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Conserved domains on  [gi|950545346|ref|WP_057421723|]
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AAA domain-containing protein [Pseudomonas amygdali]

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];
276-729 6.35e-56

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


:

Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 207.67  E-value: 6.35e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 276 APAIEHIQAVLQQLKGYLGARNAVAQLQIEISELEIERRYLTEWQRDNGVAGPSLDRYKLSPQKTTDLMAYLEQLASERI 355
Cdd:COG1112  368 ALLLLLALEELLLLALLRLLAEGLALLLLLLLAALLRLARALLLLALLLAAAAAALAALLLLALALLAALLALLLLLAAA 447
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 356 RIKDRIELLFNFRILRTRPFDNWDKRMSAFYSLQLHYYDKVLQDKKTELAAHEEALRlgNFKALLEELTSSSmlhlkhhl 435
Cdd:COG1112  448 LAALLALLLLLLLALAALLLLLAAAAALLALALLESLLEELIEEHPEELEKLIAELR--EAARLRRALRREL-------- 517
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 436 hrhisddDTFDTTYRKRLDAFLKRYPVIGSSTHSIVNSLG-GKAVLDYVIIDEASQQDIVPGVLALSCAKNLIIVGDRKQ 514
Cdd:COG1112  518 -------KKRRELRKLLWDALLELAPVVGMTPASVARLLPlGEGSFDLVIIDEASQATLAEALGALARAKRVVLVGDPKQ 590
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 515 LAHIPekLGLEAPAPWYDCEKYSFLDSCVSVFGNsiPMTLLKEHYRCHPRIIQFCNQQFYDNQLVPMT------MDNGEK 588
Cdd:COG1112  591 LPPVV--FGEEAEEVAEEGLDESLLDRLLARLPE--RGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPspkarrLADPDS 666
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 589 PLTLLVTAkGNHTR---NNSNLRELDSLLAVLEADGESLWEGEDgRGFIAPFKNQAMLSGSCLPTDFVRA-------TVH 658
Cdd:COG1112  667 PLVFIDVD-GVYERrggSRTNPEEAEAVVELVRELLEDGPDGES-IGVITPYRAQVALIRELLREALGDGlepvfvgTVD 744
                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 950545346 659 KFQGRECDEIVFSTVLDKYKS-PERLSFV-DDARMVNVAVSRAKSRFTLVTGDNVFKTSNGHIA--ALIRYMEYY 729
Cdd:COG1112  745 RFQGDERDVIIFSLVYSNDEDvPRNFGFLnGGPRRLNVAVSRARRKLIVVGSRELLDSDPSTPAlkRLLEYLERA 819
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
179-237 2.67e-19

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: 84.56  E-value: 2.67e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 950545346 179 NESQLRAVEQAFLSQVSVIEGPPGTGKTQTILNIIANILLQGKTVAVVSNNNSAVENVY 237
Cdd:cd18043    1 DSSQEAAIISARNGKNVVIQGPPGTGKSQTIANIIANALARGKRVLFVSEKKAALDVVR 59
PDDEXK_nuclease-like super family cl40440
PDDEXK family nucleases; Superfamily of PDDEXK nucleases including very short patch repair ...
820-889 5.73e-14

PDDEXK family nucleases; Superfamily of PDDEXK 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.


The actual alignment was detected with superfamily member pfam10881:

Pssm-ID: 477358  Cd Length: 126  Bit Score: 69.27  E-value: 5.73e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  820 NAARCDFVLYFKVGKTPLGVIEVDGGYHDDPLQIERDAVKNSILNKCGIPLLRLRTIESRIEEKVAAFLD 889
Cdd:pfam10881  55 SAKRFDFLLCDKADLTPVLAIELDGASHYDAKAQKRDAFKNAACESAGIPLLRLSASKSYDVSELRRQIA 124
 
Name Accession Description Interval E-value
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
276-729 6.35e-56

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 207.67  E-value: 6.35e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 276 APAIEHIQAVLQQLKGYLGARNAVAQLQIEISELEIERRYLTEWQRDNGVAGPSLDRYKLSPQKTTDLMAYLEQLASERI 355
Cdd:COG1112  368 ALLLLLALEELLLLALLRLLAEGLALLLLLLLAALLRLARALLLLALLLAAAAAALAALLLLALALLAALLALLLLLAAA 447
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 356 RIKDRIELLFNFRILRTRPFDNWDKRMSAFYSLQLHYYDKVLQDKKTELAAHEEALRlgNFKALLEELTSSSmlhlkhhl 435
Cdd:COG1112  448 LAALLALLLLLLLALAALLLLLAAAAALLALALLESLLEELIEEHPEELEKLIAELR--EAARLRRALRREL-------- 517
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 436 hrhisddDTFDTTYRKRLDAFLKRYPVIGSSTHSIVNSLG-GKAVLDYVIIDEASQQDIVPGVLALSCAKNLIIVGDRKQ 514
Cdd:COG1112  518 -------KKRRELRKLLWDALLELAPVVGMTPASVARLLPlGEGSFDLVIIDEASQATLAEALGALARAKRVVLVGDPKQ 590
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 515 LAHIPekLGLEAPAPWYDCEKYSFLDSCVSVFGNsiPMTLLKEHYRCHPRIIQFCNQQFYDNQLVPMT------MDNGEK 588
Cdd:COG1112  591 LPPVV--FGEEAEEVAEEGLDESLLDRLLARLPE--RGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPspkarrLADPDS 666
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 589 PLTLLVTAkGNHTR---NNSNLRELDSLLAVLEADGESLWEGEDgRGFIAPFKNQAMLSGSCLPTDFVRA-------TVH 658
Cdd:COG1112  667 PLVFIDVD-GVYERrggSRTNPEEAEAVVELVRELLEDGPDGES-IGVITPYRAQVALIRELLREALGDGlepvfvgTVD 744
                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 950545346 659 KFQGRECDEIVFSTVLDKYKS-PERLSFV-DDARMVNVAVSRAKSRFTLVTGDNVFKTSNGHIA--ALIRYMEYY 729
Cdd:COG1112  745 RFQGDERDVIIFSLVYSNDEDvPRNFGFLnGGPRRLNVAVSRARRKLIVVGSRELLDSDPSTPAlkRLLEYLERA 819
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
561-727 2.28e-25

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: 103.85  E-value: 2.28e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 561 CHPRIIQFCNQQFYDNQLVPMTM----------DNGEKPLTLLVTAKGNHTRNNS----NLRELDSLLAVLEADGESLWE 626
Cdd:cd18808    1 MHPEISEFPSKLFYEGKLKAGVSvaarlnppplPGPSKPLVFVDVSGGEEREESGtsksNEAEAELVVELVKYLLKSGVK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 627 GEDgRGFIAPFKNQA-----MLSGSCLPTDFVR-ATVHKFQGRECDEIVFSTVLDKyKSPERLSFVDDARMVNVAVSRAK 700
Cdd:cd18808   81 PSS-IGVITPYRAQValireLLRKRGGLLEDVEvGTVDNFQGREKDVIILSLVRSN-ESGGSIGFLSDPRRLNVALTRAK 158
                        170       180
                 ....*....|....*....|....*..
gi 950545346 701 SRFTLVtGDNVFKTSNGHIAALIRYME 727
Cdd:cd18808  159 RGLIIV-GNPDTLSKDPLWKKLLEYLE 184
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
178-731 2.74e-23

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: 105.67  E-value: 2.74e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  178 LNESQLRAVEQAFLSQ-VSVIEGPPGTGKTQTILNIIANILLQGKTVAVVSNNNSAVENVYEKLGKCglDYLVARLGknd 256
Cdd:TIGR00376 158 LNESQKEAVLFALSSKdLFLIHGPPGTGKTRTVVELIRQLVKRGLRVLVTAPSNIAVDNLLERLALC--DQKIVRLG--- 232
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  257 nqkeffanRPSRPSTDpspapAIEH-IQAVLQQLKGYlgarNAVAQLQIEISELEIERRYLTewqrdngvagpsldryKL 335
Cdd:TIGR00376 233 --------HPARLLKS-----NKQHsLDYLIENHPKY----QIVADIREKIDELIEERNKKT----------------KP 279
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  336 SPQKTtdlmaylEQLASERIRIKDRiellfnfrilrtrpfdnwdKRMSAfyslqlhyydkvlqdkktelaaheealrlgn 415
Cdd:TIGR00376 280 SPQKR-------RGLSDIKILRKAL-------------------KKREA------------------------------- 302
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  416 fkALLEELTSSSMLHLkhhlhrhisdddtfdTTYRKRLDAFLKRYPVIGS-------STHSIVNSLGGKAVL-----DYV 483
Cdd:TIGR00376 303 --RGIESLKIASMAEW---------------IETNKSIDRLLKLLPESEErimneilAESDATNSMAGSEILngqyfDVA 365
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  484 IIDEASQQDIVPGVLALSCAKNLIIVGDRKQL-----AHIPEKLgleapapwydceKYSFLDSCVSVFGNSIPMtlLKEH 558
Cdd:TIGR00376 366 VIDEASQAMEPSCLIPLLKARKLILAGDHKQLpptilSHDAEEL------------SLTLFERLIKEYPERSRT--LNVQ 431
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  559 YRCHPRIIQFCNQQFYDNQLvpmTMDNGEKPLTLLVTAKGNHTRNNSNLRELDSLLAVlEADGESLWEGEDGR------- 631
Cdd:TIGR00376 432 YRMNQKIMEFPSREFYNGKL---TAHESVANILLRDLPKVEATESEDDLETGIPLLFI-DTSGCELFELKEADstskynp 507
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  632 -----------------------GFIAPFKNQAMLSGSCLP---TDFVRATVHKFQGRECDEIVFSTVLDKYKSpeRLSF 685
Cdd:TIGR00376 508 geaelvseiiqalvkmgvpandiGVITPYDAQVDLLRQLLEhrhIDIEVSSVDGFQGREKEVIIISFVRSNRKG--EVGF 585
                         570       580       590       600
                  ....*....|....*....|....*....|....*....|....*.
gi 950545346  686 VDDARMVNVAVSRAKsRFTLVTGDNVFKTSNGHIAALIRYMEYYAD 731
Cdd:TIGR00376 586 LKDLRRLNVALTRAR-RKLIVIGDSRTLSNHKFYKRLIEWCKQHGE 630
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
179-237 2.67e-19

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: 84.56  E-value: 2.67e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 950545346 179 NESQLRAVEQAFLSQVSVIEGPPGTGKTQTILNIIANILLQGKTVAVVSNNNSAVENVY 237
Cdd:cd18043    1 DSSQEAAIISARNGKNVVIQGPPGTGKSQTIANIIANALARGKRVLFVSEKKAALDVVR 59
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
553-709 4.28e-19

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: 86.06  E-value: 4.28e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  553 TLLKEHYRCHPRIIQFCNQQFYDNQLV------------PMTMDNGEKPLTLLVTAKGNHTRNNS-----NLRE------ 609
Cdd:pfam13087  18 VMLDTQYRMHPEIMEFPSKLFYGGKLKdgpsvaerplpdDFHLPDPLGPLVFIDVDGSEEEESDGgtsysNEAEaelvvq 97
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  610 -LDSLLAVLEADGESLwegedgrGFIAPFKNQA-----MLSGSCLPTDFVR-ATVHKFQGRECDEIVFSTVldkyKSPER 682
Cdd:pfam13087  98 lVEKLIKSGPEEPSDI-------GVITPYRAQVrlirkLLKRKLGGKLEIEvNTVDGFQGREKDVIIFSCV----RSNEK 166
                         170       180
                  ....*....|....*....|....*....
gi 950545346  683 --LSFVDDARMVNVAVSRAKSRFTLVtGD 709
Cdd:pfam13087 167 ggIGFLSDPRRLNVALTRAKRGLIIV-GN 194
DUF2726 pfam10881
Protein of unknown function (DUF2726); This bacterial family of proteins has no known function.
820-889 5.73e-14

Protein of unknown function (DUF2726); This bacterial family of proteins has no known function.


Pssm-ID: 431528  Cd Length: 126  Bit Score: 69.27  E-value: 5.73e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  820 NAARCDFVLYFKVGKTPLGVIEVDGGYHDDPLQIERDAVKNSILNKCGIPLLRLRTIESRIEEKVAAFLD 889
Cdd:pfam10881  55 SAKRFDFLLCDKADLTPVLAIELDGASHYDAKAQKRDAFKNAACESAGIPLLRLSASKSYDVSELRRQIA 124
YcjD COG2852
Very-short-patch-repair endonuclease [Replication, recombination and repair];
762-882 5.34e-08

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


Pssm-ID: 442100  Cd Length: 104  Bit Score: 51.40  E-value: 5.34e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 762 LNPNDSLFksEQIVAQILREAlaqePRRGIMFHREIRLmqlaavarASFterelefmrnaaRCDFVLY-FKVgktplgVI 840
Cdd:COG2852    1 LRRNDTPA--ERRLWQRLRNR----QLRGLKFRRQVPI--------GGY------------IVDFYCPeARL------AI 48
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 950545346 841 EVDGGYHDDPLQIERDAVKNSILNKCGIPLLR-------------LRTIESRIEE 882
Cdd:COG2852   49 EVDGGYHGSPEQRERDRRRDAYLERLGWRVLRfwnedvlrnpegvLEEILAALEE 103
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
176-242 2.44e-07

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


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 54.21  E-value: 2.44e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 950545346 176 FGLNESQLRAVEQAFL-SQVSVIEGPPGTGKTQTILNIIANILLQGKTVAVVSNNNSAVENVYEKLGK 242
Cdd:COG0507  123 ITLSDEQREAVALALTtRRVSVLTGGAGTGKTTTLRALLAALEALGLRVALAAPTGKAAKRLSESTGI 190
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
177-241 2.63e-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. There is a Walker A and Walker B.


Pssm-ID: 433343 [Multi-domain]  Cd Length: 191  Bit Score: 51.80  E-value: 2.63e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 950545346  177 GLNESQLRAVEQAFLS--QVSVIEGPPGTGKTqTILNIIANILL-QGKTVAVVSNNNSAVENVYEKLG 241
Cdd:pfam13604   1 TLNAEQAAAVRALLTSgdRVAVLVGPAGTGKT-TALKALREAWEaAGYRVIGLAPTGRAAKVLGEELG 67
Endonuclease_DUF559 cd01038
Putative endonuclease; Domain of unknown function 559 (DUF559) is a putative endonuclease of ...
839-888 6.70e-06

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: 45.27  E-value: 6.70e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 950545346 839 VIEVDGGYHDDPLQIERDAVKNSILNKCGIPLLR------LRTIESrIEEKVAAFL 888
Cdd:cd01038   43 VIEIDGGQHHEKKAEEYDARRDKYLESLGYTVLRfwneevLNNIEG-VLEKIEKFL 97
 
Name Accession Description Interval E-value
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
276-729 6.35e-56

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 207.67  E-value: 6.35e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 276 APAIEHIQAVLQQLKGYLGARNAVAQLQIEISELEIERRYLTEWQRDNGVAGPSLDRYKLSPQKTTDLMAYLEQLASERI 355
Cdd:COG1112  368 ALLLLLALEELLLLALLRLLAEGLALLLLLLLAALLRLARALLLLALLLAAAAAALAALLLLALALLAALLALLLLLAAA 447
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 356 RIKDRIELLFNFRILRTRPFDNWDKRMSAFYSLQLHYYDKVLQDKKTELAAHEEALRlgNFKALLEELTSSSmlhlkhhl 435
Cdd:COG1112  448 LAALLALLLLLLLALAALLLLLAAAAALLALALLESLLEELIEEHPEELEKLIAELR--EAARLRRALRREL-------- 517
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 436 hrhisddDTFDTTYRKRLDAFLKRYPVIGSSTHSIVNSLG-GKAVLDYVIIDEASQQDIVPGVLALSCAKNLIIVGDRKQ 514
Cdd:COG1112  518 -------KKRRELRKLLWDALLELAPVVGMTPASVARLLPlGEGSFDLVIIDEASQATLAEALGALARAKRVVLVGDPKQ 590
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 515 LAHIPekLGLEAPAPWYDCEKYSFLDSCVSVFGNsiPMTLLKEHYRCHPRIIQFCNQQFYDNQLVPMT------MDNGEK 588
Cdd:COG1112  591 LPPVV--FGEEAEEVAEEGLDESLLDRLLARLPE--RGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPspkarrLADPDS 666
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 589 PLTLLVTAkGNHTR---NNSNLRELDSLLAVLEADGESLWEGEDgRGFIAPFKNQAMLSGSCLPTDFVRA-------TVH 658
Cdd:COG1112  667 PLVFIDVD-GVYERrggSRTNPEEAEAVVELVRELLEDGPDGES-IGVITPYRAQVALIRELLREALGDGlepvfvgTVD 744
                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 950545346 659 KFQGRECDEIVFSTVLDKYKS-PERLSFV-DDARMVNVAVSRAKSRFTLVTGDNVFKTSNGHIA--ALIRYMEYY 729
Cdd:COG1112  745 RFQGDERDVIIFSLVYSNDEDvPRNFGFLnGGPRRLNVAVSRARRKLIVVGSRELLDSDPSTPAlkRLLEYLERA 819
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
561-727 2.28e-25

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: 103.85  E-value: 2.28e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 561 CHPRIIQFCNQQFYDNQLVPMTM----------DNGEKPLTLLVTAKGNHTRNNS----NLRELDSLLAVLEADGESLWE 626
Cdd:cd18808    1 MHPEISEFPSKLFYEGKLKAGVSvaarlnppplPGPSKPLVFVDVSGGEEREESGtsksNEAEAELVVELVKYLLKSGVK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 627 GEDgRGFIAPFKNQA-----MLSGSCLPTDFVR-ATVHKFQGRECDEIVFSTVLDKyKSPERLSFVDDARMVNVAVSRAK 700
Cdd:cd18808   81 PSS-IGVITPYRAQValireLLRKRGGLLEDVEvGTVDNFQGREKDVIILSLVRSN-ESGGSIGFLSDPRRLNVALTRAK 158
                        170       180
                 ....*....|....*....|....*..
gi 950545346 701 SRFTLVtGDNVFKTSNGHIAALIRYME 727
Cdd:cd18808  159 RGLIIV-GNPDTLSKDPLWKKLLEYLE 184
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
178-731 2.74e-23

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: 105.67  E-value: 2.74e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  178 LNESQLRAVEQAFLSQ-VSVIEGPPGTGKTQTILNIIANILLQGKTVAVVSNNNSAVENVYEKLGKCglDYLVARLGknd 256
Cdd:TIGR00376 158 LNESQKEAVLFALSSKdLFLIHGPPGTGKTRTVVELIRQLVKRGLRVLVTAPSNIAVDNLLERLALC--DQKIVRLG--- 232
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  257 nqkeffanRPSRPSTDpspapAIEH-IQAVLQQLKGYlgarNAVAQLQIEISELEIERRYLTewqrdngvagpsldryKL 335
Cdd:TIGR00376 233 --------HPARLLKS-----NKQHsLDYLIENHPKY----QIVADIREKIDELIEERNKKT----------------KP 279
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  336 SPQKTtdlmaylEQLASERIRIKDRiellfnfrilrtrpfdnwdKRMSAfyslqlhyydkvlqdkktelaaheealrlgn 415
Cdd:TIGR00376 280 SPQKR-------RGLSDIKILRKAL-------------------KKREA------------------------------- 302
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  416 fkALLEELTSSSMLHLkhhlhrhisdddtfdTTYRKRLDAFLKRYPVIGS-------STHSIVNSLGGKAVL-----DYV 483
Cdd:TIGR00376 303 --RGIESLKIASMAEW---------------IETNKSIDRLLKLLPESEErimneilAESDATNSMAGSEILngqyfDVA 365
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  484 IIDEASQQDIVPGVLALSCAKNLIIVGDRKQL-----AHIPEKLgleapapwydceKYSFLDSCVSVFGNSIPMtlLKEH 558
Cdd:TIGR00376 366 VIDEASQAMEPSCLIPLLKARKLILAGDHKQLpptilSHDAEEL------------SLTLFERLIKEYPERSRT--LNVQ 431
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  559 YRCHPRIIQFCNQQFYDNQLvpmTMDNGEKPLTLLVTAKGNHTRNNSNLRELDSLLAVlEADGESLWEGEDGR------- 631
Cdd:TIGR00376 432 YRMNQKIMEFPSREFYNGKL---TAHESVANILLRDLPKVEATESEDDLETGIPLLFI-DTSGCELFELKEADstskynp 507
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  632 -----------------------GFIAPFKNQAMLSGSCLP---TDFVRATVHKFQGRECDEIVFSTVLDKYKSpeRLSF 685
Cdd:TIGR00376 508 geaelvseiiqalvkmgvpandiGVITPYDAQVDLLRQLLEhrhIDIEVSSVDGFQGREKEVIIISFVRSNRKG--EVGF 585
                         570       580       590       600
                  ....*....|....*....|....*....|....*....|....*.
gi 950545346  686 VDDARMVNVAVSRAKsRFTLVTGDNVFKTSNGHIAALIRYMEYYAD 731
Cdd:TIGR00376 586 LKDLRRLNVALTRAR-RKLIVIGDSRTLSNHKFYKRLIEWCKQHGE 630
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
179-237 2.67e-19

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: 84.56  E-value: 2.67e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 950545346 179 NESQLRAVEQAFLSQVSVIEGPPGTGKTQTILNIIANILLQGKTVAVVSNNNSAVENVY 237
Cdd:cd18043    1 DSSQEAAIISARNGKNVVIQGPPGTGKSQTIANIIANALARGKRVLFVSEKKAALDVVR 59
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
553-709 4.28e-19

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: 86.06  E-value: 4.28e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  553 TLLKEHYRCHPRIIQFCNQQFYDNQLV------------PMTMDNGEKPLTLLVTAKGNHTRNNS-----NLRE------ 609
Cdd:pfam13087  18 VMLDTQYRMHPEIMEFPSKLFYGGKLKdgpsvaerplpdDFHLPDPLGPLVFIDVDGSEEEESDGgtsysNEAEaelvvq 97
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  610 -LDSLLAVLEADGESLwegedgrGFIAPFKNQA-----MLSGSCLPTDFVR-ATVHKFQGRECDEIVFSTVldkyKSPER 682
Cdd:pfam13087  98 lVEKLIKSGPEEPSDI-------GVITPYRAQVrlirkLLKRKLGGKLEIEvNTVDGFQGREKDVIIFSCV----RSNEK 166
                         170       180
                  ....*....|....*....|....*....
gi 950545346  683 --LSFVDDARMVNVAVSRAKSRFTLVtGD 709
Cdd:pfam13087 167 ggIGFLSDPRRLNVALTRAKRGLIIV-GN 194
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
463-560 1.09e-15

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


Pssm-ID: 438708 [Multi-domain]  Cd Length: 121  Bit Score: 74.19  E-value: 1.09e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 463 IGSSTHSIVNslggkaVLDYVIIDEASQQDIVPGVLALSCAKNLIIVGDRKQLAHIPEklgLEAPAPWYDCEKYSFLDSC 542
Cdd:cd17934   34 VTAQSNVAVD------NVDVVIIDEASQITEPELLIALIRAKKVVLVGDPKQLPPVVQ---EDHAALLGLSFILSLLLLF 104
                         90
                 ....*....|....*...
gi 950545346 543 VSVFGNSIPmTLLKEHYR 560
Cdd:cd17934  105 RLLLPGSPK-VMLDTQYR 121
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
178-253 1.30e-15

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: 76.11  E-value: 1.30e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 950545346 178 LNESQLRAVEQAfLSQ--VSVIEGPPGTGKTQTILNIIANILLQGKTVAVVSNNNSAVENVYEKLGKCGLdyLVARLG 253
Cdd:cd18044    2 LNDSQKEAVKFA-LSQkdVALIHGPPGTGKTTTVVEIILQAVKRGEKVLACAPSNIAVDNLVERLVALKV--KVVRIG 76
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
194-236 1.63e-15

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


Pssm-ID: 438708 [Multi-domain]  Cd Length: 121  Bit Score: 73.42  E-value: 1.63e-15
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 950545346 194 VSVIEGPPGTGKTQTILNIIANIL--LQGKTVAVVSNNNSAVENV 236
Cdd:cd17934    1 ISLIQGPPGTGKTTTIAAIVLQLLkgLRGKRVLVTAQSNVAVDNV 45
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
177-288 3.46e-14

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: 72.27  E-value: 3.46e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 177 GLNESQLRAVEQAFLSQ-VSVIEGPPGTGKTQTILNIIANILLQGKTVAVVSNNNSAVENVYEKLGKCGLDYLvaRLGkn 255
Cdd:cd18041    1 GLNKDQRQAIKKVLNAKdYALILGMPGTGKTTTIAALVRILVALGKSVLLTSYTHSAVDNILLKLKKFGVNFL--RLG-- 76
                         90       100       110
                 ....*....|....*....|....*....|...
gi 950545346 256 DNQKEFFANRPSRPSTDPSPAPAIEHIQAVLQQ 288
Cdd:cd18041   77 RLKKIHPDVQEFTLEAILKSCKSVEELESKYES 109
DUF2726 pfam10881
Protein of unknown function (DUF2726); This bacterial family of proteins has no known function.
820-889 5.73e-14

Protein of unknown function (DUF2726); This bacterial family of proteins has no known function.


Pssm-ID: 431528  Cd Length: 126  Bit Score: 69.27  E-value: 5.73e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  820 NAARCDFVLYFKVGKTPLGVIEVDGGYHDDPLQIERDAVKNSILNKCGIPLLRLRTIESRIEEKVAAFLD 889
Cdd:pfam10881  55 SAKRFDFLLCDKADLTPVLAIELDGASHYDAKAQKRDAFKNAACESAGIPLLRLSASKSYDVSELRRQIA 124
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
178-252 3.44e-13

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


Pssm-ID: 350797 [Multi-domain]  Cd Length: 234  Bit Score: 69.97  E-value: 3.44e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 950545346 178 LNESQLRAVEQAFLSQVSVIEGPPGTGKTQTILNIIANILLQGKT-VAVVSNNNSAVENVYEKLGKCGLDylVARL 252
Cdd:cd18039    2 LNHSQVDAVKTALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGpVLVCAPSNVAVDQLTEKIHQTGLK--VVRL 75
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
181-515 5.82e-11

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: 63.90  E-value: 5.82e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  181 SQLRAVEQAFLSQ-VSVIEGPPGTGKTQTILNIIANILLQGKTVA-------VVSNNNSAVENVYEKLGKCGLDYL--VA 250
Cdd:pfam13086   1 SQREAIRSALSSShFTLIQGPPGTGKTTTIVELIRQLLSYPATSAaagprilVCAPSNAAVDNILERLLRKGQKYGpkIV 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  251 RLGkndnqkeffanRPSRPSTdpspapaiehiqavlqqlkgylgarnAVAQLQIEiseleierrYLTEWQRDNgvaGPSL 330
Cdd:pfam13086  81 RIG-----------HPAAISE--------------------------AVLPVSLD---------YLVESKLNN---EEDA 111
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  331 DRYKLSPQKTTDLMAYLEQLASERIRIKDRIELLFNFRILRTRPFDNWDKRmsafyslqlhyydkvlQDKKTELAAHEEA 410
Cdd:pfam13086 112 QIVKDISKELEKLAKALRAFEKEIIVEKLLKSRNKDKSKLEQERRKLRSER----------------KELRKELRRREQS 175
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346  411 LRlgnfkalleeltsssmlhlkhhlhrhisdddtfdttyrkrlDAFLKRYPVI----GSSTHSIVNSLGGkavLDYVIID 486
Cdd:pfam13086 176 LE-----------------------------------------REILDEAQIVcstlSGAGSRLLSSLAN---FDVVIID 211
                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 950545346  487 EASQqdivpgVLALSC-------AKNLIIVGDRKQL 515
Cdd:pfam13086 212 EAAQ------ALEPSTlipllrgPKKVVLVGDPKQL 241
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
459-560 2.32e-10

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: 59.13  E-value: 2.32e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 459 RYPVIGSSTHSIVNSLG-GKAVLDYVIIDEASQQDIVPGVLALSCAKNLIIVGDRKQLAhipeklgleapapwydcekys 537
Cdd:cd18043   59 RFPCWIMSPLSVSQYLPlNRNLFDLVIFDEASQIPIEEALPALFRGKQVVVVGDDKQLP--------------------- 117
                         90       100
                 ....*....|....*....|...
gi 950545346 538 fldscvsvfgnsiPMTLLKEHYR 560
Cdd:cd18043  118 -------------PSILLREHYR 127
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
177-255 8.32e-09

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


Pssm-ID: 350694 [Multi-domain]  Cd Length: 178  Bit Score: 56.01  E-value: 8.32e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 177 GLNESQLRAVEQAFLSQVSVIEGPPGTGKTQT---ILNIIANILLQGKT--VAVVSNNNSAVENVYEKLGKCGLDYLVaR 251
Cdd:cd17936    1 TLDPSQLEALKHALTSELALIQGPPGTGKTFLgvkLVRALLQNQDLSITgpILVVCYTNHALDQFLEGLLDFGPTKIV-R 79

                 ....
gi 950545346 252 LGKN 255
Cdd:cd17936   80 LGAR 83
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
178-264 2.07e-08

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: 55.68  E-value: 2.07e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 178 LNESQLRAVEQAFLSQ--VSVIEGPPGTGKTQTILNII-------------------------ANILLQGKTVAVVSNNN 230
Cdd:cd18042    1 LNESQLEAIASALQNSpgITLIQGPPGTGKTKTIVGILsvllagkyrkyyekvkkklrklqrnLNNKKKKNRILVCAPSN 80
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 950545346 231 SAV---------ENVYEKLGKCGLDYLVaRLGKNDNQKEFFAN 264
Cdd:cd18042   81 AAVdeivlrllsEGFLDGDGRSYKPNVV-RVGRQELRASILNE 122
YcjD COG2852
Very-short-patch-repair endonuclease [Replication, recombination and repair];
762-882 5.34e-08

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


Pssm-ID: 442100  Cd Length: 104  Bit Score: 51.40  E-value: 5.34e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 762 LNPNDSLFksEQIVAQILREAlaqePRRGIMFHREIRLmqlaavarASFterelefmrnaaRCDFVLY-FKVgktplgVI 840
Cdd:COG2852    1 LRRNDTPA--ERRLWQRLRNR----QLRGLKFRRQVPI--------GGY------------IVDFYCPeARL------AI 48
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 950545346 841 EVDGGYHDDPLQIERDAVKNSILNKCGIPLLR-------------LRTIESRIEE 882
Cdd:COG2852   49 EVDGGYHGSPEQRERDRRRDAYLERLGWRVLRfwnedvlrnpegvLEEILAALEE 103
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
176-242 2.44e-07

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


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 54.21  E-value: 2.44e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 950545346 176 FGLNESQLRAVEQAFL-SQVSVIEGPPGTGKTQTILNIIANILLQGKTVAVVSNNNSAVENVYEKLGK 242
Cdd:COG0507  123 ITLSDEQREAVALALTtRRVSVLTGGAGTGKTTTLRALLAALEALGLRVALAAPTGKAAKRLSESTGI 190
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
177-241 2.63e-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. There is a Walker A and Walker B.


Pssm-ID: 433343 [Multi-domain]  Cd Length: 191  Bit Score: 51.80  E-value: 2.63e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 950545346  177 GLNESQLRAVEQAFLS--QVSVIEGPPGTGKTqTILNIIANILL-QGKTVAVVSNNNSAVENVYEKLG 241
Cdd:pfam13604   1 TLNAEQAAAVRALLTSgdRVAVLVGPAGTGKT-TALKALREAWEaAGYRVIGLAPTGRAAKVLGEELG 67
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
182-225 1.38e-06

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


Pssm-ID: 350691 [Multi-domain]  Cd Length: 155  Bit Score: 49.09  E-value: 1.38e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 950545346 182 QLRAVEQAFLSQVSVIEGPPGTGKTQTILNIIANILLQGKTVAV 225
Cdd:cd17933    2 QKAAVRLVLRNRVSVLTGGAGTGKTTTLKALLAALEAEGKRVVL 45
AAA_19 pfam13245
AAA domain;
182-242 1.91e-06

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 47.98  E-value: 1.91e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 950545346  182 QLRAVEQAFLSQVSVIEGPPGTGKTQTILNIIANILLQG---KTVAVVSNNNSAVENVYEKLGK 242
Cdd:pfam13245   1 QREAVRTALPSKVVLLTGGPGTGKTTTIRHIVALLVALGgvsFPILLAAPTGRAAKRLSERTGL 64
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
451-515 2.82e-06

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: 49.16  E-value: 2.82e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 950545346 451 KRLDAFLKRYPVIGSSTHSIVNSLGGKAVLDYVIIDEASQQDiVPGVL-ALSCAKNLIIVGDRKQL 515
Cdd:cd18041  101 EELESKYESVSVVATTCLGINHPIFRRRTFDYCIVDEASQIT-LPICLgPLRLAKKFVLVGDHYQL 165
Endonuclease_DUF559 cd01038
Putative endonuclease; Domain of unknown function 559 (DUF559) is a putative endonuclease of ...
839-888 6.70e-06

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: 45.27  E-value: 6.70e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 950545346 839 VIEVDGGYHDDPLQIERDAVKNSILNKCGIPLLR------LRTIESrIEEKVAAFL 888
Cdd:cd01038   43 VIEIDGGQHHEKKAEEYDARRDKYLESLGYTVLRfwneevLNNIEG-VLEKIEKFL 97
DEXXQc_Helz-like cd18038
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ...
178-272 2.63e-05

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: 46.46  E-value: 2.63e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 178 LNESQLRAVeQAFLSQVS-----VIEGPPGTGKTQTILNIIANILLQGKT--VAVVSNNNSAVenvyeklgkcglDYLVA 250
Cdd:cd18038    2 LNDEQKLAV-RNIVTGTSrpppyIIFGPPGTGKTVTLVEAILQVLRQPPEarILVCAPSNSAA------------DLLAE 68
                         90       100
                 ....*....|....*....|....
gi 950545346 251 RL-GKNDNQKEFF-ANRPSRPSTD 272
Cdd:cd18038   69 RLlNALVTKREILrLNAPSRDRAS 92
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
656-713 1.22e-04

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


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 45.74  E-value: 1.22e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 950545346 656 TVHKFQGRECDEIVFstVLDKYKSPerlsfVDDARMVNVAVSRAKSRFTLVTGDNVFK 713
Cdd:COG0507  446 TVHKSQGSTFDRVIL--VLPSEHSP-----LLSRELLYTALTRARELLTLVGDRDALA 496
DEXXQc_Mov10L1 cd18078
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ...
178-245 1.49e-04

DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. Mov10L1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350836 [Multi-domain]  Cd Length: 230  Bit Score: 44.28  E-value: 1.49e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 950545346 178 LNESQLRAVEQaFLSQVS-----VIEGPPGTGKTQTILNIIANIL--LQGKTVAVVSNNNSAVENVYEKLGKCGL 245
Cdd:cd18078    2 LNELQKEAVKR-ILGGECrplpyILFGPPGTGKTVTIIEAILQVVynLPRSRILVCAPSNSAADLVTSRLHESKV 75
SF1_C_RecD cd18809
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ...
656-707 2.29e-04

C-terminal helicase domain of RecD family helicases; 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 family helicases 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: 350196 [Multi-domain]  Cd Length: 80  Bit Score: 40.62  E-value: 2.29e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 950545346 656 TVHKFQGRECDEIVFstVLDkyKSPERLSfvddARMVNVAVSRAKSRFTLVT 707
Cdd:cd18809   37 TIHKSQGSEFDRVIV--VLP--TSHPMLS----RGLLYTALTRARKLLTLVG 80
DEXXc_HELZ2-C cd18040
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
177-212 2.72e-04

C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known as PPAR-alpha-interacting complex protein 285 or PRIC285 and PPAR-gamma DBD-interacting protein 1 or PDIP1) acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB and RXRA. It belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350798 [Multi-domain]  Cd Length: 271  Bit Score: 43.67  E-value: 2.72e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 950545346 177 GLNESQLRAVEQAFLSQVSVIEGPPGTGKTQTILNI 212
Cdd:cd18040    1 KLNPSQNHAVRTALTKPFTLIQGPPGTGKTVTGVHI 36
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
465-515 3.05e-04

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: 42.97  E-value: 3.05e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 950545346 465 SSTHSIVNSLGGKAvlDYVIIDEASQ----QDIVPgvLALSCaKNLIIVGDRKQL 515
Cdd:cd18042  132 SSGSDLLESLPRGF--DTVIIDEAAQavelSTLIP--LRLGC-KRLILVGDPKQL 181
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
639-706 4.85e-04

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


Pssm-ID: 350173 [Multi-domain]  Cd Length: 89  Bit Score: 40.11  E-value: 4.85e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 950545346 639 NQAMLSGSCLPTDFVR---ATVHKFQGRECDEI--VFSTVldkyksperlsFVDDARMVNVAVSRAKSRFTLV 706
Cdd:cd18786   27 NQYLQGLSLDEFDLQLvgaITIDSSQGLTFDVVtlYLPTA-----------NSLTPRRLYVALTRARKRLVIY 88
EEXXQc_AQR cd17935
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ...
179-253 7.61e-04

EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds precursor-mRNA introns at a defined position and is part of a pentameric intron-binding complex (IBC). It is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350693 [Multi-domain]  Cd Length: 207  Bit Score: 41.64  E-value: 7.61e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 179 NESQLRAVEQAFLSQVSVIEGPPGTGKTQTILNIIANI---LLQGKTVaVVSNNNSAVENVYEKLGKCGLD--YLVaRLG 253
Cdd:cd17935    7 TPTQIEAIRSGMQPGLTMVVGPPGTGKTDVAVQIISNLyhnFPNQRTL-IVTHSNQALNQLFEKIMALDIDerHLL-RLG 84
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
195-234 9.67e-04

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: 9.67e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 950545346 195 SVIEGPPGTGKTQTILNIIANILLQ-----GKTVAVVSNNNSAVE 234
Cdd:cd17914    2 SLIQGPPGTGKTRVLVKIVAALMQNkngepGRILLVTPTNKAAAQ 46
CoV_Nsp13-helicase cd21718
helicase domain of coronavirus non-structural protein 13; This model represents the helicase ...
469-700 1.14e-03

helicase domain of coronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from alpha-, beta-, gamma-, and deltacoronavirus, including pathogenic human viruses such as Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core.


Pssm-ID: 409652 [Multi-domain]  Cd Length: 341  Bit Score: 42.13  E-value: 1.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 469 SIVNSLGgKAVLDYVIIDEAS-----QQDIVPGVLAlscAKNLIIVGDRKQLahipeklgleaPAPWYDCEKYSF----L 539
Cdd:cd21718  108 STINALP-ECSADIVVVDEVSmctnyDLSVVNARLK---YKHIVYVGDPAQL-----------PAPRTLLTEGSLepkdY 172
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 540 DSCVSVFGNSIPMTLLKEHYRCHPRIIQFCNQQFYDNQLVPMtmdNGEKPLTLLVTAKGNHTRNNS---NLRELDSLLAV 616
Cdd:cd21718  173 NVVTRLMVGSGPDVFLSKCYRCPKEIVDTVSKLVYDNKLKAI---KPKSRQCFKTFGKGDVRHDNGsaiNRPQLEFVKRF 249
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950545346 617 LEADGEslWegeDGRGFIAPFKNQ----AMLSGscLPTDfvraTVHKFQGRECDEIVFSTVLDKYKSPERLSFvddarmv 692
Cdd:cd21718  250 LDRNPR--W---RKAVFISPYNAMnnraSRLLG--LSTQ----TVDSSQGSEYDYVIFCQTTDTAHALNINRF------- 311

                 ....*...
gi 950545346 693 NVAVSRAK 700
Cdd:cd21718  312 NVAITRAK 319
DEXQc_UvrD cd17932
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ...
179-242 2.15e-03

DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. UvrD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350690 [Multi-domain]  Cd Length: 189  Bit Score: 40.19  E-value: 2.15e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 950545346 179 NESQLRAVEQafLSQVSVIEGPPGTGKTQTILNIIANILLQGKT----VAVVSNNNSAVENVYEKLGK 242
Cdd:cd17932    1 NPEQREAVTH--PDGPLLVLAGAGSGKTRVLTHRIAYLILEGGVpperILAVTFTNKAAKEMRERLRK 66
UvrD-helicase pfam00580
UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural ...
178-222 2.63e-03

UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyze ATP dependent unwinding of double stranded DNA to single stranded DNA. Swiss:P23478, Swiss:P08394 have large insertions near to the carboxy-terminus relative to other members of the family.


Pssm-ID: 395462 [Multi-domain]  Cd Length: 267  Bit Score: 40.69  E-value: 2.63e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 950545346  178 LNESQLRAVeqAFLSQVSVIEGPPGTGKTQTILNIIANILLQGKT 222
Cdd:pfam00580   1 LNPEQRKAV--THLGGPLLVLAGAGSGKTRVLTERIAYLILEGGI 43
DUF559 pfam04480
Protein of unknown function (DUF559);
839-877 3.62e-03

Protein of unknown function (DUF559);


Pssm-ID: 398268  Cd Length: 95  Bit Score: 37.74  E-value: 3.62e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 950545346  839 VIEVDGGYHDdpLQIERDAVKNSILNKCGIPLLRLRTIE 877
Cdd:pfam04480  42 IVELDGSQHD--EQEEYDARRTAFLESQGFTVLRFWNDE 78
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
194-246 4.03e-03

RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 39.90  E-value: 4.03e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 950545346 194 VSVIEGPPGTGKTQTILNIIANILLQGKTVAVVSNNNSAvENVYEKLGKCGLD 246
Cdd:COG0467   22 STLLSGPPGTGKTTLALQFLAEGLRRGEKGLYVSFEESP-EQLLRRAESLGLD 73
RecA-like cd01393
RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
195-226 4.30e-03

RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs RadA and RadB.


Pssm-ID: 410881 [Multi-domain]  Cd Length: 185  Bit Score: 39.26  E-value: 4.30e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 950545346 195 SVIE--GPPGTGKTQTILNIIANILLQGKTVAVV 226
Cdd:cd01393    2 KITEiyGPPGSGKTQLALQLAANALLLGGGVVWI 35
UvrD COG0210
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
177-220 6.85e-03

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


Pssm-ID: 439980 [Multi-domain]  Cd Length: 721  Bit Score: 40.30  E-value: 6.85e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 950545346 177 GLNESQLRAVEQaflsqvsvIEGP------PGTGKTQTILNIIANILLQG 220
Cdd:COG0210    6 GLNPEQRAAVEH--------PEGPllvlagAGSGKTRVLTHRIAYLIAEG 47
 
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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