NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|815890934|ref|NP_001295062|]
View 

Fanconi anemia group M protein isoform 2 [Homo sapiens]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
MPH1 super family cl34113
ERCC4-related helicase [Replication, recombination and repair];
92-593 5.70e-105

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: 354.04  E-value: 5.70e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   92 RDYQLHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRWfPSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEMTGS 171
Cdd:COG1111     5 RLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAERLHK-KGGKVLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFTGE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  172 TQASTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYC------------------------- 226
Cdd:COG1111    84 VSPEKRKELWEKARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVyiaeryhedakdplilgmtaspgsd 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  227 -QAVQQVITNLLIGQIELRSEDSPDILTYSHERKVEKLIVPLGEELAAIQKTYIQILESFARSLIQRNVLMRRDiPNLTK 305
Cdd:COG1111   164 eEKIEEVCENLGIENVEVRTEEDPDVAPYVHDTEVEWIRVELPEELKEIRDLLNEVLDDRLKKLKELGVIVSTS-PDLSK 242

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  306 YQIILARDQfrknpspnivgIQQGIIEGEF---------AICISLYHGYELLQQMGMRSLYFFLCGIMDGTKGMTRSK-- 374
Cdd:COG1111   243 KDLLALQKK-----------LQRRIREDDSegyraisilAEALKLRHALELLETQGVEALLRYLERLEEEARSSGGSKas 311

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  375 NELGRNEDFMKlynhlecmfARTRSTSANGisaiqqgdknkkfvySHPKLKKLEEVViehfkswnaENTTEKKRDEtRVM 454
Cdd:COG1111   312 KRLVSDPRFRK---------AMRLAEEADI---------------EHPKLSKLREIL---------KEQLGTNPDS-RII 357

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  455 IFSSFRDSVQEIAEMLSQhqPIIRVMTFVGHASGKSTKGFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLIIC 534
Cdd:COG1111   358 VFTQYRDTAEMIVEFLSE--PGIKAGRFVGQASKEGDKGLTQKEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIF 435

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  535 FDSQKSPIRLVQRMGRTGRKRQGRIVIILSEG-REERIYNQSQSNKRSIYKAISSNRQVL 593
Cdd:COG1111   436 YEPVPSEIRSIQRKGRTGRKREGRVVVLIAKGtRDEAYYWSSRRKEKKMKSILKKLKKLL 495
XPF_nuclease_FANCM cd20077
XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also ...
 1792-1930 1.13e-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: 244.48  E-value: 1.13e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934 1792 TCILVGGHEITSGLEVISSLRAIHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVI 1871
Cdd:cd20077     1 LVILVDSREISSGQEVISSLRIKHGIKVEVCQLGGCDYIVSNRMGVERKSLSEFANGSNRSKLVERIQHLCDLYDRPCLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 815890934 1872 VEKDREKTGDTSRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKN 1930
Cdd:cd20077    81 IEKDRVKPGETSRIFHRTKYYDSTLAALAQAGVRVLFSDSQEETARLLADLAQLEQRKN 139
FANCM-MHF_bd pfam16783
FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia ...
 649-764 4.35e-63

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: 210.29  E-value: 4.35e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   649 KKDWFLSEEEFKLWNRLYRLRDSDEIKEITLPQVQFSSLQNEENKPAQESTTGIHQLSLSEWRLWQDHPLPTHQVDHSDR 728
Cdd:pfam16783    1 KSDGFLSEEEFELWNRLYRLEEDDIKKEPTLPRSQFTTLPNEETPPKPEPGAARRELSLSEWRHWQNRPLPTHVVDHSDR 80

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 815890934   729 CRHFIGLMQMIEGMRHEEGECSYELEVESYLQMEDV 764
Cdd:pfam16783   81 CLHFIAVMEMIELMRQEEDECSYELELKPYLQMEDV 116
MRC1 super family cl09684
MRC1-like domain; This putative domain is found to be the most conserved region in mediator of ...
 1479-1562 3.84e-04

MRC1-like domain; This putative domain is found to be the most conserved region in mediator of replication checkpoint protein 1.


The actual alignment was detected with superfamily member pfam09444:

Pssm-ID: 430616  Cd Length: 141  Bit Score: 42.55  E-value: 3.84e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  1479 KHVARKFLDDEAELSEEDAEYVSSDENDESENEQDSSLLDFLNDETqlSQAINDSEMRAIYMKSLRspmmNNKYKMIHKT 1558
Cdd:pfam09444    2 KSGASEFVEEEAEESEDEYAGLGGADDEDSDDEEDSELEEMIDDES--DEDVDEDELAALKAKEER----EEDEKEVEKL 75


                   ....
gi 815890934  1559 HKNI 1562
Cdd:pfam09444   76 LKDI 79
 
Name Accession Description Interval E-value
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
92-593 5.70e-105

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 354.04  E-value: 5.70e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   92 RDYQLHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRWfPSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEMTGS 171
Cdd:COG1111     5 RLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAERLHK-KGGKVLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFTGE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  172 TQASTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYC------------------------- 226
Cdd:COG1111    84 VSPEKRKELWEKARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVyiaeryhedakdplilgmtaspgsd 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  227 -QAVQQVITNLLIGQIELRSEDSPDILTYSHERKVEKLIVPLGEELAAIQKTYIQILESFARSLIQRNVLMRRDiPNLTK 305
Cdd:COG1111   164 eEKIEEVCENLGIENVEVRTEEDPDVAPYVHDTEVEWIRVELPEELKEIRDLLNEVLDDRLKKLKELGVIVSTS-PDLSK 242

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  306 YQIILARDQfrknpspnivgIQQGIIEGEF---------AICISLYHGYELLQQMGMRSLYFFLCGIMDGTKGMTRSK-- 374
Cdd:COG1111   243 KDLLALQKK-----------LQRRIREDDSegyraisilAEALKLRHALELLETQGVEALLRYLERLEEEARSSGGSKas 311

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  375 NELGRNEDFMKlynhlecmfARTRSTSANGisaiqqgdknkkfvySHPKLKKLEEVViehfkswnaENTTEKKRDEtRVM 454
Cdd:COG1111   312 KRLVSDPRFRK---------AMRLAEEADI---------------EHPKLSKLREIL---------KEQLGTNPDS-RII 357

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  455 IFSSFRDSVQEIAEMLSQhqPIIRVMTFVGHASGKSTKGFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLIIC 534
Cdd:COG1111   358 VFTQYRDTAEMIVEFLSE--PGIKAGRFVGQASKEGDKGLTQKEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIF 435

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  535 FDSQKSPIRLVQRMGRTGRKRQGRIVIILSEG-REERIYNQSQSNKRSIYKAISSNRQVL 593
Cdd:COG1111   436 YEPVPSEIRSIQRKGRTGRKREGRVVVLIAKGtRDEAYYWSSRRKEKKMKSILKKLKKLL 495
DEXDc_FANCM cd18033
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ...
 89-244 1.03e-97

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: 312.33  E-value: 1.03e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   89 CPVRDYQLHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEM 168
Cdd:cd18033     1 VPLRDYQFTIVQKALFQNTLVALPTGLGKTFIAAVVMLNYYRWFPKGKIVFMAPTKPLVSQQIEACYKITGIPSSQTAEL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  169 TGSTQASTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYCQ--------------------- 227
Cdd:cd18033    81 TGSVPPTKRAELWASKRVFFLTPQTLENDLKEGDCDPKSIVCLVIDEAHRATGNYAYCQvvrelmrynshfrilaltatp 160

                         170       180
                  ....*....|....*....|..
gi 815890934  228 -----AVQQVITNLLIGQIELR 244
Cdd:cd18033   161 gskleAVQQVIDNLLISHIEIR 182
PRK13766 PRK13766
Hef nuclease; Provisional
 92-586 7.50e-87

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 302.56  E-value: 7.50e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   92 RDYQLHISRAALFCNTLVCLPTGLGKTFIAAVVM-YNFYRwfPSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEMTG 170
Cdd:PRK13766   17 RLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIaERLHK--KGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTG 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  171 STQASTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYC------------------------ 226
Cdd:PRK13766   95 EVSPEKRAELWEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYVyiaeryhedaknplvlgltaspgs 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  227 --QAVQQVITNLLIGQIELRSEDSPDILTYSHERKVEKLIVPLGEELAAIQKTYIQILESFARSLIQRNVLmRRDIPNLT 304
Cdd:PRK13766  175 deEKIKEVCENLGIEHVEVRTEDDPDVKPYVHKVKIEWVRVELPEELKEIRDLLNEALKDRLKKLKELGVI-VSISPDVS 253

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  305 KYQIILARDQfrknpspnivgIQQGIIEGEFAI---------CISLYHGYELLQQMGMRSL--YFFLCGIMDGTKGMTRS 373
Cdd:PRK13766  254 KKELLGLQKK-----------LQQEIANDDSEGyeaisilaeAMKLRHAVELLETQGVEALrrYLERLREEARSSGGSKA 322

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  374 KNELGRNEDFMKLYNHLecmfartrstsangisaiqqgdknKKFVYSHPKLKKLEEVVIEhfkswnaenTTEKKRDEtRV 453
Cdd:PRK13766  323 SKRLVEDPRFRKAVRKA------------------------KELDIEHPKLEKLREIVKE---------QLGKNPDS-RI 368

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  454 MIFSSFRDSVQEIAEMLSQHQpiIRVMTFVGHASGKSTKGFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLII 533
Cdd:PRK13766  369 IVFTQYRDTAEKIVDLLEKEG--IKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVI 446

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|....
gi 815890934  534 CFDSQKSPIRLVQRMGRTGRKRQGRIVIILSEG-REERIYNQSQSNKRSIYKAI 586
Cdd:PRK13766  447 FYEPVPSEIRSIQRKGRTGRQEEGRVVVLIAKGtRDEAYYWSSRRKEKKMKEEL 500
XPF_nuclease_FANCM cd20077
XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also ...
 1792-1930 1.13e-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: 244.48  E-value: 1.13e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934 1792 TCILVGGHEITSGLEVISSLRAIHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVI 1871
Cdd:cd20077     1 LVILVDSREISSGQEVISSLRIKHGIKVEVCQLGGCDYIVSNRMGVERKSLSEFANGSNRSKLVERIQHLCDLYDRPCLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 815890934 1872 VEKDREKTGDTSRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKN 1930
Cdd:cd20077    81 IEKDRVKPGETSRIFHRTKYYDSTLAALAQAGVRVLFSDSQEETARLLADLAQLEQRKN 139
FANCM-MHF_bd pfam16783
FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia ...
 649-764 4.35e-63

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: 210.29  E-value: 4.35e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   649 KKDWFLSEEEFKLWNRLYRLRDSDEIKEITLPQVQFSSLQNEENKPAQESTTGIHQLSLSEWRLWQDHPLPTHQVDHSDR 728
Cdd:pfam16783    1 KSDGFLSEEEFELWNRLYRLEEDDIKKEPTLPRSQFTTLPNEETPPKPEPGAARRELSLSEWRHWQNRPLPTHVVDHSDR 80

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 815890934   729 CRHFIGLMQMIEGMRHEEGECSYELEVESYLQMEDV 764
Cdd:pfam16783   81 CLHFIAVMEMIELMRQEEDECSYELELKPYLQMEDV 116
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 446-553 5.43e-21

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 89.96  E-value: 5.43e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   446 KKRDETRVMIFSSFRDSVQeiAEMLSQHQPIiRVMTFVGhasgkstkGFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLD 525
Cdd:pfam00271   11 KKERGGKVLIFSQTKKTLE--AELLLEKEGI-KVARLHG--------DLSQEEREEILEDFRKGKIDVLVATDVAERGLD 79

                           90       100
                   ....*....|....*....|....*...
gi 815890934   526 IGEVDLIICFDSQKSPIRLVQRMGRTGR 553
Cdd:pfam00271   80 LPDVDLVINYDLPWNPASYIQRIGRAGR 107
DEXDc smart00487
DEAD-like helicases superfamily;
90-227 6.52e-19

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 87.16  E-value: 6.52e-19
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934     90 PVRDYQLHISRAALFC--NTLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACYQVMG-IPQSHMA 166
Cdd:smart00487    8 PLRPYQKEAIEALLSGlrDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPsLGLKVVG 87

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 815890934    167 EMTGSTQASTRKEI-WCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYCQ 227
Cdd:smart00487   88 LYGGDSKREQLRKLeSGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQ 149
MUS81 COG1948
ERCC4-type crossover junction endonuclease [Replication, recombination and repair];
1816-2001 1.26e-18

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


Pssm-ID: 441551 [Multi-domain]  Cd Length: 214  Bit Score: 86.38  E-value: 1.26e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934 1816 GLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVEkdrektGD---TSRMFRRTKSY 1892
Cdd:COG1948    23 GVEVRVKTLEVGDYVVSDRVAVERKTVRDFVNSLIDGRLFEQASRLAEAYERPVLIIE------GDllyEERNIHPNAIR 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934 1893 DSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKNV-GIHVPTVVNSNKSEALQFYL--SIPNISYITALNMCHQFS 1969
Cdd:COG1948    97 GALASLALDFGIPVLPTRDAEDTAELLVTLARREQEEEKrEVSLHGKKKPKTLREQQLYVveSLPGIGPKLARRLLEHFG 176

                         170       180       190
                  ....*....|....*....|....*....|..
gi 815890934 1970 SVKRMANSSLQEISMYAQVTHQKAEEIYRYIH 2001
Cdd:COG1948   177 SVEAVFNASEEELMKVEGIGEKTAERIREVLD 208
PRK13766 PRK13766
Hef nuclease; Provisional
 1788-2000 1.83e-15

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 82.61  E-value: 1.83e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934 1788 EGKGTCILVGGHEITSGleVISSLRAIhGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNS-VNKNKFiEQIQHLQSMFE 1866
Cdd:PRK13766  559 EPEGPKIIVDSRELRSN--VARHLKRL-GAEVELKTLEVGDYVVSDRVAVERKTAEDFVDSiIDRRLF-EQVKDLKRAYE 634

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934 1867 RICVIVEkdrektGD--TSRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKN---VGIHvptvvnS 1941
Cdd:PRK13766  635 RPVLIIE------GDlyTIRNIHPNAIRGALASIAVDFGIPILFTRDEEETADLLKVIAKREQEEEkreVSVH------G 702

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 815890934 1942 NKS----EALQFYL--SIPNISYITALNMCHQFSSVKRMANSSLQEISMYAQVTHQKAEEIYRYI 2000
Cdd:PRK13766  703 EKKamtlKEQQEYIveSLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVV 767
ERCC4 pfam02732
ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an ...
 1815-1922 2.19e-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: 66.30  E-value: 2.19e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  1815 HGLQVEVCPLNGCDYIVSNR-----------MVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVE---KDREKTG 1880
Cdd:pfam02732   18 LGVEVVVETLPVGDYLWVPReydlelevvldVIVERKSLDDLVSSIIDGRLFEQKSRLKRGYKKPILLVEgldLFSRKLK 97

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 815890934  1881 DTSRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKEL 1922
Cdd:pfam02732   98 NKRRDINPNAIEGALASLQVDYGVRIIRTRSAEETAEWLASL 139
ERCC4 smart00891
ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, ...
 1793-1873 4.83e-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: 63.91  E-value: 4.83e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   1793 CILVGGHEITSGLE--VISSLRAIHGLQVEVCPLNGCDYIVSNR-------------MVVERRSQSEMLNSVNKNKFIEQ 1857
Cdd:smart00891    1 EIIVDSRELRSALEapIPRSLRWKRGVKVEYDRLEAGDFVLVARdkqsllphvnslnELVERKSLTDLVASIPDGRLFEQ 80

                            90
                    ....*....|....*..
gi 815890934   1858 IQHL-QSMFERICVIVE 1873
Cdd:smart00891   81 VRRLqQIAYPSPQLLVE 97
rad1 TIGR00596
DNA repair protein (rad1); All proteins in this family for which functions are known are ...
 1806-2001 4.38e-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: 65.22  E-value: 4.38e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  1806 EVISSLRAI---HGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVEKDREK---- 1878
Cdd:TIGR00596  595 EFRSSLPSLlhrRGIRVIPCMLTVGDYILTPDICVERKSISDLIGSLNNGRLYNQCEKMLRYYAYPVLLIEFDQNKsfsl 674

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  1879 ------TGDTSRMFRRTKSYDSLLtTLIGAGIRILFSSCQEETADLLKELSLVEQRKN------VGIHVPTVVNSNK--S 1944
Cdd:TIGR00596  675 eprndlSQEISSVNNDIQQKLALL-TLHFPKLRIIWSSSPYATAEIFEELKLGKEEPDpataaaLGSDENTTAEGLKfnD 753

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 815890934  1945 EALQFYLSIPNISYITALNMCHQFSSVKRMANSSLQEISMYAQvTHQKAEEIYRYIH 2001
Cdd:TIGR00596  754 GPQDFLLKLPGVTKKNYRNLRKKVKSIRELAKLSQNELNELIG-DEEAAKRLYDFLR 809
cas3_core TIGR01587
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ...
 449-586 2.29e-04

CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.


Pssm-ID: 273707 [Multi-domain]  Cd Length: 359  Bit Score: 45.52  E-value: 2.29e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   449 DETRVMIFSSFRDSVQEIAEMLSQHQPIIRVMTFvgHasGKSTKGFTQKEQLEVVKQFRDGGYN-TLVSTCVGEEGLDIg 527
Cdd:TIGR01587  221 KGGSIAIIVNTVDRAQEFYQQLKEKAPEEEIILY--H--SRFTEKDRAKKEAELLREMKKSNEKfVIVATQVIEASLDI- 295

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 815890934   528 EVDLIIcfdSQKSPI-RLVQRMGRTGRK----RQGRIVIILSEGREeriYNQSQSNKRSIYKAI 586
Cdd:TIGR01587  296 SADVMI---TELAPIdSLIQRLGRLHRYgrkiGENFEVYIITIAPE---GKLFPYPYELVERTI 353
MRC1 pfam09444
MRC1-like domain; This putative domain is found to be the most conserved region in mediator of ...
 1479-1562 3.84e-04

MRC1-like domain; This putative domain is found to be the most conserved region in mediator of replication checkpoint protein 1.


Pssm-ID: 430616  Cd Length: 141  Bit Score: 42.55  E-value: 3.84e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  1479 KHVARKFLDDEAELSEEDAEYVSSDENDESENEQDSSLLDFLNDETqlSQAINDSEMRAIYMKSLRspmmNNKYKMIHKT 1558
Cdd:pfam09444    2 KSGASEFVEEEAEESEDEYAGLGGADDEDSDDEEDSELEEMIDDES--DEDVDEDELAALKAKEER----EEDEKEVEKL 75


                   ....
gi 815890934  1559 HKNI 1562
Cdd:pfam09444   76 LKDI 79
 
Name Accession Description Interval E-value
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
92-593 5.70e-105

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 354.04  E-value: 5.70e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   92 RDYQLHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRWfPSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEMTGS 171
Cdd:COG1111     5 RLYQLNLAASALRKNTLVVLPTGLGKTAVALLVIAERLHK-KGGKVLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFTGE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  172 TQASTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYC------------------------- 226
Cdd:COG1111    84 VSPEKRKELWEKARIIVATPQVIENDLIAGRIDLDDVSLLIFDEAHRAVGNYAYVyiaeryhedakdplilgmtaspgsd 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  227 -QAVQQVITNLLIGQIELRSEDSPDILTYSHERKVEKLIVPLGEELAAIQKTYIQILESFARSLIQRNVLMRRDiPNLTK 305
Cdd:COG1111   164 eEKIEEVCENLGIENVEVRTEEDPDVAPYVHDTEVEWIRVELPEELKEIRDLLNEVLDDRLKKLKELGVIVSTS-PDLSK 242

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  306 YQIILARDQfrknpspnivgIQQGIIEGEF---------AICISLYHGYELLQQMGMRSLYFFLCGIMDGTKGMTRSK-- 374
Cdd:COG1111   243 KDLLALQKK-----------LQRRIREDDSegyraisilAEALKLRHALELLETQGVEALLRYLERLEEEARSSGGSKas 311

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  375 NELGRNEDFMKlynhlecmfARTRSTSANGisaiqqgdknkkfvySHPKLKKLEEVViehfkswnaENTTEKKRDEtRVM 454
Cdd:COG1111   312 KRLVSDPRFRK---------AMRLAEEADI---------------EHPKLSKLREIL---------KEQLGTNPDS-RII 357

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  455 IFSSFRDSVQEIAEMLSQhqPIIRVMTFVGHASGKSTKGFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLIIC 534
Cdd:COG1111   358 VFTQYRDTAEMIVEFLSE--PGIKAGRFVGQASKEGDKGLTQKEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIF 435

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  535 FDSQKSPIRLVQRMGRTGRKRQGRIVIILSEG-REERIYNQSQSNKRSIYKAISSNRQVL 593
Cdd:COG1111   436 YEPVPSEIRSIQRKGRTGRKREGRVVVLIAKGtRDEAYYWSSRRKEKKMKSILKKLKKLL 495
DEXDc_FANCM cd18033
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ...
 89-244 1.03e-97

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: 312.33  E-value: 1.03e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   89 CPVRDYQLHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEM 168
Cdd:cd18033     1 VPLRDYQFTIVQKALFQNTLVALPTGLGKTFIAAVVMLNYYRWFPKGKIVFMAPTKPLVSQQIEACYKITGIPSSQTAEL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  169 TGSTQASTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYCQ--------------------- 227
Cdd:cd18033    81 TGSVPPTKRAELWASKRVFFLTPQTLENDLKEGDCDPKSIVCLVIDEAHRATGNYAYCQvvrelmrynshfrilaltatp 160

                         170       180
                  ....*....|....*....|..
gi 815890934  228 -----AVQQVITNLLIGQIELR 244
Cdd:cd18033   161 gskleAVQQVIDNLLISHIEIR 182
PRK13766 PRK13766
Hef nuclease; Provisional
 92-586 7.50e-87

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 302.56  E-value: 7.50e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   92 RDYQLHISRAALFCNTLVCLPTGLGKTFIAAVVM-YNFYRwfPSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEMTG 170
Cdd:PRK13766   17 RLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIaERLHK--KGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTG 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  171 STQASTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYC------------------------ 226
Cdd:PRK13766   95 EVSPEKRAELWEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYVyiaeryhedaknplvlgltaspgs 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  227 --QAVQQVITNLLIGQIELRSEDSPDILTYSHERKVEKLIVPLGEELAAIQKTYIQILESFARSLIQRNVLmRRDIPNLT 304
Cdd:PRK13766  175 deEKIKEVCENLGIEHVEVRTEDDPDVKPYVHKVKIEWVRVELPEELKEIRDLLNEALKDRLKKLKELGVI-VSISPDVS 253

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  305 KYQIILARDQfrknpspnivgIQQGIIEGEFAI---------CISLYHGYELLQQMGMRSL--YFFLCGIMDGTKGMTRS 373
Cdd:PRK13766  254 KKELLGLQKK-----------LQQEIANDDSEGyeaisilaeAMKLRHAVELLETQGVEALrrYLERLREEARSSGGSKA 322

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  374 KNELGRNEDFMKLYNHLecmfartrstsangisaiqqgdknKKFVYSHPKLKKLEEVVIEhfkswnaenTTEKKRDEtRV 453
Cdd:PRK13766  323 SKRLVEDPRFRKAVRKA------------------------KELDIEHPKLEKLREIVKE---------QLGKNPDS-RI 368

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  454 MIFSSFRDSVQEIAEMLSQHQpiIRVMTFVGHASGKSTKGFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLII 533
Cdd:PRK13766  369 IVFTQYRDTAEKIVDLLEKEG--IKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVI 446

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|....
gi 815890934  534 CFDSQKSPIRLVQRMGRTGRKRQGRIVIILSEG-REERIYNQSQSNKRSIYKAI 586
Cdd:PRK13766  447 FYEPVPSEIRSIQRKGRTGRQEEGRVVVLIAKGtRDEAYYWSSRRKEKKMKEEL 500
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 415-563 7.93e-80

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: 259.60  E-value: 7.93e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  415 KKFVYSHPKLKKLEEVVIEHFKSWNAenttekkRDETRVMIFSSFRDSVQEIAEMLSQHQPIIRVMTFVGHASGKSTKGF 494
Cdd:cd18801     2 RKVEKIHPKLEKLEEIVKEHFKKKQE-------GSDTRVIIFSEFRDSAEEIVNFLSKIRPGIRATRFIGQASGKSSKGM 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 815890934  495 TQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLIICFDSQKSPIRLVQRMGRTGRKRQGRIVIIL 563
Cdd:cd18801    75 SQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMIQRMGRTGRKRQGRVVVLL 143
XPF_nuclease_FANCM cd20077
XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also ...
 1792-1930 1.13e-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: 244.48  E-value: 1.13e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934 1792 TCILVGGHEITSGLEVISSLRAIHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVI 1871
Cdd:cd20077     1 LVILVDSREISSGQEVISSLRIKHGIKVEVCQLGGCDYIVSNRMGVERKSLSEFANGSNRSKLVERIQHLCDLYDRPCLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 815890934 1872 VEKDREKTGDTSRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKN 1930
Cdd:cd20077    81 IEKDRVKPGETSRIFHRTKYYDSTLAALAQAGVRVLFSDSQEETARLLADLAQLEQRKN 139
FANCM-MHF_bd pfam16783
FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia ...
 649-764 4.35e-63

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: 210.29  E-value: 4.35e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   649 KKDWFLSEEEFKLWNRLYRLRDSDEIKEITLPQVQFSSLQNEENKPAQESTTGIHQLSLSEWRLWQDHPLPTHQVDHSDR 728
Cdd:pfam16783    1 KSDGFLSEEEFELWNRLYRLEEDDIKKEPTLPRSQFTTLPNEETPPKPEPGAARRELSLSEWRHWQNRPLPTHVVDHSDR 80

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 815890934   729 CRHFIGLMQMIEGMRHEEGECSYELEVESYLQMEDV 764
Cdd:pfam16783   81 CLHFIAVMEMIELMRQEEDECSYELELKPYLQMEDV 116
XPF_nuclease-like cd19940
nuclease domain of XPF/MUS81 family proteins; The XPF/MUS81 family belongs to 3'-flap ...
 1793-1924 3.30e-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: 145.22  E-value: 3.30e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934 1793 CILVGGHEITSglEVISSLRAIhGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIV 1872
Cdd:cd19940     1 SIVVDPRERRS--ELLSELQRL-GVQVEFEDLAVGDYVLSNRTCVERKSLSDLVSSINKGRLREQLQRLTRKFERRVLLV 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 815890934 1873 EKDREKTgdtsRMFRRTKSYDSLLTTLIG-AGIRILFSSCQEETADLLKELSL 1924
Cdd:cd19940    78 EKDRSKF----RSMVSSVQALSALTKLQLlTGIRLLIVASPKETADLLEELTQ 126
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 92-225 2.14e-39

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: 146.04  E-value: 2.14e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   92 RDYQLHISRAAL-FCNTLVCLPTGLGKTFIAAVVMYNFYRWFPS---GKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAE 167
Cdd:cd17927     4 RNYQLELAQPALkGKNTIICLPTGSGKTFVAVLICEHHLKKFPAgrkGKVVFLANKVPLVEQQKEVFRKHFERPGYKVTG 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  168 MTGSTQASTR-KEIWCSKRVLFLTPQVMVNDLSRGACPAAE-IKCLVIDEAHKALGNYAY 225
Cdd:cd17927    84 LSGDTSENVSvEQIVESSDVIIVTPQILVNDLKSGTIVSLSdFSLLVFDECHNTTKNHPY 143
FANCM_ID cd12091
Insert domain of FANCM and related proteins; FANCM and related proteins, like Mph1 and Fml1, ...
 272-387 5.17e-33

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: 124.33  E-value: 5.17e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  272 AAIQKTYIQILESFARSLIQRNVLMRRDIPNLTKYQIILARDQFRKNPSPNIVGiQQGIIEGEFAICISLYHGYELLQQM 351
Cdd:cd12091     1 TEIRDLLAKVLEPFLKRLNQAGILPNRDPAKLSPFRLLQARDKFRANPPGNNEG-QKGSIEGDFALLISLAHAMELLLEH 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 815890934  352 GMRSLYFFLCGIMDGTKG-MTRSKNELGRNEDFMKLY 387
Cdd:cd12091    80 GIRPFYDYLKEIKDETKAkGSKSKKELAKNPNFKALM 116
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 92-245 2.38e-27

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: 110.68  E-value: 2.38e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   92 RDYQLHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRWFpSGKVVFMAPTKPLVTQQIEACYQVMGIPQShMAEMTGS 171
Cdd:cd18035     4 RLYQVLIAAVALNGNTLIVLPTGLGKTIIAILVAADRLTKK-GGKVLILAPSRPLVEQHAENLKRVLNIPDK-ITSLTGE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  172 TQASTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYC------------------------- 226
Cdd:cd18035    82 VKPEERAERWDASKIIVATPQVIENDLLAGRITLDDVSLLIFDEAHHAVGNYAYVyiahrykreannplilgltaspgsd 161

                         170       180
                  ....*....|....*....|
gi 815890934  227 -QAVQQVITNLLIGQIELRS 245
Cdd:cd18035   162 kEKIMEICENLGIEHIEIKT 181
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 92-230 3.61e-25

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: 105.04  E-value: 3.61e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   92 RDYQLHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRWF----PSGK-VVFMAPTKPLVTQQIEA-----CYQVMGIp 161
Cdd:cd18034     4 RSYQLELFEAALKRNTIVVLPTGSGKTLIAVMLIKEMGELNrkekNPKKrAVFLVPTVPLVAQQAEAirshtDLKVGEY- 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 815890934  162 qsHMAEMTGSTQASTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYCQAVQ 230
Cdd:cd18034    83 --SGEMGVDKWTKERWKEELEKYDVLVMTAQILLDALRHGFLSLSDINLLIFDECHHATGDHPYARIMK 149
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 419-563 1.80e-22

C-terminal helicase domain of the 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. Dicer exists throughout eukaryotes, and a subset has 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 helicase domains 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: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 95.35  E-value: 1.80e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  419 YSHPKLKKLEEVVIEHFKswnaenttekKRDETRVMIFSSFRDSVQEIAEMLSQHQ---PIIRVMTFVGHASGKSTKGF- 494
Cdd:cd18802     4 VVIPKLQKLIEILREYFP----------KTPDFRGIIFVERRATAVVLSRLLKEHPstlAFIRCGFLIGRGNSSQRKRSl 73

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  495 -TQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLIICFDSQKSPIRLVQRMGRtGRKRQGRIVIIL 563
Cdd:cd18802    74 mTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGR-ARAPNSKYILMV 142
XPF_ERCC4_MUS81-like cd22367
XPF family DNA repair endonuclease; (Xeroderma Pigmentosum group F) DNA repair gene homologs ...
 1794-1923 3.28e-22

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: 93.86  E-value: 3.28e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934 1794 ILVGGHEITSGLEVISSLraiHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVE 1873
Cdd:cd22367     1 IVVDSRERRSGLPELLRK---LGVRVEVRTLEVGDYILSADIIVERKTVSDLISSIIDGRLFEQAERLKRSYERPILLIE 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 815890934 1874 KDREKTgdtsRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELS 1923
Cdd:cd22367    78 GDPDKA----RRLVRPAALGAAISSLLVIGGLLVLRTPNFETTALLLSLL 123
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 446-553 5.43e-21

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 89.96  E-value: 5.43e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   446 KKRDETRVMIFSSFRDSVQeiAEMLSQHQPIiRVMTFVGhasgkstkGFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLD 525
Cdd:pfam00271   11 KKERGGKVLIFSQTKKTLE--AELLLEKEGI-KVARLHG--------DLSQEEREEILEDFRKGKIDVLVATDVAERGLD 79

                           90       100
                   ....*....|....*....|....*...
gi 815890934   526 IGEVDLIICFDSQKSPIRLVQRMGRTGR 553
Cdd:pfam00271   80 LPDVDLVINYDLPWNPASYIQRIGRAGR 107
DEXDc smart00487
DEAD-like helicases superfamily;
90-227 6.52e-19

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 87.16  E-value: 6.52e-19
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934     90 PVRDYQLHISRAALFC--NTLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACYQVMG-IPQSHMA 166
Cdd:smart00487    8 PLRPYQKEAIEALLSGlrDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPsLGLKVVG 87

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 815890934    167 EMTGSTQASTRKEI-WCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYCQ 227
Cdd:smart00487   88 LYGGDSKREQLRKLeSGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQ 149
MUS81 COG1948
ERCC4-type crossover junction endonuclease [Replication, recombination and repair];
1816-2001 1.26e-18

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


Pssm-ID: 441551 [Multi-domain]  Cd Length: 214  Bit Score: 86.38  E-value: 1.26e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934 1816 GLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVEkdrektGD---TSRMFRRTKSY 1892
Cdd:COG1948    23 GVEVRVKTLEVGDYVVSDRVAVERKTVRDFVNSLIDGRLFEQASRLAEAYERPVLIIE------GDllyEERNIHPNAIR 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934 1893 DSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKNV-GIHVPTVVNSNKSEALQFYL--SIPNISYITALNMCHQFS 1969
Cdd:COG1948    97 GALASLALDFGIPVLPTRDAEDTAELLVTLARREQEEEKrEVSLHGKKKPKTLREQQLYVveSLPGIGPKLARRLLEHFG 176

                         170       180       190
                  ....*....|....*....|....*....|..
gi 815890934 1970 SVKRMANSSLQEISMYAQVTHQKAEEIYRYIH 2001
Cdd:COG1948   177 SVEAVFNASEEELMKVEGIGEKTAERIREVLD 208
HELICc smart00490
helicase superfamily c-terminal domain;
464-554 1.45e-18

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 81.87  E-value: 1.45e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934    464 QEIAEMLSQHQpiIRVMTFvgHAsgkstkGFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLIICFDSQKSPIR 543
Cdd:smart00490    1 EELAELLKELG--IKVARL--HG------GLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPAS 70

                            90
                    ....*....|.
gi 815890934    544 LVQRMGRTGRK 554
Cdd:smart00490   71 YIQRIGRAGRA 81
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 92-243 8.63e-17

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: 80.98  E-value: 8.63e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   92 RDYQLHISRAALFC-NTLVCLPTGLGKTFIAAVVMYNFYRWFPS----GKVVFMAPTKPLVTQQIEA-------CYQVMG 159
Cdd:cd18036     4 RNYQLELVLPALRGkNTIICAPTGSGKTRVAVYICRHHLEKRRSagekGRVVVLVNKVPLVEQQLEKffkyfrkGYKVTG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  160 IPQSHmaemtgSTQASTRKEIWCSKrVLFLTPQVMVNDLSRGACPA----AEIKCLVIDEAHKALGNYAYCQAVQQVITN 235
Cdd:cd18036    84 LSGDS------SHKVSFGQIVKASD-VIICTPQILINNLLSGREEErvylSDFSLLIFDECHHTQKEHPYNKIMRMYLDK 156


                  ....*...
gi 815890934  236 LLIGQIEL 243
Cdd:cd18036   157 KLSSQGPL 164
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
92-679 1.23e-16

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 85.85  E-value: 1.23e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   92 RDYQ------LHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRwfpSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHm 165
Cdd:COG1061    82 RPYQqealeaLLAALERGGGRGLVVAPTGTGKTVLALALAAELLR---GKRVLVLVPRRELLEQWAEELRRFLGDPLAG- 157

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  166 aemtgstqaSTRKEIWCskRVLFLTPQVMVNDLSRGACPAAeIKCLVIDEAHkalgnyaycqavqqvitnlligqielrs 245
Cdd:COG1061   158 ---------GGKKDSDA--PITVATYQSLARRAHLDELGDR-FGLVIIDEAH---------------------------- 197

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  246 edspdiltysHerkveklivplgeeLAAiqKTYIQILESFarsliqrnvlmrrdipnltKYQIILArd--qFRKNPSPNI 323
Cdd:COG1061   198 ----------H--------------AGA--PSYRRILEAF-------------------PAAYRLGltatpFRSDGREIL 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  324 VGIQQGIIegefaicislYH-GYELLQQMGmrslyfFLCGImdgtkgmtrsknelgrneDFMKLYNHLECMFARTRSTSA 402
Cdd:COG1061   233 LFLFDGIV----------YEySLKEAIEDG------YLAPP------------------EYYGIRVDLTDERAEYDALSE 278

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  403 NGISAIQQGDKNKkfvyshpkLKKLEEVVIEHfkswnaenttekkRDETRVMIFSSFRDSVQEIAEMLSQHQpiIRVMTF 482
Cdd:COG1061   279 RLREALAADAERK--------DKILRELLREH-------------PDDRKTLVFCSSVDHAEALAELLNEAG--IRAAVV 335

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  483 VGHASgkstkgftQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLIICFDSQKSPIRLVQRMGRTGRKRQGrivii 562
Cdd:COG1061   336 TGDTP--------KKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLRPTGSPREFIQRLGRGLRPAPG----- 402

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  563 lseGREERIYNQSqSNKRSIYKAISSNRQVLHFYQRSPRMVPDGINPKLHKMFITHGVYEPEKPSRNLQRKSSIFSYRDG 642
Cdd:COG1061   403 ---KEDALVYDFV-GNDVPVLEELAKDLRDLAGYRVEFLDEEESEELALLIAVKPALEVKGELEEELLEELELLEDALLL 478

                         570       580       590
                  ....*....|....*....|....*....|....*..
gi 815890934  643 MRQSSLKKDWFLSEEEFKLWNRLYRLRDSDEIKEITL 679
Cdd:COG1061   479 VLAELLLLELLALALELLELAKAEGKAEEEEEEKELL 515
DEXHc_RIG-I_DDX58 cd18073
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ...
 92-225 1.33e-16

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: 80.25  E-value: 1.33e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   92 RDYQLHISRAALFC-NTLVCLPTGLGKTFIAAVVMYNFYRWFPSG---KVVFMAPTKPLVTQQIEACYQVMGIPQSHMAE 167
Cdd:cd18073     4 RNYQLELALPAMKGkNTIICAPTGCGKTFVSLLICEHHLKKFPQGqkgKVVFFATKVPVYEQQKSVFSKYFERHGYRVTG 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  168 MTGST-QASTRKEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVI-DEAHKALGNYAY 225
Cdd:cd18073    84 ISGATaENVPVEQIIENNDIIILTPQILVNNLKKGTIPSLSIFTLMIfDECHNTSGNHPY 143
ResIII pfam04851
Type III restriction enzyme, res subunit;
88-239 1.10e-15

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 76.56  E-value: 1.10e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934    88 NCPVRDYQLHISRAALFC------NTLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACYQVMGIP 161
Cdd:pfam04851    1 KLELRPYQIEAIENLLESikngqkRGLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPRKDLLEQALEEFKKFLPNY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   162 QSHMAEMTGSTQASTRKEIwcskRVLFLTPQVMVNDLSRGACPAA--EIKCLVIDEAHKALGNyAYCQAVQQVITNLLIG 239
Cdd:pfam04851   81 VEIGEIISGDKKDESVDDN----KIVVTTIQSLYKALELASLELLpdFFDVIIIDEAHRSGAS-SYRNILEYFKPAFLLG 155
PRK13766 PRK13766
Hef nuclease; Provisional
 1788-2000 1.83e-15

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 82.61  E-value: 1.83e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934 1788 EGKGTCILVGGHEITSGleVISSLRAIhGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNS-VNKNKFiEQIQHLQSMFE 1866
Cdd:PRK13766  559 EPEGPKIIVDSRELRSN--VARHLKRL-GAEVELKTLEVGDYVVSDRVAVERKTAEDFVDSiIDRRLF-EQVKDLKRAYE 634

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934 1867 RICVIVEkdrektGD--TSRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKN---VGIHvptvvnS 1941
Cdd:PRK13766  635 RPVLIIE------GDlyTIRNIHPNAIRGALASIAVDFGIPILFTRDEEETADLLKVIAKREQEEEkreVSVH------G 702

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 815890934 1942 NKS----EALQFYL--SIPNISYITALNMCHQFSSVKRMANSSLQEISMYAQVTHQKAEEIYRYI 2000
Cdd:PRK13766  703 EKKamtlKEQQEYIveSLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVV 767
XPF_nuclease_XPF_arch cd20075
nuclease domain of XPF found in archaea; XPF, also called DNA excision repair protein ERCC-4, ...
 1806-1922 4.18e-15

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: 73.57  E-value: 4.18e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934 1806 EVISSLRAiHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVEkdrektGDTSRM 1885
Cdd:cd20075    12 GVVRELKE-LGVEVEFKQLEVGDYIVSDRVAIERKTVDDFVSSIIDGRLFDQAKRLKEAYEKPILIIE------GDLLYL 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 815890934 1886 FRRTKS---YDSLLTTLIGAGIRILFSSCQEETADLLKEL 1922
Cdd:cd20075    85 KRRIHPnaiRGALASIALDFGIPIIFTKDPEETAELLYSL 124
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 429-563 9.46e-15

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 72.93  E-value: 9.46e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  429 EVVIEHFKSWNAENTTEKKRDETRVMIFSSFRDSVQEIAEMLSQHQpiIRVMTFvgHaSGKStkgftQKEQLEVVKQFRD 508
Cdd:cd18787     6 VVVEEEEKKLLLLLLLLEKLKPGKAIIFVNTKKRVDRLAELLEELG--IKVAAL--H-GDLS-----QEERERALKKFRS 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 815890934  509 GGYNTLVSTCVGEEGLDIGEVDLIICFDSQKSPIRLVQRMGRTGRK-RQGRIVIIL 563
Cdd:cd18787    76 GKVRVLVATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAgRKGTAITFV 131
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 106-236 3.06e-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: 3.06e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  106 NTLVCLPTGLGKTFIAAVVMYNFYRWFPsGKVVFMAPTKPLVTQQIEAcYQVMGIPQSHMAEMTGSTQASTR-KEIWCSK 184
Cdd:cd00046     3 NVLITAPTGSGKTLAALLAALLLLLKKG-KKVLVLVPTKALALQTAER-LRELFGPGIRVAVLVGGSSAEEReKNKLGDA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 815890934  185 RVLFLTPQVMVNDLSRGACP-AAEIKCLVIDEAHKALGNYAYCQAVQQVITNL 236
Cdd:cd00046    81 DIIIATPDMLLNLLLREDRLfLKDLKLIIVDEAHALLIDSRGALILDLAVRKA 133
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 106-244 8.50e-13

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: 68.83  E-value: 8.50e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  106 NTLVCLPTGLGKTFIAAVVMYNfyRWFPSG-KVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEMTGSTQASTRKEIwcSK 184
Cdd:cd17921    19 SVLVSAPTSSGKTLIAELAILR--ALATSGgKAVYIAPTRALVNQKEADLRERFGPLGKNVGLLTGDPSVNKLLLA--EA 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 815890934  185 RVLFLTPQVMVNDLSRGACPAAE-IKCLVIDEAHKaLGNYAYCQAVQQVITNLLIGQIELR 244
Cdd:cd17921    95 DILVATPEKLDLLLRNGGERLIQdVRLVVVDEAHL-IGDGERGVVLELLLSRLLRINKNAR 154
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 92-219 9.03e-13

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: 67.97  E-value: 9.03e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   92 RDYQ------LHISRAALFCNTLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACYQVMgiPQSHM 165
Cdd:cd18032     2 RYYQqeaieaLEEAREKGQRRALLVMATGTGKTYTAAFLIKRLLEANRKKRILFLAHREELLEQAERSFKEVL--PDGSF 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 815890934  166 AEMTGSTQASTrkeiwcSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKA 219
Cdd:cd18032    80 GNLKGGKKKPD------DARVVFATVQTLNKRKRLEKFPPDYFDLIIIDEAHHA 127
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 106-222 1.99e-12

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: 67.27  E-value: 1.99e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   106 NTLVCLPTGLGKTFIAAVVMYN-FYRWFPSGKVVFMAPTKPLVTQQIEACYQVM-GIPQSHMAEMTGSTQASTRKEIwCS 183
Cdd:pfam00270   16 DVLVQAPTGSGKTLAFLLPALEaLDKLDNGPQALVLAPTRELAEQIYEELKKLGkGLGLKVASLLGGDSRKEQLEKL-KG 94

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 815890934   184 KRVLFLTPQvMVNDLSRGACPAAEIKCLVIDEAHKALGN 222
Cdd:pfam00270   95 PDILVGTPG-RLLDLLQERKLLKNLKLLVLDEAHRLLDM 132
ERCC4 pfam02732
ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an ...
 1815-1922 2.19e-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: 66.30  E-value: 2.19e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  1815 HGLQVEVCPLNGCDYIVSNR-----------MVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVE---KDREKTG 1880
Cdd:pfam02732   18 LGVEVVVETLPVGDYLWVPReydlelevvldVIVERKSLDDLVSSIIDGRLFEQKSRLKRGYKKPILLVEgldLFSRKLK 97

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 815890934  1881 DTSRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKEL 1922
Cdd:pfam02732   98 NKRRDINPNAIEGALASLQVDYGVRIIRTRSAEETAEWLASL 139
ERCC4 smart00891
ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, ...
 1793-1873 4.83e-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: 63.91  E-value: 4.83e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   1793 CILVGGHEITSGLE--VISSLRAIHGLQVEVCPLNGCDYIVSNR-------------MVVERRSQSEMLNSVNKNKFIEQ 1857
Cdd:smart00891    1 EIIVDSRELRSALEapIPRSLRWKRGVKVEYDRLEAGDFVLVARdkqsllphvnslnELVERKSLTDLVASIPDGRLFEQ 80

                            90
                    ....*....|....*..
gi 815890934   1858 IQHL-QSMFERICVIVE 1873
Cdd:smart00891   81 VRRLqQIAYPSPQLLVE 97
rad1 TIGR00596
DNA repair protein (rad1); All proteins in this family for which functions are known are ...
 1806-2001 4.38e-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: 65.22  E-value: 4.38e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  1806 EVISSLRAI---HGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVEKDREK---- 1878
Cdd:TIGR00596  595 EFRSSLPSLlhrRGIRVIPCMLTVGDYILTPDICVERKSISDLIGSLNNGRLYNQCEKMLRYYAYPVLLIEFDQNKsfsl 674

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  1879 ------TGDTSRMFRRTKSYDSLLtTLIGAGIRILFSSCQEETADLLKELSLVEQRKN------VGIHVPTVVNSNK--S 1944
Cdd:TIGR00596  675 eprndlSQEISSVNNDIQQKLALL-TLHFPKLRIIWSSSPYATAEIFEELKLGKEEPDpataaaLGSDENTTAEGLKfnD 753

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 815890934  1945 EALQFYLSIPNISYITALNMCHQFSSVKRMANSSLQEISMYAQvTHQKAEEIYRYIH 2001
Cdd:TIGR00596  754 GPQDFLLKLPGVTKKNYRNLRKKVKSIRELAKLSQNELNELIG-DEEAAKRLYDFLR 809
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
446-570 6.04e-10

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 63.63  E-value: 6.04e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  446 KKRDETRVMIFSSFRDSVQEIAEMLSQHqpiirvmtfvGHASGKSTKGFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLD 525
Cdd:COG0513   237 RDEDPERAIVFCNTKRGADRLAEKLQKR----------GISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGID 306

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 815890934  526 IGEVDLIICFDSQKSPIRLVQRMGRTGR-KRQGrIVIILSEGREER 570
Cdd:COG0513   307 IDDVSHVINYDLPEDPEDYVHRIGRTGRaGAEG-TAISLVTPDERR 351
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
 423-557 1.30e-09

C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase 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: 350176 [Multi-domain]  Cd Length: 153  Bit Score: 58.80  E-value: 1.30e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  423 KLKKLEEVVIEHfkswnaenttekkRDETRVMIFSSFRDSVQEIAEMLSQhqPIIrvmtfvghasgksTKGFTQKEQLEV 502
Cdd:cd18789    35 KLRALEELLKRH-------------EQGDKIIVFTDNVEALYRYAKRLLK--PFI-------------TGETPQSEREEI 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 815890934  503 VKQFRDGGYNTLVSTCVGEEGLDIGEVD-LIICFDSQKSPIRLVQRMGRTGRKRQG 557
Cdd:cd18789    87 LQNFREGEYNTLVVSKVGDEGIDLPEANvAIQISGHGGSRRQEAQRLGRILRPKKG 142
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 497-563 4.50e-09

C-terminal helicase domain of LHR family helicases; 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. LHR family helicases 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: 350183 [Multi-domain]  Cd Length: 150  Bit Score: 57.27  E-value: 4.50e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 815890934  497 KEQLEVVKQ-FRDGGYNTLVSTCVGEEGLDIGEVDLIICFDSQKSPIRLVQRMGRTGRKRQGRIVIIL 563
Cdd:cd18796    80 RELREEVEAaLKRGDLKVVVATSSLELGIDIGDVDLVIQIGSPKSVARLLQRLGRSGHRPGAASKGRL 147
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 417-550 3.65e-08

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They 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: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 54.02  E-value: 3.65e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  417 FVYShPKLKKLEEVVIEHFKSwnaenttekkrdETRVMIFSSFRDSVQEIAEMLSQHQpiIRVMTFVGhasgkSTkgfTQ 496
Cdd:cd18793     7 EVVS-GKLEALLELLEELREP------------GEKVLIFSQFTDTLDILEEALRERG--IKYLRLDG-----ST---SS 63

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 815890934  497 KEQLEVVKQFRDGGYNT--LVSTCVGEEGLDIGEVDLIICFDSQKSPIRLVQRMGR 550
Cdd:cd18793    64 KERQKLVDRFNEDPDIRvfLLSTKAGGVGLNLTAANRVILYDPWWNPAVEEQAIDR 119
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 446-553 7.25e-08

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 57.26  E-value: 7.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  446 KKRDETRVMIFSSFRDSVQEIAEMLSQHQpiIRVMTFVGHasgkstkgFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLD 525
Cdd:PRK11192  241 KQPEVTRSIVFVRTRERVHELAGWLRKAG--INCCYLEGE--------MVQAKRNEAIKRLTDGRVNVLVATDVAARGID 310

                          90       100
                  ....*....|....*....|....*...
gi 815890934  526 IGEVDLIICFDSQKSPIRLVQRMGRTGR 553
Cdd:PRK11192  311 IDDVSHVINFDMPRSADTYLHRIGRTGR 338
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
106-218 1.36e-07

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 56.44  E-value: 1.36e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  106 NTLVCLPTGLGKTFIAAVVMYNfyRWFPSGKVVFMAPTKPLVTQ---QIEACYQVMGIpqshmaEMTGSTQASTRKEIWC 182
Cdd:COG1204    40 NLVVSAPTASGKTLIAELAILK--ALLNGGKALYIVPLRALASEkyrEFKRDFEELGI------KVGVSTGDYDSDDEWL 111

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 815890934  183 SKR-VLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHK 218
Cdd:COG1204   112 GRYdILVATPEKLDSLLRNGPSWLRDVDLVVVDEAHL 148
PRK01297 PRK01297
ATP-dependent RNA helicase RhlB; Provisional
 452-553 1.89e-07

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 234938 [Multi-domain]  Cd Length: 475  Bit Score: 56.07  E-value: 1.89e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  452 RVMIFSSFRDSVQEIAEMLSQHqpiirvmtfvGHASGKSTKGFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDL 531
Cdd:PRK01297  337 RVMVFANRKDEVRRIEERLVKD----------GINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISH 406

                          90       100
                  ....*....|....*....|..
gi 815890934  532 IICFDSQKSPIRLVQRMGRTGR 553
Cdd:PRK01297  407 VINFTLPEDPDDYVHRIGRTGR 428
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 514-562 3.56e-07

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 49.24  E-value: 3.56e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 815890934  514 LVSTCVGEEGLDIGEVDLIICFDSQKSPIRLVQRMGRTGRKRQ--GRIVII 562
Cdd:cd18785    26 LVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRGGKdeGEVILF 76
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
 462-556 1.60e-06

C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. They 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: 350179 [Multi-domain]  Cd Length: 160  Bit Score: 49.96  E-value: 1.60e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  462 SVQEIAEMLSQHQPIIRVMtfVGHasGKstkgFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLIICFDSQKSP 541
Cdd:cd18792    46 SIEALAEELKELVPEARVA--LLH--GK----MTEDEKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFG 117

                          90
                  ....*....|....*.
gi 815890934  542 I-RLVQRMGRTGRKRQ 556
Cdd:cd18792   118 LsQLHQLRGRVGRGKH 133
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 92-217 2.43e-06

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: 49.23  E-value: 2.43e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   92 RDYQLHISRAALFCNT----LVCLPTGLGKTFIAAVVMynFYRWfpSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAE 167
Cdd:cd17926     2 RPYQEEALEAWLAHKNnrrgILVLPTGSGKTLTALALI--AYLK--ELRTLIVVPTDALLDQWKERFEDFLGDSSIGLIG 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 815890934  168 mTGSTQASTRKEIwcskrvLFLTPQVMVNDLSRGACPAAEIKCLVIDEAH 217
Cdd:cd17926    78 -GGKKKDFDDANV------VVATYQSLSNLAEEEKDLFDQFGLLIVDEAH 120
ComFA COG4098
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ...
 445-554 4.50e-06

Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, recombination and repair];


Pssm-ID: 443274 [Multi-domain]  Cd Length: 451  Bit Score: 51.41  E-value: 4.50e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  445 EKKRDETRVMIFSSFRDSVQEIAEMLSQHQPIIRVMTfVgHASgkstkgftQKEQLEVVKQFRDGGYNTLVSTCVGEEGL 524
Cdd:COG4098   314 KRLKEGRQLLIFVPTIELLEQLVALLQKLFPEERIAG-V-HAE--------DPERKEKVQAFRDGEIPILVTTTILERGV 383

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 815890934  525 DIGEVDLIIC------FDSQKspirLVQRMGRTGRK 554
Cdd:COG4098   384 TFPNVDVAVLgadhpvFTEAA----LVQIAGRVGRS 415
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
 462-556 4.72e-06

C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a DEAD-like helicase 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: 350197 [Multi-domain]  Cd Length: 151  Bit Score: 48.49  E-value: 4.72e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  462 SVQEIAEMLSQHQPIIRVMtfVGHasGKstkgFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLIICFDSQKSP 541
Cdd:cd18810    37 SIEKLATQLRQLVPEARIA--IAH--GQ----MTENELEEVMLEFAKGEYDILVCTTIIESGIDIPNANTIIIERADKFG 108

                          90
                  ....*....|....*.
gi 815890934  542 I-RLVQRMGRTGRKRQ 556
Cdd:cd18810   109 LaQLYQLRGRVGRSKE 124
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 412-586 6.49e-06

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 51.38  E-value: 6.49e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  412 DKNKKFVYSHPKLKKLEEVVIEHFKswnaenttekkRDEtRVMIFSSFRDSVQEIAEMLSQHQpiIRVMTFVGhasgkst 491
Cdd:COG0553   523 EEGAELSGRSAKLEALLELLEELLA-----------EGE-KVLVFSQFTDTLDLLEERLEERG--IEYAYLHG------- 581

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  492 kGFTQKEQLEVVKQFRDGGYNT--LVSTCVGEEGLDIGEVDLIICFDSQKSPIRLVQRMGRT---GRKRQGRIVIILSEG 566
Cdd:COG0553   582 -GTSAEERDELVDRFQEGPEAPvfLISLKAGGEGLNLTAADHVIHYDLWWNPAVEEQAIDRAhriGQTRDVQVYKLVAEG 660

                         170       180
                  ....*....|....*....|.
gi 815890934  567 -REERIYnQSQSNKRSIYKAI 586
Cdd:COG0553   661 tIEEKIL-ELLEEKRALAESV 680
DEXHc_ASCC3_2 cd18022
C-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ...
 105-170 1.55e-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: 1.55e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  105 CNTLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACYQ----VMGIpqsHMAEMTG 170
Cdd:cd18022    18 NNVLLGAPTGSGKTIAAELAMFRAFNKYPGSKVVYIAPLKALVRERVDDWKKrfeeKLGK---KVVELTG 84
DEXHc_DDX60 cd18025
DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an ...
 107-159 1.96e-05

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: 47.36  E-value: 1.96e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 815890934  107 TLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQqieACYQVMG 159
Cdd:cd18025    19 ALIVAPTSSGKTFISYYCMEKVLRESDDGVVVYVAPTKALVNQ---VVAEVYA 68
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 454-571 2.01e-05

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 49.46  E-value: 2.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  454 MIFSSFRDSVQEIAEMLSQHqpiirvmtfvGHASGKSTKGFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLII 533
Cdd:PRK11634  249 IIFVRTKNATLEVAEALERN----------GYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVV 318

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 815890934  534 CFDSQKSPIRLVQRMGRTGRK-RQGRiVIILSEGREERI 571
Cdd:PRK11634  319 NYDIPMDSESYVHRIGRTGRAgRAGR-ALLFVENRERRL 356
Cas3_I cd09639
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ...
 449-568 2.25e-05

CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I


Pssm-ID: 187770 [Multi-domain]  Cd Length: 353  Bit Score: 48.97  E-value: 2.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  449 DETRVMIFSSFRDSVQEIAEMLSQHQPIIRVMTFvgHasGKSTKGFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIgE 528
Cdd:cd09639   217 KGGSVAIIVNTVDRAQEFYQQLKEKGPEEEIMLI--H--SRFTEKDRAKKEAELLLEFKKSEKFVIVATQVIEASLDI-S 291

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 815890934  529 VDLIIcfdSQKSPI-RLVQRMGRTGRK--RQGRIVIILSEGRE 568
Cdd:cd09639   292 VDVMI---TELAPIdSLIQRLGRLHRYgeKNGEEVYIITDAPD 331
DEXHc_ASCC3_1 cd18020
N-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ...
 106-217 3.23e-05

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: 47.04  E-value: 3.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  106 NTLVCLPTGLGKTFIAAVVMYNFYRWF--PSG-------KVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEMTGSTQAsT 176
Cdd:cd18020    19 NMLICAPTGAGKTNIAMLTILHEIRQHvnQGGvikkddfKIVYIAPMKALAAEMVEKFSKRLAPLGIKVKELTGDMQL-T 97

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 815890934  177 RKEIwCSKRVLFLTPQ---VMVNDLSRGACPAAEIKCLVIDEAH 217
Cdd:cd18020    98 KKEI-AETQIIVTTPEkwdVVTRKSSGDVALSQLVRLLIIDEVH 140
DEXHc_RecQ cd17920
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ...
 92-217 6.68e-05

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: 45.99  E-value: 6.68e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   92 RDYQLHISRAAL-FCNTLVCLPTGLGKTfiaavVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACyQVMGIPqshMAEMTG 170
Cdd:cd17920    14 RPGQLEAINAVLaGRDVLVVMPTGGGKS-----LCYQLPALLLDGVTLVVSPLISLMQDQVDRL-QQLGIR---AAALNS 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 815890934  171 STQASTRKEIWCSK-----RVLFLTP----QVMVNDLSRGACPAAEIKCLVIDEAH 217
Cdd:cd17920    85 TLSPEEKREVLLRIkngqyKLLYVTPerllSPDFLELLQRLPERKRLALIVVDEAH 140
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 460-574 7.75e-05

CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 440816 [Multi-domain]  Cd Length: 535  Bit Score: 47.77  E-value: 7.75e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  460 RDSVQEIAEMLSQHQPIIRVMTFvgHASgkstkgFTQKEQLEVVKQ----FRDGGYNTLVSTCVGEEGLDIgevDliicF 535
Cdd:COG1203   376 VKDAQELYEALKEKLPDEEVYLL--HSR------FCPADRSEIEKEikerLERGKPCILVSTQVVEAGVDI---D----F 440

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 815890934  536 D---SQKSPIR-LVQRMGRT---GRKRQGRIVIILSEGRE--ERIYNQ 574
Cdd:COG1203   441 DvviRDLAPLDsLIQRAGRCnrhGRKEEEGNVYVFDPEDEggGYVYDK 488
PTZ00424 PTZ00424
helicase 45; Provisional
 495-553 1.38e-04

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 46.74  E-value: 1.38e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 815890934  495 TQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLIICFDSQKSPIRLVQRMGRTGR 553
Cdd:PTZ00424  302 DQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGR 360
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
 498-561 1.61e-04

C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II), and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA. Its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a DEAD-like helicase 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: 350177 [Multi-domain]  Cd Length: 171  Bit Score: 44.16  E-value: 1.61e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 815890934  498 EQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLIICFDSQK-----SPIRLVQRMGRTGRKRQGRIVI 561
Cdd:cd18790    65 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKegflrSETSLIQTIGRAARNVNGKVIL 133
SF2_C_Hrq cd18797
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...
 493-563 2.23e-04

C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases 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: 350184 [Multi-domain]  Cd Length: 146  Bit Score: 43.40  E-value: 2.23e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 815890934  493 GFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLIICFDSQKSPIRLVQRMGRTGRKRQGRIVIIL 563
Cdd:cd18797    75 GYLAEDRREIEAELFNGELLGVVATNALELGIDIGGLDAVVLAGYPGSLASLWQQAGRAGRRGKDSLVILV 145
DEXHc_RLR-2 cd18074
DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma ...
 91-217 2.29e-04

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: 44.47  E-value: 2.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   91 VRDYQLHISRAALFC-NTLVCLPTGLGKTFIAAVVMYNFY----RWFPSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHM 165
Cdd:cd18074     3 LRDYQMEVAKPALEGkNIIICLPTGSGKTRVAVYITKDHLdkkrKASEPGKVIVLVNKVPLVEQHYRKEFNPFLKHWYQV 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 815890934  166 AEMTGSTQASTR-KEIWCSKRVLFLTPQVMVNDLSRGA------CPAAEIKCLVIDEAH 217
Cdd:cd18074    83 IGLSGDSQLKISfPEVVKRYDVIICTAQILENSLLNATeeedegVQLSDFSLIIIDECH 141
cas3_core TIGR01587
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ...
 449-586 2.29e-04

CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.


Pssm-ID: 273707 [Multi-domain]  Cd Length: 359  Bit Score: 45.52  E-value: 2.29e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   449 DETRVMIFSSFRDSVQEIAEMLSQHQPIIRVMTFvgHasGKSTKGFTQKEQLEVVKQFRDGGYN-TLVSTCVGEEGLDIg 527
Cdd:TIGR01587  221 KGGSIAIIVNTVDRAQEFYQQLKEKAPEEEIILY--H--SRFTEKDRAKKEAELLREMKKSNEKfVIVATQVIEASLDI- 295

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 815890934   528 EVDLIIcfdSQKSPI-RLVQRMGRTGRK----RQGRIVIILSEGREeriYNQSQSNKRSIYKAI 586
Cdd:TIGR01587  296 SADVMI---TELAPIdSLIQRLGRLHRYgrkiGENFEVYIITIAPE---GKLFPYPYELVERTI 353
DEXHc_HFM1 cd18023
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ...
 106-217 2.38e-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: 2.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  106 NTLVCLPTGLGKTFIAAVVMYNFYRWFPSG-----KVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEMTGSTQASTRKEI 180
Cdd:cd18023    19 NFVVSAPTGSGKTVLFELAILRLLKERNPLpwgnrKVVYIAPIKALCSEKYDDWKEKFGPLGLSCAELTGDTEMDDTFEI 98

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 815890934  181 WcSKRVLFLTPQ---VMVNDLSRGACPAAEIKCLVIDEAH 217
Cdd:cd18023    99 Q-DADIILTTPEkwdSMTRRWRDNGNLVQLVALVLIDEVH 137
MRC1 pfam09444
MRC1-like domain; This putative domain is found to be the most conserved region in mediator of ...
 1479-1562 3.84e-04

MRC1-like domain; This putative domain is found to be the most conserved region in mediator of replication checkpoint protein 1.


Pssm-ID: 430616  Cd Length: 141  Bit Score: 42.55  E-value: 3.84e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  1479 KHVARKFLDDEAELSEEDAEYVSSDENDESENEQDSSLLDFLNDETqlSQAINDSEMRAIYMKSLRspmmNNKYKMIHKT 1558
Cdd:pfam09444    2 KSGASEFVEEEAEESEDEYAGLGGADDEDSDDEEDSELEEMIDDES--DEDVDEDELAALKAKEER----EEDEKEVEKL 75


                   ....
gi 815890934  1559 HKNI 1562
Cdd:pfam09444   76 LKDI 79
XPF_nuclease_XPF_euk cd20078
nuclease domain of XPF found in eukaryotes; XPF, also called DNA excision repair protein ...
 1815-1922 4.74e-04

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: 42.09  E-value: 4.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934 1815 HGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVEKDREKTGDTSRM--FRRTKSY 1892
Cdd:cd20078    20 AGIDLIPVTLEVGDYILSPDICVERKSISDLISSLNSGRLYTQLEAMCRYYKHPILLIEFDENKPFSLQSKssLSSEISS 99

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 815890934 1893 DSL---LTTLIGA--GIRILFSSCQEETADLLKEL 1922
Cdd:cd20078   100 NSLiskLVLLLLHfpKLRIIWSRSPHFTAELFREL 134
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 447-557 5.42e-04

C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins 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: 350186 [Multi-domain]  Cd Length: 116  Bit Score: 41.39  E-value: 5.42e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  447 KRDETRVMIFSSFRDSVQEIAEMLSQHQPIirvmtfVGHASGKSTKGFTQKEQLEVvKQFRDGGYNTLVSTCVGEEGLDI 526
Cdd:cd18799     3 KYVEIKTLIFCVSIEHAEFMAEAFNEAGID------AVALNSDYSDRERGDEALIL-LFFGELKPPILVTVDLLTTGVDI 75

                          90       100       110
                  ....*....|....*....|....*....|.
gi 815890934  527 GEVDLIICFDSQKSPIRLVQRMGRTGRKRQG 557
Cdd:cd18799    76 PEVDNVVFLRPTESRTLFLQMLGRGLRLHEG 106
DEAD-like_helicase_N cd17912
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 106-149 1.04e-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: 1.04e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 815890934  106 NTLVCLPTGLGKTFIAavVMYNFYRWFPSGKVVFMAPTKPLVTQ 149
Cdd:cd17912     1 NILHLGPTGSGKTLVA--IQKIASAMSSGKSVLVVTPTKLLAHE 42
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 493-563 1.09e-03

ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, recombination and repair];


Pssm-ID: 440818 [Multi-domain]  Cd Length: 758  Bit Score: 44.06  E-value: 1.09e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 815890934  493 GFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLIICFDSQKSPIRLVQRMGRTGRKRQGRIVIIL 563
Cdd:COG1205   327 GYLPEERREIERGLRSGELLGVVSTNALELGIDIGGLDAVVLAGYPGTRASFWQQAGRAGRRGQDSLVVLV 397
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
 106-217 1.55e-03

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: 41.55  E-value: 1.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  106 NTLVCLPTGLGKTFIAAVVMYNFyrWFPSGKVVFMAPTKPLVTQQIE--ACYQVMGIpqshmaEMTGSTQASTRKEIWCS 183
Cdd:cd18028    19 NLLISIPTASGKTLIAEMAMVNT--LLEGGKALYLVPLRALASEKYEefKKLEEIGL------KVGISTGDYDEDDEWLG 90

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 815890934  184 KRVLFLTPQVMVNDLSR-GACPAAEIKCLVIDEAH 217
Cdd:cd18028    91 DYDIIVATYEKFDSLLRhSPSWLRDVGVVVVDEIH 125
DEXHc_Brr2_1 cd18019
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD ...
 95-192 1.82e-03

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: 41.97  E-value: 1.82e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934   95 QLHISRAALFC--NTLVCLPTGLGKTFIAAVVM-------YNfyrwfPSG-------KVVFMAPTKPLVTQQIE------ 152
Cdd:cd18019    22 QSKLFPAAFETdeNLLLCAPTGAGKTNVALLTIlreigkhRN-----PDGtinldafKIVYIAPMKALVQEMVGnfskrl 96

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 815890934  153 ACYqvmGIpqsHMAEMTGSTQAsTRKEIwCSKRVLFLTPQ 192
Cdd:cd18019    97 APY---GI---TVAELTGDQQL-TKEQI-SETQIIVTTPE 128
PTZ00110 PTZ00110
helicase; Provisional
 496-553 2.21e-03

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 42.84  E-value: 2.21e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 815890934  496 QKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLIICFDSQKSPIRLVQRMGRTGR 553
Cdd:PTZ00110  413 QEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGR 470
PRK13767 PRK13767
ATP-dependent helicase; Provisional
 521-560 2.48e-03

ATP-dependent helicase; Provisional


Pssm-ID: 237497 [Multi-domain]  Cd Length: 876  Bit Score: 42.95  E-value: 2.48e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 815890934  521 EEGLDIGEVDLIICFDSQKSPIRLVQRMGRTG-RKRQ---GRIV 560
Cdd:PRK13767  351 ELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAGhRLGEvskGRII 394
PRK00254 PRK00254
ski2-like helicase; Provisional
 106-237 2.63e-03

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 42.88  E-value: 2.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  106 NTLVCLPTGLGKTFIAAVVMYN-FYRwfPSGKVVFMAPTKPLVTQQIEAC--YQVMGIpqsHMAEMTGSTQAstrKEIWC 182
Cdd:PRK00254   41 NLVLAIPTASGKTLVAEIVMVNkLLR--EGGKAVYLVPLKALAEEKYREFkdWEKLGL---RVAMTTGDYDS---TDEWL 112

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 815890934  183 SK-RVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHkALGNYAYCQAVQQVITNLL 237
Cdd:PRK00254  113 GKyDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIH-LIGSYDRGATLEMILTHML 167
DEXHc_Brr2_2 cd18021
C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type ...
 106-192 3.45e-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: 40.70  E-value: 3.45e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  106 NTLVCLPTGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACYQVMG-IPQSHMAEMTGSTQASTRkeIWCSK 184
Cdd:cd18021    21 NVFVGAPTGSGKTVCAELALLRHWRQNPKGRAVYIAPMQELVDARYKDWRAKFGpLLGKKVVKLTGETSTDLK--LLAKS 98


                  ....*...
gi 815890934  185 RVLFLTPQ 192
Cdd:cd18021    99 DVILATPE 106
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 462-553 5.50e-03

C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It is a DEAD-like helicase 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: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 39.63  E-value: 5.50e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 815890934  462 SVQEIAEMLSQHqpiIRVMTFVGHASGKstkgFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLIICFDSQKSP 541
Cdd:cd18811    46 AAVAMYEYLKER---FRPELNVGLLHGR----LKSDEKDAVMAEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFG 118

                          90
                  ....*....|...
gi 815890934  542 I-RLVQRMGRTGR 553
Cdd:cd18811   119 LsQLHQLRGRVGR 131
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH