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Conserved domains on  [gi|3319366|gb|AAC28215|]
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contains similarity to helicases [Arabidopsis thaliana]

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 ...
 18-162 3.69e-57

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: 186.43  E-value: 3.69e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3319366     18 PNDGEVLIGIPEEFLITEGEDPIKAISLEICGDptLLLENKDLKFIQERAILSPTNEDVNTINQRLLEKLPGEEIQYLSI 97
Cdd:pfam05970 219 ENEREQLIDIPIDILLNTGGDPIEAIVSEVYPD--ILQNSTDPNYLEERAILCPTNEDVDEINNYRLSQLPGEEKEYLSS 296

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 3319366     98 DSIDLSDTTSEYNPVFTPDFLNSIKISGLPNHCLRLNIGAPIMLLRNLDPKGGLCNGTRLQMIQM 162
Cdd:pfam05970 297 DSISKSDNDSEIDALYPTEFLNSLNANGLPNHVLKLKVGAPVMLLRNLDQSRGLCNGTRLIVTQL 361
SF1_C_RecD cd18809
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ...
 209-252 8.10e-10

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: 54.10  E-value: 8.10e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 3319366  209 AFAMTINKSQGQSLKEIGLYLP--RPVFSHDQLYVALSRVTSKKGL 252
Cdd:cd18809  33 AYAMTIHKSQGSEFDRVIVVLPtsHPMLSRGLLYTALTRARKLLTL 78
 
Name Accession Description Interval E-value
PIF1 pfam05970
PIF1-like helicase; This family includes homologs of the PIF1 helicase, which inhibits ...
 18-162 3.69e-57

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: 186.43  E-value: 3.69e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3319366     18 PNDGEVLIGIPEEFLITEGEDPIKAISLEICGDptLLLENKDLKFIQERAILSPTNEDVNTINQRLLEKLPGEEIQYLSI 97
Cdd:pfam05970 219 ENEREQLIDIPIDILLNTGGDPIEAIVSEVYPD--ILQNSTDPNYLEERAILCPTNEDVDEINNYRLSQLPGEEKEYLSS 296

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 3319366     98 DSIDLSDTTSEYNPVFTPDFLNSIKISGLPNHCLRLNIGAPIMLLRNLDPKGGLCNGTRLQMIQM 162
Cdd:pfam05970 297 DSISKSDNDSEIDALYPTEFLNSLNANGLPNHVLKLKVGAPVMLLRNLDQSRGLCNGTRLIVTQL 361
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 68-252 3.58e-14

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: 71.55  E-value: 3.58e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3319366   68 ILSPTNEDVNTINQRLLEKLPGEeiqylsidsidlsdttSEYNPVFTPDFLNSIKIsglpnhclrlniGAPIMLLRNlDP 147
Cdd:COG0507 347 VLAPTNAGVDALNQAIREALNPA----------------GELERELAEDGELELYV------------GDRVMFTRN-DY 397

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3319366  148 KGGLCNGTRLQMIQMTPPILQAVIITGGRigdkvliSKILITPSDtkLPfnmrrkqfPIVVAFAMTINKSQGQSLKEIGL 227
Cdd:COG0507 398 DLGVFNGDIGTVLSIDEDEGRLTVRFDGR-------EIVTYDPSE--LD--------QLELAYAITVHKSQGSTFDRVIL 460

                       170       180
                ....*....|....*....|....*...
gi 3319366  228 YLP---RPVFSHDQLYVALSRVTSKKGL 252
Cdd:COG0507 461 VLPsehSPLLSRELLYTALTRARELLTL 488
SF1_C_RecD cd18809
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ...
 209-252 8.10e-10

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: 54.10  E-value: 8.10e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 3319366  209 AFAMTINKSQGQSLKEIGLYLP--RPVFSHDQLYVALSRVTSKKGL 252
Cdd:cd18809  33 AYAMTIHKSQGSEFDRVIVVLPtsHPMLSRGLLYTALTRARKLLTL 78
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 135-254 7.33e-07

exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273631 [Multi-domain]  Cd Length: 582  Bit Score: 49.76  E-value: 7.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3319366    135 IGAPIMLLRNlDPKGGLCNGTrlqmiqmtppilqaviiTGGRIGDKVLISKILITPSDTKLPFNMRRkqFPIVV-AFAMT 213
Cdd:TIGR01447 462 IGRPIMVTEN-DYTLGLFNGD-----------------IGVLLRDPDGILTVWFHFADGSKAVLPSR--LPNYEtAFAMT 521

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 3319366    214 INKSQGQSLKEIGLYLPR---PVFSHDQLYVALSRvtSKKGLKV 254
Cdd:TIGR01447 522 VHKSQGSEFDHVILILPNgnsPVLTRELLYTGITR--AKDQLSV 563
PHA03311 PHA03311
helicase-primase subunit BBLF4; Provisional
 211-253 6.84e-04

helicase-primase subunit BBLF4; Provisional


Pssm-ID: 223040  Cd Length: 782  Bit Score: 40.66  E-value: 6.84e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 3319366   211 AMTINKSQGQSLKEIGLylprpVFSHD------QLYVALSRVTSKKGLK 253
Cdd:PHA03311 706 AMTIAKSQGLSLDKVAI-----CFGNHknlklsHVYVAMSRVTSSNFLV 749
 
Name Accession Description Interval E-value
PIF1 pfam05970
PIF1-like helicase; This family includes homologs of the PIF1 helicase, which inhibits ...
 18-162 3.69e-57

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: 186.43  E-value: 3.69e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3319366     18 PNDGEVLIGIPEEFLITEGEDPIKAISLEICGDptLLLENKDLKFIQERAILSPTNEDVNTINQRLLEKLPGEEIQYLSI 97
Cdd:pfam05970 219 ENEREQLIDIPIDILLNTGGDPIEAIVSEVYPD--ILQNSTDPNYLEERAILCPTNEDVDEINNYRLSQLPGEEKEYLSS 296

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 3319366     98 DSIDLSDTTSEYNPVFTPDFLNSIKISGLPNHCLRLNIGAPIMLLRNLDPKGGLCNGTRLQMIQM 162
Cdd:pfam05970 297 DSISKSDNDSEIDALYPTEFLNSLNANGLPNHVLKLKVGAPVMLLRNLDQSRGLCNGTRLIVTQL 361
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 68-252 3.58e-14

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: 71.55  E-value: 3.58e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3319366   68 ILSPTNEDVNTINQRLLEKLPGEeiqylsidsidlsdttSEYNPVFTPDFLNSIKIsglpnhclrlniGAPIMLLRNlDP 147
Cdd:COG0507 347 VLAPTNAGVDALNQAIREALNPA----------------GELERELAEDGELELYV------------GDRVMFTRN-DY 397

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3319366  148 KGGLCNGTRLQMIQMTPPILQAVIITGGRigdkvliSKILITPSDtkLPfnmrrkqfPIVVAFAMTINKSQGQSLKEIGL 227
Cdd:COG0507 398 DLGVFNGDIGTVLSIDEDEGRLTVRFDGR-------EIVTYDPSE--LD--------QLELAYAITVHKSQGSTFDRVIL 460

                       170       180
                ....*....|....*....|....*...
gi 3319366  228 YLP---RPVFSHDQLYVALSRVTSKKGL 252
Cdd:COG0507 461 VLPsehSPLLSRELLYTALTRARELLTL 488
SF1_C_RecD cd18809
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ...
 209-252 8.10e-10

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: 54.10  E-value: 8.10e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 3319366  209 AFAMTINKSQGQSLKEIGLYLP--RPVFSHDQLYVALSRVTSKKGL 252
Cdd:cd18809  33 AYAMTIHKSQGSEFDRVIVVLPtsHPMLSRGLLYTALTRARKLLTL 78
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 135-254 7.33e-07

exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273631 [Multi-domain]  Cd Length: 582  Bit Score: 49.76  E-value: 7.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3319366    135 IGAPIMLLRNlDPKGGLCNGTrlqmiqmtppilqaviiTGGRIGDKVLISKILITPSDTKLPFNMRRkqFPIVV-AFAMT 213
Cdd:TIGR01447 462 IGRPIMVTEN-DYTLGLFNGD-----------------IGVLLRDPDGILTVWFHFADGSKAVLPSR--LPNYEtAFAMT 521

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 3319366    214 INKSQGQSLKEIGLYLPR---PVFSHDQLYVALSRvtSKKGLKV 254
Cdd:TIGR01447 522 VHKSQGSEFDHVILILPNgnsPVLTRELLYTGITR--AKDQLSV 563
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 159-252 5.44e-05

C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Similar to SF2 helicases, they do not form toroidal, predominantly hexameric structures like SF3-6. SF1 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: 350173 [Multi-domain]  Cd Length: 89  Bit Score: 40.88  E-value: 5.44e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3319366  159 MIQMTPPILQAVIITGGRIGDKVLISKILitpsdtklpFNMRrKQFPIVVAFAMTINKSQGQSLKEIGLYLPRPvFSHD- 237
Cdd:cd18786   3 IVNAANGLYKGVVLTPYHRDRAYLNQYLQ---------GLSL-DEFDLQLVGAITIDSSQGLTFDVVTLYLPTA-NSLTp 71

                        90
                ....*....|....*.
gi 3319366  238 -QLYVALSRvtSKKGL 252
Cdd:cd18786  72 rRLYVALTR--ARKRL 85
PHA03311 PHA03311
helicase-primase subunit BBLF4; Provisional
 211-253 6.84e-04

helicase-primase subunit BBLF4; Provisional


Pssm-ID: 223040  Cd Length: 782  Bit Score: 40.66  E-value: 6.84e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 3319366   211 AMTINKSQGQSLKEIGLylprpVFSHD------QLYVALSRVTSKKGLK 253
Cdd:PHA03311 706 AMTIAKSQGLSLDKVAI-----CFGNHknlklsHVYVAMSRVTSSNFLV 749
 
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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