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Conserved domains on  [gi|62327127|ref|YP_223915|]
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DNA helicase [Lactobacillus phage phiJL-1]

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];
1-322 2.67e-78

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


:

Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 254.18  E-value: 2.67e-78
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127   1 MFKLYDYQQRIVDETRNKLRQGNKGVLIVSPPGSGKSVIIGEITRlTTLKKNRVLFTVHRQELVDQITDTF-------DA 73
Cdd:COG1061  78 SFELRPYQQEALEALLAALERGGGRGLVVAPTGTGKTVLALALAA-ELLRGKRVLVLVPRRELLEQWAEELrrflgdpLA 156

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127  74 MGVNQDY------TTVMTVGRvKNRLDKLEK-PDLIIVDESQHTRAKTYTDILDYYSDVPRLGFSGSPWRMNGQgfdDIY 146
Cdd:COG1061 157 GGGKKDSdapitvATYQSLAR-RAHLDELGDrFGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPFRSDGR---EIL 232

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127 147 PAMVEGP----SVKWLIDNYHLAPFTYYAPQTleGFKKRNGEYD--KKSVDEVL--GSKIFGDAVSSYLS-NANGKQAIL 217
Cdd:COG1061 233 LFLFDGIvyeySLKEAIEDGYLAPPEYYGIRV--DLTDERAEYDalSERLREALaaDAERKDKILRELLReHPDDRKTLV 310

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127 218 YAHSVEYAKKYAVAFEEAGVNAASVDGKTPKAERDRIINDFRSGKLKVLCNNDLISEGFDVPNCEVVIMCRPTASLVLYL 297
Cdd:COG1061 311 FCSSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLRPTGSPREFI 390

                       330       340
                ....*....|....*....|....*.
gi 62327127 298 QQSMRCMRYVNGKQ-AMIIDHVGNYV 322
Cdd:COG1061 391 QRLGRGLRPAPGKEdALVYDFVGNDV 416
 
Name Accession Description Interval E-value
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
1-322 2.67e-78

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 254.18  E-value: 2.67e-78
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127   1 MFKLYDYQQRIVDETRNKLRQGNKGVLIVSPPGSGKSVIIGEITRlTTLKKNRVLFTVHRQELVDQITDTF-------DA 73
Cdd:COG1061  78 SFELRPYQQEALEALLAALERGGGRGLVVAPTGTGKTVLALALAA-ELLRGKRVLVLVPRRELLEQWAEELrrflgdpLA 156

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127  74 MGVNQDY------TTVMTVGRvKNRLDKLEK-PDLIIVDESQHTRAKTYTDILDYYSDVPRLGFSGSPWRMNGQgfdDIY 146
Cdd:COG1061 157 GGGKKDSdapitvATYQSLAR-RAHLDELGDrFGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPFRSDGR---EIL 232

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127 147 PAMVEGP----SVKWLIDNYHLAPFTYYAPQTleGFKKRNGEYD--KKSVDEVL--GSKIFGDAVSSYLS-NANGKQAIL 217
Cdd:COG1061 233 LFLFDGIvyeySLKEAIEDGYLAPPEYYGIRV--DLTDERAEYDalSERLREALaaDAERKDKILRELLReHPDDRKTLV 310

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127 218 YAHSVEYAKKYAVAFEEAGVNAASVDGKTPKAERDRIINDFRSGKLKVLCNNDLISEGFDVPNCEVVIMCRPTASLVLYL 297
Cdd:COG1061 311 FCSSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLRPTGSPREFI 390

                       330       340
                ....*....|....*....|....*.
gi 62327127 298 QQSMRCMRYVNGKQ-AMIIDHVGNYV 322
Cdd:COG1061 391 QRLGRGLRPAPGKEdALVYDFVGNDV 416
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 4-146 9.20e-26

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: 102.64  E-value: 9.20e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127   4 LYDYQQRIVDETRNKLRQGNKGVLIVSPPGSGKSVIIGEITR--LTTLKKNRVLFTVHRQELVDQITDTF------DAMG 75
Cdd:cd18032   1 PRYYQQEAIEALEEAREKGQRRALLVMATGTGKTYTAAFLIKrlLEANRKKRILFLAHREELLEQAERSFkevlpdGSFG 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127  76 V-------NQDY----TTVMTVGRVKnRLDKLEK--PDLIIVDESQHTRAKTYTDILDYYSDVPRLGFSGSPWRMNGQgf 142
Cdd:cd18032  81 NlkggkkkPDDArvvfATVQTLNKRK-RLEKFPPdyFDLIIIDEAHHAIASSYRKILEYFEPAFLLGLTATPERTDGL-- 157


                ....
gi 62327127 143 dDIY 146
Cdd:cd18032 158 -DTY 160
ResIII pfam04851
Type III restriction enzyme, res subunit;
2-134 1.18e-24

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 99.67  E-value: 1.18e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127     2 FKLYDYQQRIVDETRNKLRQGNKGVLIVSPPGSGKSVIIGEITRLTTLK--KNRVLFTVHRQELVDQITDTFDAMG---- 75
Cdd:pfam04851   2 LELRPYQIEAIENLLESIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKgpIKKVLFLVPRKDLLEQALEEFKKFLpnyv 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62327127    76 --------------VNQDYTTVMTVGRVKNRLDK------LEKPDLIIVDESQHTRAKTYTDILDYYSDVPRLGFSGSP 134
Cdd:pfam04851  82 eigeiisgdkkdesVDDNKIVVTTIQSLYKALELaslellPDFFDVIIIDEAHRSGASSYRNILEYFKPAFLLGLTATP 160
DEXDc smart00487
DEAD-like helicases superfamily;
2-134 1.66e-16

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 77.92  E-value: 1.66e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127      2 FKLYDYQQRIVdetrNKLRQGNKGVLIVSPPGSGKSVIIGE--ITRLTTLKKNRVLFTVHRQELVDQITDTFDAMGVNQD 79
Cdd:smart00487   7 EPLRPYQKEAI----EALLSGLRDVILAAPTGSGKTLAALLpaLEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLG 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127     80 YT------------------------TVMTVGRVKNRLDK----LEKPDLIIVDESQHTRAKTYTDILDYY-----SDVP 126
Cdd:smart00487  83 LKvvglyggdskreqlrklesgktdiLVTTPGRLLDLLENdklsLSNVDLVILDEAHRLLDGGFGDQLEKLlkllpKNVQ 162


                   ....*...
gi 62327127    127 RLGFSGSP 134
Cdd:smart00487 163 LLLLSATP 170
hsdR PRK11448
type I restriction enzyme EcoKI subunit R; Provisional
 2-321 4.18e-09

type I restriction enzyme EcoKI subunit R; Provisional


Pssm-ID: 236912 [Multi-domain]  Cd Length: 1123  Bit Score: 59.19  E-value: 4.18e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127     2 FKLYDYQQRIVDETRNKLRQGNKGVLIVSPPGSGKS-VIIGEITRLTTLKK-NRVLFTVHRQELVDQITDTFDAMGVNQD 79
Cdd:PRK11448  412 LGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTrTAIALMYRLLKAKRfRRILFLVDRSALGEQAEDAFKDTKIEGD 491

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127    80 YT------------------------TV--MtVGRVKNRLDKLEKP-----DLIIVDE-------------------SQH 109
Cdd:PRK11448  492 QTfasiydikgledkfpedetkvhvaTVqgM-VKRILYSDDPMDKPpvdqyDCIIVDEahrgytldkemsegelqfrDQL 570

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127   110 TRAKTYTDILDYYsDVPRLGFSGSPWRMNGQGFDD-IY-----PAMVEGpsvkWLIDnyHLAPFTYYAPQTLEG--FKKr 181
Cdd:PRK11448  571 DYVSKYRRVLDYF-DAVKIGLTATPALHTTEIFGEpVYtysyrEAVIDG----YLID--HEPPIRIETRLSQEGihFEK- 642

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127   182 nGE----YDKKS--------VDEV----------LGSKIFGDAVSSYLSN-----ANGKQAILYA---HS---VEYAKKy 228
Cdd:PRK11448  643 -GEevevINTQTgeidlatlEDEVdfevedfnrrVITESFNRVVCEELAKyldptGEGKTLIFAAtdaHAdmvVRLLKE- 720

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127   229 avAFEEAG--VNAASVDGKTPKAER-DRIINDFRSGKL-KVLCNNDLISEGFDVPN-CEVVIMcRPTASLVLYLQQSMRC 303
Cdd:PRK11448  721 --AFKKKYgqVEDDAVIKITGSIDKpDQLIRRFKNERLpNIVVTVDLLTTGIDVPSiCNLVFL-RRVRSRILYEQMLGRA 797

                         410       420
                  ....*....|....*....|.
gi 62327127   304 MRYVN--GKQA-MIIDHVGNY 321
Cdd:PRK11448  798 TRLCPeiGKTHfRIFDAVDIY 818
 
Name Accession Description Interval E-value
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
1-322 2.67e-78

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 254.18  E-value: 2.67e-78
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127   1 MFKLYDYQQRIVDETRNKLRQGNKGVLIVSPPGSGKSVIIGEITRlTTLKKNRVLFTVHRQELVDQITDTF-------DA 73
Cdd:COG1061  78 SFELRPYQQEALEALLAALERGGGRGLVVAPTGTGKTVLALALAA-ELLRGKRVLVLVPRRELLEQWAEELrrflgdpLA 156

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127  74 MGVNQDY------TTVMTVGRvKNRLDKLEK-PDLIIVDESQHTRAKTYTDILDYYSDVPRLGFSGSPWRMNGQgfdDIY 146
Cdd:COG1061 157 GGGKKDSdapitvATYQSLAR-RAHLDELGDrFGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPFRSDGR---EIL 232

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127 147 PAMVEGP----SVKWLIDNYHLAPFTYYAPQTleGFKKRNGEYD--KKSVDEVL--GSKIFGDAVSSYLS-NANGKQAIL 217
Cdd:COG1061 233 LFLFDGIvyeySLKEAIEDGYLAPPEYYGIRV--DLTDERAEYDalSERLREALaaDAERKDKILRELLReHPDDRKTLV 310

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127 218 YAHSVEYAKKYAVAFEEAGVNAASVDGKTPKAERDRIINDFRSGKLKVLCNNDLISEGFDVPNCEVVIMCRPTASLVLYL 297
Cdd:COG1061 311 FCSSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLRPTGSPREFI 390

                       330       340
                ....*....|....*....|....*.
gi 62327127 298 QQSMRCMRYVNGKQ-AMIIDHVGNYV 322
Cdd:COG1061 391 QRLGRGLRPAPGKEdALVYDFVGNDV 416
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 4-146 9.20e-26

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: 102.64  E-value: 9.20e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127   4 LYDYQQRIVDETRNKLRQGNKGVLIVSPPGSGKSVIIGEITR--LTTLKKNRVLFTVHRQELVDQITDTF------DAMG 75
Cdd:cd18032   1 PRYYQQEAIEALEEAREKGQRRALLVMATGTGKTYTAAFLIKrlLEANRKKRILFLAHREELLEQAERSFkevlpdGSFG 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127  76 V-------NQDY----TTVMTVGRVKnRLDKLEK--PDLIIVDESQHTRAKTYTDILDYYSDVPRLGFSGSPWRMNGQgf 142
Cdd:cd18032  81 NlkggkkkPDDArvvfATVQTLNKRK-RLEKFPPdyFDLIIIDEAHHAIASSYRKILEYFEPAFLLGLTATPERTDGL-- 157


                ....
gi 62327127 143 dDIY 146
Cdd:cd18032 158 -DTY 160
ResIII pfam04851
Type III restriction enzyme, res subunit;
2-134 1.18e-24

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 99.67  E-value: 1.18e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127     2 FKLYDYQQRIVDETRNKLRQGNKGVLIVSPPGSGKSVIIGEITRLTTLK--KNRVLFTVHRQELVDQITDTFDAMG---- 75
Cdd:pfam04851   2 LELRPYQIEAIENLLESIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKgpIKKVLFLVPRKDLLEQALEEFKKFLpnyv 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62327127    76 --------------VNQDYTTVMTVGRVKNRLDK------LEKPDLIIVDESQHTRAKTYTDILDYYSDVPRLGFSGSP 134
Cdd:pfam04851  82 eigeiisgdkkdesVDDNKIVVTTIQSLYKALELaslellPDFFDVIIIDEAHRSGASSYRNILEYFKPAFLLGLTATP 160
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 201-306 5.31e-21

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


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 87.65  E-value: 5.31e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127   201 DAVSSYLSNANGKQAILYAHSVEYAKkYAVAFEEAGVNAASVDGKTPKAERDRIINDFRSGKLKVLCNNDLISEGFDVPN 280
Cdd:pfam00271   4 EALLELLKKERGGKVLIFSQTKKTLE-AELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPD 82

                          90       100
                  ....*....|....*....|....*.
gi 62327127   281 CEVVIMCRPTASLVLYLQQSMRCMRY 306
Cdd:pfam00271  83 VDLVINYDLPWNPASYIQRIGRAGRA 108
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 215-318 3.36e-18

C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350186 [Multi-domain]  Cd Length: 116  Bit Score: 79.91  E-value: 3.36e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127 215 AILYAHSVEYAKKYAVAFEEAGVNAASVDGKTPKAER-DRIINDFRSGKLK--VLCNNDLISEGFDVPNCEVVIMCRPTA 291
Cdd:cd18799   9 TLIFCVSIEHAEFMAEAFNEAGIDAVALNSDYSDRERgDEALILLFFGELKppILVTVDLLTTGVDIPEVDNVVFLRPTE 88

                        90       100
                ....*....|....*....|....*...
gi 62327127 292 SLVLYLQQSMRCMRYVNGKQAM-IIDHV 318
Cdd:cd18799  89 SRTLFLQMLGRGLRLHEGKDFFtILDFI 116
DEXDc smart00487
DEAD-like helicases superfamily;
2-134 1.66e-16

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 77.92  E-value: 1.66e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127      2 FKLYDYQQRIVdetrNKLRQGNKGVLIVSPPGSGKSVIIGE--ITRLTTLKKNRVLFTVHRQELVDQITDTFDAMGVNQD 79
Cdd:smart00487   7 EPLRPYQKEAI----EALLSGLRDVILAAPTGSGKTLAALLpaLEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLG 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127     80 YT------------------------TVMTVGRVKNRLDK----LEKPDLIIVDESQHTRAKTYTDILDYY-----SDVP 126
Cdd:smart00487  83 LKvvglyggdskreqlrklesgktdiLVTTPGRLLDLLENdklsLSNVDLVILDEAHRLLDGGFGDQLEKLlkllpKNVQ 162


                   ....*...
gi 62327127    127 RLGFSGSP 134
Cdd:smart00487 163 LLLLSATP 170
HELICc smart00490
helicase superfamily c-terminal domain;
226-306 9.69e-16

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 71.86  E-value: 9.69e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127    226 KKYAVAFEEAGVNAASVDGKTPKAERDRIINDFRSGKLKVLCNNDLISEGFDVPNCEVVIMCRPTASLVLYLQQSMRCMR 305
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGR 80


                   .
gi 62327127    306 Y 306
Cdd:smart00490  81 A 81
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 4-134 1.88e-15

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: 73.11  E-value: 1.88e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127   4 LYDYQQRIVDETRNKlrQGNKGVLIVSPPGSGKSVIIGEITRLttLKKNRVLFTVHRQELVDQITDTF------------ 71
Cdd:cd17926   1 LRPYQEEALEAWLAH--KNNRRGILVLPTGSGKTLTALALIAY--LKELRTLIVVPTDALLDQWKERFedflgdssigli 76

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127  72 ------DAMGVNQDYTTVMTVGR-VKNRLDKLEKPDLIIVDESQHTRAKTYTDILDYYSDVPRLGFSGSP 134
Cdd:cd17926  77 gggkkkDFDDANVVVATYQSLSNlAEEEKDLFDQFGLLIVDEAHHLPAKTFSEILKELNAKYRLGLTATP 146
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 205-285 3.15e-12

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 63.68  E-value: 3.15e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127 205 SYLSNANGKQAILYAHSVEYAKKYAVAFEEAGVNAASVDGKTPKAERDRIINDFRSGKLKVLCNNDLISEGFDVPNCEVV 284
Cdd:cd18787  20 LLLEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDHV 99


                .
gi 62327127 285 I 285
Cdd:cd18787 100 I 100
HsdR COG4096
Type I site-specific restriction endonuclease, part of a restriction-modification system ...
 6-329 3.63e-10

Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms];


Pssm-ID: 443272 [Multi-domain]  Cd Length: 806  Bit Score: 62.17  E-value: 3.63e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127   6 DYQQRIVDETRNKLRQGNKGVLIVSPPGSGKS-VIIGEITRLttLK---KNRVLFTVHRQELVDQITDTFDAMGVNQD-- 79
Cdd:COG4096 161 YYQIEAIRRVEEAIAKGQRRALLVMATGTGKTrTAIALIYRL--LKagrAKRILFLADRNALVDQAKNAFKPFLPDLDaf 238

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127  80 ---YTT-----------VMTVGRVKNRLDKLEKP-----------DLIIVDESqHtR--AKTYTDILDYYSDV------- 125
Cdd:COG4096 239 tklYNKskdidksarvyFSTYQTMMNRIDGEEEEpgyrqfppdffDLIIIDEC-H-RgiYSKWRAILDYFDALqigltat 316

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127 126 PRLG--------FSGSPwrmngqgfddiypamvegpsvkwlIDNY---------HLAPF--------------TYYAPQT 174
Cdd:COG4096 317 PKDTidrntyeyFNGNP------------------------VYTYsleqavadgFLVPYkviridtkfdregiRYDAGED 372

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127 175 L---EGFKKR------NGEYDKKSVDEVLGSKIFGDAVSSYLSNaNGKQA--------ILYAHSVEYAK--KYAV--AFE 233
Cdd:COG4096 373 LsdeEGEEIEleeleeDREYEAKDFNRKVVNEDTTRKVLEELME-YLDKPggdrlgktIIFAKNDDHADriVQALreLYP 451

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127 234 EAGVNAASV-DGKTPKAErdRIINDFRSGK--LKVLCNNDLISEGFDVPNCE-VVIMcRPTASLVLYLQqsM------RC 303
Cdd:COG4096 452 ELGGDFVKKiTGDDDYGK--SLIDNFKNPEkyPRIAVTVDMLDTGIDVPEVVnLVFM-RPVKSRIKFEQ--MigrgtrLC 526

                       410       420
                ....*....|....*....|....*..
gi 62327127 304 MRYVNGKQA-MIIDHVGNYVRFGLPDD 329
Cdd:COG4096 527 PDLFPGKTHfTIFDFVGNTELFADPSF 553
hsdR PRK11448
type I restriction enzyme EcoKI subunit R; Provisional
 2-321 4.18e-09

type I restriction enzyme EcoKI subunit R; Provisional


Pssm-ID: 236912 [Multi-domain]  Cd Length: 1123  Bit Score: 59.19  E-value: 4.18e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127     2 FKLYDYQQRIVDETRNKLRQGNKGVLIVSPPGSGKS-VIIGEITRLTTLKK-NRVLFTVHRQELVDQITDTFDAMGVNQD 79
Cdd:PRK11448  412 LGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTrTAIALMYRLLKAKRfRRILFLVDRSALGEQAEDAFKDTKIEGD 491

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127    80 YT------------------------TV--MtVGRVKNRLDKLEKP-----DLIIVDE-------------------SQH 109
Cdd:PRK11448  492 QTfasiydikgledkfpedetkvhvaTVqgM-VKRILYSDDPMDKPpvdqyDCIIVDEahrgytldkemsegelqfrDQL 570

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127   110 TRAKTYTDILDYYsDVPRLGFSGSPWRMNGQGFDD-IY-----PAMVEGpsvkWLIDnyHLAPFTYYAPQTLEG--FKKr 181
Cdd:PRK11448  571 DYVSKYRRVLDYF-DAVKIGLTATPALHTTEIFGEpVYtysyrEAVIDG----YLID--HEPPIRIETRLSQEGihFEK- 642

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127   182 nGE----YDKKS--------VDEV----------LGSKIFGDAVSSYLSN-----ANGKQAILYA---HS---VEYAKKy 228
Cdd:PRK11448  643 -GEevevINTQTgeidlatlEDEVdfevedfnrrVITESFNRVVCEELAKyldptGEGKTLIFAAtdaHAdmvVRLLKE- 720

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127   229 avAFEEAG--VNAASVDGKTPKAER-DRIINDFRSGKL-KVLCNNDLISEGFDVPN-CEVVIMcRPTASLVLYLQQSMRC 303
Cdd:PRK11448  721 --AFKKKYgqVEDDAVIKITGSIDKpDQLIRRFKNERLpNIVVTVDLLTTGIDVPSiCNLVFL-RRVRSRILYEQMLGRA 797

                         410       420
                  ....*....|....*....|.
gi 62327127   304 MRYVN--GKQA-MIIDHVGNY 321
Cdd:PRK11448  798 TRLCPeiGKTHfRIFDAVDIY 818
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
 210-285 2.15e-07

C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350176 [Multi-domain]  Cd Length: 153  Bit Score: 50.33  E-value: 2.15e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62327127 210 ANGKQAILYAHSVEYAKKYAVAFeeagvNAASVDGKTPKAERDRIINDFRSGKLKVLCNNDLISEGFDVPNCEVVI 285
Cdd:cd18789  47 EQGDKIIVFTDNVEALYRYAKRL-----LKPFITGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEANVAI 117
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
201-285 2.53e-06

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 49.76  E-value: 2.53e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127 201 DAVSSYLSNANGKQAILYAHSVEYAKKYAVAFEEAGVNAASVDGKTPKAERDRIINDFRSGKLKVLCNNDLISEGFDVPN 280
Cdd:COG0513 230 ELLRRLLRDEDPERAIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDD 309


                ....*
gi 62327127 281 CEVVI 285
Cdd:COG0513 310 VSHVI 314
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 23-106 4.49e-06

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 46.21  E-value: 4.49e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127     23 NKGVLIVSPPGSGKSVIIGEITRLTTLKKNRVLFtVHRQELVDQITDTFDAMGVNQDYTTVMTVGRVKNRLDKLEK--PD 100
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIY-IDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKlkPD 80


                   ....*.
gi 62327127    101 LIIVDE 106
Cdd:smart00382  81 VLILDE 86
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 262-316 1.37e-05

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


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 43.08  E-value: 1.37e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 62327127 262 KLKVLCNNDLISEGFDVPNCEVVIMCRPTASLVLYLQQSMRCMRYvNGKQAMIID 316
Cdd:cd18785  22 SLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRG-GKDEGEVIL 75
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 190-262 1.43e-05

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 44.39  E-value: 1.43e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62327127 190 VDEVLGSKIfgDAVSSYLSN--ANGKQAILYAHSVEYAKKYAVAFEEAGVNAASVDGKTPKAERDRIINDFRSGK 262
Cdd:cd18793   5 IEEVVSGKL--EALLELLEElrEPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDP 77
PTZ00424 PTZ00424
helicase 45; Provisional
 214-318 1.88e-05

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 46.74  E-value: 1.88e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127  214 QAILYAHSVEYAKKYAVAFEEAGVNAASVDGKTPKAERDRIINDFRSGKLKVLCNNDLISEGFDVPNCEVVIMCRPTASL 293
Cdd:PTZ00424 269 QAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASP 348

                         90       100
                 ....*....|....*....|....*
gi 62327127  294 VLYLQQSMRCMRYvnGKQAMIIDHV 318
Cdd:PTZ00424 349 ENYIHRIGRSGRF--GRKGVAINFV 371
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 210-262 4.08e-05

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 45.99  E-value: 4.08e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 62327127 210 ANGKQAILYAHSVEYAKKYAVAFEEAGVNAASVDGKTPKAERDRIINDFRSGK 262
Cdd:COG0553 547 AEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQEGP 599
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 23-132 7.41e-05

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: 42.78  E-value: 7.41e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127  23 NKGVLIVSPPGSGKSVIIGEITRLTTLKKN-RVLFTVHRQELVDQITDTFDA-------MGVNQDYTT------------ 82
Cdd:cd00046   1 GENVLITAPTGSGKTLAALLAALLLLLKKGkKVLVLVPTKALALQTAERLRElfgpgirVAVLVGGSSaeereknklgda 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62327127  83 ---VMTVGRV---KNRLDKLEKPD--LIIVDE-------SQHTRAKTYTDILDYYSDVPRLGFSG 132
Cdd:cd00046  81 diiIATPDMLlnlLLREDRLFLKDlkLIIVDEahallidSRGALILDLAVRKAGLKNAQVILLSA 145
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 2-134 1.72e-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: 42.64  E-value: 1.72e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127   2 FKLYDYQQRIVDETRNKlrqgNkgVLIVSPPGSGKSVI-------IGEITRLTTLKKNRVLFTVHRQELVDQ----ITDT 70
Cdd:cd18034   1 FTPRSYQLELFEAALKR----N--TIVVLPTGSGKTLIavmlikeMGELNRKEKNPKKRAVFLVPTVPLVAQqaeaIRSH 74

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127  71 FDA------MGVNQDYTT--------------VMTVGRVKNRLD----KLEKPDLIIVDESQHTRAK-TYTDIL-DYY-- 122
Cdd:cd18034  75 TDLkvgeysGEMGVDKWTkerwkeelekydvlVMTAQILLDALRhgflSLSDINLLIFDECHHATGDhPYARIMkEFYhl 154

                       170
                ....*....|....*.
gi 62327127 123 ---SDVPR-LGFSGSP 134
Cdd:cd18034 155 egrTSRPRiLGLTASP 170
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
 232-318 1.95e-04

C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II), and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA. Its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350177 [Multi-domain]  Cd Length: 171  Bit Score: 41.85  E-value: 1.95e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127 232 FEEAGVNAASVDGKTPKAERDRIINDFRSGKLKVLCNNDLISEGFDVPNCEVV-IM-------CRPTASLVlylQQSMRC 303
Cdd:cd18790  47 LQELGVKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVaILdadkegfLRSETSLI---QTIGRA 123

                        90
                ....*....|....*
gi 62327127 304 MRYVNGKQAMIIDHV 318
Cdd:cd18790 124 ARNVNGKVILYADKI 138
DEXHc_RE_I_HsdR cd18030
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of ...
 7-134 2.45e-04

DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of type I restriction-modification enzymes contains the DNA cleavage and ATP-dependent DNA translocation activities of the heteromeric complex. 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: 350788 [Multi-domain]  Cd Length: 208  Bit Score: 42.21  E-value: 2.45e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127   7 YQQ-----RIVDETRNKLRQG--NKGVLIVSPPGSGKSVIIGEITR-LTTLKKN-RVLFTVHRQELVDQITDTFDAMG-- 75
Cdd:cd18030  24 YYQyyaveAALERIKTATNKDgdKKGGYIWHTQGSGKSLTMFKAAKlLIEDPKNpKVVFVVDRKDLDYQTSSTFSRFAae 103

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127  76 --VNQDYTT--------------VMTVGRVKNRLDKLEKPDLI-------IVDESQHTRA-KTYTDILDYYSDVPRLGFS 131
Cdd:cd18030 104 dvVRANSTKelkellknlsggiiVTTIQKFNNAVKEESKPVLIyrknivvIVDEAHRSQFgELAKALKKALPNATFIGFT 183


                ...
gi 62327127 132 GSP 134
Cdd:cd18030 184 GTP 186
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 4-103 3.93e-04

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: 41.09  E-value: 3.93e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127   4 LYDYQQRIVDETRNKlrqgNKGVLIVSPPGSGKSViIGE--ITRLTTLKKNRVLFTVHRQELVDQITDTFDAMGVNQDYT 81
Cdd:cd17921   2 LNPIQREALRALYLS----GDSVLVSAPTSSGKTL-IAElaILRALATSGGKAVYIAPTRALVNQKEADLRERFGPLGKN 76

                        90       100
                ....*....|....*....|..
gi 62327127  82 TVMTVGRVKNRLDKLEKPDLII 103
Cdd:cd17921  77 VGLLTGDPSVNKLLLAEADILV 98
DnaC COG1484
DNA replication protein DnaC [Replication, recombination and repair];
5-106 5.39e-04

DNA replication protein DnaC [Replication, recombination and repair];


Pssm-ID: 441093 [Multi-domain]  Cd Length: 242  Bit Score: 41.69  E-value: 5.39e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127   5 YDY-QQRIVDETR-NKLRQG-----NKGVLIVSPPGSGKSVIIGEITRLTTLKKNRVLFTvHRQELVDQITDTFDAmgvn 77
Cdd:COG1484  74 FDFdAQPGLDRRQiLELATLdfierGENLILLGPPGTGKTHLAIALGHEACRAGYRVRFT-TAPDLVNELKEARAD---- 148

                        90       100
                ....*....|....*....|....*....
gi 62327127  78 qdyttvmtvGRVKNRLDKLEKPDLIIVDE 106
Cdd:COG1484 149 ---------GRLERLLKRLAKVDLLILDE 168
COG0610 COG0610
Type I site-specific restriction-modification system, R (restriction) subunit and related ...
 7-73 6.03e-04

Type I site-specific restriction-modification system, R (restriction) subunit and related helicases ... [Defense mechanisms];


Pssm-ID: 440375 [Multi-domain]  Cd Length: 936  Bit Score: 42.55  E-value: 6.03e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62327127   7 YQQ-----RIVDETRNKLRQGNKGVlivsppGSGKSVII----GEITRLTTLKKNRVLFTVHRQELVDQITDTFDA 73
Cdd:COG0610 258 YHQyfavrKAVERVKEAEGDGKGGViwh-tqGSGKSLTMvflaQKLARLPDLDNPTVVVVTDRKDLDDQLFDTFKA 332
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 26-126 4.61e-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: 38.37  E-value: 4.61e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62327127  26 VLIVSPPGSGKSVIIGEITRLTTLKKNRVLFTVHRQELVDQITDTFDAMGVNqdyttVMTVGRVKNRLDKLEKPDLiivd 105
Cdd:cd18041  20 ALILGMPGTGKTTTIAALVRILVALGKSVLLTSYTHSAVDNILLKLKKFGVN-----FLRLGRLKKIHPDVQEFTL---- 90

                        90       100
                ....*....|....*....|.
gi 62327127 106 ESQHTRAKTYTDILDYYSDVP 126
Cdd:cd18041  91 EAILKSCKSVEELESKYESVS 111
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 246-285 6.23e-03

C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 37.19  E-value: 6.23e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 62327127 246 TPKAERDrIINDFRSGKLKVLCNNDLISEGFDVPNCEVVI 285
Cdd:cd18802  75 TQRKQKE-TLDKFRDGELNLLIATSVLEEGIDVPACNLVI 113
 
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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