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Conserved domains on  [gi|835584282|ref|WP_047570842|]
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MULTISPECIES: DEAD/DEAH box helicase [Serratia]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 11437332)

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

CATH:  1.20.1320.20|3.40.50.300
EC:  3.6.4.-
Gene Ontology:  GO:0016887|GO:0003676|GO:0004386|GO:0005524
PubMed:  20206133|20225155

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
2-342 6.37e-72

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


:

Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 238.77  E-value: 6.37e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282   2 TLTIQPREKQIVALNMLRAAWKQ-YASFMMYAPVGFGKTAIAALIASGFIsRNMRIMFVAPYTVLLDQTATRFIEYGLPA 80
Cdd:COG1061   76 GTSFELRPYQQEALEALLAALERgGGRGLVVAPTGTGKTVLALALAAELL-RGKRVLVLVPRRELLEQWAEELRRFLGDP 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  81 EEIGyiwrdhPAYDPSRLIQIASADTLIRRD----FPDNIDLLIIDEAH-LKRKKMLEFIDELTAKgvKVIGLSGTPFSA 155
Cdd:COG1061  155 LAGG------GKKDSDAPITVATYQSLARRAhldeLGDRFGLVIIDEAHhAGAPSYRRILEAFPAA--YRLGLTATPFRS 226

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 156 W----LGTYYQKLIKPTTMKELIAIGALSKYEFYaPSHPDLSDvktsEQAGYgRDYNETQSAEVMSDPTLVGDIVKNWL- 230
Cdd:COG1061  227 DgreiLLFLFDGIVYEYSLKEAIEDGYLAPPEYY-GIRVDLTD----ERAEY-DALSERLREALAADAERKDKILRELLr 300

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 231 ENGEDRPTICFCVNVAHANYVTVEFSKAGVTVEVMTAATPHEDRQMTIRRFEQGITKIIINVGVLVAGFD-SDVRCIIFA 309
Cdd:COG1061  301 EHPDDRKTLVFCSSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDvPRLDVAILL 380

                        330       340       350
                 ....*....|....*....|....*....|...
gi 835584282 310 RPTKSEMRWIQILGRGLRPASGKDHCLIFDHTG 342
Cdd:COG1061  381 RPTGSPREFIQRLGRGLRPAPGKEDALVYDFVG 413
COG2888 COG2888
Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 ...
 379-405 9.30e-03

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: 34.32  E-value: 9.30e-03
                         10        20
                 ....*....|....*....|....*..
gi 835584282 379 ERLPKECTQCHYVKpVGVYICPKCGFK 405
Cdd:COG2888   25 EALIIRCPKCRKQS-NALYFCPKCGFE 50
 
Name Accession Description Interval E-value
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
2-342 6.37e-72

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 238.77  E-value: 6.37e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282   2 TLTIQPREKQIVALNMLRAAWKQ-YASFMMYAPVGFGKTAIAALIASGFIsRNMRIMFVAPYTVLLDQTATRFIEYGLPA 80
Cdd:COG1061   76 GTSFELRPYQQEALEALLAALERgGGRGLVVAPTGTGKTVLALALAAELL-RGKRVLVLVPRRELLEQWAEELRRFLGDP 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  81 EEIGyiwrdhPAYDPSRLIQIASADTLIRRD----FPDNIDLLIIDEAH-LKRKKMLEFIDELTAKgvKVIGLSGTPFSA 155
Cdd:COG1061  155 LAGG------GKKDSDAPITVATYQSLARRAhldeLGDRFGLVIIDEAHhAGAPSYRRILEAFPAA--YRLGLTATPFRS 226

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 156 W----LGTYYQKLIKPTTMKELIAIGALSKYEFYaPSHPDLSDvktsEQAGYgRDYNETQSAEVMSDPTLVGDIVKNWL- 230
Cdd:COG1061  227 DgreiLLFLFDGIVYEYSLKEAIEDGYLAPPEYY-GIRVDLTD----ERAEY-DALSERLREALAADAERKDKILRELLr 300

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 231 ENGEDRPTICFCVNVAHANYVTVEFSKAGVTVEVMTAATPHEDRQMTIRRFEQGITKIIINVGVLVAGFD-SDVRCIIFA 309
Cdd:COG1061  301 EHPDDRKTLVFCSSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDvPRLDVAILL 380

                        330       340       350
                 ....*....|....*....|....*....|...
gi 835584282 310 RPTKSEMRWIQILGRGLRPASGKDHCLIFDHTG 342
Cdd:COG1061  381 RPTGSPREFIQRLGRGLRPAPGKEDALVYDFVG 413
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 234-339 1.80e-22

C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins 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: 350186 [Multi-domain]  Cd Length: 116  Bit Score: 92.24  E-value: 1.80e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 234 EDRPTICFCVNVAHANYVTVEFSKAGVTVEVMTAATPHEDRQM-TIRRFEQGITK--IIINVGVLVAGFD-SDVRCIIFA 309
Cdd:cd18799    5 VEIKTLIFCVSIEHAEFMAEAFNEAGIDAVALNSDYSDRERGDeALILLFFGELKppILVTVDLLTTGVDiPEVDNVVFL 84

                         90       100       110
                 ....*....|....*....|....*....|
gi 835584282 310 RPTKSEMRWIQILGRGLRPASGKDHCLIFD 339
Cdd:cd18799   85 RPTESRTLFLQMLGRGLRLHEGKDFFTILD 114
DEXDc smart00487
DEAD-like helicases superfamily;
5-152 5.80e-15

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 73.68  E-value: 5.80e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282     5 IQPREKQIVALNMLRAAWKqyaSFMMYAPVGFGKTAIAALIASGFISRNM--RIMFVAPYTVLLDQTATRFIEYG--LPA 80
Cdd:smart00487   7 EPLRPYQKEAIEALLSGLR---DVILAAPTGSGKTLAALLPALEALKRGKggRVLVLVPTRELAEQWAEELKKLGpsLGL 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282    81 EEIGYIWRDHPAYDPSRL------IQIASADTLIR-----RDFPDNIDLLIIDEAH----LKRKKMLEFIDELTAKGVKV 145
Cdd:smart00487  84 KVVGLYGGDSKREQLRKLesgktdILVTTPGRLLDllendKLSLSNVDLVILDEAHrlldGGFGDQLEKLLKLLPKNVQL 163


                   ....*..
gi 835584282   146 IGLSGTP 152
Cdd:smart00487 164 LLLSATP 170
ResIII pfam04851
Type III restriction enzyme, res subunit;
5-153 2.66e-13

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 67.70  E-value: 2.66e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282    5 IQPREKQIVALNMLRAAWKQY-ASFMMYAPVGFGKTAIAALIASGFIS--RNMRIMFVAPYTVLLDQTATRFIEYGLPAE 81
Cdd:pfam04851   2 LELRPYQIEAIENLLESIKNGqKRGLIVMATGSGKTLTAAKLIARLFKkgPIKKVLFLVPRKDLLEQALEEFKKFLPNYV 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282   82 EIGYIW---RDHPAYDPSRLIqIASADTLIR-------RDFPDNIDLLIIDEAH----LKRKKMLEFIDELTakgvkVIG 147
Cdd:pfam04851  82 EIGEIIsgdKKDESVDDNKIV-VTTIQSLYKalelaslELLPDFFDVIIIDEAHrsgaSSYRNILEYFKPAF-----LLG 155


                  ....*.
gi 835584282  148 LSGTPF 153
Cdd:pfam04851 156 LTATPE 161
uvsW PHA02558
UvsW helicase; Provisional
 32-339 2.82e-13

UvsW helicase; Provisional


Pssm-ID: 222875 [Multi-domain]  Cd Length: 501  Bit Score: 71.96  E-value: 2.82e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  32 APVGFGKTAIAALIASGFISRNM-RIMFVAPYTVLLDQTATRFIEYGLPAEEIGYIWRDHPAYDPSRLIQIASADTLIR- 109
Cdd:PHA02558 136 LPTSAGKSLIQYLLSRYYLENYEgKVLIIVPTTSLVTQMIDDFVDYRLFPREAMHKIYSGTAKDTDAPIVVSTWQSAVKq 215

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 110 -RDFPDNIDLLIIDEAHL-KRKKMLEFIDELTAKGVKvIGLSGTP---------FSAWLGTYYqkliKPTTMKELIAIGA 178
Cdd:PHA02558 216 pKEWFDQFGMVIVDECHLfTGKSLTSIITKLDNCKFK-FGLTGSLrdgkanilqYVGLFGDIF----KPVTTSQLMEEGQ 290

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 179 LSKYEFYAP--SHPDLSDVKTseqagYGRDYNEtqSAEVMSDPT----LVGDIVKNWLENGEDrpTICFCVNVAHANYVT 252
Cdd:PHA02558 291 VTDLKINSIflRYPDEDRVKL-----KGEDYQE--EIKYITSHTkrnkWIANLALKLAKKGEN--TFVMFKYVEHGKPLY 361

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 253 VEFSKAGVTVEVMTAATPHEDRQmTIRRFEQGITKIII--NVGVLVAGFD-SDVRCIIFARPTKSEMRWIQILGRGLRPA 329
Cdd:PHA02558 362 EMLKKVYDKVYYVSGEVDTEDRN-EMKKIAEGGKGIIIvaSYGVFSTGISiKNLHHVIFAHPSKSKIIVLQSIGRVLRKH 440

                        330
                 ....*....|
gi 835584282 330 SGKDHCLIFD 339
Cdd:PHA02558 441 GSKSIATVWD 450
COG2888 COG2888
Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 ...
 379-405 9.30e-03

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: 34.32  E-value: 9.30e-03
                         10        20
                 ....*....|....*....|....*..
gi 835584282 379 ERLPKECTQCHYVKpVGVYICPKCGFK 405
Cdd:COG2888   25 EALIIRCPKCRKQS-NALYFCPKCGFE 50
 
Name Accession Description Interval E-value
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
2-342 6.37e-72

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 238.77  E-value: 6.37e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282   2 TLTIQPREKQIVALNMLRAAWKQ-YASFMMYAPVGFGKTAIAALIASGFIsRNMRIMFVAPYTVLLDQTATRFIEYGLPA 80
Cdd:COG1061   76 GTSFELRPYQQEALEALLAALERgGGRGLVVAPTGTGKTVLALALAAELL-RGKRVLVLVPRRELLEQWAEELRRFLGDP 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  81 EEIGyiwrdhPAYDPSRLIQIASADTLIRRD----FPDNIDLLIIDEAH-LKRKKMLEFIDELTAKgvKVIGLSGTPFSA 155
Cdd:COG1061  155 LAGG------GKKDSDAPITVATYQSLARRAhldeLGDRFGLVIIDEAHhAGAPSYRRILEAFPAA--YRLGLTATPFRS 226

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 156 W----LGTYYQKLIKPTTMKELIAIGALSKYEFYaPSHPDLSDvktsEQAGYgRDYNETQSAEVMSDPTLVGDIVKNWL- 230
Cdd:COG1061  227 DgreiLLFLFDGIVYEYSLKEAIEDGYLAPPEYY-GIRVDLTD----ERAEY-DALSERLREALAADAERKDKILRELLr 300

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 231 ENGEDRPTICFCVNVAHANYVTVEFSKAGVTVEVMTAATPHEDRQMTIRRFEQGITKIIINVGVLVAGFD-SDVRCIIFA 309
Cdd:COG1061  301 EHPDDRKTLVFCSSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDvPRLDVAILL 380

                        330       340       350
                 ....*....|....*....|....*....|...
gi 835584282 310 RPTKSEMRWIQILGRGLRPASGKDHCLIFDHTG 342
Cdd:COG1061  381 RPTGSPREFIQRLGRGLRPAPGKEDALVYDFVG 413
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 234-339 1.80e-22

C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins 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: 350186 [Multi-domain]  Cd Length: 116  Bit Score: 92.24  E-value: 1.80e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 234 EDRPTICFCVNVAHANYVTVEFSKAGVTVEVMTAATPHEDRQM-TIRRFEQGITK--IIINVGVLVAGFD-SDVRCIIFA 309
Cdd:cd18799    5 VEIKTLIFCVSIEHAEFMAEAFNEAGIDAVALNSDYSDRERGDeALILLFFGELKppILVTVDLLTTGVDiPEVDNVVFL 84

                         90       100       110
                 ....*....|....*....|....*....|
gi 835584282 310 RPTKSEMRWIQILGRGLRPASGKDHCLIFD 339
Cdd:cd18799   85 RPTESRTLFLQMLGRGLRLHEGKDFFTILD 114
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 7-152 4.15e-18

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: 80.81  E-value: 4.15e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282   7 PREKQIVALNMLRAAWKQYASfMMYAPVGFGKTAIAALIAsgFISRNMRIMFVAPYTVLLDQTATRFIEYGLPAeEIGYI 86
Cdd:cd17926    1 LRPYQEEALEAWLAHKNNRRG-ILVLPTGSGKTLTALALI--AYLKELRTLIVVPTDALLDQWKERFEDFLGDS-SIGLI 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 835584282  87 WRDHPAYDPSRLIQIASADTLIR-----RDFPDNIDLLIIDEAHLKRKKMLE-FIDELTAKgvKVIGLSGTP 152
Cdd:cd17926   77 GGGKKKDFDDANVVVATYQSLSNlaeeeKDLFDQFGLLIVDEAHHLPAKTFSeILKELNAK--YRLGLTATP 146
DEXDc smart00487
DEAD-like helicases superfamily;
5-152 5.80e-15

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 73.68  E-value: 5.80e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282     5 IQPREKQIVALNMLRAAWKqyaSFMMYAPVGFGKTAIAALIASGFISRNM--RIMFVAPYTVLLDQTATRFIEYG--LPA 80
Cdd:smart00487   7 EPLRPYQKEAIEALLSGLR---DVILAAPTGSGKTLAALLPALEALKRGKggRVLVLVPTRELAEQWAEELKKLGpsLGL 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282    81 EEIGYIWRDHPAYDPSRL------IQIASADTLIR-----RDFPDNIDLLIIDEAH----LKRKKMLEFIDELTAKGVKV 145
Cdd:smart00487  84 KVVGLYGGDSKREQLRKLesgktdILVTTPGRLLDllendKLSLSNVDLVILDEAHrlldGGFGDQLEKLLKLLPKNVQL 163


                   ....*..
gi 835584282   146 IGLSGTP 152
Cdd:smart00487 164 LLLSATP 170
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 7-152 1.15e-13

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: 68.74  E-value: 1.15e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282   7 PREKQIVALNMLRAAWKQ-YASFMMYAPVGFGKTAIAALIASGFISRNM--RIMFVAPYTVLLDQTATRFIEYgLPAEEI 83
Cdd:cd18032    1 PRYYQQEAIEALEEAREKgQRRALLVMATGTGKTYTAAFLIKRLLEANRkkRILFLAHREELLEQAERSFKEV-LPDGSF 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 835584282  84 GYIWRDHPAYDPSRlIQIASADTLIRRDF-----PDNIDLLIIDEAHlkR---KKMLEFIDELtaKGVKVIGLSGTP 152
Cdd:cd18032   80 GNLKGGKKKPDDAR-VVFATVQTLNKRKRlekfpPDYFDLIIIDEAH--HaiaSSYRKILEYF--EPAFLLGLTATP 151
ResIII pfam04851
Type III restriction enzyme, res subunit;
5-153 2.66e-13

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 67.70  E-value: 2.66e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282    5 IQPREKQIVALNMLRAAWKQY-ASFMMYAPVGFGKTAIAALIASGFIS--RNMRIMFVAPYTVLLDQTATRFIEYGLPAE 81
Cdd:pfam04851   2 LELRPYQIEAIENLLESIKNGqKRGLIVMATGSGKTLTAAKLIARLFKkgPIKKVLFLVPRKDLLEQALEEFKKFLPNYV 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282   82 EIGYIW---RDHPAYDPSRLIqIASADTLIR-------RDFPDNIDLLIIDEAH----LKRKKMLEFIDELTakgvkVIG 147
Cdd:pfam04851  82 EIGEIIsgdKKDESVDDNKIV-VTTIQSLYKalelaslELLPDFFDVIIIDEAHrsgaSSYRNILEYFKPAF-----LLG 155


                  ....*.
gi 835584282  148 LSGTPF 153
Cdd:pfam04851 156 LTATPE 161
uvsW PHA02558
UvsW helicase; Provisional
 32-339 2.82e-13

UvsW helicase; Provisional


Pssm-ID: 222875 [Multi-domain]  Cd Length: 501  Bit Score: 71.96  E-value: 2.82e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  32 APVGFGKTAIAALIASGFISRNM-RIMFVAPYTVLLDQTATRFIEYGLPAEEIGYIWRDHPAYDPSRLIQIASADTLIR- 109
Cdd:PHA02558 136 LPTSAGKSLIQYLLSRYYLENYEgKVLIIVPTTSLVTQMIDDFVDYRLFPREAMHKIYSGTAKDTDAPIVVSTWQSAVKq 215

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 110 -RDFPDNIDLLIIDEAHL-KRKKMLEFIDELTAKGVKvIGLSGTP---------FSAWLGTYYqkliKPTTMKELIAIGA 178
Cdd:PHA02558 216 pKEWFDQFGMVIVDECHLfTGKSLTSIITKLDNCKFK-FGLTGSLrdgkanilqYVGLFGDIF----KPVTTSQLMEEGQ 290

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 179 LSKYEFYAP--SHPDLSDVKTseqagYGRDYNEtqSAEVMSDPT----LVGDIVKNWLENGEDrpTICFCVNVAHANYVT 252
Cdd:PHA02558 291 VTDLKINSIflRYPDEDRVKL-----KGEDYQE--EIKYITSHTkrnkWIANLALKLAKKGEN--TFVMFKYVEHGKPLY 361

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 253 VEFSKAGVTVEVMTAATPHEDRQmTIRRFEQGITKIII--NVGVLVAGFD-SDVRCIIFARPTKSEMRWIQILGRGLRPA 329
Cdd:PHA02558 362 EMLKKVYDKVYYVSGEVDTEDRN-EMKKIAEGGKGIIIvaSYGVFSTGISiKNLHHVIFAHPSKSKIIVLQSIGRVLRKH 440

                        330
                 ....*....|
gi 835584282 330 SGKDHCLIFD 339
Cdd:PHA02558 441 GSKSIATVWD 450
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 32-151 4.01e-12

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: 63.96  E-value: 4.01e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  32 APVGFGKTAIAALIA-SGFISRNMRIMFVAPYTVLLDQTATRFIEYGLPAEEIGYIWRDHPAYDPSRL------IQIASA 104
Cdd:cd00046    8 APTGSGKTLAALLAAlLLLLKKGKKVLVLVPTKALALQTAERLRELFGPGIRVAVLVGGSSAEEREKNklgdadIIIATP 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 835584282 105 DTLIR------RDFPDNIDLLIIDEAH--LKRKK----MLEFIDELTAKGVKVIGLSGT 151
Cdd:cd00046   88 DMLLNlllredRLFLKDLKLIIVDEAHalLIDSRgaliLDLAVRKAGLKNAQVILLSAT 146
HsdR COG4096
Type I site-specific restriction endonuclease, part of a restriction-modification system ...
 35-342 2.09e-10

Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms];


Pssm-ID: 443272 [Multi-domain]  Cd Length: 806  Bit Score: 63.32  E-value: 2.09e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  35 GFGKT--AIAA---LIASGfisRNMRIMFVAPYTVLLDQTATRFIEYGLPAEEIGYIWRDHPAYDPSRLIQIA------- 102
Cdd:COG4096  188 GTGKTrtAIALiyrLLKAG---RAKRILFLADRNALVDQAKNAFKPFLPDLDAFTKLYNKSKDIDKSARVYFStyqtmmn 264

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 103 ----SADTLIRRDF-PDNIDLLIIDEAHlkR------KKMLEFIDELTakgvkvIGLSGTPfsawlgtyyqKLIK----- 166
Cdd:COG4096  265 ridgEEEEPGYRQFpPDFFDLIIIDECH--RgiyskwRAILDYFDALQ------IGLTATP----------KDTIdrnty 326

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 167 ------PT---TMKELIAIGALSKYE-------------FYAPSHpDLSDVKT----SEQAGYGRDYNETQ-SAEVMSDP 219
Cdd:COG4096  327 eyfngnPVytySLEQAVADGFLVPYKviridtkfdregiRYDAGE-DLSDEEGeeieLEELEEDREYEAKDfNRKVVNED 405

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 220 TL---VGDIVKNWLENGEDRP--TICFCVNVAHANYVTVEFSKA-----GVTVEVMTAATphEDRQMTIRRFEQGIT--K 287
Cdd:COG4096  406 TTrkvLEELMEYLDKPGGDRLgkTIIFAKNDDHADRIVQALRELypelgGDFVKKITGDD--DYGKSLIDNFKNPEKypR 483

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 288 IIINVGVLVAGFDS-DVRCIIFARPTKSEMRWIQILGRG--LRP--ASGKDHCLIFDHTG 342
Cdd:COG4096  484 IAVTVDMLDTGIDVpEVVNLVFMRPVKSRIKFEQMIGRGtrLCPdlFPGKTHFTIFDFVG 543
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 32-154 7.22e-10

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: 58.02  E-value: 7.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282   32 APVGFGKTA---IAALIASGFISRNMRIMFVAPYTVLLDQTATRFIEYG----------LPAEEIGYIWRDHPAYD---- 94
Cdd:pfam00270  21 APTGSGKTLaflLPALEALDKLDNGPQALVLAPTRELAEQIYEELKKLGkglglkvaslLGGDSRKEQLEKLKGPDilvg 100

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 835584282   95 -PSRLIqiasaDTLIRRDFPDNIDLLIIDEAHL----KRKKMLEFIDELTAKGVKVIGLSGTPFS 154
Cdd:pfam00270 101 tPGRLL-----DLLQERKLLKNLKLLVLDEAHRlldmGFGPDLEEILRRLPKKRQILLLSATLPR 160
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 224-327 2.77e-08

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: 51.83  E-value: 2.77e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  224 DIVKNWLENGEDRPTICFC--VNVAHANYVtveFSKAGVTVEVMTAATPHEDRQMTIRRFEQGITKIIINVGVLVAGFD- 300
Cdd:pfam00271   4 EALLELLKKERGGKVLIFSqtKKTLEAELL---LEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDl 80

                          90       100
                  ....*....|....*....|....*..
gi 835584282  301 SDVRCIIFARPTKSEMRWIQILGRGLR 327
Cdd:pfam00271  81 PDVDLVINYDLPWNPASYIQRIGRAGR 107
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
19-333 2.82e-08

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 56.06  E-value: 2.82e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  19 RAAWKQ----YASFMMYAPVGFGKTAIAALIASGFISRNMRIMFVAPYTVLLDQTATRFI----EYGLPAEEI--GYIWR 88
Cdd:COG1204   28 AEALEAglleGKNLVVSAPTASGKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKrdfeELGIKVGVStgDYDSD 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  89 DHPAYDPSrlIQIA---SADTLIRR--DFPDNIDLLIIDEAHL----KRKKMLEFIdeLT-----AKGVKVIGLSGT--- 151
Cdd:COG1204  108 DEWLGRYD--ILVAtpeKLDSLLRNgpSWLRDVDLVVVDEAHLiddeSRGPTLEVL--LArlrrlNPEAQIVALSATign 183

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 152 --PFSAWLGtyyQKLIK----PTTMKELIAI-GALS---KYEFYAPSHPDLSDvKTSEQAG------YGRDYNET---QS 212
Cdd:COG1204  184 aeEIAEWLD---AELVKsdwrPVPLNEGVLYdGVLRfddGSRRSKDPTLALAL-DLLEEGGqvlvfvSSRRDAESlakKL 259

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 213 AEVMsDPTLVGDIVKNWLENGEDrptICFCVNVAHANYVTVEFSKAGVTVEvmTAATPHEDRQMTIRRFEQGITKIIINV 292
Cdd:COG1204  260 ADEL-KRRLTPEEREELEELAEE---LLEVSEETHTNEKLADCLEKGVAFH--HAGLPSELRRLVEDAFREGLIKVLVAT 333

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*..
gi 835584282 293 GVLVAGFDSDVRCIIFARPTKSEMRWI------QILGRGLRPasGKD 333
Cdd:COG1204  334 PTLAAGVNLPARRVIIRDTKRGGMVPIpvlefkQMAGRAGRP--GYD 378
HELICc smart00490
helicase superfamily c-terminal domain;
250-328 8.40e-08

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 49.52  E-value: 8.40e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282   250 YVTVEFSKAGVTVEVMTAATPHEDRQMTIRRFEQGITKIIINVGVLVAGFD-SDVRCIIFARPTKSEMRWIQILGRGLRP 328
Cdd:smart00490   2 ELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDlPGVDLVIIYDLPWSPASYIQRIGRAGRA 81
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 17-158 5.42e-07

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: 49.95  E-value: 5.42e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  17 MLRAAWKQYASFMMYAPVGFGKTAIAAL-IASGFISRNMRIMFVAPYTVLLDQTATRFIE-----YGLPAEEIG-YIWRD 89
Cdd:cd17921    9 ALRALYLSGDSVLVSAPTSSGKTLIAELaILRALATSGGKAVYIAPTRALVNQKEADLRErfgplGKNVGLLTGdPSVNK 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  90 HPAYDPSRLIQIA-SADTLIRR---DFPDNIDLLIIDEAHL----KRKKMLEFIDELT---AKGVKVIGLSGT-----PF 153
Cdd:cd17921   89 LLLAEADILVATPeKLDLLLRNggeRLIQDVRLVVVDEAHLigdgERGVVLELLLSRLlriNKNARFVGLSATlpnaeDL 168


                 ....*
gi 835584282 154 SAWLG 158
Cdd:cd17921  169 AEWLG 173
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
 34-154 6.06e-07

DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350769 [Multi-domain]  Cd Length: 207  Bit Score: 49.98  E-value: 6.06e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  34 VGFGKTAIAALIASGFISRNM--RIMFVAPyTVLLDQ----TATRFieyGLPA-----EEIGYIWRDHPAYDPSRLIQIA 102
Cdd:cd18011   26 VGLGKTIEAGLIIKELLLRGDakRVLILCP-ASLVEQwqdeLQDKF---GLPFlildrETAAQLRRLIGNPFEEFPIVIV 101

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 835584282 103 SADTL-----IRRDF-PDNIDLLIIDEAH-------LKRKKMLEFIDELTAKGVKVIGLSGTPFS 154
Cdd:cd18011  102 SLDLLkrseeRRGLLlSEEWDLVVVDEAHklrnsggGKETKRYKLGRLLAKRARHVLLLTATPHN 166
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
 27-158 9.15e-07

DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type 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: 350786 [Multi-domain]  Cd Length: 177  Bit Score: 49.25  E-value: 9.15e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  27 SFMMYAPVGFGKTAIAALIASGFISRNMRIMFVAPYTVLLDQTATRFIEYGLPAEEIGYI---WRDHPAYDPSRLIQIAS 103
Cdd:cd18028   19 NLLISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFKKLEEIGLKVGIStgdYDEDDEWLGDYDIIVAT 98

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 835584282 104 A---DTLIRR--DFPDNIDLLIIDEAHL----KRKKMLEFI---DELTAKGVKVIGLSGT-----PFSAWLG 158
Cdd:cd18028   99 YekfDSLLRHspSWLRDVGVVVVDEIHLisdeERGPTLESIvarLRRLNPNTQIIGLSATignpdELAEWLN 170
PRK13766 PRK13766
Hef nuclease; Provisional
 4-125 2.83e-06

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 49.87  E-value: 2.83e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282   4 TIQPREKQI-VALNMLRAawkqyaSFMMYAPVGFGKTAIAALIASGFIS-RNMRIMFVAPYTVLLDQTATRFIEY-GLPA 80
Cdd:PRK13766  13 TIEARLYQQlLAATALKK------NTLVVLPTGLGKTAIALLVIAERLHkKGGKVLILAPTKPLVEQHAEFFRKFlNIPE 86

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 835584282  81 EEI----GYIWRDHPA--YDPSRLI----QIASADTLIRRDFPDNIDLLIIDEAH 125
Cdd:PRK13766  87 EKIvvftGEVSPEKRAelWEKAKVIvatpQVIENDLIAGRISLEDVSLLIFDEAH 141
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 5-153 7.51e-06

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: 46.88  E-value: 7.51e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282   5 IQPREKQIValnMLRAAWKQyaSFMMYAPVGFGKTAIAALIASGFISRNM-------RIMFVAPYTVLLDQTATrFIEYG 77
Cdd:cd18034    1 FTPRSYQLE---LFEAALKR--NTIVVLPTGSGKTLIAVMLIKEMGELNRkeknpkkRAVFLVPTVPLVAQQAE-AIRSH 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  78 LPAEEIGY-------IWRDHPAYDPSRLIQI--ASADTL---IRRDF--PDNIDLLIIDEAHLKRKK------MLEF-ID 136
Cdd:cd18034   75 TDLKVGEYsgemgvdKWTKERWKEELEKYDVlvMTAQILldaLRHGFlsLSDINLLIFDECHHATGDhpyariMKEFyHL 154

                        170
                 ....*....|....*..
gi 835584282 137 ELTAKGVKVIGLSGTPF 153
Cdd:cd18034  155 EGRTSRPRILGLTASPV 171
Helicase_RecD pfam05127
Helicase; This domain contains a P-loop (Walker A) motif, suggesting that it has ATPase ...
 32-124 8.47e-06

Helicase; This domain contains a P-loop (Walker A) motif, suggesting that it has ATPase activity, and a Walker B motif. In tRNA(Met) cytidine acetyltransferase (TmcA) it may function as an RNA helicase motor (driven by ATP hydrolysis) which delivers the wobble base to the active centre of the GCN5-related N-acetyltransferase (GNAT) domain. It is found in the bacterial exodeoxyribonuclease V alpha chain (RecD), which has 5'-3' helicase activity. It is structurally similar to the motor domain 1A in other SF1 helicases.


Pssm-ID: 461555 [Multi-domain]  Cd Length: 171  Bit Score: 45.99  E-value: 8.47e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282   32 APVGFGKTAIAALIASGFISRNM-RIMFVAP--YTVlldQTATRFIEYGLPAEEIGYIWRDHPAYDPSRLIQIASADTLI 108
Cdd:pfam05127   4 ADRGRGKSAALGLAAAALIAQGYsRIIVTAPspANV---QTLFEFAIKGLDALGLTPKFRDGIIRGNGQRIRFIAPDELL 80

                          90
                  ....*....|....*.
gi 835584282  109 RRdfPDNIDLLIIDEA 124
Cdd:pfam05127  81 KL--PGQADLLVVDEA 94
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 5-125 2.21e-05

DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef 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: 350793 [Multi-domain]  Cd Length: 181  Bit Score: 45.20  E-value: 2.21e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282   5 IQPREKQIVALNMLRAAwkqyaSFMMYAPVGFGKTAIAALIASGFISR-NMRIMFVAPYTVLLDQTATRFIEY-GLPAEE 82
Cdd:cd18035    1 EERRLYQVLIAAVALNG-----NTLIVLPTGLGKTIIAILVAADRLTKkGGKVLILAPSRPLVEQHAENLKRVlNIPDKI 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 835584282  83 IGYIWRDHP-----AYDPSRLI----QIASADTLIRRDFPDNIDLLIIDEAH 125
Cdd:cd18035   76 TSLTGEVKPeeraeRWDASKIIvatpQVIENDLLAGRITLDDVSLLIFDEAH 127
DEXHc_RecG cd17918
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ...
 34-140 5.14e-05

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: 43.94  E-value: 5.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  34 VGFGKTAIAALIASGFISRNMRIMFVAPYTVLLDQTATRFIEYgLPAEEIGYIWRDHPAYDPSRLIQIASADTLIRRD-F 112
Cdd:cd17918   45 VGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEARKF-LPFINVELVTGGTKAQILSGISLLVGTHALLHLDvK 123

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 835584282 113 PDNIDLLIIDEAH---------LKRKKMLEFIdELTA 140
Cdd:cd17918  124 FKNLDLVIVDEQHrfgvaqreaLYNLGATHFL-EATA 159
AAA_22 pfam13401
AAA domain;
23-152 9.69e-05

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 42.33  E-value: 9.69e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282   23 KQYASFMM-YAPVGFGKTAIAALIASGFISRNMRIMFVapyTVLLDQTATRFI-----EYGLPAEEigyiwrDHPAYDPS 96
Cdd:pfam13401   2 RFGAGILVlTGESGTGKTTLLRRLLEQLPEVRDSVVFV---DLPSGTSPKDLLrallrALGLPLSG------RLSKEELL 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 835584282   97 RLIQIASADTLIRRdfpdnidLLIIDEAHLKRKKMLEF---IDELTAKGVKVIgLSGTP 152
Cdd:pfam13401  73 AALQQLLLALAVAV-------VLIIDEAQHLSLEALEElrdLLNLSSKLLQLI-LVGTP 123
hsdR PRK11448
type I restriction enzyme EcoKI subunit R; Provisional
 35-339 1.65e-04

type I restriction enzyme EcoKI subunit R; Provisional


Pssm-ID: 236912 [Multi-domain]  Cd Length: 1123  Bit Score: 44.56  E-value: 1.65e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282   35 GFGKT--AIAA---LIASgfiSRNMRIMFVAPYTVLLDQTATRF----IEYGLPAEEIGYIWR-DHPAYDPSRLIQIASA 104
Cdd:PRK11448  443 GTGKTrtAIALmyrLLKA---KRFRRILFLVDRSALGEQAEDAFkdtkIEGDQTFASIYDIKGlEDKFPEDETKVHVATV 519

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  105 DTLIRRDF----------PDNIDLLIIDEAH---LKRKKM----LEFIDEL--TAKGVKV--------IGLSGTP----- 152
Cdd:PRK11448  520 QGMVKRILysddpmdkppVDQYDCIIVDEAHrgyTLDKEMsegeLQFRDQLdyVSKYRRVldyfdavkIGLTATPalhtt 599

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  153 -------FS---------AWL----------------GTYYQK-----LIKPTTmkeliaiGALSKyeFYAPSHPDLsDV 195
Cdd:PRK11448  600 eifgepvYTysyreavidGYLidheppirietrlsqeGIHFEKgeeveVINTQT-------GEIDL--ATLEDEVDF-EV 669

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  196 KTSEQAGYGRDYNETQSAEVMS--DPTLVGDivknwlengedrpTICFCVNVAHANYV----TVEFSKAGVTVE---VM- 265
Cdd:PRK11448  670 EDFNRRVITESFNRVVCEELAKylDPTGEGK-------------TLIFAATDAHADMVvrllKEAFKKKYGQVEddaVIk 736

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 835584282  266 -TAATPHEDRqmTIRRFE-QGITKIIINVGVLVAGFDSDVRC-IIFARPTKSEMRWIQILGRGLR--PASGKDHCLIFD 339
Cdd:PRK11448  737 iTGSIDKPDQ--LIRRFKnERLPNIVVTVDLLTTGIDVPSICnLVFLRRVRSRILYEQMLGRATRlcPEIGKTHFRIFD 813
DEXHc_HFM1 cd18023
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ...
 27-159 2.77e-04

DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box helicase, required for crossover formation and complete synapsis of homologous chromosomes during meiosis. HFM1 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: 350781 [Multi-domain]  Cd Length: 206  Bit Score: 42.34  E-value: 2.77e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  27 SFMMYAPVGFGKTAIAAL-IASGFISRNM------RIMFVAPYTVLLDQTAT----RFIEYGLP-AEEIGyiwrDHPAYD 94
Cdd:cd18023   19 NFVVSAPTGSGKTVLFELaILRLLKERNPlpwgnrKVVYIAPIKALCSEKYDdwkeKFGPLGLScAELTG----DTEMDD 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  95 psrLIQIASADTLI----------RRD-----FPDNIDLLIIDEAHL-------------KRKKMLEFIDEL---TAKGV 143
Cdd:cd18023   95 ---TFEIQDADIILttpekwdsmtRRWrdngnLVQLVALVLIDEVHIikenrgatlevvvSRMKTLSSSSELrgsTVRPM 171

                        170       180
                 ....*....|....*....|.
gi 835584282 144 KVIGLSGT-P----FSAWLGT 159
Cdd:cd18023  172 RFVAVSATiPniedLAEWLGD 192
DDXDc_reverse_gyrase cd17924
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ...
 27-82 7.99e-04

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: 7.99e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 835584282  27 SFMMYAPVGFGKTAIAALIASGFISRNMRIMFVAPYTVLLDQTATRFIEYGLPAEE 82
Cdd:cd17924   34 SFAIIAPTGVGKTTFGLATSLYLASKGKRSYLIFPTKSLVKQAYERLSKYAEKAGV 89
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 29-125 1.45e-03

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 39.28  E-value: 1.45e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282    29 MMYAPVGFGKTAIAALIASGFISRNMRIMFVAPytvlldqtaTRFIEYGLPAEEIGYIWRDHPAYDPSRLIQIASAdtLI 108
Cdd:smart00382   6 LIVGPPGSGKTTLARALARELGPPGGGVIYIDG---------EDILEEVLDQLLLIIVGGKKASGSGELRLRLALA--LA 74

                           90
                   ....*....|....*..
gi 835584282   109 RRDFPDnidLLIIDEAH 125
Cdd:smart00382  75 RKLKPD---VLILDEIT 88
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 5-152 2.00e-03

DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350685 [Multi-domain]  Cd Length: 201  Bit Score: 39.72  E-value: 2.00e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282   5 IQPREKQivaLNMLRAAWKQYASfMMYAPVGFGKTAIAALIA----SGFISRNM-RIMFVAPYTVLLDQTATRFIEY-GL 78
Cdd:cd17927    1 FKPRNYQ---LELAQPALKGKNT-IICLPTGSGKTFVAVLICehhlKKFPAGRKgKVVFLANKVPLVEQQKEVFRKHfER 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  79 PAEEIGYIWRDHPAYDPSRLIqIASADTLI------RRDFPD-------NIDLLIIDEAHLKRKK------MLEFIDELT 139
Cdd:cd17927   77 PGYKVTGLSGDTSENVSVEQI-VESSDVIIvtpqilVNDLKSgtivslsDFSLLVFDECHNTTKNhpyneiMFRYLDQKL 155

                        170
                 ....*....|....*.
gi 835584282 140 AKGVK---VIGLSGTP 152
Cdd:cd17927  156 GSSGPlpqILGLTASP 171
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 1-284 2.13e-03

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 40.59  E-value: 2.13e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282   1 MTLTIQPREKQIVALNMLRAAWKqyasfmmYAP-------VGFGKT-----AIAALIASGfisRNMRIMFVAPyTVLLDQ 68
Cdd:COG0553  236 AGLKATLRPYQLEGAAWLLFLRR-------LGLgglladdMGLGKTiqalaLLLELKERG---LARPVLIVAP-TSLVGN 304

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  69 ---TATRF-------IEYGLPAEEigyiwRDHPAYDPSRLIqIASADTLiRRDFPD----NIDLLIIDEAH-LK--RKKM 131
Cdd:COG0553  305 wqrELAKFapglrvlVLDGTRERA-----KGANPFEDADLV-ITSYGLL-RRDIELlaavDWDLVILDEAQhIKnpATKR 377

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 132 LEFIDELTAKGvkVIGLSGTP-----FSAW----------LGTYY---------------------QKLIKPT---TMKE 172
Cdd:COG0553  378 AKAVRALKARH--RLALTGTPvenrlEELWslldflnpglLGSLKafrerfarpiekgdeealerlRRLLRPFllrRTKE 455

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282 173 LIAIG-----------ALSKYE--FYApshpdlsDVKTSEQAGYGRDYNETQSAEVM----------SDPTLV------- 222
Cdd:COG0553  456 DVLKDlpekteetlyvELTPEQraLYE-------AVLEYLRRELEGAEGIRRRGLILaaltrlrqicSHPALLleegael 528

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 835584282 223 ----------GDIVKNWLENGEdrPTICFCVNVAHANYVTVEFSKAGVTVEVMTAATPHEDRQMTIRRFEQG 284
Cdd:COG0553  529 sgrsaklealLELLEELLAEGE--KVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQEG 598
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 32-75 3.41e-03

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: 40.06  E-value: 3.41e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 835584282  32 APVGFGKTaIAALIasgFISRNM------RIMFVAPYTVLLDQTATRFIE 75
Cdd:COG1203  154 APTGGGKT-EAALL---FALRLAakhggrRIIYALPFTSIINQTYDRLRD 199
DEXHc_UvsW cd18031
DEXH-box helicase domain of bacteriophage UvsW; Bacteriophage UvsW is part of the WXY system ...
 29-152 5.24e-03

DEXH-box helicase domain of bacteriophage UvsW; Bacteriophage UvsW is part of the WXY system that repairs DNA damage by a process that involves homologous recombination. UvsW 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: 350789 [Multi-domain]  Cd Length: 161  Bit Score: 37.80  E-value: 5.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  29 MMYAPVGFGKTAIAALIASGFISR-NMRIMFVAPYTVLLDQTATRFIEYGL-PAEEIGYIWR---DHPAYDPSRLIQIAS 103
Cdd:cd18031   19 ILNLPTSAGRSLIQALLARYYLENyEGKILIIVPTTALTTQMADDFVDYRLfSHAMIKKIGGgasKDDKYKNDAPVVVGT 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 835584282 104 ADTLIRR--DFPDNIDLLIIDEAH-LKRKKMLEFIDELTAKGVKvIGLSGTP 152
Cdd:cd18031   99 WQTVVKQpkEWFSQFGMMMNDECHlATGKSISSIISGLNNCMFK-FGLSGSL 149
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 37-146 8.80e-03

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 38.80  E-value: 8.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835584282  37 GKTAIAALIASGFISRNMRIMFVAPytvlldqT---ATRFIEY-GLPAEEIgyiwrdHpaydpsRLIQIASADTLIRRDf 112
Cdd:COG0507  152 GKTTTLRALLAALEALGLRVALAAP-------TgkaAKRLSEStGIEARTI------H------RLLGLRPDSGRFRHN- 211

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 835584282 113 PDNI----DLLIIDEA-----HLkrkkMLEFIDELTAKGVKVI 146
Cdd:COG0507  212 RDNPltpaDLLVVDEAsmvdtRL----MAALLEALPRAGARLI 250
COG2888 COG2888
Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 ...
 379-405 9.30e-03

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: 34.32  E-value: 9.30e-03
                         10        20
                 ....*....|....*....|....*..
gi 835584282 379 ERLPKECTQCHYVKpVGVYICPKCGFK 405
Cdd:COG2888   25 EALIIRCPKCRKQS-NALYFCPKCGFE 50
 
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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