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Conserved domains on  [gi|1519541156|gb|AZB02080|]
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primosomal protein N' [Chryseobacterium joostei]

Protein Classification

primosomal protein N'( domain architecture ID 11439891)

primosomal protein N' is involved in the restart of stalled replication forks, as well as in initiation of normal DNA replication in various plasmids and phages

EC:  3.6.4.-
Gene Ontology:  GO:0006268|GO:0005524|GO:0003678|GO:0006260|GO:0032508|GO:0003677
PubMed:  1667219|23264623|17483094

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PriA COG1198
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ...
 1-782 0e+00

Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];


:

Pssm-ID: 440811 [Multi-domain]  Cd Length: 728  Bit Score: 770.44  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156   1 MQYTQIVLPLNLKGSFTYRVPEElMSEIQLGMRVLVPFGGKKIyTGIVFELH---DLAPENFvaKDVISILDDKPILPEE 77
Cdd:COG1198     1 MKIAEVALPVPLDRPFDYLVPEG-LELVQPGSRVLVPFGRRQV-VGIVVGLKeesDVDPAKL--KPILAVLDDEPLLPEE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156  78 QISFWNWLSEYYLCNLGEIYRFAFPSSLKLESETYLKLKPGVVVdfenldvnemylvqalevrqlvnltdieafipkkei 157
Cdd:COG1198    77 LLELLRWVADYYLCPLGEVLRLALPAGLRQGYPARIKTERYVRL------------------------------------ 120

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 158 iktinslidlqyieidekiaekykakevayvkvngdvlnnqNLTEILLKLnkAPKQKELfLLILEKQTEKpdlhIKKAEL 237
Cdd:COG1198   121 -----------------------------------------TLGEELPKR--APKQRRV-LEALREHGGP----LTLSEL 152

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 238 FEDGYFGSSHFKALADKGLVEEYHMQKDR-IESYDGEIEELEELSEQQKIAKSEIDEAFEEKKNVLLHGVTSSGKTHIYL 316
Cdd:COG1198   153 AKEAGVSRSVLKALVKKGLLEIEEREVDRdPFAPDVPAEPPPTLNEEQQAAVEAIRAAAGGFSVFLLHGVTGSGKTEVYL 232

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 317 EKIEECVRNGQNVLFLLPEISLTKQITQRLEKKYGRQLGFYHQKLTDFERVEVWRRVKQNDIRILVGTRNALFLPYQNLG 396
Cdd:COG1198   233 QAIAEVLAQGKQALVLVPEIALTPQTVERFRARFGARVAVLHSGLSDGERLDEWRRARRGEARIVIGTRSALFAPFPNLG 312

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 397 LIVVDEEHDSAYKPREvSPYFNAKDAALVLGGLYEAGVILGSATPSVESYYRARKDKMKYIFLDARFGNVNLPEYELINF 476
Cdd:COG1198   313 LIIVDEEHDSSYKQED-GPRYHARDVAVVRAKLEGAPVVLGSATPSLESLYNAQKGRYRLLELPERAGGAPLPEVELVDM 391

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 477 KEaqESKKVSGNFSLRLIDEIKKTVDEKNQAIVLHNRRGYANVVECETCGYVNYCSNCDVVMTYHKAANEMKCHYCGQRA 556
Cdd:COG1198   392 RE--EPLEGGRILSPPLLEAIEETLERGEQVLLFLNRRGYAPFLLCRDCGWVAKCPNCDVSLTYHRSRRRLRCHYCGYEE 469

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 557 SKPKTCPKCNSEKLNERGVGVEQIHEEVSKIFPENEVDRMDVDSMRKKFAYEKLYEKIEDGETDIVVGTQMISKGLDFDH 636
Cdd:COG1198   470 PVPKQCPECGSDSLRPFGPGTERVEEELAELFPDARVLRMDRDTTRRKGALEKLLEAFARGEADILVGTQMLAKGHDFPN 549

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 637 IELVAIPKADSLLYVQDFRAEERAYQLITQVSGRAGRVSGKGRILIQTYNPDHSVFQLIKMNNPAKIYKYILTERQKFNY 716
Cdd:COG1198   550 VTLVGVLDADLGLNSPDFRAAERTFQLLTQVAGRAGRAEKPGEVLIQTYNPEHPVIQALLNHDYEAFYEEELAERKAAGY 629

                         730       740       750       760       770       780
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1519541156 717 PPFTKLIMIELKHRRDDKVDRASQFLGSILRKYLPED--CILGPERAQIARLNNLYQFQILLKLPRGK 782
Cdd:COG1198   630 PPFGRLALLRASGKDEEAAEEFAQALARALRALLSADgvEVLGPAPAPIARLRGRYRWQLLLKAPSRA 697
 
Name Accession Description Interval E-value
PriA COG1198
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ...
 1-782 0e+00

Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];


Pssm-ID: 440811 [Multi-domain]  Cd Length: 728  Bit Score: 770.44  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156   1 MQYTQIVLPLNLKGSFTYRVPEElMSEIQLGMRVLVPFGGKKIyTGIVFELH---DLAPENFvaKDVISILDDKPILPEE 77
Cdd:COG1198     1 MKIAEVALPVPLDRPFDYLVPEG-LELVQPGSRVLVPFGRRQV-VGIVVGLKeesDVDPAKL--KPILAVLDDEPLLPEE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156  78 QISFWNWLSEYYLCNLGEIYRFAFPSSLKLESETYLKLKPGVVVdfenldvnemylvqalevrqlvnltdieafipkkei 157
Cdd:COG1198    77 LLELLRWVADYYLCPLGEVLRLALPAGLRQGYPARIKTERYVRL------------------------------------ 120

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 158 iktinslidlqyieidekiaekykakevayvkvngdvlnnqNLTEILLKLnkAPKQKELfLLILEKQTEKpdlhIKKAEL 237
Cdd:COG1198   121 -----------------------------------------TLGEELPKR--APKQRRV-LEALREHGGP----LTLSEL 152

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 238 FEDGYFGSSHFKALADKGLVEEYHMQKDR-IESYDGEIEELEELSEQQKIAKSEIDEAFEEKKNVLLHGVTSSGKTHIYL 316
Cdd:COG1198   153 AKEAGVSRSVLKALVKKGLLEIEEREVDRdPFAPDVPAEPPPTLNEEQQAAVEAIRAAAGGFSVFLLHGVTGSGKTEVYL 232

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 317 EKIEECVRNGQNVLFLLPEISLTKQITQRLEKKYGRQLGFYHQKLTDFERVEVWRRVKQNDIRILVGTRNALFLPYQNLG 396
Cdd:COG1198   233 QAIAEVLAQGKQALVLVPEIALTPQTVERFRARFGARVAVLHSGLSDGERLDEWRRARRGEARIVIGTRSALFAPFPNLG 312

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 397 LIVVDEEHDSAYKPREvSPYFNAKDAALVLGGLYEAGVILGSATPSVESYYRARKDKMKYIFLDARFGNVNLPEYELINF 476
Cdd:COG1198   313 LIIVDEEHDSSYKQED-GPRYHARDVAVVRAKLEGAPVVLGSATPSLESLYNAQKGRYRLLELPERAGGAPLPEVELVDM 391

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 477 KEaqESKKVSGNFSLRLIDEIKKTVDEKNQAIVLHNRRGYANVVECETCGYVNYCSNCDVVMTYHKAANEMKCHYCGQRA 556
Cdd:COG1198   392 RE--EPLEGGRILSPPLLEAIEETLERGEQVLLFLNRRGYAPFLLCRDCGWVAKCPNCDVSLTYHRSRRRLRCHYCGYEE 469

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 557 SKPKTCPKCNSEKLNERGVGVEQIHEEVSKIFPENEVDRMDVDSMRKKFAYEKLYEKIEDGETDIVVGTQMISKGLDFDH 636
Cdd:COG1198   470 PVPKQCPECGSDSLRPFGPGTERVEEELAELFPDARVLRMDRDTTRRKGALEKLLEAFARGEADILVGTQMLAKGHDFPN 549

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 637 IELVAIPKADSLLYVQDFRAEERAYQLITQVSGRAGRVSGKGRILIQTYNPDHSVFQLIKMNNPAKIYKYILTERQKFNY 716
Cdd:COG1198   550 VTLVGVLDADLGLNSPDFRAAERTFQLLTQVAGRAGRAEKPGEVLIQTYNPEHPVIQALLNHDYEAFYEEELAERKAAGY 629

                         730       740       750       760       770       780
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1519541156 717 PPFTKLIMIELKHRRDDKVDRASQFLGSILRKYLPED--CILGPERAQIARLNNLYQFQILLKLPRGK 782
Cdd:COG1198   630 PPFGRLALLRASGKDEEAAEEFAQALARALRALLSADgvEVLGPAPAPIARLRGRYRWQLLLKAPSRA 697
PRK05580 PRK05580
primosome assembly protein PriA; Validated
 1-787 0e+00

primosome assembly protein PriA; Validated


Pssm-ID: 235514 [Multi-domain]  Cd Length: 679  Bit Score: 669.17  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156   1 MQYTQIVLPLNLKGSFTYRVPEELmsEIQLGMRVLVPFGGKKIyTGIVFELHDLAP-ENFVAKDVISILDDKPILPEEQI 79
Cdd:PRK05580    2 MKIARVLLPVPLPRPFDYLIPEGL--EVQPGDRVRVPFGNRKL-IGVVVGVEEGSEvPADKLKPILEVLDLEPLLPPELL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156  80 SFWNWLSEYYLCNLGEIYRFAFPSSLKLEsetylklkpgvvvdfenldvnemylvqalevrqlvnltdieafipkkeiik 159
Cdd:PRK05580   79 RLLDWAADYYLSPLGEVLRLALLAELALA--------------------------------------------------- 107

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 160 tinslidlqyieidekiaekykakevayvkvngdvlnnqnlteillklnkapkqkelfllilekqtekpdlhikkaelfe 239
Cdd:PRK05580      --------------------------------------------------------------------------------

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 240 dgyFGSSHFKALADKGLVEEYHMQKDRIESYDGEIEELEELSEQQKIAKSEIDEAfEEKKNVLLHGVTSSGKTHIYLEKI 319
Cdd:PRK05580  108 ---ASSAVLKGLVKKGLIELEEVEVLRLRPPPDPAFEPPTLNPEQAAAVEAIRAA-AGFSPFLLDGVTGSGKTEVYLQAI 183

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 320 EECVRNGQNVLFLLPEISLTKQITQRLEKKYGRQLGFYHQKLTDFERVEVWRRVKQNDIRILVGTRNALFLPYQNLGLIV 399
Cdd:PRK05580  184 AEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALFLPFKNLGLII 263

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 400 VDEEHDSAYKPREvSPYFNAKDAALVLGGLYEAGVILGSATPSVESYYRARKDKMKYIFLDARFGNVNLPEYELINFKEA 479
Cdd:PRK05580  264 VDEEHDSSYKQQE-GPRYHARDLAVVRAKLENIPVVLGSATPSLESLANAQQGRYRLLRLTKRAGGARLPEVEIIDMREL 342

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 480 QESKKVSGnFSLRLIDEIKKTVDEKNQAIVLHNRRGYANVVECETCGYVNYCSNCDVVMTYHKAANEMKCHYCGQRASKP 559
Cdd:PRK05580  343 LRGENGSF-LSPPLLEAIKQRLERGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIP 421

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 560 KTCPKCNSEKLNERGVGVEQIHEEVSKIFPENEVDRMDVDSMRKKFAYEKLYEKIEDGETDIVVGTQMISKGLDFDHIEL 639
Cdd:PRK05580  422 KACPECGSTDLVPVGPGTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTL 501

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 640 VAIPKADSLLYVQDFRAEERAYQLITQVSGRAGRVSGKGRILIQTYNPDHSVFQLIKMNNPAKIYKYILTERQKFNYPPF 719
Cdd:PRK05580  502 VGVLDADLGLFSPDFRASERTFQLLTQVAGRAGRAEKPGEVLIQTYHPEHPVIQALLAQDYDAFAEQELEERRAAGYPPF 581

                         730       740       750       760       770       780       790
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 720 TKLIMIELKHRRDDKVDRASQFLGSILRKYLPED--CILGPERAQIARLNNLYQFQILLKLPRGKNYERF 787
Cdd:PRK05580  582 GRLALLRASAKDEEKAEKFAQQLAALLPNLLPLLdvEVLGPAPAPIAKIAGRYRYQLLLKSPSRADLQKL 651
priA TIGR00595
primosomal protein N'; All proteins in this family for which functions are known are ...
 302-781 0e+00

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: 531.19  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 302 LLHGVTSSGKTHIYLEKIEECVRNGQNVLFLLPEISLTKQITQRLEKKYGRQLGFYHQKLTDFERVEVWRRVKQNDIRIL 381
Cdd:TIGR00595   1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 382 VGTRNALFLPYQNLGLIVVDEEHDSAYKPREVsPYFNAKDAALVLGGLYEAGVILGSATPSVESYYRARKDKMKYIFLDA 461
Cdd:TIGR00595  81 IGTRSALFLPFKNLGLIIVDEEHDSSYKQEEG-PRYHARDVAVYRAKKFNCPVVLGSATPSLESYHNAKQKAYRLLVLTR 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 462 RFGNVNLPEYELINFKEAqeskKVSGNFSLRLIDEIKKTVDEKNQAIVLHNRRGYANVVECETCGYVNYCSNCDVVMTYH 541
Cdd:TIGR00595 160 RVSGRKPPEVKLIDMRKE----PRQSFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLTYH 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 542 KAANEMKCHYCGQRASKPKTCPKCNSEKLNERGVGVEQIHEEVSKIFPENEVDRMDVDSMRKKFAYEKLYEKIEDGETDI 621
Cdd:TIGR00595 236 KKEGKLRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADI 315

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 622 VVGTQMISKGLDFDHIELVAIPKADSLLYVQDFRAEERAYQLITQVSGRAGRVSGKGRILIQTYNPDHSVFQLIKMNNPA 701
Cdd:TIGR00595 316 LIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVIIQTYNPNHPAIQAALTGDYE 395

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 702 KIYKYILTERQKFNYPPFTKLIMIELKHRRDDKVDRASQFLGSILRKYLPEDC-ILGPERAQIARLNNLYQFQILLKLPR 780
Cdd:TIGR00595 396 AFYEQELAQRRALNYPPFTRLIRLIFRGKNEEKAQQTAQAAHELLKQNLDEKLeVLGPSPAPIAKIAGRYRYQILLKSKS 475


                  .
gi 1519541156 781 G 781
Cdd:TIGR00595 476 F 476
SF2_C_priA cd18804
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ...
 472-712 4.30e-111

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: 338.45  E-value: 4.30e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 472 ELINFKEaqesKKVSGNFSLRLIDEIKKTVDEKNQAIVLHNRRGYANVVECETCGYVNYCSNCDVVMTYHKAANEMKCHY 551
Cdd:cd18804     2 EIVDMKE----EELKSGFSPKLLDAIKETLEKGEQVILFLNRRGYSPSVLCRDCGYVPECPNCDVSMTYHKSTNKLKCHY 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 552 CGQRASKPKTCPKCNSEKLNERGVGVEQIHEEVSKIFPENEVDRMDVDSMRKKFAYEKLYEKIEDGETDIVVGTQMISKG 631
Cdd:cd18804    78 CGYQEPIPKQCPECGSEDLVFKGIGTERVEEELKTLFPEARIARIDRDTTRKKGALEKLLDQFERGEIDILIGTQMIAKG 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 632 LDFDHIELVAIPKADSLLYVQDFRAEERAYQLITQVSGRAGRVSGKGRILIQTYNPDHSVFQLIKMNNPAKIYKYILTER 711
Cdd:cd18804   158 LDFPNVTLVGILNADSGLNSPDFRASERAFQLLTQVSGRAGRGDKPGKVIIQTYNPEHPLIQAAKEEDYEAFYEEELAER 237


                  .
gi 1519541156 712 Q 712
Cdd:cd18804   238 K 238
PriA_3primeBD pfam17764
3'DNA-binding domain (3'BD); This domain represents the N-terminal DNA-binding domain found in ...
 5-102 3.95e-34

3'DNA-binding domain (3'BD); This domain represents the N-terminal DNA-binding domain found in the PriA protein. The 3'BD, which has been shown to bind the 3' end of the leading-strand arm of replication fork structures.


Pssm-ID: 465491 [Multi-domain]  Cd Length: 96  Bit Score: 125.65  E-value: 3.95e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156   5 QIVLPLNLKGSFTYRVPEELmsEIQLGMRVLVPFGGKKiYTGIVFELHDLAP-ENFVAKDVISILDDKPILPEEQISFWN 83
Cdd:pfam17764   1 EVAVPLPLDRPFDYRVPEEL--AVKIGMRVLVPFGKRK-VTGIVVGLSEESEvDPEKLKPILEVLDEEPLLTPELLELAR 77

                          90
                  ....*....|....*....
gi 1519541156  84 WLSEYYLCNLGEIYRFAFP 102
Cdd:pfam17764  78 WMAEYYLCPLGEVLRAALP 96
DEXDc smart00487
DEAD-like helicases superfamily;
291-466 2.25e-15

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 75.61  E-value: 2.25e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156  291 IDEAFEEKKNVLLHGVTSSGKTHIYLEKIEECVRNGQN--VLFLLPEISLTKQITQRLEKKYGRQLGFYHQKLTDFERVE 368
Cdd:smart00487  17 IEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGgrVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKRE 96

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156  369 VWRRVKQNDIRILVGTRNALF-------LPYQNLGLIVVDEEHdsaykprEVSPYFNAKDAALVLGGLYEAG-VILGSAT 440
Cdd:smart00487  97 QLRKLESGKTDILVTTPGRLLdllendkLSLSNVDLVILDEAH-------RLLDGGFGDQLEKLLKLLPKNVqLLLLSAT 169

                          170       180
                   ....*....|....*....|....*.
gi 1519541156  441 PSVESYYRARKDKMKYIFLDARFGNV 466
Cdd:smart00487 170 PPEEIENLLELFLNDPVFIDVGFTPL 195
 
Name Accession Description Interval E-value
PriA COG1198
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ...
 1-782 0e+00

Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];


Pssm-ID: 440811 [Multi-domain]  Cd Length: 728  Bit Score: 770.44  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156   1 MQYTQIVLPLNLKGSFTYRVPEElMSEIQLGMRVLVPFGGKKIyTGIVFELH---DLAPENFvaKDVISILDDKPILPEE 77
Cdd:COG1198     1 MKIAEVALPVPLDRPFDYLVPEG-LELVQPGSRVLVPFGRRQV-VGIVVGLKeesDVDPAKL--KPILAVLDDEPLLPEE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156  78 QISFWNWLSEYYLCNLGEIYRFAFPSSLKLESETYLKLKPGVVVdfenldvnemylvqalevrqlvnltdieafipkkei 157
Cdd:COG1198    77 LLELLRWVADYYLCPLGEVLRLALPAGLRQGYPARIKTERYVRL------------------------------------ 120

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 158 iktinslidlqyieidekiaekykakevayvkvngdvlnnqNLTEILLKLnkAPKQKELfLLILEKQTEKpdlhIKKAEL 237
Cdd:COG1198   121 -----------------------------------------TLGEELPKR--APKQRRV-LEALREHGGP----LTLSEL 152

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 238 FEDGYFGSSHFKALADKGLVEEYHMQKDR-IESYDGEIEELEELSEQQKIAKSEIDEAFEEKKNVLLHGVTSSGKTHIYL 316
Cdd:COG1198   153 AKEAGVSRSVLKALVKKGLLEIEEREVDRdPFAPDVPAEPPPTLNEEQQAAVEAIRAAAGGFSVFLLHGVTGSGKTEVYL 232

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 317 EKIEECVRNGQNVLFLLPEISLTKQITQRLEKKYGRQLGFYHQKLTDFERVEVWRRVKQNDIRILVGTRNALFLPYQNLG 396
Cdd:COG1198   233 QAIAEVLAQGKQALVLVPEIALTPQTVERFRARFGARVAVLHSGLSDGERLDEWRRARRGEARIVIGTRSALFAPFPNLG 312

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 397 LIVVDEEHDSAYKPREvSPYFNAKDAALVLGGLYEAGVILGSATPSVESYYRARKDKMKYIFLDARFGNVNLPEYELINF 476
Cdd:COG1198   313 LIIVDEEHDSSYKQED-GPRYHARDVAVVRAKLEGAPVVLGSATPSLESLYNAQKGRYRLLELPERAGGAPLPEVELVDM 391

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 477 KEaqESKKVSGNFSLRLIDEIKKTVDEKNQAIVLHNRRGYANVVECETCGYVNYCSNCDVVMTYHKAANEMKCHYCGQRA 556
Cdd:COG1198   392 RE--EPLEGGRILSPPLLEAIEETLERGEQVLLFLNRRGYAPFLLCRDCGWVAKCPNCDVSLTYHRSRRRLRCHYCGYEE 469

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 557 SKPKTCPKCNSEKLNERGVGVEQIHEEVSKIFPENEVDRMDVDSMRKKFAYEKLYEKIEDGETDIVVGTQMISKGLDFDH 636
Cdd:COG1198   470 PVPKQCPECGSDSLRPFGPGTERVEEELAELFPDARVLRMDRDTTRRKGALEKLLEAFARGEADILVGTQMLAKGHDFPN 549

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 637 IELVAIPKADSLLYVQDFRAEERAYQLITQVSGRAGRVSGKGRILIQTYNPDHSVFQLIKMNNPAKIYKYILTERQKFNY 716
Cdd:COG1198   550 VTLVGVLDADLGLNSPDFRAAERTFQLLTQVAGRAGRAEKPGEVLIQTYNPEHPVIQALLNHDYEAFYEEELAERKAAGY 629

                         730       740       750       760       770       780
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1519541156 717 PPFTKLIMIELKHRRDDKVDRASQFLGSILRKYLPED--CILGPERAQIARLNNLYQFQILLKLPRGK 782
Cdd:COG1198   630 PPFGRLALLRASGKDEEAAEEFAQALARALRALLSADgvEVLGPAPAPIARLRGRYRWQLLLKAPSRA 697
PRK05580 PRK05580
primosome assembly protein PriA; Validated
 1-787 0e+00

primosome assembly protein PriA; Validated


Pssm-ID: 235514 [Multi-domain]  Cd Length: 679  Bit Score: 669.17  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156   1 MQYTQIVLPLNLKGSFTYRVPEELmsEIQLGMRVLVPFGGKKIyTGIVFELHDLAP-ENFVAKDVISILDDKPILPEEQI 79
Cdd:PRK05580    2 MKIARVLLPVPLPRPFDYLIPEGL--EVQPGDRVRVPFGNRKL-IGVVVGVEEGSEvPADKLKPILEVLDLEPLLPPELL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156  80 SFWNWLSEYYLCNLGEIYRFAFPSSLKLEsetylklkpgvvvdfenldvnemylvqalevrqlvnltdieafipkkeiik 159
Cdd:PRK05580   79 RLLDWAADYYLSPLGEVLRLALLAELALA--------------------------------------------------- 107

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 160 tinslidlqyieidekiaekykakevayvkvngdvlnnqnlteillklnkapkqkelfllilekqtekpdlhikkaelfe 239
Cdd:PRK05580      --------------------------------------------------------------------------------

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 240 dgyFGSSHFKALADKGLVEEYHMQKDRIESYDGEIEELEELSEQQKIAKSEIDEAfEEKKNVLLHGVTSSGKTHIYLEKI 319
Cdd:PRK05580  108 ---ASSAVLKGLVKKGLIELEEVEVLRLRPPPDPAFEPPTLNPEQAAAVEAIRAA-AGFSPFLLDGVTGSGKTEVYLQAI 183

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 320 EECVRNGQNVLFLLPEISLTKQITQRLEKKYGRQLGFYHQKLTDFERVEVWRRVKQNDIRILVGTRNALFLPYQNLGLIV 399
Cdd:PRK05580  184 AEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALFLPFKNLGLII 263

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 400 VDEEHDSAYKPREvSPYFNAKDAALVLGGLYEAGVILGSATPSVESYYRARKDKMKYIFLDARFGNVNLPEYELINFKEA 479
Cdd:PRK05580  264 VDEEHDSSYKQQE-GPRYHARDLAVVRAKLENIPVVLGSATPSLESLANAQQGRYRLLRLTKRAGGARLPEVEIIDMREL 342

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 480 QESKKVSGnFSLRLIDEIKKTVDEKNQAIVLHNRRGYANVVECETCGYVNYCSNCDVVMTYHKAANEMKCHYCGQRASKP 559
Cdd:PRK05580  343 LRGENGSF-LSPPLLEAIKQRLERGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIP 421

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 560 KTCPKCNSEKLNERGVGVEQIHEEVSKIFPENEVDRMDVDSMRKKFAYEKLYEKIEDGETDIVVGTQMISKGLDFDHIEL 639
Cdd:PRK05580  422 KACPECGSTDLVPVGPGTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTL 501

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 640 VAIPKADSLLYVQDFRAEERAYQLITQVSGRAGRVSGKGRILIQTYNPDHSVFQLIKMNNPAKIYKYILTERQKFNYPPF 719
Cdd:PRK05580  502 VGVLDADLGLFSPDFRASERTFQLLTQVAGRAGRAEKPGEVLIQTYHPEHPVIQALLAQDYDAFAEQELEERRAAGYPPF 581

                         730       740       750       760       770       780       790
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 720 TKLIMIELKHRRDDKVDRASQFLGSILRKYLPED--CILGPERAQIARLNNLYQFQILLKLPRGKNYERF 787
Cdd:PRK05580  582 GRLALLRASAKDEEKAEKFAQQLAALLPNLLPLLdvEVLGPAPAPIAKIAGRYRYQLLLKSPSRADLQKL 651
priA TIGR00595
primosomal protein N'; All proteins in this family for which functions are known are ...
 302-781 0e+00

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: 531.19  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 302 LLHGVTSSGKTHIYLEKIEECVRNGQNVLFLLPEISLTKQITQRLEKKYGRQLGFYHQKLTDFERVEVWRRVKQNDIRIL 381
Cdd:TIGR00595   1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 382 VGTRNALFLPYQNLGLIVVDEEHDSAYKPREVsPYFNAKDAALVLGGLYEAGVILGSATPSVESYYRARKDKMKYIFLDA 461
Cdd:TIGR00595  81 IGTRSALFLPFKNLGLIIVDEEHDSSYKQEEG-PRYHARDVAVYRAKKFNCPVVLGSATPSLESYHNAKQKAYRLLVLTR 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 462 RFGNVNLPEYELINFKEAqeskKVSGNFSLRLIDEIKKTVDEKNQAIVLHNRRGYANVVECETCGYVNYCSNCDVVMTYH 541
Cdd:TIGR00595 160 RVSGRKPPEVKLIDMRKE----PRQSFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLTYH 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 542 KAANEMKCHYCGQRASKPKTCPKCNSEKLNERGVGVEQIHEEVSKIFPENEVDRMDVDSMRKKFAYEKLYEKIEDGETDI 621
Cdd:TIGR00595 236 KKEGKLRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADI 315

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 622 VVGTQMISKGLDFDHIELVAIPKADSLLYVQDFRAEERAYQLITQVSGRAGRVSGKGRILIQTYNPDHSVFQLIKMNNPA 701
Cdd:TIGR00595 316 LIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVIIQTYNPNHPAIQAALTGDYE 395

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 702 KIYKYILTERQKFNYPPFTKLIMIELKHRRDDKVDRASQFLGSILRKYLPEDC-ILGPERAQIARLNNLYQFQILLKLPR 780
Cdd:TIGR00595 396 AFYEQELAQRRALNYPPFTRLIRLIFRGKNEEKAQQTAQAAHELLKQNLDEKLeVLGPSPAPIAKIAGRYRYQILLKSKS 475


                  .
gi 1519541156 781 G 781
Cdd:TIGR00595 476 F 476
SF2_C_priA cd18804
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ...
 472-712 4.30e-111

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: 338.45  E-value: 4.30e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 472 ELINFKEaqesKKVSGNFSLRLIDEIKKTVDEKNQAIVLHNRRGYANVVECETCGYVNYCSNCDVVMTYHKAANEMKCHY 551
Cdd:cd18804     2 EIVDMKE----EELKSGFSPKLLDAIKETLEKGEQVILFLNRRGYSPSVLCRDCGYVPECPNCDVSMTYHKSTNKLKCHY 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 552 CGQRASKPKTCPKCNSEKLNERGVGVEQIHEEVSKIFPENEVDRMDVDSMRKKFAYEKLYEKIEDGETDIVVGTQMISKG 631
Cdd:cd18804    78 CGYQEPIPKQCPECGSEDLVFKGIGTERVEEELKTLFPEARIARIDRDTTRKKGALEKLLDQFERGEIDILIGTQMIAKG 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 632 LDFDHIELVAIPKADSLLYVQDFRAEERAYQLITQVSGRAGRVSGKGRILIQTYNPDHSVFQLIKMNNPAKIYKYILTER 711
Cdd:cd18804   158 LDFPNVTLVGILNADSGLNSPDFRASERAFQLLTQVSGRAGRGDKPGKVIIQTYNPEHPLIQAAKEEDYEAFYEEELAER 237


                  .
gi 1519541156 712 Q 712
Cdd:cd18804   238 K 238
DEXHc_priA cd17929
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ...
 284-462 1.95e-78

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: 250.59  E-value: 1.95e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 284 QKIAKSEIDEAFEEKKNVLLHGVTSSGKTHIYLEKIEECVRNGQNVLFLLPEISLTKQITQRLEKKYGRQLGFYHQKLTD 363
Cdd:cd17929     1 QRKAYEAIVSSLGGFKTFLLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGDKVAVLHSKLSD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 364 FERVEVWRRVKQNDIRILVGTRNALFLPYQNLGLIVVDEEHDSAYKPREvSPYFNAKDAALVLGGLYEAGVILGSATPSV 443
Cdd:cd17929    81 KERADEWRKIKRGEAKVVIGARSALFAPFKNLGLIIVDEEHDSSYKQDS-GPRYHARDVAIYRAKLENAPVVLGSATPSL 159

                         170
                  ....*....|....*....
gi 1519541156 444 ESYYRARKDKMKYIFLDAR 462
Cdd:cd17929   160 ESYYNAQQGKYRLLQLTER 178
PriA_3primeBD pfam17764
3'DNA-binding domain (3'BD); This domain represents the N-terminal DNA-binding domain found in ...
 5-102 3.95e-34

3'DNA-binding domain (3'BD); This domain represents the N-terminal DNA-binding domain found in the PriA protein. The 3'BD, which has been shown to bind the 3' end of the leading-strand arm of replication fork structures.


Pssm-ID: 465491 [Multi-domain]  Cd Length: 96  Bit Score: 125.65  E-value: 3.95e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156   5 QIVLPLNLKGSFTYRVPEELmsEIQLGMRVLVPFGGKKiYTGIVFELHDLAP-ENFVAKDVISILDDKPILPEEQISFWN 83
Cdd:pfam17764   1 EVAVPLPLDRPFDYRVPEEL--AVKIGMRVLVPFGKRK-VTGIVVGLSEESEvDPEKLKPILEVLDEEPLLTPELLELAR 77

                          90
                  ....*....|....*....
gi 1519541156  84 WLSEYYLCNLGEIYRFAFP 102
Cdd:pfam17764  78 WMAEYYLCPLGEVLRAALP 96
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 293-442 3.11e-16

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: 76.90  E-value: 3.11e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 293 EAFEEKKNVLLHGVTSSGKTHIY----LEKIEECVRNGQnVLFLLPEISLTKQITQRLEKKYGRQLGFYHQKLTDFERVE 368
Cdd:pfam00270   9 PAILEGRDVLVQAPTGSGKTLAFllpaLEALDKLDNGPQ-ALVLAPTRELAEQIYEELKKLGKGLGLKVASLLGGDSRKE 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 369 VWRRVKqnDIRILVGTRNALFL------PYQNLGLIVVDEEHDSAYKPREvspyfnaKDAALVLGGLYEAG-VILGSATP 441
Cdd:pfam00270  88 QLEKLK--GPDILVGTPGRLLDllqerkLLKNLKLLVLDEAHRLLDMGFG-------PDLEEILRRLPKKRqILLLSATL 158


                  .
gi 1519541156 442 S 442
Cdd:pfam00270 159 P 159
DEXDc smart00487
DEAD-like helicases superfamily;
291-466 2.25e-15

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 75.61  E-value: 2.25e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156  291 IDEAFEEKKNVLLHGVTSSGKTHIYLEKIEECVRNGQN--VLFLLPEISLTKQITQRLEKKYGRQLGFYHQKLTDFERVE 368
Cdd:smart00487  17 IEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGgrVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKRE 96

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156  369 VWRRVKQNDIRILVGTRNALF-------LPYQNLGLIVVDEEHdsaykprEVSPYFNAKDAALVLGGLYEAG-VILGSAT 440
Cdd:smart00487  97 QLRKLESGKTDILVTTPGRLLdllendkLSLSNVDLVILDEAH-------RLLDGGFGDQLEKLLKLLPKNVqLLLLSAT 169

                          170       180
                   ....*....|....*....|....*.
gi 1519541156  441 PSVESYYRARKDKMKYIFLDARFGNV 466
Cdd:smart00487 170 PPEEIENLLELFLNDPVFIDVGFTPL 195
PriA_C pfam18074
Primosomal protein N C-terminal domain; This is the C-terminal domain found in PriA DNA ...
 718-797 1.67e-12

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: 64.16  E-value: 1.67e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 718 PFTKLIMIELKHRRDDKVDRASQFLGSILRKYLPEDC--ILGPERAQIARLNNLYQFQILLKLPRGKNYERFKGLVLISL 795
Cdd:pfam18074   1 PFSRLALIRVSGKDEEKAEKFAEELAELLKELLKLQGveILGPAPAPIAKIKGRYRYQLLLKSKSRKALHQLLRELLEEL 80


                  ..
gi 1519541156 796 KE 797
Cdd:pfam18074  81 QK 82
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 299-440 3.29e-11

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: 62.04  E-value: 3.29e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 299 KNVLLHGVTSSGKTHIYLEKIE-ECVRNGQNVLFLLPEISLTKQITQRLekkygRQLGFYHQK---LTDFERVEVWRRVK 374
Cdd:cd00046     2 ENVLITAPTGSGKTLAALLAALlLLLKKGKKVLVLVPTKALALQTAERL-----RELFGPGIRvavLVGGSSAEEREKNK 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1519541156 375 QNDIRILVGTRNALFLPYQ--------NLGLIVVDEEHDSAYKprevSPYFNAKDAALVLGGLYEAGVILGSAT 440
Cdd:cd00046    77 LGDADIIIATPDMLLNLLLredrlflkDLKLIIVDEAHALLID----SRGALILDLAVRKAGLKNAQVILLSAT 146
ResIII pfam04851
Type III restriction enzyme, res subunit;
283-441 4.21e-11

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 61.92  E-value: 4.21e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 283 QQKIAKSEIDEAFEEKKNVLLHGVTSSGKTHIYLEKIEECVRNG--QNVLFLLPEISLTKQITQRLEK---KYGRQLGFY 357
Cdd:pfam04851   8 QIEAIENLLESIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGpiKKVLFLVPRKDLLEQALEEFKKflpNYVEIGEII 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 358 HQKLTDFERvevwrrvkqNDIRILVGTRNALF---------LPYQNLGLIVVDEEHDSAYKP-REVSPYFNAKdaalvlg 427
Cdd:pfam04851  88 SGDKKDESV---------DDNKIVVTTIQSLYkalelasleLLPDFFDVIIIDEAHRSGASSyRNILEYFKPA------- 151

                         170
                  ....*....|....*
gi 1519541156 428 glyeagVILG-SATP 441
Cdd:pfam04851 152 ------FLLGlTATP 160
PRK14873 PRK14873
primosomal protein N';
365-589 8.76e-11

primosomal protein N';


Pssm-ID: 237844 [Multi-domain]  Cd Length: 665  Bit Score: 65.34  E-value: 8.76e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 365 ERVEVWRRVKQNDIRILVGTRNALFLPYQNLGLIVVDEEHDSAY-KPRevSPYFNAKDAALVLGGLYEAGVILGSATPSV 443
Cdd:PRK14873  228 DRYRRWLAVLRGQARVVVGTRSAVFAPVEDLGLVAIWDDGDDLLaEPR--APYPHAREVALLRAHQHGCALLIGGHARTA 305

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 444 ESYY-------------RAR-KDKMKYIFLdarfgnVNLPEYELinfkEAQESKKvsgnfSLRL----IDEIKKTVDEkN 505
Cdd:PRK14873  306 EAQAlvesgwahdlvapRPVvRARAPRVRA------LGDSGLAL----ERDPAAR-----AARLpslaFRAARDALEH-G 369

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 506 QAIVLHNRRGYANVVECETCGYVNYCSNCDVVMTYHKAANEMKCHYCGqRASKPKTCPKCNSEKLNERGVGVEQIHEEVS 585
Cdd:PRK14873  370 PVLVQVPRRGYVPSLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCG-RAAPDWRCPRCGSDRLRAVVVGARRTAEELG 448


                  ....
gi 1519541156 586 KIFP 589
Cdd:PRK14873  449 RAFP 452
PriA_CRR pfam18319
PriA DNA helicase Cys-rich region (CRR) domain; This is a cys-rich region (CRR) domain found ...
 531-555 7.75e-10

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: 54.46  E-value: 7.75e-10
                          10        20
                  ....*....|....*....|....*
gi 1519541156 531 CSNCDVVMTYHKAANEMKCHYCGQR 555
Cdd:pfam18319   1 CPNCDVSLTYHKSRNRLRCHYCGYT 25
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 291-476 6.68e-08

DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong 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: 350679 [Multi-domain]  Cd Length: 181  Bit Score: 53.03  E-value: 6.68e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 291 IDEAFEEKKNVLLHGVTSSGKTHIYLEKIEECVR-NGQNVLFLLPEISLTKQITQRLEKKYGRQLGfyhqKLTDFERVEV 369
Cdd:cd17921    10 LRALYLSGDSVLVSAPTSSGKTLIAELAILRALAtSGGKAVYIAPTRALVNQKEADLRERFGPLGK----NVGLLTGDPS 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 370 WRRVKQNDIRILVGT--------RNALFLPYQNLGLIVVDEEHDSAYKPRevspyfnakdaalvlGGLYEAGVilgsatp 441
Cdd:cd17921    86 VNKLLLAEADILVATpekldlllRNGGERLIQDVRLVVVDEAHLIGDGER---------------GVVLELLL------- 143

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1519541156 442 sveSYYRARKDKMKYIFLDARFGNVN-----LPEYELINF 476
Cdd:cd17921   144 ---SRLLRINKNARFVGLSATLPNAEdlaewLGVEDLIRF 180
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 293-404 8.93e-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: 53.04  E-value: 8.93e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 293 EAFEE--KKNVLLHGVTSSGKTHIYL----EKIEECVRNGQN---VLFLLPEISLTKQITQRLEKKYGRQLGFYH-QKLT 362
Cdd:cd18034     9 ELFEAalKRNTIVVLPTGSGKTLIAVmlikEMGELNRKEKNPkkrAVFLVPTVPLVAQQAEAIRSHTDLKVGEYSgEMGV 88

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1519541156 363 DFERVEVWRRVKQNdIRILVGT----RNAL---FLPYQNLGLIVVDEEH 404
Cdd:cd18034    89 DKWTKERWKEELEK-YDVLVMTaqilLDALrhgFLSLSDINLLIFDECH 136
DEXHc_RecG cd17918
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ...
 284-412 1.63e-06

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: 48.95  E-value: 1.63e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 284 QKIAKSEIDEAF--EEKKNVLLHGVTSSGKTHIYLEKIEECVRNGQNVLFLLPEISLTKQITQRLEKKYgrqlgfyhqkl 361
Cdd:cd17918    20 QAQAIKDIEKDLhsPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEARKFL----------- 88

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1519541156 362 tDFERVEVWRRVKQNDIR----ILVGTRNALFL--PYQNLGLIVVDEEHDSAYKPRE 412
Cdd:cd17918    89 -PFINVELVTGGTKAQILsgisLLVGTHALLHLdvKFKNLDLVIVDEQHRFGVAQRE 144
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
291-517 1.75e-06

Replicative superfamily II helicase [Replication, recombination and repair];


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 51.43  E-value: 1.75e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 291 IDEAFEEKKNVLLHGVTSSGKTHIYLEKIEECVRNGQNVLFLLPEISLTKQITQRLEKKYgRQLGFYHQKLT-DFERVEV 369
Cdd:COG1204    31 LEAGLLEGKNLVVSAPTASGKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKRDF-EELGIKVGVSTgDYDSDDE 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 370 WrrVKQNDirILVGT---------RNALFLpyQNLGLIVVDEEH--DSAYKprevspyfnakdaalvlGGLYEagVILgs 438
Cdd:COG1204   110 W--LGRYD--ILVATpekldsllrNGPSWL--RDVDLVVVDEAHliDDESR-----------------GPTLE--VLL-- 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 439 atpsveSYYRARKDKMKYIFLDARFGNVNL-----------------PEYELINFKEAQESKKVSGNFSLRLIDEIKKTV 501
Cdd:COG1204   163 ------ARLRRLNPEAQIVALSATIGNAEEiaewldaelvksdwrpvPLNEGVLYDGVLRFDDGSRRSKDPTLALALDLL 236

                         250
                  ....*....|....*.
gi 1519541156 502 DEKNQAIVLHNRRGYA 517
Cdd:COG1204   237 EEGGQVLVFVSSRRDA 252
DEXHc_RecG cd17992
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ...
 284-404 1.84e-06

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: 49.84  E-value: 1.84e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 284 QKIAKSEI--DEAFEEKKNVLLHGVTSSGKTHIYLEKIEECVRNGQNVLFLLP-EIsLTKQITQRLEK---KYGRQLGFY 357
Cdd:cd17992    50 QKRVIDEIlrDLASEKPMNRLLQGDVGSGKTVVAALAMLAAVENGYQVALMAPtEI-LAEQHYDSLKKllePLGIRVALL 128

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1519541156 358 HQKLTDFERVEVWRRVKQNDIRILVGTrNALF---LPYQNLGLIVVDEEH 404
Cdd:cd17992   129 TGSTKAKEKREILEKIASGEIDIVIGT-HALIqedVEFHNLGLVIIDEQH 177
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
284-652 3.07e-06

Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 50.79  E-value: 3.07e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 284 QKIAKSEIDEAFEEK-KNVLLHGVTSSGKTHIYLEKIEEcVRNGQNVLFLLPEISLTKQITQRLEKKYGRQLGFyhqklt 362
Cdd:COG1061    85 QQEALEALLAALERGgGRGLVVAPTGTGKTVLALALAAE-LLRGKRVLVLVPRRELLEQWAEELRRFLGDPLAG------ 157

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 363 dfervevwRRVKQNDIRILVGT------RNALFLPYQNLGLIVVDEEHD-SAYKPREVSPYFNAKdaalvlgglyeagVI 435
Cdd:COG1061   158 --------GGKKDSDAPITVATyqslarRAHLDELGDRFGLVIIDEAHHaGAPSYRRILEAFPAA-------------YR 216

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 436 LG-SATPsvesyyrARKDKmKYIFLDaRFGNV--NLPEYELIN---FKEAQ-ESKKVSGNFSLRLIDEIKKTVDEK---- 504
Cdd:COG1061   217 LGlTATP-------FRSDG-REILLF-LFDGIvyEYSLKEAIEdgyLAPPEyYGIRVDLTDERAEYDALSERLREAlaad 287

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 505 ---NQAIVLHNRRGYANvvecETCGYVnYCSNcdvvmtyHKAANEMkchycgqraskpktcpkcnSEKLNERGVGVEQIH 581
Cdd:COG1061   288 aerKDKILRELLREHPD----DRKTLV-FCSS-------VDHAEAL-------------------AELLNEAGIRAAVVT 336

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1519541156 582 EEVSKifpeneVDRmdvdsmrkkfayEKLYEKIEDGETDIVVGTQMISKGLDFDHIELVAI--PKADSLLYVQ 652
Cdd:COG1061   337 GDTPK------KER------------EEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILlrPTGSPREFIQ 391
HELICc smart00490
helicase superfamily c-terminal domain;
567-673 9.34e-06

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 44.51  E-value: 9.34e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156  567 SEKLNERGVGVEQIHEEVSKIfpenevDRmdvdsmrkkfayEKLYEKIEDGETDIVVGTQMISKGLDFDHIELVAIPKAD 646
Cdd:smart00490   4 AELLKELGIKVARLHGGLSQE------ER------------EEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP 65

                           90       100
                   ....*....|....*....|....*..
gi 1519541156  647 sllyvqdfraeeRAYQLITQVSGRAGR 673
Cdd:smart00490  66 ------------WSPASYIQRIGRAGR 80
DEXDc_ComFA cd17925
DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon ...
 283-402 1.13e-05

DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon protein 1) is part of the complex mediating the binding and uptake of single-stranded DNA. ComFA is required for DNA uptake but not for binding. It 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: 350683 [Multi-domain]  Cd Length: 143  Bit Score: 45.75  E-value: 1.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 283 QQKIAKsEIDEAFEEKKNVLLHGVTSSGKTHIYLEKIEECVRNGQNVLFLLPEISLTKQITQRLEKKY-GRQLGFYHQKL 361
Cdd:cd17925     2 QQKASN-ALVETIDAKEDLLVWAVTGAGKTEMLFPAIAQALRQGGRVAIASPRIDVCLELAPRLKAAFpGAAIVLLHGGS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1519541156 362 TDFERVEvwrrvkqndiRILVGTRNALFLPYQNLGLIVVDE 402
Cdd:cd17925    81 EDQYQRS----------PLVIATTHQLLRFYRAFDLLIIDE 111
PRK14873 PRK14873
primosomal protein N';
16-103 4.55e-05

primosomal protein N';


Pssm-ID: 237844 [Multi-domain]  Cd Length: 665  Bit Score: 46.85  E-value: 4.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156  16 FTYRVPEELMSEIQLGMRVLVPFGGKKIyTGIVFELHDlaPENFVAK-----DVISildDKPILPEEQISFWNWLSEYYL 90
Cdd:PRK14873   29 FDYLVPEELSDDAQPGVRVRVRFGGRLV-DGFVLERRS--DSDHEGKlrwleRVVS---PEPVLTPEIRRLARAVADRYA 102

                          90
                  ....*....|...
gi 1519541156  91 CNLGEIYRFAFPS 103
Cdd:PRK14873  103 GTRADVLRLAVPP 115
DEXHc_TRCF cd17991
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ...
 310-404 7.58e-05

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: 44.48  E-value: 7.58e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 310 GKTHIYLEKIEECVRNGQNVLFLLPEISLTKQITQRLEKK---YGRQLGFYHQKLTDFERVEVWRRVKQNDIRILVGTRN 386
Cdd:cd17991    48 GKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYETFKERfanFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHR 127

                          90       100
                  ....*....|....*....|
gi 1519541156 387 ALF--LPYQNLGLIVVDEEH 404
Cdd:cd17991   128 LLSkdVEFKNLGLLIIDEEQ 147
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 284-441 2.10e-04

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: 42.29  E-value: 2.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 284 QKIAKSEIDEAFEEKKNVLLHgVTSSGKTHIYLEKIEECVRngQNVLFLLPEISLTKQITQRLEKKYG-RQLGfyhqklt 362
Cdd:cd17926     5 QEEALEAWLAHKNNRRGILVL-PTGSGKTLTALALIAYLKE--LRTLIVVPTDALLDQWKERFEDFLGdSSIG------- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 363 dfeRVEVWRRVKQNDIRILVGTRNALF-------LPYQNLGLIVVDEEHD-SAYKPREVSPYFNAKdaaLVLgGLyeagv 434
Cdd:cd17926    75 ---LIGGGKKKDFDDANVVVATYQSLSnlaeeekDLFDQFGLLIVDEAHHlPAKTFSEILKELNAK---YRL-GL----- 142


                  ....*..
gi 1519541156 435 ilgSATP 441
Cdd:cd17926   143 ---TATP 146
RecG COG1200
RecG-like helicase [Replication, recombination and repair];
365-404 5.30e-04

RecG-like helicase [Replication, recombination and repair];


Pssm-ID: 440813 [Multi-domain]  Cd Length: 684  Bit Score: 43.50  E-value: 5.30e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1519541156 365 ERVEVWRRVKQNDIRILVGTrNALF---LPYQNLGLIVVDEEH 404
Cdd:COG1200   350 ERREILAALASGEADIVVGT-HALIqddVEFKNLGLVVIDEQH 391
COG2888 COG2888
Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 ...
 522-568 6.79e-04

Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 family [General function prediction only];


Pssm-ID: 442134 [Multi-domain]  Cd Length: 52  Bit Score: 38.17  E-value: 6.79e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1519541156 522 CETCG--------YVNYCSNCDVVMTYhkaanemKCHYCGQRASKPKTCPKCNSE 568
Cdd:COG2888     3 CPSCGreiapeggVAFYCPNCGEALII-------RCPKCRKQSNALYFCPKCGFE 50
DDXDc_reverse_gyrase cd17924
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ...
 307-409 1.36e-03

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: 40.77  E-value: 1.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 307 TSSGKT------HIYLekieecVRNGQNVLFLLPEISLTKQITQRLEKKYGRQ-----LGFYHQKLTDFERVEVWRRVKQ 375
Cdd:cd17924    41 TGVGKTtfglatSLYL------ASKGKRSYLIFPTKSLVKQAYERLSKYAEKAgvevkILVYHSRLKKKEKEELLEKIEK 114

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1519541156 376 NDIRILVGT-----RNALFLPYQNLGLIVVDEEhDSAYK 409
Cdd:cd17924   115 GDFDILVTTnqflsKNFDLLSNKKFDFVFVDDV-DAVLK 152
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 608-673 1.97e-03

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 41.76  E-value: 1.97e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1519541156 608 EKLYEKIEDGETDIVVGTQMISKGLDFDHIELVA---IPkADSLLYVQDFRAEERAyqlitqvsGRAGR 673
Cdd:PRK11634  285 EQTLERLKDGRLDILIATDVAARGLDVERISLVVnydIP-MDSESYVHRIGRTGRA--------GRAGR 344
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
 567-677 3.82e-03

C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II), and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA. Its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB 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: 350177 [Multi-domain]  Cd Length: 171  Bit Score: 39.15  E-value: 3.82e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 567 SEKLNERGVGVEQIHEEVSKIfpenevDRMDV-DSMRKkfayeklyekiedGETDIVVGTQMISKGLDFDHIELVAIPKA 645
Cdd:cd18790    44 TEYLQELGVKVRYLHSEIDTL------ERVEIiRDLRL-------------GEFDVLVGINLLREGLDLPEVSLVAILDA 104

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1519541156 646 DsllyVQDFRAEERAyqLItQVSGRAGR-VSGK 677
Cdd:cd18790   105 D----KEGFLRSETS--LI-QTIGRAARnVNGK 130
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 284-442 3.98e-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: 38.70  E-value: 3.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 284 QKIAKSEIDEAFEE-KKNVLLHGVTSSGKTHIYLEKIEECVRNGQN--VLFLLPEISLTKQitqrLEKKYGRQLGFyhqk 360
Cdd:cd18032     5 QQEAIEALEEAREKgQRRALLVMATGTGKTYTAAFLIKRLLEANRKkrILFLAHREELLEQ----AERSFKEVLPD---- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519541156 361 lTDFERVEVWRRVKQNDiRILVGT--------RNALFLPYQnLGLIVVDEEHDSAYKP-REVSPYFNakDAALVlgGLye 431
Cdd:cd18032    77 -GSFGNLKGGKKKPDDA-RVVFATvqtlnkrkRLEKFPPDY-FDLIIIDEAHHAIASSyRKILEYFE--PAFLL--GL-- 147

                         170
                  ....*....|.
gi 1519541156 432 agvilgSATPS 442
Cdd:cd18032   148 ------TATPE 152
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
 365-404 4.08e-03

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 40.52  E-value: 4.08e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1519541156 365 ERVEVWRRVKQNDIRILVGTrNALF---LPYQNLGLIVVDEEH 404
Cdd:PRK10917  352 ERREILEAIASGEADIVIGT-HALIqddVEFHNLGLVIIDEQH 393
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
 578-642 6.75e-03

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 40.13  E-value: 6.75e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1519541156 578 EQIHEEVSKIFPEnevdrMDVD------SMRKKfAYEKLYEKIEDGETDIVVGTQ-MISKGLDFDHIELVAI 642
Cdd:PRK10917  324 EQHYENLKKLLEP-----LGIRvalltgSLKGK-ERREILEAIASGEADIVIGTHaLIQDDVEFHNLGLVII 389
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 608-674 8.82e-03

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: 36.80  E-value: 8.82e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1519541156 608 EKLYEKIEDGETDIVVGTQMISKGLDFDHIELVAIpkadsllyvqdFRAEERAYQLItQVSGRAGRV 674
Cdd:pfam00271  54 EEILEDFRKGKIDVLVATDVAERGLDLPDVDLVIN-----------YDLPWNPASYI-QRIGRAGRA 108
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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