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Conserved domains on  [gi|392887892|ref|NP_493597|]
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ATP-dependent DNA helicase [Caenorhabditis elegans]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 13209511)

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

CATH:  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
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 46-263 6.12e-08

N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.


The actual alignment was detected with superfamily member pfam05970:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 361  Bit Score: 54.31  E-value: 6.12e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392887892   46 LNQFQQPIALEIVN--NWKMQKLHYIEGISGTGKTYLLNAI----------------CGL-------------FKNFSLN 94
Cdd:pfam05970   1 LNDEQKKVFDAIIEsvINNKGGVFFVYGYGGTGKTFLWKAIitslrsegkivlavasSGVaalllpggrtahsRFGIPLD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392887892   95 IEIISPCPFPR--EHKSILK---------ILSNHDVFLEEIDKLKRAMQ---NDKPFGGKAIVMAADFGQLLPFSLN--- 157
Cdd:pfam05970  81 IDELSTCKIKRgsKLAELLEktslivwdeAPMTHRHCFEALDRTLRDILsetDDKPFGGKTVVLGGDFRQILPVIPKgsr 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392887892  158 ---FNQKVKNS--LKH-----LAEN--LVAPFKKHVLPTPTDDWSQFMYMVR-------QTPK--IVIPDANVVSS---- 212
Cdd:pfam05970 161 peiVNASITNSylWKHvkvleLTKNmrLLADSLDQTEAKELQDFSDWLLAIGdgkindeNEREqlIDIPIDILLNTggdp 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 392887892  213 LDELIDFTFGPLYTEIPNLNGI----ILTPKKADVEYINLKIMDQIKGKDLVFEA 263
Cdd:pfam05970 241 IEAIVSEVYPDILQNSTDPNYLeeraILCPTNEDVDEINNYRLSQLPGEEKEYLS 295
SF1_C_RecD cd18809
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ...
 369-409 3.90e-07

C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350196 [Multi-domain]  Cd Length: 80  Bit Score: 47.56  E-value: 3.90e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 392887892 369 LNFASTIHGSQGKSFEKLGLY--KLNECFEHGMIYTAISRVRR 409
Cdd:cd18809   32 QAYAMTIHKSQGSEFDRVIVVlpTSHPMLSRGLLYTALTRARK 74
 
Name Accession Description Interval E-value
PIF1 pfam05970
PIF1-like helicase; This family includes homologs of the PIF1 helicase, which inhibits ...
 46-263 6.12e-08

PIF1-like helicase; This family includes homologs of the PIF1 helicase, which inhibits telomerase activity and is cell cycle regulated. This family includes a large number of largely uncharacterized plant proteins. This family includes a P-loop motif that is involved in nucleotide binding.


Pssm-ID: 428699 [Multi-domain]  Cd Length: 361  Bit Score: 54.31  E-value: 6.12e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392887892   46 LNQFQQPIALEIVN--NWKMQKLHYIEGISGTGKTYLLNAI----------------CGL-------------FKNFSLN 94
Cdd:pfam05970   1 LNDEQKKVFDAIIEsvINNKGGVFFVYGYGGTGKTFLWKAIitslrsegkivlavasSGVaalllpggrtahsRFGIPLD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392887892   95 IEIISPCPFPR--EHKSILK---------ILSNHDVFLEEIDKLKRAMQ---NDKPFGGKAIVMAADFGQLLPFSLN--- 157
Cdd:pfam05970  81 IDELSTCKIKRgsKLAELLEktslivwdeAPMTHRHCFEALDRTLRDILsetDDKPFGGKTVVLGGDFRQILPVIPKgsr 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392887892  158 ---FNQKVKNS--LKH-----LAEN--LVAPFKKHVLPTPTDDWSQFMYMVR-------QTPK--IVIPDANVVSS---- 212
Cdd:pfam05970 161 peiVNASITNSylWKHvkvleLTKNmrLLADSLDQTEAKELQDFSDWLLAIGdgkindeNEREqlIDIPIDILLNTggdp 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 392887892  213 LDELIDFTFGPLYTEIPNLNGI----ILTPKKADVEYINLKIMDQIKGKDLVFEA 263
Cdd:pfam05970 241 IEAIVSEVYPDILQNSTDPNYLeeraILCPTNEDVDEINNYRLSQLPGEEKEYLS 295
SF1_C_RecD cd18809
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ...
 369-409 3.90e-07

C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350196 [Multi-domain]  Cd Length: 80  Bit Score: 47.56  E-value: 3.90e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 392887892 369 LNFASTIHGSQGKSFEKLGLY--KLNECFEHGMIYTAISRVRR 409
Cdd:cd18809   32 QAYAMTIHKSQGSEFDRVIVVlpTSHPMLSRGLLYTALTRARK 74
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 367-410 9.57e-04

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: 41.50  E-value: 9.57e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 392887892 367 VSLNFASTIHGSQGKSFEK---LGLYKLNECFEHGMIYTAISRVRRF 410
Cdd:COG0507  439 LELAYAITVHKSQGSTFDRvilVLPSEHSPLLSRELLYTALTRAREL 485
 
Name Accession Description Interval E-value
PIF1 pfam05970
PIF1-like helicase; This family includes homologs of the PIF1 helicase, which inhibits ...
 46-263 6.12e-08

PIF1-like helicase; This family includes homologs of the PIF1 helicase, which inhibits telomerase activity and is cell cycle regulated. This family includes a large number of largely uncharacterized plant proteins. This family includes a P-loop motif that is involved in nucleotide binding.


Pssm-ID: 428699 [Multi-domain]  Cd Length: 361  Bit Score: 54.31  E-value: 6.12e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392887892   46 LNQFQQPIALEIVN--NWKMQKLHYIEGISGTGKTYLLNAI----------------CGL-------------FKNFSLN 94
Cdd:pfam05970   1 LNDEQKKVFDAIIEsvINNKGGVFFVYGYGGTGKTFLWKAIitslrsegkivlavasSGVaalllpggrtahsRFGIPLD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392887892   95 IEIISPCPFPR--EHKSILK---------ILSNHDVFLEEIDKLKRAMQ---NDKPFGGKAIVMAADFGQLLPFSLN--- 157
Cdd:pfam05970  81 IDELSTCKIKRgsKLAELLEktslivwdeAPMTHRHCFEALDRTLRDILsetDDKPFGGKTVVLGGDFRQILPVIPKgsr 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392887892  158 ---FNQKVKNS--LKH-----LAEN--LVAPFKKHVLPTPTDDWSQFMYMVR-------QTPK--IVIPDANVVSS---- 212
Cdd:pfam05970 161 peiVNASITNSylWKHvkvleLTKNmrLLADSLDQTEAKELQDFSDWLLAIGdgkindeNEREqlIDIPIDILLNTggdp 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 392887892  213 LDELIDFTFGPLYTEIPNLNGI----ILTPKKADVEYINLKIMDQIKGKDLVFEA 263
Cdd:pfam05970 241 IEAIVSEVYPDILQNSTDPNYLeeraILCPTNEDVDEINNYRLSQLPGEEKEYLS 295
SF1_C_RecD cd18809
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ...
 369-409 3.90e-07

C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350196 [Multi-domain]  Cd Length: 80  Bit Score: 47.56  E-value: 3.90e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 392887892 369 LNFASTIHGSQGKSFEKLGLY--KLNECFEHGMIYTAISRVRR 409
Cdd:cd18809   32 QAYAMTIHKSQGSEFDRVIVVlpTSHPMLSRGLLYTALTRARK 74
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 367-410 9.57e-04

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: 41.50  E-value: 9.57e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 392887892 367 VSLNFASTIHGSQGKSFEK---LGLYKLNECFEHGMIYTAISRVRRF 410
Cdd:COG0507  439 LELAYAITVHKSQGSTFDRvilVLPSEHSPLLSRELLYTALTRAREL 485
 
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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