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Conserved domains on  [gi|1622955504|ref|XP_014999116|]
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Fanconi anemia group M protein isoform X3 [Macaca mulatta]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEXDc_FANCM cd18033
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ...
 89-270 3.93e-119

DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. In complex with CENPS and CENPX, it binds double-stranded DNA (dsDNA), fork-structured DNA (fsDNA), and Holliday junction substrates. Its ATP-dependent DNA branch migration activity can process branched DNA structures such as a movable replication fork. This activity is strongly stimulated in the presence of CENPS and CENPX. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, it strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA. FANCM 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: 350791 [Multi-domain]  Cd Length: 182  Bit Score: 373.58  E-value: 3.93e-119
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   89 CPVRDYQLHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEM 168
Cdd:cd18033      1 VPLRDYQFTIVQKALFQNTLVALPTGLGKTFIAAVVMLNYYRWFPKGKIVFMAPTKPLVSQQIEACYKITGIPSSQTAEL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  169 TGSTQAFTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYCQVVRELVKYTNHFRILALSATP 248
Cdd:cd18033     81 TGSVPPTKRAELWASKRVFFLTPQTLENDLKEGDCDPKSIVCLVIDEAHRATGNYAYCQVVRELMRYNSHFRILALTATP 160

                          170       180
                   ....*....|....*....|..
gi 1622955504  249 GSDIKAVQQVITNLLIGQIELR 270
Cdd:cd18033    161 GSKLEAVQQVIDNLLISHIEIR 182
MPH1 super family cl34113
ERCC4-related helicase [Replication, recombination and repair];
92-528 8.21e-83

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


The actual alignment was detected with superfamily member COG1111:

Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 288.94  E-value: 8.21e-83
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   92 RDYQLHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRWfPSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEMTGS 171
Cdd:COG1111      5 RLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAERLHK-KGGKVLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFTGE 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  172 TQAFTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYCQVVRELVKYTNHFRILALSATPGSD 251
Cdd:COG1111     84 VSPEKRKELWEKARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKDPLILGMTASPGSD 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  252 IKAVQQVITNLLIGQIELRSEDSPDILAYSYERKIEKLIVPLGEELAAIQKTYIQILESFAHSLIQRNVLMRRDiPNLTK 331
Cdd:COG1111    164 EEKIEEVCENLGIENVEVRTEEDPDVAPYVHDTEVEWIRVELPEELKEIRDLLNEVLDDRLKKLKELGVIVSTS-PDLSK 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  332 YQIILARDQ-FRKNPSPNIVGIQQGVIegeFAICISLYHGYELLQQMGMRSLYFFLCGIMDGTKGMTRSK--NELGRNED 408
Cdd:COG1111    243 KDLLALQKKlQRRIREDDSEGYRAISI---LAEALKLRHALELLETQGVEALLRYLERLEEEARSSGGSKasKRLVSDPR 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  409 FMKLYNHLEcmfahtrstsadsvsaiqqgdknkKFVYSHPKLKKLEEVVIEHFKswnaentsekKRDETRVMIFSSFRDS 488
Cdd:COG1111    320 FRKAMRLAE------------------------EADIEHPKLSKLREILKEQLG----------TNPDSRIIVFTQYRDT 365

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|
gi 1622955504  489 VQEIAEMLSQhqPIIRVMTFVGHASGKSTKGFTQKEQLEI 528
Cdd:COG1111    366 AEMIVEFLSE--PGIKAGRFVGQASKEGDKGLTQKEQIEI 403
XPF_nuclease_FANCM cd20077
XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also ...
 1751-1889 5.07e-74

XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also called Fanconi anemia-associated polypeptide of 250 kDa (FAAP250), or protein Hef ortholog, or ATP-dependent RNA helicase FANCM, is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. In complex with CENPS and CENPX, it binds double-stranded DNA (dsDNA), fork-structured DNA (fsDNA) and Holliday junction substrates. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, FANCM strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA.


:

Pssm-ID: 410853 [Multi-domain]  Cd Length: 139  Bit Score: 242.56  E-value: 5.07e-74
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1751 TCILVGGHEITSGLEVISSLRAIHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSINKNKLIEQIQHLQSMFERICVI 1830
Cdd:cd20077      1 LVILVDSREISSGQEVISSLRIKHGIKVEVCQLGGCDYIVSNRMGVERKSLSEFANGSNRSKLVERIQHLCDLYDRPCLI 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1622955504 1831 VEKDREKTGDASRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKN 1889
Cdd:cd20077     81 IEKDRVKPGETSRIFHRTKYYDSTLAALAQAGVRVLFSDSQEETARLLADLAQLEQRKN 139
FANCM-MHF_bd pfam16783
FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia ...
 606-721 5.61e-62

FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia complementation group protein M that binds to a two-histone-fold-containing protein complex MHF. MHF binds double-strand DNA, stimulates the DNA-binding activity of FANCM, and contributes to the targeting of FANCM to chromatin.


:

Pssm-ID: 465270  Cd Length: 116  Bit Score: 207.21  E-value: 5.61e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  606 KKDWFLSEEEFKLWNRLYRLRDSDEIKEITLPQVQFSSLQNEESKPTQESATGIRQLSLSEWRLWQDHPLPTHQVDHSDR 685
Cdd:pfam16783    1 KSDGFLSEEEFELWNRLYRLEEDDIKKEPTLPRSQFTTLPNEETPPKPEPGAARRELSLSEWRHWQNRPLPTHVVDHSDR 80

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1622955504  686 CRHFIGLMQMIEGMRHEEGECSYKLEVESYLQMEDV 721
Cdd:pfam16783   81 CLHFIAVMEMIELMRQEEDECSYELELKPYLQMEDV 116
 
Name Accession Description Interval E-value
DEXDc_FANCM cd18033
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ...
 89-270 3.93e-119

DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. In complex with CENPS and CENPX, it binds double-stranded DNA (dsDNA), fork-structured DNA (fsDNA), and Holliday junction substrates. Its ATP-dependent DNA branch migration activity can process branched DNA structures such as a movable replication fork. This activity is strongly stimulated in the presence of CENPS and CENPX. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, it strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA. FANCM 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: 350791 [Multi-domain]  Cd Length: 182  Bit Score: 373.58  E-value: 3.93e-119
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   89 CPVRDYQLHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEM 168
Cdd:cd18033      1 VPLRDYQFTIVQKALFQNTLVALPTGLGKTFIAAVVMLNYYRWFPKGKIVFMAPTKPLVSQQIEACYKITGIPSSQTAEL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  169 TGSTQAFTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYCQVVRELVKYTNHFRILALSATP 248
Cdd:cd18033     81 TGSVPPTKRAELWASKRVFFLTPQTLENDLKEGDCDPKSIVCLVIDEAHRATGNYAYCQVVRELMRYNSHFRILALTATP 160

                          170       180
                   ....*....|....*....|..
gi 1622955504  249 GSDIKAVQQVITNLLIGQIELR 270
Cdd:cd18033    161 GSKLEAVQQVIDNLLISHIEIR 182
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
92-528 8.21e-83

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 288.94  E-value: 8.21e-83
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   92 RDYQLHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRWfPSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEMTGS 171
Cdd:COG1111      5 RLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAERLHK-KGGKVLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFTGE 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  172 TQAFTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYCQVVRELVKYTNHFRILALSATPGSD 251
Cdd:COG1111     84 VSPEKRKELWEKARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKDPLILGMTASPGSD 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  252 IKAVQQVITNLLIGQIELRSEDSPDILAYSYERKIEKLIVPLGEELAAIQKTYIQILESFAHSLIQRNVLMRRDiPNLTK 331
Cdd:COG1111    164 EEKIEEVCENLGIENVEVRTEEDPDVAPYVHDTEVEWIRVELPEELKEIRDLLNEVLDDRLKKLKELGVIVSTS-PDLSK 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  332 YQIILARDQ-FRKNPSPNIVGIQQGVIegeFAICISLYHGYELLQQMGMRSLYFFLCGIMDGTKGMTRSK--NELGRNED 408
Cdd:COG1111    243 KDLLALQKKlQRRIREDDSEGYRAISI---LAEALKLRHALELLETQGVEALLRYLERLEEEARSSGGSKasKRLVSDPR 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  409 FMKLYNHLEcmfahtrstsadsvsaiqqgdknkKFVYSHPKLKKLEEVVIEHFKswnaentsekKRDETRVMIFSSFRDS 488
Cdd:COG1111    320 FRKAMRLAE------------------------EADIEHPKLSKLREILKEQLG----------TNPDSRIIVFTQYRDT 365

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|
gi 1622955504  489 VQEIAEMLSQhqPIIRVMTFVGHASGKSTKGFTQKEQLEI 528
Cdd:COG1111    366 AEMIVEFLSE--PGIKAGRFVGQASKEGDKGLTQKEQIEI 403
XPF_nuclease_FANCM cd20077
XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also ...
 1751-1889 5.07e-74

XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also called Fanconi anemia-associated polypeptide of 250 kDa (FAAP250), or protein Hef ortholog, or ATP-dependent RNA helicase FANCM, is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. In complex with CENPS and CENPX, it binds double-stranded DNA (dsDNA), fork-structured DNA (fsDNA) and Holliday junction substrates. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, FANCM strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA.


Pssm-ID: 410853 [Multi-domain]  Cd Length: 139  Bit Score: 242.56  E-value: 5.07e-74
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1751 TCILVGGHEITSGLEVISSLRAIHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSINKNKLIEQIQHLQSMFERICVI 1830
Cdd:cd20077      1 LVILVDSREISSGQEVISSLRIKHGIKVEVCQLGGCDYIVSNRMGVERKSLSEFANGSNRSKLVERIQHLCDLYDRPCLI 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1622955504 1831 VEKDREKTGDASRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKN 1889
Cdd:cd20077     81 IEKDRVKPGETSRIFHRTKYYDSTLAALAQAGVRVLFSDSQEETARLLADLAQLEQRKN 139
PRK13766 PRK13766
Hef nuclease; Provisional
 92-528 1.75e-65

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 239.00  E-value: 1.75e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   92 RDYQLHISRAALFCNTLVCLPTGLGKTFIAAVVM-YNFYRwfPSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEMTG 170
Cdd:PRK13766    17 RLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIaERLHK--KGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTG 94

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  171 STQAFTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYCQVVRELVKYTNHFRILALSATPGS 250
Cdd:PRK13766    95 EVSPEKRAELWEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKNPLVLGLTASPGS 174

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  251 DIKAVQQVITNLLIGQIELRSEDSPDILAYSYERKIEKLIVPLGEELAAIQKTYIQILESFAHSLIQRNVLmRRDIPNLT 330
Cdd:PRK13766   175 DEEKIKEVCENLGIEHVEVRTEDDPDVKPYVHKVKIEWVRVELPEELKEIRDLLNEALKDRLKKLKELGVI-VSISPDVS 253

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  331 KYQIILARDQFRKNpspnivgIQQGVIEGEFAI-----CISLYHGYELLQQMGMRSL--YFFLCGIMDGTKGMTRSKNEL 403
Cdd:PRK13766   254 KKELLGLQKKLQQE-------IANDDSEGYEAIsilaeAMKLRHAVELLETQGVEALrrYLERLREEARSSGGSKASKRL 326

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  404 GRNEDFMKLYNHLecmfahtrstsadsvsaiqqgdknKKFVYSHPKLKKLEEVVIEHFkswnaentseKKRDETRVMIFS 483
Cdd:PRK13766   327 VEDPRFRKAVRKA------------------------KELDIEHPKLEKLREIVKEQL----------GKNPDSRIIVFT 372

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*
gi 1622955504  484 SFRDSVQEIAEMLSQHQpiIRVMTFVGHASGKSTKGFTQKEQLEI 528
Cdd:PRK13766   373 QYRDTAEKIVDLLEKEG--IKAVRFVGQASKDGDKGMSQKEQIEI 415
FANCM-MHF_bd pfam16783
FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia ...
 606-721 5.61e-62

FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia complementation group protein M that binds to a two-histone-fold-containing protein complex MHF. MHF binds double-strand DNA, stimulates the DNA-binding activity of FANCM, and contributes to the targeting of FANCM to chromatin.


Pssm-ID: 465270  Cd Length: 116  Bit Score: 207.21  E-value: 5.61e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  606 KKDWFLSEEEFKLWNRLYRLRDSDEIKEITLPQVQFSSLQNEESKPTQESATGIRQLSLSEWRLWQDHPLPTHQVDHSDR 685
Cdd:pfam16783    1 KSDGFLSEEEFELWNRLYRLEEDDIKKEPTLPRSQFTTLPNEETPPKPEPGAARRELSLSEWRHWQNRPLPTHVVDHSDR 80

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1622955504  686 CRHFIGLMQMIEGMRHEEGECSYKLEVESYLQMEDV 721
Cdd:pfam16783   81 CLHFIAVMEMIELMRQEEDECSYELELKPYLQMEDV 116
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 441-544 3.04e-34

C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 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: 350188 [Multi-domain]  Cd Length: 143  Bit Score: 129.01  E-value: 3.04e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  441 KKFVYSHPKLKKLEEVVIEHFKSWNAentsekkRDETRVMIFSSFRDSVQEIAEMLSQHQPIIRVMTFVGHASGKSTKGF 520
Cdd:cd18801      2 RKVEKIHPKLEKLEEIVKEHFKKKQE-------GSDTRVIIFSEFRDSAEEIVNFLSKIRPGIRATRFIGQASGKSSKGM 74

                           90       100
                   ....*....|....*....|....
gi 1622955504  521 TQKEQLEIYNQSQSNKRNICKAIS 544
Cdd:cd18801     75 SQKEQKEVIEQFRKGGYNVLVATS 98
DEXDc smart00487
DEAD-like helicases superfamily;
90-264 4.47e-25

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 104.88  E-value: 4.47e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504    90 PVRDYQLHISRAALFC--NTLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACYQVMG-IPQSHMA 166
Cdd:smart00487    8 PLRPYQKEAIEALLSGlrDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPsLGLKVVG 87

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   167 EMTG-STQAFTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYCQVVRELVKYTNHFRILALS 245
Cdd:smart00487   88 LYGGdSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLS 167

                           170
                    ....*....|....*....
gi 1622955504   246 ATPGSDIKAVQQVITNLLI 264
Cdd:smart00487  168 ATPPEEIENLLELFLNDPV 186
ResIII pfam04851
Type III restriction enzyme, res subunit;
88-248 1.63e-20

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 90.42  E-value: 1.63e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   88 NCPVRDYQLHISRAALFC------NTLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACYQVMGIP 161
Cdd:pfam04851    1 KLELRPYQIEAIENLLESikngqkRGLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPRKDLLEQALEEFKKFLPNY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  162 QSHMAEMTGSTQAFTRKEIwcskRVLFLTPQVMVNDLSRGACPAA--EIKCLVIDEAHKALGNyAYcqvvRELVKYTNHF 239
Cdd:pfam04851   81 VEIGEIISGDKKDESVDDN----KIVVTTIQSLYKALELASLELLpdFFDVIIIDEAHRSGAS-SY----RNILEYFKPA 151


                   ....*....
gi 1622955504  240 RILALSATP 248
Cdd:pfam04851  152 FLLGLTATP 160
MUS81 COG1948
ERCC4-type crossover junction endonuclease [Replication, recombination and repair];
1775-1960 1.06e-18

ERCC4-type crossover junction endonuclease [Replication, recombination and repair];


Pssm-ID: 441551 [Multi-domain]  Cd Length: 214  Bit Score: 86.77  E-value: 1.06e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1775 GLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSINKNKLIEQIQHLQSMFERICVIVEkdrektGD---ASRMFRRTKSY 1851
Cdd:COG1948     23 GVEVRVKTLEVGDYVVSDRVAVERKTVRDFVNSLIDGRLFEQASRLAEAYERPVLIIE------GDllyEERNIHPNAIR 96

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1852 DSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKNVGIHVPTVVNSSKS-EALQFYL--SIPNISYITALNMCHQFS 1928
Cdd:COG1948     97 GALASLALDFGIPVLPTRDAEDTAELLVTLARREQEEEKREVSLHGKKKPKTlREQQLYVveSLPGIGPKLARRLLEHFG 176

                          170       180       190
                   ....*....|....*....|....*....|..
gi 1622955504 1929 SVKRMANSTPQEISMYAQVTHQKAEEIYRYIH 1960
Cdd:COG1948    177 SVEAVFNASEEELMKVEGIGEKTAERIREVLD 208
PRK13766 PRK13766
Hef nuclease; Provisional
 1753-1959 4.85e-16

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 84.54  E-value: 4.85e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1753 ILVGGHEITSGleVISSLRAIhGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSINKNKLIEQIQHLQSMFERICVIVE 1832
Cdd:PRK13766   565 IIVDSRELRSN--VARHLKRL-GAEVELKTLEVGDYVVSDRVAVERKTAEDFVDSIIDRRLFEQVKDLKRAYERPVLIIE 641

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1833 kdrektGD--ASRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKN---VGIHvptvvnSSKS---- 1903
Cdd:PRK13766   642 ------GDlyTIRNIHPNAIRGALASIAVDFGIPILFTRDEEETADLLKVIAKREQEEEkreVSVH------GEKKamtl 709

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1622955504 1904 EALQFYL--SIPNISYITALNMCHQFSSVKRMANSTPQEISMYAQVTHQKAEEIYRYI 1959
Cdd:PRK13766   710 KEQQEYIveSLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVV 767
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
92-248 7.89e-14

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 76.60  E-value: 7.89e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   92 RDYQ------LHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRwfpSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHm 165
Cdd:COG1061     82 RPYQqealeaLLAALERGGGRGLVVAPTGTGKTVLALALAAELLR---GKRVLVLVPRRELLEQWAEELRRFLGDPLAG- 157

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  166 aemtgstqaFTRKEIWCskRVLFLTPQVMVNDLSRGACPAAeIKCLVIDEAHKALGNyaycqVVRELVKYTNHFRILALS 245
Cdd:COG1061    158 ---------GGKKDSDA--PITVATYQSLARRAHLDELGDR-FGLVIIDEAHHAGAP-----SYRRILEAFPAAYRLGLT 220


                   ...
gi 1622955504  246 ATP 248
Cdd:COG1061    221 ATP 223
ERCC4 pfam02732
ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an ...
 1774-1881 1.00e-12

ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.


Pssm-ID: 426945 [Multi-domain]  Cd Length: 139  Bit Score: 67.07  E-value: 1.00e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1774 HGLQVEVCPLNGCDYIVSNR-----------MVVERRSQSEMLNSINKNKLIEQIQHLQSMFERICVIVE---KDREKTG 1839
Cdd:pfam02732   18 LGVEVVVETLPVGDYLWVPReydlelevvldVIVERKSLDDLVSSIIDGRLFEQKSRLKRGYKKPILLVEgldLFSRKLK 97

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1622955504 1840 DASRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKEL 1881
Cdd:pfam02732   98 NKRRDINPNAIEGALASLQVDYGVRIIRTRSAEETAEWLASL 139
ERCC4 smart00891
ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, ...
 1752-1832 1.13e-12

ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases, and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases.


Pssm-ID: 214888 [Multi-domain]  Cd Length: 98  Bit Score: 65.83  E-value: 1.13e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  1752 CILVGGHEITSGLE--VISSLRAIHGLQVEVCPLNGCDYIVSNR-------------MVVERRSQSEMLNSINKNKLIEQ 1816
Cdd:smart00891    1 EIIVDSRELRSALEapIPRSLRWKRGVKVEYDRLEAGDFVLVARdkqsllphvnslnELVERKSLTDLVASIPDGRLFEQ 80

                            90
                    ....*....|....*..
gi 1622955504  1817 IQHL-QSMFERICVIVE 1832
Cdd:smart00891   81 VRRLqQIAYPSPQLLVE 97
rad1 TIGR00596
DNA repair protein (rad1); All proteins in this family for which functions are known are ...
 1723-1960 7.94e-10

DNA repair protein (rad1); All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombinational repair in some species. Most Archaeal species also have homologs of these genes, but the function of these Archaeal genes is not known, so we have set our cutoff to only pick up the eukaryotic genes.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273163 [Multi-domain]  Cd Length: 814  Bit Score: 64.06  E-value: 7.94e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1723 ASGASSSNSRphlagtHTSLRLPQEGKET-CILVGGHEITSGLeviSSLRAIHGLQVEVCPLNGCDYIVSNRMVVERRSQ 1801
Cdd:TIGR00596  564 ISKLRKSKTR------NAGGQLGFANLTQpKVIVDMREFRSSL---PSLLHRRGIRVIPCMLTVGDYILTPDICVERKSI 634

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1802 SEMLNSINKNKLIEQIQHLQSMFERICVIVEKDREKT------GDAS---RMFRRTKSYDSLLTTLIGAGIRILFSSCQE 1872
Cdd:TIGR00596  635 SDLIGSLNNGRLYNQCEKMLRYYAYPVLLIEFDQNKSfsleprNDLSqeiSSVNNDIQQKLALLTLHFPKLRIIWSSSPY 714

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1873 ETADLLKELSLVEQRKN------VGIHVPTVVNSSK--SEALQFYLSIPNISYITALNMCHQFSSVKRMANSTPQEISMY 1944
Cdd:TIGR00596  715 ATAEIFEELKLGKEEPDpataaaLGSDENTTAEGLKfnDGPQDFLLKLPGVTKKNYRNLRKKVKSIRELAKLSQNELNEL 794

                          250
                   ....*....|....*.
gi 1622955504 1945 AQvTHQKAEEIYRYIH 1960
Cdd:TIGR00596  795 IG-DEEAAKRLYDFLR 809
PRK00254 PRK00254
ski2-like helicase; Provisional
 106-250 1.17e-04

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 47.12  E-value: 1.17e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  106 NTLVCLPTGLGKTFIAAVVMYN-FYRwfPSGKVVFMAPTKPLVTQQIEAC--YQVMGIpqsHMAEMTGStqaFTRKEIWC 182
Cdd:PRK00254    41 NLVLAIPTASGKTLVAEIVMVNkLLR--EGGKAVYLVPLKALAEEKYREFkdWEKLGL---RVAMTTGD---YDSTDEWL 112

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622955504  183 SK-RVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHkALGNY---AYCQVVreLVKYTNHFRILALSATPGS 250
Cdd:PRK00254   113 GKyDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIH-LIGSYdrgATLEMI--LTHMLGRAQILGLSATVGN 181
 
Name Accession Description Interval E-value
DEXDc_FANCM cd18033
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ...
 89-270 3.93e-119

DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. In complex with CENPS and CENPX, it binds double-stranded DNA (dsDNA), fork-structured DNA (fsDNA), and Holliday junction substrates. Its ATP-dependent DNA branch migration activity can process branched DNA structures such as a movable replication fork. This activity is strongly stimulated in the presence of CENPS and CENPX. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, it strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA. FANCM 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: 350791 [Multi-domain]  Cd Length: 182  Bit Score: 373.58  E-value: 3.93e-119
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   89 CPVRDYQLHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEM 168
Cdd:cd18033      1 VPLRDYQFTIVQKALFQNTLVALPTGLGKTFIAAVVMLNYYRWFPKGKIVFMAPTKPLVSQQIEACYKITGIPSSQTAEL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  169 TGSTQAFTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYCQVVRELVKYTNHFRILALSATP 248
Cdd:cd18033     81 TGSVPPTKRAELWASKRVFFLTPQTLENDLKEGDCDPKSIVCLVIDEAHRATGNYAYCQVVRELMRYNSHFRILALTATP 160

                          170       180
                   ....*....|....*....|..
gi 1622955504  249 GSDIKAVQQVITNLLIGQIELR 270
Cdd:cd18033    161 GSKLEAVQQVIDNLLISHIEIR 182
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
92-528 8.21e-83

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 288.94  E-value: 8.21e-83
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   92 RDYQLHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRWfPSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEMTGS 171
Cdd:COG1111      5 RLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAERLHK-KGGKVLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFTGE 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  172 TQAFTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYCQVVRELVKYTNHFRILALSATPGSD 251
Cdd:COG1111     84 VSPEKRKELWEKARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKDPLILGMTASPGSD 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  252 IKAVQQVITNLLIGQIELRSEDSPDILAYSYERKIEKLIVPLGEELAAIQKTYIQILESFAHSLIQRNVLMRRDiPNLTK 331
Cdd:COG1111    164 EEKIEEVCENLGIENVEVRTEEDPDVAPYVHDTEVEWIRVELPEELKEIRDLLNEVLDDRLKKLKELGVIVSTS-PDLSK 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  332 YQIILARDQ-FRKNPSPNIVGIQQGVIegeFAICISLYHGYELLQQMGMRSLYFFLCGIMDGTKGMTRSK--NELGRNED 408
Cdd:COG1111    243 KDLLALQKKlQRRIREDDSEGYRAISI---LAEALKLRHALELLETQGVEALLRYLERLEEEARSSGGSKasKRLVSDPR 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  409 FMKLYNHLEcmfahtrstsadsvsaiqqgdknkKFVYSHPKLKKLEEVVIEHFKswnaentsekKRDETRVMIFSSFRDS 488
Cdd:COG1111    320 FRKAMRLAE------------------------EADIEHPKLSKLREILKEQLG----------TNPDSRIIVFTQYRDT 365

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|
gi 1622955504  489 VQEIAEMLSQhqPIIRVMTFVGHASGKSTKGFTQKEQLEI 528
Cdd:COG1111    366 AEMIVEFLSE--PGIKAGRFVGQASKEGDKGLTQKEQIEI 403
XPF_nuclease_FANCM cd20077
XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also ...
 1751-1889 5.07e-74

XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also called Fanconi anemia-associated polypeptide of 250 kDa (FAAP250), or protein Hef ortholog, or ATP-dependent RNA helicase FANCM, is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. In complex with CENPS and CENPX, it binds double-stranded DNA (dsDNA), fork-structured DNA (fsDNA) and Holliday junction substrates. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, FANCM strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA.


Pssm-ID: 410853 [Multi-domain]  Cd Length: 139  Bit Score: 242.56  E-value: 5.07e-74
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1751 TCILVGGHEITSGLEVISSLRAIHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSINKNKLIEQIQHLQSMFERICVI 1830
Cdd:cd20077      1 LVILVDSREISSGQEVISSLRIKHGIKVEVCQLGGCDYIVSNRMGVERKSLSEFANGSNRSKLVERIQHLCDLYDRPCLI 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1622955504 1831 VEKDREKTGDASRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKN 1889
Cdd:cd20077     81 IEKDRVKPGETSRIFHRTKYYDSTLAALAQAGVRVLFSDSQEETARLLADLAQLEQRKN 139
PRK13766 PRK13766
Hef nuclease; Provisional
 92-528 1.75e-65

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 239.00  E-value: 1.75e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   92 RDYQLHISRAALFCNTLVCLPTGLGKTFIAAVVM-YNFYRwfPSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEMTG 170
Cdd:PRK13766    17 RLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIaERLHK--KGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTG 94

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  171 STQAFTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYCQVVRELVKYTNHFRILALSATPGS 250
Cdd:PRK13766    95 EVSPEKRAELWEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKNPLVLGLTASPGS 174

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  251 DIKAVQQVITNLLIGQIELRSEDSPDILAYSYERKIEKLIVPLGEELAAIQKTYIQILESFAHSLIQRNVLmRRDIPNLT 330
Cdd:PRK13766   175 DEEKIKEVCENLGIEHVEVRTEDDPDVKPYVHKVKIEWVRVELPEELKEIRDLLNEALKDRLKKLKELGVI-VSISPDVS 253

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  331 KYQIILARDQFRKNpspnivgIQQGVIEGEFAI-----CISLYHGYELLQQMGMRSL--YFFLCGIMDGTKGMTRSKNEL 403
Cdd:PRK13766   254 KKELLGLQKKLQQE-------IANDDSEGYEAIsilaeAMKLRHAVELLETQGVEALrrYLERLREEARSSGGSKASKRL 326

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  404 GRNEDFMKLYNHLecmfahtrstsadsvsaiqqgdknKKFVYSHPKLKKLEEVVIEHFkswnaentseKKRDETRVMIFS 483
Cdd:PRK13766   327 VEDPRFRKAVRKA------------------------KELDIEHPKLEKLREIVKEQL----------GKNPDSRIIVFT 372

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*
gi 1622955504  484 SFRDSVQEIAEMLSQHQpiIRVMTFVGHASGKSTKGFTQKEQLEI 528
Cdd:PRK13766   373 QYRDTAEKIVDLLEKEG--IKAVRFVGQASKDGDKGMSQKEQIEI 415
FANCM-MHF_bd pfam16783
FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia ...
 606-721 5.61e-62

FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia complementation group protein M that binds to a two-histone-fold-containing protein complex MHF. MHF binds double-strand DNA, stimulates the DNA-binding activity of FANCM, and contributes to the targeting of FANCM to chromatin.


Pssm-ID: 465270  Cd Length: 116  Bit Score: 207.21  E-value: 5.61e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  606 KKDWFLSEEEFKLWNRLYRLRDSDEIKEITLPQVQFSSLQNEESKPTQESATGIRQLSLSEWRLWQDHPLPTHQVDHSDR 685
Cdd:pfam16783    1 KSDGFLSEEEFELWNRLYRLEEDDIKKEPTLPRSQFTTLPNEETPPKPEPGAARRELSLSEWRHWQNRPLPTHVVDHSDR 80

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1622955504  686 CRHFIGLMQMIEGMRHEEGECSYKLEVESYLQMEDV 721
Cdd:pfam16783   81 CLHFIAVMEMIELMRQEEDECSYELELKPYLQMEDV 116
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 92-270 2.55e-45

DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350685 [Multi-domain]  Cd Length: 201  Bit Score: 162.99  E-value: 2.55e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   92 RDYQLHISRAAL-FCNTLVCLPTGLGKTFIAAVVMYNFYRWFPS---GKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAE 167
Cdd:cd17927      4 RNYQLELAQPALkGKNTIICLPTGSGKTFVAVLICEHHLKKFPAgrkGKVVFLANKVPLVEQQKEVFRKHFERPGYKVTG 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  168 MTGSTQAFTR-KEIWCSKRVLFLTPQVMVNDLSRGACPAAE-IKCLVIDEAHKALGNYAYCQVVRELVKYTNH-----FR 240
Cdd:cd17927     84 LSGDTSENVSvEQIVESSDVIIVTPQILVNDLKSGTIVSLSdFSLLVFDECHNTTKNHPYNEIMFRYLDQKLGssgplPQ 163

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 1622955504  241 ILALSATPGSD--------IKAVQQVITNLLIGQIELR 270
Cdd:cd17927    164 ILGLTASPGVGgaknteeaLEHICKLCANLDISVIATV 201
XPF_nuclease-like cd19940
nuclease domain of XPF/MUS81 family proteins; The XPF/MUS81 family belongs to 3'-flap ...
 1752-1883 1.66e-40

nuclease domain of XPF/MUS81 family proteins; The XPF/MUS81 family belongs to 3'-flap endonuclease that act upon 3'-flap structures and involved in DNA repair pathways that are necessary for the removal of UV-light-induced DNA lesions and cross-links between DNA strands. Family members exist either as heterodimers or as homodimers in their functionally competent states which consist of a catalytic and a noncatalytic subunit. The catalytic subunits have a DX(n)RKX(3)D motif. This motif is required for metal-dependent endonuclease activity but not for DNA junction binding. The equivalent regions of the noncatalytic subunits (ERCC1, EME1, and FAAP24) have diverged. The noncatalytic subunits have roles such as binding ssDNA or an ability to target the endonuclease to defined DNA structures or sites of DNA damage.


Pssm-ID: 410849 [Multi-domain]  Cd Length: 126  Bit Score: 146.37  E-value: 1.66e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1752 CILVGGHEITSglEVISSLRAIhGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSINKNKLIEQIQHLQSMFERICVIV 1831
Cdd:cd19940      1 SIVVDPRERRS--ELLSELQRL-GVQVEFEDLAVGDYVLSNRTCVERKSLSDLVSSINKGRLREQLQRLTRKFERRVLLV 77

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1622955504 1832 EKDREKTgdasRMFRRTKSYDSLLTTLIG-AGIRILFSSCQEETADLLKELSL 1883
Cdd:cd19940     78 EKDRSKF----RSMVSSVQALSALTKLQLlTGIRLLIVASPKETADLLEELTQ 126
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 92-271 8.76e-39

DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef 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: 350793 [Multi-domain]  Cd Length: 181  Bit Score: 143.42  E-value: 8.76e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   92 RDYQLHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRWFpSGKVVFMAPTKPLVTQQIEACYQVMGIPQShMAEMTGS 171
Cdd:cd18035      4 RLYQVLIAAVALNGNTLIVLPTGLGKTIIAILVAADRLTKK-GGKVLILAPSRPLVEQHAENLKRVLNIPDK-ITSLTGE 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  172 TQAFTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYCQVVRELVKYTNHFRILALSATPGSD 251
Cdd:cd18035     82 VKPEERAERWDASKIIVATPQVIENDLLAGRITLDDVSLLIFDEAHHAVGNYAYVYIAHRYKREANNPLILGLTASPGSD 161

                          170       180
                   ....*....|....*....|
gi 1622955504  252 IKAVQQVITNLLIGQIELRS 271
Cdd:cd18035    162 KEKIMEICENLGIEHIEIKT 181
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 441-544 3.04e-34

C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 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: 350188 [Multi-domain]  Cd Length: 143  Bit Score: 129.01  E-value: 3.04e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  441 KKFVYSHPKLKKLEEVVIEHFKSWNAentsekkRDETRVMIFSSFRDSVQEIAEMLSQHQPIIRVMTFVGHASGKSTKGF 520
Cdd:cd18801      2 RKVEKIHPKLEKLEEIVKEHFKKKQE-------GSDTRVIIFSEFRDSAEEIVNFLSKIRPGIRATRFIGQASGKSSKGM 74

                           90       100
                   ....*....|....*....|....
gi 1622955504  521 TQKEQLEIYNQSQSNKRNICKAIS 544
Cdd:cd18801     75 SQKEQKEVIEQFRKGGYNVLVATS 98
FANCM_ID cd12091
Insert domain of FANCM and related proteins; FANCM and related proteins, like Mph1 and Fml1, ...
 298-413 2.85e-32

Insert domain of FANCM and related proteins; FANCM and related proteins, like Mph1 and Fml1, are DNA junction-specific helicases/translocases that bind to and process perturbed replication forks and intermediates of homologous recombination. FANCM contains an N-terminal superfamily 2 helicase (SF2) domain, although FANCM, in contrast to other members of this family, does not exhibit DNA helicase activity. The SF2 helicase domain is comprised of 3 structural domains, the 2 generally conserved helicase domains and a helical domain inserted between the two domains. FANCM is a component of the Fanconi anaemia (FA) core complex. FA is a rare genetic disease in humans that is associated with progressive bone marrow failure, a variety of developmental abnormalities, and a high incidence of cancer. A key role of this complex is to monoubiquitination of FANCD2 and FANCI during S-phase and in response to DNA damage. The role of FANCM during this process seems to be the recruitment of the complex to chromatin.


Pssm-ID: 277190 [Multi-domain]  Cd Length: 116  Bit Score: 122.40  E-value: 2.85e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  298 AAIQKTYIQILESFAHSLIQRNVLMRRDIPNLTKYQIILARDQFRKNPSPNIVGiQQGVIEGEFAICISLYHGYELLQQM 377
Cdd:cd12091      1 TEIRDLLAKVLEPFLKRLNQAGILPNRDPAKLSPFRLLQARDKFRANPPGNNEG-QKGSIEGDFALLISLAHAMELLLEH 79

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1622955504  378 GMRSLYFFLCGIMDGTKG-MTRSKNELGRNEDFMKLY 413
Cdd:cd12091     80 GIRPFYDYLKEIKDETKAkGSKSKKELAKNPNFKALM 116
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 92-268 1.53e-29

DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer 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: 350792 [Multi-domain]  Cd Length: 200  Bit Score: 117.75  E-value: 1.53e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   92 RDYQLHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRWF----PSGK-VVFMAPTKPLVTQQIEA-----CYQVMGIp 161
Cdd:cd18034      4 RSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNrkekNPKKrAVFLVPTVPLVAQQAEAirshtDLKVGEY- 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  162 qsHMAEMTGSTQAFTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYCQVVRELVKYTNHF-- 239
Cdd:cd18034     83 --SGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMKEFYHLEGRTsr 160

                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 1622955504  240 -RILALSATP---GSDIKAVQ---QVITNLLIGQIE 268
Cdd:cd18034    161 pRILGLTASPvngKGDPKSVEkkiQQLEELLNSTIK 196
DEXDc smart00487
DEAD-like helicases superfamily;
90-264 4.47e-25

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 104.88  E-value: 4.47e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504    90 PVRDYQLHISRAALFC--NTLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACYQVMG-IPQSHMA 166
Cdd:smart00487    8 PLRPYQKEAIEALLSGlrDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPsLGLKVVG 87

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   167 EMTG-STQAFTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYCQVVRELVKYTNHFRILALS 245
Cdd:smart00487   88 LYGGdSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLS 167

                           170
                    ....*....|....*....
gi 1622955504   246 ATPGSDIKAVQQVITNLLI 264
Cdd:smart00487  168 ATPPEEIENLLELFLNDPV 186
XPF_ERCC4_MUS81-like cd22367
XPF family DNA repair endonuclease; (Xeroderma Pigmentosum group F) DNA repair gene homologs ...
 1753-1878 2.76e-23

XPF family DNA repair endonuclease; (Xeroderma Pigmentosum group F) DNA repair gene homologs are members of the XPF/Rad1/Mus81-dependent nuclease family which specifically cleave branched structures generated during DNA repair, replication, and recombination, and they are essential for maintaining genome stability. They belong to a wider superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411771 [Multi-domain]  Cd Length: 123  Bit Score: 96.95  E-value: 2.76e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1753 ILVGGHEITSGLEVISSLraiHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSINKNKLIEQIQHLQSMFERICVIVE 1832
Cdd:cd22367      1 IVVDSRERRSGLPELLRK---LGVRVEVRTLEVGDYILSADIIVERKTVSDLISSIIDGRLFEQAERLKRSYERPILLIE 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1622955504 1833 KDREKtgdASRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLL 1878
Cdd:cd22367     78 GDPDK---ARRLVRPAALGAAISSLLVIGGLLVLRTPNFETTALLL 120
ResIII pfam04851
Type III restriction enzyme, res subunit;
88-248 1.63e-20

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 90.42  E-value: 1.63e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   88 NCPVRDYQLHISRAALFC------NTLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACYQVMGIP 161
Cdd:pfam04851    1 KLELRPYQIEAIENLLESikngqkRGLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPRKDLLEQALEEFKKFLPNY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  162 QSHMAEMTGSTQAFTRKEIwcskRVLFLTPQVMVNDLSRGACPAA--EIKCLVIDEAHKALGNyAYcqvvRELVKYTNHF 239
Cdd:pfam04851   81 VEIGEIISGDKKDESVDDN----KIVVTTIQSLYKALELASLELLpdFFDVIIIDEAHRSGAS-SY----RNILEYFKPA 151


                   ....*....
gi 1622955504  240 RILALSATP 248
Cdd:pfam04851  152 FLLGLTATP 160
MUS81 COG1948
ERCC4-type crossover junction endonuclease [Replication, recombination and repair];
1775-1960 1.06e-18

ERCC4-type crossover junction endonuclease [Replication, recombination and repair];


Pssm-ID: 441551 [Multi-domain]  Cd Length: 214  Bit Score: 86.77  E-value: 1.06e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1775 GLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSINKNKLIEQIQHLQSMFERICVIVEkdrektGD---ASRMFRRTKSY 1851
Cdd:COG1948     23 GVEVRVKTLEVGDYVVSDRVAVERKTVRDFVNSLIDGRLFEQASRLAEAYERPVLIIE------GDllyEERNIHPNAIR 96

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1852 DSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKNVGIHVPTVVNSSKS-EALQFYL--SIPNISYITALNMCHQFS 1928
Cdd:COG1948     97 GALASLALDFGIPVLPTRDAEDTAELLVTLARREQEEEKREVSLHGKKKPKTlREQQLYVveSLPGIGPKLARRLLEHFG 176

                          170       180       190
                   ....*....|....*....|....*....|..
gi 1622955504 1929 SVKRMANSTPQEISMYAQVTHQKAEEIYRYIH 1960
Cdd:COG1948    177 SVEAVFNASEEELMKVEGIGEKTAERIREVLD 208
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 92-249 2.78e-18

DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350794 [Multi-domain]  Cd Length: 204  Bit Score: 85.22  E-value: 2.78e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   92 RDYQLHISRAALFC-NTLVCLPTGLGKTFIAAVVMYNFYRWFPS----GKVVFMAPTKPLVTQQIEA-------CYQVMG 159
Cdd:cd18036      4 RNYQLELVLPALRGkNTIICAPTGSGKTRVAVYICRHHLEKRRSagekGRVVVLVNKVPLVEQQLEKffkyfrkGYKVTG 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  160 IPQSHmaemtgSTQAFTRKEIWCSKrVLFLTPQVMVNDLSRGACPA----AEIKCLVIDEAHKALGNYAYCQVVRELVKY 235
Cdd:cd18036     84 LSGDS------SHKVSFGQIVKASD-VIICTPQILINNLLSGREEErvylSDFSLLIFDECHHTQKEHPYNKIMRMYLDK 156

                          170
                   ....*....|....*....
gi 1622955504  236 TNHFR-----ILALSATPG 249
Cdd:cd18036    157 KLSSQgplpqILGLTASPG 175
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 106-255 1.75e-17

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 81.91  E-value: 1.75e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  106 NTLVCLPTGLGKTFIAAVVMYN-FYRWFPSGKVVFMAPTKPLVTQQIEACYQVM-GIPQSHMAEMTGSTQAFTRKEIwCS 183
Cdd:pfam00270   16 DVLVQAPTGSGKTLAFLLPALEaLDKLDNGPQALVLAPTRELAEQIYEELKKLGkGLGLKVASLLGGDSRKEQLEKL-KG 94

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1622955504  184 KRVLFLTPQvMVNDLSRGACPAAEIKCLVIDEAHKaLGNYAYCQVVRELVKYTN-HFRILALSATPGSDIKAV 255
Cdd:pfam00270   95 PDILVGTPG-RLLDLLQERKLLKNLKLLVLDEAHR-LLDMGFGPDLEEILRRLPkKRQILLLSATLPRNLEDL 165
XPF_nuclease_XPF_arch cd20075
nuclease domain of XPF found in archaea; XPF, also called DNA excision repair protein ERCC-4, ...
 1765-1881 6.32e-17

nuclease domain of XPF found in archaea; XPF, also called DNA excision repair protein ERCC-4, or DNA repair protein complementing XP-F cells, or Xeroderma pigmentosum group F-complementing protein, is a 3'-flap repair endonuclease that cleaves 5' of ds/ssDNA interfaces in 3' flap structures, although it also cuts bubble, Y-DNA structures and mobile and immobile Holliday junctions. XPF cuts preferentially after pyrimidines, may continue to progressively cleave substrate upstream of the initial cleavage, at least in vitro. It may be involved in nucleotide excision repair. The nuclease domains of the catalytic subunits XPF have the GDX(n)ERKX(3)D motif which is required for metal-dependent endonuclease activity but not for DNA junction binding. XPF-ERRC1 and its yeast homolog Rad1-Rad10 play key roles in the excision of DNA lesions and are required for certain types of homologous recombination events and for the repair of DNA cross-links.


Pssm-ID: 410851 [Multi-domain]  Cd Length: 127  Bit Score: 78.97  E-value: 6.32e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1765 EVISSLRAiHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSINKNKLIEQIQHLQSMFERICVIVEkdrektGDASRM 1844
Cdd:cd20075     12 GVVRELKE-LGVEVEFKQLEVGDYIVSDRVAIERKTVDDFVSSIIDGRLFDQAKRLKEAYEKPILIIE------GDLLYL 84

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1622955504 1845 FRRTKS---YDSLLTTLIGAGIRILFSSCQEETADLLKEL 1881
Cdd:cd20075     85 KRRIHPnaiRGALASIALDFGIPIIFTKDPEETAELLYSL 124
DEXHc_RIG-I_DDX58 cd18073
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ...
 92-228 8.48e-17

DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called DEAD box protein 58 (DDX58), is a pathogen-recognition receptor that recognizes viral 5'-triphosphates carrying double-stranded RNA. Upon binding to these microbe-associated molecular patterns (MAMPs), RIG-I forms oligomers and promotes downstream processes that result in type I interferon production and induction of an antiviral state. The optimal ligand for RIG-I has been found to be base-paired or double-stranded RNA (dsRNA) molecules containing a 5' triphosphate (5'-ppp-dsRNA). RIG-I contains two N-terminal caspase activation and recruitment domains (CARDs), which are required for interaction with IPS-1, a superfamily 2 helicase/translocase/ATPase (SF2) domain and a C-terminal regulatory/repressor domain (RD). RIG-I 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: 350831 [Multi-domain]  Cd Length: 202  Bit Score: 81.02  E-value: 8.48e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   92 RDYQLHISRAALFC-NTLVCLPTGLGKTFIAAVVMYNFYRWFPSG---KVVFMAPTKPLVTQQIEACYQVMGIPQSHMAE 167
Cdd:cd18073      4 RNYQLELALPAMKGkNTIICAPTGCGKTFVSLLICEHHLKKFPQGqkgKVVFFATKVPVYEQQKSVFSKYFERHGYRVTG 83

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1622955504  168 MTGST-QAFTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVI-DEAHKALGNYAYCQV 228
Cdd:cd18073     84 ISGATaENVPVEQIIENNDIIILTPQILVNNLKKGTIPSLSIFTLMIfDECHNTSGNHPYNMI 146
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 92-248 1.44e-16

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: 79.14  E-value: 1.44e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   92 RDYQ------LHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACYQVMgiPQSHM 165
Cdd:cd18032      2 RYYQqeaieaLEEAREKGQRRALLVMATGTGKTYTAAFLIKRLLEANRKKRILFLAHREELLEQAERSFKEVL--PDGSF 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  166 AEMTGSTQAFTrkeiwcSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKAL-GNYaycqvvRELVKYTNHFRILAL 244
Cdd:cd18032     80 GNLKGGKKKPD------DARVVFATVQTLNKRKRLEKFPPDYFDLIIIDEAHHAIaSSY------RKILEYFEPAFLLGL 147


                   ....
gi 1622955504  245 SATP 248
Cdd:cd18032    148 TATP 151
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 106-247 2.43e-16

DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350679 [Multi-domain]  Cd Length: 181  Bit Score: 78.84  E-value: 2.43e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  106 NTLVCLPTGLGKTFIAAVVMYNfyRWFPSG-KVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEMTGSTQAFTRKEIwcSK 184
Cdd:cd17921     19 SVLVSAPTSSGKTLIAELAILR--ALATSGgKAVYIAPTRALVNQKEADLRERFGPLGKNVGLLTGDPSVNKLLLA--EA 94

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622955504  185 RVLFLTPQVMVNDLSRGACPAAE-IKCLVIDEAHKaLGNYAYCQVVRELVKYTN----HFRILALSAT 247
Cdd:cd17921     95 DILVATPEKLDLLLRNGGERLIQdVRLVVVDEAHL-IGDGERGVVLELLLSRLLrinkNARFVGLSAT 161
PRK13766 PRK13766
Hef nuclease; Provisional
 1753-1959 4.85e-16

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 84.54  E-value: 4.85e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1753 ILVGGHEITSGleVISSLRAIhGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSINKNKLIEQIQHLQSMFERICVIVE 1832
Cdd:PRK13766   565 IIVDSRELRSN--VARHLKRL-GAEVELKTLEVGDYVVSDRVAVERKTAEDFVDSIIDRRLFEQVKDLKRAYERPVLIIE 641

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1833 kdrektGD--ASRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKN---VGIHvptvvnSSKS---- 1903
Cdd:PRK13766   642 ------GDlyTIRNIHPNAIRGALASIAVDFGIPILFTRDEEETADLLKVIAKREQEEEkreVSVH------GEKKamtl 709

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1622955504 1904 EALQFYL--SIPNISYITALNMCHQFSSVKRMANSTPQEISMYAQVTHQKAEEIYRYI 1959
Cdd:PRK13766   710 KEQQEYIveSLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVV 767
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
92-248 7.89e-14

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 76.60  E-value: 7.89e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   92 RDYQ------LHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRwfpSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHm 165
Cdd:COG1061     82 RPYQqealeaLLAALERGGGRGLVVAPTGTGKTVLALALAAELLR---GKRVLVLVPRRELLEQWAEELRRFLGDPLAG- 157

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  166 aemtgstqaFTRKEIWCskRVLFLTPQVMVNDLSRGACPAAeIKCLVIDEAHKALGNyaycqVVRELVKYTNHFRILALS 245
Cdd:COG1061    158 ---------GGKKDSDA--PITVATYQSLARRAHLDELGDR-FGLVIIDEAHHAGAP-----SYRRILEAFPAAYRLGLT 220


                   ...
gi 1622955504  246 ATP 248
Cdd:COG1061    221 ATP 223
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 106-247 2.82e-13

N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 68.97  E-value: 2.82e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  106 NTLVCLPTGLGKTFIAAVVMYNFYRWFPsGKVVFMAPTKPLVTQQIEAcYQVMGIPQSHMAEMTGSTQAFTR-KEIWCSK 184
Cdd:cd00046      3 NVLITAPTGSGKTLAALLAALLLLLKKG-KKVLVLVPTKALALQTAER-LRELFGPGIRVAVLVGGSSAEEReKNKLGDA 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622955504  185 RVLFLTPQVMVNDLSRGACP-AAEIKCLVIDEAHKALGNYAY----CQVVRELVKYTNhfRILALSAT 247
Cdd:cd00046     81 DIIIATPDMLLNLLLREDRLfLKDLKLIIVDEAHALLIDSRGalilDLAVRKAGLKNA--QVILLSAT 146
ERCC4 pfam02732
ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an ...
 1774-1881 1.00e-12

ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.


Pssm-ID: 426945 [Multi-domain]  Cd Length: 139  Bit Score: 67.07  E-value: 1.00e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1774 HGLQVEVCPLNGCDYIVSNR-----------MVVERRSQSEMLNSINKNKLIEQIQHLQSMFERICVIVE---KDREKTG 1839
Cdd:pfam02732   18 LGVEVVVETLPVGDYLWVPReydlelevvldVIVERKSLDDLVSSIIDGRLFEQKSRLKRGYKKPILLVEgldLFSRKLK 97

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1622955504 1840 DASRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKEL 1881
Cdd:pfam02732   98 NKRRDINPNAIEGALASLQVDYGVRIIRTRSAEETAEWLASL 139
ERCC4 smart00891
ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, ...
 1752-1832 1.13e-12

ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases, and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases.


Pssm-ID: 214888 [Multi-domain]  Cd Length: 98  Bit Score: 65.83  E-value: 1.13e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  1752 CILVGGHEITSGLE--VISSLRAIHGLQVEVCPLNGCDYIVSNR-------------MVVERRSQSEMLNSINKNKLIEQ 1816
Cdd:smart00891    1 EIIVDSRELRSALEapIPRSLRWKRGVKVEYDRLEAGDFVLVARdkqsllphvnslnELVERKSLTDLVASIPDGRLFEQ 80

                            90
                    ....*....|....*..
gi 1622955504  1817 IQHL-QSMFERICVIVE 1832
Cdd:smart00891   81 VRRLqQIAYPSPQLLVE 97
rad1 TIGR00596
DNA repair protein (rad1); All proteins in this family for which functions are known are ...
 1723-1960 7.94e-10

DNA repair protein (rad1); All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombinational repair in some species. Most Archaeal species also have homologs of these genes, but the function of these Archaeal genes is not known, so we have set our cutoff to only pick up the eukaryotic genes.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273163 [Multi-domain]  Cd Length: 814  Bit Score: 64.06  E-value: 7.94e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1723 ASGASSSNSRphlagtHTSLRLPQEGKET-CILVGGHEITSGLeviSSLRAIHGLQVEVCPLNGCDYIVSNRMVVERRSQ 1801
Cdd:TIGR00596  564 ISKLRKSKTR------NAGGQLGFANLTQpKVIVDMREFRSSL---PSLLHRRGIRVIPCMLTVGDYILTPDICVERKSI 634

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1802 SEMLNSINKNKLIEQIQHLQSMFERICVIVEKDREKT------GDAS---RMFRRTKSYDSLLTTLIGAGIRILFSSCQE 1872
Cdd:TIGR00596  635 SDLIGSLNNGRLYNQCEKMLRYYAYPVLLIEFDQNKSfsleprNDLSqeiSSVNNDIQQKLALLTLHFPKLRIIWSSSPY 714

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1873 ETADLLKELSLVEQRKN------VGIHVPTVVNSSK--SEALQFYLSIPNISYITALNMCHQFSSVKRMANSTPQEISMY 1944
Cdd:TIGR00596  715 ATAEIFEELKLGKEEPDpataaaLGSDENTTAEGLKfnDGPQDFLLKLPGVTKKNYRNLRKKVKSIRELAKLSQNELNEL 794

                          250
                   ....*....|....*.
gi 1622955504 1945 AQvTHQKAEEIYRYIH 1960
Cdd:TIGR00596  795 IG-DEEAAKRLYDFLR 809
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 92-248 1.22e-09

DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 58.47  E-value: 1.22e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   92 RDYQLHISRAALFCNT----LVCLPTGLGKTFIAAVVMynFYRWfpSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAE 167
Cdd:cd17926      2 RPYQEEALEAWLAHKNnrrgILVLPTGSGKTLTALALI--AYLK--ELRTLIVVPTDALLDQWKERFEDFLGDSSIGLIG 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  168 mTGSTQAFTRKEIwcskrvLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHK--ALGNyaycqvvRELVKYTNHFRILALS 245
Cdd:cd17926     78 -GGKKKDFDDANV------VVATYQSLSNLAEEEKDLFDQFGLLIVDEAHHlpAKTF-------SEILKELNAKYRLGLT 143


                   ...
gi 1622955504  246 ATP 248
Cdd:cd17926    144 ATP 146
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
106-247 1.86e-09

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 62.61  E-value: 1.86e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  106 NTLVCLPTGLGKTFIAAVVMYNfyRWFPSGKVVFMAPTKPLVTQ---QIEACYQVMGIpqshmaEMTGSTQAFTRKEIWC 182
Cdd:COG1204     40 NLVVSAPTASGKTLIAELAILK--ALLNGGKALYIVPLRALASEkyrEFKRDFEELGI------KVGVSTGDYDSDDEWL 111

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622955504  183 SKR-VLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKaLGNYAycqvvR----ELV----KYTNH-FRILALSAT 247
Cdd:COG1204    112 GRYdILVATPEKLDSLLRNGPSWLRDVDLVVVDEAHL-IDDES-----RgptlEVLlarlRRLNPeAQIVALSAT 180
DEXHc_ASCC3_1 cd18020
N-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ...
 106-247 8.27e-07

N-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; Activating signal cointegrator 1 complex subunit 3 (ASCC3) is a type II DEAD box helicase that plays a role in the repair of N-alkylated nucleotides. ASCC3 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350778 [Multi-domain]  Cd Length: 199  Bit Score: 51.66  E-value: 8.27e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  106 NTLVCLPTGLGKTFIAAVVMYNFYRWF--PSG-------KVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEMTGSTQaFT 176
Cdd:cd18020     19 NMLICAPTGAGKTNIAMLTILHEIRQHvnQGGvikkddfKIVYIAPMKALAAEMVEKFSKRLAPLGIKVKELTGDMQ-LT 97

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  177 RKEIwCSKRVLFLTPQ---VMVNDLSRGACPAAEIKCLVIDEAH---KALGNYAYCQVVREL--VKYTNHF-RILALSAT 247
Cdd:cd18020     98 KKEI-AETQIIVTTPEkwdVVTRKSSGDVALSQLVRLLIIDEVHllhDDRGPVIESLVARTLrqVESTQSMiRIVGLSAT 176
DEXHc_RecQ cd17920
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ...
 92-247 2.10e-06

DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box helicase superfamily is a family of highly conserved DNA repair helicases. This domain contains the ATP-binding region.


Pssm-ID: 350678 [Multi-domain]  Cd Length: 200  Bit Score: 50.61  E-value: 2.10e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   92 RDYQLHISRAAL-FCNTLVCLPTGLGKTfiaavVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACyQVMGIPqshMAEMTG 170
Cdd:cd17920     14 RPGQLEAINAVLaGRDVLVVMPTGGGKS-----LCYQLPALLLDGVTLVVSPLISLMQDQVDRL-QQLGIR---AAALNS 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  171 STQAFTRKEIWCSK-----RVLFLTP----QVMVNDLSRGACPAAEIKCLVIDEAH-------------KALGnyaycqv 228
Cdd:cd17920     85 TLSPEEKREVLLRIkngqyKLLYVTPerllSPDFLELLQRLPERKRLALIVVDEAHcvsqwghdfrpdyLRLG------- 157

                          170
                   ....*....|....*....
gi 1622955504  229 vrELVKYTNHFRILALSAT 247
Cdd:cd17920    158 --RLRRALPGVPILALTAT 174
DEXHc_DDX60 cd18025
DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an ...
 107-250 4.75e-06

DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an IFN-inducible cytoplasmic helicase that plays a role in RIG-I-mediated type I interferon (IFN) nuclease-mediated viral RNA degradation. DDX60 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350783 [Multi-domain]  Cd Length: 192  Bit Score: 49.29  E-value: 4.75e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  107 TLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQqieACYQVMGIPQSHMAEMTGS-----TQAFtRKEIW 181
Cdd:cd18025     19 ALIVAPTSSGKTFISYYCMEKVLRESDDGVVVYVAPTKALVNQ---VVAEVYARFSKKYPPSGKSlwgvfTRDY-RHNNP 94

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1622955504  182 CSKRVLFLTPQV---MVndLSRGacPAA---EIKCLVIDEAHK--ALGNYAycqvVRELVKYTNHFRILALSATPGS 250
Cdd:cd18025     95 MNCQVLITVPECleiLL--LSPH--NASwvpRIKYVIFDEIHSigQSEDGA----VWEQLLLLIPCPFLALSATIGN 163
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
 106-249 5.67e-06

DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350786 [Multi-domain]  Cd Length: 177  Bit Score: 48.87  E-value: 5.67e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  106 NTLVCLPTGLGKTFIAAVVMYNFyrWFPSGKVVFMAPTKPLVTQQIE--ACYQVMGIpqshmaEMTGSTQAFTRKEIWCS 183
Cdd:cd18028     19 NLLISIPTASGKTLIAEMAMVNT--LLEGGKALYLVPLRALASEKYEefKKLEEIGL------KVGISTGDYDEDDEWLG 90

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1622955504  184 KRVLFLTPQVMVNDLSR-GACPAAEIKCLVIDEAHkALGNYAYCQVVRELVKYTNHF----RILALSATPG 249
Cdd:cd18028     91 DYDIIVATYEKFDSLLRhSPSWLRDVGVVVVDEIH-LISDEERGPTLESIVARLRRLnpntQIIGLSATIG 160
XPF_nuclease_XPF_euk cd20078
nuclease domain of XPF found in eukaryotes; XPF, also called DNA excision repair protein ...
 1774-1881 1.11e-05

nuclease domain of XPF found in eukaryotes; XPF, also called DNA excision repair protein ERCC-4, or DNA repair protein complementing XP-F cells, or Xeroderma pigmentosum group F-complementing protein, is a DNA repair endonuclease that is a catalytic component of a structure-specific DNA repair endonuclease responsible for the 5-prime incision during DNA repair. It is involved in homologous recombination that assists in removing interstrand cross-link. The nuclease domains of the catalytic subunits XPF have the GDX(n)ERKX(3)D motif which is required for metal-dependent endonuclease activity but not for DNA junction binding. XPF-ERRC1 and its yeast homolog Rad1-Rad10 play key roles in the excision of DNA lesions and are required for certain types of homologous recombination events and for the repair of DNA cross-links.


Pssm-ID: 410854 [Multi-domain]  Cd Length: 136  Bit Score: 46.71  E-value: 1.11e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504 1774 HGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSINKNKLIEQIQHLQSMFERICVIVEKDREKTG--DASRMFRRTKSY 1851
Cdd:cd20078     20 AGIDLIPVTLEVGDYILSPDICVERKSISDLISSLNSGRLYTQLEAMCRYYKHPILLIEFDENKPFslQSKSSLSSEISS 99

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1622955504 1852 DSL---LTTLIGA--GIRILFSSCQEETADLLKEL 1881
Cdd:cd20078    100 NSLiskLVLLLLHfpKLRIIWSRSPHFTAELFREL 134
DEXHc_RLR-2 cd18074
DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma ...
 91-249 1.49e-05

DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma differentiation-associated protein 5 or Mda5 and IFIH1) is a viral double-stranded RNA (dsRNA) receptor that shares sequence similarity and signaling pathways with RIG-I, yet plays essential functions in antiviral immunity through distinct specificity for viral RNA. RLR-2 recognizes the internal duplex structure, whereas RIG-I recognizes the terminus of dsRNA. RLR-2 uses direct protein-protein contacts to stack along dsRNA in a head-to-tail arrangement. The signaling domain (tandem CARD), which decorates the outside of the core RLR-2 filament, also has an intrinsic propensity to oligomerize into an elongated structure that activates the signaling adaptor, MAVS. RLR-2 uses long dsRNA as a signaling platform to cooperatively assemble the core filament, which in turn promotes stochastic assembly of the tandem CARD oligomers for signaling. LGP2 appears to positively and negatively regulate RLR-2 and RIG-I signaling, respectively. RLR-2 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: 350832 [Multi-domain]  Cd Length: 216  Bit Score: 48.32  E-value: 1.49e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   91 VRDYQLHISRAALFC-NTLVCLPTGLGKTFIAAVVMYNFY----RWFPSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHM 165
Cdd:cd18074      3 LRDYQMEVAKPALEGkNIIICLPTGSGKTRVAVYITKDHLdkkrKASEPGKVIVLVNKVPLVEQHYRKEFNPFLKHWYQV 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  166 AEMTGSTQ---AFTrkEIWCSKRVLFLTPQVMVNDLSRGA------CPAAEIKCLVIDEAHKALGNYAYCQVVRELVKYT 236
Cdd:cd18074     83 IGLSGDSQlkiSFP--EVVKRYDVIICTAQILENSLLNATeeedegVQLSDFSLIIIDECHHTQKEAVYNNIMRRYLKQK 160

                          170       180
                   ....*....|....*....|....*..
gi 1622955504  237 NHFR--------------ILALSATPG 249
Cdd:cd18074    161 IKNRkqkkenkpliplpqILGLTASPG 187
DEXHc_ASCC3_2 cd18022
C-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ...
 105-170 1.52e-05

C-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; Activating signal cointegrator 1 complex subunit 3 (ASCC3) is a type II DEAD box helicase that plays a role in the repair of N-alkylated nucleotides. ASCC3 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350780 [Multi-domain]  Cd Length: 189  Bit Score: 47.75  E-value: 1.52e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  105 CNTLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACYQ----VMGIpqsHMAEMTG 170
Cdd:cd18022     18 NNVLLGAPTGSGKTIAAELAMFRAFNKYPGSKVVYIAPLKALVRERVDDWKKrfeeKLGK---KVVELTG 84
DEXHc_RLR-3 cd18075
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ...
 91-250 3.23e-05

DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of genetics and physiology 2 or LGP2 and DHX58) appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. RLR-3 resembles a chimera combining a MDA5-like helicase domain and RIG-I like CTD supporting both stem and end binding. RNA binding is required for RLR-3-mediated enhancement of MDA5 activation. RLR-3 end-binding may promote nucleation of MDA5 oligomerization on dsRNA. RLR-3 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: 350833 [Multi-domain]  Cd Length: 200  Bit Score: 46.77  E-value: 3.23e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   91 VRDYQLHISRAALFC-NTLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACYQVMgIPQSHMAEMT 169
Cdd:cd18075      3 LHGYQWEVVAPALRGkNSIIWLPTGAGKTRAAVYVARRHLETKRGAKVAVLVNKVHLVDQHLEKEFHVL-LDKYTVTAIS 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  170 GST--QAFTRKEIWCSKrVLFLTPQVMVNDLSRGACPA----AEIKCLVIDEAHKALGNYAYCQVV-----RELVKYTNH 238
Cdd:cd18075     82 GDSshKCFFGQLARGSD-VVICTAQILQNALLSGEEEAhvelTDFSLLVIDECHHTHKEAVYNKIMlsyleKKLSRQGDL 160

                          170
                   ....*....|..
gi 1622955504  239 FRILALSATPGS 250
Cdd:cd18075    161 PQILGLTASPGT 172
PRK00254 PRK00254
ski2-like helicase; Provisional
 106-250 1.17e-04

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 47.12  E-value: 1.17e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  106 NTLVCLPTGLGKTFIAAVVMYN-FYRwfPSGKVVFMAPTKPLVTQQIEAC--YQVMGIpqsHMAEMTGStqaFTRKEIWC 182
Cdd:PRK00254    41 NLVLAIPTASGKTLVAEIVMVNkLLR--EGGKAVYLVPLKALAEEKYREFkdWEKLGL---RVAMTTGD---YDSTDEWL 112

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622955504  183 SK-RVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHkALGNY---AYCQVVreLVKYTNHFRILALSATPGS 250
Cdd:PRK00254   113 GKyDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIH-LIGSYdrgATLEMI--LTHMLGRAQILGLSATVGN 181
DEXHc_HFM1 cd18023
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ...
 106-217 2.80e-04

DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box helicase, required for crossover formation and complete synapsis of homologous chromosomes during meiosis. HFM1 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350781 [Multi-domain]  Cd Length: 206  Bit Score: 44.27  E-value: 2.80e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  106 NTLVCLPTGLGKTFIAAVVMYNFYRWFPSG-----KVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEMTGSTQAFTRKEI 180
Cdd:cd18023     19 NFVVSAPTGSGKTVLFELAILRLLKERNPLpwgnrKVVYIAPIKALCSEKYDDWKEKFGPLGLSCAELTGDTEMDDTFEI 98

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1622955504  181 WcSKRVLFLTPQ---VMVNDLSRGACPAAEIKCLVIDEAH 217
Cdd:cd18023     99 Q-DADIILTTPEkwdSMTRRWRDNGNLVQLVALVLIDEVH 137
DEXHc_Brr2_1 cd18019
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD ...
 95-247 7.91e-04

N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD box helicase that mediates spliceosome catalytic activation. It is a stable subunit of the spliceosome, required during splicing catalysis and spliceosome disassembly. Brr2 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350777 [Multi-domain]  Cd Length: 214  Bit Score: 43.13  E-value: 7.91e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504   95 QLHISRAALFC--NTLVCLPTGLGKTFIAAVVM-------YNfyrwfPSG-------KVVFMAPTKPLVTQQIE------ 152
Cdd:cd18019     22 QSKLFPAAFETdeNLLLCAPTGAGKTNVALLTIlreigkhRN-----PDGtinldafKIVYIAPMKALVQEMVGnfskrl 96

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  153 ACYqvmGIpqsHMAEMTGSTQaFTRKEIwCSKRVLFLTPQVMvNDLSRGACPAAE---IKCLVIDEA---HKALGNYAYC 226
Cdd:cd18019     97 APY---GI---TVAELTGDQQ-LTKEQI-SETQIIVTTPEKW-DIITRKSGDRTYtqlVRLIIIDEIhllHDDRGPVLES 167

                          170       180
                   ....*....|....*....|....
gi 1622955504  227 QVVREL--VKYTNHF-RILALSAT 247
Cdd:cd18019    168 IVARTIrqIEQTQEYvRLVGLSAT 191
DEAD-like_helicase_N cd17912
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 106-149 1.02e-03

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.


Pssm-ID: 350670 [Multi-domain]  Cd Length: 81  Bit Score: 39.81  E-value: 1.02e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1622955504  106 NTLVCLPTGLGKTFIAavVMYNFYRWFPSGKVVFMAPTKPLVTQ 149
Cdd:cd17912      1 NILHLGPTGSGKTLVA--IQKIASAMSSGKSVLVVTPTKLLAHE 42
DEXHc_LHR-like cd17922
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ...
 106-250 2.80e-03

DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases from the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350680 [Multi-domain]  Cd Length: 166  Bit Score: 40.64  E-value: 2.80e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  106 NTLVCLPTGLGKTFiaAVVMYNFYRWF----PSGKVVFMAPTKPLVTQQ---IEACYQVMGIPQSHmAEMTGSTQAFTRK 178
Cdd:cd17922      3 NVLIAAPTGSGKTE--AAFLPALSSLAdepeKGVQVLYISPLKALINDQerrLEEPLDEIDLEIPV-AVRHGDTSQSEKA 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622955504  179 EIwcSKR---VLFLTP---QVMVNdlSRGACPA-AEIKCLVIDEAHKALGN----YAYCQVVReLVKYT-NHFRILALSA 246
Cdd:cd17922     80 KQ--LKNppgILITTPeslELLLV--NKKLRELfAGLRYVVVDEIHALLGSkrgvQLELLLER-LRKLTgRPLRRIGLSA 154


                   ....
gi 1622955504  247 TPGS 250
Cdd:cd17922    155 TLGN 158
DEXHc_Brr2_2 cd18021
C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type ...
 106-152 7.53e-03

C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD box helicase that mediates spliceosome catalytic activation. It is a stable subunit of the spliceosome, required during splicing catalysis and spliceosome disassembly. Brr2 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350779 [Multi-domain]  Cd Length: 191  Bit Score: 39.55  E-value: 7.53e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1622955504  106 NTLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIE 152
Cdd:cd18021     21 NVFVGAPTGSGKTVCAELALLRHWRQNPKGRAVYIAPMQELVDARYK 67
 
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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