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Conserved domains on  [gi|28971393|ref|NP_803205|]
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NS3 proteinase/ATPase/helicase [GB virus C]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Peptidase_S29 super family cl03772
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ...
 30-177 8.74e-75

Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a trypsin-like fold. The non-structural (NS) protein NS3 is one of the NS proteins involved in replication of the HCV genome. NS2-3 proteinase, a zinc-dependent enzyme, performs a single proteolytic cut to release the N-terminus of NS3. The action of NS3 proteinase (NS3P), which resides in the N-terminal one-third of the NS3 protein, then yields all remaining non-structural proteins. The C-terminal two-thirds of the NS3 protein contain a helicase. The functional relationship between the proteinase and helicase domains is unknown. NS3 has a structural zinc-binding site and requires cofactor NS4A.


The actual alignment was detected with superfamily member pfam02907:

Pssm-ID: 427049  Cd Length: 149  Bit Score: 235.78  E-value: 8.74e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393    30 GNVMVLGTATSRSMGTCLNGLLFTTFHGASSRTIATPVGALNPRWWSASDDVTVYPLPDGATSLTPCTCQAESCWVIRSD 109
Cdd:pfam02907   2 GEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTRD 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 28971393   110 GALCHGLSKGD-KVELDVAMEVSDFRGSSGSPVLCDEGHAVGMLVSVLHSGGRVTAARFTrPWTQVPTD 177
Cdd:pfam02907  82 GDLIPGRRRGDpRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFV-PWETLPTT 149
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 344-453 1.35e-19

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd18806:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 145  Bit Score: 85.78  E-value: 1.35e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393 344 GEIPFYGHGIPLERmrTGRHLVFCHSKAECERLAGQFSARGVNAIAYYRGKDSSIIKD----GDLVVCATDALSTGYTGN 419
Cdd:cd18806  10 GRIWFYGKAWITIY--GGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEYPKiktiDWDFVVTTDISEMGANFD 87

                        90       100       110
                ....*....|....*....|....*....|....
gi 28971393 420 FDSVTDCGLVVEEVVEVTLDPTItISLRTVPASA 453
Cdd:cd18806  88 ADRVIDCRTCVKPTILFSGDFRV-ILTGPVPQTA 120
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 198-335 7.74e-19

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


The actual alignment was detected with superfamily member cd17931:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 151  Bit Score: 83.75  E-value: 7.74e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393 198 LFMPTGAGKSTRVPLEY----DNMGHKVLILNPSVATVRAMGPYMErlaGKHPSIYCGHDTTafTRITDSPLTYSTYGRF 273
Cdd:cd17931   6 LDLHPGAGKTTRVLPQIireaIKKRLRTLVLAPTRVVAAEMYEALR---GLPIRYRTGAVKE--EHGGNEIVDYMCHGTF 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 28971393 274 LAnprQMLRGVSV-----VICDECHSHDSTVLLGIGRVRELARgCGVQLVLYATATPPGSPMTQHPS 335
Cdd:cd17931  81 TC---RLLSPKRVpnynlIIMDEAHFTDPASIAARGYIHTRVE-MGEAAVIFMTATPPGTVTPFPQS 143
 
Name Accession Description Interval E-value
Peptidase_S29 pfam02907
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ...
 30-177 8.74e-75

Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a trypsin-like fold. The non-structural (NS) protein NS3 is one of the NS proteins involved in replication of the HCV genome. NS2-3 proteinase, a zinc-dependent enzyme, performs a single proteolytic cut to release the N-terminus of NS3. The action of NS3 proteinase (NS3P), which resides in the N-terminal one-third of the NS3 protein, then yields all remaining non-structural proteins. The C-terminal two-thirds of the NS3 protein contain a helicase. The functional relationship between the proteinase and helicase domains is unknown. NS3 has a structural zinc-binding site and requires cofactor NS4A.


Pssm-ID: 427049  Cd Length: 149  Bit Score: 235.78  E-value: 8.74e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393    30 GNVMVLGTATSRSMGTCLNGLLFTTFHGASSRTIATPVGALNPRWWSASDDVTVYPLPDGATSLTPCTCQAESCWVIRSD 109
Cdd:pfam02907   2 GEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTRD 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 28971393   110 GALCHGLSKGD-KVELDVAMEVSDFRGSSGSPVLCDEGHAVGMLVSVLHSGGRVTAARFTrPWTQVPTD 177
Cdd:pfam02907  82 GDLIPGRRRGDpRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFV-PWETLPTT 149
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 344-453 1.35e-19

C-terminal helicase domain of viral helicase; Viral helicases in this family here 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: 350193 [Multi-domain]  Cd Length: 145  Bit Score: 85.78  E-value: 1.35e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393 344 GEIPFYGHGIPLERmrTGRHLVFCHSKAECERLAGQFSARGVNAIAYYRGKDSSIIKD----GDLVVCATDALSTGYTGN 419
Cdd:cd18806  10 GRIWFYGKAWITIY--GGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEYPKiktiDWDFVVTTDISEMGANFD 87

                        90       100       110
                ....*....|....*....|....*....|....
gi 28971393 420 FDSVTDCGLVVEEVVEVTLDPTItISLRTVPASA 453
Cdd:cd18806  88 ADRVIDCRTCVKPTILFSGDFRV-ILTGPVPQTA 120
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 198-335 7.74e-19

DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 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: 350689 [Multi-domain]  Cd Length: 151  Bit Score: 83.75  E-value: 7.74e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393 198 LFMPTGAGKSTRVPLEY----DNMGHKVLILNPSVATVRAMGPYMErlaGKHPSIYCGHDTTafTRITDSPLTYSTYGRF 273
Cdd:cd17931   6 LDLHPGAGKTTRVLPQIireaIKKRLRTLVLAPTRVVAAEMYEALR---GLPIRYRTGAVKE--EHGGNEIVDYMCHGTF 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 28971393 274 LAnprQMLRGVSV-----VICDECHSHDSTVLLGIGRVRELARgCGVQLVLYATATPPGSPMTQHPS 335
Cdd:cd17931  81 TC---RLLSPKRVpnynlIIMDEAHFTDPASIAARGYIHTRVE-MGEAAVIFMTATPPGTVTPFPQS 143
DEXDc smart00487
DEAD-like helicases superfamily;
198-327 3.04e-14

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 71.75  E-value: 3.04e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393    198 LFMPTGAGKSTRVPL-----EYDNMGHKVLILNPSVATVRAMGPYMERLA----GKHPSIYCGHDTTAFTRIT---DSPL 265
Cdd:smart00487  29 LAAPTGSGKTLAALLpaleaLKRGKGGRVLVLVPTRELAEQWAEELKKLGpslgLKVVGLYGGDSKREQLRKLesgKTDI 108

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 28971393    266 TYSTYGRF---LANPRQMLRGVSVVICDECHSHDS----TVLLGIGRVRELARgcgvqLVLYATATPPG 327
Cdd:smart00487 109 LVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLDggfgDQLEKLLKLLPKNV-----QLLLLSATPPE 172
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 200-326 5.51e-07

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: 49.93  E-value: 5.51e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393   200 MPTGAGKST--RVP----LEYDNMGHKVLILNPSVA----TVRAMGPYMERLAGKHPSIYCGHDTTA-FTRITDSPLTYS 268
Cdd:pfam00270  21 APTGSGKTLafLLPaleaLDKLDNGPQALVLAPTRElaeqIYEELKKLGKGLGLKVASLLGGDSRKEqLEKLKGPDILVG 100

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 28971393   269 TYGRFLA--NPRQMLRGVSVVICDECHshdstVLLGIGRVRELARGCG-----VQLVLYaTATPP 326
Cdd:pfam00270 101 TPGRLLDllQERKLLKNLKLLVLDEAH-----RLLDMGFGPDLEEILRrlpkkRQILLL-SATLP 159
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
198-416 5.97e-06

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 49.25  E-value: 5.97e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393 198 LFMPTGAGKST---RVPLEYDNmGHKVLILNPSVATVRAMgpyMERLAgkhpSIYCGHDTTAFTRITDSPLTYSTYGRFL 274
Cdd:COG1061 105 VVAPTGTGKTVlalALAAELLR-GKRVLVLVPRRELLEQW---AEELR----RFLGDPLAGGGKKDSDAPITVATYQSLA 176

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393 275 ANP--RQMLRGVSVVICDECHshdstvLLGIGRVRELARGCGVQLVLYATATP---PGSPMTQHPSI-IETKLDVGEI-- 346
Cdd:COG1061 177 RRAhlDELGDRFGLVIIDEAH------HAGAPSYRRILEAFPAAYRLGLTATPfrsDGREILLFLFDgIVYEYSLKEAie 250

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393 347 -----PFYGHGIP-----------------------------------LERMRTGRH-LVFCHSKAECERLAGQFSARGV 385
Cdd:COG1061 251 dgylaPPEYYGIRvdltderaeydalserlrealaadaerkdkilrelLREHPDDRKtLVFCSSVDHAEALAELLNEAGI 330

                       250       260       270       280
                ....*....|....*....|....*....|....*....|
gi 28971393 386 NAIAYYrGKDSS-----II---KDGDL-VVCATDALSTGY 416
Cdd:COG1061 331 RAAVVT-GDTPKkereeILeafRDGELrILVTVDVLNEGV 369
 
Name Accession Description Interval E-value
Peptidase_S29 pfam02907
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ...
 30-177 8.74e-75

Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a trypsin-like fold. The non-structural (NS) protein NS3 is one of the NS proteins involved in replication of the HCV genome. NS2-3 proteinase, a zinc-dependent enzyme, performs a single proteolytic cut to release the N-terminus of NS3. The action of NS3 proteinase (NS3P), which resides in the N-terminal one-third of the NS3 protein, then yields all remaining non-structural proteins. The C-terminal two-thirds of the NS3 protein contain a helicase. The functional relationship between the proteinase and helicase domains is unknown. NS3 has a structural zinc-binding site and requires cofactor NS4A.


Pssm-ID: 427049  Cd Length: 149  Bit Score: 235.78  E-value: 8.74e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393    30 GNVMVLGTATSRSMGTCLNGLLFTTFHGASSRTIATPVGALNPRWWSASDDVTVYPLPDGATSLTPCTCQAESCWVIRSD 109
Cdd:pfam02907   2 GEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTRD 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 28971393   110 GALCHGLSKGD-KVELDVAMEVSDFRGSSGSPVLCDEGHAVGMLVSVLHSGGRVTAARFTrPWTQVPTD 177
Cdd:pfam02907  82 GDLIPGRRRGDpRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFV-PWETLPTT 149
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 344-453 1.35e-19

C-terminal helicase domain of viral helicase; Viral helicases in this family here 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: 350193 [Multi-domain]  Cd Length: 145  Bit Score: 85.78  E-value: 1.35e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393 344 GEIPFYGHGIPLERmrTGRHLVFCHSKAECERLAGQFSARGVNAIAYYRGKDSSIIKD----GDLVVCATDALSTGYTGN 419
Cdd:cd18806  10 GRIWFYGKAWITIY--GGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEYPKiktiDWDFVVTTDISEMGANFD 87

                        90       100       110
                ....*....|....*....|....*....|....
gi 28971393 420 FDSVTDCGLVVEEVVEVTLDPTItISLRTVPASA 453
Cdd:cd18806  88 ADRVIDCRTCVKPTILFSGDFRV-ILTGPVPQTA 120
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 198-335 7.74e-19

DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 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: 350689 [Multi-domain]  Cd Length: 151  Bit Score: 83.75  E-value: 7.74e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393 198 LFMPTGAGKSTRVPLEY----DNMGHKVLILNPSVATVRAMGPYMErlaGKHPSIYCGHDTTafTRITDSPLTYSTYGRF 273
Cdd:cd17931   6 LDLHPGAGKTTRVLPQIireaIKKRLRTLVLAPTRVVAAEMYEALR---GLPIRYRTGAVKE--EHGGNEIVDYMCHGTF 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 28971393 274 LAnprQMLRGVSV-----VICDECHSHDSTVLLGIGRVRELARgCGVQLVLYATATPPGSPMTQHPS 335
Cdd:cd17931  81 TC---RLLSPKRVpnynlIIMDEAHFTDPASIAARGYIHTRVE-MGEAAVIFMTATPPGTVTPFPQS 143
DEXDc smart00487
DEAD-like helicases superfamily;
198-327 3.04e-14

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 71.75  E-value: 3.04e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393    198 LFMPTGAGKSTRVPL-----EYDNMGHKVLILNPSVATVRAMGPYMERLA----GKHPSIYCGHDTTAFTRIT---DSPL 265
Cdd:smart00487  29 LAAPTGSGKTLAALLpaleaLKRGKGGRVLVLVPTRELAEQWAEELKKLGpslgLKVVGLYGGDSKREQLRKLesgKTDI 108

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 28971393    266 TYSTYGRF---LANPRQMLRGVSVVICDECHSHDS----TVLLGIGRVRELARgcgvqLVLYATATPPG 327
Cdd:smart00487 109 LVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLDggfgDQLEKLLKLLPKNV-----QLLLLSATPPE 172
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 201-312 2.02e-07

DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA two-partner secretion (TPS) system, a secretion pathway important to the secretion of large virulence-associated proteins. HrpB belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438711 [Multi-domain]  Cd Length: 174  Bit Score: 51.18  E-value: 2.02e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393 201 PTGAGKSTRVPL----EYDNMGHKVLILNPSVATVRAMGPYMERLAGKHPSIYCGHDTTAFTRIT-DSPLTYSTYG---- 271
Cdd:cd17990  25 PPGAGKTTRVPLallaELWIAGGKIIVLEPRRVAARAAARRLATLLGEAPGETVGYRVRGESRVGrRTRVEVVTEGvllr 104

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 28971393 272 RFLANPRqmLRGVSVVICDECHSHDSTVLLGIGRVRELARG 312
Cdd:cd17990 105 RLQRDPE--LSGVGAVILDEFHERSLDADLALALLLEVQQL 143
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 200-326 5.51e-07

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: 49.93  E-value: 5.51e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393   200 MPTGAGKST--RVP----LEYDNMGHKVLILNPSVA----TVRAMGPYMERLAGKHPSIYCGHDTTA-FTRITDSPLTYS 268
Cdd:pfam00270  21 APTGSGKTLafLLPaleaLDKLDNGPQALVLAPTRElaeqIYEELKKLGKGLGLKVASLLGGDSRKEqLEKLKGPDILVG 100

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 28971393   269 TYGRFLA--NPRQMLRGVSVVICDECHshdstVLLGIGRVRELARGCG-----VQLVLYaTATPP 326
Cdd:pfam00270 101 TPGRLLDllQERKLLKNLKLLVLDEAH-----RLLDMGFGPDLEEILRrlpkkRQILLL-SATLP 159
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 200-324 1.31e-06

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: 48.17  E-value: 1.31e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393 200 MPTGAGKSTRVPL----EYDNMGHKVLILNPSVATVRAMGPYMERLAGKHPSI-YCGHDTTAFTR----ITDSPLTYSTY 270
Cdd:cd00046   8 APTGSGKTLAALLaallLLLKKGKKVLVLVPTKALALQTAERLRELFGPGIRVaVLVGGSSAEEReknkLGDADIIIATP 87

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 28971393 271 GRF----LANPRQMLRGVSVVICDECH----SHDSTVLLGIgRVRELARGcGVQLVLyATAT 324
Cdd:cd00046  88 DMLlnllLREDRLFLKDLKLIIVDEAHalliDSRGALILDL-AVRKAGLK-NAQVIL-LSAT 146
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
198-416 5.97e-06

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 49.25  E-value: 5.97e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393 198 LFMPTGAGKST---RVPLEYDNmGHKVLILNPSVATVRAMgpyMERLAgkhpSIYCGHDTTAFTRITDSPLTYSTYGRFL 274
Cdd:COG1061 105 VVAPTGTGKTVlalALAAELLR-GKRVLVLVPRRELLEQW---AEELR----RFLGDPLAGGGKKDSDAPITVATYQSLA 176

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393 275 ANP--RQMLRGVSVVICDECHshdstvLLGIGRVRELARGCGVQLVLYATATP---PGSPMTQHPSI-IETKLDVGEI-- 346
Cdd:COG1061 177 RRAhlDELGDRFGLVIIDEAH------HAGAPSYRRILEAFPAAYRLGLTATPfrsDGREILLFLFDgIVYEYSLKEAie 250

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393 347 -----PFYGHGIP-----------------------------------LERMRTGRH-LVFCHSKAECERLAGQFSARGV 385
Cdd:COG1061 251 dgylaPPEYYGIRvdltderaeydalserlrealaadaerkdkilrelLREHPDDRKtLVFCSSVDHAEALAELLNEAGI 330

                       250       260       270       280
                ....*....|....*....|....*....|....*....|
gi 28971393 386 NAIAYYrGKDSS-----II---KDGDL-VVCATDALSTGY 416
Cdd:COG1061 331 RAAVVT-GDTPKkereeILeafRDGELrILVTVDVLNEGV 369
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 364-411 4.08e-04

C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. 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: 350181 [Multi-domain]  Cd Length: 134  Bit Score: 40.65  E-value: 4.08e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 28971393 364 LVFCHSKAECERLAGQFSARGVNAIAYYRGKDSSI--------IKDGDLVVCATDA 411
Cdd:cd18794  34 IIYCLSRKECEQVAARLQSKGISAAAYHAGLEPSDrrdvqrkwLRDKIQVIVATVA 89
DEXHc_RHA-like cd17917
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ...
 202-311 3.87e-03

DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438707 [Multi-domain]  Cd Length: 159  Bit Score: 38.59  E-value: 3.87e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393 202 TGAGKSTRVP---LE--YDNMGH-KVLILNP------SVAtvramgpymERLAGKHpSIYCGHD---TTAFTRIT--DSP 264
Cdd:cd17917  10 TGSGKTTQVPqflLEdgLAKGGKgRIVCTQPrriaaiSVA---------ERVAEER-GEKLGEEvgyQIRFESKTssKTR 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 28971393 265 LTYSTYG----RFLANPrqMLRGVSVVICDECH--SHDSTVLLGIgrVRELAR 311
Cdd:cd17917  80 IKFCTDGillrELLSDP--LLSGYSHVILDEAHerSLDTDFLLGL--LKDLLR 128
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 190-325 5.69e-03

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: 37.67  E-value: 5.69e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393 190 KGVFKeaplfMPTGAGKS-TRVPLEYDNMGHKVLILNPSVATVRAMGPYMERLAGKHPSIYCGHDTTAFtrITDSPLTYS 268
Cdd:cd17926  20 RGILV-----LPTGSGKTlTALALIAYLKELRTLIVVPTDALLDQWKERFEDFLGDSSIGLIGGGKKKD--FDDANVVVA 92

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 28971393 269 TY---GRFLANPRQMLRGVSVVICDECHsHDSTVLLgigrvRELARGCGVQLVLYATATP 325
Cdd:cd17926  93 TYqslSNLAEEEKDLFDQFGLLIVDEAH-HLPAKTF-----SEILKELNAKYRLGLTATP 146
 
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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