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Conserved domains on  [gi|402659418|gb|EJW90345|]
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helicase, putative, RecD/TraA family, partial [gut metagenome]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AAA_19 pfam13245
AAA domain;
18-116 2.08e-29

AAA domain;


:

Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 102.68  E-value: 2.08e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402659418   18 QLQAIEEAIRSKVMVLTGGPGTGKTTTTQGIIAALKHMG---LRILLAAPTGRAAKRMSEATGMEAKTIHRLLEFNPK-- 92
Cdd:pfam13245   1 QREAVRTALPSKVVLLTGGPGTGKTTTIRHIVALLVALGgvsFPILLAAPTGRAAKRLSERTGLPASTIHRLLGFDDLea 80

                          90       100
                  ....*....|....*....|....
gi 402659418   93 DGYKRNDENPLEGDALIVDECSMI 116
Cdd:pfam13245  81 GGFLRDEEEPLDGDLLIVDEFSMV 104
 
Name Accession Description Interval E-value
AAA_19 pfam13245
AAA domain;
18-116 2.08e-29

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 102.68  E-value: 2.08e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402659418   18 QLQAIEEAIRSKVMVLTGGPGTGKTTTTQGIIAALKHMG---LRILLAAPTGRAAKRMSEATGMEAKTIHRLLEFNPK-- 92
Cdd:pfam13245   1 QREAVRTALPSKVVLLTGGPGTGKTTTIRHIVALLVALGgvsFPILLAAPTGRAAKRLSERTGLPASTIHRLLGFDDLea 80

                          90       100
                  ....*....|....*....|....
gi 402659418   93 DGYKRNDENPLEGDALIVDECSMI 116
Cdd:pfam13245  81 GGFLRDEEEPLDGDLLIVDEFSMV 104
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 18-116 7.69e-29

DEXS-box helicase domain of RecD and similar proteins; 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 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: 350691 [Multi-domain]  Cd Length: 155  Bit Score: 101.86  E-value: 7.69e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402659418  18 QLQAIEEAIRSKVMVLTGGPGTGKTTTTQGIIAALKHMGLRILLAAPTGRAAKRMSEATGMEAKTIHRLLEFNP-KDGYK 96
Cdd:cd17933    2 QKAAVRLVLRNRVSVLTGGAGTGKTTTLKALLAALEAEGKRVVLAAPTGKAAKRLSESTGIEASTIHRLLGINPgGGGFY 81

                         90       100
                 ....*....|....*....|
gi 402659418  97 RNDENPLEGDALIVDECSMI 116
Cdd:cd17933   82 YNEENPLDADLLIVDEASMV 101
recD_rel TIGR01448
helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the ...
 1-116 6.33e-27

helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273632 [Multi-domain]  Cd Length: 720  Bit Score: 103.33  E-value: 6.33e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402659418    1 MDVKALSKETGIEYDEVQLQAIEEAIRSKVMVLTGGPGTGKTTTTQGII--AALKHMGLRILLAAPTGRAAKRMSEATGM 78
Cdd:TIGR01448 311 EHIWEVEKKLRKGLSEEQKQALDTAIQHKVVILTGGPGTGKTTITRAIIelAEELGGLLPVGLAAPTGRAAKRLGEVTGL 390

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 402659418   79 EAKTIHRLLEFNPKDGYKRNDENPLEGDALIVDECSMI 116
Cdd:TIGR01448 391 TASTIHRLLGYGPDTFRHNHLEDPIDCDLLIVDESSMM 428
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 3-116 3.22e-26

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: 101.21  E-value: 3.22e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402659418   3 VKALSKETGIEYDEVQLQAIEEAI-RSKVMVLTGGPGTGKTTTTQGIIAALKHMGLRILLAAPTGRAAKRMSEATGMEAK 81
Cdd:COG0507  114 LAALEPRAGITLSDEQREAVALALtTRRVSVLTGGAGTGKTTTLRALLAALEALGLRVALAAPTGKAAKRLSESTGIEAR 193

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 402659418  82 TIHRLLEFNP-KDGYKRNDENPL-EGDALIVDECSMI 116
Cdd:COG0507  194 TIHRLLGLRPdSGRFRHNRDNPLtPADLLVVDEASMV 230
recD PRK10875
exodeoxyribonuclease V subunit alpha;
15-116 2.27e-10

exodeoxyribonuclease V subunit alpha;


Pssm-ID: 236783 [Multi-domain]  Cd Length: 615  Bit Score: 56.10  E-value: 2.27e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402659418  15 DEVQLQAIEEA--IRSKVMVLTGGPGTGKTTTTQGIIAALKHMG----LRILLAAPTGRAAKRMSEATGM---------- 78
Cdd:PRK10875 152 DEVDWQKVAAAvaLTRRISVISGGPGTGKTTTVAKLLAALIQLAdgerCRIRLAAPTGKAAARLTESLGKalrqlpltde 231

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 402659418  79 -------EAKTIHRLLEFNPKDGYKRNDE-NPLEGDALIVDECSMI 116
Cdd:PRK10875 232 qkkripeEASTLHRLLGAQPGSQRLRYHAgNPLHLDVLVVDEASMV 277
 
Name Accession Description Interval E-value
AAA_19 pfam13245
AAA domain;
18-116 2.08e-29

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 102.68  E-value: 2.08e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402659418   18 QLQAIEEAIRSKVMVLTGGPGTGKTTTTQGIIAALKHMG---LRILLAAPTGRAAKRMSEATGMEAKTIHRLLEFNPK-- 92
Cdd:pfam13245   1 QREAVRTALPSKVVLLTGGPGTGKTTTIRHIVALLVALGgvsFPILLAAPTGRAAKRLSERTGLPASTIHRLLGFDDLea 80

                          90       100
                  ....*....|....*....|....
gi 402659418   93 DGYKRNDENPLEGDALIVDECSMI 116
Cdd:pfam13245  81 GGFLRDEEEPLDGDLLIVDEFSMV 104
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 18-116 7.69e-29

DEXS-box helicase domain of RecD and similar proteins; 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 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: 350691 [Multi-domain]  Cd Length: 155  Bit Score: 101.86  E-value: 7.69e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402659418  18 QLQAIEEAIRSKVMVLTGGPGTGKTTTTQGIIAALKHMGLRILLAAPTGRAAKRMSEATGMEAKTIHRLLEFNP-KDGYK 96
Cdd:cd17933    2 QKAAVRLVLRNRVSVLTGGAGTGKTTTLKALLAALEAEGKRVVLAAPTGKAAKRLSESTGIEASTIHRLLGINPgGGGFY 81

                         90       100
                 ....*....|....*....|
gi 402659418  97 RNDENPLEGDALIVDECSMI 116
Cdd:cd17933   82 YNEENPLDADLLIVDEASMV 101
recD_rel TIGR01448
helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the ...
 1-116 6.33e-27

helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273632 [Multi-domain]  Cd Length: 720  Bit Score: 103.33  E-value: 6.33e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402659418    1 MDVKALSKETGIEYDEVQLQAIEEAIRSKVMVLTGGPGTGKTTTTQGII--AALKHMGLRILLAAPTGRAAKRMSEATGM 78
Cdd:TIGR01448 311 EHIWEVEKKLRKGLSEEQKQALDTAIQHKVVILTGGPGTGKTTITRAIIelAEELGGLLPVGLAAPTGRAAKRLGEVTGL 390

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 402659418   79 EAKTIHRLLEFNPKDGYKRNDENPLEGDALIVDECSMI 116
Cdd:TIGR01448 391 TASTIHRLLGYGPDTFRHNHLEDPIDCDLLIVDESSMM 428
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 3-116 3.22e-26

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: 101.21  E-value: 3.22e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402659418   3 VKALSKETGIEYDEVQLQAIEEAI-RSKVMVLTGGPGTGKTTTTQGIIAALKHMGLRILLAAPTGRAAKRMSEATGMEAK 81
Cdd:COG0507  114 LAALEPRAGITLSDEQREAVALALtTRRVSVLTGGAGTGKTTTLRALLAALEALGLRVALAAPTGKAAKRLSESTGIEAR 193

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 402659418  82 TIHRLLEFNP-KDGYKRNDENPL-EGDALIVDECSMI 116
Cdd:COG0507  194 TIHRLLGLRPdSGRFRHNRDNPLtPADLLVVDEASMV 230
recD PRK10875
exodeoxyribonuclease V subunit alpha;
15-116 2.27e-10

exodeoxyribonuclease V subunit alpha;


Pssm-ID: 236783 [Multi-domain]  Cd Length: 615  Bit Score: 56.10  E-value: 2.27e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402659418  15 DEVQLQAIEEA--IRSKVMVLTGGPGTGKTTTTQGIIAALKHMG----LRILLAAPTGRAAKRMSEATGM---------- 78
Cdd:PRK10875 152 DEVDWQKVAAAvaLTRRISVISGGPGTGKTTTVAKLLAALIQLAdgerCRIRLAAPTGKAAARLTESLGKalrqlpltde 231

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 402659418  79 -------EAKTIHRLLEFNPKDGYKRNDE-NPLEGDALIVDECSMI 116
Cdd:PRK10875 232 qkkripeEASTLHRLLGAQPGSQRLRYHAgNPLHLDVLVVDEASMV 277
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 40-116 5.38e-10

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: 55.15  E-value: 5.38e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402659418   40 GKTTTTQGIIAAL-----KHMGLRILLAAPTGRAAKRMSEATG-----------------MEAKTIHRLLEFNPKDGYKR 97
Cdd:TIGR01447 171 GKTTTVARLLLALvkqspKQGKLRIALAAPTGKAAARLAESLRkavknlaaaealiaalpSEAVTIHRLLGIKPDTKRFR 250

                          90       100
                  ....*....|....*....|
gi 402659418   98 NDE-NPLEGDALIVDECSMI 116
Cdd:TIGR01447 251 HHErNPLPLDVLVVDEASMV 270
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 18-116 5.21e-09

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.


Pssm-ID: 433343 [Multi-domain]  Cd Length: 191  Bit Score: 51.41  E-value: 5.21e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402659418   18 QLQAIEEAIRS--KVMVLTGGPGTGKTTTTQGIIAALKHMGLRILLAAPTGRAAKRMSEATGMEAKTIHRLLefnpkdgY 95
Cdd:pfam13604   6 QAAAVRALLTSgdRVAVLVGPAGTGKTTALKALREAWEAAGYRVIGLAPTGRAAKVLGEELGIPADTIAKLL-------H 78

                          90       100
                  ....*....|....*....|..
gi 402659418   96 KRNDENPLE-GDALIVDECSMI 116
Cdd:pfam13604  79 RLGGRAGLDpGTLLIVDEAGMV 100
DEXSc_Pif1_like cd18037
DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like ...
 39-116 1.02e-03

DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like helicases involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. The members of Pif1 helicase subfamily studied so far all appear to contribute to telomere maintenance. Pif1 is a member of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350795 [Multi-domain]  Cd Length: 183  Bit Score: 36.84  E-value: 1.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402659418  39 TGKTTTTQGIIAALKHMGLRILLAAPTGRAakrmseATGMEAKTIHRLLEFNPKDGY-----------KRNDENPLEGDA 107
Cdd:cd18037   23 TGKSYLLRRIIRALPSRPKRVAVTASTGIA------ACNIGGTTLHSFAGIGLGSEPaedllervkrsPYLVQRWRKCDV 96


                 ....*....
gi 402659418 108 LIVDECSMI 116
Cdd:cd18037   97 LIIDEISML 105
 
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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