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Conserved domains on  [gi|14318453|ref|NP_116589|]
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Y' element ATP-dependent helicase [Saccharomyces cerevisiae S288C]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 11423521)

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:0005524
PubMed:  20206133
SCOP:  4000282|3002019

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 238-333 3.47e-14

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: 68.01  E-value: 3.47e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453   238 FEIEPESKAIVVASTTNEVEELACSWRKYFRVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQLMMVIM 317
Cdd:pfam00271  10 LKKERGGKVLIFSQTKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDF-RKGKIDVLVATDVAERGLDLPDVDLVIN 88

                          90
                  ....*....|....*.
gi 14318453   318 LDNRLNIIELIQGVGR 333
Cdd:pfam00271  89 YDLPWNPASYIQRIGR 104
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 6-163 3.60e-13

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: 66.88  E-value: 3.60e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453     6 SVAVQAPPGYGKTELFHLPLIALASKGDVKYVSFLFVPYTVLLANCMIRLGRRGclnvAPVRNFIEEGYDGVTDLYvgIY 85
Cdd:pfam00270  16 DVLVQAPTGSGKTLAFLLPALEALDKLDNGPQALVLAPTRELAEQIYEELKKLG----KGLGLKVASLLGGDSRKE--QL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453    86 DDLASTNFTdrIA---AWENIVECTFRTNNVKlgYLIVDEFHNFETEVYRQSQFGGITNLDFDAfeKAIFLSGTAPEAVA 162
Cdd:pfam00270  90 EKLKGPDIL--VGtpgRLLDLLQERKLLKNLK--LLVLDEAHRLLDMGFGPDLEEILRRLPKKR--QILLLSATLPRNLE 163


                  .
gi 14318453   163 D 163
Cdd:pfam00270 164 D 164
 
Name Accession Description Interval E-value
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 238-333 3.47e-14

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: 68.01  E-value: 3.47e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453   238 FEIEPESKAIVVASTTNEVEELACSWRKYFRVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQLMMVIM 317
Cdd:pfam00271  10 LKKERGGKVLIFSQTKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDF-RKGKIDVLVATDVAERGLDLPDVDLVIN 88

                          90
                  ....*....|....*.
gi 14318453   318 LDNRLNIIELIQGVGR 333
Cdd:pfam00271  89 YDLPWNPASYIQRIGR 104
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 6-163 3.60e-13

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: 66.88  E-value: 3.60e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453     6 SVAVQAPPGYGKTELFHLPLIALASKGDVKYVSFLFVPYTVLLANCMIRLGRRGclnvAPVRNFIEEGYDGVTDLYvgIY 85
Cdd:pfam00270  16 DVLVQAPTGSGKTLAFLLPALEALDKLDNGPQALVLAPTRELAEQIYEELKKLG----KGLGLKVASLLGGDSRKE--QL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453    86 DDLASTNFTdrIA---AWENIVECTFRTNNVKlgYLIVDEFHNFETEVYRQSQFGGITNLDFDAfeKAIFLSGTAPEAVA 162
Cdd:pfam00270  90 EKLKGPDIL--VGtpgRLLDLLQERKLLKNLK--LLVLDEAHRLLDMGFGPDLEEILRRLPKKR--QILLLSATLPRNLE 163


                  .
gi 14318453   163 D 163
Cdd:pfam00270 164 D 164
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
9-335 1.97e-11

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 65.43  E-value: 1.97e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453   9 VQAPPGYGKTELFhlplIALASKGDVKYVSFLFVPYTVLLANCMIRLgRRGCLNVAPVRNFIEEGYDGVtdlyVGIYDDL 88
Cdd:COG1061 105 VVAPTGTGKTVLA----LALAAELLRGKRVLVLVPRRELLEQWAEEL-RRFLGDPLAGGGKKDSDAPIT----VATYQSL 175

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453  89 ASTNFTDRIAAwenivectfrtnnvKLGYLIVDEFHNFETEVYRQSqfggitnldFDAFEKAIFL--SGTaPEAVADAAL 166
Cdd:COG1061 176 ARRAHLDELGD--------------RFGLVIIDEAHHAGAPSYRRI---------LEAFPAAYRLglTAT-PFRSDGREI 231

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453 167 QRIGLTGLAKkSMDINELKRSE------------DLSRGLSSYPT---RMFNLIKEKSEvplgHVHKIWKKVESqpeeal 231
Cdd:COG1061 232 LLFLFDGIVY-EYSLKEAIEDGylappeyygirvDLTDERAEYDAlseRLREALAADAE----RKDKILRELLR------ 300

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453 232 klllalfEIEPESKAIVVASTTNEVEELACSWRKY-FRVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIK 310
Cdd:COG1061 301 -------EHPDDRKTLVFCSSVDHAEALAELLNEAgIRAAVVTGDTPKKEREEILEAF-RDGELRILVTVDVLNEGVDVP 372

                       330       340
                ....*....|....*....|....*.
gi 14318453 311 QLMMVIMLDNRLNIIELIQGVGR-LR 335
Cdd:COG1061 373 RLDVAILLRPTGSPREFIQRLGRgLR 398
HELICc smart00490
helicase superfamily c-terminal domain;
257-337 3.77e-10

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 56.07  E-value: 3.77e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453    257 EELACSWRKY-FRVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQLMMVIMLDNRLNIIELIQGVGR-L 334
Cdd:smart00490   1 EELAELLKELgIKVARLHGGLSQEEREEILDKF-NNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRaG 79


                   ...
gi 14318453    335 RDG 337
Cdd:smart00490  80 RAG 82
DEXDc smart00487
DEAD-like helicases superfamily;
6-165 1.77e-07

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 51.34  E-value: 1.77e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453      6 SVAVQAPPGYGKTELFHLPLIALASKGDVKYVSFLfVPYTVLLANCMIRLgrrgclnvapvRNFIEEGYDGVTDLYVGiy 85
Cdd:smart00487  26 DVILAAPTGSGKTLAALLPALEALKRGKGGRVLVL-VPTRELAEQWAEEL-----------KKLGPSLGLKVVGLYGG-- 91

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453     86 ddlasTNFTDRIAAWEN----IVECTF----------RTNNVKLGYLIVDEFHNFETEVYRQSqfggITNLDFDAFEKA- 150
Cdd:smart00487  92 -----DSKREQLRKLESgktdILVTTPgrlldllendKLSLSNVDLVILDEAHRLLDGGFGDQ----LEKLLKLLPKNVq 162

                          170
                   ....*....|....*.
gi 14318453    151 -IFLSGTAPEAVADAA 165
Cdd:smart00487 163 lLLLSATPPEEIENLL 178
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 240-354 6.72e-06

C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It 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: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 45.80  E-value: 6.72e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453 240 IEpESKAIVVASTTNEVEELACSWRKYFRVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQL-MMVIML 318
Cdd:cd18811  36 IE-ESEKLDLKAAVAMYEYLKERFRPELNVGLLHGRLKSDEKDAVMAEF-REGEVDILVSTTVIEVGVDVPNAtVMVIED 113

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 14318453 319 DNRLNIIELIQGVGRLRDGGL---CYLLSR-KNSWAARNR 354
Cdd:cd18811 114 AERFGLSQLHQLRGRVGRGDHqsyCLLVYKdPLTETAKQR 153
PTZ00424 PTZ00424
helicase 45; Provisional
 244-333 1.06e-04

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 44.05  E-value: 1.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453  244 SKAIVVASTTNEVEELACSWR-KYFRVVWIHGKLGAAEKVSRTKEFVTdGSMQVLIGTKLVTEGIDIKQLMMVIMLDNRL 322
Cdd:PTZ00424 268 TQAIIYCNTRRKVDYLTKKMHeRDFTVSCMHGDMDQKDRDLIMREFRS-GSTRVLITTDLLARGIDVQQVSLVINYDLPA 346

                         90
                 ....*....|.
gi 14318453  323 NIIELIQGVGR 333
Cdd:PTZ00424 347 SPENYIHRIGR 357
 
Name Accession Description Interval E-value
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 238-333 3.47e-14

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: 68.01  E-value: 3.47e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453   238 FEIEPESKAIVVASTTNEVEELACSWRKYFRVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQLMMVIM 317
Cdd:pfam00271  10 LKKERGGKVLIFSQTKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDF-RKGKIDVLVATDVAERGLDLPDVDLVIN 88

                          90
                  ....*....|....*.
gi 14318453   318 LDNRLNIIELIQGVGR 333
Cdd:pfam00271  89 YDLPWNPASYIQRIGR 104
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 6-163 3.60e-13

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: 66.88  E-value: 3.60e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453     6 SVAVQAPPGYGKTELFHLPLIALASKGDVKYVSFLFVPYTVLLANCMIRLGRRGclnvAPVRNFIEEGYDGVTDLYvgIY 85
Cdd:pfam00270  16 DVLVQAPTGSGKTLAFLLPALEALDKLDNGPQALVLAPTRELAEQIYEELKKLG----KGLGLKVASLLGGDSRKE--QL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453    86 DDLASTNFTdrIA---AWENIVECTFRTNNVKlgYLIVDEFHNFETEVYRQSQFGGITNLDFDAfeKAIFLSGTAPEAVA 162
Cdd:pfam00270  90 EKLKGPDIL--VGtpgRLLDLLQERKLLKNLK--LLVLDEAHRLLDMGFGPDLEEILRRLPKKR--QILLLSATLPRNLE 163


                  .
gi 14318453   163 D 163
Cdd:pfam00270 164 D 164
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
9-335 1.97e-11

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 65.43  E-value: 1.97e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453   9 VQAPPGYGKTELFhlplIALASKGDVKYVSFLFVPYTVLLANCMIRLgRRGCLNVAPVRNFIEEGYDGVtdlyVGIYDDL 88
Cdd:COG1061 105 VVAPTGTGKTVLA----LALAAELLRGKRVLVLVPRRELLEQWAEEL-RRFLGDPLAGGGKKDSDAPIT----VATYQSL 175

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453  89 ASTNFTDRIAAwenivectfrtnnvKLGYLIVDEFHNFETEVYRQSqfggitnldFDAFEKAIFL--SGTaPEAVADAAL 166
Cdd:COG1061 176 ARRAHLDELGD--------------RFGLVIIDEAHHAGAPSYRRI---------LEAFPAAYRLglTAT-PFRSDGREI 231

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453 167 QRIGLTGLAKkSMDINELKRSE------------DLSRGLSSYPT---RMFNLIKEKSEvplgHVHKIWKKVESqpeeal 231
Cdd:COG1061 232 LLFLFDGIVY-EYSLKEAIEDGylappeyygirvDLTDERAEYDAlseRLREALAADAE----RKDKILRELLR------ 300

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453 232 klllalfEIEPESKAIVVASTTNEVEELACSWRKY-FRVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIK 310
Cdd:COG1061 301 -------EHPDDRKTLVFCSSVDHAEALAELLNEAgIRAAVVTGDTPKKEREEILEAF-RDGELRILVTVDVLNEGVDVP 372

                       330       340
                ....*....|....*....|....*.
gi 14318453 311 QLMMVIMLDNRLNIIELIQGVGR-LR 335
Cdd:COG1061 373 RLDVAILLRPTGSPREFIQRLGRgLR 398
HELICc smart00490
helicase superfamily c-terminal domain;
257-337 3.77e-10

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 56.07  E-value: 3.77e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453    257 EELACSWRKY-FRVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQLMMVIMLDNRLNIIELIQGVGR-L 334
Cdd:smart00490   1 EELAELLKELgIKVARLHGGLSQEEREEILDKF-NNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRaG 79


                   ...
gi 14318453    335 RDG 337
Cdd:smart00490  80 RAG 82
DEXDc smart00487
DEAD-like helicases superfamily;
6-165 1.77e-07

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 51.34  E-value: 1.77e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453      6 SVAVQAPPGYGKTELFHLPLIALASKGDVKYVSFLfVPYTVLLANCMIRLgrrgclnvapvRNFIEEGYDGVTDLYVGiy 85
Cdd:smart00487  26 DVILAAPTGSGKTLAALLPALEALKRGKGGRVLVL-VPTRELAEQWAEEL-----------KKLGPSLGLKVVGLYGG-- 91

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453     86 ddlasTNFTDRIAAWEN----IVECTF----------RTNNVKLGYLIVDEFHNFETEVYRQSqfggITNLDFDAFEKA- 150
Cdd:smart00487  92 -----DSKREQLRKLESgktdILVTTPgrlldllendKLSLSNVDLVILDEAHRLLDGGFGDQ----LEKLLKLLPKNVq 162

                          170
                   ....*....|....*.
gi 14318453    151 -IFLSGTAPEAVADAA 165
Cdd:smart00487 163 lLLLSATPPEEIENLL 178
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 240-354 6.72e-06

C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It 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: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 45.80  E-value: 6.72e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453 240 IEpESKAIVVASTTNEVEELACSWRKYFRVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQL-MMVIML 318
Cdd:cd18811  36 IE-ESEKLDLKAAVAMYEYLKERFRPELNVGLLHGRLKSDEKDAVMAEF-REGEVDILVSTTVIEVGVDVPNAtVMVIED 113

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 14318453 319 DNRLNIIELIQGVGRLRDGGL---CYLLSR-KNSWAARNR 354
Cdd:cd18811 114 AERFGLSQLHQLRGRVGRGDHqsyCLLVYKdPLTETAKQR 153
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 293-343 1.40e-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: 42.69  E-value: 1.40e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 14318453 293 SMQVLIGTKLVTEGIDIKQLMMVIMLDNRLNIIELIQGVGRLR----DGGLCYLL 343
Cdd:cd18785  22 SLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGrggkDEGEVILF 76
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
 255-345 2.38e-05

C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. 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: 350179 [Multi-domain]  Cd Length: 160  Bit Score: 44.18  E-value: 2.38e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453 255 EVEELACSWRKYF---RVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQL-MMVIMLDNRLNIIELIQ- 329
Cdd:cd18792  46 SIEALAEELKELVpeaRVALLHGKMTEDEKEAVMLEF-REGEYDILVSTTVIEVGIDVPNAnTMIIEDADRFGLSQLHQl 124

                        90
                ....*....|....*...
gi 14318453 330 -G-VGRLRDGGLCYLLSR 345
Cdd:cd18792 125 rGrVGRGKHQSYCYLLYP 142
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 238-333 8.68e-05

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: 42.11  E-value: 8.68e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453 238 FEIEPESKAIVVASTTNEVEELAcswrKYFR-----VVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQL 312
Cdd:cd18787  22 LEKLKPGKAIIFVNTKKRVDRLA----ELLEelgikVAALHGDLSQEERERALKKF-RSGKVRVLVATDVAARGLDIPGV 96

                        90       100
                ....*....|....*....|.
gi 14318453 313 MMVIMLDNRLNIIELIQGVGR 333
Cdd:cd18787  97 DHVINYDLPRDAEDYVHRIGR 117
PTZ00424 PTZ00424
helicase 45; Provisional
 244-333 1.06e-04

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 44.05  E-value: 1.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453  244 SKAIVVASTTNEVEELACSWR-KYFRVVWIHGKLGAAEKVSRTKEFVTdGSMQVLIGTKLVTEGIDIKQLMMVIMLDNRL 322
Cdd:PTZ00424 268 TQAIIYCNTRRKVDYLTKKMHeRDFTVSCMHGDMDQKDRDLIMREFRS-GSTRVLITTDLLARGIDVQQVSLVINYDLPA 346

                         90
                 ....*....|.
gi 14318453  323 NIIELIQGVGR 333
Cdd:PTZ00424 347 SPENYIHRIGR 357
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
 240-354 3.75e-04

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 42.44  E-value: 3.75e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453  240 IEpESKAIVVASttneVEELACSWRKYF---RVVWIHGKLGAAEKVSRTKEFVtDGSMQVLIGTKLVTEGIDIKQL-MMV 315
Cdd:PRK10917 481 IE-ESEKLDLQS----AEETYEELQEAFpelRVGLLHGRMKPAEKDAVMAAFK-AGEIDILVATTVIEVGVDVPNAtVMV 554

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 14318453  316 IMLDNRLNIIELIQ--G-VGRLRDGGLCYLLSR-KNSWAARNR 354
Cdd:PRK10917 555 IENAERFGLAQLHQlrGrVGRGAAQSYCVLLYKdPLSETARER 597
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
239-316 1.20e-03

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 40.90  E-value: 1.20e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453 239 EIEPESKAIVVASTTNEVEELACSWRKY-FRVVWIHGKLGAAEkvsRTK---EFvTDGSMQVLIGTKLVTEGIDIKQLMM 314
Cdd:COG0513 237 RDEDPERAIVFCNTKRGADRLAEKLQKRgISAAALHGDLSQGQ---RERaldAF-RNGKIRVLVATDVAARGIDIDDVSH 312


                ..
gi 14318453 315 VI 316
Cdd:COG0513 313 VI 314
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
 266-343 2.45e-03

C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF 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: 350197 [Multi-domain]  Cd Length: 151  Bit Score: 38.09  E-value: 2.45e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453 266 YFRVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQLMMVIMLD-NRLNIIELIQ---GVGRLRDGGLCY 341
Cdd:cd18810  51 EARIAIAHGQMTENELEEVMLEF-AKGEYDILVCTTIIESGIDIPNANTIIIERaDKFGLAQLYQlrgRVGRSKERAYAY 129


                ..
gi 14318453 342 LL 343
Cdd:cd18810 130 FL 131
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 243-335 2.80e-03

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: 37.15  E-value: 2.80e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453 243 ESKAIVVASTTNEVEELAcswrKYFRVVWIHgklgAAEKVSRTKEFVTDGSM-----------QVLIGTKLVTEGIDIKQ 311
Cdd:cd18799   6 EIKTLIFCVSIEHAEFMA----EAFNEAGID----AVALNSDYSDRERGDEAlillffgelkpPILVTVDLLTTGVDIPE 77

                        90       100
                ....*....|....*....|....*
gi 14318453 312 LMMVIMLDNRLNIIELIQGVGR-LR 335
Cdd:cd18799  78 VDNVVFLRPTESRTLFLQMLGRgLR 102
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
 245-357 5.22e-03

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: 37.61  E-value: 5.22e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318453 245 KAIVVASTTNEVEELAcswrKYF-----RVVWIHGKLGAAEKVsrtkEFVTD---GSMQVLIGTKLVTEGIDIKQLMMVI 316
Cdd:cd18790  29 RVLVTTLTKRMAEDLT----EYLqelgvKVRYLHSEIDTLERV----EIIRDlrlGEFDVLVGINLLREGLDLPEVSLVA 100

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 14318453 317 MLDN------RlNIIELIQGVGRlrdgglcyllsrknswAARNRKGE 357
Cdd:cd18790 101 ILDAdkegflR-SETSLIQTIGR----------------AARNVNGK 130
 
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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