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Conserved domains on  [gi|881012556|ref|WP_048733265|]
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MULTISPECIES: DEAD/DEAH box helicase [Corynebacterium]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 11437332)

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

CATH:  1.20.1320.20|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
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
3-477 1.62e-76

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


:

Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 253.02  E-value: 1.62e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556   3 GLRKWQQEALDKYLAT---NPKDFLAVATPGAGKTTFALRIASELLSRRiveRIIVVVPTEHLKVQWAASAARsgiaLDP 79
Cdd:COG1061   80 ELRPYQQEALEALLAAlerGGGRGLVVAPTGTGKTVLALALAAELLRGK---RVLVLVPRRELLEQWAEELRR----FLG 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556  80 KFTNAKGVVNPSYQGIVVTYAQVAVHPfkHHAVATARPTLVILDEVHHGGdAKSWGDGISeaYGDVERRLCLTGTPFRSD 159
Cdd:COG1061  153 DPLAGGGKKDSDAPITVATYQSLARRA--HLDELGDRFGLVIIDEAHHAG-APSYRRILE--AFPAAYRLGLTATPFRSD 227

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556 160 DAAIPFVRYspdgDGysrsVAdYTYGYSNALADGVVRPVVFLAYSGEARWRDSAGDEFAARLgtvmspeettrawRTALD 239
Cdd:COG1061  228 GREILLFLF----DG----IV-YEYSLKEAIEDGYLAPPEYYGIRVDLTDERAEYDALSERL-------------REALA 285

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556 240 PKGEWMPSVLRAAhtrlsqMRQHIPDAGGLVIASDAATARAYKRILEQiASTPVALVLSDEPGS--SERIKTFSESTDEW 317
Cdd:COG1061  286 ADAERKDKILREL------LREHPDDRKTLVFCSSVDHAEALAELLNE-AGIRAAVVTGDTPKKerEEILEAFRDGELRI 358

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556 318 MVAVRMVSEGVDVPRLAVGVYATSSSTPLFFAQAIGRFVRSRMPGETASVFL---PSIPVLLDLAS--QMEVQRNHVLGK 392
Cdd:COG1061  359 LVTVDVLNEGVDVPRLDVAILLRPTGSPREFIQRLGRGLRPAPGKEDALVYDfvgNDVPVLEELAKdlRDLAGYRVEFLD 438

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556 393 PDRPSEGWEDDLVAEANRRKDEPDELLPAYESIGADAELDYLIYDGSSYGTATVAGSAEEADYLGLPGLLDADQMRLLLR 472
Cdd:COG1061  439 EEESEELALLIAVKPALEVKGELEEELLEELELLEDALLLVLAELLLLELLALALELLELAKAEGKAEEEEEEKELLLLL 518


                 ....*
gi 881012556 473 QRQDE 477
Cdd:COG1061  519 ALAKL 523
 
Name Accession Description Interval E-value
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
3-477 1.62e-76

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 253.02  E-value: 1.62e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556   3 GLRKWQQEALDKYLAT---NPKDFLAVATPGAGKTTFALRIASELLSRRiveRIIVVVPTEHLKVQWAASAARsgiaLDP 79
Cdd:COG1061   80 ELRPYQQEALEALLAAlerGGGRGLVVAPTGTGKTVLALALAAELLRGK---RVLVLVPRRELLEQWAEELRR----FLG 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556  80 KFTNAKGVVNPSYQGIVVTYAQVAVHPfkHHAVATARPTLVILDEVHHGGdAKSWGDGISeaYGDVERRLCLTGTPFRSD 159
Cdd:COG1061  153 DPLAGGGKKDSDAPITVATYQSLARRA--HLDELGDRFGLVIIDEAHHAG-APSYRRILE--AFPAAYRLGLTATPFRSD 227

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556 160 DAAIPFVRYspdgDGysrsVAdYTYGYSNALADGVVRPVVFLAYSGEARWRDSAGDEFAARLgtvmspeettrawRTALD 239
Cdd:COG1061  228 GREILLFLF----DG----IV-YEYSLKEAIEDGYLAPPEYYGIRVDLTDERAEYDALSERL-------------REALA 285

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556 240 PKGEWMPSVLRAAhtrlsqMRQHIPDAGGLVIASDAATARAYKRILEQiASTPVALVLSDEPGS--SERIKTFSESTDEW 317
Cdd:COG1061  286 ADAERKDKILREL------LREHPDDRKTLVFCSSVDHAEALAELLNE-AGIRAAVVTGDTPKKerEEILEAFRDGELRI 358

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556 318 MVAVRMVSEGVDVPRLAVGVYATSSSTPLFFAQAIGRFVRSRMPGETASVFL---PSIPVLLDLAS--QMEVQRNHVLGK 392
Cdd:COG1061  359 LVTVDVLNEGVDVPRLDVAILLRPTGSPREFIQRLGRGLRPAPGKEDALVYDfvgNDVPVLEELAKdlRDLAGYRVEFLD 438

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556 393 PDRPSEGWEDDLVAEANRRKDEPDELLPAYESIGADAELDYLIYDGSSYGTATVAGSAEEADYLGLPGLLDADQMRLLLR 472
Cdd:COG1061  439 EEESEELALLIAVKPALEVKGELEEELLEELELLEDALLLVLAELLLLELLALALELLELAKAEGKAEEEEEEKELLLLL 518


                 ....*
gi 881012556 473 QRQDE 477
Cdd:COG1061  519 ALAKL 523
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 4-155 9.81e-20

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


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 85.82  E-value: 9.81e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556   4 LRKWQQEALDKYLATNPKDF-LAVATPGAGKTTFALRIASELLSrrivERIIVVVPTEHLKVQWAASAAR-SGIALDPKF 81
Cdd:cd17926    1 LRPYQEEALEAWLAHKNNRRgILVLPTGSGKTLTALALIAYLKE----LRTLIVVPTDALLDQWKERFEDfLGDSSIGLI 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 881012556  82 tnaKGVVNPSYQGIVVTYA--QVAVHPFKHHAVATARPTLVILDEVHHGGdAKSWGDGISEAYGdvERRLCLTGTP 155
Cdd:cd17926   77 ---GGGKKKDFDDANVVVAtyQSLSNLAEEEKDLFDQFGLLIVDEAHHLP-AKTFSEILKELNA--KYRLGLTATP 146
DEXDc smart00487
DEAD-like helicases superfamily;
4-155 7.85e-19

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 84.85  E-value: 7.85e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556     4 LRKWQQEALDKyLATNPKDFLAVATPGAGKTTFALRIASELLSRRIVERIIVVVPTEHLKVQWAASAARSGIAL------ 77
Cdd:smart00487   9 LRPYQKEAIEA-LLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLglkvvg 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556    78 ----DPKFTNAKGVVNPSYQGIVVTYaQVAVHPFKHHAVATARPTLVILDEVHHGGDAKSWGD--GISEAYGDVERRLCL 151
Cdd:smart00487  88 lyggDSKREQLRKLESGKTDILVTTP-GRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQleKLLKLLPKNVQLLLL 166


                   ....
gi 881012556   152 TGTP 155
Cdd:smart00487 167 SATP 170
ResIII pfam04851
Type III restriction enzyme, res subunit;
4-157 4.57e-15

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 73.09  E-value: 4.57e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556    4 LRKWQQEALDKYLA---TNPKDFLAVATPGAGKTTFALRIASELLSRRIVERIIVVVPTEHLKVQWAASAARSGialdPK 80
Cdd:pfam04851   4 LRPYQIEAIENLLEsikNGQKRGLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPRKDLLEQALEEFKKFL----PN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556   81 FTNAKGVVNP--------SYQGIVVTY--AQVAVHPFKHHAVATARPtLVILDEVHHGGdAKSWG---DGISEAYgdver 147
Cdd:pfam04851  80 YVEIGEIISGdkkdesvdDNKIVVTTIqsLYKALELASLELLPDFFD-VIIIDEAHRSG-ASSYRnilEYFKPAF----- 152

                         170
                  ....*....|
gi 881012556  148 RLCLTGTPFR 157
Cdd:pfam04851 153 LLGLTATPER 162
 
Name Accession Description Interval E-value
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
3-477 1.62e-76

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 253.02  E-value: 1.62e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556   3 GLRKWQQEALDKYLAT---NPKDFLAVATPGAGKTTFALRIASELLSRRiveRIIVVVPTEHLKVQWAASAARsgiaLDP 79
Cdd:COG1061   80 ELRPYQQEALEALLAAlerGGGRGLVVAPTGTGKTVLALALAAELLRGK---RVLVLVPRRELLEQWAEELRR----FLG 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556  80 KFTNAKGVVNPSYQGIVVTYAQVAVHPfkHHAVATARPTLVILDEVHHGGdAKSWGDGISeaYGDVERRLCLTGTPFRSD 159
Cdd:COG1061  153 DPLAGGGKKDSDAPITVATYQSLARRA--HLDELGDRFGLVIIDEAHHAG-APSYRRILE--AFPAAYRLGLTATPFRSD 227

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556 160 DAAIPFVRYspdgDGysrsVAdYTYGYSNALADGVVRPVVFLAYSGEARWRDSAGDEFAARLgtvmspeettrawRTALD 239
Cdd:COG1061  228 GREILLFLF----DG----IV-YEYSLKEAIEDGYLAPPEYYGIRVDLTDERAEYDALSERL-------------REALA 285

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556 240 PKGEWMPSVLRAAhtrlsqMRQHIPDAGGLVIASDAATARAYKRILEQiASTPVALVLSDEPGS--SERIKTFSESTDEW 317
Cdd:COG1061  286 ADAERKDKILREL------LREHPDDRKTLVFCSSVDHAEALAELLNE-AGIRAAVVTGDTPKKerEEILEAFRDGELRI 358

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556 318 MVAVRMVSEGVDVPRLAVGVYATSSSTPLFFAQAIGRFVRSRMPGETASVFL---PSIPVLLDLAS--QMEVQRNHVLGK 392
Cdd:COG1061  359 LVTVDVLNEGVDVPRLDVAILLRPTGSPREFIQRLGRGLRPAPGKEDALVYDfvgNDVPVLEELAKdlRDLAGYRVEFLD 438

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556 393 PDRPSEGWEDDLVAEANRRKDEPDELLPAYESIGADAELDYLIYDGSSYGTATVAGSAEEADYLGLPGLLDADQMRLLLR 472
Cdd:COG1061  439 EEESEELALLIAVKPALEVKGELEEELLEELELLEDALLLVLAELLLLELLALALELLELAKAEGKAEEEEEEKELLLLL 518


                 ....*
gi 881012556 473 QRQDE 477
Cdd:COG1061  519 ALAKL 523
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 4-155 9.81e-20

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


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 85.82  E-value: 9.81e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556   4 LRKWQQEALDKYLATNPKDF-LAVATPGAGKTTFALRIASELLSrrivERIIVVVPTEHLKVQWAASAAR-SGIALDPKF 81
Cdd:cd17926    1 LRPYQEEALEAWLAHKNNRRgILVLPTGSGKTLTALALIAYLKE----LRTLIVVPTDALLDQWKERFEDfLGDSSIGLI 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 881012556  82 tnaKGVVNPSYQGIVVTYA--QVAVHPFKHHAVATARPTLVILDEVHHGGdAKSWGDGISEAYGdvERRLCLTGTP 155
Cdd:cd17926   77 ---GGGKKKDFDDANVVVAtyQSLSNLAEEEKDLFDQFGLLIVDEAHHLP-AKTFSEILKELNA--KYRLGLTATP 146
DEXDc smart00487
DEAD-like helicases superfamily;
4-155 7.85e-19

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 84.85  E-value: 7.85e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556     4 LRKWQQEALDKyLATNPKDFLAVATPGAGKTTFALRIASELLSRRIVERIIVVVPTEHLKVQWAASAARSGIAL------ 77
Cdd:smart00487   9 LRPYQKEAIEA-LLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLglkvvg 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556    78 ----DPKFTNAKGVVNPSYQGIVVTYaQVAVHPFKHHAVATARPTLVILDEVHHGGDAKSWGD--GISEAYGDVERRLCL 151
Cdd:smart00487  88 lyggDSKREQLRKLESGKTDILVTTP-GRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQleKLLKLLPKNVQLLLL 166


                   ....
gi 881012556   152 TGTP 155
Cdd:smart00487 167 SATP 170
ResIII pfam04851
Type III restriction enzyme, res subunit;
4-157 4.57e-15

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 73.09  E-value: 4.57e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556    4 LRKWQQEALDKYLA---TNPKDFLAVATPGAGKTTFALRIASELLSRRIVERIIVVVPTEHLKVQWAASAARSGialdPK 80
Cdd:pfam04851   4 LRPYQIEAIENLLEsikNGQKRGLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPRKDLLEQALEEFKKFL----PN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556   81 FTNAKGVVNP--------SYQGIVVTY--AQVAVHPFKHHAVATARPtLVILDEVHHGGdAKSWG---DGISEAYgdver 147
Cdd:pfam04851  80 YVEIGEIISGdkkdesvdDNKIVVTTIqsLYKALELASLELLPDFFD-VIIIDEAHRSG-ASSYRnilEYFKPAF----- 152

                         170
                  ....*....|
gi 881012556  148 RLCLTGTPFR 157
Cdd:pfam04851 153 LLGLTATPER 162
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
 4-163 2.28e-10

DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350769 [Multi-domain]  Cd Length: 207  Bit Score: 60.38  E-value: 2.28e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556   4 LRKWQQEALDKYLATNPKDFLAVATPGAGKTTFALRIASELLSRRIVERIIVVVPTeHLKVQWAAS-AARSGI---ALDP 79
Cdd:cd18011    1 PLPHQIDAVLRALRKPPVRLLLADEVGLGKTIEAGLIIKELLLRGDAKRVLILCPA-SLVEQWQDElQDKFGLpflILDR 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556  80 K--FTNAKGVVNP-SYQGIVVT-YAQVAVHPFKHHAVATARPTLVILDEVHHggdAKSWGDGISEAYGDVERRLC----- 150
Cdd:cd18011   80 EtaAQLRRLIGNPfEEFPIVIVsLDLLKRSEERRGLLLSEEWDLVVVDEAHK---LRNSGGGKETKRYKLGRLLAkrarh 156

                        170
                 ....*....|....*.
gi 881012556 151 ---LTGTPFRSDDAAI 163
Cdd:cd18011  157 vllLTATPHNGKEEDF 172
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 4-163 3.68e-10

DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350790 [Multi-domain]  Cd Length: 163  Bit Score: 58.73  E-value: 3.68e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556   4 LRKWQQEALDKYLATNPKDF---LAVATPGAGKTTFALRIASELLSRRIVERIIVVVPTEHLKVQwAASAARsGIALDPK 80
Cdd:cd18032    1 PRYYQQEAIEALEEAREKGQrraLLVMATGTGKTYTAAFLIKRLLEANRKKRILFLAHREELLEQ-AERSFK-EVLPDGS 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556  81 FTNAKG---------VVNPSYQGIV--VTYAQVAVHPFKhhavatarptLVILDEVHHGGdAKSWGdGISEAYGDVeRRL 149
Cdd:cd18032   79 FGNLKGgkkkpddarVVFATVQTLNkrKRLEKFPPDYFD----------LIIIDEAHHAI-ASSYR-KILEYFEPA-FLL 145

                        170
                 ....*....|....
gi 881012556 150 CLTGTPFRSDDAAI 163
Cdd:cd18032  146 GLTATPERTDGLDT 159
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 29-155 1.72e-08

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 57.54  E-value: 1.72e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556  29 PGAGKTTFALRIASELLSRRIVERIIVVVPTeHLKVQWAASAARSGIALD------PKFTNAKGVVNPSYQGIVVTYAQV 102
Cdd:COG0553  269 MGLGKTIQALALLLELKERGLARPVLIVAPT-SLVGNWQRELAKFAPGLRvlvldgTRERAKGANPFEDADLVITSYGLL 347

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 881012556 103 AVHpfkHHAVATARPTLVILDEVHHggdAKSWGDGISEAygdVER-----RLCLTGTP 155
Cdd:COG0553  348 RRD---IELLAAVDWDLVILDEAQH---IKNPATKRAKA---VRAlkarhRLALTGTP 396
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 8-158 3.60e-08

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


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 53.02  E-value: 3.60e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556    8 QQEALDkyLATNPKDFLAVATPGAGKTT-FALRIASELLSRRIVERIIVVVPTEHLKVQWAASAARSGIALDPKFTNAKG 86
Cdd:pfam00270   4 QAEAIP--AILEGRDVLVQAPTGSGKTLaFLLPALEALDKLDNGPQALVLAPTRELAEQIYEELKKLGKGLGLKVASLLG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556   87 VVNPSYQG--------IVVTYAQVAVHpfKHHAVATARPTLVILDEVHHGGDaKSWGDGISEAYGDVE---RRLCLTGTP 155
Cdd:pfam00270  82 GDSRKEQLeklkgpdiLVGTPGRLLDL--LQERKLLKNLKLLVLDEAHRLLD-MGFGPDLEEILRRLPkkrQILLLSATL 158


                  ...
gi 881012556  156 FRS 158
Cdd:pfam00270 159 PRN 161
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 21-127 9.79e-07

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


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 48.55  E-value: 9.79e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556  21 KDFLAVATPGAGKTTFALRIA-SELLSRRivERIIVVVPTEHLKVQWAA---SAARSGIALDP--KFTNAK---GVVNPS 91
Cdd:cd00046    2 ENVLITAPTGSGKTLAALLAAlLLLLKKG--KKVLVLVPTKALALQTAErlrELFGPGIRVAVlvGGSSAEereKNKLGD 79

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 881012556  92 YQGIVVTYAQVAVHPFKHHAVATARPTLVILDEVHH 127
Cdd:cd00046   80 ADIIIATPDMLLNLLLREDRLFLKDLKLIIVDEAHA 115
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 2-59 5.78e-05

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


Pssm-ID: 440816 [Multi-domain]  Cd Length: 535  Bit Score: 45.84  E-value: 5.78e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 881012556   2 SGLRKWQQEALD---KYLATNPKDFLAVATPGAGKTTFALRIASELLSRRIVERIIVVVPT 59
Cdd:COG1203  126 TPINPLQNEALElalEAAEEEPGLFILTAPTGGGKTEAALLFALRLAAKHGGRRIIYALPF 186
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 4-129 1.35e-04

DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350792 [Multi-domain]  Cd Length: 200  Bit Score: 43.41  E-value: 1.35e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556   4 LRKWQQEALDKYLATNpkdFLAVATPGAGKTTFALRIASELLSRRIVE-----RIIVVVPTEHLkVQWAASAARSGIALD 78
Cdd:cd18034    3 PRSYQLELFEAALKRN---TIVVLPTGSGKTLIAVMLIKEMGELNRKEknpkkRAVFLVPTVPL-VAQQAEAIRSHTDLK 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 881012556  79 -PKFTNAKGVVNP----------SYQGIVVTyAQVAVHPFKHHAVATARPTLVILDEVHHGG 129
Cdd:cd18034   79 vGEYSGEMGVDKWtkerwkeeleKYDVLVMT-AQILLDALRHGFLSLSDINLLIFDECHHAT 139
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
 4-155 2.29e-04

DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350677 [Multi-domain]  Cd Length: 182  Bit Score: 42.17  E-value: 2.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556   4 LRKWQQEALdKYLATNPKDFLAVA---TPGAGKT--TFALrIASELLSRRIVERIIVVVP--------------TEHLKV 64
Cdd:cd17919    1 LRPYQLEGL-NFLLELYENGPGGIladEMGLGKTlqAIAF-LAYLLKEGKERGPVLVVCPlsvlenwerefekwTPDLRV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556  65 Q--WAASAARSGIALDPKFtnakgvvnPSYQGIVVTYAQVAVHPFKHHAVataRPTLVILDEVHHggdAKSWGDGISEAY 142
Cdd:cd17919   79 VvyHGSQRERAQIRAKEKL--------DKFDVVLTTYETLRRDKASLRKF---RWDLVVVDEAHR---LKNPKSQLSKAL 144

                        170
                 ....*....|....*
gi 881012556 143 GDV--ERRLCLTGTP 155
Cdd:cd17919  145 KALraKRRLLLTGTP 159
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 4-127 4.25e-04

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


Pssm-ID: 350685 [Multi-domain]  Cd Length: 201  Bit Score: 41.65  E-value: 4.25e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556   4 LRKWQQEALDKylATNPKDFLAVATPGAGKTTFALRIASELLSRRIVE---RIIVVVPTEHLKVQWAASAAR-------- 72
Cdd:cd17927    3 PRNYQLELAQP--ALKGKNTIICLPTGSGKTFVAVLICEHHLKKFPAGrkgKVVFLANKVPLVEQQKEVFRKhferpgyk 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 881012556  73 -SGIALDPKFTNAKGVVNPSYQGIVVTyAQVAVHPFKH-HAVATARPTLVILDEVHH 127
Cdd:cd17927   81 vTGLSGDTSENVSVEQIVESSDVIIVT-PQILVNDLKSgTIVSLSDFSLLVFDECHN 136
AAA_22 pfam13401
AAA domain;
24-127 1.11e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 39.25  E-value: 1.11e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556   24 LAVATPGAGKTTFALRIASELLSRRiVERIIVVVPtehlkvqwaasAARSGIALDPKFTNAKGVVNPSYQGIVVTYAQVA 103
Cdd:pfam13401   9 VLTGESGTGKTTLLRRLLEQLPEVR-DSVVFVDLP-----------SGTSPKDLLRALLRALGLPLSGRLSKEELLAALQ 76

                          90       100
                  ....*....|....*....|....
gi 881012556  104 vhpfkHHAVATARPTLVILDEVHH 127
Cdd:pfam13401  77 -----QLLLALAVAVVLIIDEAQH 95
DEXHc_DDX60 cd18025
DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an ...
 7-156 1.11e-03

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


Pssm-ID: 350783 [Multi-domain]  Cd Length: 192  Bit Score: 40.43  E-value: 1.11e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556   7 WQQEALDkyLATNPKDFLAVATPGAGKTtFALRIASELLSRRIVERIIV-VVPTEHLKVQWAASA-AR-------SGIAL 77
Cdd:cd18025    5 WQRELLD--IVDRRESALIVAPTSSGKT-FISYYCMEKVLRESDDGVVVyVAPTKALVNQVVAEVyARfskkyppSGKSL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556  78 DPKFTNAKGVVNPSYQGIVVTYAQVAVHPF--KHHAVATARPTLVILDEVHHGGdakswgdgiSEAYGDV-ERRLCLTGT 154
Cdd:cd18025   82 WGVFTRDYRHNNPMNCQVLITVPECLEILLlsPHNASWVPRIKYVIFDEIHSIG---------QSEDGAVwEQLLLLIPC 152


                 ..
gi 881012556 155 PF 156
Cdd:cd18025  153 PF 154
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 6-126 3.45e-03

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


Pssm-ID: 350679 [Multi-domain]  Cd Length: 181  Bit Score: 38.78  E-value: 3.45e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556   6 KWQQEALDKYLATNpkDFLAVATP-GAGKTTFA-LRIASELLSRRIveRIIVVVPTEHLKVQ----WAASAARSGIAL-- 77
Cdd:cd17921    4 PIQREALRALYLSG--DSVLVSAPtSSGKTLIAeLAILRALATSGG--KAVYIAPTRALVNQkeadLRERFGPLGKNVgl 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 881012556  78 ---DPKFTNAKgvvNPSYQGIVVTYAQVAVHPFKHHAVATARPTLVILDEVH 126
Cdd:cd17921   80 ltgDPSVNKLL---LAEADILVATPEKLDLLLRNGGERLIQDVRLVVVDEAH 128
DEXHc_cas3 cd17930
DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase ...
 20-126 4.32e-03

DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase responsible for degradation of dsDNA. The two enzymatic units of Cas3, a histidine-aspartate (HD) nuclease and a Superfamily 2 (SF2) helicase, may be expressed from separate genes as Cas3' (SF2 helicase) and Cas3'' (HD nuclease) or may be fused as a single HD-SF2 polypeptide. The nucleolytic activity of most Cas3 enzymes is transition metal ion-dependent. Cas3 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: 350688 [Multi-domain]  Cd Length: 186  Bit Score: 38.43  E-value: 4.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881012556  20 PKDFLAVATPGAGKTTFALRIASELLSRRIVERIIVVVPT--------EHLKvQWAASAAR--------SGIALDPKFTN 83
Cdd:cd17930    1 PGLVILEAPTGSGKTEAALLWALKLAARGGKRRIIYALPTratinqmyERIR-EILGRLDDedkvlllhSKAALELLESD 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 881012556  84 AKGVVNPSYQG-------------IVVTYA-QV--AVHPFKH-----HAVATArptLVILDEVH 126
Cdd:cd17930   80 EEPDDDPVEAVdwalllkrswlapIVVTTIdQLleSLLKYKHferrlHGLANS---VVVLDEVQ 140
 
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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