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Conserved domains on  [gi|1958657566|ref|XP_038941571|]
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probable helicase with zinc finger domain isoform X5 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 658-850 3.58e-121

N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.


The actual alignment was detected with superfamily member cd18077:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 226  Bit Score: 381.06  E-value: 3.58e-121
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  658 RLNAKQKEAVLAITTPLCIQLPPVLIIGPYGTGKTFTLAQAVKHILQQQET----------------------------- 708
Cdd:cd18077      1 RLNAKQKEAVLAITTPLSIQLPPVLLIGPFGTGKTFTLAQAVKHILQQPETrilicthsnsaadlyikeylhpyvetgnp 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  709 -----RVYFRNRWVKTVHPVVHQYCLIsSAHSTFQMPQKEDILKHRVVVVTLNTSQYLCQLDLEPGFFTHILLDEAAQAM 783
Cdd:cd18077     81 rarplRVYYRNRWVKTVHPVVQKYCLI-DEHGTFRMPTREDVMRHRVVVVTLSTSQYLCQLDLEPGFFTHILLDEAAQAM 159

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958657566  784 ECETIMPLALATKNTRIVLAGDHMQLSPFVYSEFARERNLHVSLLDRLYEHYPAEFPCRILLCENYR 850
Cdd:cd18077    160 ECEAIMPLALATKSTRIVLAGDHMQLSPEVYSEFARERNLHISLLERLYEHYPSEHPCRILLCENYR 226
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
748-1057 9.07e-42

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


:

Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 167.23  E-value: 9.07e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  748 HRVVVVTLNTSQYLcqLDLEPGFFTHILLDEAAQAMECETIMPLALATkntRIVLAGDHMQLSPFV---YSEFARERNLH 824
Cdd:COG1112    535 APVVGMTPASVARL--LPLGEGSFDLVIIDEASQATLAEALGALARAK---RVVLVGDPKQLPPVVfgeEAEEVAEEGLD 609

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  825 VSLLDRLYEHYPaefPCRILLCENYRSHEAIINYTSELFYEGKLMA---SGKQPAHKDFYPLTFFTARGedVQEKNSTAF 901
Cdd:COG1112    610 ESLLDRLLARLP---ERGVMLREHYRMHPEIIAFSNRLFYDGKLVPlpsPKARRLADPDSPLVFIDVDG--VYERRGGSR 684

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  902 YNnaevfevverveelrrkwP------VAW------GKLDDGSIGVVTPYADQVFRIRAELRKKRLSDV------NVERv 963
Cdd:COG1112    685 TN------------------PeeaeavVELvrelleDGPDGESIGVITPYRAQVALIRELLREALGDGLepvfvgTVDR- 745

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  964 lnVQGKQFRVLFLSTVRTRhtckhkqtpikkkeqlleDSTEDLDYGFLS-NYKLLNTAITRAQSLVAVVGDPvALCSIGR 1042
Cdd:COG1112    746 --FQGDERDVIIFSLVYSN------------------DEDVPRNFGFLNgGPRRLNVAVSRARRKLIVVGSR-ELLDSDP 804

                          330
                   ....*....|....*
gi 1958657566 1043 CRKFWERFIALCHEN 1057
Cdd:COG1112    805 STPALKRLLEYLERA 819
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
181-205 6.55e-06

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


:

Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 44.49  E-value: 6.55e-06
                           10        20
                   ....*....|....*....|....*
gi 1958657566  181 YTLCKRFLEQGICRYGAQCTSAHSQ 205
Cdd:pfam00642    3 TELCRFFLRTGYCKYGDRCKFAHGQ 27
PRK10263 super family cl35903
DNA translocase FtsK; Provisional
 1301-1395 8.97e-05

DNA translocase FtsK; Provisional


The actual alignment was detected with superfamily member PRK10263:

Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 47.77  E-value: 8.97e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566 1301 PESRPGVVYSNTKFPRKDNLNPRHINLPLPAPHTQYAIPSRHFHPLPQLPRPPFPISQQHTLLNQQQnnlPEQPNQMTPQ 1380
Cdd:PRK10263   743 PLFTPIVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQ---PVAPQPQYQQ 819

                           90
                   ....*....|....*.
gi 1958657566 1381 PNQ-VAPQPNQMAPQP 1395
Cdd:PRK10263   820 PQQpVAPQPQYQQPQQ 835
Atrophin-1 super family cl38111
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1226-1501 6.78e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


The actual alignment was detected with superfamily member pfam03154:

Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 44.76  E-value: 6.78e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566 1226 HGRGSPIPYglghhpPVNLGQPQNQHAEKDQQEQNRNGKTDTNNP-GPEINKIRTPEKKPTEPKqidlesnPQNRSPESR 1304
Cdd:pfam03154  272 HGQMPPMPH------SLQTGPSHMQHPVPPQPFPLTPQSSQSQVPpGPSPAAPGQSQQRIHTPP-------SQSQLQSQQ 338

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566 1305 PgvvysntkfPRKDNLNPRhinlPLPAPHTQyaipsrhfhPLPQLPRPPFPISQQHTLLN--------QQQNNLPEQP-- 1374
Cdd:pfam03154  339 P---------PREQPLPPA----PLSMPHIK---------PPPTTPIPQLPNPQSHKHPPhlsgpspfQMNSNLPPPPal 396

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566 1375 ----NQMTPQPNQVAPQPNQMAPQPNQMAPQPNQVVQQQNQAPPQAPQPAPQLSPAFQAGPTNAFFnnavahrPQSP--- 1447
Cdd:pfam03154  397 kplsSLSTHHPPSAHPPPLQLMPQSQQLPPPPAQPPVLTQSQSLPPPAASHPPTSGLHQVPSQSPF-------PQHPfvp 469

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958657566 1448 -AAEAVGPEQQVPPGLSDGHSPLRAITQPGPILASPLNNFVDESSPGLPI-EEALD 1501
Cdd:pfam03154  470 gGPPPITPPSGPPTSTSSAMPGIQPPSSASVSSSGPVPAAVSCPLPPVQIkEEALD 525
 
Name Accession Description Interval E-value
DEXXQc_HELZ cd18077
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ...
 658-850 3.58e-121

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: 381.06  E-value: 3.58e-121
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  658 RLNAKQKEAVLAITTPLCIQLPPVLIIGPYGTGKTFTLAQAVKHILQQQET----------------------------- 708
Cdd:cd18077      1 RLNAKQKEAVLAITTPLSIQLPPVLLIGPFGTGKTFTLAQAVKHILQQPETrilicthsnsaadlyikeylhpyvetgnp 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  709 -----RVYFRNRWVKTVHPVVHQYCLIsSAHSTFQMPQKEDILKHRVVVVTLNTSQYLCQLDLEPGFFTHILLDEAAQAM 783
Cdd:cd18077     81 rarplRVYYRNRWVKTVHPVVQKYCLI-DEHGTFRMPTREDVMRHRVVVVTLSTSQYLCQLDLEPGFFTHILLDEAAQAM 159

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958657566  784 ECETIMPLALATKNTRIVLAGDHMQLSPFVYSEFARERNLHVSLLDRLYEHYPAEFPCRILLCENYR 850
Cdd:cd18077    160 ECEAIMPLALATKSTRIVLAGDHMQLSPEVYSEFARERNLHISLLERLYEHYPSEHPCRILLCENYR 226
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
748-1057 9.07e-42

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 167.23  E-value: 9.07e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  748 HRVVVVTLNTSQYLcqLDLEPGFFTHILLDEAAQAMECETIMPLALATkntRIVLAGDHMQLSPFV---YSEFARERNLH 824
Cdd:COG1112    535 APVVGMTPASVARL--LPLGEGSFDLVIIDEASQATLAEALGALARAK---RVVLVGDPKQLPPVVfgeEAEEVAEEGLD 609

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  825 VSLLDRLYEHYPaefPCRILLCENYRSHEAIINYTSELFYEGKLMA---SGKQPAHKDFYPLTFFTARGedVQEKNSTAF 901
Cdd:COG1112    610 ESLLDRLLARLP---ERGVMLREHYRMHPEIIAFSNRLFYDGKLVPlpsPKARRLADPDSPLVFIDVDG--VYERRGGSR 684

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  902 YNnaevfevverveelrrkwP------VAW------GKLDDGSIGVVTPYADQVFRIRAELRKKRLSDV------NVERv 963
Cdd:COG1112    685 TN------------------PeeaeavVELvrelleDGPDGESIGVITPYRAQVALIRELLREALGDGLepvfvgTVDR- 745

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  964 lnVQGKQFRVLFLSTVRTRhtckhkqtpikkkeqlleDSTEDLDYGFLS-NYKLLNTAITRAQSLVAVVGDPvALCSIGR 1042
Cdd:COG1112    746 --FQGDERDVIIFSLVYSN------------------DEDVPRNFGFLNgGPRRLNVAVSRARRKLIVVGSR-ELLDSDP 804

                          330
                   ....*....|....*
gi 1958657566 1043 CRKFWERFIALCHEN 1057
Cdd:COG1112    805 STPALKRLLEYLERA 819
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 851-1051 6.36e-36

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: 135.44  E-value: 6.36e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  851 SHEAIINYTSELFYEGKLMAS-------GKQPAHKDFYPLTFFTARGEDVQEKNSTAFYNNAEVFEVVERVEELRRKWpv 923
Cdd:cd18808      1 MHPEISEFPSKLFYEGKLKAGvsvaarlNPPPLPGPSKPLVFVDVSGGEEREESGTSKSNEAEAELVVELVKYLLKSG-- 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  924 awgkLDDGSIGVVTPYADQVFRIRAELRKKR--LSDVNVERVLNVQGKQFRVLFLSTVRTRHTCKHkqtpikkkeqlled 1001
Cdd:cd18808     79 ----VKPSSIGVITPYRAQVALIRELLRKRGglLEDVEVGTVDNFQGREKDVIILSLVRSNESGGS-------------- 140

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 1958657566 1002 stedldYGFLSNYKLLNTAITRAQSLVAVVGDPVALCSIGRCRKFWERFI 1051
Cdd:cd18808    141 ------IGFLSDPRRLNVALTRAKRGLIIVGNPDTLSKDPLWKKLLEYLE 184
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 823-1034 4.84e-35

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: 133.06  E-value: 4.84e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  823 LHVSLLDRLYEHYPAefpCRILLCENYRSHEAIINYTSELFYEGKLMASGKQPAH---------KDFYPLTFF-TARGED 892
Cdd:pfam13087    1 LDRSLFERLQELGPS---AVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERplpddfhlpDPLGPLVFIdVDGSEE 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  893 VQEKNSTAFYNNAEVFEVVERVEELRRKWPVAWGKlddgsIGVVTPYADQVFRIRAELRKKRLSDVNVErVLNV---QGK 969
Cdd:pfam13087   78 EESDGGTSYSNEAEAELVVQLVEKLIKSGPEEPSD-----IGVITPYRAQVRLIRKLLKRKLGGKLEIE-VNTVdgfQGR 151

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958657566  970 QFRVLFLSTVRtrhtckhkqtpikkkeqlledSTEDLDYGFLSNYKLLNTAITRAQSLVAVVGDP 1034
Cdd:pfam13087  152 EKDVIIFSCVR---------------------SNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNA 195
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 741-816 3.06e-09

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


Pssm-ID: 404072 [Multi-domain]  Cd Length: 248  Bit Score: 59.66  E-value: 3.06e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958657566  741 QKEDILKHRVVVVTLNTS--QYLCQLDlepGFFThILLDEAAQAMECETIMPLALATKntRIVLAGDHMQLSPFVYSE 816
Cdd:pfam13086  177 EREILDEAQIVCSTLSGAgsRLLSSLA---NFDV-VIIDEAAQALEPSTLIPLLRGPK--KVVLVGDPKQLPPTVISK 248
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
181-205 6.55e-06

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 44.49  E-value: 6.55e-06
                           10        20
                   ....*....|....*....|....*
gi 1958657566  181 YTLCKRFLEQGICRYGAQCTSAHSQ 205
Cdd:pfam00642    3 TELCRFFLRTGYCKYGDRCKFAHGQ 27
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 1301-1395 8.97e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 47.77  E-value: 8.97e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566 1301 PESRPGVVYSNTKFPRKDNLNPRHINLPLPAPHTQYAIPSRHFHPLPQLPRPPFPISQQHTLLNQQQnnlPEQPNQMTPQ 1380
Cdd:PRK10263   743 PLFTPIVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQ---PVAPQPQYQQ 819

                           90
                   ....*....|....*.
gi 1958657566 1381 PNQ-VAPQPNQMAPQP 1395
Cdd:PRK10263   820 PQQpVAPQPQYQQPQQ 835
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1226-1501 6.78e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 44.76  E-value: 6.78e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566 1226 HGRGSPIPYglghhpPVNLGQPQNQHAEKDQQEQNRNGKTDTNNP-GPEINKIRTPEKKPTEPKqidlesnPQNRSPESR 1304
Cdd:pfam03154  272 HGQMPPMPH------SLQTGPSHMQHPVPPQPFPLTPQSSQSQVPpGPSPAAPGQSQQRIHTPP-------SQSQLQSQQ 338

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566 1305 PgvvysntkfPRKDNLNPRhinlPLPAPHTQyaipsrhfhPLPQLPRPPFPISQQHTLLN--------QQQNNLPEQP-- 1374
Cdd:pfam03154  339 P---------PREQPLPPA----PLSMPHIK---------PPPTTPIPQLPNPQSHKHPPhlsgpspfQMNSNLPPPPal 396

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566 1375 ----NQMTPQPNQVAPQPNQMAPQPNQMAPQPNQVVQQQNQAPPQAPQPAPQLSPAFQAGPTNAFFnnavahrPQSP--- 1447
Cdd:pfam03154  397 kplsSLSTHHPPSAHPPPLQLMPQSQQLPPPPAQPPVLTQSQSLPPPAASHPPTSGLHQVPSQSPF-------PQHPfvp 469

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958657566 1448 -AAEAVGPEQQVPPGLSDGHSPLRAITQPGPILASPLNNFVDESSPGLPI-EEALD 1501
Cdd:pfam03154  470 gGPPPITPPSGPPTSTSSAMPGIQPPSSASVSSSGPVPAAVSCPLPPVQIkEEALD 525
UvrD COG0210
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
658-706 7.05e-04

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


Pssm-ID: 439980 [Multi-domain]  Cd Length: 721  Bit Score: 44.54  E-value: 7.05e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1958657566  658 RLNAKQKEAVLAITTPLciqlppvLII-GPyGTGKTFTLAQAVKHILQQQ 706
Cdd:COG0210      6 GLNPEQRAAVEHPEGPL-------LVLaGA-GSGKTRVLTHRIAYLIAEG 47
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
 1313-1398 4.09e-03

Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide.


Pssm-ID: 197891 [Multi-domain]  Cd Length: 165  Bit Score: 40.16  E-value: 4.09e-03
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  1313 KFPRKDNLNPRHINLPLPAPHTqyAIPSRHFHP-LPQLPRPPFpisqqhtllnQQQNNLPEQPNQMTPQPNQVAPQPNQM 1391
Cdd:smart00818   60 VLPAQQPVVPQQPLMPVPGQHS--MTPTQHHQPnLPQPAQQPF----------QPQPLQPPQPQQPMQPQPPVHPIPPLP 127


                    ....*..
gi 1958657566  1392 APQPNQM 1398
Cdd:smart00818  128 PQPPLPP 134
dnaA PRK14086
chromosomal replication initiator protein DnaA;
1279-1482 6.18e-03

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 41.35  E-value: 6.18e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566 1279 TPEKKPTEPKQIDLESNPQNRSPESRPGVVYSNTKFPRKDNLNPRHINLPLPAPhtqyAIPSRHFHPLP-QLPRPPFPIS 1357
Cdd:PRK14086    91 SAGEPAPPPPHARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQDQLPTARP----AYPAYQQRPEPgAWPRAADDYG 166

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566 1358 QQHTLLNQQQNNLPEQPNQMTPQPNQVAPQPNQMAPQPNQMAPQPNQvvqqqnqappqapqpapqlsPAFQAGPTNAFFN 1437
Cdd:PRK14086   167 WQQQRLGFPPRAPYASPASYAPEQERDREPYDAGRPEYDQRRRDYDH--------------------PRPDWDRPRRDRT 226

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1958657566 1438 NavahRPQ-SPAAEAVGPEQQVPPGLSDGHSPLRAITQPGPILASP 1482
Cdd:PRK14086   227 D----RPEpPPGAGHVHRGGPGPPERDDAPVVPIRPSAPGPLAAQP 268
 
Name Accession Description Interval E-value
DEXXQc_HELZ cd18077
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ...
 658-850 3.58e-121

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: 381.06  E-value: 3.58e-121
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  658 RLNAKQKEAVLAITTPLCIQLPPVLIIGPYGTGKTFTLAQAVKHILQQQET----------------------------- 708
Cdd:cd18077      1 RLNAKQKEAVLAITTPLSIQLPPVLLIGPFGTGKTFTLAQAVKHILQQPETrilicthsnsaadlyikeylhpyvetgnp 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  709 -----RVYFRNRWVKTVHPVVHQYCLIsSAHSTFQMPQKEDILKHRVVVVTLNTSQYLCQLDLEPGFFTHILLDEAAQAM 783
Cdd:cd18077     81 rarplRVYYRNRWVKTVHPVVQKYCLI-DEHGTFRMPTREDVMRHRVVVVTLSTSQYLCQLDLEPGFFTHILLDEAAQAM 159

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958657566  784 ECETIMPLALATKNTRIVLAGDHMQLSPFVYSEFARERNLHVSLLDRLYEHYPAEFPCRILLCENYR 850
Cdd:cd18077    160 ECEAIMPLALATKSTRIVLAGDHMQLSPEVYSEFARERNLHISLLERLYEHYPSEHPCRILLCENYR 226
DEXXQc_Helz-like cd18038
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ...
 658-850 8.64e-76

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: 251.38  E-value: 8.64e-76
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  658 RLNAKQKEAVLAITTPLCiQLPPVLIIGPYGTGKTFTLAQAVKHILQQQET----------------------------- 708
Cdd:cd18038      1 ELNDEQKLAVRNIVTGTS-RPPPYIIFGPPGTGKTVTLVEAILQVLRQPPEarilvcapsnsaadllaerllnalvtkre 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  709 --RVYFRNRWVKTVHPVVHQYClISSAHSTFQMPQKEDILKHRVVVVTLNTSQYLCQLDLEPGFFTHILLDEAAQAMECE 786
Cdd:cd18038     80 ilRLNAPSRDRASVPPELLPYC-NSKAEGTFRLPSLEELKKYRIVVCTLMTAGRLVQAGVPNGHFTHIFIDEAGQATEPE 158

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958657566  787 TIMPLA-LATKNTRIVLAGDHMQLSPFVYSEFARERNLHVSLLDRLYEHYP------AEFPCRILLCENYR 850
Cdd:cd18038    159 ALIPLSeLASKNTQIVLAGDPKQLGPVVRSPLARKYGLGKSLLERLMERPLyykdgeYNPSYITKLLKNYR 229
DEXXQc_HELZ2-N cd18076
N-terminal DEXXQ-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 658-850 5.27e-43

N-terminal DEXXQ-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: 350834 [Multi-domain]  Cd Length: 230  Bit Score: 157.36  E-value: 5.27e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  658 RLNAKQKEAVLAIT--TPLCIQLPPVLIIGPYGTGKTFTLAQAVKHILQQQETRV----------------YFR------ 713
Cdd:cd18076      1 AGNNKQQLAFNFIAgkPSEARFVPPLLIYGPFGTGKTFTLAMAALEVIREPGTKVlicthtnsaadiyireYFHpyvdkg 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  714 NRWVKTVH------------PVVHQYCLISSAHSTFQMPQKEDILKHRVVVVTLNTSQylcQLDLEPGFFTHILLDEAAQ 781
Cdd:cd18076     81 HPEARPLRikatdrpnaitdPDTITYCCLTKDRQCFRLPTRDELDFHNIVITTTAMAF---NLHVLSGFFTHIFIDEAAQ 157

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958657566  782 AMECETIMPLALATKNTRIVLAGDHMQLSPFVYSeFARERNLHVSLLDRLYEHYPAE-----FPCRILLCENYR 850
Cdd:cd18076    158 MLECEALIPLSYAGPKTRVVLAGDHMQMTPKLFS-VADYNRANHTLLNRLFHYYQGEkhevaVKSRVIFSENYR 230
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
748-1057 9.07e-42

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 167.23  E-value: 9.07e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  748 HRVVVVTLNTSQYLcqLDLEPGFFTHILLDEAAQAMECETIMPLALATkntRIVLAGDHMQLSPFV---YSEFARERNLH 824
Cdd:COG1112    535 APVVGMTPASVARL--LPLGEGSFDLVIIDEASQATLAEALGALARAK---RVVLVGDPKQLPPVVfgeEAEEVAEEGLD 609

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  825 VSLLDRLYEHYPaefPCRILLCENYRSHEAIINYTSELFYEGKLMA---SGKQPAHKDFYPLTFFTARGedVQEKNSTAF 901
Cdd:COG1112    610 ESLLDRLLARLP---ERGVMLREHYRMHPEIIAFSNRLFYDGKLVPlpsPKARRLADPDSPLVFIDVDG--VYERRGGSR 684

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  902 YNnaevfevverveelrrkwP------VAW------GKLDDGSIGVVTPYADQVFRIRAELRKKRLSDV------NVERv 963
Cdd:COG1112    685 TN------------------PeeaeavVELvrelleDGPDGESIGVITPYRAQVALIRELLREALGDGLepvfvgTVDR- 745

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  964 lnVQGKQFRVLFLSTVRTRhtckhkqtpikkkeqlleDSTEDLDYGFLS-NYKLLNTAITRAQSLVAVVGDPvALCSIGR 1042
Cdd:COG1112    746 --FQGDERDVIIFSLVYSN------------------DEDVPRNFGFLNgGPRRLNVAVSRARRKLIVVGSR-ELLDSDP 804

                          330
                   ....*....|....*
gi 1958657566 1043 CRKFWERFIALCHEN 1057
Cdd:COG1112    805 STPALKRLLEYLERA 819
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 851-1051 6.36e-36

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: 135.44  E-value: 6.36e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  851 SHEAIINYTSELFYEGKLMAS-------GKQPAHKDFYPLTFFTARGEDVQEKNSTAFYNNAEVFEVVERVEELRRKWpv 923
Cdd:cd18808      1 MHPEISEFPSKLFYEGKLKAGvsvaarlNPPPLPGPSKPLVFVDVSGGEEREESGTSKSNEAEAELVVELVKYLLKSG-- 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  924 awgkLDDGSIGVVTPYADQVFRIRAELRKKR--LSDVNVERVLNVQGKQFRVLFLSTVRTRHTCKHkqtpikkkeqlled 1001
Cdd:cd18808     79 ----VKPSSIGVITPYRAQVALIRELLRKRGglLEDVEVGTVDNFQGREKDVIILSLVRSNESGGS-------------- 140

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 1958657566 1002 stedldYGFLSNYKLLNTAITRAQSLVAVVGDPVALCSIGRCRKFWERFI 1051
Cdd:cd18808    141 ------IGFLSDPRRLNVALTRAKRGLIIVGNPDTLSKDPLWKKLLEYLE 184
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 823-1034 4.84e-35

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: 133.06  E-value: 4.84e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  823 LHVSLLDRLYEHYPAefpCRILLCENYRSHEAIINYTSELFYEGKLMASGKQPAH---------KDFYPLTFF-TARGED 892
Cdd:pfam13087    1 LDRSLFERLQELGPS---AVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERplpddfhlpDPLGPLVFIdVDGSEE 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  893 VQEKNSTAFYNNAEVFEVVERVEELRRKWPVAWGKlddgsIGVVTPYADQVFRIRAELRKKRLSDVNVErVLNV---QGK 969
Cdd:pfam13087   78 EESDGGTSYSNEAEAELVVQLVEKLIKSGPEEPSD-----IGVITPYRAQVRLIRKLLKRKLGGKLEIE-VNTVdgfQGR 151

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958657566  970 QFRVLFLSTVRtrhtckhkqtpikkkeqlledSTEDLDYGFLSNYKLLNTAITRAQSLVAVVGDP 1034
Cdd:pfam13087  152 EKDVIIFSCVR---------------------SNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNA 195
DEXXQc_Mov10L1 cd18078
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ...
 659-850 1.41e-30

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: 121.71  E-value: 1.41e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  659 LNAKQKEAVLAITTPLCIQLPPVlIIGPYGTGKTFTLAQAV--------------------------------KHILQQQ 706
Cdd:cd18078      2 LNELQKEAVKRILGGECRPLPYI-LFGPPGTGKTVTIIEAIlqvvynlprsrilvcapsnsaadlvtsrlhesKVLKPGD 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  707 ETRVYFRNRWVKTVHPVVHQYCLISSahstfqmpQKEDILKHRVVVVTLNTSQYLCQLDLEPGFFTHILLDEAAQAMECE 786
Cdd:cd18078     81 MVRLNAVNRFESTVIDARKLYCRLGE--------DLSKASRHRIVISTCSTAGLLYQMGLPVGHFTHVFVDEAGQATEPE 152

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958657566  787 TIMPLALATKNT-RIVLAGDHMQLSPFVYSEFARERNLHVSLLDRL-----YEHYPAEFP-CRIL-------LCENYR 850
Cdd:cd18078    153 SLIPLGLISSRDgQIILAGDPMQLGPVIKSRLASAYGLGVSFLERLmnrplYLRDPNRFGeSGGYnpllvtkLVDNYR 230
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 658-850 1.78e-19

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: 88.44  E-value: 1.78e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  658 RLNAKQKEAVLaittpLCIQLPPVLII-GPYGTGKTFTLAQAvkhILQ--QQETRVY------------------FRNRW 716
Cdd:cd18044      1 NLNDSQKEAVK-----FALSQKDVALIhGPPGTGKTTTVVEI---ILQavKRGEKVLacapsniavdnlverlvaLKVKV 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  717 VKTVHPV-----VHQYCLissahstfqmpqkEDILKHRVVVVTLNTSqylCQLDLEPG-FFTHILLDEAAQAMECETIMP 790
Cdd:cd18044     73 VRIGHPArllesVLDHSL-------------DALVAAQVVLATNTGA---GSRQLLPNeLFDVVVIDEAAQALEASCWIP 136

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  791 LalaTKNTRIVLAGDHMQLSPFVYSEFARERNLHVSLLDRLYEHYPAEfpCRILLCENYR 850
Cdd:cd18044    137 L---LKARRCILAGDHKQLPPTILSDKAARGGLGVTLFERLVNLYGES--VVRMLTVQYR 191
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 658-836 7.84e-19

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: 86.91  E-value: 7.84e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  658 RLNAKQKEAVLAITTPLCIqlppVLIIGPYGTGKTFTLAQAVKhILQQQETRV-----------------------YFRN 714
Cdd:cd18041      1 GLNKDQRQAIKKVLNAKDY----ALILGMPGTGKTTTIAALVR-ILVALGKSVlltsythsavdnillklkkfgvnFLRL 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  715 RWVKTVHPVVHQYCLISSAHSTFQMPQKEDIL-KHRVVVVTL--NTSQYLCQldlepGFFTHILLDEAAQAMECETIMPL 791
Cdd:cd18041     76 GRLKKIHPDVQEFTLEAILKSCKSVEELESKYeSVSVVATTClgINHPIFRR-----RTFDYCIVDEASQITLPICLGPL 150

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 1958657566  792 ALATKntrIVLAGDHMQLSPFVYSEFARERNLHVSLLDRLYEHYP 836
Cdd:cd18041    151 RLAKK---FVLVGDHYQLPPLVKSREARELGMDESLFKRLSEAHP 192
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 659-850 4.98e-17

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: 81.88  E-value: 4.98e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  659 LNAKQKEAVLAIttplCIQLPPV-LIIGPYGTGKTFTLAQAVKHILQQQETRVYFRNRWVKTVHPVVHQ---------YC 728
Cdd:cd18042      1 LNESQLEAIASA----LQNSPGItLIQGPPGTGKTKTIVGILSVLLAGKYRKYYEKVKKKLRKLQRNLNnkkkknrilVC 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  729 LISSA-----------------HSTFQMPQ---------KEDILKH-RVVVVTLNTSQYLcQLDLEPGFFTHILLDEAAQ 781
Cdd:cd18042     77 APSNAavdeivlrllsegfldgDGRSYKPNvvrvgrqelRASILNEaDIVCTTLSSSGSD-LLESLPRGFDTVIIDEAAQ 155

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958657566  782 AMECETIMPLALATKntRIVLAGDHMQLSPFVYSEFARERNLHVSLLDRLYEhypAEFPCrILLCENYR 850
Cdd:cd18042    156 AVELSTLIPLRLGCK--RLILVGDPKQLPATVFSKVAQKLGYDRSLFERLQL---AGYPV-LMLTTQYR 218
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
 659-831 1.06e-13

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: 72.66  E-value: 1.06e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  659 LNAKQKEAV-LAITTPLCiqlppvLIIGPYGTGKTFTLAQAVKHILQQQET---------------------------RV 710
Cdd:cd18039      2 LNHSQVDAVkTALQRPLS------LIQGPPGTGKTVTSATIVYHLVKQGNGpvlvcapsnvavdqltekihqtglkvvRL 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  711 YFRNRW-----VK--TVHPVVHQY-----------------CLISSAHSTFQM----PQKEDILKHRVVVVTLNTSqylc 762
Cdd:cd18039     76 CAKSREavespVSflALHNQVRNLdsaeklellkllkletgELSSADEKRYRKlkrkAERELLRNADVICCTCVGA---- 151

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958657566  763 qLD--LEPGFFTHILLDEAAQAMECETIMPLALATKntRIVLAGDHMQLSPFVYSEFARERNLHVSLLDRL 831
Cdd:cd18039    152 -GDprLSKMKFRTVLIDEATQATEPECLIPLVHGAK--QVILVGDHCQLGPVVMCKKAAKAGLSQSLFERL 219
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 681-850 1.40e-13

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: 69.19  E-value: 1.40e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  681 VLIIGPYGTGKTFTLAQAVKHILQQQETrvyfrnrwvKTVhpvvhqycLISsAHStfqmpqkedilkHRVVVVtlntsqy 760
Cdd:cd17934      2 SLIQGPPGTGKTTTIAAIVLQLLKGLRG---------KRV--------LVT-AQS------------NVAVDN------- 44

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  761 lcqLDlepgfftHILLDEAAQAMECETIMPLALATKntrIVLAGDHMQLSPFVYSEFARE--RNLHVSLLDRLYEHYPAE 838
Cdd:cd17934     45 ---VD-------VVIIDEASQITEPELLIALIRAKK---VVLVGDPKQLPPVVQEDHAALlgLSFILSLLLLFRLLLPGS 111

                          170
                   ....*....|..
gi 1958657566  839 FPcrILLCENYR 850
Cdd:cd17934    112 PK--VMLDTQYR 121
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 658-831 1.37e-12

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: 67.95  E-value: 1.37e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  658 RLNAKQKEA-VLAITTPLciqlppVLIIGPYGTGKTFTLAQAVkhilqqqetRVYFRNRWVKTVHPVVhqyCLISSAHST 736
Cdd:cd17936      1 TLDPSQLEAlKHALTSEL------ALIQGPPGTGKTFLGVKLV---------RALLQNQDLSITGPIL---VVCYTNHAL 62

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  737 FQMpqKEDILKH----------RVVVVTLNTSQYLCQL--DLEPgffTHILLDEAAQAMECETIMPLalaTKNTR-IVLA 803
Cdd:cd17936     63 DQF--LEGLLDFgptkivrlgaRVIGMTTTGAAKYRELlqALGP---KVVIVEEAAEVLEAHILAAL---TPSTEhLILI 134

                          170       180       190
                   ....*....|....*....|....*....|
gi 1958657566  804 GDHMQLSPFV--YSEFARERNLHVSLLDRL 831
Cdd:cd17936    135 GDHKQLRPKVnvYELTAKKYNLDVSLFERL 164
EEXXQc_AQR cd17935
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ...
 658-831 1.26e-09

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: 60.13  E-value: 1.26e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  658 RLNAKQKEAVLAITTPLCiqlppVLIIGPYGTGKTFTLAQAVKHILqqqetrvyfrnrwvktvHPVVHQYCLISSaHSTF 737
Cdd:cd17935      5 KFTPTQIEAIRSGMQPGL-----TMVVGPPGTGKTDVAVQIISNLY-----------------HNFPNQRTLIVT-HSNQ 61

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  738 QMPQ------KEDI-------LKH--RVVVVTLnTSQYLCQLDL-EPGF-FTHILLDEAAQAMECETIMPLALATKNT-- 798
Cdd:cd17935     62 ALNQlfekimALDIderhllrLGHgaKIIAMTC-THAALKRGELvELGFkYDNILMEEAAQILEIETFIPLLLQNPEDgp 140

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 1958657566  799 ----RIVLAGDHMQLSPFVYS-EFARERNLHVSLLDRL 831
Cdd:cd17935    141 nrlkRLIMIGDHHQLPPVIKNmAFQKYSNMEQSLFTRL 178
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 660-814 2.12e-09

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: 57.21  E-value: 2.12e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  660 NAKQKEAVLAIttplcIQLPPVLIIGPYGTGKTFTLAQAVKHILQQQetrvyfrnrwvKTVhpvvhqycLISSahstfqm 739
Cdd:cd18043      1 DSSQEAAIISA-----RNGKNVVIQGPPGTGKSQTIANIIANALARG-----------KRV--------LFVS------- 49

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958657566  740 pQKE---DILKHRVVVVTLNT-SQYLcqlDLEPGFFTHILLDEAAQAMECETImPLALATKntRIVLAGDHMQLSPFVY 814
Cdd:cd18043     50 -EKKaalDVVRFPCWIMSPLSvSQYL---PLNRNLFDLVIFDEASQIPIEEAL-PALFRGK--QVVVVGDDKQLPPSIL 121
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 741-816 3.06e-09

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


Pssm-ID: 404072 [Multi-domain]  Cd Length: 248  Bit Score: 59.66  E-value: 3.06e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958657566  741 QKEDILKHRVVVVTLNTS--QYLCQLDlepGFFThILLDEAAQAMECETIMPLALATKntRIVLAGDHMQLSPFVYSE 816
Cdd:pfam13086  177 EREILDEAQIVCSTLSGAgsRLLSSLA---NFDV-VIIDEAAQALEPSTLIPLLRGPK--KVVLVGDPKQLPPTVISK 248
DEXXc_HELZ2-C cd18040
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 774-833 1.62e-08

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: 57.92  E-value: 1.62e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  774 ILLDEAAQAMECETIMPLALATKNTRIVLAGDHMQLSPFVYSEFARERNLHVSLLDRLYE 833
Cdd:cd18040    202 CIVDECGMCTEPESLIPIVSAPRAEQVVLIGDHKQLRPVVQNKEAQKLGLGRSLFERYAE 261
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 680-811 1.76e-07

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: 51.72  E-value: 1.76e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  680 PVLIIGPYGTGKTFTLAQAVKHILQQQETRVYfrnrwvktvhpvvhqyclissahstfqmpqkedilkhRVVVVTLnTSQ 759
Cdd:cd17914      1 LSLIQGPPGTGKTRVLVKIVAALMQNKNGEPG-------------------------------------RILLVTP-TNK 42

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1958657566  760 YLCQLDlepgfftHILLDEAAQAMECETIMPLALATKNTRIVLAGDHMQLSP 811
Cdd:cd17914     43 AAAQLD-------NILVDEAAQILEPETSRLIDLALDQGRVILVGDHDQLGP 87
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 649-1055 2.93e-07

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: 55.37  E-value: 2.93e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  649 RQWDEQLDPRLNAKQKEAV--LAITTPLCIqlppvlIIGPYGTGKTFTLAqAVKHILQQQETRVYF-------------- 712
Cdd:COG0507    115 AALEPRAGITLSDEQREAValALTTRRVSV------LTGGAGTGKTTTLR-ALLAALEALGLRVALaaptgkaakrlses 187

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  713 RNRWVKTVHPVVHqyclISSAHSTFQMPQKEDILKHRVVVVtlntsqylcqldlepgffthillDEA--------AQAME 784
Cdd:COG0507    188 TGIEARTIHRLLG----LRPDSGRFRHNRDNPLTPADLLVV-----------------------DEAsmvdtrlmAALLE 240

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  785 cetimplALATKNTRIVLAGDHMQLSP----FVYSEFARERNLHVSLLDrlyehypaefpcrillcENYRSHEAI-INYT 859
Cdd:COG0507    241 -------ALPRAGARLILVGDPDQLPSvgagAVLRDLIESGTVPVVELT-----------------EVYRQADDSrIIEL 296

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  860 SELFYEGKlMASGKQPAHKDFYPL----------------TFFTARGEDVQ-----EKnSTAFYN-------NAEVFEVV 911
Cdd:COG0507    297 AHAIREGD-APEALNARYADVVFVeaedaeeaaeaivelyADRPAGGEDIQvlaptNA-GVDALNqairealNPAGELER 374

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  912 ERVEELRRKW----PV-------AWGkLDDGSIGVVTPYADQVFRIRAELRKKRLSDVNVERVLNV-----------QGK 969
Cdd:COG0507    375 ELAEDGELELyvgdRVmftrndyDLG-VFNGDIGTVLSIDEDEGRLTVRFDGREIVTYDPSELDQLelayaitvhksQGS 453

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  970 QF-RVLFLSTvrtrhtckhkqtpikkkeqlledsteDLDYGFLSNyKLLNTAITRAQSLVAVVGDPVALCSIgrCRKFWE 1048
Cdd:COG0507    454 TFdRVILVLP--------------------------SEHSPLLSR-ELLYTALTRARELLTLVGDRDALARA--VRRDTA 504


                   ....*..
gi 1958657566 1049 RFIALCH 1055
Cdd:COG0507    505 RATGLAE 511
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 662-811 5.53e-06

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: 48.32  E-value: 5.53e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  662 KQKEAVLAITT-PLCIqlppvlIIGPYGTGKTFTLAQAVKhILQQQETRVYF--------------RNRWVKTVHPVvhq 726
Cdd:cd17933      1 EQKAAVRLVLRnRVSV------LTGGAGTGKTTTLKALLA-ALEAEGKRVVLaaptgkaakrlsesTGIEASTIHRL--- 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  727 ycLISSAHSTFQMPQKEDILKHRVVVVtlntsqylcqldlepgffthillDEAaqAMecetiMPLALATK-------NTR 799
Cdd:cd17933     71 --LGINPGGGGFYYNEENPLDADLLIV-----------------------DEA--SM-----VDTRLMAAllsaipaGAR 118

                          170
                   ....*....|..
gi 1958657566  800 IVLAGDHMQLSP 811
Cdd:cd17933    119 LILVGDPDQLPS 130
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
181-205 6.55e-06

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 44.49  E-value: 6.55e-06
                           10        20
                   ....*....|....*....|....*
gi 1958657566  181 YTLCKRFLEQGICRYGAQCTSAHSQ 205
Cdd:pfam00642    3 TELCRFFLRTGYCKYGDRCKFAHGQ 27
ResIII pfam04851
Type III restriction enzyme, res subunit;
659-779 1.65e-05

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 46.90  E-value: 1.65e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  659 LNAKQKEAVLAITTPLCIQLPPVLIIGPYGTGKTFTLAQAVKHILQQQ-ETRVYFrnrwvktvhpVVHQYCLISSAHSTF 737
Cdd:pfam04851    4 LRPYQIEAIENLLESIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGpIKKVLF----------LVPRKDLLEQALEEF 73

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  738 Q-------------MPQKEDILKH--RVVVVT---LNTSQYLCQLDLEPGFFTHILLDEA 779
Cdd:pfam04851   74 KkflpnyveigeiiSGDKKDESVDdnKIVVTTiqsLYKALELASLELLPDFFDVIIIDEA 133
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 1301-1395 8.97e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 47.77  E-value: 8.97e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566 1301 PESRPGVVYSNTKFPRKDNLNPRHINLPLPAPHTQYAIPSRHFHPLPQLPRPPFPISQQHTLLNQQQnnlPEQPNQMTPQ 1380
Cdd:PRK10263   743 PLFTPIVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQ---PVAPQPQYQQ 819

                           90
                   ....*....|....*.
gi 1958657566 1381 PNQ-VAPQPNQMAPQP 1395
Cdd:PRK10263   820 PQQpVAPQPQYQQPQQ 835
DEXQc_UvrD cd17932
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ...
 660-849 2.88e-04

DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. UvrD 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: 350690 [Multi-domain]  Cd Length: 189  Bit Score: 44.04  E-value: 2.88e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  660 NAKQKEAVLAITTPLCIqlppvlIIGPyGTGKTFTLAQAVKHILQQQETRVY------FRNR------------------ 715
Cdd:cd17932      1 NPEQREAVTHPDGPLLV------LAGA-GSGKTRVLTHRIAYLILEGGVPPErilavtFTNKaakemrerlrkllgeqla 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  716 ---WVKTVHPVvhqyCL-ISSAHSTFqmpqkEDILkHRVVVVtLNTSQYLCQLDLEPgfFTHILLDEA-----AQamecE 786
Cdd:cd17932     74 sgvWIGTFHSF----ALrILRRYGDF-----DDLL-LYALEL-LEENPDVREKLQSR--FRYILVDEYqdtnpLQ----Y 136

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958657566  787 TIMpLALATKNTRIVLAGDHMQlSpfVYSeFareRNLHVSLLDRLYEHYPAefPCRILLCENY 849
Cdd:cd17932    137 ELL-KLLAGDGKNLFVVGDDDQ-S--IYG-F---RGADPENILDFEKDFPD--AKVIKLEENY 189
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 658-811 5.58e-04

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: 42.94  E-value: 5.58e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  658 RLNAKQKEAVLAITT-PLCIQLppvlIIGPYGTGKTFTLAQAVKHILQQQetrvyfrnrwvKTVHPVvhqyclissAHST 736
Cdd:pfam13604    1 TLNAEQAAAVRALLTsGDRVAV----LVGPAGTGKTTALKALREAWEAAG-----------YRVIGL---------APTG 56

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  737 fqmpQKEDILKHRVVVVTLNTSQYLCQLDLEPGFFTH--ILLDEAAQA----MEcetiMPLALATK-NTRIVLAGDHMQL 809
Cdd:pfam13604   57 ----RAAKVLGEELGIPADTIAKLLHRLGGRAGLDPGtlLIVDEAGMVgtrqMA----RLLKLAEDaGARVILVGDPRQL 128


                   ..
gi 1958657566  810 SP 811
Cdd:pfam13604  129 PS 130
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1226-1501 6.78e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 44.76  E-value: 6.78e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566 1226 HGRGSPIPYglghhpPVNLGQPQNQHAEKDQQEQNRNGKTDTNNP-GPEINKIRTPEKKPTEPKqidlesnPQNRSPESR 1304
Cdd:pfam03154  272 HGQMPPMPH------SLQTGPSHMQHPVPPQPFPLTPQSSQSQVPpGPSPAAPGQSQQRIHTPP-------SQSQLQSQQ 338

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566 1305 PgvvysntkfPRKDNLNPRhinlPLPAPHTQyaipsrhfhPLPQLPRPPFPISQQHTLLN--------QQQNNLPEQP-- 1374
Cdd:pfam03154  339 P---------PREQPLPPA----PLSMPHIK---------PPPTTPIPQLPNPQSHKHPPhlsgpspfQMNSNLPPPPal 396

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566 1375 ----NQMTPQPNQVAPQPNQMAPQPNQMAPQPNQVVQQQNQAPPQAPQPAPQLSPAFQAGPTNAFFnnavahrPQSP--- 1447
Cdd:pfam03154  397 kplsSLSTHHPPSAHPPPLQLMPQSQQLPPPPAQPPVLTQSQSLPPPAASHPPTSGLHQVPSQSPF-------PQHPfvp 469

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958657566 1448 -AAEAVGPEQQVPPGLSDGHSPLRAITQPGPILASPLNNFVDESSPGLPI-EEALD 1501
Cdd:pfam03154  470 gGPPPITPPSGPPTSTSSAMPGIQPPSSASVSSSGPVPAAVSCPLPPVQIkEEALD 525
UvrD COG0210
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
658-706 7.05e-04

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


Pssm-ID: 439980 [Multi-domain]  Cd Length: 721  Bit Score: 44.54  E-value: 7.05e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1958657566  658 RLNAKQKEAVLAITTPLciqlppvLII-GPyGTGKTFTLAQAVKHILQQQ 706
Cdd:COG0210      6 GLNPEQRAAVEHPEGPL-------LVLaGA-GSGKTRVLTHRIAYLIAEG 47
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 682-779 1.73e-03

DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs 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: 350790 [Multi-domain]  Cd Length: 163  Bit Score: 41.01  E-value: 1.73e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  682 LIIGPYGTGKTFTLAQAVKHILQQqetrvyfrnRWVKTVHPVVHQYCLISSAHSTFQMP-----------QKEDILKHRV 750
Cdd:cd18032     24 LLVMATGTGKTYTAAFLIKRLLEA---------NRKKRILFLAHREELLEQAERSFKEVlpdgsfgnlkgGKKKPDDARV 94

                           90       100       110
                   ....*....|....*....|....*....|
gi 1958657566  751 VVVTLNTSQYLCQLD-LEPGFFTHILLDEA 779
Cdd:cd18032     95 VFATVQTLNKRKRLEkFPPDYFDLIIIDEA 124
UvrD-helicase pfam00580
UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural ...
 659-705 2.69e-03

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: 41.85  E-value: 2.69e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1958657566  659 LNAKQKEAVLAITTPLciqlppvLIIGPYGTGKTFTLAQAVKHILQQ 705
Cdd:pfam00580    1 LNPEQRKAVTHLGGPL-------LVLAGAGSGKTRVLTERIAYLILE 40
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
654-779 2.95e-03

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 42.32  E-value: 2.95e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  654 QLDPRLNAKQKEAVLAITTPLCIQLPPVLIIGPYGTGKTFTLAQAVKHILQQQETRVyfrnrwvktvhpVVHQYCLISSA 733
Cdd:COG1061     76 GTSFELRPYQQEALEALLAALERGGGRGLVVAPTGTGKTVLALALAAELLRGKRVLV------------LVPRRELLEQW 143

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1958657566  734 HSTFQM-------PQKEDILKHRVVVVTLNTSQYLCQLDLEPGFFTHILLDEA 779
Cdd:COG1061    144 AEELRRflgdplaGGGKKDSDAPITVATYQSLARRAHLDELGDRFGLVIIDEA 196
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
 1313-1398 4.09e-03

Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide.


Pssm-ID: 197891 [Multi-domain]  Cd Length: 165  Bit Score: 40.16  E-value: 4.09e-03
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566  1313 KFPRKDNLNPRHINLPLPAPHTqyAIPSRHFHP-LPQLPRPPFpisqqhtllnQQQNNLPEQPNQMTPQPNQVAPQPNQM 1391
Cdd:smart00818   60 VLPAQQPVVPQQPLMPVPGQHS--MTPTQHHQPnLPQPAQQPF----------QPQPLQPPQPQQPMQPQPPVHPIPPLP 127


                    ....*..
gi 1958657566  1392 APQPNQM 1398
Cdd:smart00818  128 PQPPLPP 134
dnaA PRK14086
chromosomal replication initiator protein DnaA;
1279-1482 6.18e-03

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 41.35  E-value: 6.18e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566 1279 TPEKKPTEPKQIDLESNPQNRSPESRPGVVYSNTKFPRKDNLNPRHINLPLPAPhtqyAIPSRHFHPLP-QLPRPPFPIS 1357
Cdd:PRK14086    91 SAGEPAPPPPHARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQDQLPTARP----AYPAYQQRPEPgAWPRAADDYG 166

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657566 1358 QQHTLLNQQQNNLPEQPNQMTPQPNQVAPQPNQMAPQPNQMAPQPNQvvqqqnqappqapqpapqlsPAFQAGPTNAFFN 1437
Cdd:PRK14086   167 WQQQRLGFPPRAPYASPASYAPEQERDREPYDAGRPEYDQRRRDYDH--------------------PRPDWDRPRRDRT 226

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1958657566 1438 NavahRPQ-SPAAEAVGPEQQVPPGLSDGHSPLRAITQPGPILASP 1482
Cdd:PRK14086   227 D----RPEpPPGAGHVHRGGPGPPERDDAPVVPIRPSAPGPLAAQP 268
 
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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