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Conserved domains on  [gi|2212216228|ref|WP_242456480|]
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AAA domain-containing protein [Prosthecochloris ethylica]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
518-1347 2.11e-67

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


:

Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 245.42  E-value: 2.11e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  518 QSIAEGAYRGTAARIAEAVNRDRADYRWFTDSVPLDKTCQIDIIDLQNVLVALRLFTPEKRRELGLAWPEAMPSSERFAN 597
Cdd:COG1112      3 ALLLDAARALLALLALALLALLLALALLLDLLLLLLLAAALLLLALALALLLLALRALELLDLLAALALLLLLLLLDAEL 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  598 LVKNEKSAIEEEQKSAHDADERLADLLAENNPLTIEKIRDALSTFRDTQSRLRVAPHSWMNEALRDVLGNNSFLWHELLR 677
Cdd:COG1112     83 LLLALRALLLLLAAELLLLLLLLLLLAALLLALAALLLALALLLLALALLALLALLLAELLDLLAALAALAALLAALLLL 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  678 VTRDVIASIEELVTTADETRIELSDTIDIKSLHEDARKLKEHMESGGKLGWGMLRPKLVKELLYVIKDVKISGRPCSAVE 757
Cdd:COG1112    163 LLLLAALLLLDLRLLALLELLLAAALALALLALLALALEDELALLLLLLLLALLLLLALLLLLDALLLLLAALALLALAL 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  758 HFSTLADALHVRIECEKAWGFwkgRREKVEGPYALQLTVLKSLRDTLESALTLEGLIAECRKAISHCSVLSEPVWADESQ 837
Cdd:COG1112    243 LLALLLLLLALLLLAALALLR---AALRLDLLAALELLAALSLALLALLAALALALLLLAALALLLALALAALLALLALL 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  838 IERIIASCRLGLIRIRKLLAAEEIQDIEGPISQIAAGSGVHPVTDEVLTAIRGRDIDKFALCANKIQDLEKDRQRLQKVD 917
Cdd:COG1112    320 ALLAARLAAALAALLLLLLLEELALLAALLLLLELALLRLLAALLLALALLLLLALEELLLLALLRLLAEGLALLLLLLL 399

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  918 EDLSNLRSLLPKFTKSLEETCNDPYWEELIPRIGDAWHWAQARYWIEDYIRREDVPALSKRAKQIEDEISSIIAKLASLH 997
Cdd:COG1112    400 AALLRLARALLLLALLLAAAAAALAALLLLALALLAALLALLLLLAAALAALLALLLLLLLALAALLLLLAAAAALLALA 479

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  998 AWSFCFSRLKEDHRRHMEAWQQSMR---RLGKGTGKHAPRHRREAQGHLNECREAVPAWVMPLHRVWDTVYPAPGMFDVI 1074
Cdd:COG1112    480 LLESLLEELIEEHPEELEKLIAELReaaRLRRALRRELKKRRELRKLLWDALLELAPVVGMTPASVARLLPLGEGSFDLV 559

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1075 IVDEASQCGV-EALPLFYLGKKILIVGDDKQISPDAVGLPRDSVHRlmeeflhdfhfkssFDIESSLFDHGKLRYGTRRI 1153
Cdd:COG1112    560 IIDEASQATLaEALGALARAKRVVLVGDPKQLPPVVFGEEAEEVAE--------------EGLDESLLDRLLARLPERGV 625

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1154 TLREHFRCMPEIIRFSNDLCYSDTpLIPLRQYGPNRLP----PLEHVFVgDGHREGSNNRTINRPEAEAIVNRIAEMCDD 1229
Cdd:COG1112    626 MLREHYRMHPEIIAFSNRLFYDGK-LVPLPSPKARRLAdpdsPLVFIDV-DGVYERRGGSRTNPEEAEAVVELVRELLED 703

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1230 srRYDDKTMGVVVLQgEAQAALIENQLLERLGaeeMERRRLVCGNPYSFQGDERDIIFLSLVAASNE----RIGPLTKaa 1305
Cdd:COG1112    704 --GPDGESIGVITPY-RAQVALIRELLREALG---DGLEPVFVGTVDRFQGDERDVIIFSLVYSNDEdvprNFGFLNG-- 775

                          810       820       830       840
                   ....*....|....*....|....*....|....*....|...
gi 2212216228 1306 DERRFNVAASRARDMMILFHSVTSNDLSASC-LRKQLLDFFEN 1347
Cdd:COG1112    776 GPRRLNVAVSRARRKLIVVGSRELLDSDPSTpALKRLLEYLER 818
MTES_1575 pfam18741
REase_MTES_1575; Vsr REase Fold. Fused to HEPN (SWT1/Abi2 family), along with Transglutaminase ...
 1383-1475 2.72e-33

REase_MTES_1575; Vsr REase Fold. Fused to HEPN (SWT1/Abi2 family), along with Transglutaminase and wHTH.


:

Pssm-ID: 465853  Cd Length: 96  Bit Score: 124.12  E-value: 2.72e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1383 FEVDVALELLRKDFSVLAQHEVAGKRIDLVVEG--GQARLAVECDGDHWHGA-DRYEDDMQRQRQLERCGWEFFRVRESA 1459
Cdd:pfam18741    1 FEEEVAEALRERGYRVVPQVGVGGYRIDLVVVDppGRYRLGIECDGATYHSSkSARDRDRLRQRVLERLGWKFHRIWSTD 80

                           90
                   ....*....|....*.
gi 2212216228 1460 FYANKESALAGLWQAL 1475
Cdd:pfam18741   81 WYRDPEAELERLWEAL 96
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 380-437 1.13e-23

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


The actual alignment was detected with superfamily member cd18043:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 127  Bit Score: 98.04  E-value: 1.13e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2212216228  380 NDEQRRIVDKMRAASGVLVQGPPGTGKSHTIANLICHLLATGQRTLITAKTPRALQVL 437
Cdd:cd18043      1 DSSQEAAIISARNGKNVVIQGPPGTGKSQTIANIIANALARGKRVLFVSEKKAALDVV 58
AAA_11 super family cl38386
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 383-516 1.15e-07

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


The actual alignment was detected with superfamily member pfam13086:

Pssm-ID: 404072 [Multi-domain]  Cd Length: 248  Bit Score: 54.66  E-value: 1.15e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  383 QRRIVDKMRAASGV-LVQGPPGTGKSHTIANLICHLLAT-------GQRTLITAKTPRALQVLEGLVPDELRPLCINLLG 454
Cdd:pfam13086    2 QREAIRSALSSSHFtLIQGPPGTGKTTTIVELIRQLLSYpatsaaaGPRILVCAPSNAAVDNILERLLRKGQKYGPKIVR 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2212216228  455 SGLEERR-------SLESSVGGILRKNEEWNDDRAKRERTELEERLRKLREEKARVNRRLRDIRESETH 516
Cdd:pfam13086   82 IGHPAAIseavlpvSLDYLVESKLNNEEDAQIVKDISKELEKLAKALRAFEKEIIVEKLLKSRNKDKSK 150
 
Name Accession Description Interval E-value
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
518-1347 2.11e-67

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 245.42  E-value: 2.11e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  518 QSIAEGAYRGTAARIAEAVNRDRADYRWFTDSVPLDKTCQIDIIDLQNVLVALRLFTPEKRRELGLAWPEAMPSSERFAN 597
Cdd:COG1112      3 ALLLDAARALLALLALALLALLLALALLLDLLLLLLLAAALLLLALALALLLLALRALELLDLLAALALLLLLLLLDAEL 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  598 LVKNEKSAIEEEQKSAHDADERLADLLAENNPLTIEKIRDALSTFRDTQSRLRVAPHSWMNEALRDVLGNNSFLWHELLR 677
Cdd:COG1112     83 LLLALRALLLLLAAELLLLLLLLLLLAALLLALAALLLALALLLLALALLALLALLLAELLDLLAALAALAALLAALLLL 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  678 VTRDVIASIEELVTTADETRIELSDTIDIKSLHEDARKLKEHMESGGKLGWGMLRPKLVKELLYVIKDVKISGRPCSAVE 757
Cdd:COG1112    163 LLLLAALLLLDLRLLALLELLLAAALALALLALLALALEDELALLLLLLLLALLLLLALLLLLDALLLLLAALALLALAL 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  758 HFSTLADALHVRIECEKAWGFwkgRREKVEGPYALQLTVLKSLRDTLESALTLEGLIAECRKAISHCSVLSEPVWADESQ 837
Cdd:COG1112    243 LLALLLLLLALLLLAALALLR---AALRLDLLAALELLAALSLALLALLAALALALLLLAALALLLALALAALLALLALL 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  838 IERIIASCRLGLIRIRKLLAAEEIQDIEGPISQIAAGSGVHPVTDEVLTAIRGRDIDKFALCANKIQDLEKDRQRLQKVD 917
Cdd:COG1112    320 ALLAARLAAALAALLLLLLLEELALLAALLLLLELALLRLLAALLLALALLLLLALEELLLLALLRLLAEGLALLLLLLL 399

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  918 EDLSNLRSLLPKFTKSLEETCNDPYWEELIPRIGDAWHWAQARYWIEDYIRREDVPALSKRAKQIEDEISSIIAKLASLH 997
Cdd:COG1112    400 AALLRLARALLLLALLLAAAAAALAALLLLALALLAALLALLLLLAAALAALLALLLLLLLALAALLLLLAAAAALLALA 479

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  998 AWSFCFSRLKEDHRRHMEAWQQSMR---RLGKGTGKHAPRHRREAQGHLNECREAVPAWVMPLHRVWDTVYPAPGMFDVI 1074
Cdd:COG1112    480 LLESLLEELIEEHPEELEKLIAELReaaRLRRALRRELKKRRELRKLLWDALLELAPVVGMTPASVARLLPLGEGSFDLV 559

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1075 IVDEASQCGV-EALPLFYLGKKILIVGDDKQISPDAVGLPRDSVHRlmeeflhdfhfkssFDIESSLFDHGKLRYGTRRI 1153
Cdd:COG1112    560 IIDEASQATLaEALGALARAKRVVLVGDPKQLPPVVFGEEAEEVAE--------------EGLDESLLDRLLARLPERGV 625

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1154 TLREHFRCMPEIIRFSNDLCYSDTpLIPLRQYGPNRLP----PLEHVFVgDGHREGSNNRTINRPEAEAIVNRIAEMCDD 1229
Cdd:COG1112    626 MLREHYRMHPEIIAFSNRLFYDGK-LVPLPSPKARRLAdpdsPLVFIDV-DGVYERRGGSRTNPEEAEAVVELVRELLED 703

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1230 srRYDDKTMGVVVLQgEAQAALIENQLLERLGaeeMERRRLVCGNPYSFQGDERDIIFLSLVAASNE----RIGPLTKaa 1305
Cdd:COG1112    704 --GPDGESIGVITPY-RAQVALIRELLREALG---DGLEPVFVGTVDRFQGDERDVIIFSLVYSNDEdvprNFGFLNG-- 775

                          810       820       830       840
                   ....*....|....*....|....*....|....*....|...
gi 2212216228 1306 DERRFNVAASRARDMMILFHSVTSNDLSASC-LRKQLLDFFEN 1347
Cdd:COG1112    776 GPRRLNVAVSRARRKLIVVGSRELLDSDPSTpALKRLLEYLER 818
MTES_1575 pfam18741
REase_MTES_1575; Vsr REase Fold. Fused to HEPN (SWT1/Abi2 family), along with Transglutaminase ...
 1383-1475 2.72e-33

REase_MTES_1575; Vsr REase Fold. Fused to HEPN (SWT1/Abi2 family), along with Transglutaminase and wHTH.


Pssm-ID: 465853  Cd Length: 96  Bit Score: 124.12  E-value: 2.72e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1383 FEVDVALELLRKDFSVLAQHEVAGKRIDLVVEG--GQARLAVECDGDHWHGA-DRYEDDMQRQRQLERCGWEFFRVRESA 1459
Cdd:pfam18741    1 FEEEVAEALRERGYRVVPQVGVGGYRIDLVVVDppGRYRLGIECDGATYHSSkSARDRDRLRQRVLERLGWKFHRIWSTD 80

                           90
                   ....*....|....*.
gi 2212216228 1460 FYANKESALAGLWQAL 1475
Cdd:pfam18741   81 WYRDPEAELERLWEAL 96
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 1161-1346 6.95e-33

C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), and similar proteins. They are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350195 [Multi-domain]  Cd Length: 184  Bit Score: 126.19  E-value: 6.95e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1161 CMPEIIRFSNDLCYSDTPLI-------PLRQYGPNRLPPLEHVFVGDGH-REGSNNRTINRPEAEAIVNRIAEMCDdsRR 1232
Cdd:cd18808      1 MHPEISEFPSKLFYEGKLKAgvsvaarLNPPPLPGPSKPLVFVDVSGGEeREESGTSKSNEAEAELVVELVKYLLK--SG 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1233 YDDKTMGVVVLQgEAQAALIENQLLERLGaeemERRRLVCGNPYSFQGDERDIIFLSLVaASNERIGPLTKAADERRFNV 1312
Cdd:cd18808     79 VKPSSIGVITPY-RAQVALIRELLRKRGG----LLEDVEVGTVDNFQGREKDVIILSLV-RSNESGGSIGFLSDPRRLNV 152

                          170       180       190
                   ....*....|....*....|....*....|....
gi 2212216228 1313 AASRARDMMILFHSvtSNDLSASCLRKQLLDFFE 1346
Cdd:cd18808    153 ALTRAKRGLIIVGN--PDTLSKDPLWKKLLEYLE 184
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 380-437 1.13e-23

DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. This is central to many aspects of cellular DNA and RNA metabolism and accordingly, they are implicated in a wide range of nucleic acid processing events including DNA replication, recombination, and repair as well as many aspects of RNA metabolism. Superfamily 1 helicases are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350801 [Multi-domain]  Cd Length: 127  Bit Score: 98.04  E-value: 1.13e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2212216228  380 NDEQRRIVDKMRAASGVLVQGPPGTGKSHTIANLICHLLATGQRTLITAKTPRALQVL 437
Cdd:cd18043      1 DSSQEAAIISARNGKNVVIQGPPGTGKSQTIANIIANALARGKRVLFVSEKKAALDVV 58
YcjD COG2852
Very-short-patch-repair endonuclease [Replication, recombination and repair];
1377-1478 1.09e-19

Very-short-patch-repair endonuclease [Replication, recombination and repair];


Pssm-ID: 442100  Cd Length: 104  Bit Score: 85.69  E-value: 1.09e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1377 PPFDSWFEVDVALELLRKDFS---VLAQHEVAGKRIDLVVEGgqARLAVECDGDHWHGADRYEDDMQRQRQLERCGWEFF 1453
Cdd:COG2852      2 RRNDTPAERRLWQRLRNRQLRglkFRRQVPIGGYIVDFYCPE--ARLAIEVDGGYHGSPEQRERDRRRDAYLERLGWRVL 79

                           90       100
                   ....*....|....*....|....*
gi 2212216228 1454 RVRESAFYANKESALAGLWQALEER 1478
Cdd:COG2852     80 RFWNEDVLRNPEGVLEEILAALEER 104
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 1139-1318 4.71e-15

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


Pssm-ID: 463780 [Multi-domain]  Cd Length: 196  Bit Score: 75.28  E-value: 4.71e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1139 SLFDHGKLRYGTRRITLREHFRCMPEIIRFSNDLCY-----SDTPLIPLRQYGPNRLPPLEH--VFVG-DGHREGSNNRT 1210
Cdd:pfam13087    4 SLFERLQELGPSAVVMLDTQYRMHPEIMEFPSKLFYggklkDGPSVAERPLPDDFHLPDPLGplVFIDvDGSEEEESDGG 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1211 ---INRPEAEAIVNRIAEMCDDSRRyDDKTMGVVVLQGeAQAALIEnqllERLGAEEMERRRLVCGNPYSFQGDERDIIF 1287
Cdd:pfam13087   84 tsySNEAEAELVVQLVEKLIKSGPE-EPSDIGVITPYR-AQVRLIR----KLLKRKLGGKLEIEVNTVDGFQGREKDVII 157

                          170       180       190
                   ....*....|....*....|....*....|..
gi 2212216228 1288 LSLVAASNE-RIGPLtkaADERRFNVAASRAR 1318
Cdd:pfam13087  158 FSCVRSNEKgGIGFL---SDPRRLNVALTRAK 186
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 383-516 1.15e-07

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


Pssm-ID: 404072 [Multi-domain]  Cd Length: 248  Bit Score: 54.66  E-value: 1.15e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  383 QRRIVDKMRAASGV-LVQGPPGTGKSHTIANLICHLLAT-------GQRTLITAKTPRALQVLEGLVPDELRPLCINLLG 454
Cdd:pfam13086    2 QREAIRSALSSSHFtLIQGPPGTGKTTTIVELIRQLLSYpatsaaaGPRILVCAPSNAAVDNILERLLRKGQKYGPKIVR 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2212216228  455 SGLEERR-------SLESSVGGILRKNEEWNDDRAKRERTELEERLRKLREEKARVNRRLRDIRESETH 516
Cdd:pfam13086   82 IGHPAAIseavlpvSLDYLVESKLNNEEDAQIVKDISKELEKLAKALRAFEKEIIVEKLLKSRNKDKSK 150
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 374-511 1.77e-05

DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273041 [Multi-domain]  Cd Length: 636  Bit Score: 49.43  E-value: 1.77e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  374 FFPKPSNDEQRRIVDKMRAASGV-LVQGPPGTGKSHTIANLICHLLATGQRTLITAKTPRAL-QVLEGLVPDELRplCIN 451
Cdd:TIGR00376  153 FFDPNLNESQKEAVLFALSSKDLfLIHGPPGTGKTRTVVELIRQLVKRGLRVLVTAPSNIAVdNLLERLALCDQK--IVR 230

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2212216228  452 LLGSGLEERRSLESSVGGILRKNEEWNDDRAKRERT-ELEERLRKLREEKARVNRRLRDIR 511
Cdd:TIGR00376  231 LGHPARLLKSNKQHSLDYLIENHPKYQIVADIREKIdELIEERNKKTKPSPQKRRGLSDIK 291
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 380-438 2.16e-05

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


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 49.20  E-value: 2.16e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  380 NDEQRRIVDKMRAASGVLV-QGPPGTGKSHTIANLICHLLATGQRTLITAKTPRALQVLE 438
Cdd:COG0507    126 SDEQREAVALALTTRRVSVlTGGAGTGKTTTLRALLAALEALGLRVALAAPTGKAAKRLS 185
AAA_19 pfam13245
AAA domain;
383-437 6.26e-04

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 41.43  E-value: 6.26e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2212216228  383 QRRIVDKMRAASGVLVQGPPGTGKSHTIANLICHLLATGQ---RTLITAKTPRALQVL 437
Cdd:pfam13245    1 QREAVRTALPSKVVLLTGGPGTGKTTTIRHIVALLVALGGvsfPILLAAPTGRAAKRL 58
Endonuclease_DUF559 cd01038
Putative endonuclease; Domain of unknown function 559 (DUF559) is a putative endonuclease of ...
 1417-1475 2.48e-03

Putative endonuclease; Domain of unknown function 559 (DUF559) is a putative endonuclease of unknown function, belongs to a 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: 411708  Cd Length: 97  Bit Score: 38.72  E-value: 2.48e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2212216228 1417 QARLAVECDGDHWHGADRYEDDMQRQRQLERCGWEFFRVRESAFYANKESALAGLWQAL 1475
Cdd:cd01038     39 EKKLVIEIDGGQHHEKKAEEYDARRDKYLESLGYTVLRFWNEEVLNNIEGVLEKIEKFL 97
 
Name Accession Description Interval E-value
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
518-1347 2.11e-67

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 245.42  E-value: 2.11e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  518 QSIAEGAYRGTAARIAEAVNRDRADYRWFTDSVPLDKTCQIDIIDLQNVLVALRLFTPEKRRELGLAWPEAMPSSERFAN 597
Cdd:COG1112      3 ALLLDAARALLALLALALLALLLALALLLDLLLLLLLAAALLLLALALALLLLALRALELLDLLAALALLLLLLLLDAEL 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  598 LVKNEKSAIEEEQKSAHDADERLADLLAENNPLTIEKIRDALSTFRDTQSRLRVAPHSWMNEALRDVLGNNSFLWHELLR 677
Cdd:COG1112     83 LLLALRALLLLLAAELLLLLLLLLLLAALLLALAALLLALALLLLALALLALLALLLAELLDLLAALAALAALLAALLLL 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  678 VTRDVIASIEELVTTADETRIELSDTIDIKSLHEDARKLKEHMESGGKLGWGMLRPKLVKELLYVIKDVKISGRPCSAVE 757
Cdd:COG1112    163 LLLLAALLLLDLRLLALLELLLAAALALALLALLALALEDELALLLLLLLLALLLLLALLLLLDALLLLLAALALLALAL 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  758 HFSTLADALHVRIECEKAWGFwkgRREKVEGPYALQLTVLKSLRDTLESALTLEGLIAECRKAISHCSVLSEPVWADESQ 837
Cdd:COG1112    243 LLALLLLLLALLLLAALALLR---AALRLDLLAALELLAALSLALLALLAALALALLLLAALALLLALALAALLALLALL 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  838 IERIIASCRLGLIRIRKLLAAEEIQDIEGPISQIAAGSGVHPVTDEVLTAIRGRDIDKFALCANKIQDLEKDRQRLQKVD 917
Cdd:COG1112    320 ALLAARLAAALAALLLLLLLEELALLAALLLLLELALLRLLAALLLALALLLLLALEELLLLALLRLLAEGLALLLLLLL 399

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  918 EDLSNLRSLLPKFTKSLEETCNDPYWEELIPRIGDAWHWAQARYWIEDYIRREDVPALSKRAKQIEDEISSIIAKLASLH 997
Cdd:COG1112    400 AALLRLARALLLLALLLAAAAAALAALLLLALALLAALLALLLLLAAALAALLALLLLLLLALAALLLLLAAAAALLALA 479

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  998 AWSFCFSRLKEDHRRHMEAWQQSMR---RLGKGTGKHAPRHRREAQGHLNECREAVPAWVMPLHRVWDTVYPAPGMFDVI 1074
Cdd:COG1112    480 LLESLLEELIEEHPEELEKLIAELReaaRLRRALRRELKKRRELRKLLWDALLELAPVVGMTPASVARLLPLGEGSFDLV 559

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1075 IVDEASQCGV-EALPLFYLGKKILIVGDDKQISPDAVGLPRDSVHRlmeeflhdfhfkssFDIESSLFDHGKLRYGTRRI 1153
Cdd:COG1112    560 IIDEASQATLaEALGALARAKRVVLVGDPKQLPPVVFGEEAEEVAE--------------EGLDESLLDRLLARLPERGV 625

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1154 TLREHFRCMPEIIRFSNDLCYSDTpLIPLRQYGPNRLP----PLEHVFVgDGHREGSNNRTINRPEAEAIVNRIAEMCDD 1229
Cdd:COG1112    626 MLREHYRMHPEIIAFSNRLFYDGK-LVPLPSPKARRLAdpdsPLVFIDV-DGVYERRGGSRTNPEEAEAVVELVRELLED 703

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1230 srRYDDKTMGVVVLQgEAQAALIENQLLERLGaeeMERRRLVCGNPYSFQGDERDIIFLSLVAASNE----RIGPLTKaa 1305
Cdd:COG1112    704 --GPDGESIGVITPY-RAQVALIRELLREALG---DGLEPVFVGTVDRFQGDERDVIIFSLVYSNDEdvprNFGFLNG-- 775

                          810       820       830       840
                   ....*....|....*....|....*....|....*....|...
gi 2212216228 1306 DERRFNVAASRARDMMILFHSVTSNDLSASC-LRKQLLDFFEN 1347
Cdd:COG1112    776 GPRRLNVAVSRARRKLIVVGSRELLDSDPSTpALKRLLEYLER 818
MTES_1575 pfam18741
REase_MTES_1575; Vsr REase Fold. Fused to HEPN (SWT1/Abi2 family), along with Transglutaminase ...
 1383-1475 2.72e-33

REase_MTES_1575; Vsr REase Fold. Fused to HEPN (SWT1/Abi2 family), along with Transglutaminase and wHTH.


Pssm-ID: 465853  Cd Length: 96  Bit Score: 124.12  E-value: 2.72e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1383 FEVDVALELLRKDFSVLAQHEVAGKRIDLVVEG--GQARLAVECDGDHWHGA-DRYEDDMQRQRQLERCGWEFFRVRESA 1459
Cdd:pfam18741    1 FEEEVAEALRERGYRVVPQVGVGGYRIDLVVVDppGRYRLGIECDGATYHSSkSARDRDRLRQRVLERLGWKFHRIWSTD 80

                           90
                   ....*....|....*.
gi 2212216228 1460 FYANKESALAGLWQAL 1475
Cdd:pfam18741   81 WYRDPEAELERLWEAL 96
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 1161-1346 6.95e-33

C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), and similar proteins. They are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350195 [Multi-domain]  Cd Length: 184  Bit Score: 126.19  E-value: 6.95e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1161 CMPEIIRFSNDLCYSDTPLI-------PLRQYGPNRLPPLEHVFVGDGH-REGSNNRTINRPEAEAIVNRIAEMCDdsRR 1232
Cdd:cd18808      1 MHPEISEFPSKLFYEGKLKAgvsvaarLNPPPLPGPSKPLVFVDVSGGEeREESGTSKSNEAEAELVVELVKYLLK--SG 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1233 YDDKTMGVVVLQgEAQAALIENQLLERLGaeemERRRLVCGNPYSFQGDERDIIFLSLVaASNERIGPLTKAADERRFNV 1312
Cdd:cd18808     79 VKPSSIGVITPY-RAQVALIRELLRKRGG----LLEDVEVGTVDNFQGREKDVIILSLV-RSNESGGSIGFLSDPRRLNV 152

                          170       180       190
                   ....*....|....*....|....*....|....
gi 2212216228 1313 AASRARDMMILFHSvtSNDLSASCLRKQLLDFFE 1346
Cdd:cd18808    153 ALTRAKRGLIIVGN--PDTLSKDPLWKKLLEYLE 184
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 380-437 1.13e-23

DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. This is central to many aspects of cellular DNA and RNA metabolism and accordingly, they are implicated in a wide range of nucleic acid processing events including DNA replication, recombination, and repair as well as many aspects of RNA metabolism. Superfamily 1 helicases are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350801 [Multi-domain]  Cd Length: 127  Bit Score: 98.04  E-value: 1.13e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2212216228  380 NDEQRRIVDKMRAASGVLVQGPPGTGKSHTIANLICHLLATGQRTLITAKTPRALQVL 437
Cdd:cd18043      1 DSSQEAAIISARNGKNVVIQGPPGTGKSQTIANIIANALARGKRVLFVSEKKAALDVV 58
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 1049-1107 2.90e-22

DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. This is central to many aspects of cellular DNA and RNA metabolism and accordingly, they are implicated in a wide range of nucleic acid processing events including DNA replication, recombination, and repair as well as many aspects of RNA metabolism. Superfamily 1 helicases are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350801 [Multi-domain]  Cd Length: 127  Bit Score: 93.80  E-value: 2.90e-22
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1049 AVPAWVMPLHRVWDTVYPAPGMFDVIIVDEASQCGVE-ALPLFYLGKKILIVGDDKQISP 1107
Cdd:cd18043     59 RFPCWIMSPLSVSQYLPLNRNLFDLVIFDEASQIPIEeALPALFRGKQVVVVGDDKQLPP 118
YcjD COG2852
Very-short-patch-repair endonuclease [Replication, recombination and repair];
1377-1478 1.09e-19

Very-short-patch-repair endonuclease [Replication, recombination and repair];


Pssm-ID: 442100  Cd Length: 104  Bit Score: 85.69  E-value: 1.09e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1377 PPFDSWFEVDVALELLRKDFS---VLAQHEVAGKRIDLVVEGgqARLAVECDGDHWHGADRYEDDMQRQRQLERCGWEFF 1453
Cdd:COG2852      2 RRNDTPAERRLWQRLRNRQLRglkFRRQVPIGGYIVDFYCPE--ARLAIEVDGGYHGSPEQRERDRRRDAYLERLGWRVL 79

                           90       100
                   ....*....|....*....|....*
gi 2212216228 1454 RVRESAFYANKESALAGLWQALEER 1478
Cdd:COG2852     80 RFWNEDVLRNPEGVLEEILAALEER 104
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 1139-1318 4.71e-15

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


Pssm-ID: 463780 [Multi-domain]  Cd Length: 196  Bit Score: 75.28  E-value: 4.71e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1139 SLFDHGKLRYGTRRITLREHFRCMPEIIRFSNDLCY-----SDTPLIPLRQYGPNRLPPLEH--VFVG-DGHREGSNNRT 1210
Cdd:pfam13087    4 SLFERLQELGPSAVVMLDTQYRMHPEIMEFPSKLFYggklkDGPSVAERPLPDDFHLPDPLGplVFIDvDGSEEEESDGG 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1211 ---INRPEAEAIVNRIAEMCDDSRRyDDKTMGVVVLQGeAQAALIEnqllERLGAEEMERRRLVCGNPYSFQGDERDIIF 1287
Cdd:pfam13087   84 tsySNEAEAELVVQLVEKLIKSGPE-EPSDIGVITPYR-AQVRLIR----KLLKRKLGGKLEIEVNTVDGFQGREKDVII 157

                          170       180       190
                   ....*....|....*....|....*....|..
gi 2212216228 1288 LSLVAASNE-RIGPLtkaADERRFNVAASRAR 1318
Cdd:pfam13087  158 FSCVRSNEKgGIGFL---SDPRRLNVALTRAK 186
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 1071-1160 1.63e-12

DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438708 [Multi-domain]  Cd Length: 121  Bit Score: 65.72  E-value: 1.63e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228 1071 FDVIIVDEASQC-GVEALPLFYLGKKILIVGDDKQISPdavglPRDSVHRLMEEFLHDFHFKSSFdiesslfdhGKLRYG 1149
Cdd:cd17934     45 VDVVIIDEASQItEPELLIALIRAKKVVLVGDPKQLPP-----VVQEDHAALLGLSFILSLLLLF---------RLLLPG 110

                           90
                   ....*....|.
gi 2212216228 1150 TRRITLREHFR 1160
Cdd:cd17934    111 SPKVMLDTQYR 121
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 396-444 6.55e-10

DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438708 [Multi-domain]  Cd Length: 121  Bit Score: 58.40  E-value: 6.55e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2212216228  396 VLVQGPPGTGKSHTIANLICHLLAT--GQRTLITAKTPRALQVLEGLVPDE 444
Cdd:cd17934      2 SLIQGPPGTGKTTTIAAIVLQLLKGlrGKRVLVTAQSNVAVDNVDVVIIDE 52
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 383-516 1.15e-07

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


Pssm-ID: 404072 [Multi-domain]  Cd Length: 248  Bit Score: 54.66  E-value: 1.15e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  383 QRRIVDKMRAASGV-LVQGPPGTGKSHTIANLICHLLAT-------GQRTLITAKTPRALQVLEGLVPDELRPLCINLLG 454
Cdd:pfam13086    2 QREAIRSALSSSHFtLIQGPPGTGKTTTIVELIRQLLSYpatsaaaGPRILVCAPSNAAVDNILERLLRKGQKYGPKIVR 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2212216228  455 SGLEERR-------SLESSVGGILRKNEEWNDDRAKRERTELEERLRKLREEKARVNRRLRDIRESETH 516
Cdd:pfam13086   82 IGHPAAIseavlpvSLDYLVESKLNNEEDAQIVKDISKELEKLAKALRAFEKEIIVEKLLKSRNKDKSK 150
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 380-430 1.38e-07

DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses different enzymatic activities, such as single-stranded DNA (ssDNA)-dependent ATPase, 5-3 helicase, and endonuclease activities, and is involved in DNA replication and DNA repair in the nucleus and mitochondrion. It is involved in Okazaki fragment processing by cleaving long flaps that escape FEN1: flaps that are longer than 27 nucleotides are coated by replication protein A complex (RPA), leading to recruit DNA2 which cleaves the flap until it is too short to bind RPA and becomes a substrate for FEN1. It is also involved in 5-end resection of DNA during double-strand break (DSB) repair; it is recruited by BLM and mediates the cleavage of 5-ssDNA, while the 3-ssDNA cleavage is prevented by the presence of RPA. DNA2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350799 [Multi-domain]  Cd Length: 203  Bit Score: 53.78  E-value: 1.38e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2212216228  380 NDEQRRIVDK-MRAASGVLVQGPPGTGKSHTIANLICHLLATGQRTLITAKT 430
Cdd:cd18041      3 NKDQRQAIKKvLNAKDYALILGMPGTGKTTTIAALVRILVALGKSVLLTSYT 54
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 380-428 1.56e-06

DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, or IGHMBP2) is a 5' to 3' helicase that unwinds RNA and DNA duplexes in an ATP-dependent reaction. It is a DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence (5'-GGGCT-3') related to the immunoglobulin mu chain switch region. The IGHMBP2 gene is responsible for Charcot-Marie-Tooth disease (CMT) type 2S and spinal muscular atrophy with respiratory distress type 1 (SMARD1). It is also thought to play a role in frontotemporal dementia (FTD) with amyotrophic lateral sclerosis (ALS) and major depressive disorder (MDD). SMUBP2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350802 [Multi-domain]  Cd Length: 191  Bit Score: 50.30  E-value: 1.56e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2212216228  380 NDEQRRIVDKMRAASGV-LVQGPPGTGKSHTIANLICHLLATGQRTLITA 428
Cdd:cd18044      3 NDSQKEAVKFALSQKDVaLIHGPPGTGKTTTVVEIILQAVKRGEKVLACA 52
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 1071-1107 1.25e-05

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


Pssm-ID: 404072 [Multi-domain]  Cd Length: 248  Bit Score: 48.49  E-value: 1.25e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 2212216228 1071 FDVIIVDEASQCgVEA---LPLFYLGKKILIVGDDKQISP 1107
Cdd:pfam13086  205 FDVVIIDEAAQA-LEPstlIPLLRGPKKVVLVGDPKQLPP 243
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 374-511 1.77e-05

DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273041 [Multi-domain]  Cd Length: 636  Bit Score: 49.43  E-value: 1.77e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  374 FFPKPSNDEQRRIVDKMRAASGV-LVQGPPGTGKSHTIANLICHLLATGQRTLITAKTPRAL-QVLEGLVPDELRplCIN 451
Cdd:TIGR00376  153 FFDPNLNESQKEAVLFALSSKDLfLIHGPPGTGKTRTVVELIRQLVKRGLRVLVTAPSNIAVdNLLERLALCDQK--IVR 230

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2212216228  452 LLGSGLEERRSLESSVGGILRKNEEWNDDRAKRERT-ELEERLRKLREEKARVNRRLRDIR 511
Cdd:TIGR00376  231 LGHPARLLKSNKQHSLDYLIENHPKYQIVADIREKIdELIEERNKKTKPSPQKRRGLSDIK 291
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 380-438 2.16e-05

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


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 49.20  E-value: 2.16e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2212216228  380 NDEQRRIVDKMRAASGVLV-QGPPGTGKSHTIANLICHLLATGQRTLITAKTPRALQVLE 438
Cdd:COG0507    126 SDEQREAVALALTTRRVSVlTGGAGTGKTTTLRALLAALEALGLRVALAAPTGKAAKRLS 185
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 382-437 3.52e-05

DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350691 [Multi-domain]  Cd Length: 155  Bit Score: 45.62  E-value: 3.52e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2212216228  382 EQRRIVDKMRAASGVLVQGPPGTGKSHTIANLICHLLATGQRTLITAKTPRALQVL 437
Cdd:cd17933      1 EQKAAVRLVLRNRVSVLTGGAGTGKTTTLKALLAALEAEGKRVVLAAPTGKAAKRL 56
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 396-420 7.16e-05

DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in transcription, neurogenesis, and antiviral response. SEXT is an R-loop-associated protein that is thought to function as an RNA/DNA helicase. R-loops consist of RNA/DNA hybrids, formed during transcription when nascent RNA hybridizes to the DNA template strand, displacing the non-template DNA strand. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). S. cerevisiae homolog splicing endonuclease 1 (Sen1) is an exclusively nuclear protein, important for nucleolar organization. S. cerevisiae Sen1 and its ortholog, the Schizosaccharomyces pombe Sen1, share conserved domains and belong to the family I class of helicases. Both proteins translocate 5' to 3' and unwind both DNA and RNA duplexes and also RNA/DNA hybrids in vitro. SETX is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438712 [Multi-domain]  Cd Length: 218  Bit Score: 45.67  E-value: 7.16e-05
                           10        20
                   ....*....|....*....|....*
gi 2212216228  396 VLVQGPPGTGKSHTIANLICHLLAT 420
Cdd:cd18042     20 TLIQGPPGTGKTKTIVGILSVLLAG 44
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 1071-1109 9.61e-05

DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in transcription, neurogenesis, and antiviral response. SEXT is an R-loop-associated protein that is thought to function as an RNA/DNA helicase. R-loops consist of RNA/DNA hybrids, formed during transcription when nascent RNA hybridizes to the DNA template strand, displacing the non-template DNA strand. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). S. cerevisiae homolog splicing endonuclease 1 (Sen1) is an exclusively nuclear protein, important for nucleolar organization. S. cerevisiae Sen1 and its ortholog, the Schizosaccharomyces pombe Sen1, share conserved domains and belong to the family I class of helicases. Both proteins translocate 5' to 3' and unwind both DNA and RNA duplexes and also RNA/DNA hybrids in vitro. SETX is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438712 [Multi-domain]  Cd Length: 218  Bit Score: 45.28  E-value: 9.61e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2212216228 1071 FDVIIVDEASQCgVEA---LPLFYLGKKILIVGDDKQ-----ISPDA 1109
Cdd:cd18042    145 FDTVIIDEAAQA-VELstlIPLRLGCKRLILVGDPKQlpatvFSKVA 190
AAA_19 pfam13245
AAA domain;
383-437 6.26e-04

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 41.43  E-value: 6.26e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2212216228  383 QRRIVDKMRAASGVLVQGPPGTGKSHTIANLICHLLATGQ---RTLITAKTPRALQVL 437
Cdd:pfam13245    1 QREAVRTALPSKVVLLTGGPGTGKTTTIRHIVALLVALGGvsfPILLAAPTGRAAKRL 58
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 380-438 8.28e-04

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


Pssm-ID: 433343 [Multi-domain]  Cd Length: 191  Bit Score: 42.17  E-value: 8.28e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2212216228  380 NDEQRRIVDKMrAASG---VLVQGPPGTGKSHTIANLICHLLATGQRTLITAKTPRALQVLE 438
Cdd:pfam13604    3 NAEQAAAVRAL-LTSGdrvAVLVGPAGTGKTTALKALREAWEAAGYRVIGLAPTGRAAKVLG 63
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 1070-1107 8.37e-04

DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses different enzymatic activities, such as single-stranded DNA (ssDNA)-dependent ATPase, 5-3 helicase, and endonuclease activities, and is involved in DNA replication and DNA repair in the nucleus and mitochondrion. It is involved in Okazaki fragment processing by cleaving long flaps that escape FEN1: flaps that are longer than 27 nucleotides are coated by replication protein A complex (RPA), leading to recruit DNA2 which cleaves the flap until it is too short to bind RPA and becomes a substrate for FEN1. It is also involved in 5-end resection of DNA during double-strand break (DSB) repair; it is recruited by BLM and mediates the cleavage of 5-ssDNA, while the 3-ssDNA cleavage is prevented by the presence of RPA. DNA2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350799 [Multi-domain]  Cd Length: 203  Bit Score: 42.61  E-value: 8.37e-04
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 2212216228 1070 MFDVIIVDEASQCGV-EALPLFYLGKKILIVGDDKQISP 1107
Cdd:cd18041    129 TFDYCIVDEASQITLpICLGPLRLAKKFVLVGDHYQLPP 167
DEXXQc_Helz-like cd18038
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ...
 380-428 1.28e-03

DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and similar proteins. Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. All are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350796 [Multi-domain]  Cd Length: 229  Bit Score: 42.22  E-value: 1.28e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2212216228  380 NDEQRRIVdkMRAASG------VLVQGPPGTGKSHTIANLICHLLATGQ--RTLITA 428
Cdd:cd18038      3 NDEQKLAV--RNIVTGtsrpppYIIFGPPGTGKTVTLVEAILQVLRQPPeaRILVCA 57
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 397-444 2.14e-03

DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. Their helicase core is surrounded by C and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains or domains engaged in protein-protein interactions. SF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438706 [Multi-domain]  Cd Length: 121  Bit Score: 39.78  E-value: 2.14e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2212216228  397 LVQGPPGTGKSHTIANLICHLLATG----QRTLITAKTPRALQVLEGLVPDE 444
Cdd:cd17914      3 LIQGPPGTGKTRVLVKIVAALMQNKngepGRILLVTPTNKAAAQLDNILVDE 54
Endonuclease_DUF559 cd01038
Putative endonuclease; Domain of unknown function 559 (DUF559) is a putative endonuclease of ...
 1417-1475 2.48e-03

Putative endonuclease; Domain of unknown function 559 (DUF559) is a putative endonuclease of unknown function, belongs to a 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: 411708  Cd Length: 97  Bit Score: 38.72  E-value: 2.48e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2212216228 1417 QARLAVECDGDHWHGADRYEDDMQRQRQLERCGWEFFRVRESAFYANKESALAGLWQAL 1475
Cdd:cd01038     39 EKKLVIEIDGGQHHEKKAEEYDARRDKYLESLGYTVLRFWNEEVLNNIEGVLEKIEKFL 97
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 397-440 3.56e-03

EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that represses class II MHC (major histocompatibility complex) gene expression. NFX1 binds a conserved cis-acting element, termed the X-box, in promoters of human class II MHC genes. The Cys-rich region contains several NFX1-type zinc finger domains. Frequently, a R3H domain is present in the C-terminus, and a RING finger domain and a PAM2 motif are present in the N-terminus. The lack of R3H and PAM2 motifs in the plant proteins indicates functional differences. Plant NFX1-like proteins are proposed to modulate growth and survival by coordinating reactive oxygen species, salicylic acid, further biotic stress and abscisic acid responses. A common feature of all members may be E3 ubiquitin ligase, due to the presence of a RING finger domain, as well as DNA binding. NFX1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350694 [Multi-domain]  Cd Length: 178  Bit Score: 40.22  E-value: 3.56e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2212216228  397 LVQGPPGTGKSHtIANLICHLLATGQRT------LITAKTPRAL-QVLEGL 440
Cdd:cd17936     20 LIQGPPGTGKTF-LGVKLVRALLQNQDLsitgpiLVVCYTNHALdQFLEGL 69
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
 397-428 8.45e-03

DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of Nonsense Transcripts, or ATP-Dependent Helicase RENT1) is an RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. It is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. It is recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) located downstream from the termination codon through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Diseases associated with UPF1 include juvenile amyotrophic lateral sclerosis and epidermolysis bullosa, junctional, non-Herlitz type. UPF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350797 [Multi-domain]  Cd Length: 234  Bit Score: 39.54  E-value: 8.45e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 2212216228  397 LVQGPPGTGKSHTIANLICHLL-ATGQRTLITA 428
Cdd:cd18039     20 LIQGPPGTGKTVTSATIVYHLVkQGNGPVLVCA 52
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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