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Conserved domains on  [gi|2711542876|ref|WP_339099563|]
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AAA domain-containing protein [Yersinia enterocolitica]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 13208672)

DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA

CATH:  3.40.50.300
EC:  3.6.4.-
Gene Ontology:  GO:0016887|GO:0003676|GO:0004386|GO:0005524
PubMed:  20206133|20225155

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];
397-1084 7.06e-59

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


:

Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 218.07  E-value: 7.06e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  397 AAVENISKELPQKKSLAEEFRSLDYLAPVANQIAAQSRPKKEHKRDKNGEGKERDYYLFRPLEEKNQCWGIISAALGKKA 476
Cdd:COG1112    154 ALLAALLLLLLLLAALLLLDLRLLALLELLLAAALALALLALLALALEDELALLLLLLLLALLLLLALLLLLDALLLLLA 233

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  477 NREKFTQRLFIDEHFLRETLAETSRPADENFLSLWRNWKTQPNKASFADAKKHFIECLKQTEELQQQLvLYANILAKQPD 556
Cdd:COG1112    234 ALALLALALLLALLLLLLALLLLAALALLRAALRLDLLAALELLAALSLALLALLAALALALLLLAAL-ALLLALALAAL 312

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  557 NSLDTLSITRLQTEKLCDEYSDGLKQLEAERDLLEKRVHHASQQQKIIENDAPGWLTHLINRKHVQAYQEVLRKSQYQLV 636
Cdd:COG1112    313 LALLALLALLAARLAAALAALLLLLLLEELALLAALLLLLELALLRLLAALLLALALLLLLALEELLLLALLRLLAEGLA 392

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  637 TLTASLVKNAQEIAEQRKQLNGIEIKKRNIQRNIALITQQQADEELERLKLQQRFPDITLPDSDKRIDDSALQRTAFWQN 716
Cdd:COG1112    393 LLLLLLLAALLRLARALLLLALLLAAAAAALAALLLLALALLAALLALLLLLAAALAALLALLLLLLLALAALLLLLAAA 472

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  717 eqinRQRSVLFIAAVKLHQAWFYEALGINRFRSNIMNLGNFLTSPHAEITPLR-----WWQILFMLVPVVSTTFASVGRM 791
Cdd:COG1112    473 ----AALLALALLESLLEELIEEHPEELEKLIAELREAARLRRALRRELKKRRelrklLWDALLELAPVVGMTPASVARL 548

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  792 FhGVKSEELGWLMIDEAGQASPQQAVGAIWRAKRVLVVGDPLQIEPVFTtspalvrhlcqnilHEHAEDWNPGKL--SIQ 869
Cdd:COG1112    549 L-PLGEGSFDLVIIDEASQATLAEALGALARAKRVVLVGDPKQLPPVVF--------------GEEAEEVAEEGLdeSLL 613

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  870 QVADRVNHwgcelnvmnhqvWIGIPLWVHRRCIEPMFSLANKMAYDNRMIHGLSDDKICSQRVNGAVenHWLAsVGGLGE 949
Cdd:COG1112    614 DRLLARLP------------ERGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPSPKARRLADPDSPL--VFID-VDGVYE 678

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  950 K----QYRDSHGKSLLKLLDRLLSENVAIQTIYIITPFKAVKTALLDLLEQRDlkvwqqysplikrkeIKEWQKNCVGTV 1025
Cdd:COG1112    679 RrggsRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELLREAL---------------GDGLEPVFVGTV 743

                          650       660       670       680       690       700
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2711542876 1026 HTFQGKENDIVIFVLGC--DEQDAGGAKWASSKPNLLNVALTRAKKHIFVIGDPKVWLQLP 1084
Cdd:COG1112    744 DRFQGDERDVIIFSLVYsnDEDVPRNFGFLNGGPRRLNVAVSRARRKLIVVGSRELLDSDP 804
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 324-364 8.81e-04

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: 40.26  E-value: 8.81e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2711542876  324 TAVEELSKGGLLSVNGPPGTGKTTLLRDLIAHNIVERAKVL 364
Cdd:cd18043      6 AAIISARNGKNVVIQGPPGTGKSQTIANIIANALARGKRVL 46
RecD super family cl33920
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 251-355 2.61e-03

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


The actual alignment was detected with superfamily member COG0507:

Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 41.50  E-value: 2.61e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  251 EDIENAIAAIKRKEPCNPLKT-YLSRnmprnpdLYSQE-GLELIINKLHPTRMPQ-------GRWPSEPGHAMSLMQQFA 321
Cdd:COG0507     60 EDIEAALAALVESGPLVLDGRrYLTR-------LLEAEqRLARRLRRLARPALDEadveaalAALEPRAGITLSDEQREA 132

                           90       100       110
                   ....*....|....*....|....*....|....
gi 2711542876  322 INTAveeLSKGGLLSVNGPPGTGKTTLLRDLIAH 355
Cdd:COG0507    133 VALA---LTTRRVSVLTGGAGTGKTTTLRALLAA 163
 
Name Accession Description Interval E-value
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
397-1084 7.06e-59

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 218.07  E-value: 7.06e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  397 AAVENISKELPQKKSLAEEFRSLDYLAPVANQIAAQSRPKKEHKRDKNGEGKERDYYLFRPLEEKNQCWGIISAALGKKA 476
Cdd:COG1112    154 ALLAALLLLLLLLAALLLLDLRLLALLELLLAAALALALLALLALALEDELALLLLLLLLALLLLLALLLLLDALLLLLA 233

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  477 NREKFTQRLFIDEHFLRETLAETSRPADENFLSLWRNWKTQPNKASFADAKKHFIECLKQTEELQQQLvLYANILAKQPD 556
Cdd:COG1112    234 ALALLALALLLALLLLLLALLLLAALALLRAALRLDLLAALELLAALSLALLALLAALALALLLLAAL-ALLLALALAAL 312

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  557 NSLDTLSITRLQTEKLCDEYSDGLKQLEAERDLLEKRVHHASQQQKIIENDAPGWLTHLINRKHVQAYQEVLRKSQYQLV 636
Cdd:COG1112    313 LALLALLALLAARLAAALAALLLLLLLEELALLAALLLLLELALLRLLAALLLALALLLLLALEELLLLALLRLLAEGLA 392

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  637 TLTASLVKNAQEIAEQRKQLNGIEIKKRNIQRNIALITQQQADEELERLKLQQRFPDITLPDSDKRIDDSALQRTAFWQN 716
Cdd:COG1112    393 LLLLLLLAALLRLARALLLLALLLAAAAAALAALLLLALALLAALLALLLLLAAALAALLALLLLLLLALAALLLLLAAA 472

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  717 eqinRQRSVLFIAAVKLHQAWFYEALGINRFRSNIMNLGNFLTSPHAEITPLR-----WWQILFMLVPVVSTTFASVGRM 791
Cdd:COG1112    473 ----AALLALALLESLLEELIEEHPEELEKLIAELREAARLRRALRRELKKRRelrklLWDALLELAPVVGMTPASVARL 548

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  792 FhGVKSEELGWLMIDEAGQASPQQAVGAIWRAKRVLVVGDPLQIEPVFTtspalvrhlcqnilHEHAEDWNPGKL--SIQ 869
Cdd:COG1112    549 L-PLGEGSFDLVIIDEASQATLAEALGALARAKRVVLVGDPKQLPPVVF--------------GEEAEEVAEEGLdeSLL 613

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  870 QVADRVNHwgcelnvmnhqvWIGIPLWVHRRCIEPMFSLANKMAYDNRMIHGLSDDKICSQRVNGAVenHWLAsVGGLGE 949
Cdd:COG1112    614 DRLLARLP------------ERGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPSPKARRLADPDSPL--VFID-VDGVYE 678

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  950 K----QYRDSHGKSLLKLLDRLLSENVAIQTIYIITPFKAVKTALLDLLEQRDlkvwqqysplikrkeIKEWQKNCVGTV 1025
Cdd:COG1112    679 RrggsRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELLREAL---------------GDGLEPVFVGTV 743

                          650       660       670       680       690       700
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2711542876 1026 HTFQGKENDIVIFVLGC--DEQDAGGAKWASSKPNLLNVALTRAKKHIFVIGDPKVWLQLP 1084
Cdd:COG1112    744 DRFQGDERDVIIFSLVYsnDEDVPRNFGFLNGGPRRLNVAVSRARRKLIVVGSRELLDSDP 804
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 975-1089 1.58e-17

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: 81.51  E-value: 1.58e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  975 QTIYIITPFKAVKTALLDLLEQRDlkvwqqysplIKRKEIKewqkncVGTVHTFQGKENDIVIF--VLGCDEQDAGGAKw 1052
Cdd:cd18808     82 SSIGVITPYRAQVALIRELLRKRG----------GLLEDVE------VGTVDNFQGREKDVIILslVRSNESGGSIGFL- 144

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 2711542876 1053 asSKPNLLNVALTRAKKHIFVIGDPKVWLQLPWFGEV 1089
Cdd:cd18808    145 --SDPRRLNVALTRAKRGLIIVGNPDTLSKDPLWKKL 179
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 977-1078 2.87e-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: 463780 [Multi-domain]  Cd Length: 196  Bit Score: 63.72  E-value: 2.87e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  977 IYIITPFKAVKTALLDLLEQRDLKvwqqySPLIKrkeikewqkncVGTVHTFQGKENDIVIF--VLGCDEQDAGGAkwas 1054
Cdd:pfam13087  113 IGVITPYRAQVRLIRKLLKRKLGG-----KLEIE-----------VNTVDGFQGREKDVIIFscVRSNEKGGIGFL---- 172

                           90       100
                   ....*....|....*....|....
gi 2711542876 1055 SKPNLLNVALTRAKKHIFVIGDPK 1078
Cdd:pfam13087  173 SDPRRLNVALTRAKRGLIIVGNAK 196
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 324-364 8.81e-04

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: 40.26  E-value: 8.81e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2711542876  324 TAVEELSKGGLLSVNGPPGTGKTTLLRDLIAHNIVERAKVL 364
Cdd:cd18043      6 AAIISARNGKNVVIQGPPGTGKSQTIANIIANALARGKRVL 46
SpoIIIAA COG3854
Stage III sporulation protein SpoIIIAA [Cell cycle control, cell division, chromosome ...
 339-353 2.57e-03

Stage III sporulation protein SpoIIIAA [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443063  Cd Length: 309  Bit Score: 41.29  E-value: 2.57e-03
                           10
                   ....*....|....*
gi 2711542876  339 GPPGTGKTTLLRDLI 353
Cdd:COG3854    147 SPPGCGKTTLLRDIA 161
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 251-355 2.61e-03

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: 41.50  E-value: 2.61e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  251 EDIENAIAAIKRKEPCNPLKT-YLSRnmprnpdLYSQE-GLELIINKLHPTRMPQ-------GRWPSEPGHAMSLMQQFA 321
Cdd:COG0507     60 EDIEAALAALVESGPLVLDGRrYLTR-------LLEAEqRLARRLRRLARPALDEadveaalAALEPRAGITLSDEQREA 132

                           90       100       110
                   ....*....|....*....|....*....|....
gi 2711542876  322 INTAveeLSKGGLLSVNGPPGTGKTTLLRDLIAH 355
Cdd:COG0507    133 VALA---LTTRRVSVLTGGAGTGKTTTLRALLAA 163
 
Name Accession Description Interval E-value
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
397-1084 7.06e-59

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 218.07  E-value: 7.06e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  397 AAVENISKELPQKKSLAEEFRSLDYLAPVANQIAAQSRPKKEHKRDKNGEGKERDYYLFRPLEEKNQCWGIISAALGKKA 476
Cdd:COG1112    154 ALLAALLLLLLLLAALLLLDLRLLALLELLLAAALALALLALLALALEDELALLLLLLLLALLLLLALLLLLDALLLLLA 233

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  477 NREKFTQRLFIDEHFLRETLAETSRPADENFLSLWRNWKTQPNKASFADAKKHFIECLKQTEELQQQLvLYANILAKQPD 556
Cdd:COG1112    234 ALALLALALLLALLLLLLALLLLAALALLRAALRLDLLAALELLAALSLALLALLAALALALLLLAAL-ALLLALALAAL 312

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  557 NSLDTLSITRLQTEKLCDEYSDGLKQLEAERDLLEKRVHHASQQQKIIENDAPGWLTHLINRKHVQAYQEVLRKSQYQLV 636
Cdd:COG1112    313 LALLALLALLAARLAAALAALLLLLLLEELALLAALLLLLELALLRLLAALLLALALLLLLALEELLLLALLRLLAEGLA 392

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  637 TLTASLVKNAQEIAEQRKQLNGIEIKKRNIQRNIALITQQQADEELERLKLQQRFPDITLPDSDKRIDDSALQRTAFWQN 716
Cdd:COG1112    393 LLLLLLLAALLRLARALLLLALLLAAAAAALAALLLLALALLAALLALLLLLAAALAALLALLLLLLLALAALLLLLAAA 472

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  717 eqinRQRSVLFIAAVKLHQAWFYEALGINRFRSNIMNLGNFLTSPHAEITPLR-----WWQILFMLVPVVSTTFASVGRM 791
Cdd:COG1112    473 ----AALLALALLESLLEELIEEHPEELEKLIAELREAARLRRALRRELKKRRelrklLWDALLELAPVVGMTPASVARL 548

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  792 FhGVKSEELGWLMIDEAGQASPQQAVGAIWRAKRVLVVGDPLQIEPVFTtspalvrhlcqnilHEHAEDWNPGKL--SIQ 869
Cdd:COG1112    549 L-PLGEGSFDLVIIDEASQATLAEALGALARAKRVVLVGDPKQLPPVVF--------------GEEAEEVAEEGLdeSLL 613

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  870 QVADRVNHwgcelnvmnhqvWIGIPLWVHRRCIEPMFSLANKMAYDNRMIHGLSDDKICSQRVNGAVenHWLAsVGGLGE 949
Cdd:COG1112    614 DRLLARLP------------ERGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPSPKARRLADPDSPL--VFID-VDGVYE 678

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  950 K----QYRDSHGKSLLKLLDRLLSENVAIQTIYIITPFKAVKTALLDLLEQRDlkvwqqysplikrkeIKEWQKNCVGTV 1025
Cdd:COG1112    679 RrggsRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELLREAL---------------GDGLEPVFVGTV 743

                          650       660       670       680       690       700
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2711542876 1026 HTFQGKENDIVIFVLGC--DEQDAGGAKWASSKPNLLNVALTRAKKHIFVIGDPKVWLQLP 1084
Cdd:COG1112    744 DRFQGDERDVIIFSLVYsnDEDVPRNFGFLNGGPRRLNVAVSRARRKLIVVGSRELLDSDP 804
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 975-1089 1.58e-17

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: 81.51  E-value: 1.58e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  975 QTIYIITPFKAVKTALLDLLEQRDlkvwqqysplIKRKEIKewqkncVGTVHTFQGKENDIVIF--VLGCDEQDAGGAKw 1052
Cdd:cd18808     82 SSIGVITPYRAQVALIRELLRKRG----------GLLEDVE------VGTVDNFQGREKDVIILslVRSNESGGSIGFL- 144

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 2711542876 1053 asSKPNLLNVALTRAKKHIFVIGDPKVWLQLPWFGEV 1089
Cdd:cd18808    145 --SDPRRLNVALTRAKRGLIIVGNPDTLSKDPLWKKL 179
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 977-1078 2.87e-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: 463780 [Multi-domain]  Cd Length: 196  Bit Score: 63.72  E-value: 2.87e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  977 IYIITPFKAVKTALLDLLEQRDLKvwqqySPLIKrkeikewqkncVGTVHTFQGKENDIVIF--VLGCDEQDAGGAkwas 1054
Cdd:pfam13087  113 IGVITPYRAQVRLIRKLLKRKLGG-----KLEIE-----------VNTVDGFQGREKDVIIFscVRSNEKGGIGFL---- 172

                           90       100
                   ....*....|....*....|....
gi 2711542876 1055 SKPNLLNVALTRAKKHIFVIGDPK 1078
Cdd:pfam13087  173 SDPRRLNVALTRAKRGLIIVGNAK 196
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 780-838 8.70e-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: 57.63  E-value: 8.70e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2711542876  780 VVSTTFASVgrmfhgvksEELGWLMIDEAGQASPQQAVGAIWRAKRVLVVGDPLQIEPV 838
Cdd:cd17934     34 VTAQSNVAV---------DNVDVVIIDEASQITEPELLIALIRAKKVVLVGDPKQLPPV 83
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 778-838 7.90e-09

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


Pssm-ID: 350801 [Multi-domain]  Cd Length: 127  Bit Score: 54.90  E-value: 7.90e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2711542876  778 VPVVSTTFASVGRMFhGVKSEELGWLMIDEAGQASPQQAVGAIWRAKRVLVVGDPLQIEPV 838
Cdd:cd18043     60 FPCWIMSPLSVSQYL-PLNRNLFDLVIFDEASQIPIEEALPALFRGKQVVVVGDDKQLPPS 119
SF1_C_RecD cd18809
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ...
 1024-1075 6.43e-06

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: 45.25  E-value: 6.43e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2711542876 1024 TVHTFQGKENDIVIFVLgcdeqdaGGAKWASSKpNLLNVALTRAKKHIFVIG 1075
Cdd:cd18809     37 TIHKSQGSEFDRVIVVL-------PTSHPMLSR-GLLYTALTRARKLLTLVG 80
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 1022-1075 2.04e-05

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: 43.97  E-value: 2.04e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2711542876 1022 VGTVHTFQGKENDIVIFVlgCDEQDaggakwaSSKPNLLNVALTRAKKHIFVIG 1075
Cdd:cd18786     45 AITIDSSQGLTFDVVTLY--LPTAN-------SLTPRRLYVALTRARKRLVIYD 89
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 1024-1082 1.32e-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: 1.32e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2711542876 1024 TVHTFQGKENDIVIFVLGcdeqdagGAKWASSKPNLLNVALTRAKKHIFVIGDPKVWLQ 1082
Cdd:COG0507    446 TVHKSQGSTFDRVILVLP-------SEHSPLLSRELLYTALTRARELLTLVGDRDALAR 497
CoV_Nsp13-helicase cd21718
helicase domain of coronavirus non-structural protein 13; This model represents the helicase ...
 1022-1074 8.21e-04

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: 42.90  E-value: 8.21e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2711542876 1022 VGTVHTFQGKENDIVIFVLGCDEQDAggakwasSKPNLLNVALTRAKKHIFVI 1074
Cdd:cd21718    280 TQTVDSSQGSEYDYVIFCQTTDTAHA-------LNINRFNVAITRAKHGILVI 325
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 324-364 8.81e-04

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: 40.26  E-value: 8.81e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2711542876  324 TAVEELSKGGLLSVNGPPGTGKTTLLRDLIAHNIVERAKVL 364
Cdd:cd18043      6 AAIISARNGKNVVIQGPPGTGKSQTIANIIANALARGKRVL 46
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 334-402 1.31e-03

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: 39.91  E-value: 1.31e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2711542876  334 LLSVNGPPGTGKTTllrdLIAHNIVERAKVLSsfnqvddtldnqgfirpeltGYEMVMASSNNAAVENI 402
Cdd:cd17934      1 ISLIQGPPGTGKTT----TIAAIVLQLLKGLR--------------------GKRVLVTAQSNVAVDNV 45
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 805-869 1.60e-03

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: 41.07  E-value: 1.60e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2711542876  805 IDEAGQASPQQAVGAIWRAKRVLVVGDPLQIEPVFTTSPA--------LVRHLCQNILHEHAEdwnpgkLSIQ 869
Cdd:cd18041    135 VDEASQITLPICLGPLRLAKKFVLVGDHYQLPPLVKSREArelgmdesLFKRLSEAHPDAVVQ------LTIQ 201
SpoIIIAA COG3854
Stage III sporulation protein SpoIIIAA [Cell cycle control, cell division, chromosome ...
 339-353 2.57e-03

Stage III sporulation protein SpoIIIAA [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443063  Cd Length: 309  Bit Score: 41.29  E-value: 2.57e-03
                           10
                   ....*....|....*
gi 2711542876  339 GPPGTGKTTLLRDLI 353
Cdd:COG3854    147 SPPGCGKTTLLRDIA 161
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 251-355 2.61e-03

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: 41.50  E-value: 2.61e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  251 EDIENAIAAIKRKEPCNPLKT-YLSRnmprnpdLYSQE-GLELIINKLHPTRMPQ-------GRWPSEPGHAMSLMQQFA 321
Cdd:COG0507     60 EDIEAALAALVESGPLVLDGRrYLTR-------LLEAEqRLARRLRRLARPALDEadveaalAALEPRAGITLSDEQREA 132

                           90       100       110
                   ....*....|....*....|....*....|....
gi 2711542876  322 INTAveeLSKGGLLSVNGPPGTGKTTLLRDLIAH 355
Cdd:COG0507    133 VALA---LTTRRVSVLTGGAGTGKTTTLRALLAA 163
UvrD_C_2 pfam13538
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ...
 1021-1074 3.81e-03

UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.


Pssm-ID: 463913 [Multi-domain]  Cd Length: 52  Bit Score: 36.40  E-value: 3.81e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2711542876 1021 CVGTVHTFQGKENDIVIFVLGcdeqDAGGAKWASSKPNLLNVALTRAKKHIFVI 1074
Cdd:pfam13538    3 YALTVHKAQGSEFPAVFLVDP----DLTAHYHSMLRRRLLYTAVTRARKKLVLV 52
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 318-364 6.87e-03

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: 39.13  E-value: 6.87e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2711542876  318 QQFAINTAveeLSKGGLLSVNGPPGTGKTTLLRDLIAHNIVERAKVL 364
Cdd:cd18044      6 QKEAVKFA---LSQKDVALIHGPPGTGKTTTVVEIILQAVKRGEKVL 49
gammaCoV_Nsp13-helicase cd21720
helicase domain of gammacoronavirus non-structural protein 13; This model represents the ...
 1015-1074 7.20e-03

helicase domain of gammacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from gammacoronavirus, including Avian infectious bronchitis virus. 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. Coronavirus (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: 409653 [Multi-domain]  Cd Length: 343  Bit Score: 39.90  E-value: 7.20e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2711542876 1015 KEWQKNC-------------------VGTVHTFQGKENDIVIFVLGCDEQDAggakwasSKPNLLNVALTRAKKHIFVI 1074
Cdd:cd21720    256 KEWREATfispynamnqrayrmlglnVQTVDSSQGSEYDYVIFCVTADSQHA-------LNINRFNVALTRAKRGILVV 327
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
559-724 9.66e-03

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 40.28  E-value: 9.66e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  559 LDTLSITRLQTEKLCDEYSDGLKQLEAERDLLEKRVHHASQQQKII--ENDAPGWLTHLINRKhvQAYQEvLRKSQYQLV 636
Cdd:COG4913    612 LAALEAELAELEEELAEAEERLEALEAELDALQERREALQRLAEYSwdEIDVASAEREIAELE--AELER-LDASSDDLA 688

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711542876  637 TLTASLVKNAQEIAEQRKQLNGIEIKKRNIQRNIALITQQQADEELERLKLQQRFPDITLPDSDKR----IDDSALQRTA 712
Cdd:COG4913    689 ALEEQLEELEAELEELEEELDELKGEIGRLEKELEQAEEELDELQDRLEAAEDLARLELRALLEERfaaaLGDAVERELR 768

                          170
                   ....*....|..
gi 2711542876  713 FWQNEQINRQRS 724
Cdd:COG4913    769 ENLEERIDALRA 780
 
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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