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Conserved domains on  [gi|767956714|ref|XP_011516708|]
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probable helicase senataxin isoform X3 [Homo sapiens]

Protein Classification

DEXXQc_SETX and SF1_C_Upf1 domain-containing protein( domain architecture ID 13132286)

protein containing domains SEN1_N, DEXXQc_SETX, and SF1_C_Upf1

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 ...
 1934-2259 2.54e-78

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: 258.68  E-value: 2.54e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 1934 FNEDQKKAIETAYAMVKhspsvaKICLIHGPPGTGKSKTIVGLLYRLLTENQRKGHSD---------ENSNAKIKQNRVL 2004
Cdd:cd18042     1 LNESQLEAIASALQNSP------GITLIQGPPGTGKTKTIVGILSVLLAGKYRKYYEKvkkklrklqRNLNNKKKKNRIL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2005 VCAPSNAAVDELMKKIILEFKEKCKdkknplGNCGDINLVRLGPeksinsevlkfsldsqvnhrmkkelpshvqamhkrk 2084
Cdd:cd18042    75 VCAPSNAAVDEIVLRLLSEGFLDGD------GRSYKPNVVRVGR------------------------------------ 112

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2085 efldyqldelsrqralcrggreiqrqeldeniskvskerqelaskikevqgrpQKTQSIIILESHIICCTLSTSGGLLLE 2164
Cdd:cd18042   113 -----------------------------------------------------QELRASILNEADIVCTTLSSSGSDLLE 139

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2165 SafrgqGGVPFSCVIVDEAGQSCEIETLTPLIHRCNKLILVGDPKQLPPTVISMKAQEYGYDQSMMARFCRlleenvehn 2244
Cdd:cd18042   140 S-----LPRGFDTVIIDEAAQAVELSTLIPLRLGCKRLILVGDPKQLPATVFSKVAQKLGYDRSLFERLQL--------- 205

                         330
                  ....*....|....*
gi 767956714 2245 miSRLPILQLTVQYR 2259
Cdd:cd18042   206 --AGYPVLMLTTQYR 218
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 2225-2400 4.80e-52

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: 182.36  E-value: 4.80e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2225 YDQSMMARFCRLLEENVehnmisrlpiLQLTVQYRMHPDICLFPSNYVYNRNLKTNRQTEAIRCSSDW----PFQPYLVF 2300
Cdd:pfam13087    1 LDRSLFERLQELGPSAV----------VMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPDDFhlpdPLGPLVFI 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2301 DVGDGSERRDN--DSYINVQEIKLVMEIIKLIKdKRKDVSFRNIGIITHYKAQKTMIQKDLDKEFDRKGPAEVDTVDAFQ 2378
Cdd:pfam13087   71 DVDGSEEEESDggTSYSNEAEAELVVQLVEKLI-KSGPEEPSDIGVITPYRAQVRLIRKLLKRKLGGKLEIEVNTVDGFQ 149

                          170       180
                   ....*....|....*....|..
gi 767956714  2379 GRQKDCVIVTCVRANSiQGSIG 2400
Cdd:pfam13087  150 GREKDVIIFSCVRSNE-KGGIG 170
SEN1_N super family cl20462
SEN1 N terminal; This domain is found at the N terminal of the helicase SEN1. SEN1 is a Pol II ...
 37-351 7.37e-08

SEN1 N terminal; This domain is found at the N terminal of the helicase SEN1. SEN1 is a Pol II termination factor for noncoding RNA genes. The N terminal of SEN1, unlike the C terminal, is not required for growth.


The actual alignment was detected with superfamily member pfam12726:

Pssm-ID: 432746  Cd Length: 744  Bit Score: 58.10  E-value: 7.37e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714    37 LCYCLECVAEYHKARDEL------PFLHEVL---------WELEtlRLINHFEKSMKaeigdddelyIVDNNGEMPLFDI 101
Cdd:pfam12726    9 LSSCDKCVRNFHRGKKELrqtfaeRFPEETVaqfldkldeWDIE--RILPGLDKAKE----------ILEKRGIFSKSSL 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714   102 TGQDfeNKLRVPLLEILKYP-YLLLHERVNELcVEALCRMEQANcsfQVFDKH----PGIYLFLVHPNEMVRRWAILTAR 176
Cdd:pfam12726   77 SSHL--KEVLLALYEALCCPpYLRSDPELRAL-FDYVFKLLQTK---KKPLRLgtllPGMTYFLFDGDPEERRWARRQLE 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714   177 NLGKVDRDDYYDLQevllclfkvIELGLLESPDIYTSSVLEKGKLILLpshmydttnyksyWLGICMLLTILEEQAMDSL 256
Cdd:pfam12726  151 RLKRSLTPEEFDWA---------VHDLLEEAIVHLSNIQLDPSFIERF-------------WSGFSLILRLLDKDLITHR 208

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714   257 LLGSDKQNDFmQSILHTMEREADDDSVDPFWPALHCFMVILDRLGSKVWGQLMD--PIVAFQTIINNASYNREIRHIRNS 334
Cdd:pfam12726  209 LRALEVNPPI-EDIYRLLLNHLSSTLDPPLPDLLRALSLLLEKSGKAFWDAMGPisPQVVLDQIFDNPAFAKLLAQSLEE 287

                          330
                   ....*....|....*..
gi 767956714   335 svRTKLEPESYLDDMVT 351
Cdd:pfam12726  288 --EMDPPDDDSLSDLLS 302
 
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 ...
 1934-2259 2.54e-78

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: 258.68  E-value: 2.54e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 1934 FNEDQKKAIETAYAMVKhspsvaKICLIHGPPGTGKSKTIVGLLYRLLTENQRKGHSD---------ENSNAKIKQNRVL 2004
Cdd:cd18042     1 LNESQLEAIASALQNSP------GITLIQGPPGTGKTKTIVGILSVLLAGKYRKYYEKvkkklrklqRNLNNKKKKNRIL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2005 VCAPSNAAVDELMKKIILEFKEKCKdkknplGNCGDINLVRLGPeksinsevlkfsldsqvnhrmkkelpshvqamhkrk 2084
Cdd:cd18042    75 VCAPSNAAVDEIVLRLLSEGFLDGD------GRSYKPNVVRVGR------------------------------------ 112

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2085 efldyqldelsrqralcrggreiqrqeldeniskvskerqelaskikevqgrpQKTQSIIILESHIICCTLSTSGGLLLE 2164
Cdd:cd18042   113 -----------------------------------------------------QELRASILNEADIVCTTLSSSGSDLLE 139

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2165 SafrgqGGVPFSCVIVDEAGQSCEIETLTPLIHRCNKLILVGDPKQLPPTVISMKAQEYGYDQSMMARFCRlleenvehn 2244
Cdd:cd18042   140 S-----LPRGFDTVIIDEAAQAVELSTLIPLRLGCKRLILVGDPKQLPATVFSKVAQKLGYDRSLFERLQL--------- 205

                         330
                  ....*....|....*
gi 767956714 2245 miSRLPILQLTVQYR 2259
Cdd:cd18042   206 --AGYPVLMLTTQYR 218
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 1937-2218 3.24e-72

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: 242.25  E-value: 3.24e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  1937 DQKKAIETAYamvKHSPsvakICLIHGPPGTGKSKTIVGLLYRLLTENQrkghsdensNAKIKQNRVLVCAPSNAAVDEL 2016
Cdd:pfam13086    1 SQREAIRSAL---SSSH----FTLIQGPPGTGKTTTIVELIRQLLSYPA---------TSAAAGPRILVCAPSNAAVDNI 64

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2017 MKKIILEfkekckdkknplGNCGDINLVRLGPEKSINSEVLKFSLDSQVNHRMKKE-LPSHVQAMHKRKEFLDYQLDELS 2095
Cdd:pfam13086   65 LERLLRK------------GQKYGPKIVRIGHPAAISEAVLPVSLDYLVESKLNNEeDAQIVKDISKELEKLAKALRAFE 132

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2096 RQRA--LCRGGREIQRQELDENISKVSKERQELASKIKEVQgrpQKTQSIIILESHIICCTLSTSGGLLLESAFrgqggv 2173
Cdd:pfam13086  133 KEIIveKLLKSRNKDKSKLEQERRKLRSERKELRKELRRRE---QSLEREILDEAQIVCSTLSGAGSRLLSSLA------ 203

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*
gi 767956714  2174 PFSCVIVDEAGQSCEIETLTPLIHRCNKLILVGDPKQLPPTVISM 2218
Cdd:pfam13086  204 NFDVVIIDEAAQALEPSTLIPLLRGPKKVVLVGDPKQLPPTVISK 248
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 2225-2400 4.80e-52

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: 182.36  E-value: 4.80e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2225 YDQSMMARFCRLLEENVehnmisrlpiLQLTVQYRMHPDICLFPSNYVYNRNLKTNRQTEAIRCSSDW----PFQPYLVF 2300
Cdd:pfam13087    1 LDRSLFERLQELGPSAV----------VMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPDDFhlpdPLGPLVFI 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2301 DVGDGSERRDN--DSYINVQEIKLVMEIIKLIKdKRKDVSFRNIGIITHYKAQKTMIQKDLDKEFDRKGPAEVDTVDAFQ 2378
Cdd:pfam13087   71 DVDGSEEEESDggTSYSNEAEAELVVQLVEKLI-KSGPEEPSDIGVITPYRAQVRLIRKLLKRKLGGKLEIEVNTVDGFQ 149

                          170       180
                   ....*....|....*....|..
gi 767956714  2379 GRQKDCVIVTCVRANSiQGSIG 2400
Cdd:pfam13087  150 GREKDVIIFSCVRSNE-KGGIG 170
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
2105-2393 9.99e-49

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 189.18  E-value: 9.99e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2105 REIQRQELDENISKVSKERQELASKIKEVQGRPQKTQSIIILESHIICCTLSTSGGLLLEsafrgqGGVPFSCVIVDEAG 2184
Cdd:COG1112   492 HPEELEKLIAELREAARLRRALRRELKKRRELRKLLWDALLELAPVVGMTPASVARLLPL------GEGSFDLVIIDEAS 565

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2185 QSCEIETLtPLIHRCNKLILVGDPKQLPPTVIS---MKAQEYGYDQSMMARFCRLLEENVehnmisrlpiLQLTVQYRMH 2261
Cdd:COG1112   566 QATLAEAL-GALARAKRVVLVGDPKQLPPVVFGeeaEEVAEEGLDESLLDRLLARLPERG----------VMLREHYRMH 634

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2262 PDICLFPSNYVYNRNLKTNRQTEAIRCssDWPFQPYLVFDVgDGSERRDNDSYINVQEIKLVMEIIKLIKDKRKDVsfRN 2341
Cdd:COG1112   635 PEIIAFSNRLFYDGKLVPLPSPKARRL--ADPDSPLVFIDV-DGVYERRGGSRTNPEEAEAVVELVRELLEDGPDG--ES 709

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 767956714 2342 IGIITHYKAQKTMIQKDLDKEFDRKG-PAEVDTVDAFQGRQKDCVIVTCVRAN 2393
Cdd:COG1112   710 IGVITPYRAQVALIRELLREALGDGLePVFVGTVDRFQGDERDVIIFSLVYSN 762
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 1935-2400 4.91e-46

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: 178.08  E-value: 4.91e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  1935 NEDQKKAIETAYamvkhspSVAKICLIHGPPGTGKSKTIVGLLYRLLTENQrkghsdensnakikqnRVLVCAPSNAAVD 2014
Cdd:TIGR00376  159 NESQKEAVLFAL-------SSKDLFLIHGPPGTGKTRTVVELIRQLVKRGL----------------RVLVTAPSNIAVD 215

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2015 ELMKKIILEfkekckdkknplgncgDINLVRLGPEKSINSEVLKFSLDSQV-NHrmkkelpshvqamHKRKEFLDYQ--L 2091
Cdd:TIGR00376  216 NLLERLALC----------------DQKIVRLGHPARLLKSNKQHSLDYLIeNH-------------PKYQIVADIRekI 266

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2092 DELSRQR-ALCRGGREIQRQELDENISKVSKERQE---LASKI----KEVQGRPQKTQSIIIL----ESHIICCTLSTSG 2159
Cdd:TIGR00376  267 DELIEERnKKTKPSPQKRRGLSDIKILRKALKKREargIESLKiasmAEWIETNKSIDRLLKLlpesEERIMNEILAESD 346

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2160 GLLLESAFRGQGGVPFSCVIVDEAGQSCEIETLTPLIhRCNKLILVGDPKQLPPTVISMKAQEygydqsmmarfcrlLEE 2239
Cdd:TIGR00376  347 ATNSMAGSEILNGQYFDVAVIDEASQAMEPSCLIPLL-KARKLILAGDHKQLPPTILSHDAEE--------------LSL 411

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2240 NVEHNMISRLP--ILQLTVQYRMHPDICLFPSNYVYNRNLKTNRQTEAI-------------RCSSDWPfQPYLVFDVG- 2303
Cdd:TIGR00376  412 TLFERLIKEYPerSRTLNVQYRMNQKIMEFPSREFYNGKLTAHESVANIllrdlpkveatesEDDLETG-IPLLFIDTSg 490

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2304 -DGSERRDND--SYINVQEIKLVMEIIKliKDKRKDVSFRNIGIITHYKAQKTMIQKDLDkefDRKGPAEVDTVDAFQGR 2380
Cdd:TIGR00376  491 cELFELKEADstSKYNPGEAELVSEIIQ--ALVKMGVPANDIGVITPYDAQVDLLRQLLE---HRHIDIEVSSVDGFQGR 565

                          490       500
                   ....*....|....*....|
gi 767956714  2381 QKDCVIVTCVRANSiQGSIG 2400
Cdd:TIGR00376  566 EKEVIIISFVRSNR-KGEVG 584
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 2260-2400 3.43e-38

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: 141.99  E-value: 3.43e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2260 MHPDICLFPSNYVYNRNLKTNRQTEAIRCSSDWP--FQPYLVFDVGDGSERRDND-SYINVQEIKLVMEIIKLIKdkRKD 2336
Cdd:cd18808     1 MHPEISEFPSKLFYEGKLKAGVSVAARLNPPPLPgpSKPLVFVDVSGGEEREESGtSKSNEAEAELVVELVKYLL--KSG 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767956714 2337 VSFRNIGIITHYKAQKTMIQKDLDKEFDRKGPAEVDTVDAFQGRQKDCVIVTCVRANSIQGSIG 2400
Cdd:cd18808    79 VKPSSIGVITPYRAQVALIRELLRKRGGLLEDVEVGTVDNFQGREKDVIILSLVRSNESGGSIG 142
SEN1_N pfam12726
SEN1 N terminal; This domain is found at the N terminal of the helicase SEN1. SEN1 is a Pol II ...
 37-351 7.37e-08

SEN1 N terminal; This domain is found at the N terminal of the helicase SEN1. SEN1 is a Pol II termination factor for noncoding RNA genes. The N terminal of SEN1, unlike the C terminal, is not required for growth.


Pssm-ID: 432746  Cd Length: 744  Bit Score: 58.10  E-value: 7.37e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714    37 LCYCLECVAEYHKARDEL------PFLHEVL---------WELEtlRLINHFEKSMKaeigdddelyIVDNNGEMPLFDI 101
Cdd:pfam12726    9 LSSCDKCVRNFHRGKKELrqtfaeRFPEETVaqfldkldeWDIE--RILPGLDKAKE----------ILEKRGIFSKSSL 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714   102 TGQDfeNKLRVPLLEILKYP-YLLLHERVNELcVEALCRMEQANcsfQVFDKH----PGIYLFLVHPNEMVRRWAILTAR 176
Cdd:pfam12726   77 SSHL--KEVLLALYEALCCPpYLRSDPELRAL-FDYVFKLLQTK---KKPLRLgtllPGMTYFLFDGDPEERRWARRQLE 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714   177 NLGKVDRDDYYDLQevllclfkvIELGLLESPDIYTSSVLEKGKLILLpshmydttnyksyWLGICMLLTILEEQAMDSL 256
Cdd:pfam12726  151 RLKRSLTPEEFDWA---------VHDLLEEAIVHLSNIQLDPSFIERF-------------WSGFSLILRLLDKDLITHR 208

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714   257 LLGSDKQNDFmQSILHTMEREADDDSVDPFWPALHCFMVILDRLGSKVWGQLMD--PIVAFQTIINNASYNREIRHIRNS 334
Cdd:pfam12726  209 LRALEVNPPI-EDIYRLLLNHLSSTLDPPLPDLLRALSLLLEKSGKAFWDAMGPisPQVVLDQIFDNPAFAKLLAQSLEE 287

                          330
                   ....*....|....*..
gi 767956714   335 svRTKLEPESYLDDMVT 351
Cdd:pfam12726  288 --EMDPPDDDSLSDLLS 302
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 1868-2023 2.17e-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: 2.17e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 1868 PANLNELVNCIVISSLVTTQRKLKAMSLLGSRNQLARAVLNPNPMDFCTKDLLTTTSERIIAYLRDFNEDQKKAIETAYA 1947
Cdd:COG0507    59 AEDIEAALAALVESGPLVLDGRRYLTRLLEAEQRLARRLRRLARPALDEADVEAALAALEPRAGITLSDEQREAVALALT 138

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767956714 1948 MvkhspsvAKICLIHGPPGTGKSKTIVGLLyRLLTENQRkghsdensnakikqnRVLVCAPSNAAVDELMKKIILE 2023
Cdd:COG0507   139 T-------RRVSVLTGGAGTGKTTTLRALL-AALEALGL---------------RVALAAPTGKAAKRLSESTGIE 191
hsdR PRK11448
type I restriction enzyme EcoKI subunit R; Provisional
 1895-1982 7.55e-04

type I restriction enzyme EcoKI subunit R; Provisional


Pssm-ID: 236912 [Multi-domain]  Cd Length: 1123  Bit Score: 44.94  E-value: 7.55e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 1895 LLGSRNQLARAVLNPNPMDFCTKdlltttseriiayLRDFNEDQKKAIETAYAMVKhspsvaKICLIHGPPGTGKSKTIV 1974
Cdd:PRK11448  391 LLESDIEAANQWLADEPFDYGLG-------------LRYYQEDAIQAVEKAIVEGQ------REILLAMATGTGKTRTAI 451


                  ....*...
gi 767956714 1975 GLLYRLLT 1982
Cdd:PRK11448  452 ALMYRLLK 459
 
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 ...
 1934-2259 2.54e-78

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: 258.68  E-value: 2.54e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 1934 FNEDQKKAIETAYAMVKhspsvaKICLIHGPPGTGKSKTIVGLLYRLLTENQRKGHSD---------ENSNAKIKQNRVL 2004
Cdd:cd18042     1 LNESQLEAIASALQNSP------GITLIQGPPGTGKTKTIVGILSVLLAGKYRKYYEKvkkklrklqRNLNNKKKKNRIL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2005 VCAPSNAAVDELMKKIILEFKEKCKdkknplGNCGDINLVRLGPeksinsevlkfsldsqvnhrmkkelpshvqamhkrk 2084
Cdd:cd18042    75 VCAPSNAAVDEIVLRLLSEGFLDGD------GRSYKPNVVRVGR------------------------------------ 112

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2085 efldyqldelsrqralcrggreiqrqeldeniskvskerqelaskikevqgrpQKTQSIIILESHIICCTLSTSGGLLLE 2164
Cdd:cd18042   113 -----------------------------------------------------QELRASILNEADIVCTTLSSSGSDLLE 139

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2165 SafrgqGGVPFSCVIVDEAGQSCEIETLTPLIHRCNKLILVGDPKQLPPTVISMKAQEYGYDQSMMARFCRlleenvehn 2244
Cdd:cd18042   140 S-----LPRGFDTVIIDEAAQAVELSTLIPLRLGCKRLILVGDPKQLPATVFSKVAQKLGYDRSLFERLQL--------- 205

                         330
                  ....*....|....*
gi 767956714 2245 miSRLPILQLTVQYR 2259
Cdd:cd18042   206 --AGYPVLMLTTQYR 218
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 1937-2218 3.24e-72

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: 242.25  E-value: 3.24e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  1937 DQKKAIETAYamvKHSPsvakICLIHGPPGTGKSKTIVGLLYRLLTENQrkghsdensNAKIKQNRVLVCAPSNAAVDEL 2016
Cdd:pfam13086    1 SQREAIRSAL---SSSH----FTLIQGPPGTGKTTTIVELIRQLLSYPA---------TSAAAGPRILVCAPSNAAVDNI 64

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2017 MKKIILEfkekckdkknplGNCGDINLVRLGPEKSINSEVLKFSLDSQVNHRMKKE-LPSHVQAMHKRKEFLDYQLDELS 2095
Cdd:pfam13086   65 LERLLRK------------GQKYGPKIVRIGHPAAISEAVLPVSLDYLVESKLNNEeDAQIVKDISKELEKLAKALRAFE 132

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2096 RQRA--LCRGGREIQRQELDENISKVSKERQELASKIKEVQgrpQKTQSIIILESHIICCTLSTSGGLLLESAFrgqggv 2173
Cdd:pfam13086  133 KEIIveKLLKSRNKDKSKLEQERRKLRSERKELRKELRRRE---QSLEREILDEAQIVCSTLSGAGSRLLSSLA------ 203

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*
gi 767956714  2174 PFSCVIVDEAGQSCEIETLTPLIHRCNKLILVGDPKQLPPTVISM 2218
Cdd:pfam13086  204 NFDVVIIDEAAQALEPSTLIPLLRGPKKVVLVGDPKQLPPTVISK 248
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 2225-2400 4.80e-52

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: 182.36  E-value: 4.80e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2225 YDQSMMARFCRLLEENVehnmisrlpiLQLTVQYRMHPDICLFPSNYVYNRNLKTNRQTEAIRCSSDW----PFQPYLVF 2300
Cdd:pfam13087    1 LDRSLFERLQELGPSAV----------VMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPDDFhlpdPLGPLVFI 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2301 DVGDGSERRDN--DSYINVQEIKLVMEIIKLIKdKRKDVSFRNIGIITHYKAQKTMIQKDLDKEFDRKGPAEVDTVDAFQ 2378
Cdd:pfam13087   71 DVDGSEEEESDggTSYSNEAEAELVVQLVEKLI-KSGPEEPSDIGVITPYRAQVRLIRKLLKRKLGGKLEIEVNTVDGFQ 149

                          170       180
                   ....*....|....*....|..
gi 767956714  2379 GRQKDCVIVTCVRANSiQGSIG 2400
Cdd:pfam13087  150 GREKDVIIFSCVRSNE-KGGIG 170
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
2105-2393 9.99e-49

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 189.18  E-value: 9.99e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2105 REIQRQELDENISKVSKERQELASKIKEVQGRPQKTQSIIILESHIICCTLSTSGGLLLEsafrgqGGVPFSCVIVDEAG 2184
Cdd:COG1112   492 HPEELEKLIAELREAARLRRALRRELKKRRELRKLLWDALLELAPVVGMTPASVARLLPL------GEGSFDLVIIDEAS 565

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2185 QSCEIETLtPLIHRCNKLILVGDPKQLPPTVIS---MKAQEYGYDQSMMARFCRLLEENVehnmisrlpiLQLTVQYRMH 2261
Cdd:COG1112   566 QATLAEAL-GALARAKRVVLVGDPKQLPPVVFGeeaEEVAEEGLDESLLDRLLARLPERG----------VMLREHYRMH 634

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2262 PDICLFPSNYVYNRNLKTNRQTEAIRCssDWPFQPYLVFDVgDGSERRDNDSYINVQEIKLVMEIIKLIKDKRKDVsfRN 2341
Cdd:COG1112   635 PEIIAFSNRLFYDGKLVPLPSPKARRL--ADPDSPLVFIDV-DGVYERRGGSRTNPEEAEAVVELVRELLEDGPDG--ES 709

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 767956714 2342 IGIITHYKAQKTMIQKDLDKEFDRKG-PAEVDTVDAFQGRQKDCVIVTCVRAN 2393
Cdd:COG1112   710 IGVITPYRAQVALIRELLREALGDGLePVFVGTVDRFQGDERDVIIFSLVYSN 762
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 1935-2400 4.91e-46

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: 178.08  E-value: 4.91e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  1935 NEDQKKAIETAYamvkhspSVAKICLIHGPPGTGKSKTIVGLLYRLLTENQrkghsdensnakikqnRVLVCAPSNAAVD 2014
Cdd:TIGR00376  159 NESQKEAVLFAL-------SSKDLFLIHGPPGTGKTRTVVELIRQLVKRGL----------------RVLVTAPSNIAVD 215

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2015 ELMKKIILEfkekckdkknplgncgDINLVRLGPEKSINSEVLKFSLDSQV-NHrmkkelpshvqamHKRKEFLDYQ--L 2091
Cdd:TIGR00376  216 NLLERLALC----------------DQKIVRLGHPARLLKSNKQHSLDYLIeNH-------------PKYQIVADIRekI 266

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2092 DELSRQR-ALCRGGREIQRQELDENISKVSKERQE---LASKI----KEVQGRPQKTQSIIIL----ESHIICCTLSTSG 2159
Cdd:TIGR00376  267 DELIEERnKKTKPSPQKRRGLSDIKILRKALKKREargIESLKiasmAEWIETNKSIDRLLKLlpesEERIMNEILAESD 346

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2160 GLLLESAFRGQGGVPFSCVIVDEAGQSCEIETLTPLIhRCNKLILVGDPKQLPPTVISMKAQEygydqsmmarfcrlLEE 2239
Cdd:TIGR00376  347 ATNSMAGSEILNGQYFDVAVIDEASQAMEPSCLIPLL-KARKLILAGDHKQLPPTILSHDAEE--------------LSL 411

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2240 NVEHNMISRLP--ILQLTVQYRMHPDICLFPSNYVYNRNLKTNRQTEAI-------------RCSSDWPfQPYLVFDVG- 2303
Cdd:TIGR00376  412 TLFERLIKEYPerSRTLNVQYRMNQKIMEFPSREFYNGKLTAHESVANIllrdlpkveatesEDDLETG-IPLLFIDTSg 490

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2304 -DGSERRDND--SYINVQEIKLVMEIIKliKDKRKDVSFRNIGIITHYKAQKTMIQKDLDkefDRKGPAEVDTVDAFQGR 2380
Cdd:TIGR00376  491 cELFELKEADstSKYNPGEAELVSEIIQ--ALVKMGVPANDIGVITPYDAQVDLLRQLLE---HRHIDIEVSSVDGFQGR 565

                          490       500
                   ....*....|....*....|
gi 767956714  2381 QKDCVIVTCVRANSiQGSIG 2400
Cdd:TIGR00376  566 EKEVIIISFVRSNR-KGEVG 584
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
 1933-2259 2.50e-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: 152.79  E-value: 2.50e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 1933 DFNEDQKKAIETAYAmvkhspsvAKICLIHGPPGTGKSKTIVGLLYRLltenqrkghsdensnAKIKQNRVLVCAPSNAA 2012
Cdd:cd18039     1 ELNHSQVDAVKTALQ--------RPLSLIQGPPGTGKTVTSATIVYHL---------------VKQGNGPVLVCAPSNVA 57

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2013 VDELMKKIilefkekckdkkNPLGncgdINLVRLgPEKS---INSEVLKFSLDSQVNHRMKKELpshvqamHKRKEFLDY 2089
Cdd:cd18039    58 VDQLTEKI------------HQTG----LKVVRL-CAKSreaVESPVSFLALHNQVRNLDSAEK-------LELLKLLKL 113

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2090 QLDELSrqralcrggreiqrqELDENISKVSKERQElaskiKEvqgrpqktqsiIILESHIICCTLSTSGGLLLesafrg 2169
Cdd:cd18039   114 ETGELS---------------SADEKRYRKLKRKAE-----RE-----------LLRNADVICCTCVGAGDPRL------ 156

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2170 qGGVPFSCVIVDEAGQSCEIETLTPLIHRCNKLILVGDPKQLPPTVISMKAQEYGYDQSMMARFcrlleenVEHNMIsrl 2249
Cdd:cd18039   157 -SKMKFRTVLIDEATQATEPECLIPLVHGAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERL-------VQLGIR--- 225

                         330
                  ....*....|
gi 767956714 2250 PILqLTVQYR 2259
Cdd:cd18039   226 PIR-LQVQYR 234
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 2260-2400 3.43e-38

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: 141.99  E-value: 3.43e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2260 MHPDICLFPSNYVYNRNLKTNRQTEAIRCSSDWP--FQPYLVFDVGDGSERRDND-SYINVQEIKLVMEIIKLIKdkRKD 2336
Cdd:cd18808     1 MHPEISEFPSKLFYEGKLKAGVSVAARLNPPPLPgpSKPLVFVDVSGGEEREESGtSKSNEAEAELVVELVKYLL--KSG 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767956714 2337 VSFRNIGIITHYKAQKTMIQKDLDKEFDRKGPAEVDTVDAFQGRQKDCVIVTCVRANSIQGSIG 2400
Cdd:cd18808    79 VKPSSIGVITPYRAQVALIRELLRKRGGLLEDVEVGTVDNFQGREKDVIILSLVRSNESGGSIG 142
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 1934-2259 4.00e-36

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: 136.59  E-value: 4.00e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 1934 FNEDQKKAIETAYAmvkhSPSVAkicLIHGPPGTGKSKTIVGLLYRLLTENQRkghsdensnakikqnrVLVCAPSNAAV 2013
Cdd:cd18044     2 LNDSQKEAVKFALS----QKDVA---LIHGPPGTGKTTTVVEIILQAVKRGEK----------------VLACAPSNIAV 58

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2014 DELMKKIIlefkekckdkknplgNCGdINLVRLGPEKSINSEVLKFSLDSQVnhrmkkelpshvqamhkrkefldyqlde 2093
Cdd:cd18044    59 DNLVERLV---------------ALK-VKVVRIGHPARLLESVLDHSLDALV---------------------------- 94

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2094 lsrqralcrggreiqrqeldeniskvskerqelaskikevqgrpqktqsiiilESHIICCTLSTSGGLLLesafrgQGGV 2173
Cdd:cd18044    95 -----------------------------------------------------AAQVVLATNTGAGSRQL------LPNE 115

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2174 PFSCVIVDEAGQSCEIETLTPLIhRCNKLILVGDPKQLPPTVISMKAQEYGYDQSMMARFcrlleENVEHNMISRLpilq 2253
Cdd:cd18044   116 LFDVVVIDEAAQALEASCWIPLL-KARRCILAGDHKQLPPTILSDKAARGGLGVTLFERL-----VNLYGESVVRM---- 185


                  ....*.
gi 767956714 2254 LTVQYR 2259
Cdd:cd18044   186 LTVQYR 191
DEXXQc_Helz-like cd18038
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ...
 1935-2259 1.24e-28

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: 116.18  E-value: 1.24e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 1935 NEDQKKAIETAYAMVKHSPSVakicLIHGPPGTGKSKTIVGLLYRLLTENQrkghsdensnakikQNRVLVCAPSNAAVD 2014
Cdd:cd18038     3 NDEQKLAVRNIVTGTSRPPPY----IIFGPPGTGKTVTLVEAILQVLRQPP--------------EARILVCAPSNSAAD 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2015 ELMKKIILEFKEKckdkknplgncgdINLVRLgpeksinsevlkfsLDSQvnhRMKKELPSHVQAMHKRKEFLDYQLDEL 2094
Cdd:cd18038    65 LLAERLLNALVTK-------------REILRL--------------NAPS---RDRASVPPELLPYCNSKAEGTFRLPSL 114

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2095 SRqralcrggreiqrqeldeniskvskerqelaskikevqgrpqktqsiiILESHIICCTLSTSGglLLESAFRGQGGvp 2174
Cdd:cd18038   115 EE------------------------------------------------LKKYRIVVCTLMTAG--RLVQAGVPNGH-- 142

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2175 FSCVIVDEAGQSCEIETLTPLIHRCNK---LILVGDPKQLPPTVISMKAQEYGYDQSMMArfcRLLEENVEHNMISRLP- 2250
Cdd:cd18038   143 FTHIFIDEAGQATEPEALIPLSELASKntqIVLAGDPKQLGPVVRSPLARKYGLGKSLLE---RLMERPLYYKDGEYNPs 219

                         330
                  ....*....|
gi 767956714 2251 -ILQLTVQYR 2259
Cdd:cd18038   220 yITKLLKNYR 229
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 1935-2259 3.39e-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: 102.70  E-value: 3.39e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 1935 NEDQKKAIETAYamvkhspsVAK-ICLIHGPPGTGKSKTIVGLLYRLLTENqrkghsdensnakikqNRVLVCAPSNAAV 2013
Cdd:cd18041     3 NKDQRQAIKKVL--------NAKdYALILGMPGTGKTTTIAALVRILVALG----------------KSVLLTSYTHSAV 58

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2014 DelmkKIILEFKEKckdkknplgncgDINLVRLGPEKSINSEVLKFSLdsqvnhrmkkelpshvqamhkrkefldyqlde 2093
Cdd:cd18041    59 D----NILLKLKKF------------GVNFLRLGRLKKIHPDVQEFTL-------------------------------- 90

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2094 lsrqralcrggreiqrqeldENISKVSKERQELASKIKEVQgrpqktqsiiileshIICCTLSTsgglLLESAFRGQggv 2173
Cdd:cd18041    91 --------------------EAILKSCKSVEELESKYESVS---------------VVATTCLG----INHPIFRRR--- 128

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2174 PFSCVIVDEAGQSCEIETLTPLIHrCNKLILVGDPKQLPPTVISMKAQEYGYDQSMMARFCrlleeNVEHNMISrlpilQ 2253
Cdd:cd18041   129 TFDYCIVDEASQITLPICLGPLRL-AKKFVLVGDHYQLPPLVKSREARELGMDESLFKRLS-----EAHPDAVV-----Q 197


                  ....*.
gi 767956714 2254 LTVQYR 2259
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 ...
 1935-2233 8.80e-24

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: 103.37  E-value: 8.80e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 1935 NEDQKKAIETAYAmvkhspsvAKICLIHGPPGTGKSKTIVGLLYRLLTENQRKGHSDENSNAKikqNRVLVCAPSNAAVD 2014
Cdd:cd18040     3 NPSQNHAVRTALT--------KPFTLIQGPPGTGKTVTGVHIAYWFAKQNREIQSVSGEGDGG---PCVLYCGPSNKSVD 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2015 ---ELMK-----KIILEFKEKCKDKKNPLGNCGDINLVRLGPEKSINSEVLKFSLdsqvNHRMKKELPSHVQAMhkrKEF 2086
Cdd:cd18040    72 vvaELLLkvpglKILRVYSEQIETTEYPIPNEPRHPNKKSERESKPNSELSSITL----HHRIRQPSNPHSQQI---KAF 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2087 ldyqldelsrQRALCRGGREIQRQELDENISKVSKER-QELASKikevqgrpqktqsiiilesHIICCTLSTSGGLLLES 2165
Cdd:cd18040   145 ----------EARFERTQEKITEEDIKTYKILIWEARfEELETV-------------------DVILCTCSEAASQKMRT 195

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2166 AfrgqggVPFSCVIVDEAGQSCEIETLTPLI--HRCNKLILVGDPKQLPPTVISMKAQEYGYDQSMMARF 2233
Cdd:cd18040   196 H------ANVKQCIVDECGMCTEPESLIPIVsaPRAEQVVLIGDHKQLRPVVQNKEAQKLGLGRSLFERY 259
DEXXQc_Mov10L1 cd18078
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ...
 1933-2259 3.82e-17

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: 82.80  E-value: 3.82e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 1933 DFNEDQKKAIETAYAMV-KHSPSVakiclIHGPPGTGKSKTIVGLLYRLLTEnqrkghsdensnakIKQNRVLVCAPSNA 2011
Cdd:cd18078     1 DLNELQKEAVKRILGGEcRPLPYI-----LFGPPGTGKTVTIIEAILQVVYN--------------LPRSRILVCAPSNS 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2012 AVDELMKKIIlefkekckdkknplgncgDINLVRLGPEKSINSevlkfsldsqVNHRMKKELPshvqamhkrkEFLDYql 2091
Cdd:cd18078    62 AADLVTSRLH------------------ESKVLKPGDMVRLNA----------VNRFESTVID----------ARKLY-- 101

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2092 delsrqralCRGGreiqrqeldENISKVSKERqelaskikevqgrpqktqsiiileshIICCTLSTSGGLLlesafrgQG 2171
Cdd:cd18078   102 ---------CRLG---------EDLSKASRHR--------------------------IVISTCSTAGLLY-------QM 130

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2172 GVP---FSCVIVDEAGQSCEIETLTPL--IH-RCNKLILVGDPKQLPPTVISMKAQEYGYDQSMMARF------CRLLEE 2239
Cdd:cd18078   131 GLPvghFTHVFVDEAGQATEPESLIPLglISsRDGQIILAGDPMQLGPVIKSRLASAYGLGVSFLERLmnrplyLRDPNR 210

                         330       340
                  ....*....|....*....|
gi 767956714 2240 NVEHNMISRLPILQLTVQYR 2259
Cdd:cd18078   211 FGESGGYNPLLVTKLVDNYR 230
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 2178-2259 2.86e-15

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: 74.19  E-value: 2.86e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2178 VIVDEAGQSCEIETLtPLIHRCNKLILVGDPKQLPPTVISMKAQEYGydqsMMARFCRLLEENVEHNMIsrlPILQLTVQ 2257
Cdd:cd17934    48 VIIDEASQITEPELL-IALIRAKKVVLVGDPKQLPPVVQEDHAALLG----LSFILSLLLLFRLLLPGS---PKVMLDTQ 119


                  ..
gi 767956714 2258 YR 2259
Cdd:cd17934   120 YR 121
EEXXQc_AQR cd17935
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ...
 2147-2271 3.08e-14

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: 74.00  E-value: 3.08e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2147 ESHIICCT---LSTSGGLLLESAFRgqggvpFSCVIVDEAGQSCEIETLTPLI--------HRCNKLILVGDPKQLPPTV 2215
Cdd:cd17935    86 GAKIIAMTcthAALKRGELVELGFK------YDNILMEEAAQILEIETFIPLLlqnpedgpNRLKRLIMIGDHHQLPPVI 159

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 767956714 2216 ISMKAQEYGY-DQSMMARFCRLleenvehnmisRLPILQLTVQYRMHPDIC-LFPSNY 2271
Cdd:cd17935   160 KNMAFQKYSNmEQSLFTRLVRL-----------GVPTVDLDAQGRARASISsLYNWRY 206
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 2141-2247 1.77e-08

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: 56.40  E-value: 1.77e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2141 QSIIILESHIICCTlsTSGGLLLESAFRGQGgvpFSCVIVDEAGQSCEIETLTPLIHRCNKLILVGDPKQLPPTVISMK- 2219
Cdd:cd17936    75 TKIVRLGARVIGMT--TTGAAKYRELLQALG---PKVVIVEEAAEVLEAHILAALTPSTEHLILIGDHKQLRPKVNVYEl 149

                          90       100
                  ....*....|....*....|....*....
gi 767956714 2220 -AQEYGYDQSMmarFCRLLEENVEHNMIS 2247
Cdd:cd17936   150 tAKKYNLDVSL---FERLVKNGLPFVTLN 175
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 2175-2213 2.16e-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: 54.51  E-value: 2.16e-08
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 767956714 2175 FSCVIVDEAGQsCEIETLTPLIHRCNKLILVGDPKQLPP 2213
Cdd:cd18043    81 FDLVIFDEASQ-IPIEEALPALFRGKQVVVVGDDKQLPP 118
SEN1_N pfam12726
SEN1 N terminal; This domain is found at the N terminal of the helicase SEN1. SEN1 is a Pol II ...
 37-351 7.37e-08

SEN1 N terminal; This domain is found at the N terminal of the helicase SEN1. SEN1 is a Pol II termination factor for noncoding RNA genes. The N terminal of SEN1, unlike the C terminal, is not required for growth.


Pssm-ID: 432746  Cd Length: 744  Bit Score: 58.10  E-value: 7.37e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714    37 LCYCLECVAEYHKARDEL------PFLHEVL---------WELEtlRLINHFEKSMKaeigdddelyIVDNNGEMPLFDI 101
Cdd:pfam12726    9 LSSCDKCVRNFHRGKKELrqtfaeRFPEETVaqfldkldeWDIE--RILPGLDKAKE----------ILEKRGIFSKSSL 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714   102 TGQDfeNKLRVPLLEILKYP-YLLLHERVNELcVEALCRMEQANcsfQVFDKH----PGIYLFLVHPNEMVRRWAILTAR 176
Cdd:pfam12726   77 SSHL--KEVLLALYEALCCPpYLRSDPELRAL-FDYVFKLLQTK---KKPLRLgtllPGMTYFLFDGDPEERRWARRQLE 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714   177 NLGKVDRDDYYDLQevllclfkvIELGLLESPDIYTSSVLEKGKLILLpshmydttnyksyWLGICMLLTILEEQAMDSL 256
Cdd:pfam12726  151 RLKRSLTPEEFDWA---------VHDLLEEAIVHLSNIQLDPSFIERF-------------WSGFSLILRLLDKDLITHR 208

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714   257 LLGSDKQNDFmQSILHTMEREADDDSVDPFWPALHCFMVILDRLGSKVWGQLMD--PIVAFQTIINNASYNREIRHIRNS 334
Cdd:pfam12726  209 LRALEVNPPI-EDIYRLLLNHLSSTLDPPLPDLLRALSLLLEKSGKAFWDAMGPisPQVVLDQIFDNPAFAKLLAQSLEE 287

                          330
                   ....*....|....*..
gi 767956714   335 svRTKLEPESYLDDMVT 351
Cdd:pfam12726  288 --EMDPPDDDSLSDLLS 302
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 1935-2022 1.16e-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: 52.58  E-value: 1.16e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 1935 NEDQKKAIETAYamvkHSPSVakicLIHGPPGTGKSKTIVGLLYRLLTENQrkghsdensnakikqnRVLVCAPSNAAVD 2014
Cdd:cd18043     1 DSSQEAAIISAR----NGKNV----VIQGPPGTGKSQTIANIIANALARGK----------------RVLFVSEKKAALD 56


                  ....*...
gi 767956714 2015 ELMKKIIL 2022
Cdd:cd18043    57 VVRFPCWI 64
DEXXQc_HELZ cd18077
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ...
 2145-2240 3.94e-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: 53.26  E-value: 3.94e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2145 ILESHIICCTLSTSGGLLLESAFRGQggvpFSCVIVDEAGQSCEIETLTP--LIHRCNKLILVGDPKQLPPTVISMKAQE 2222
Cdd:cd18077   121 VMRHRVVVVTLSTSQYLCQLDLEPGF----FTHILLDEAAQAMECEAIMPlaLATKSTRIVLAGDHMQLSPEVYSEFARE 196

                          90       100
                  ....*....|....*....|....*...
gi 767956714 2223 YGYDQSMMARF---------CR-LLEEN 2240
Cdd:cd18077   197 RNLHISLLERLyehypsehpCRiLLCEN 224
UvrD-helicase pfam00580
UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural ...
 1935-2210 1.30e-06

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: 52.25  E-value: 1.30e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  1935 NEDQKKAIEtayamvkhspSVAKICLIHGPPGTGKSKTIVGLLYRLLTENQrkghsdensnakIKQNRVLVCAPSNAAVD 2014
Cdd:pfam00580    2 NPEQRKAVT----------HLGGPLLVLAGAGSGKTRVLTERIAYLILEGG------------IDPEEILAVTFTNKAAR 59

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2015 ELMKKIILEFKEKCKDKKNpLGN----CGDInLVRLGPEKSINSEVLKFSLDSQvnhrmkkelpshVQAMHKRKEFLDYQ 2090
Cdd:pfam00580   60 EMKERILKLLGKAELSELN-ISTfhsfCLRI-LRKYANRIGLLPNFSILDELDQ------------LALLKELLEKDRLN 125

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2091 LD-ELSRQRALCrggreiqrqeldENISKVsKERQELASKIKEVQGRPQKTQSIIILESH----------------IICC 2153
Cdd:pfam00580  126 LDpKLLRKLELK------------ELISKA-KNRLLSPEELQQGAADPRDKLAAEFYQEYqerlkennaldfddllLLTL 192

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  2154 TLSTSGGLLLEsAFRGQggvpFSCVIVDEAgQ---SCEIETLTPLIHRCNKLILVGDPKQ 2210
Cdd:pfam00580  193 ELLRSDPELLE-AYRER----FKYILVDEF-QdtnPIQYRLLKLLAGGHENLFLVGDPDQ 246
AAA_19 pfam13245
AAA domain;
1938-2016 2.27e-05

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 46.44  E-value: 2.27e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767956714  1938 QKKAIETAyamvkhspSVAKICLIHGPPGTGKSKTIVGLLYRLLTENQRKghsdensnakikqNRVLVCAPSNAAVDEL 2016
Cdd:pfam13245    1 QREAVRTA--------LPSKVVLLTGGPGTGKTTTIRHIVALLVALGGVS-------------FPILLAAPTGRAAKRL 58
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 1960-2026 4.32e-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: 4.32e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767956714 1960 LIHGPPGTGKSKTIVGLLYRLLTenqrkghsdensNAKIKQNRVLVCAPSNAAVDELMKKIILEFKE 2026
Cdd:cd17914     3 LIQGPPGTGKTRVLVKIVAALMQ------------NKNGEPGRILLVTPTNKAAAQLDNILVDEAAQ 57
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 2178-2258 4.58e-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: 4.58e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2178 VIVDEAGQSCEIET--LTPLIHRCNKLILVGDPKQLPPTVISMKAQEYGYDQSmmarfcrLLEENVEHNmisrLPILQLT 2255
Cdd:cd17914    50 ILVDEAAQILEPETsrLIDLALDQGRVILVGDHDQLGPVWRGAVLAKICNEQS-------LFTRLVRLG----VSLIRLQ 118


                  ...
gi 767956714 2256 VQY 2258
Cdd:cd17914   119 VQY 121
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 1868-2023 2.17e-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: 2.17e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 1868 PANLNELVNCIVISSLVTTQRKLKAMSLLGSRNQLARAVLNPNPMDFCTKDLLTTTSERIIAYLRDFNEDQKKAIETAYA 1947
Cdd:COG0507    59 AEDIEAALAALVESGPLVLDGRRYLTRLLEAEQRLARRLRRLARPALDEADVEAALAALEPRAGITLSDEQREAVALALT 138

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767956714 1948 MvkhspsvAKICLIHGPPGTGKSKTIVGLLyRLLTENQRkghsdensnakikqnRVLVCAPSNAAVDELMKKIILE 2023
Cdd:COG0507   139 T-------RRVSVLTGGAGTGKTTTLRALL-AALEALGL---------------RVALAAPTGKAAKRLSESTGIE 191
hsdR PRK11448
type I restriction enzyme EcoKI subunit R; Provisional
 1895-1982 7.55e-04

type I restriction enzyme EcoKI subunit R; Provisional


Pssm-ID: 236912 [Multi-domain]  Cd Length: 1123  Bit Score: 44.94  E-value: 7.55e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 1895 LLGSRNQLARAVLNPNPMDFCTKdlltttseriiayLRDFNEDQKKAIETAYAMVKhspsvaKICLIHGPPGTGKSKTIV 1974
Cdd:PRK11448  391 LLESDIEAANQWLADEPFDYGLG-------------LRYYQEDAIQAVEKAIVEGQ------REILLAMATGTGKTRTAI 451


                  ....*...
gi 767956714 1975 GLLYRLLT 1982
Cdd:PRK11448  452 ALMYRLLK 459
CoV_Nsp13-helicase cd21718
helicase domain of coronavirus non-structural protein 13; This model represents the helicase ...
 2198-2394 1.24e-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: 43.67  E-value: 1.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2198 RCNKLILVGDPKQLP-PTVI----SMKAQEYGydqsmmaRFCRLleenvehnMISRLPILQLTVQYRMHPDICLFPSNYV 2272
Cdd:cd21718   142 KYKHIVYVGDPAQLPaPRTLltegSLEPKDYN-------VVTRL--------MVGSGPDVFLSKCYRCPKEIVDTVSKLV 206

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2273 YNRNLKtnrqteAIRCSSDwpfQPYLVFdvGDGSERRDNDSYINVQEIKLVMEIIKLIKDKRKDVsfrnigIITHYKAQK 2352
Cdd:cd21718   207 YDNKLK------AIKPKSR---QCFKTF--GKGDVRHDNGSAINRPQLEFVKRFLDRNPRWRKAV------FISPYNAMN 269

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 767956714 2353 TMIQKDLDkefdrkgpAEVDTVDAFQGRQKDCVIVtCVRANS 2394
Cdd:cd21718   270 NRASRLLG--------LSTQTVDSSQGSEYDYVIF-CQTTDT 302
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 1937-2020 1.33e-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: 41.39  E-value: 1.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 1937 DQKKAIETAyamVKHspsvaKICLIHGPPGTGKSKTIVGLLyRLLtenQRKGHsdensnakikqnRVLVCAPSNAAVDEL 2016
Cdd:cd17933     1 EQKAAVRLV---LRN-----RVSVLTGGAGTGKTTTLKALL-AAL---EAEGK------------RVVLAAPTGKAAKRL 56


                  ....
gi 767956714 2017 MKKI 2020
Cdd:cd17933    57 SEST 60
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 1935-2018 1.94e-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: 41.78  E-value: 1.94e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714  1935 NEDQKKAIETAYAmvkhspSVAKICLIHGPPGTGKSkTIVGLLYRLLTENqrkGHsdensnakikqnRVLVCAPSNAAVD 2014
Cdd:pfam13604    3 NAEQAAAVRALLT------SGDRVAVLVGPAGTGKT-TALKALREAWEAA---GY------------RVIGLAPTGRAAK 60


                   ....
gi 767956714  2015 ELMK 2018
Cdd:pfam13604   61 VLGE 64
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 2342-2394 2.44e-03

C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Similar to SF2 helicases, they do not form toroidal, predominantly hexameric structures like SF3-6. SF1 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350173 [Multi-domain]  Cd Length: 89  Bit Score: 39.34  E-value: 2.44e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 767956714 2342 IGIITHYKAQKTMIQKDLDKE-FDRKGPAEVD--TVDAFQGRQKDCVIVTCVRANS 2394
Cdd:cd18786    13 GVVLTPYHRDRAYLNQYLQGLsLDEFDLQLVGaiTIDSSQGLTFDVVTLYLPTANS 68
betaCoV_Nsp13-helicase cd21722
helicase domain of betacoronavirus non-structural protein 13; This model represents the ...
 2198-2388 7.75e-03

helicase domain of betacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from betacoronavirus, 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: 409655 [Multi-domain]  Cd Length: 340  Bit Score: 40.94  E-value: 7.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2198 RCNKLILVGDPKQLPP--TVISMKAQEYGYDQSMmarfCRLleenvehnMISRLPILQLTVQYRMHPDICLFPSNYVYNR 2275
Cdd:cd21722   142 RAKHIVYIGDPAQLPAprTLLTKGTLEPEYFNSV----TRL--------MCCLGPDIFLGTCYRCPKEIVDTVSALVYDN 209

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767956714 2276 NLKTNRQTEAiRCssdwpFQPYLvfdvgDGSERRDNDSYINVQEIKLVMEIIKlikdkrKDVSFRNIGIITHYKAQKTMI 2355
Cdd:cd21722   210 KLKAKKDNSG-QC-----FKVYY-----KGSVTHDSSSAINRPQIYLVKKFLK------ANPAWSKAVFISPYNSQNAVA 272

                         170       180       190
                  ....*....|....*....|....*....|...
gi 767956714 2356 QKDLDkefdrkgpAEVDTVDAFQGRQKDCVIVT 2388
Cdd:cd21722   273 RRVLG--------LQTQTVDSSQGSEYDYVIYC 297
 
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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