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Conserved domains on  [gi|1039789631|ref|XP_017168187|]
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probable ATP-dependent RNA helicase DDX60 isoform X7 [Mus musculus]

Protein Classification

DEAD/DEAH box helicase family protein( domain architecture ID 1000205)

DEAD/DEAH box helicase family protein such as a DEAD/DEAH box-containing ATP-dependent helicase, which catalyzes the unwinding of DNA or RNA

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 ...
 761-858 2.57e-58

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 cd18025:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 192  Bit Score: 197.59  E-value: 2.57e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039789631 761 IPDTWQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVEYRYAKNM-PAGES 839
Cdd:cd18025     1 NPDAWQRELLDIVDRRESALIVAPTSSGKTFISYYCMEKVLRESDDGVVVYVAPTKALVNQVVAEVYARFSKKYpPSGKS 80

                          90       100
                  ....*....|....*....|
gi 1039789631 840 LCGVFTRDYRHD-ALNCQVL 858
Cdd:cd18025    81 LWGVFTRDYRHNnPMNCQVL 100
Cas3 super family cl34179
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 635-827 5.55e-05

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


The actual alignment was detected with superfamily member COG1203:

Pssm-ID: 440816 [Multi-domain]  Cd Length: 535  Bit Score: 46.61  E-value: 5.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039789631 635 KAQVERVGLQACLKAWKEHCQAEGETTKDLSIAVNMMKRIHSLLDKHSELLQEADQKLIARCLKYLGFCELAVSLYPTQD 714
Cdd:COG1203    11 GALALAALLLLLLALLLAALLLLLLAALLLALLLALLLLAALELALLLLLLLLLLLLLLLLLLDLLLDDLAFLFLLLLID 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039789631 715 A----SDGIKMKKKNKysvgigpARFQLQYMGHYLirEERKDPDPRVqdfipDTWQRELLDVVDNYESA-----VIVAPT 785
Cdd:COG1203    91 AdwldSANFDMARQAL-------DHLLAERLERLL--PKKSKPRTPI-----NPLQNEALELALEAAEEepglfILTAPT 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1039789631 786 SSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVE 827
Cdd:COG1203   157 GGGKTEAALLFALRLAAKHGGRRIIYALPFTSIINQTYDRLR 198
 
Name Accession Description Interval E-value
DEXHc_DDX60 cd18025
DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an ...
 761-858 2.57e-58

DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an IFN-inducible cytoplasmic helicase that plays a role in RIG-I-mediated type I interferon (IFN) nuclease-mediated viral RNA degradation. DDX60 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: 350783 [Multi-domain]  Cd Length: 192  Bit Score: 197.59  E-value: 2.57e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039789631 761 IPDTWQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVEYRYAKNM-PAGES 839
Cdd:cd18025     1 NPDAWQRELLDIVDRRESALIVAPTSSGKTFISYYCMEKVLRESDDGVVVYVAPTKALVNQVVAEVYARFSKKYpPSGKS 80

                          90       100
                  ....*....|....*....|
gi 1039789631 840 LCGVFTRDYRHD-ALNCQVL 858
Cdd:cd18025    81 LWGVFTRDYRHNnPMNCQVL 100
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 766-859 5.11e-09

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: 56.10  E-value: 5.11e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039789631 766 QRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGV-VVYVAPTKALVNQVAATVEYRYAKNMPAGESLCGVF 844
Cdd:pfam00270   4 QAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALEALDKLDNGPqALVLAPTRELAEQIYEELKKLGKGLGLKVASLLGGD 83

                          90
                  ....*....|....*.
gi 1039789631 845 TRDYRHDAL-NCQVLY 859
Cdd:pfam00270  84 SRKEQLEKLkGPDILV 99
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
766-848 2.98e-08

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 57.21  E-value: 2.98e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039789631 766 QRELLD-VVDNYESAVIVAPTSSGKTYASYYCMEKVLKESdeGVVVYVAPTKALVNQVAATVEYRYAKNmpaGESLcGVF 844
Cdd:COG1204    27 QAEALEaGLLEGKNLVVSAPTASGKTLIAELAILKALLNG--GKALYIVPLRALASEKYREFKRDFEEL---GIKV-GVS 100


                  ....
gi 1039789631 845 TRDY 848
Cdd:COG1204   101 TGDY 104
DEXDc smart00487
DEAD-like helicases superfamily;
760-827 8.18e-08

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 53.65  E-value: 8.18e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1039789631  760 FIPDTWQRELLD-VVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVE 827
Cdd:smart00487   7 EPLRPYQKEAIEaLLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELK 75
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 635-827 5.55e-05

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: 46.61  E-value: 5.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039789631 635 KAQVERVGLQACLKAWKEHCQAEGETTKDLSIAVNMMKRIHSLLDKHSELLQEADQKLIARCLKYLGFCELAVSLYPTQD 714
Cdd:COG1203    11 GALALAALLLLLLALLLAALLLLLLAALLLALLLALLLLAALELALLLLLLLLLLLLLLLLLLDLLLDDLAFLFLLLLID 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039789631 715 A----SDGIKMKKKNKysvgigpARFQLQYMGHYLirEERKDPDPRVqdfipDTWQRELLDVVDNYESA-----VIVAPT 785
Cdd:COG1203    91 AdwldSANFDMARQAL-------DHLLAERLERLL--PKKSKPRTPI-----NPLQNEALELALEAAEEepglfILTAPT 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1039789631 786 SSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVE 827
Cdd:COG1203   157 GGGKTEAALLFALRLAAKHGGRRIIYALPFTSIINQTYDRLR 198
 
Name Accession Description Interval E-value
DEXHc_DDX60 cd18025
DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an ...
 761-858 2.57e-58

DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an IFN-inducible cytoplasmic helicase that plays a role in RIG-I-mediated type I interferon (IFN) nuclease-mediated viral RNA degradation. DDX60 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: 350783 [Multi-domain]  Cd Length: 192  Bit Score: 197.59  E-value: 2.57e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039789631 761 IPDTWQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVEYRYAKNM-PAGES 839
Cdd:cd18025     1 NPDAWQRELLDIVDRRESALIVAPTSSGKTFISYYCMEKVLRESDDGVVVYVAPTKALVNQVVAEVYARFSKKYpPSGKS 80

                          90       100
                  ....*....|....*....|
gi 1039789631 840 LCGVFTRDYRHD-ALNCQVL 858
Cdd:cd18025    81 LWGVFTRDYRHNnPMNCQVL 100
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 763-858 4.08e-19

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: 85.78  E-value: 4.08e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039789631 763 DTWQRELLDVVDNY-ESAVIVAPTSSGKTYASYYCMEKVLKESdEGVVVYVAPTKALVNQVAATVEYRYAKNMpageSLC 841
Cdd:cd17921     3 NPIQREALRALYLSgDSVLVSAPTSSGKTLIAELAILRALATS-GGKAVYIAPTRALVNQKEADLRERFGPLG----KNV 77

                          90       100
                  ....*....|....*....|
gi 1039789631 842 GVFTRDYRHDAL---NCQVL 858
Cdd:cd17921    78 GLLTGDPSVNKLllaEADIL 97
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 766-859 5.11e-09

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: 56.10  E-value: 5.11e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039789631 766 QRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGV-VVYVAPTKALVNQVAATVEYRYAKNMPAGESLCGVF 844
Cdd:pfam00270   4 QAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALEALDKLDNGPqALVLAPTRELAEQIYEELKKLGKGLGLKVASLLGGD 83

                          90
                  ....*....|....*.
gi 1039789631 845 TRDYRHDAL-NCQVLY 859
Cdd:pfam00270  84 SRKEQLEKLkGPDILV 99
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
766-848 2.98e-08

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 57.21  E-value: 2.98e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039789631 766 QRELLD-VVDNYESAVIVAPTSSGKTYASYYCMEKVLKESdeGVVVYVAPTKALVNQVAATVEYRYAKNmpaGESLcGVF 844
Cdd:COG1204    27 QAEALEaGLLEGKNLVVSAPTASGKTLIAELAILKALLNG--GKALYIVPLRALASEKYREFKRDFEEL---GIKV-GVS 100


                  ....
gi 1039789631 845 TRDY 848
Cdd:COG1204   101 TGDY 104
DEXDc smart00487
DEAD-like helicases superfamily;
760-827 8.18e-08

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 53.65  E-value: 8.18e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1039789631  760 FIPDTWQRELLD-VVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVE 827
Cdd:smart00487   7 EPLRPYQKEAIEaLLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELK 75
DEXHc_Mtr4-like cd18024
DEXH-box helicase domain of ATP-dependent RNA helicase Mtr4; Mtr4 (also known as DOB1 or ...
 744-821 1.73e-07

DEXH-box helicase domain of ATP-dependent RNA helicase Mtr4; Mtr4 (also known as DOB1 or SKIV2L2) is a type II DEAD box helicase that plays a role in the processing of structured RNAs, including the maturation of 5.8S ribosomal RNA (rRNA)and is part of the TRAMP complex that is involved in exosome-mediated degradation of aberrant RNAs. Mtr4 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: 350782 [Multi-domain]  Cd Length: 205  Bit Score: 52.45  E-value: 1.73e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039789631 744 YLIREERKDPDPRVQDFIPDTWQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEgvVVYVAPTKALVNQ 821
Cdd:cd18024    15 PISAHKPPGNPARTYPFTLDPFQKTAIACIERNESVLVSAHTSAGKTVVAEYAIAQSLRDKQR--VIYTSPIKALSNQ 90
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
743-827 6.05e-06

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 50.02  E-value: 6.05e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039789631 743 HYLIREERKDPDPRVQ-DFIPDTWQRELLD-----VVDNYESAVIVAPTSSGKTYASYYCMEKVLKesdEGVVVYVAPTK 816
Cdd:COG1061    61 ELAEAEALEAGDEASGtSFELRPYQQEALEallaaLERGGGRGLVVAPTGTGKTVLALALAAELLR---GKRVLVLVPRR 137

                          90
                  ....*....|.
gi 1039789631 817 ALVNQVAATVE 827
Cdd:COG1061   138 ELLEQWAEELR 148
DEXHc_LHR-like cd17922
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ...
 777-827 7.34e-06

DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases from 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: 350680 [Multi-domain]  Cd Length: 166  Bit Score: 46.81  E-value: 7.34e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1039789631 777 ESAVIVAPTSSGKTYASYYC-MEKVLKESDEGV-VVYVAPTKALVNQVAATVE 827
Cdd:cd17922     2 RNVLIAAPTGSGKTEAAFLPaLSSLADEPEKGVqVLYISPLKALINDQERRLE 54
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
758-821 9.13e-06

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


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 49.55  E-value: 9.13e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1039789631 758 QDFIPDTWQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESdeGVVVYVAPTKALVNQ 821
Cdd:COG4581    22 RGFELDPFQEEAILALEAGRSVLVAAPTGSGKTLVAEFAIFLALARG--RRSFYTAPIKALSNQ 83
DEXHc_HFM1 cd18023
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ...
 766-821 1.03e-05

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: 47.35  E-value: 1.03e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039789631 766 QRELL-DVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEG-----VVVYVAPTKALVNQ 821
Cdd:cd18023     6 QSEVFpDLLYSDKNFVVSAPTGSGKTVLFELAILRLLKERNPLpwgnrKVVYIAPIKALCSE 67
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 760-834 2.47e-05

DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) 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: 350794 [Multi-domain]  Cd Length: 204  Bit Score: 46.31  E-value: 2.47e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1039789631 760 FIPDTWQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKE----SDEGVVVYVAPTKALVNQvAATVEYRYAKNM 834
Cdd:cd18036     1 LELRNYQLELVLPALRGKNTIICAPTGSGKTRVAVYICRHHLEKrrsaGEKGRVVVLVNKVPLVEQ-QLEKFFKYFRKG 78
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 766-824 3.57e-05

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


Pssm-ID: 440818 [Multi-domain]  Cd Length: 758  Bit Score: 47.52  E-value: 3.57e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039789631 766 QRELLDVVDNYESAVIVAPTSSGKTYAsyYC---MEKVLKESDeGVVVYVAPTKALVN-QVAA 824
Cdd:COG1205    61 QAEAIEAARAGKNVVIATPTASGKSLA--YLlpvLEALLEDPG-ATALYLYPTKALARdQLRR 120
DEXHc_ASCC3_2 cd18022
C-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ...
 777-819 4.27e-05

C-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; Activating signal cointegrator 1 complex subunit 3 (ASCC3) is a type II DEAD box helicase that plays a role in the repair of N-alkylated nucleotides. ASCC3 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: 350780 [Multi-domain]  Cd Length: 189  Bit Score: 45.06  E-value: 4.27e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1039789631 777 ESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALV 819
Cdd:cd18022    18 NNVLLGAPTGSGKTIAAELAMFRAFNKYPGSKVVYIAPLKALV 60
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 762-830 5.35e-05

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: 45.12  E-value: 5.35e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039789631 762 PDTWQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLK---ESDEGVVVYVAPTKALVNQvAATVEYRY 830
Cdd:cd17927     3 PRNYQLELAQPALKGKNTIICLPTGSGKTFVAVLICEHHLKkfpAGRKGKVVFLANKVPLVEQ-QKEVFRKH 73
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 635-827 5.55e-05

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: 46.61  E-value: 5.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039789631 635 KAQVERVGLQACLKAWKEHCQAEGETTKDLSIAVNMMKRIHSLLDKHSELLQEADQKLIARCLKYLGFCELAVSLYPTQD 714
Cdd:COG1203    11 GALALAALLLLLLALLLAALLLLLLAALLLALLLALLLLAALELALLLLLLLLLLLLLLLLLLDLLLDDLAFLFLLLLID 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039789631 715 A----SDGIKMKKKNKysvgigpARFQLQYMGHYLirEERKDPDPRVqdfipDTWQRELLDVVDNYESA-----VIVAPT 785
Cdd:COG1203    91 AdwldSANFDMARQAL-------DHLLAERLERLL--PKKSKPRTPI-----NPLQNEALELALEAAEEepglfILTAPT 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1039789631 786 SSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVE 827
Cdd:COG1203   157 GGGKTEAALLFALRLAAKHGGRRIIYALPFTSIINQTYDRLR 198
Lhr COG1201
Lhr-like helicase [Replication, recombination and repair];
754-823 5.78e-05

Lhr-like helicase [Replication, recombination and repair];


Pssm-ID: 440814 [Multi-domain]  Cd Length: 850  Bit Score: 47.02  E-value: 5.78e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039789631 754 DPRVQDFIPDTW------QRELLDVVDNYESAVIVAPTSSGKTYASY------YCMEKVLKESDEGV-VVYVAPTKALVN 820
Cdd:COG1201    11 HPAVRAWFAARFgaptppQREAWPAIAAGESTLLIAPTGSGKTLAAFlpaldeLARRPRPGELPDGLrVLYISPLKALAN 90


                  ...
gi 1039789631 821 QVA 823
Cdd:COG1201    91 DIE 93
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 765-821 1.52e-04

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: 42.68  E-value: 1.52e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039789631 765 WQRELLDVVDNYES---AVIVAPTSSGKTYASYYCMEKVLKESdegvVVYVAPTKALVNQ 821
Cdd:cd17926     4 YQEEALEAWLAHKNnrrGILVLPTGSGKTLTALALIAYLKELR----TLIVVPTDALLDQ 59
DEXHc_SKIV2L cd18027
DEXH-box helicase domain of SKIV2L; Superkiller viralicidic activity 2-like (SKIV2L, also ...
 760-821 9.39e-04

DEXH-box helicase domain of SKIV2L; Superkiller viralicidic activity 2-like (SKIV2L, also called SKI2 or DHX13) plays a role in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. SKIV2L 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: 350785 [Multi-domain]  Cd Length: 179  Bit Score: 41.10  E-value: 9.39e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039789631 760 FIPDTWQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEgvVVYVAPTKALVNQ 821
Cdd:cd18027     7 FELDVFQKQAILHLEAGDSVFVAAHTSAGKTVVAEYAIALAQKHMTR--TIYTSPIKALSNQ 66
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 777-848 1.12e-03

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: 40.08  E-value: 1.12e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039789631 777 ESAVIVAPTSSGKTYASYYCMEKVLkESDEGVVVYVAPTKALVNQVAATVEYRYAKNMPageslCGVFTRDY 848
Cdd:cd00046     2 ENVLITAPTGSGKTLAALLAALLLL-LKKGKKVLVLVPTKALALQTAERLRELFGPGIR-----VAVLVGGS 67
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
781-845 1.19e-03

ERCC4-related helicase [Replication, recombination and repair];


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 42.41  E-value: 1.19e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1039789631 781 IVAPTSSGKTYASYYCMEKVLKESDeGVVVYVAPTKALVNQVAATveyrYAKNMPAGESLCGVFT 845
Cdd:COG1111    22 VVLPTGLGKTAVALLVIAERLHKKG-GKVLFLAPTKPLVEQHAEF----FKEALNIPEDEIVVFT 81
DEXHc_cas3 cd17930
DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase ...
 780-821 3.46e-03

DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase responsible for degradation of dsDNA. The two enzymatic units of Cas3, a histidine-aspartate (HD) nuclease and a Superfamily 2 (SF2) helicase, may be expressed from separate genes as Cas3' (SF2 helicase) and Cas3'' (HD nuclease) or may be fused as a single HD-SF2 polypeptide. The nucleolytic activity of most Cas3 enzymes is transition metal ion-dependent. Cas3 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: 350688 [Multi-domain]  Cd Length: 186  Bit Score: 39.58  E-value: 3.46e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1039789631 780 VIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQ 821
Cdd:cd17930     5 ILEAPTGSGKTEAALLWALKLAARGGKRRIIYALPTRATINQ 46
ResIII pfam04851
Type III restriction enzyme, res subunit;
779-858 4.16e-03

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 38.81  E-value: 4.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039789631 779 AVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQvaaTVEyRYAKNMPAGESLCGVFT-RDYRHDALNCQV 857
Cdd:pfam04851  26 GLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPRKDLLEQ---ALE-EFKKFLPNYVEIGEIISgDKKDESVDDNKI 101


                  .
gi 1039789631 858 L 858
Cdd:pfam04851 102 V 102
DEXHc_Brr2_2 cd18021
C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type ...
 777-835 8.02e-03

C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD box helicase that mediates spliceosome catalytic activation. It is a stable subunit of the spliceosome, required during splicing catalysis and spliceosome disassembly. Brr2 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: 350779 [Multi-domain]  Cd Length: 191  Bit Score: 38.39  E-value: 8.02e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1039789631 777 ESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVEYRYAKNMP 835
Cdd:cd18021    20 DNVFVGAPTGSGKTVCAELALLRHWRQNPKGRAVYIAPMQELVDARYKDWRAKFGPLLG 78
DDXDc_reverse_gyrase cd17924
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ...
 764-827 8.61e-03

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: 38.46  E-value: 8.61e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1039789631 764 TWQRELLdvvdNYESAVIVAPTSSGKT-----YASYYcmekvlkESDEGVVVYVAPTKALVNQVAATVE 827
Cdd:cd17924    24 TWAKRLL----RGKSFAIIAPTGVGKTtfglaTSLYL-------ASKGKRSYLIFPTKSLVKQAYERLS 81
 
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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