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Conserved domains on  [gi|1958764762|ref|XP_038962080|]
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probable helicase senataxin isoform X2 [Rattus norvegicus]

Protein Classification

ATP-binding protein; ATP-binding protein; DNA2/NAM7 family helicase; ATP-dependent helicase; DNA2/NAM7 family helicase; DNA2/NAM7 family helicase; bifunctional RecB family nuclease/DEAD/DEAH box helicase( domain architecture ID 13030308)

ATP-binding protein containing an AAA (ATPases Associated with various cellular Activities) domain, similar to superfamily I DNA and RNA helicases, which are ubiquitous enzymes mediating ATP-dependent unwinding of DNA and RNA duplexes; ATP-binding protein containing an AAA (ATPases Associated with various cellular Activities) domain, similar to superfamily I DNA and RNA helicases, which are ubiquitous enzymes mediating ATP-dependent unwinding of DNA and RNA duplexes; DNA2/NAM7 family helicase similar to Saccharomyces cerevisiae NAM7 which is a helicase involved in mitochondrial functions; ATP-dependent helicase utilizes the energy from ATP hydrolysis to unwind double-stranded DNA or RNA; contains a PD-(D/E)XK nuclease domain; DNA2/NAM7 family helicase similar to Saccharomyces cerevisiae NAM7 which is a helicase involved in mitochondrial functions; DNA2/NAM7 family helicase similar to Saccharomyces cerevisiae NAM7 which is a helicase involved in mitochondrial functions; bifunctional RecB family nuclease/DEAD/DEAH box containing ATP-dependent helicase contains a nuclease domain belonging to the DnaQ-like (or DEDD) 3'-5' exonuclease superfamily and may catalyze the unwinding of DNA or RNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 1911-2236 2.76e-77

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: 255.60  E-value: 2.76e-77
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1911 FNEDQKKAIETAYAMVKhspsvaKICLIHGPPGTGKSKTIVGLLYRLLTESQRKGHSD---------ENFNAKIKQNRVL 1981
Cdd:cd18042      1 LNESQLEAIASALQNSP------GITLIQGPPGTGKTKTIVGILSVLLAGKYRKYYEKvkkklrklqRNLNNKKKKNRIL 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1982 VCAPSNAAVDELMKKIILEFKEKCKdkknplGNCGDINLVRLGPEKsintevlkfsldsqvshrmkkdlpshiqemlrrk 2061
Cdd:cd18042     75 VCAPSNAAVDEIVLRLLSEGFLDGD------GRSYKPNVVRVGRQE---------------------------------- 114

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2062 eildaqldelsrqralcrggremqrqeldehivivskerqelaskikevqgrpqrAQNTIILESHVICCTLSTSGGLLLE 2141
Cdd:cd18042    115 -------------------------------------------------------LRASILNEADIVCTTLSSSGSDLLE 139

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2142 SafrgqGGVPFSCVIVDEAGQSCEVETLSPLIHRCNKLVLVGDPKQLPPTVISMKAQEYGYDQSMMARFCKLLEenveqn 2221
Cdd:cd18042    140 S-----LPRGFDTVIIDEAAQAVELSTLIPLRLGCKRLILVGDPKQLPATVFSKVAQKLGYDRSLFERLQLAGY------ 208

                          330
                   ....*....|....*
gi 1958764762 2222 migrlPVLQLTIQYR 2236
Cdd:cd18042    209 -----PVLMLTTQYR 218
 
Name Accession Description Interval E-value
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 1911-2236 2.76e-77

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: 255.60  E-value: 2.76e-77
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1911 FNEDQKKAIETAYAMVKhspsvaKICLIHGPPGTGKSKTIVGLLYRLLTESQRKGHSD---------ENFNAKIKQNRVL 1981
Cdd:cd18042      1 LNESQLEAIASALQNSP------GITLIQGPPGTGKTKTIVGILSVLLAGKYRKYYEKvkkklrklqRNLNNKKKKNRIL 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1982 VCAPSNAAVDELMKKIILEFKEKCKdkknplGNCGDINLVRLGPEKsintevlkfsldsqvshrmkkdlpshiqemlrrk 2061
Cdd:cd18042     75 VCAPSNAAVDEIVLRLLSEGFLDGD------GRSYKPNVVRVGRQE---------------------------------- 114

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2062 eildaqldelsrqralcrggremqrqeldehivivskerqelaskikevqgrpqrAQNTIILESHVICCTLSTSGGLLLE 2141
Cdd:cd18042    115 -------------------------------------------------------LRASILNEADIVCTTLSSSGSDLLE 139

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2142 SafrgqGGVPFSCVIVDEAGQSCEVETLSPLIHRCNKLVLVGDPKQLPPTVISMKAQEYGYDQSMMARFCKLLEenveqn 2221
Cdd:cd18042    140 S-----LPRGFDTVIIDEAAQAVELSTLIPLRLGCKRLILVGDPKQLPATVFSKVAQKLGYDRSLFERLQLAGY------ 208

                          330
                   ....*....|....*
gi 1958764762 2222 migrlPVLQLTIQYR 2236
Cdd:cd18042    209 -----PVLMLTTQYR 218
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 1914-2195 2.43e-69

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: 233.77  E-value: 2.43e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1914 DQKKAIETAYamvKHSPsvakICLIHGPPGTGKSKTIVGLLYRLLTESQrkghsdenfNAKIKQNRVLVCAPSNAAVDEL 1993
Cdd:pfam13086    1 SQREAIRSAL---SSSH----FTLIQGPPGTGKTTTIVELIRQLLSYPA---------TSAAAGPRILVCAPSNAAVDNI 64

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1994 MKKIILEfkekckdkknplGNCGDINLVRLGPEKSINTEVLKFSLDSQVSHRMKK-DLPSHIQEMLRRKEILDAQLDELS 2072
Cdd:pfam13086   65 LERLLRK------------GQKYGPKIVRIGHPAAISEAVLPVSLDYLVESKLNNeEDAQIVKDISKELEKLAKALRAFE 132

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2073 RQRALCRGGREM------QRQELDEhiviVSKERQELASKIKEVQgrpQRAQNTIILESHVICCTLSTSGGLLLESAFrg 2146
Cdd:pfam13086  133 KEIIVEKLLKSRnkdkskLEQERRK----LRSERKELRKELRRRE---QSLEREILDEAQIVCSTLSGAGSRLLSSLA-- 203

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*....
gi 1958764762 2147 qggvPFSCVIVDEAGQSCEVETLSPLIHRCNKLVLVGDPKQLPPTVISM 2195
Cdd:pfam13086  204 ----NFDVVIIDEAAQALEPSTLIPLLRGPKKVVLVGDPKQLPPTVISK 248
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 1906-2255 7.99e-32

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: 134.56  E-value: 7.99e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1906 AYLKDFNEDQKKAIETAYamvkhspSVAKICLIHGPPGTGKSKTIVGLLYRLLtesqrkghsdenfnakIKQNRVLVCAP 1985
Cdd:TIGR00376  153 FFDPNLNESQKEAVLFAL-------SSKDLFLIHGPPGTGKTRTVVELIRQLV----------------KRGLRVLVTAP 209

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1986 SNAAVDELMKKIILEfkekckdkknplgncgDINLVRLGPEKSINTEVLKFSLDSQVSHRMK----KDLPSHIQEMLRRK 2061
Cdd:TIGR00376  210 SNIAVDNLLERLALC----------------DQKIVRLGHPARLLKSNKQHSLDYLIENHPKyqivADIREKIDELIEER 273

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2062 EILDAQLDELSRQR--------ALCRGGREMQRQELDEHIVIVSKERQELASKIKEVQGRPQRAQNTIILESHViccTLS 2133
Cdd:TIGR00376  274 NKKTKPSPQKRRGLsdikilrkALKKREARGIESLKIASMAEWIETNKSIDRLLKLLPESEERIMNEILAESDA---TNS 350

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2134 TSGGLLLEsafrgqgGVPFSCVIVDEAGQSCEVETLSPLIhRCNKLVLVGDPKQLPPTVISMKAQEygydqsmmarfckl 2213
Cdd:TIGR00376  351 MAGSEILN-------GQYFDVAVIDEASQAMEPSCLIPLL-KARKLILAGDHKQLPPTILSHDAEE-------------- 408

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....
gi 1958764762 2214 LEENVEQNMIGRLP--VLQLTIQYRMHPDICLFPSNYVYNKNLK 2255
Cdd:TIGR00376  409 LSLTLFERLIKEYPerSRTLNVQYRMNQKIMEFPSREFYNGKLT 452
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
2058-2258 4.23e-26

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 117.15  E-value: 4.23e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2058 LRRKEILDAQLDELSRQRALCRGGREMQRQELDEHIvivsKERQELASKIKEVQGRPQRAQNTIILESHVICCTLSTSGG 2137
Cdd:COG1112    472 AAALLALALLESLLEELIEEHPEELEKLIAELREAA----RLRRALRRELKKRRELRKLLWDALLELAPVVGMTPASVAR 547

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2138 LLLEsafrgqGGVPFSCVIVDEAGQSCEVETLsPLIHRCNKLVLVGDPKQLPPTVIS---MKAQEYGYDQSMMARFCKLL 2214
Cdd:COG1112    548 LLPL------GEGSFDLVIIDEASQATLAEAL-GALARAKRVVLVGDPKQLPPVVFGeeaEEVAEEGLDESLLDRLLARL 620

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 1958764762 2215 EEnveqnmigrlPVLQLTIQYRMHPDICLFPSNYVYNKNLKTNR 2258
Cdd:COG1112    621 PE----------RGVMLREHYRMHPEIIAFSNRLFYDGKLVPLP 654
 
Name Accession Description Interval E-value
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 1911-2236 2.76e-77

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: 255.60  E-value: 2.76e-77
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1911 FNEDQKKAIETAYAMVKhspsvaKICLIHGPPGTGKSKTIVGLLYRLLTESQRKGHSD---------ENFNAKIKQNRVL 1981
Cdd:cd18042      1 LNESQLEAIASALQNSP------GITLIQGPPGTGKTKTIVGILSVLLAGKYRKYYEKvkkklrklqRNLNNKKKKNRIL 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1982 VCAPSNAAVDELMKKIILEFKEKCKdkknplGNCGDINLVRLGPEKsintevlkfsldsqvshrmkkdlpshiqemlrrk 2061
Cdd:cd18042     75 VCAPSNAAVDEIVLRLLSEGFLDGD------GRSYKPNVVRVGRQE---------------------------------- 114

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2062 eildaqldelsrqralcrggremqrqeldehivivskerqelaskikevqgrpqrAQNTIILESHVICCTLSTSGGLLLE 2141
Cdd:cd18042    115 -------------------------------------------------------LRASILNEADIVCTTLSSSGSDLLE 139

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2142 SafrgqGGVPFSCVIVDEAGQSCEVETLSPLIHRCNKLVLVGDPKQLPPTVISMKAQEYGYDQSMMARFCKLLEenveqn 2221
Cdd:cd18042    140 S-----LPRGFDTVIIDEAAQAVELSTLIPLRLGCKRLILVGDPKQLPATVFSKVAQKLGYDRSLFERLQLAGY------ 208

                          330
                   ....*....|....*
gi 1958764762 2222 migrlPVLQLTIQYR 2236
Cdd:cd18042    209 -----PVLMLTTQYR 218
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 1914-2195 2.43e-69

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: 233.77  E-value: 2.43e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1914 DQKKAIETAYamvKHSPsvakICLIHGPPGTGKSKTIVGLLYRLLTESQrkghsdenfNAKIKQNRVLVCAPSNAAVDEL 1993
Cdd:pfam13086    1 SQREAIRSAL---SSSH----FTLIQGPPGTGKTTTIVELIRQLLSYPA---------TSAAAGPRILVCAPSNAAVDNI 64

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1994 MKKIILEfkekckdkknplGNCGDINLVRLGPEKSINTEVLKFSLDSQVSHRMKK-DLPSHIQEMLRRKEILDAQLDELS 2072
Cdd:pfam13086   65 LERLLRK------------GQKYGPKIVRIGHPAAISEAVLPVSLDYLVESKLNNeEDAQIVKDISKELEKLAKALRAFE 132

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2073 RQRALCRGGREM------QRQELDEhiviVSKERQELASKIKEVQgrpQRAQNTIILESHVICCTLSTSGGLLLESAFrg 2146
Cdd:pfam13086  133 KEIIVEKLLKSRnkdkskLEQERRK----LRSERKELRKELRRRE---QSLEREILDEAQIVCSTLSGAGSRLLSSLA-- 203

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*....
gi 1958764762 2147 qggvPFSCVIVDEAGQSCEVETLSPLIHRCNKLVLVGDPKQLPPTVISM 2195
Cdd:pfam13086  204 ----NFDVVIIDEAAQALEPSTLIPLLRGPKKVVLVGDPKQLPPTVISK 248
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
 1910-2236 1.28e-41

DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of Nonsense Transcripts, or ATP-Dependent Helicase RENT1) is an RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. It is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. It is recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) located downstream from the termination codon through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Diseases associated with UPF1 include juvenile amyotrophic lateral sclerosis and epidermolysis bullosa, junctional, non-Herlitz type. UPF1 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: 350797 [Multi-domain]  Cd Length: 234  Bit Score: 153.56  E-value: 1.28e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1910 DFNEDQKKAIETAYAmvkhspsvAKICLIHGPPGTGKSKTIVGLLYRLltesqrkghsdenfnAKIKQNRVLVCAPSNAA 1989
Cdd:cd18039      1 ELNHSQVDAVKTALQ--------RPLSLIQGPPGTGKTVTSATIVYHL---------------VKQGNGPVLVCAPSNVA 57

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1990 VDELMKKIilefkekckdkkNPLGncgdINLVRLgPEKSINTevlkfsLDSQVS----HRMKKDLPSHIQEMLRRKEILD 2065
Cdd:cd18039     58 VDQLTEKI------------HQTG----LKVVRL-CAKSREA------VESPVSflalHNQVRNLDSAEKLELLKLLKLE 114

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2066 aqLDELSrqralcrggremqrqELDEhivivsKERQELASKIKevqgrpqraqNTIILESHVICCTLSTSGGLLLesafr 2145
Cdd:cd18039    115 --TGELS---------------SADE------KRYRKLKRKAE----------RELLRNADVICCTCVGAGDPRL----- 156

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2146 gqGGVPFSCVIVDEAGQSCEVETLSPLIHRCNKLVLVGDPKQLPPTVISMKAQEYGYDQSMMARFCKLleenveqnmiGR 2225
Cdd:cd18039    157 --SKMKFRTVLIDEATQATEPECLIPLVHGAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVQL----------GI 224

                          330
                   ....*....|.
gi 1958764762 2226 LPVLqLTIQYR 2236
Cdd:cd18039    225 RPIR-LQVQYR 234
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 1911-2236 4.21e-35

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: 133.50  E-value: 4.21e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1911 FNEDQKKAIETAYAmvkhSPSVAkicLIHGPPGTGKSKTIVGLLYRLLTESQRkghsdenfnakikqnrVLVCAPSNAAV 1990
Cdd:cd18044      2 LNDSQKEAVKFALS----QKDVA---LIHGPPGTGKTTTVVEIILQAVKRGEK----------------VLACAPSNIAV 58

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1991 DELMKKIIlefkekckdkknplgNCGdINLVRLGPEKSINTEVLKFSLDSQVshrmkkdlpshiqemlrrkeildaqlde 2070
Cdd:cd18044     59 DNLVERLV---------------ALK-VKVVRIGHPARLLESVLDHSLDALV---------------------------- 94

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2071 lsrqralcrggremqrqeldehivivskerqelaskikevqgrpqraqntiilESHVICCTLSTSGGLLLesafrgQGGV 2150
Cdd:cd18044     95 -----------------------------------------------------AAQVVLATNTGAGSRQL------LPNE 115

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2151 PFSCVIVDEAGQSCEVETLSPLIhRCNKLVLVGDPKQLPPTVISMKAQEYGYDQSMMARfcklLEenveqNMIGRLPVLQ 2230
Cdd:cd18044    116 LFDVVVIDEAAQALEASCWIPLL-KARRCILAGDHKQLPPTILSDKAARGGLGVTLFER----LV-----NLYGESVVRM 185


                   ....*.
gi 1958764762 2231 LTIQYR 2236
Cdd:cd18044    186 LTVQYR 191
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 1906-2255 7.99e-32

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: 134.56  E-value: 7.99e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1906 AYLKDFNEDQKKAIETAYamvkhspSVAKICLIHGPPGTGKSKTIVGLLYRLLtesqrkghsdenfnakIKQNRVLVCAP 1985
Cdd:TIGR00376  153 FFDPNLNESQKEAVLFAL-------SSKDLFLIHGPPGTGKTRTVVELIRQLV----------------KRGLRVLVTAP 209

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1986 SNAAVDELMKKIILEfkekckdkknplgncgDINLVRLGPEKSINTEVLKFSLDSQVSHRMK----KDLPSHIQEMLRRK 2061
Cdd:TIGR00376  210 SNIAVDNLLERLALC----------------DQKIVRLGHPARLLKSNKQHSLDYLIENHPKyqivADIREKIDELIEER 273

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2062 EILDAQLDELSRQR--------ALCRGGREMQRQELDEHIVIVSKERQELASKIKEVQGRPQRAQNTIILESHViccTLS 2133
Cdd:TIGR00376  274 NKKTKPSPQKRRGLsdikilrkALKKREARGIESLKIASMAEWIETNKSIDRLLKLLPESEERIMNEILAESDA---TNS 350

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2134 TSGGLLLEsafrgqgGVPFSCVIVDEAGQSCEVETLSPLIhRCNKLVLVGDPKQLPPTVISMKAQEygydqsmmarfckl 2213
Cdd:TIGR00376  351 MAGSEILN-------GQYFDVAVIDEASQAMEPSCLIPLL-KARKLILAGDHKQLPPTILSHDAEE-------------- 408

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....
gi 1958764762 2214 LEENVEQNMIGRLP--VLQLTIQYRMHPDICLFPSNYVYNKNLK 2255
Cdd:TIGR00376  409 LSLTLFERLIKEYPerSRTLNVQYRMNQKIMEFPSREFYNGKLT 452
DEXXQc_Helz-like cd18038
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ...
 1912-2236 6.08e-29

DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and similar proteins. Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. All 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: 350796 [Multi-domain]  Cd Length: 229  Bit Score: 116.95  E-value: 6.08e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1912 NEDQKKAIETAYAMVKHSPSVakicLIHGPPGTGKSKTIVGLLYRLLTesQRKGHsdenfnakikqnRVLVCAPSNAAVD 1991
Cdd:cd18038      3 NDEQKLAVRNIVTGTSRPPPY----IIFGPPGTGKTVTLVEAILQVLR--QPPEA------------RILVCAPSNSAAD 64

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1992 ELMKKIILEFKEKckdkknplgncgdINLVRLG----PEKSINTEVLKFSLDSQVSHRmkkDLPShiqemlrrkeildaq 2067
Cdd:cd18038     65 LLAERLLNALVTK-------------REILRLNapsrDRASVPPELLPYCNSKAEGTF---RLPS--------------- 113

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2068 ldelsrqralcrggremqRQELDEHIVIVskerqelaskikevqgrpqraqntiileshvicCTLSTSGglLLESAFRGQ 2147
Cdd:cd18038    114 ------------------LEELKKYRIVV---------------------------------CTLMTAG--RLVQAGVPN 140

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2148 GGvpFSCVIVDEAGQSCEVETLSPLIHRCNK---LVLVGDPKQLPPTVISMKAQEYGYDQSMMARFCKL--LEENVEQNM 2222
Cdd:cd18038    141 GH--FTHIFIDEAGQATEPEALIPLSELASKntqIVLAGDPKQLGPVVRSPLARKYGLGKSLLERLMERplYYKDGEYNP 218

                          330
                   ....*....|....
gi 1958764762 2223 igrLPVLQLTIQYR 2236
Cdd:cd18038    219 ---SYITKLLKNYR 229
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
2058-2258 4.23e-26

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 117.15  E-value: 4.23e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2058 LRRKEILDAQLDELSRQRALCRGGREMQRQELDEHIvivsKERQELASKIKEVQGRPQRAQNTIILESHVICCTLSTSGG 2137
Cdd:COG1112    472 AAALLALALLESLLEELIEEHPEELEKLIAELREAA----RLRRALRRELKKRRELRKLLWDALLELAPVVGMTPASVAR 547

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2138 LLLEsafrgqGGVPFSCVIVDEAGQSCEVETLsPLIHRCNKLVLVGDPKQLPPTVIS---MKAQEYGYDQSMMARFCKLL 2214
Cdd:COG1112    548 LLPL------GEGSFDLVIIDEASQATLAEAL-GALARAKRVVLVGDPKQLPPVVFGeeaEEVAEEGLDESLLDRLLARL 620

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 1958764762 2215 EEnveqnmigrlPVLQLTIQYRMHPDICLFPSNYVYNKNLKTNR 2258
Cdd:COG1112    621 PE----------RGVMLREHYRMHPEIIAFSNRLFYDGKLVPLP 654
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 1912-2236 4.87e-24

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: 101.93  E-value: 4.87e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1912 NEDQKKAIETAYamvkhspsVAK-ICLIHGPPGTGKSKTIVgLLYRLLtESQRKghsdenfnakikqnRVLVCAPSNAAV 1990
Cdd:cd18041      3 NKDQRQAIKKVL--------NAKdYALILGMPGTGKTTTIA-ALVRIL-VALGK--------------SVLLTSYTHSAV 58

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1991 DelmkKIILEFKEKckdkknplgncgDINLVRLGPEKSINTEVLKFSLDSqvshrmkkdlpshiqemlrrkeildaqlde 2070
Cdd:cd18041     59 D----NILLKLKKF------------GVNFLRLGRLKKIHPDVQEFTLEA------------------------------ 92

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2071 lsrqralcrggremqrqeldehIVIVSKERQELASKIKEVQgrpqraqntiileshVICCTLSTsgglLLESAFRGQggv 2150
Cdd:cd18041     93 ----------------------ILKSCKSVEELESKYESVS---------------VVATTCLG----INHPIFRRR--- 128

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2151 PFSCVIVDEAGQSCEVETLSPLIHrCNKLVLVGDPKQLPPTVISMKAQEYGYDQSMMARFCKLLEENveqnmigrlpVLQ 2230
Cdd:cd18041    129 TFDYCIVDEASQITLPICLGPLRL-AKKFVLVGDHYQLPPLVKSREARELGMDESLFKRLSEAHPDA----------VVQ 197


                   ....*.
gi 1958764762 2231 LTIQYR 2236
Cdd:cd18041    198 LTIQYR 203
DEXXc_HELZ2-C cd18040
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 1912-2236 7.33e-22

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: 97.60  E-value: 7.33e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1912 NEDQKKAIETAYAmvkhspsvAKICLIHGPPGTGKSKTIVGLLYRLLTESQRKGHSDENFNAKikqNRVLVCAPSNAAVD 1991
Cdd:cd18040      3 NPSQNHAVRTALT--------KPFTLIQGPPGTGKTVTGVHIAYWFAKQNREIQSVSGEGDGG---PCVLYCGPSNKSVD 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1992 ---ELMK-----KIILEFKEKCKDKKNPLGNCGDINLVRLGPEKSINTEVLKFSLdsqvSHRMKKDLPSHIQEMLrrkei 2063
Cdd:cd18040     72 vvaELLLkvpglKILRVYSEQIETTEYPIPNEPRHPNKKSERESKPNSELSSITL----HHRIRQPSNPHSQQIK----- 142

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2064 ldaQLDELSRQRalcrgGREMQRQELDEHIVIVSKER-QELASKikevqgrpqraqntiilesHVICCTLSTSGGLLLES 2142
Cdd:cd18040    143 ---AFEARFERT-----QEKITEEDIKTYKILIWEARfEELETV-------------------DVILCTCSEAASQKMRT 195

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2143 AfrgqggVPFSCVIVDEAGQSCEVETLSPLI--HRCNKLVLVGDPKQLPPTVISMKAQEYGYDQSMMARFCKlleenveq 2220
Cdd:cd18040    196 H------ANVKQCIVDECGMCTEPESLIPIVsaPRAEQVVLIGDHKQLRPVVQNKEAQKLGLGRSLFERYAE-------- 261

                          330
                   ....*....|....*.
gi 1958764762 2221 nmigrlPVLQLTIQYR 2236
Cdd:cd18040    262 ------KACMLDTQYR 271
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 2155-2236 5.28e-16

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: 76.12  E-value: 5.28e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2155 VIVDEAGQSCEVETLsPLIHRCNKLVLVGDPKQLPPTVISMKAQEYGYDQSMMARFcklleenVEQNMIGRLPVLQLTIQ 2234
Cdd:cd17934     48 VIIDEASQITEPELL-IALIRAKKVVLVGDPKQLPPVVQEDHAALLGLSFILSLLL-------LFRLLLPGSPKVMLDTQ 119


                   ..
gi 1958764762 2235 YR 2236
Cdd:cd17934    120 YR 121
DEXXQc_Mov10L1 cd18078
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ...
 1910-2210 1.27e-15

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: 78.56  E-value: 1.27e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1910 DFNEDQKKAIETAYAMV-KHSPSVakiclIHGPPGTGKSKTIVGLLYRLLTEsqrkghsdenfnakIKQNRVLVCAPSNA 1988
Cdd:cd18078      1 DLNELQKEAVKRILGGEcRPLPYI-----LFGPPGTGKTVTIIEAILQVVYN--------------LPRSRILVCAPSNS 61

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1989 AVDELMKKIIlefkekckdkknplgncgDINLVRLGPEKSINTevlkfsldsqvSHRMKKDLPSHIQEMLRRKEildaQL 2068
Cdd:cd18078     62 AADLVTSRLH------------------ESKVLKPGDMVRLNA-----------VNRFESTVIDARKLYCRLGE----DL 108

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2069 DELSRQRalcrggremqrqeldehIVIVskerqelaskikevqgrpqraqntiileshviccTLSTSGGLLlesafrgQG 2148
Cdd:cd18078    109 SKASRHR-----------------IVIS----------------------------------TCSTAGLLY-------QM 130

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958764762 2149 GVP---FSCVIVDEAGQSCEVETLSPL--IH-RCNKLVLVGDPKQLPPTVISMKAQEYGYDQSMMARF 2210
Cdd:cd18078    131 GLPvghFTHVFVDEAGQATEPESLIPLglISsRDGQIILAGDPMQLGPVIKSRLASAYGLGVSFLERL 198
EEXXQc_AQR cd17935
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ...
 2124-2248 3.51e-12

EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds precursor-mRNA introns at a defined position and is part of a pentameric intron-binding complex (IBC). It 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: 350693 [Multi-domain]  Cd Length: 207  Bit Score: 67.84  E-value: 3.51e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2124 ESHVICCT---LSTSGGLLLESAFRgqggvpFSCVIVDEAGQSCEVETLSPLI--------HRCNKLVLVGDPKQLPPTV 2192
Cdd:cd17935     86 GAKIIAMTcthAALKRGELVELGFK------YDNILMEEAAQILEIETFIPLLlqnpedgpNRLKRLIMIGDHHQLPPVI 159

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958764762 2193 ISMKAQEYGY-DQSMMARFCKLleenveqnmigRLPVLQLTIQYRMHPDIC-LFPSNY 2248
Cdd:cd17935    160 KNMAFQKYSNmEQSLFTRLVRL-----------GVPTVDLDAQGRARASISsLYNWRY 206
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 2202-2256 1.69e-11

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: 65.65  E-value: 1.69e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1958764762 2202 YDQSMMARFCKLleenveqnmiGRLPVLQLTIQYRMHPDICLFPSNYVYNKNLKT 2256
Cdd:pfam13087    1 LDRSLFERLQEL----------GPSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKD 45
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 2152-2190 6.57e-08

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: 53.36  E-value: 6.57e-08
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1958764762 2152 FSCVIVDEAGQsCEVETLSPLIHRCNKLVLVGDPKQLPP 2190
Cdd:cd18043     81 FDLVIFDEASQ-IPIEEALPALFRGKQVVVVGDDKQLPP 118
DEXXQc_HELZ cd18077
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ...
 1912-2217 1.28e-07

DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. HELZ is a member of the family I class of RNA helicases 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: 350835 [Multi-domain]  Cd Length: 226  Bit Score: 54.80  E-value: 1.28e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1912 NEDQKKAI-ETAYAMVKHSPSVakicLIHGPPGTGKSKTIVGLLYRLLTESQrkghsdenfnakikqNRVLVCAPSNAAV 1990
Cdd:cd18077      3 NAKQKEAVlAITTPLSIQLPPV----LLIGPFGTGKTFTLAQAVKHILQQPE---------------TRILICTHSNSAA 63

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1991 DELMKKIILEFKEKCKDKKNPLgncgdinlvrlgpeksintevlkfsldsQVSHRMKKDLPSHiqemlrrkeildaqldE 2070
Cdd:cd18077     64 DLYIKEYLHPYVETGNPRARPL----------------------------RVYYRNRWVKTVH----------------P 99

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2071 LSRQRALcrggremqrqeLDEHivivskerqelaskikevqGRPQRAQNTIILESHVICCTLSTSGGLLLESAFRGQggv 2150
Cdd:cd18077    100 VVQKYCL-----------IDEH-------------------GTFRMPTREDVMRHRVVVVTLSTSQYLCQLDLEPGF--- 146

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958764762 2151 pFSCVIVDEAGQSCEVETLSP--LIHRCNKLVLVGDPKQLPPTVISMKAQEYGYDQSMMARF---------CK-LLEEN 2217
Cdd:cd18077    147 -FTHILLDEAAQAMECEAIMPlaLATKSTRIVLAGDHMQLSPEVYSEFARERNLHISLLERLyehypsehpCRiLLCEN 224
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 2127-2235 2.65e-07

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: 52.93  E-value: 2.65e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2127 VICCTlsTSGGLLLESAFRGQGgvpFSCVIVDEAGQSCEVETLSPLIHRCNKLVLVGDPKQLPPTVISMK--AQEYGYDQ 2204
Cdd:cd17936     84 VIGMT--TTGAAKYRELLQALG---PKVVIVEEAAEVLEAHILAALTPSTEHLILIGDHKQLRPKVNVYEltAKKYNLDV 158

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1958764762 2205 SMMARFCKLleenveqnmigRLPVLQLTIQY 2235
Cdd:cd17936    159 SLFERLVKN-----------GLPFVTLNVQR 178
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 1912-1999 5.20e-07

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: 50.66  E-value: 5.20e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1912 NEDQKKAIETAYamvkHSPSVakicLIHGPPGTGKSKTIVGLLYRLLTESQrkghsdenfnakikqnRVLVCAPSNAAVD 1991
Cdd:cd18043      1 DSSQEAAIISAR----NGKNV----VIQGPPGTGKSQTIANIIANALARGK----------------RVLFVSEKKAALD 56


                   ....*...
gi 1958764762 1992 ELMKKIIL 1999
Cdd:cd18043     57 VVRFPCWI 64
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 1937-2003 4.04e-05

DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. Their helicase core is surrounded by C and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains or domains engaged in protein-protein interactions. SF1 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: 438706 [Multi-domain]  Cd Length: 121  Bit Score: 45.17  E-value: 4.04e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958764762 1937 LIHGPPGTGKSKTIVGLLYRLLTesqrkghsdenfNAKIKQNRVLVCAPSNAAVDELMKKIILEFKE 2003
Cdd:cd17914      3 LIQGPPGTGKTRVLVKIVAALMQ------------NKNGEPGRILLVTPTNKAAAQLDNILVDEAAQ 57
AAA_19 pfam13245
AAA domain;
1915-1993 5.09e-05

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 45.29  E-value: 5.09e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958764762 1915 QKKAIETAyamvkhspSVAKICLIHGPPGTGKSKTIVGLLYRLLtesQRKGHSDenfnakikqnRVLVCAPSNAAVDEL 1993
Cdd:pfam13245    1 QREAVRTA--------LPSKVVLLTGGPGTGKTTTIRHIVALLV---ALGGVSF----------PILLAAPTGRAAKRL 58
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 1877-2000 1.95e-04

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 46.51  E-value: 1.95e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1877 NQLARAVLNPNPMDFCTKDLLTTTSERIIAYLKDFNEDQKKAIETAYAMvkhspsvAKICLIHGPPGTGKSKTIVGLLyR 1956
Cdd:COG0507     91 QRLARRLRRLARPALDEADVEAALAALEPRAGITLSDEQREAVALALTT-------RRVSVLTGGAGTGKTTTLRALL-A 162

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1958764762 1957 LLTESQRkghsdenfnakikqnRVLVCAPSNAAVDELMKKIILE 2000
Cdd:COG0507    163 ALEALGL---------------RVALAAPTGKAAKRLSESTGIE 191
UvrD-helicase pfam00580
UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural ...
 1912-2187 2.51e-04

UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyze ATP dependent unwinding of double stranded DNA to single stranded DNA. Swiss:P23478, Swiss:P08394 have large insertions near to the carboxy-terminus relative to other members of the family.


Pssm-ID: 395462 [Multi-domain]  Cd Length: 267  Bit Score: 45.31  E-value: 2.51e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1912 NEDQKKAIEtayamvkhspSVAKICLIHGPPGTGKSKTIVGLLYRLLTEsqrkghsdenfnAKIKQNRVLVCAPSNAAVD 1991
Cdd:pfam00580    2 NPEQRKAVT----------HLGGPLLVLAGAGSGKTRVLTERIAYLILE------------GGIDPEEILAVTFTNKAAR 59

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1992 ELMKKIILEFKEKCKDKKNpLGN----CGDInLVRLGPEKSINTEVLKFSLDSQVSHrMKKDLpshiqemlrrkEILDAQ 2067
Cdd:pfam00580   60 EMKERILKLLGKAELSELN-ISTfhsfCLRI-LRKYANRIGLLPNFSILDELDQLAL-LKELL-----------EKDRLN 125

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2068 LD-ELSRQRALCrggremqrqeldEHIVIVsKERQELASKIKEVQGRPQRAQNTIILESHV----------------ICC 2130
Cdd:pfam00580  126 LDpKLLRKLELK------------ELISKA-KNRLLSPEELQQGAADPRDKLAAEFYQEYQerlkennaldfddlllLTL 192

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 2131 TLSTSGGLLLEsAFRGQggvpFSCVIVDEAgQ---SCEVETLSPLIHRCNKLVLVGDPKQ 2187
Cdd:pfam00580  193 ELLRSDPELLE-AYRER----FKYILVDEF-QdtnPIQYRLLKLLAGGHENLFLVGDPDQ 246
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 2155-2213 7.77e-04

DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. Their helicase core is surrounded by C and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains or domains engaged in protein-protein interactions. SF1 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: 438706 [Multi-domain]  Cd Length: 121  Bit Score: 41.32  E-value: 7.77e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958764762 2155 VIVDEAGQSCEVET--LSPLIHRCNKLVLVGDPKQLPPTVISMKAQEYGYDQSMMARFCKL 2213
Cdd:cd17914     50 ILVDEAAQILEPETsrLIDLALDQGRVILVGDHDQLGPVWRGAVLAKICNEQSLFTRLVRL 110
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 1912-1995 1.02e-03

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: 42.55  E-value: 1.02e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1912 NEDQKKAIETAYAmvkhspSVAKICLIHGPPGTGKSkTIVGLLYRLLTESqrkGHsdenfnakikqnRVLVCAPSNAAVD 1991
Cdd:pfam13604    3 NAEQAAAVRALLT------SGDRVAVLVGPAGTGKT-TALKALREAWEAA---GY------------RVIGLAPTGRAAK 60


                   ....
gi 1958764762 1992 ELMK 1995
Cdd:pfam13604   61 VLGE 64
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 1914-1997 1.18e-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: 41.77  E-value: 1.18e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958764762 1914 DQKKAIETAyamVKHspsvaKICLIHGPPGTGKSKTIVGLLyrlltesqrkghsdENFNAKIKqnRVLVCAPSNAAVDEL 1993
Cdd:cd17933      1 EQKAAVRLV---LRN-----RVSVLTGGAGTGKTTTLKALL--------------AALEAEGK--RVVLAAPTGKAAKRL 56


                   ....
gi 1958764762 1994 MKKI 1997
Cdd:cd17933     57 SEST 60
 
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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