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Conserved domains on  [gi|2728048274|ref|WP_343251668|]
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ATP-binding protein [Mycoplasma amphoriforme]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 13208672)

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
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
603-990 1.92e-66

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


:

Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 240.80  E-value: 1.92e-66
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  603 DELQFNFSQFQSLFSQSVYEYIEACKRNLKSKIIKNFFQIYESDKKQLLEICRQGRN--SNPKEIPWWFSINRKIINRLY 680
Cdd:COG1112    456 LLLLLALAALLLLLAAAAALLALALLESLLEELIEEHPEELEKLIAELREAARLRRAlrRELKKRRELRKLLWDALLELA 535

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  681 PIHIMSFESASILLENQRDLYDYVIIDEASQVFLERALPALYRGKRYIIAGDTKQLHPSSFFQSRanyEDDAFAEIDEnn 760
Cdd:COG1112    536 PVVGMTPASVARLLPLGEGSFDLVIIDEASQATLAEALGALARAKRVVLVGDPKQLPPVVFGEEA---EEVAEEGLDE-- 610

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  761 aietdeavnaiSLIHFLKERA-RLSSMLKYHYRSNFSnLIAFTNSHIYGNELIFMDKAIR-----PNQTFIVHEIsSGKW 834
Cdd:COG1112    611 -----------SLLDRLLARLpERGVMLREHYRMHPE-IIAFSNRLFYDGKLVPLPSPKArrladPDSPLVFIDV-DGVY 677

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  835 Q----NNRNIEEAQEVVKRLQKLVLSDDYQKTVGIITFNKTQADFIENLLDKVNDplinewrerttpnGEYIGLFVKNVE 910
Cdd:COG1112    678 ErrggSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELLREALG-------------DGLEPVFVGTVD 744

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  911 NVQGDERDIIIFSLGYDKSVN---NYGPISKeeGANRLNVAITRAKSRIELFkTNKAneysgWASNSEGARLLVEYLSYC 987
Cdd:COG1112    745 RFQGDERDVIIFSLVYSNDEDvprNFGFLNG--GPRRLNVAVSRARRKLIVV-GSRE-----LLDSDPSTPALKRLLEYL 816


                   ...
gi 2728048274  988 EEQ 990
Cdd:COG1112    817 ERA 819
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 298-355 8.38e-18

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 cd18043:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 127  Bit Score: 80.70  E-value: 8.38e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2728048274  298 DIYQQLAVKHALVG-DIVVEGPPGTGKSETILNILINIVLNNKTALFVSEKATAMEVVY 355
Cdd:cd18043      1 DSSQEAAIISARNGkNVVIQGPPGTGKSQTIANIIANALARGKRVLFVSEKKAALDVVR 59
 
Name Accession Description Interval E-value
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
603-990 1.92e-66

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 240.80  E-value: 1.92e-66
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  603 DELQFNFSQFQSLFSQSVYEYIEACKRNLKSKIIKNFFQIYESDKKQLLEICRQGRN--SNPKEIPWWFSINRKIINRLY 680
Cdd:COG1112    456 LLLLLALAALLLLLAAAAALLALALLESLLEELIEEHPEELEKLIAELREAARLRRAlrRELKKRRELRKLLWDALLELA 535

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  681 PIHIMSFESASILLENQRDLYDYVIIDEASQVFLERALPALYRGKRYIIAGDTKQLHPSSFFQSRanyEDDAFAEIDEnn 760
Cdd:COG1112    536 PVVGMTPASVARLLPLGEGSFDLVIIDEASQATLAEALGALARAKRVVLVGDPKQLPPVVFGEEA---EEVAEEGLDE-- 610

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  761 aietdeavnaiSLIHFLKERA-RLSSMLKYHYRSNFSnLIAFTNSHIYGNELIFMDKAIR-----PNQTFIVHEIsSGKW 834
Cdd:COG1112    611 -----------SLLDRLLARLpERGVMLREHYRMHPE-IIAFSNRLFYDGKLVPLPSPKArrladPDSPLVFIDV-DGVY 677

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  835 Q----NNRNIEEAQEVVKRLQKLVLSDDYQKTVGIITFNKTQADFIENLLDKVNDplinewrerttpnGEYIGLFVKNVE 910
Cdd:COG1112    678 ErrggSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELLREALG-------------DGLEPVFVGTVD 744

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  911 NVQGDERDIIIFSLGYDKSVN---NYGPISKeeGANRLNVAITRAKSRIELFkTNKAneysgWASNSEGARLLVEYLSYC 987
Cdd:COG1112    745 RFQGDERDVIIFSLVYSNDEDvprNFGFLNG--GPRRLNVAVSRARRKLIVV-GSRE-----LLDSDPSTPALKRLLEYL 816


                   ...
gi 2728048274  988 EEQ 990
Cdd:COG1112    817 ERA 819
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 796-955 2.67e-27

C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), and similar proteins. They 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: 350195 [Multi-domain]  Cd Length: 184  Bit Score: 109.63  E-value: 2.67e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  796 SNLIAFTNSHIYGNELIFMDKAIR-----------PNQTFIVH---EISSGKWQNNRNIEEAQEVVKRLQKLVLSDDYQK 861
Cdd:cd18808      3 PEISEFPSKLFYEGKLKAGVSVAArlnppplpgpsKPLVFVDVsggEEREESGTSKSNEAEAELVVELVKYLLKSGVKPS 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  862 TVGIITFNKTQADFIENLLDKVNdplinewrerttpnGEYIGLFVKNVENVQGDERDIIIFSLGYDKSVNnyGPISKEEG 941
Cdd:cd18808     83 SIGVITPYRAQVALIRELLRKRG--------------GLLEDVEVGTVDNFQGREKDVIILSLVRSNESG--GSIGFLSD 146

                          170
                   ....*....|....
gi 2728048274  942 ANRLNVAITRAKSR 955
Cdd:cd18808    147 PRRLNVALTRAKRG 160
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 298-355 8.38e-18

DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. This is central to many aspects of cellular DNA and RNA metabolism and accordingly, they are implicated in a wide range of nucleic acid processing events including DNA replication, recombination, and repair as well as many aspects of RNA metabolism. Superfamily 1 helicases 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: 350801 [Multi-domain]  Cd Length: 127  Bit Score: 80.70  E-value: 8.38e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2728048274  298 DIYQQLAVKHALVG-DIVVEGPPGTGKSETILNILINIVLNNKTALFVSEKATAMEVVY 355
Cdd:cd18043      1 DSSQEAAIISARNGkNVVIQGPPGTGKSQTIANIIANALARGKRVLFVSEKKAALDVVR 59
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 784-954 9.49e-18

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.


Pssm-ID: 463780 [Multi-domain]  Cd Length: 196  Bit Score: 82.60  E-value: 9.49e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  784 SSMLKYHYRSNfSNLIAFTNSHIYGNELI-----------FMDKAIRPNQTFIVHEISSGKWQNNR------NIEEAQEV 846
Cdd:pfam13087   17 VVMLDTQYRMH-PEIMEFPSKLFYGGKLKdgpsvaerplpDDFHLPDPLGPLVFIDVDGSEEEESDggtsysNEAEAELV 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  847 VKRLQKLVLS-DDYQKTVGIITFNKTQADFIENLLDKVNDPLInewrerttpngeyiGLFVKNVENVQGDERDIIIFSLg 925
Cdd:pfam13087   96 VQLVEKLIKSgPEEPSDIGVITPYRAQVRLIRKLLKRKLGGKL--------------EIEVNTVDGFQGREKDVIIFSC- 160

                          170       180       190
                   ....*....|....*....|....*....|....
gi 2728048274  926 ydksV-----NNYGPISKEegaNRLNVAITRAKS 954
Cdd:pfam13087  161 ----VrsnekGGIGFLSDP---RRLNVALTRAKR 187
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 295-956 5.36e-07

DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273041 [Multi-domain]  Cd Length: 636  Bit Score: 53.67  E-value: 5.36e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  295 SHLDIYQQLAVKHALVGD--IVVEGPPGTGKSETILNILINIVLNNKTALFVSEKATAMEVVYNRLgnlkhiamyipslt 372
Cdd:TIGR00376  156 PNLNESQKEAVLFALSSKdlFLIHGPPGTGKTRTVVELIRQLVKRGLRVLVTAPSNIAVDNLLERL-------------- 221

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  373 enkkqfykqfadfeqyfsenysnqllntpmATFDNKLVpsyyklaseienfynqkintgtqthlfkdillnfklmdvsfi 452
Cdd:TIGR00376  222 ------------------------------ALCDQKIV------------------------------------------ 229

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  453 KLDDVARFEEWLSVFTNQSWLEQHVAYNELHNqlinswgrdtfnafyhawhqepenykrfmliihnfYKKKLIEVPKLSN 532
Cdd:TIGR00376  230 RLGHPARLLKSNKQHSLDYLIENHPKYQIVAD-----------------------------------IREKIDELIEERN 274

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  533 PFFKPTPkeektfnllslQIKRFDS----LKKFASKSKYQTIKhclennvlankkavfyswfmqeqsapyiakidelqfn 608
Cdd:TIGR00376  275 KKTKPSP-----------QKRRGLSdikiLRKALKKREARGIE------------------------------------- 306

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  609 fsqfqSLFSQSVYEYIEACKRnlKSKIIKNffqIYESDKKQLLEICRQGRNSNpkeipwwfsinrkiinrlypihimSFE 688
Cdd:TIGR00376  307 -----SLKIASMAEWIETNKS--IDRLLKL---LPESEERIMNEILAESDATN------------------------SMA 352

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  689 SASILLEnqrDLYDYVIIDEASQVFLERALPALYRGKRYIIAGDTKQLHPSSFFQSRANYEDDAFAEIdennaietdeav 768
Cdd:TIGR00376  353 GSEILNG---QYFDVAVIDEASQAMEPSCLIPLLKARKLILAGDHKQLPPTILSHDAEELSLTLFERL------------ 417

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  769 naislihfLKERARLSSMLKYHYRSNfSNLIAFTNSHIYGNELI--------------------FMDKAIRPNQTFIVHE 828
Cdd:TIGR00376  418 --------IKEYPERSRTLNVQYRMN-QKIMEFPSREFYNGKLTahesvanillrdlpkveateSEDDLETGIPLLFIDT 488

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  829 ISSGKW-------QNNRNIEEAQEVVKRLQKLVLSDDYQKTVGIITFNKTQADFIENLLDKvndplinewrerttpngEY 901
Cdd:TIGR00376  489 SGCELFelkeadsTSKYNPGEAELVSEIIQALVKMGVPANDIGVITPYDAQVDLLRQLLEH-----------------RH 551

                          650       660       670       680       690
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2728048274  902 IGLFVKNVENVQGDERDIIIFSLgydKSVNNYGPISKEEGANRLNVAITRAKSRI 956
Cdd:TIGR00376  552 IDIEVSSVDGFQGREKEVIIISF---VRSNRKGEVGFLKDLRRLNVALTRARRKL 603
 
Name Accession Description Interval E-value
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
603-990 1.92e-66

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 240.80  E-value: 1.92e-66
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  603 DELQFNFSQFQSLFSQSVYEYIEACKRNLKSKIIKNFFQIYESDKKQLLEICRQGRN--SNPKEIPWWFSINRKIINRLY 680
Cdd:COG1112    456 LLLLLALAALLLLLAAAAALLALALLESLLEELIEEHPEELEKLIAELREAARLRRAlrRELKKRRELRKLLWDALLELA 535

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  681 PIHIMSFESASILLENQRDLYDYVIIDEASQVFLERALPALYRGKRYIIAGDTKQLHPSSFFQSRanyEDDAFAEIDEnn 760
Cdd:COG1112    536 PVVGMTPASVARLLPLGEGSFDLVIIDEASQATLAEALGALARAKRVVLVGDPKQLPPVVFGEEA---EEVAEEGLDE-- 610

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  761 aietdeavnaiSLIHFLKERA-RLSSMLKYHYRSNFSnLIAFTNSHIYGNELIFMDKAIR-----PNQTFIVHEIsSGKW 834
Cdd:COG1112    611 -----------SLLDRLLARLpERGVMLREHYRMHPE-IIAFSNRLFYDGKLVPLPSPKArrladPDSPLVFIDV-DGVY 677

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  835 Q----NNRNIEEAQEVVKRLQKLVLSDDYQKTVGIITFNKTQADFIENLLDKVNDplinewrerttpnGEYIGLFVKNVE 910
Cdd:COG1112    678 ErrggSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELLREALG-------------DGLEPVFVGTVD 744

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  911 NVQGDERDIIIFSLGYDKSVN---NYGPISKeeGANRLNVAITRAKSRIELFkTNKAneysgWASNSEGARLLVEYLSYC 987
Cdd:COG1112    745 RFQGDERDVIIFSLVYSNDEDvprNFGFLNG--GPRRLNVAVSRARRKLIVV-GSRE-----LLDSDPSTPALKRLLEYL 816


                   ...
gi 2728048274  988 EEQ 990
Cdd:COG1112    817 ERA 819
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 796-955 2.67e-27

C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), and similar proteins. They 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: 350195 [Multi-domain]  Cd Length: 184  Bit Score: 109.63  E-value: 2.67e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  796 SNLIAFTNSHIYGNELIFMDKAIR-----------PNQTFIVH---EISSGKWQNNRNIEEAQEVVKRLQKLVLSDDYQK 861
Cdd:cd18808      3 PEISEFPSKLFYEGKLKAGVSVAArlnppplpgpsKPLVFVDVsggEEREESGTSKSNEAEAELVVELVKYLLKSGVKPS 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  862 TVGIITFNKTQADFIENLLDKVNdplinewrerttpnGEYIGLFVKNVENVQGDERDIIIFSLGYDKSVNnyGPISKEEG 941
Cdd:cd18808     83 SIGVITPYRAQVALIRELLRKRG--------------GLLEDVEVGTVDNFQGREKDVIILSLVRSNESG--GSIGFLSD 146

                          170
                   ....*....|....
gi 2728048274  942 ANRLNVAITRAKSR 955
Cdd:cd18808    147 PRRLNVALTRAKRG 160
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 680-741 1.14e-24

DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. This is central to many aspects of cellular DNA and RNA metabolism and accordingly, they are implicated in a wide range of nucleic acid processing events including DNA replication, recombination, and repair as well as many aspects of RNA metabolism. Superfamily 1 helicases 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: 350801 [Multi-domain]  Cd Length: 127  Bit Score: 100.35  E-value: 1.14e-24
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2728048274  680 YPIHIMSFESASILLENQRDLYDYVIIDEASQVFLERALPALYRGKRYIIAGDTKQLHPSSF 741
Cdd:cd18043     60 FPCWIMSPLSVSQYLPLNRNLFDLVIFDEASQIPIEEALPALFRGKQVVVVGDDKQLPPSIL 121
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 298-355 8.38e-18

DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. This is central to many aspects of cellular DNA and RNA metabolism and accordingly, they are implicated in a wide range of nucleic acid processing events including DNA replication, recombination, and repair as well as many aspects of RNA metabolism. Superfamily 1 helicases 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: 350801 [Multi-domain]  Cd Length: 127  Bit Score: 80.70  E-value: 8.38e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2728048274  298 DIYQQLAVKHALVG-DIVVEGPPGTGKSETILNILINIVLNNKTALFVSEKATAMEVVY 355
Cdd:cd18043      1 DSSQEAAIISARNGkNVVIQGPPGTGKSQTIANIIANALARGKRVLFVSEKKAALDVVR 59
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 784-954 9.49e-18

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.


Pssm-ID: 463780 [Multi-domain]  Cd Length: 196  Bit Score: 82.60  E-value: 9.49e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  784 SSMLKYHYRSNfSNLIAFTNSHIYGNELI-----------FMDKAIRPNQTFIVHEISSGKWQNNR------NIEEAQEV 846
Cdd:pfam13087   17 VVMLDTQYRMH-PEIMEFPSKLFYGGKLKdgpsvaerplpDDFHLPDPLGPLVFIDVDGSEEEESDggtsysNEAEAELV 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  847 VKRLQKLVLS-DDYQKTVGIITFNKTQADFIENLLDKVNDPLInewrerttpngeyiGLFVKNVENVQGDERDIIIFSLg 925
Cdd:pfam13087   96 VQLVEKLIKSgPEEPSDIGVITPYRAQVRLIRKLLKRKLGGKL--------------EIEVNTVDGFQGREKDVIIFSC- 160

                          170       180       190
                   ....*....|....*....|....*....|....
gi 2728048274  926 ydksV-----NNYGPISKEegaNRLNVAITRAKS 954
Cdd:pfam13087  161 ----VrsnekGGIGFLSDP---RRLNVALTRAKR 187
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 702-792 1.36e-10

DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to 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: 438708 [Multi-domain]  Cd Length: 121  Bit Score: 59.94  E-value: 1.36e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  702 DYVIIDEASQVFLERALPALYRGKRYIIAGDTKQLHPSSFFQSRANYEDdafaeIDENNAIETDEAVNAISLIHflkera 781
Cdd:cd17934     46 DVVIIDEASQITEPELLIALIRAKKVVLVGDPKQLPPVVQEDHAALLGL-----SFILSLLLLFRLLLPGSPKV------ 114

                           90
                   ....*....|.
gi 2728048274  782 rlssMLKYHYR 792
Cdd:cd17934    115 ----MLDTQYR 121
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 295-956 5.36e-07

DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273041 [Multi-domain]  Cd Length: 636  Bit Score: 53.67  E-value: 5.36e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  295 SHLDIYQQLAVKHALVGD--IVVEGPPGTGKSETILNILINIVLNNKTALFVSEKATAMEVVYNRLgnlkhiamyipslt 372
Cdd:TIGR00376  156 PNLNESQKEAVLFALSSKdlFLIHGPPGTGKTRTVVELIRQLVKRGLRVLVTAPSNIAVDNLLERL-------------- 221

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  373 enkkqfykqfadfeqyfsenysnqllntpmATFDNKLVpsyyklaseienfynqkintgtqthlfkdillnfklmdvsfi 452
Cdd:TIGR00376  222 ------------------------------ALCDQKIV------------------------------------------ 229

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  453 KLDDVARFEEWLSVFTNQSWLEQHVAYNELHNqlinswgrdtfnafyhawhqepenykrfmliihnfYKKKLIEVPKLSN 532
Cdd:TIGR00376  230 RLGHPARLLKSNKQHSLDYLIENHPKYQIVAD-----------------------------------IREKIDELIEERN 274

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  533 PFFKPTPkeektfnllslQIKRFDS----LKKFASKSKYQTIKhclennvlankkavfyswfmqeqsapyiakidelqfn 608
Cdd:TIGR00376  275 KKTKPSP-----------QKRRGLSdikiLRKALKKREARGIE------------------------------------- 306

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  609 fsqfqSLFSQSVYEYIEACKRnlKSKIIKNffqIYESDKKQLLEICRQGRNSNpkeipwwfsinrkiinrlypihimSFE 688
Cdd:TIGR00376  307 -----SLKIASMAEWIETNKS--IDRLLKL---LPESEERIMNEILAESDATN------------------------SMA 352

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  689 SASILLEnqrDLYDYVIIDEASQVFLERALPALYRGKRYIIAGDTKQLHPSSFFQSRANYEDDAFAEIdennaietdeav 768
Cdd:TIGR00376  353 GSEILNG---QYFDVAVIDEASQAMEPSCLIPLLKARKLILAGDHKQLPPTILSHDAEELSLTLFERL------------ 417

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  769 naislihfLKERARLSSMLKYHYRSNfSNLIAFTNSHIYGNELI--------------------FMDKAIRPNQTFIVHE 828
Cdd:TIGR00376  418 --------IKEYPERSRTLNVQYRMN-QKIMEFPSREFYNGKLTahesvanillrdlpkveateSEDDLETGIPLLFIDT 488

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  829 ISSGKW-------QNNRNIEEAQEVVKRLQKLVLSDDYQKTVGIITFNKTQADFIENLLDKvndplinewrerttpngEY 901
Cdd:TIGR00376  489 SGCELFelkeadsTSKYNPGEAELVSEIIQALVKMGVPANDIGVITPYDAQVDLLRQLLEH-----------------RH 551

                          650       660       670       680       690
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2728048274  902 IGLFVKNVENVQGDERDIIIFSLgydKSVNNYGPISKEEGANRLNVAITRAKSRI 956
Cdd:TIGR00376  552 IDIEVSSVDGFQGREKEVIIISF---VRSNRKGEVGFLKDLRRLNVALTRARRKL 603
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 701-738 8.27e-06

DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses different enzymatic activities, such as single-stranded DNA (ssDNA)-dependent ATPase, 5-3 helicase, and endonuclease activities, and is involved in DNA replication and DNA repair in the nucleus and mitochondrion. It is involved in Okazaki fragment processing by cleaving long flaps that escape FEN1: flaps that are longer than 27 nucleotides are coated by replication protein A complex (RPA), leading to recruit DNA2 which cleaves the flap until it is too short to bind RPA and becomes a substrate for FEN1. It is also involved in 5-end resection of DNA during double-strand break (DSB) repair; it is recruited by BLM and mediates the cleavage of 5-ssDNA, while the 3-ssDNA cleavage is prevented by the presence of RPA. DNA2 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: 350799 [Multi-domain]  Cd Length: 203  Bit Score: 48.00  E-value: 8.27e-06
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 2728048274  701 YDYVIIDEASQVFLERALPALYRGKRYIIAGDTKQLHP 738
Cdd:cd18041    130 FDYCIVDEASQITLPICLGPLRLAKKFVLVGDHYQLPP 167
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 689-738 1.10e-05

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.


Pssm-ID: 404072 [Multi-domain]  Cd Length: 248  Bit Score: 48.11  E-value: 1.10e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2728048274  689 SASILLENQRDlYDYVIIDEASQ-VFLERALPALYRGKRYIIAGDTKQLHP 738
Cdd:pfam13086  194 AGSRLLSSLAN-FDVVIIDEAAQaLEPSTLIPLLRGPKKVVLVGDPKQLPP 243
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 689-749 1.61e-05

DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in transcription, neurogenesis, and antiviral response. SEXT is an R-loop-associated protein that is thought to function as an RNA/DNA helicase. R-loops consist of RNA/DNA hybrids, formed during transcription when nascent RNA hybridizes to the DNA template strand, displacing the non-template DNA strand. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). S. cerevisiae homolog splicing endonuclease 1 (Sen1) is an exclusively nuclear protein, important for nucleolar organization. S. cerevisiae Sen1 and its ortholog, the Schizosaccharomyces pombe Sen1, share conserved domains and belong to the family I class of helicases. Both proteins translocate 5' to 3' and unwind both DNA and RNA duplexes and also RNA/DNA hybrids in vitro. SETX 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: 438712 [Multi-domain]  Cd Length: 218  Bit Score: 47.21  E-value: 1.61e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2728048274  689 SASILLENQRDLYDYVIIDEASQ-VFLERALPALYRGKRYIIAGDTKQLHPSSFFQS--RANYE 749
Cdd:cd18042    133 SGSDLLESLPRGFDTVIIDEAAQaVELSTLIPLRLGCKRLILVGDPKQLPATVFSKVaqKLGYD 196
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 314-354 1.90e-05

DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to 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: 438708 [Multi-domain]  Cd Length: 121  Bit Score: 44.92  E-value: 1.90e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 2728048274  314 VVEGPPGTGKSETILNILINIV--LNNKTALFVSEKATAMEVV 354
Cdd:cd17934      3 LIQGPPGTGKTTTIAAIVLQLLkgLRGKRVLVTAQSNVAVDNV 45
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 699-792 2.33e-05

DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, or IGHMBP2) is a 5' to 3' helicase that unwinds RNA and DNA duplexes in an ATP-dependent reaction. It is a DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence (5'-GGGCT-3') related to the immunoglobulin mu chain switch region. The IGHMBP2 gene is responsible for Charcot-Marie-Tooth disease (CMT) type 2S and spinal muscular atrophy with respiratory distress type 1 (SMARD1). It is also thought to play a role in frontotemporal dementia (FTD) with amyotrophic lateral sclerosis (ALS) and major depressive disorder (MDD). SMUBP2 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: 350802 [Multi-domain]  Cd Length: 191  Bit Score: 46.45  E-value: 2.33e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  699 DLYDYVIIDEASQVfLERA-LPALYRGKRYIIAGDTKQLHPSsffqsranyeddafaeidennaIETDEAVNAiSLIHFL 777
Cdd:cd18044    115 ELFDVVVIDEAAQA-LEAScWIPLLKARRCILAGDHKQLPPT----------------------ILSDKAARG-GLGVTL 170

                           90       100
                   ....*....|....*....|.
gi 2728048274  778 KERA------RLSSMLKYHYR 792
Cdd:cd18044    171 FERLvnlygeSVVRMLTVQYR 191
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 297-345 3.80e-04

DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses different enzymatic activities, such as single-stranded DNA (ssDNA)-dependent ATPase, 5-3 helicase, and endonuclease activities, and is involved in DNA replication and DNA repair in the nucleus and mitochondrion. It is involved in Okazaki fragment processing by cleaving long flaps that escape FEN1: flaps that are longer than 27 nucleotides are coated by replication protein A complex (RPA), leading to recruit DNA2 which cleaves the flap until it is too short to bind RPA and becomes a substrate for FEN1. It is also involved in 5-end resection of DNA during double-strand break (DSB) repair; it is recruited by BLM and mediates the cleavage of 5-ssDNA, while the 3-ssDNA cleavage is prevented by the presence of RPA. DNA2 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: 350799 [Multi-domain]  Cd Length: 203  Bit Score: 42.99  E-value: 3.80e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2728048274  297 LDIYQQLAVKHALVGD--IVVEGPPGTGKSETILNILINIVLNNKTALFVS 345
Cdd:cd18041      2 LNKDQRQAIKKVLNAKdyALILGMPGTGKTTTIAALVRILVALGKSVLLTS 52
DEXXc_HELZ2-C cd18040
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 297-354 1.06e-03

C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known as PPAR-alpha-interacting complex protein 285 or PRIC285 and PPAR-gamma DBD-interacting protein 1 or PDIP1) acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB and RXRA. It belongs to 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: 350798 [Multi-domain]  Cd Length: 271  Bit Score: 42.13  E-value: 1.06e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2728048274  297 LDIYQQLAVKHALVGDI-VVEGPPGTGKSETILNILINIVLNNKTALFVSEKATAMEVV 354
Cdd:cd18040      2 LNPSQNHAVRTALTKPFtLIQGPPGTGKTVTGVHIAYWFAKQNREIQSVSGEGDGGPCV 60
gammaCoV_Nsp13-helicase cd21720
helicase domain of gammacoronavirus non-structural protein 13; This model represents the ...
 868-969 1.38e-03

helicase domain of gammacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from gammacoronavirus, including Avian infectious bronchitis virus. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Coronavirus (CoV) Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core.


Pssm-ID: 409653 [Multi-domain]  Cd Length: 343  Bit Score: 42.21  E-value: 1.38e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  868 FNKTQADFIENLLDKVNdplinEWRERT--TPNG-------EYIGLFVKNVENVQGDERDIIIFSLGYDKsvnnygpiSK 938
Cdd:cd21720    240 YNTTQLEFVKDFVCRNK-----EWREATfiSPYNamnqrayRMLGLNVQTVDSSQGSEYDYVIFCVTADS--------QH 306

                           90       100       110
                   ....*....|....*....|....*....|.
gi 2728048274  939 EEGANRLNVAITRAKSRIELFKTNKANEYSG 969
Cdd:cd21720    307 ALNINRFNVALTRAKRGILVVMRQRDELYSA 337
DEXXQc_Mov10L1 cd18078
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ...
 297-337 1.45e-03

DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. Mov10L1 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: 350836 [Multi-domain]  Cd Length: 230  Bit Score: 41.59  E-value: 1.45e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2728048274  297 LDIYQQLAVKHALVGD-----IVVEGPPGTGKSETILNILINIVLN 337
Cdd:cd18078      2 LNELQKEAVKRILGGEcrplpYILFGPPGTGKTVTIIEAILQVVYN 47
CoV_Nsp13-helicase cd21718
helicase domain of coronavirus non-structural protein 13; This model represents the helicase ...
 868-956 2.42e-03

helicase domain of coronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from alpha-, beta-, gamma-, and deltacoronavirus, including pathogenic human viruses such as Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core.


Pssm-ID: 409652 [Multi-domain]  Cd Length: 341  Bit Score: 41.36  E-value: 2.42e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  868 FNKTQADFIENLLDKvnDPlinEWRERT--TP-------NGEYIGLFVKNVENVQGDERDIIIFSLGYDK--SVNnygpi 936
Cdd:cd21718    238 INRPQLEFVKRFLDR--NP---RWRKAVfiSPynamnnrASRLLGLSTQTVDSSQGSEYDYVIFCQTTDTahALN----- 307

                           90       100
                   ....*....|....*....|
gi 2728048274  937 skeegANRLNVAITRAKSRI 956
Cdd:cd21718    308 -----INRFNVAITRAKHGI 322
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 701-759 2.97e-03

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: 39.46  E-value: 2.97e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2728048274  701 YDYVIIDEASQV---FLERALPALYRGKRYIIAGDTKQLhPS----SFFQSRANYEDDAFAEIDEN 759
Cdd:cd17933     90 ADLLIVDEASMVdtrLMAALLSAIPAGARLILVGDPDQL-PSvgagNVLRDLIASKGVPTVELTEV 154
RecA-like_superfamily cd01120
RecA-like_NTPases; RecA-like NTPases. This superfamily includes the NTP binding domain of F1 ...
 313-372 3.19e-03

RecA-like_NTPases; RecA-like NTPases. This superfamily includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410865 [Multi-domain]  Cd Length: 119  Bit Score: 38.64  E-value: 3.19e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2728048274  313 IVVEGPPGTGKSETILNILINIVLNNKTALFVSEKATAMEVVYNRLGNLKHIAMYIPSLT 372
Cdd:cd01120      1 ILITGPPGSGKTTLLLQFAEQALLSDEPVIFISFLDTILEAIEDLIEEKKLDIIIIDSLS 60
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 301-362 3.92e-03

DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in transcription, neurogenesis, and antiviral response. SEXT is an R-loop-associated protein that is thought to function as an RNA/DNA helicase. R-loops consist of RNA/DNA hybrids, formed during transcription when nascent RNA hybridizes to the DNA template strand, displacing the non-template DNA strand. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). S. cerevisiae homolog splicing endonuclease 1 (Sen1) is an exclusively nuclear protein, important for nucleolar organization. S. cerevisiae Sen1 and its ortholog, the Schizosaccharomyces pombe Sen1, share conserved domains and belong to the family I class of helicases. Both proteins translocate 5' to 3' and unwind both DNA and RNA duplexes and also RNA/DNA hybrids in vitro. SETX 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: 438712 [Multi-domain]  Cd Length: 218  Bit Score: 39.89  E-value: 3.92e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2728048274  301 QQLAVKHAL--VGDIV-VEGPPGTGKSETILNIlINIVLNNKTALFvSEKATAMEVVYNRLGNLK 362
Cdd:cd18042      5 QLEAIASALqnSPGITlIQGPPGTGKTKTIVGI-LSVLLAGKYRKY-YEKVKKKLRKLQRNLNNK 67
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 296-339 8.96e-03

EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that represses class II MHC (major histocompatibility complex) gene expression. NFX1 binds a conserved cis-acting element, termed the X-box, in promoters of human class II MHC genes. The Cys-rich region contains several NFX1-type zinc finger domains. Frequently, a R3H domain is present in the C-terminus, and a RING finger domain and a PAM2 motif are present in the N-terminus. The lack of R3H and PAM2 motifs in the plant proteins indicates functional differences. Plant NFX1-like proteins are proposed to modulate growth and survival by coordinating reactive oxygen species, salicylic acid, further biotic stress and abscisic acid responses. A common feature of all members may be E3 ubiquitin ligase, due to the presence of a RING finger domain, as well as DNA binding. NFX1 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: 350694 [Multi-domain]  Cd Length: 178  Bit Score: 38.29  E-value: 8.96e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2728048274  296 HLDIYQQLAVKHALVGDI-VVEGPPGTGKSeTILNILINIVLNNK 339
Cdd:cd17936      1 TLDPSQLEALKHALTSELaLIQGPPGTGKT-FLGVKLVRALLQNQ 44
 
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.
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