQEYLECFCKGEVLLVAGARSALF--LPFRNLGLI 230
Cdd:PRK10689 651 QVAVLVPTTLLAQQHYDN----FRDRFANWPVRIemlsrfrSAKEQTQILAEAAEGKIDILIGTHKLLQsdVKWKDLGLL 726
|
....*.
gi 1160598055 231 VVDEEH 236
Cdd:PRK10689 727 IVDEEH 732
|
|
| DEXHc_LHR-like |
cd17922 |
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ... |
131-236 |
3.43e-06 |
|
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases from the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350680 [Multi-domain] Cd Length: 166 Bit Score: 47.58 E-value: 3.43e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 131 NNSLLFADTGSGKTE-----IYISLIKEClEQGKQALLLMPEIALTPQMQKRLEVYFKDNFF-----LWHSKISKKKKQE 200
Cdd:cd17922 2 RNVLIAAPTGSGKTEaaflpALSSLADEP-EKGVQVLYISPLKALINDQERRLEEPLDEIDLeipvaVRHGDTSQSEKAK 80
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 1160598055 201 YL-----------ECFckgEVLLVAGARSALflpFRNLGLIVVDEEH 236
Cdd:cd17922 81 QLknppgilittpESL---ELLLVNKKLREL---FAGLRYVVVDEIH 121
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
115-490 |
5.67e-06 |
|
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, recombination and repair];
Pssm-ID: 443274 [Multi-domain] Cd Length: 451 Bit Score: 49.10 E-value: 5.67e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 115 KLSNQQQNA----LSFLQKENNSLLFADTGSGKTEIYISLIKECLEQGKQALLLMPEIALTPQMQKRLEVYFKD-NFFLW 189
Cdd:COG4098 110 TLTPAQQKAsdelLEAIKKKEEHLVWAVCGAGKTEMLFPAIAEALKQGGRVCIATPRVDVVLELAPRLQQAFPGvDIAAL 189
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 190 HSKiSKKKKqeylecfcKGEVLLVAGARSAL-FlpFRNLGLIVVDEE-----HDNS--YKASNQpfinARdlalflgqKN 261
Cdd:COG4098 190 YGG-SEEKY--------RYAQLVIATTHQLLrF--YQAFDLLIIDEVdafpySGDPmlQYAVKR----AR--------KP 246
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 262 NIKVVLGSATPSlTSFYKQ-KSFRLKGTF--------------FESKKHFLYDENELGITPMLLSELEKSLKHQKQAIVF 326
Cdd:COG4098 247 DGKLIYLTATPS-KALQRQvKRGKLKVVKlparyhghplpvpkFKWLGNWKKRLRRGKLPRKLLKWLKKRLKEGRQLLIF 325
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 327 LPTRanfrqiickdcgetikcpfcsiamsmhkkknilkchycnytSLIEQncpsckgemlearkigtaeLLELLQNALPL 406
Cdd:COG4098 326 VPTI-----------------------------------------ELLEQ-------------------LVALLQKLFPE 345
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 407 AKI----AKfDSDEITSVKKlntilknFNENKIDILIGTSMLAKGHDYHSVDLsVILGLDEYLlrpsFraSEETLalaMQ 482
Cdd:COG4098 346 ERIagvhAE-DPERKEKVQA-------FRDGEIPILVTTTILERGVTFPNVDV-AVLGADHPV----F--TEAAL---VQ 407
|
....*...
gi 1160598055 483 VAGRAGRK 490
Cdd:COG4098 408 IAGRVGRS 415
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
120-272 |
1.03e-05 |
|
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350684 [Multi-domain] Cd Length: 146 Bit Score: 45.76 E-value: 1.03e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 120 QQNAL-SFLQKENN--SLLFADTGSGKTEIYISLIKECLEQGkqALLLMPEIALTPQMQKRLEVYFkdnfflwHSKISKK 196
Cdd:cd17926 5 QEEALeAWLAHKNNrrGILVLPTGSGKTLTALALIAYLKELR--TLIVVPTDALLDQWKERFEDFL-------GDSSIGL 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 197 KKQEYLECFcKGEVLLVAGARSA------LFLPFRNLGLIVVDEEHDnsykasnqpfINARDLALFLGQKNNIKVVLGSA 270
Cdd:cd17926 76 IGGGKKKDF-DDANVVVATYQSLsnlaeeEKDLFDQFGLLIVDEAHH----------LPAKTFSEILKELNAKYRLGLTA 144
|
..
gi 1160598055 271 TP 272
Cdd:cd17926 145 TP 146
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
120-496 |
1.56e-05 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 48.10 E-value: 1.56e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 120 QQNALS-----FLQKENNSLLFADTGSGKTEIYISLIKEcLEQGKQALLLMPEIALTPQMQKRLEVYFKDnfflwhSKIS 194
Cdd:COG1061 85 QQEALEallaaLERGGGRGLVVAPTGTGKTVLALALAAE-LLRGKRVLVLVPRRELLEQWAEELRRFLGD------PLAG 157
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 195 KKKKQEylecfckGEVLLVAG----ARSALFLPFRNL-GLIVVDEEH---DNSYKASNQPFINARDLALflgqknnikvv 266
Cdd:COG1061 158 GGKKDS-------DAPITVATyqslARRAHLDELGDRfGLVIIDEAHhagAPSYRRILEAFPAAYRLGL----------- 219
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 267 lgSATPsltsfykqksFRLKGtffESKKHFLYDENELGITpmlLSELEKSlKHQKQAIVF-LPTRANFRQIICKDCGETI 345
Cdd:COG1061 220 --TATP----------FRSDG---REILLFLFDGIVYEYS---LKEAIED-GYLAPPEYYgIRVDLTDERAEYDALSERL 280
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 346 KcpfcsIAMSMHKKKNILKChycnyTSLIEQNCPSCKGeMLEARKIGTAELL-ELLQNAlpLAKIAKFDSDeiTSVKKLN 424
Cdd:COG1061 281 R-----EALAADAERKDKIL-----RELLREHPDDRKT-LVFCSSVDHAEALaELLNEA--GIRAAVVTGD--TPKKERE 345
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1160598055 425 TILKNFNENKIDILIGTSMLAKGHDYHSVDLSVIlgldeylLRPSfraseETLALAMQVAGR----AGRKGKARVL 496
Cdd:COG1061 346 EILEAFRDGELRILVTVDVLNEGVDVPRLDVAIL-------LRPT-----GSPREFIQRLGRglrpAPGKEDALVY 409
|
|
| PRK14873 |
PRK14873 |
primosomal protein N'; |
208-273 |
2.34e-05 |
|
primosomal protein N';
Pssm-ID: 237844 [Multi-domain] Cd Length: 665 Bit Score: 47.24 E-value: 2.34e-05
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1160598055 208 GEVLLVAGARSALFLPFRNLGLIVVDEEHDNSYKASNQPFINARDLALFLGQKNNIKVVLGSATPS 273
Cdd:PRK14873 239 GQARVVVGTRSAVFAPVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAHQHGCALLIGGHART 304
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
109-233 |
3.88e-05 |
|
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350682 [Multi-domain] Cd Length: 189 Bit Score: 44.63 E-value: 3.88e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 109 FFKD---TPKLSNQQQNALSFLQKENNSLLfADTGSGKT------EIYISLikecleQGKQALLLMPEIALTPQMQKRLE 179
Cdd:cd17924 9 FFKKktgFPPWGAQRTWAKRLLRGKSFAII-APTGVGKTtfglatSLYLAS------KGKRSYLIFPTKSLVKQAYERLS 81
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1160598055 180 VY-----FKDNFFLWHSKISKKKKQEYLECFCKGEV-LLVAgarSALFLP--FRNLG-----LIVVD 233
Cdd:cd17924 82 KYaekagVEVKILVYHSRLKKKEKEELLEKIEKGDFdILVT---TNQFLSknFDLLSnkkfdFVFVD 145
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
418-492 |
1.29e-04 |
|
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350172 [Multi-domain] Cd Length: 77 Bit Score: 40.77 E-value: 1.29e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1160598055 418 TSVKKLNTIlknfnENKIDILIGTSMLAKGHDYHSVDLSVILGldeyllRPSFRASeetlalAMQVAGRAGRKGK 492
Cdd:cd18785 11 NSIEHAEEI-----ASSLEILVATNVLGEGIDVPSLDTVIFFD------PPSSAAS------YIQRVGRAGRGGK 68
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
120-241 |
9.63e-03 |
|
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350790 [Multi-domain] Cd Length: 163 Bit Score: 37.16 E-value: 9.63e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160598055 120 QQNAL-----SFLQKENNSLLFADTGSGKTEIYISLIKECLEQG--KQALLLMPEIALTPQMQKRLEVYFKDNFFlwhSK 192
Cdd:cd18032 5 QQEAIealeeAREKGQRRALLVMATGTGKTYTAAFLIKRLLEANrkKRILFLAHREELLEQAERSFKEVLPDGSF---GN 81
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 1160598055 193 ISKKKKQEYlecfcKGEVL------LVAGARSALFLP--FrnlGLIVVDEEHDNSYK 241
Cdd:cd18032 82 LKGGKKKPD-----DARVVfatvqtLNKRKRLEKFPPdyF---DLIIIDEAHHAIAS 130
|
|
| |
