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Conserved domains on  [gi|827480655|ref|WP_047235421|]
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DEAD/DEAH box helicase [Streptococcus pyogenes]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 11467865)

DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ComFA COG4098
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ...
 1-433 0e+00

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: 632.29  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655   1 MESI-ENSYGRLLLESQLPDS--------ARQLAQPLKSVVISRGKMICQRCHYQLDEE-----ARLPSGAYYCRFCLVF 66
Cdd:COG4098    1 MEELqEFLYGRLLLREELPFSlellqallLRGYVQTLPAIKKEPGKWRCQRCGNTDRKLfafpcARCGQGCYYCRNCIQM 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  67 GRNQSDKLLYAIPPMHF--PKGNYLVWSGQLTAYQEMISQQLLINMQNQKTTLVHAVTGAGKTEMIYAAIEAVINTGGWV 144
Cdd:COG4098   81 GRVSSCTPLYYWPGPNKkePKSNPLTWEGTLTPAQQKASDELLEAIKKKEEHLVWAVCGAGKTEMLFPAIAEALKQGGRV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 145 CIASPRVDVCVEVATRLSQAF-SCSICLMHAES-LPYQRAPIIVATTHQLLKFHKAFDLLIIDEVDAFPFVNNIQLHYAA 222
Cdd:COG4098  161 CIATPRVDVVLELAPRLQQAFpGVDIAALYGGSeEKYRYAQLVIATTHQLLRFYQAFDLLIIDEVDAFPYSGDPMLQYAV 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 223 SQALKEGGAKILLTATSTRTLERKVNKGEVVKLTLARRFHNRPLVIPKFIRSFNLFKMIHRQKLPPKILKYLKKQRKTGY 302
Cdd:COG4098  241 KRARKPDGKLIYLTATPSKALQRQVKRGKLKVVKLPARYHGHPLPVPKFKWLGNWKKRLRRGKLPRKLLKWLKKRLKEGR 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 303 PLLIFLPTIIMAESVTAILKELLPAEQIACVSSQSQNRKEDITAFRQGKKTILITTTILERGVTFPQIDVFVLGSHHRVY 382
Cdd:COG4098  321 QLLIFVPTIELLEQLVALLQKLFPEERIAGVHAEDPERKEKVQAFRDGEIPILVTTTILERGVTFPNVDVAVLGADHPVF 400

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|.
gi 827480655 383 SSQSLVQIAGRVGRSIDRPDGTLYFFHEGISKAMLLARKEIKEMNYKGYSH 433
Cdd:COG4098  401 TEAALVQIAGRVGRSADYPTGEVIFFHHGKTRAMKRAIREIKRMNREAKKR 451
 
Name Accession Description Interval E-value
ComFA COG4098
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ...
 1-433 0e+00

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: 632.29  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655   1 MESI-ENSYGRLLLESQLPDS--------ARQLAQPLKSVVISRGKMICQRCHYQLDEE-----ARLPSGAYYCRFCLVF 66
Cdd:COG4098    1 MEELqEFLYGRLLLREELPFSlellqallLRGYVQTLPAIKKEPGKWRCQRCGNTDRKLfafpcARCGQGCYYCRNCIQM 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  67 GRNQSDKLLYAIPPMHF--PKGNYLVWSGQLTAYQEMISQQLLINMQNQKTTLVHAVTGAGKTEMIYAAIEAVINTGGWV 144
Cdd:COG4098   81 GRVSSCTPLYYWPGPNKkePKSNPLTWEGTLTPAQQKASDELLEAIKKKEEHLVWAVCGAGKTEMLFPAIAEALKQGGRV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 145 CIASPRVDVCVEVATRLSQAF-SCSICLMHAES-LPYQRAPIIVATTHQLLKFHKAFDLLIIDEVDAFPFVNNIQLHYAA 222
Cdd:COG4098  161 CIATPRVDVVLELAPRLQQAFpGVDIAALYGGSeEKYRYAQLVIATTHQLLRFYQAFDLLIIDEVDAFPYSGDPMLQYAV 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 223 SQALKEGGAKILLTATSTRTLERKVNKGEVVKLTLARRFHNRPLVIPKFIRSFNLFKMIHRQKLPPKILKYLKKQRKTGY 302
Cdd:COG4098  241 KRARKPDGKLIYLTATPSKALQRQVKRGKLKVVKLPARYHGHPLPVPKFKWLGNWKKRLRRGKLPRKLLKWLKKRLKEGR 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 303 PLLIFLPTIIMAESVTAILKELLPAEQIACVSSQSQNRKEDITAFRQGKKTILITTTILERGVTFPQIDVFVLGSHHRVY 382
Cdd:COG4098  321 QLLIFVPTIELLEQLVALLQKLFPEERIAGVHAEDPERKEKVQAFRDGEIPILVTTTILERGVTFPNVDVAVLGADHPVF 400

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|.
gi 827480655 383 SSQSLVQIAGRVGRSIDRPDGTLYFFHEGISKAMLLARKEIKEMNYKGYSH 433
Cdd:COG4098  401 TEAALVQIAGRVGRSADYPTGEVIFFHHGKTRAMKRAIREIKRMNREAKKR 451
DEXDc_ComFA cd17925
DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon ...
 98-238 9.69e-68

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: 212.16  E-value: 9.69e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  98 YQEMISQQLLINMQNQKTTLVHAVTGAGKTEMIYAAIEAVINTGGWVCIASPRVDVCVEVATRLSQAFS-CSICLMHAES 176
Cdd:cd17925    1 GQQKASNALVETIDAKEDLLVWAVTGAGKTEMLFPAIAQALRQGGRVAIASPRIDVCLELAPRLKAAFPgAAIVLLHGGS 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 827480655 177 L-PYQRAPIIVATTHQLLKFHKAFDLLIIDEVDAFPFVNNIQLHYAASQALKEGGAKILLTAT 238
Cdd:cd17925   81 EdQYQRSPLVIATTHQLLRFYRAFDLLIIDEVDAFPYAGDPMLYYAVEKARKEEGSLIYLTAT 143
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 289-396 4.24e-13

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: 65.31  E-value: 4.24e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  289 KILKYLKKQRktGYPLLIFLPTIIMAEsvtaiLKELLPAEQIACV---SSQSQN-RKEDITAFRQGKKTILITTTILERG 364
Cdd:pfam00271   5 ALLELLKKER--GGKVLIFSQTKKTLE-----AELLLEKEGIKVArlhGDLSQEeREEILEDFRKGKIDVLVATDVAERG 77

                          90       100       110
                  ....*....|....*....|....*....|...
gi 827480655  365 VTFPQID-VFVLGSHhrvYSSQSLVQIAGRVGR 396
Cdd:pfam00271  78 LDLPDVDlVINYDLP---WNPASYIQRIGRAGR 107
DEXDc smart00487
DEAD-like helicases superfamily;
94-245 4.49e-11

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 62.12  E-value: 4.49e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655    94 QLTAYQEMISQQLLINMQNqktTLVHAVTGAGKTE-MIYAAIEAVINTGGW-VCIASPRVDVCVEVATRLSQAFSC---- 167
Cdd:smart00487   8 PLRPYQKEAIEALLSGLRD---VILAAPTGSGKTLaALLPALEALKRGKGGrVLVLVPTRELAEQWAEELKKLGPSlglk 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655   168 SICLMHAESLPYQR-------APIIVATTHQLLKF-------HKAFDLLIIDEVDAFPFVNNIQLHYAASQALKEGGAKI 233
Cdd:smart00487  85 VVGLYGGDSKREQLrklesgkTDILVTTPGRLLDLlendklsLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLL 164

                          170
                   ....*....|..
gi 827480655   234 LLTATSTRTLER 245
Cdd:smart00487 165 LLSATPPEEIEN 176
priA TIGR00595
primosomal protein N'; All proteins in this family for which functions are known are ...
 117-399 1.91e-10

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: 62.79  E-value: 1.91e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  117 LVHAVTGAGKTEMIYAAIEAVINTGGWVCIASPRVDVCVEVATRLSQAFSCSICLMHA-----------ESLPYQRAPII 185
Cdd:TIGR00595   1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSglsdseklqawRKVKNGEILVV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  186 VATTHQLLKFHKAFDLLIIDEVDAFPFVN-NIQLHYAASQAL---KEGGAKILLtATSTRTLE--RKVNKGEVVKLTLAR 259
Cdd:TIGR00595  81 IGTRSALFLPFKNLGLIIVDEEHDSSYKQeEGPRYHARDVAVyraKKFNCPVVL-GSATPSLEsyHNAKQKAYRLLVLTR 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  260 RFHNRPLVIPKFIrsfNLFKMIHRQKLPPKILKYLKKQRKTGYPLLIFLP----------------------TIIMA--- 314
Cdd:TIGR00595 160 RVSGRKPPEVKLI---DMRKEPRQSFLSPELITAIEQTLAAGEQSILFLNrrgysknllcrscgyilccpncDVSLTyhk 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  315 -----------------------------------ESVTAILKELLPAEQIACVSSQSQNRKED----ITAFRQGKKTIL 355
Cdd:TIGR00595 237 kegklrchycgyqepipktcpqcgsedlvykgygtEQVEEELAKLFPGARIARIDSDTTSRKGAhealLNQFANGKADIL 316

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 827480655  356 ITTTILERGVTFPQID-VFVLGSHHRVYSS---------QSLVQIAGRVGRSID 399
Cdd:TIGR00595 317 IGTQMIAKGHHFPNVTlVGVLDADSGLHSPdfraaergfQLLTQVAGRAGRAED 370
 
Name Accession Description Interval E-value
ComFA COG4098
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ...
 1-433 0e+00

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: 632.29  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655   1 MESI-ENSYGRLLLESQLPDS--------ARQLAQPLKSVVISRGKMICQRCHYQLDEE-----ARLPSGAYYCRFCLVF 66
Cdd:COG4098    1 MEELqEFLYGRLLLREELPFSlellqallLRGYVQTLPAIKKEPGKWRCQRCGNTDRKLfafpcARCGQGCYYCRNCIQM 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  67 GRNQSDKLLYAIPPMHF--PKGNYLVWSGQLTAYQEMISQQLLINMQNQKTTLVHAVTGAGKTEMIYAAIEAVINTGGWV 144
Cdd:COG4098   81 GRVSSCTPLYYWPGPNKkePKSNPLTWEGTLTPAQQKASDELLEAIKKKEEHLVWAVCGAGKTEMLFPAIAEALKQGGRV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 145 CIASPRVDVCVEVATRLSQAF-SCSICLMHAES-LPYQRAPIIVATTHQLLKFHKAFDLLIIDEVDAFPFVNNIQLHYAA 222
Cdd:COG4098  161 CIATPRVDVVLELAPRLQQAFpGVDIAALYGGSeEKYRYAQLVIATTHQLLRFYQAFDLLIIDEVDAFPYSGDPMLQYAV 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 223 SQALKEGGAKILLTATSTRTLERKVNKGEVVKLTLARRFHNRPLVIPKFIRSFNLFKMIHRQKLPPKILKYLKKQRKTGY 302
Cdd:COG4098  241 KRARKPDGKLIYLTATPSKALQRQVKRGKLKVVKLPARYHGHPLPVPKFKWLGNWKKRLRRGKLPRKLLKWLKKRLKEGR 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 303 PLLIFLPTIIMAESVTAILKELLPAEQIACVSSQSQNRKEDITAFRQGKKTILITTTILERGVTFPQIDVFVLGSHHRVY 382
Cdd:COG4098  321 QLLIFVPTIELLEQLVALLQKLFPEERIAGVHAEDPERKEKVQAFRDGEIPILVTTTILERGVTFPNVDVAVLGADHPVF 400

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|.
gi 827480655 383 SSQSLVQIAGRVGRSIDRPDGTLYFFHEGISKAMLLARKEIKEMNYKGYSH 433
Cdd:COG4098  401 TEAALVQIAGRVGRSADYPTGEVIFFHHGKTRAMKRAIREIKRMNREAKKR 451
DEXDc_ComFA cd17925
DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon ...
 98-238 9.69e-68

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: 212.16  E-value: 9.69e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  98 YQEMISQQLLINMQNQKTTLVHAVTGAGKTEMIYAAIEAVINTGGWVCIASPRVDVCVEVATRLSQAFS-CSICLMHAES 176
Cdd:cd17925    1 GQQKASNALVETIDAKEDLLVWAVTGAGKTEMLFPAIAQALRQGGRVAIASPRIDVCLELAPRLKAAFPgAAIVLLHGGS 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 827480655 177 L-PYQRAPIIVATTHQLLKFHKAFDLLIIDEVDAFPFVNNIQLHYAASQALKEGGAKILLTAT 238
Cdd:cd17925   81 EdQYQRSPLVIATTHQLLRFYRAFDLLIIDEVDAFPYAGDPMLYYAVEKARKEEGSLIYLTAT 143
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
92-394 1.21e-22

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 100.48  E-value: 1.21e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  92 SGQLTAYQEMISQQLLINM-QNQKTTLVHAVTGAGKTEMIYAAIEAVInTGGWVCIASPRVDVCVEVATRLSQAFSCSIC 170
Cdd:COG1061   78 SFELRPYQQEALEALLAALeRGGGRGLVVAPTGTGKTVLALALAAELL-RGKRVLVLVPRRELLEQWAEELRRFLGDPLA 156

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 171 LMHAESLpyqRAPIIVATTHQLLK------FHKAFDLLIIDEVdafpfvnniqlHYAAS----QALKEGGAKILL--TAT 238
Cdd:COG1061  157 GGGKKDS---DAPITVATYQSLARrahldeLGDRFGLVIIDEA-----------HHAGApsyrRILEAFPAAYRLglTAT 222

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 239 ----STRTLERKVNKGEVVKLTLAR----------RFHNRPLVIPKFIRSFNLFK------MIHRQKLPPKILKYLKKQR 298
Cdd:COG1061  223 pfrsDGREILLFLFDGIVYEYSLKEaiedgylappEYYGIRVDLTDERAEYDALSerlreaLAADAERKDKILRELLREH 302

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 299 KTGYPLLIFLPTIIMAESVTAILKELlpAEQIACVSSQSQN--RKEDITAFRQGKKTILITTTILERGVTFPQIDVFVLG 376
Cdd:COG1061  303 PDDRKTLVFCSSVDHAEALAELLNEA--GIRAAVVTGDTPKkeREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILL 380

                        330
                 ....*....|....*...
gi 827480655 377 SHHRvySSQSLVQIAGRV 394
Cdd:COG1061  381 RPTG--SPREFIQRLGRG 396
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 116-238 4.59e-14

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: 69.35  E-value: 4.59e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 116 TLVHAVTGAGKTEMIY-AAIEAVINTGGWVCIASPRVDVCVEVATRLSQAFSC--SICLMHAESLPYQR-------APII 185
Cdd:cd00046    4 VLITAPTGSGKTLAALlAALLLLLKKGKKVLVLVPTKALALQTAERLRELFGPgiRVAVLVGGSSAEEReknklgdADII 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 827480655 186 VATTHQLLK--------FHKAFDLLIIDEVDAFPFVN-NIQLHYAASQALKEGGAK-ILLTAT 238
Cdd:cd00046   84 IATPDMLLNlllredrlFLKDLKLIIVDEAHALLIDSrGALILDLAVRKAGLKNAQvILLSAT 146
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 289-396 4.24e-13

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: 65.31  E-value: 4.24e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  289 KILKYLKKQRktGYPLLIFLPTIIMAEsvtaiLKELLPAEQIACV---SSQSQN-RKEDITAFRQGKKTILITTTILERG 364
Cdd:pfam00271   5 ALLELLKKER--GGKVLIFSQTKKTLE-----AELLLEKEGIKVArlhGDLSQEeREEILEDFRKGKIDVLVATDVAERG 77

                          90       100       110
                  ....*....|....*....|....*....|...
gi 827480655  365 VTFPQID-VFVLGSHhrvYSSQSLVQIAGRVGR 396
Cdd:pfam00271  78 LDLPDVDlVINYDLP---WNPASYIQRIGRAGR 107
DEXDc smart00487
DEAD-like helicases superfamily;
94-245 4.49e-11

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 62.12  E-value: 4.49e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655    94 QLTAYQEMISQQLLINMQNqktTLVHAVTGAGKTE-MIYAAIEAVINTGGW-VCIASPRVDVCVEVATRLSQAFSC---- 167
Cdd:smart00487   8 PLRPYQKEAIEALLSGLRD---VILAAPTGSGKTLaALLPALEALKRGKGGrVLVLVPTRELAEQWAEELKKLGPSlglk 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655   168 SICLMHAESLPYQR-------APIIVATTHQLLKF-------HKAFDLLIIDEVDAFPFVNNIQLHYAASQALKEGGAKI 233
Cdd:smart00487  85 VVGLYGGDSKREQLrklesgkTDILVTTPGRLLDLlendklsLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLL 164

                          170
                   ....*....|..
gi 827480655   234 LLTATSTRTLER 245
Cdd:smart00487 165 LLSATPPEEIEN 176
priA TIGR00595
primosomal protein N'; All proteins in this family for which functions are known are ...
 117-399 1.91e-10

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: 62.79  E-value: 1.91e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  117 LVHAVTGAGKTEMIYAAIEAVINTGGWVCIASPRVDVCVEVATRLSQAFSCSICLMHA-----------ESLPYQRAPII 185
Cdd:TIGR00595   1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSglsdseklqawRKVKNGEILVV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  186 VATTHQLLKFHKAFDLLIIDEVDAFPFVN-NIQLHYAASQAL---KEGGAKILLtATSTRTLE--RKVNKGEVVKLTLAR 259
Cdd:TIGR00595  81 IGTRSALFLPFKNLGLIIVDEEHDSSYKQeEGPRYHARDVAVyraKKFNCPVVL-GSATPSLEsyHNAKQKAYRLLVLTR 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  260 RFHNRPLVIPKFIrsfNLFKMIHRQKLPPKILKYLKKQRKTGYPLLIFLP----------------------TIIMA--- 314
Cdd:TIGR00595 160 RVSGRKPPEVKLI---DMRKEPRQSFLSPELITAIEQTLAAGEQSILFLNrrgysknllcrscgyilccpncDVSLTyhk 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  315 -----------------------------------ESVTAILKELLPAEQIACVSSQSQNRKED----ITAFRQGKKTIL 355
Cdd:TIGR00595 237 kegklrchycgyqepipktcpqcgsedlvykgygtEQVEEELAKLFPGARIARIDSDTTSRKGAhealLNQFANGKADIL 316

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 827480655  356 ITTTILERGVTFPQID-VFVLGSHHRVYSS---------QSLVQIAGRVGRSID 399
Cdd:TIGR00595 317 IGTQMIAKGHHFPNVTlVGVLDADSGLHSPdfraaergfQLLTQVAGRAGRAED 370
HELICc smart00490
helicase superfamily c-terminal domain;
320-396 2.77e-10

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 56.45  E-value: 2.77e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655   320 ILKELLPAEQIACV---SSQSQNRKEDI-TAFRQGKKTILITTTILERGVTFPQID-VFVLGSHhrvYSSQSLVQIAGRV 394
Cdd:smart00490   2 ELAELLKELGIKVArlhGGLSQEEREEIlDKFNNGKIKVLVATDVAERGLDLPGVDlVIIYDLP---WSPASYIQRIGRA 78


                   ..
gi 827480655   395 GR 396
Cdd:smart00490  79 GR 80
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 91-425 2.44e-09

CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 440816 [Multi-domain]  Cd Length: 535  Bit Score: 59.32  E-value: 2.44e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  91 WSGQLTAYQEMISQQLLINMQNQK--TTLVhAVTGAGKTEMIYAAIEAVINTGGwvciaSPRVDVCV-------EVATRL 161
Cdd:COG1203  124 PRTPINPLQNEALELALEAAEEEPglFILT-APTGGGKTEAALLFALRLAAKHG-----GRRIIYALpftsiinQTYDRL 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 162 SQAFSCSICLMHAESLPYQR---------------------APIIVAT------------THQLLKFHKAFD-LLIIDEV 207
Cdd:COG1203  198 RDLFGEDVLLHHSLADLDLLeeeeeyesearwlkllkelwdAPVVVTTidqlfeslfsnrKGQERRLHNLANsVIILDEV 277

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 208 DAFPfVNNIQLHYAASQALKEGGAK-ILLTAT-STRTLERKVNKGEVVKltlarrfhNRPLVIPKFIRSFN------LFK 279
Cdd:COG1203  278 QAYP-PYMLALLLRLLEWLKNLGGSvILMTATlPPLLREELLEAYELIP--------DEPEELPEYFRAFVrkrvelKEG 348

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 280 MIHRQKLPPKILKYLKKQRKTgyplLIFLPTIIMAESVTAILKELLPAEQIACVSSQ----SQNRKED--ITAFRQGKKT 353
Cdd:COG1203  349 PLSDEELAELILEALHKGKSV----LVIVNTVKDAQELYEALKEKLPDEEVYLLHSRfcpaDRSEIEKeiKERLERGKPC 424

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 827480655 354 ILITTTILERGV--TFPqidvfvlgshhRVYSS----QSLVQIAGRVGRSIDRPD-GTLYFFHEGISKAMLLARKEIKE 425
Cdd:COG1203  425 ILVSTQVVEAGVdiDFD-----------VVIRDlaplDSLIQRAGRCNRHGRKEEeGNVYVFDPEDEGGGYVYDKPLLE 492
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 290-401 4.89e-08

C-terminal helicase domain of LHR family helicases; 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. LHR family helicases are DEAD-like helicases 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: 350183 [Multi-domain]  Cd Length: 150  Bit Score: 51.88  E-value: 4.89e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 290 ILKYLKKQRKTgyplLIFLPTIIMAESVTAILKELLPA----EQIAC-VSSQSQNRKEDI-TAFRQGKKTILITTTILER 363
Cdd:cd18796   31 VIFLLERHKST----LVFTNTRSQAERLAQRLRELCPDrvppDFIALhHGSLSRELREEVeAALKRGDLKVVVATSSLEL 106

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 827480655 364 GVTFPQID-VFVLGShhrVYSSQSLVQIAGRVGRSIDRP 401
Cdd:cd18796  107 GIDIGDVDlVIQIGS---PKSVARLLQRLGRSGHRPGAA 142
DEXHc_priA cd17929
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ...
 94-260 1.23e-07

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: 51.44  E-value: 1.23e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  94 QLTAYqEMISQQLLINmqnqKTTLVHAVTGAGKTEMIYAAIEAVINTGGWVCIASPRVDVCVEVATRLSQAFSCSICLMH 173
Cdd:cd17929    1 QRKAY-EAIVSSLGGF----KTFLLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGDKVAVLH 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 174 AESLPYQR-----------APIIVATTHQLLKFHKAFDLLIIDE-------VDAFPFVNNIQLhyAASQALKEgGAKILL 235
Cdd:cd17929   76 SKLSDKERadewrkikrgeAKVVIGARSALFAPFKNLGLIIVDEehdssykQDSGPRYHARDV--AIYRAKLE-NAPVVL 152

                        170       180
                 ....*....|....*....|....*..
gi 827480655 236 tATSTRTLE--RKVNKGEVVKLTLARR 260
Cdd:cd17929  153 -GSATPSLEsyYNAQQGKYRLLQLTER 178
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 289-396 1.29e-07

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 50.20  E-value: 1.29e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 289 KILKYLKKQRKTGYPLLIFLPTIIMAESVTAILKELlpaeQIACV---SSQSQN-RKEDITAFRQGKKTILITTTILERG 364
Cdd:cd18787   15 LLLLLLLLEKLKPGKAIIFVNTKKRVDRLAELLEEL----GIKVAalhGDLSQEeRERALKKFRSGKVRVLVATDVAARG 90

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 827480655 365 VTFPQIDV------------FVlgshHRVyssqslvqiaGRVGR 396
Cdd:cd18787   91 LDIPGVDHvinydlprdaedYV----HRI----------GRTGR 120
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
 302-397 5.48e-07

C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. They are DEAD-like helicases 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: 350179 [Multi-domain]  Cd Length: 160  Bit Score: 49.19  E-value: 5.48e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 302 YPLlIFLPTIIMAESVTAI---LKELLPAEQIACVSSQ-SQNRKEDI-TAFRQGKKTILITTTILERGVTFPQIDVFVLG 376
Cdd:cd18792   33 YPR-IEESEKLDLKSIEALaeeLKELVPEARVALLHGKmTEDEKEAVmLEFREGEYDILVSTTVIEVGIDVPNANTMIIE 111

                         90       100
                 ....*....|....*....|.
gi 827480655 377 SHHRVYSSQsLVQIAGRVGRS 397
Cdd:cd18792  112 DADRFGLSQ-LHQLRGRVGRG 131
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 280-397 6.01e-07

C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It 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: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 48.88  E-value: 6.01e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 280 MIHRQKLPPKILKYLKKQRKTGYPLLIFLPTIIMAE-----SVTAI---LKELLPAE-QIACVSSQ-SQNRKEDI-TAFR 348
Cdd:cd18811    5 YLIFHTRLDKVYEFVREEIAKGRQAYVIYPLIEESEkldlkAAVAMyeyLKERFRPElNVGLLHGRlKSDEKDAVmAEFR 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 827480655 349 QGKKTILITTTILERGVTFPQIDVFVLGSHHRVYSSQsLVQIAGRVGRS 397
Cdd:cd18811   85 EGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQ-LHQLRGRVGRG 132
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 96-245 7.97e-06

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: 45.70  E-value: 7.97e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655   96 TAYQEMISQQLLinmqNQKTTLVHAVTGAGKTEM-IYAAIEAV--INTGGWVCIASPRVDVCVEVATRLSQAFSCS---- 168
Cdd:pfam00270   1 TPIQAEAIPAIL----EGRDVLVQAPTGSGKTLAfLLPALEALdkLDNGPQALVLAPTRELAEQIYEELKKLGKGLglkv 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  169 ICLMHAESLPYQR-----APIIVATTHQLL------KFHKAFDLLIIDEVDAFpFVNNIQLHYAAS-QALKEGGAKILLT 236
Cdd:pfam00270  77 ASLLGGDSRKEQLeklkgPDILVGTPGRLLdllqerKLLKNLKLLVLDEAHRL-LDMGFGPDLEEIlRRLPKKRQILLLS 155


                  ....*....
gi 827480655  237 ATSTRTLER 245
Cdd:pfam00270 156 ATLPRNLED 164
SF2_C_priA cd18804
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ...
 315-400 2.42e-05

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: 45.31  E-value: 2.42e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 315 ESVTAILKELLPAEQIACVSSQSQNRKED----ITAFRQGKKTILITTTILERGVTFPQID-VFVL----GSHHRVYSS- 384
Cdd:cd18804  104 ERVEEELKTLFPEARIARIDRDTTRKKGAleklLDQFERGEIDILIGTQMIAKGLDFPNVTlVGILnadsGLNSPDFRAs 183

                         90       100
                 ....*....|....*....|
gi 827480655 385 ----QSLVQIAGRVGRSIDR 400
Cdd:cd18804  184 erafQLLTQVSGRAGRGDKP 203
ResIII pfam04851
Type III restriction enzyme, res subunit;
94-207 3.21e-05

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 44.20  E-value: 3.21e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655   94 QLTAYQEMISQQLLINM-QNQKTTLVHAVTGAGKTEMIYAAIEAVINTGGwvciaSPRVDVCV---EVATRLSQAFSC-- 167
Cdd:pfam04851   3 ELRPYQIEAIENLLESIkNGQKRGLIVMATGSGKTLTAAKLIARLFKKGP-----IKKVLFLVprkDLLEQALEEFKKfl 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 827480655  168 SICLMHAESL-------PYQRAPIIVATTHQL---------LKFHKAFDLLIIDEV 207
Cdd:pfam04851  78 PNYVEIGEIIsgdkkdeSVDDNKIVVTTIQSLykalelaslELLPDFFDVIIIDEA 133
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
 315-397 1.61e-04

C-terminal 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 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: 350197 [Multi-domain]  Cd Length: 151  Bit Score: 41.95  E-value: 1.61e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 315 ESVTAILKELLPAEQIACVSSQSQNRKEDIT--AFRQGKKTILITTTILERGVTFPQIDVFVLGSHHRVYSSQsLVQIAG 392
Cdd:cd18810   39 EKLATQLRQLVPEARIAIAHGQMTENELEEVmlEFAKGEYDILVCTTIIESGIDIPNANTIIIERADKFGLAQ-LYQLRG 117


                 ....*
gi 827480655 393 RVGRS 397
Cdd:cd18810  118 RVGRS 122
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 294-397 2.82e-04

ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, recombination and repair];


Pssm-ID: 440818 [Multi-domain]  Cd Length: 758  Bit Score: 43.29  E-value: 2.82e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 294 LKKQRKTgyplLIFLPTIIMAESVTAILKELLPAEQIA-CVSS-----QSQNRKEDITAFRQGKKTILITTTILERGVTF 367
Cdd:COG1205  285 VREGLRT----LVFTRSRRGAELLARYARRALREPDLAdRVAAyragyLPEERREIERGLRSGELLGVVSTNALELGIDI 360

                         90       100       110
                 ....*....|....*....|....*....|....
gi 827480655 368 PQIDVFVL----GSHhrvyssQSLVQIAGRVGRS 397
Cdd:COG1205  361 GGLDAVVLagypGTR------ASFWQQAGRAGRR 388
mfd TIGR00580
transcription-repair coupling factor (mfd); All proteins in this family for which functions ...
 185-397 3.41e-04

transcription-repair coupling factor (mfd); All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273152 [Multi-domain]  Cd Length: 926  Bit Score: 43.11  E-value: 3.41e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  185 IVATTHQLL----KFhKAFDLLIIDEVDAFPfVNniqlhyaASQALKEGGAKI-LLTATST---RTLE---RKVNKGEVV 253
Cdd:TIGR00580 557 ILIGTHKLLqkdvKF-KDLGLLIIDEEQRFG-VK-------QKEKLKELRTSVdVLTLSATpipRTLHmsmSGIRDLSII 627

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  254 KLTLARRfhnrpLVIPKFIRSFNlfkmihrqklpPKILK--YLKKQRKTGYPLLIFlPTIIMAESVTAILKELLPAEQIA 331
Cdd:TIGR00580 628 ATPPEDR-----LPVRTFVMEYD-----------PELVReaIRRELLRGGQVFYVH-NRIESIEKLATQLRELVPEARIA 690

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 827480655  332 CVSSQ-SQNRKEDI-TAFRQGKKTILITTTILERGVTFPQIDVFVLGSHHRVYSSQsLVQIAGRVGRS 397
Cdd:TIGR00580 691 IAHGQmTENELEEVmLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQ-LYQLRGRVGRS 757
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 305-396 2.11e-03

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: 36.91  E-value: 2.11e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 305 LIFLPTIIMAESVTAILKellpaeqiacvssqsqnrkeditafrqgkktILITTTILERGVTFPQID-VFVLGshhRVYS 383
Cdd:cd18785    7 IVFTNSIEHAEEIASSLE-------------------------------ILVATNVLGEGIDVPSLDtVIFFD---PPSS 52

                         90
                 ....*....|...
gi 827480655 384 SQSLVQIAGRVGR 396
Cdd:cd18785   53 AASYIQRVGRAGR 65
PriA COG1198
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ...
 94-173 6.32e-03

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


Pssm-ID: 440811 [Multi-domain]  Cd Length: 728  Bit Score: 38.95  E-value: 6.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655  94 QLTAYQEMISQQLLINMQNQKTTLVHAVTGAGKTEmIY-AAIEAVINTGGWVCIASPrvdvcvEVA------TRLSQAFS 166
Cdd:COG1198  195 TLNEEQQAAVEAIRAAAGGFSVFLLHGVTGSGKTE-VYlQAIAEVLAQGKQALVLVP------EIAltpqtvERFRARFG 267


                 ....*..
gi 827480655 167 CSICLMH 173
Cdd:COG1198  268 ARVAVLH 274
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 116-207 6.95e-03

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: 37.63  E-value: 6.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 116 TLVHAVTGAGKTEMIYAAIEAVINTGGWVCI-ASPRVDVCVEVATRLSQAFS-----CSICLMHAESLPYQ--RAPIIVA 187
Cdd:cd17921   20 VLVSAPTSSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGplgknVGLLTGDPSVNKLLlaEADILVA 99

                         90       100
                 ....*....|....*....|....*...
gi 827480655 188 TTHQLL--------KFHKAFDLLIIDEV 207
Cdd:cd17921  100 TPEKLDlllrnggeRLIQDVRLVVVDEA 127
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
 290-429 7.95e-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: 37.22  E-value: 7.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 827480655 290 ILKYLKKQRKTGYPLLIFLPTIIMAESVTAILKELlpAEQIACVSSQ--SQNRKEDITAFRQGKKTILITTTILERGVTF 367
Cdd:cd18790   16 LLGEIRKRVARGERVLVTTLTKRMAEDLTEYLQEL--GVKVRYLHSEidTLERVEIIRDLRLGEFDVLVGINLLREGLDL 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 827480655 368 PQID-VFVLGSHHRVY--SSQSLVQIAGRVGRSIdrpDGTLYFFHEGISKAMllaRKEIKEMNYK 429
Cdd:cd18790   94 PEVSlVAILDADKEGFlrSETSLIQTIGRAARNV---NGKVILYADKITDSM---QKAIEETERR 152
 
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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