NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|6322237|ref|NP_012311|]
View 

Y' element ATP-dependent helicase [Saccharomyces cerevisiae S288C]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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, ...
 908-1003 9.52e-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: 69.16  E-value: 9.52e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237     908 FESEPESKAIVVASTTNEVEELACSWRKYFRVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQLMMVIM 987
Cdd:pfam00271   10 LKKERGGKVLIFSQTKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDF-RKGKIDVLVATDVAERGLDLPDVDLVIN 88

                           90
                   ....*....|....*.
gi 6322237     988 LDNRLNIIELIQGVGR 1003
Cdd:pfam00271   89 YDLPWNPASYIQRIGR 104
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 676-833 3.88e-12

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 pfam00270:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 165  Bit Score: 66.11  E-value: 3.88e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237     676 SVAVQAPPGYGKTELFHLPLIALASKGDVEYVSFLFVPYTVLLANCMIRLGRRGclnvAPVRNFIEEGYDGVTDLYvgIY 755
Cdd:pfam00270   16 DVLVQAPTGSGKTLAFLLPALEALDKLDNGPQALVLAPTRELAEQIYEELKKLG----KGLGLKVASLLGGDSRKE--QL 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237     756 DDLASTNFTdrIA---AWENIVECTFRTNNVKlgYLIVDEFHNFETEVYRQSQFGGITNLDFDAfeKAIFLSGTAPEAVA 832
Cdd:pfam00270   90 EKLKGPDIL--VGtpgRLLDLLQERKLLKNLK--LLVLDEAHRLLDMGFGPDLEEILRRLPKKR--QILLLSATLPRNLE 163


                   .
gi 6322237     833 D 833
Cdd:pfam00270  164 D 164
Sir1 super family cl13110
Sir1, ORC-binding domain; This entry represents the ORC-binding domain of Sir1. Sir1 interacts ...
 13-88 1.40e-06

Sir1, ORC-binding domain; This entry represents the ORC-binding domain of Sir1. Sir1 interacts with the BAH domain of the Orc1 subunit of the origin recognition complex (ORC) resulting in the establishment of silent chromatin at HMR and HML in S.cerevisiae. The amino acids from the ORC interaction region of Sir1 are presented on a conserved, convex surface that forms a complementary interface with the Orc1 BAH domain, critical for transcriptional silencing. Proteins containing this domain also include Y' element ATP-dependent helicase protein 1, which catalyzes DNA unwinding and is involved in telomerase-independent telomere maintenance.


The actual alignment was detected with superfamily member pfam11603:

Pssm-ID: 431955  Cd Length: 120  Bit Score: 48.77  E-value: 1.40e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6322237      13 NFDEFEsalNNKNDLVHCPSITLFESIPTEVRSFYEDEkSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFL 88
Cdd:pfam11603   48 DLNELK---LENSDLIPCDSKELFEHVTTETKEFYRTE-DGFIIVNSTRTSKKKIRNAITYRVIPIRLKNKGVKYL 119
YccJ super family cl23921
YccJ-like protein; The YccJ-like family of proteins includes the E. coli YccJ protein which is ...
 1556-1609 3.85e-03

YccJ-like protein; The YccJ-like family of proteins includes the E. coli YccJ protein which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length.


The actual alignment was detected with superfamily member PRK10174:

Pssm-ID: 451607  Cd Length: 75  Bit Score: 37.95  E-value: 3.85e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 6322237   1556 MSGRQIKELYFKVWSNLRESKTEVLQYFL---NWDEKKCQEEWEAKDDTVVVEALEK 1609
Cdd:PRK10174    1 MPTQEAKAHHVGEWASLRNTSPEIAEAIFevaGYDEKLAEKIWEEGSDEVLVKAFAK 57
 
Name Accession Description Interval E-value
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 908-1003 9.52e-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: 69.16  E-value: 9.52e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237     908 FESEPESKAIVVASTTNEVEELACSWRKYFRVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQLMMVIM 987
Cdd:pfam00271   10 LKKERGGKVLIFSQTKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDF-RKGKIDVLVATDVAERGLDLPDVDLVIN 88

                           90
                   ....*....|....*.
gi 6322237     988 LDNRLNIIELIQGVGR 1003
Cdd:pfam00271   89 YDLPWNPASYIQRIGR 104
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 676-833 3.88e-12

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: 66.11  E-value: 3.88e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237     676 SVAVQAPPGYGKTELFHLPLIALASKGDVEYVSFLFVPYTVLLANCMIRLGRRGclnvAPVRNFIEEGYDGVTDLYvgIY 755
Cdd:pfam00270   16 DVLVQAPTGSGKTLAFLLPALEALDKLDNGPQALVLAPTRELAEQIYEELKKLG----KGLGLKVASLLGGDSRKE--QL 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237     756 DDLASTNFTdrIA---AWENIVECTFRTNNVKlgYLIVDEFHNFETEVYRQSQFGGITNLDFDAfeKAIFLSGTAPEAVA 832
Cdd:pfam00270   90 EKLKGPDIL--VGtpgRLLDLLQERKLLKNLK--LLVLDEAHRLLDMGFGPDLEEILRRLPKKR--QILLLSATLPRNLE 163


                   .
gi 6322237     833 D 833
Cdd:pfam00270  164 D 164
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
626-1005 2.12e-11

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 68.90  E-value: 2.12e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237   626 ISRVTRKRPREPKSTNDILVAGQKLFGSSFEFRDlHQ---LRLCYEIYMADTPSVAVQAPPGYGKTELFhlpliALASKG 702
Cdd:COG1061   50 GRRLPEEDTERELAEAEALEAGDEASGTSFELRP-YQqeaLEALLAALERGGGRGLVVAPTGTGKTVLA-----LALAAE 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237   703 DVEYVSFLF-VPYTVLLANCMIRLgRRGCLNVAPVRNFIEEGYDGVtdlyVGIYDDLASTNFTDRIAAwenivectfrtn 781
Cdd:COG1061  124 LLRGKRVLVlVPRRELLEQWAEEL-RRFLGDPLAGGGKKDSDAPIT----VATYQSLARRAHLDELGD------------ 186

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237   782 nvKLGYLIVDEFHNFETEVYRQSqfggitnldFDAFEKAIFL--SGTaPEAVADAALQRIGLTGLAKkSMDINELKRSED 859
Cdd:COG1061  187 --RFGLVIIDEAHHAGAPSYRRI---------LEAFPAAYRLglTAT-PFRSDGREILLFLFDGIVY-EYSLKEAIEDGY 253

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237   860 LSR----GLSSYPTRMFNLIKEKSEvplghvhKIRKKVESQPEEALKLLLALFESEPES-KAIVVASTTNEVEELACSWR 934
Cdd:COG1061  254 LAPpeyyGIRVDLTDERAEYDALSE-------RLREALAADAERKDKILRELLREHPDDrKTLVFCSSVDHAEALAELLN 326

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6322237   935 KY-FRVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQLMMVIMLDNRLNIIELIQGVGR-LR 1005
Cdd:COG1061  327 EAgIRAAVVTGDTPKKEREEILEAF-RDGELRILVTVDVLNEGVDVPRLDVAILLRPTGSPREFIQRLGRgLR 398
HELICc smart00490
helicase superfamily c-terminal domain;
927-1007 1.75e-09

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 56.07  E-value: 1.75e-09
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237      927 EELACSWRKY-FRVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQLMMVIMLDNRLNIIELIQGVGR-L 1004
Cdd:smart00490    1 EELAELLKELgIKVARLHGGLSQEEREEILDKF-NNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRaG 79


                    ...
gi 6322237     1005 RDG 1007
Cdd:smart00490   80 RAG 82
DEXDc smart00487
DEAD-like helicases superfamily;
655-835 3.40e-07

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 52.49  E-value: 3.40e-07
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237      655 FEFRDlHQLRLCYEIyMADTPSVAVQAPPGYGKTELFHLPLIALASKGDVEYVSFLfVPYTVLLANCMIRLgrrgclnva 734
Cdd:smart00487    7 EPLRP-YQKEAIEAL-LSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVL-VPTRELAEQWAEEL--------- 74

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237      735 pvRNFIEEGYDGVTDLYVGiyddlasTNFTDRIAAWEN----IVECTF----------RTNNVKLGYLIVDEFHNFETEV 800
Cdd:smart00487   75 --KKLGPSLGLKVVGLYGG-------DSKREQLRKLESgktdILVTTPgrlldllendKLSLSNVDLVILDEAHRLLDGG 145

                           170       180       190
                    ....*....|....*....|....*....|....*..
gi 6322237      801 YRQSqfggITNLDFDAFEKA--IFLSGTAPEAVADAA 835
Cdd:smart00487  146 FGDQ----LEKLLKLLPKNVqlLLLSATPPEEIENLL 178
Sir1 pfam11603
Sir1, ORC-binding domain; This entry represents the ORC-binding domain of Sir1. Sir1 interacts ...
 13-88 1.40e-06

Sir1, ORC-binding domain; This entry represents the ORC-binding domain of Sir1. Sir1 interacts with the BAH domain of the Orc1 subunit of the origin recognition complex (ORC) resulting in the establishment of silent chromatin at HMR and HML in S.cerevisiae. The amino acids from the ORC interaction region of Sir1 are presented on a conserved, convex surface that forms a complementary interface with the Orc1 BAH domain, critical for transcriptional silencing. Proteins containing this domain also include Y' element ATP-dependent helicase protein 1, which catalyzes DNA unwinding and is involved in telomerase-independent telomere maintenance.


Pssm-ID: 431955  Cd Length: 120  Bit Score: 48.77  E-value: 1.40e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6322237      13 NFDEFEsalNNKNDLVHCPSITLFESIPTEVRSFYEDEkSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFL 88
Cdd:pfam11603   48 DLNELK---LENSDLIPCDSKELFEHVTTETKEFYRTE-DGFIIVNSTRTSKKKIRNAITYRVIPIRLKNKGVKYL 119
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 963-1013 3.17e-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: 43.85  E-value: 3.17e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 6322237   963 SMQVLIGTKLVTEGIDIKQLMMVIMLDNRLNIIELIQGVGRLR----DGGLCYLL 1013
Cdd:cd18785   22 SLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGrggkDEGEVILF 76
PTZ00424 PTZ00424
helicase 45; Provisional
 908-1003 5.70e-04

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 44.43  E-value: 5.70e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237    908 FESEPESKAIVVASTTNEVEELACSWR-KYFRVVWIHGKLGAAEKVSRTKEFVTdGSMQVLIGTKLVTEGIDIKQLMMVI 986
Cdd:PTZ00424  262 YETLTITQAIIYCNTRRKVDYLTKKMHeRDFTVSCMHGDMDQKDRDLIMREFRS-GSTRVLITTDLLARGIDVQQVSLVI 340

                          90
                  ....*....|....*..
gi 6322237    987 MLDNRLNIIELIQGVGR 1003
Cdd:PTZ00424  341 NYDLPASPENYIHRIGR 357
PRK10174 PRK10174
hypothetical protein; Provisional
 1556-1609 3.85e-03

hypothetical protein; Provisional


Pssm-ID: 182285  Cd Length: 75  Bit Score: 37.95  E-value: 3.85e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 6322237   1556 MSGRQIKELYFKVWSNLRESKTEVLQYFL---NWDEKKCQEEWEAKDDTVVVEALEK 1609
Cdd:PRK10174    1 MPTQEAKAHHVGEWASLRNTSPEIAEAIFevaGYDEKLAEKIWEEGSDEVLVKAFAK 57
 
Name Accession Description Interval E-value
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 908-1003 9.52e-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: 69.16  E-value: 9.52e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237     908 FESEPESKAIVVASTTNEVEELACSWRKYFRVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQLMMVIM 987
Cdd:pfam00271   10 LKKERGGKVLIFSQTKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDF-RKGKIDVLVATDVAERGLDLPDVDLVIN 88

                           90
                   ....*....|....*.
gi 6322237     988 LDNRLNIIELIQGVGR 1003
Cdd:pfam00271   89 YDLPWNPASYIQRIGR 104
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 676-833 3.88e-12

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: 66.11  E-value: 3.88e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237     676 SVAVQAPPGYGKTELFHLPLIALASKGDVEYVSFLFVPYTVLLANCMIRLGRRGclnvAPVRNFIEEGYDGVTDLYvgIY 755
Cdd:pfam00270   16 DVLVQAPTGSGKTLAFLLPALEALDKLDNGPQALVLAPTRELAEQIYEELKKLG----KGLGLKVASLLGGDSRKE--QL 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237     756 DDLASTNFTdrIA---AWENIVECTFRTNNVKlgYLIVDEFHNFETEVYRQSQFGGITNLDFDAfeKAIFLSGTAPEAVA 832
Cdd:pfam00270   90 EKLKGPDIL--VGtpgRLLDLLQERKLLKNLK--LLVLDEAHRLLDMGFGPDLEEILRRLPKKR--QILLLSATLPRNLE 163


                   .
gi 6322237     833 D 833
Cdd:pfam00270  164 D 164
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
626-1005 2.12e-11

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 68.90  E-value: 2.12e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237   626 ISRVTRKRPREPKSTNDILVAGQKLFGSSFEFRDlHQ---LRLCYEIYMADTPSVAVQAPPGYGKTELFhlpliALASKG 702
Cdd:COG1061   50 GRRLPEEDTERELAEAEALEAGDEASGTSFELRP-YQqeaLEALLAALERGGGRGLVVAPTGTGKTVLA-----LALAAE 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237   703 DVEYVSFLF-VPYTVLLANCMIRLgRRGCLNVAPVRNFIEEGYDGVtdlyVGIYDDLASTNFTDRIAAwenivectfrtn 781
Cdd:COG1061  124 LLRGKRVLVlVPRRELLEQWAEEL-RRFLGDPLAGGGKKDSDAPIT----VATYQSLARRAHLDELGD------------ 186

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237   782 nvKLGYLIVDEFHNFETEVYRQSqfggitnldFDAFEKAIFL--SGTaPEAVADAALQRIGLTGLAKkSMDINELKRSED 859
Cdd:COG1061  187 --RFGLVIIDEAHHAGAPSYRRI---------LEAFPAAYRLglTAT-PFRSDGREILLFLFDGIVY-EYSLKEAIEDGY 253

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237   860 LSR----GLSSYPTRMFNLIKEKSEvplghvhKIRKKVESQPEEALKLLLALFESEPES-KAIVVASTTNEVEELACSWR 934
Cdd:COG1061  254 LAPpeyyGIRVDLTDERAEYDALSE-------RLREALAADAERKDKILRELLREHPDDrKTLVFCSSVDHAEALAELLN 326

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6322237   935 KY-FRVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQLMMVIMLDNRLNIIELIQGVGR-LR 1005
Cdd:COG1061  327 EAgIRAAVVTGDTPKKEREEILEAF-RDGELRILVTVDVLNEGVDVPRLDVAILLRPTGSPREFIQRLGRgLR 398
HELICc smart00490
helicase superfamily c-terminal domain;
927-1007 1.75e-09

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 56.07  E-value: 1.75e-09
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237      927 EELACSWRKY-FRVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQLMMVIMLDNRLNIIELIQGVGR-L 1004
Cdd:smart00490    1 EELAELLKELgIKVARLHGGLSQEEREEILDKF-NNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRaG 79


                    ...
gi 6322237     1005 RDG 1007
Cdd:smart00490   80 RAG 82
DEXDc smart00487
DEAD-like helicases superfamily;
655-835 3.40e-07

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 52.49  E-value: 3.40e-07
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237      655 FEFRDlHQLRLCYEIyMADTPSVAVQAPPGYGKTELFHLPLIALASKGDVEYVSFLfVPYTVLLANCMIRLgrrgclnva 734
Cdd:smart00487    7 EPLRP-YQKEAIEAL-LSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVL-VPTRELAEQWAEEL--------- 74

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237      735 pvRNFIEEGYDGVTDLYVGiyddlasTNFTDRIAAWEN----IVECTF----------RTNNVKLGYLIVDEFHNFETEV 800
Cdd:smart00487   75 --KKLGPSLGLKVVGLYGG-------DSKREQLRKLESgktdILVTTPgrlldllendKLSLSNVDLVILDEAHRLLDGG 145

                           170       180       190
                    ....*....|....*....|....*....|....*..
gi 6322237      801 YRQSqfggITNLDFDAFEKA--IFLSGTAPEAVADAA 835
Cdd:smart00487  146 FGDQ----LEKLLKLLPKNVqlLLLSATPPEEIENLL 178
Sir1 pfam11603
Sir1, ORC-binding domain; This entry represents the ORC-binding domain of Sir1. Sir1 interacts ...
 13-88 1.40e-06

Sir1, ORC-binding domain; This entry represents the ORC-binding domain of Sir1. Sir1 interacts with the BAH domain of the Orc1 subunit of the origin recognition complex (ORC) resulting in the establishment of silent chromatin at HMR and HML in S.cerevisiae. The amino acids from the ORC interaction region of Sir1 are presented on a conserved, convex surface that forms a complementary interface with the Orc1 BAH domain, critical for transcriptional silencing. Proteins containing this domain also include Y' element ATP-dependent helicase protein 1, which catalyzes DNA unwinding and is involved in telomerase-independent telomere maintenance.


Pssm-ID: 431955  Cd Length: 120  Bit Score: 48.77  E-value: 1.40e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6322237      13 NFDEFEsalNNKNDLVHCPSITLFESIPTEVRSFYEDEkSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFL 88
Cdd:pfam11603   48 DLNELK---LENSDLIPCDSKELFEHVTTETKEFYRTE-DGFIIVNSTRTSKKKIRNAITYRVIPIRLKNKGVKYL 119
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 963-1013 3.17e-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: 43.85  E-value: 3.17e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 6322237   963 SMQVLIGTKLVTEGIDIKQLMMVIMLDNRLNIIELIQGVGRLR----DGGLCYLL 1013
Cdd:cd18785   22 SLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGrggkDEGEVILF 76
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 913-1024 3.40e-05

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: 3.40e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237   913 ESKAIVVASTTNEVEELACSWRKYFRVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQL-MMVIMLDNR 991
Cdd:cd18811   38 ESEKLDLKAAVAMYEYLKERFRPELNVGLLHGRLKSDEKDAVMAEF-REGEVDILVSTTVIEVGVDVPNAtVMVIEDAER 116

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 6322237   992 LNIIELIQGVGRLRDGGL---CYLLSR-KNSWAARNR 1024
Cdd:cd18811  117 FGLSQLHQLRGRVGRGDHqsyCLLVYKdPLTETAKQR 153
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
 925-1015 9.69e-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: 44.57  E-value: 9.69e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237   925 EVEELACSWRKYF---RVVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQL-MMVIMLDNRLNIIELIQ- 999
Cdd:cd18792   46 SIEALAEELKELVpeaRVALLHGKMTEDEKEAVMLEF-REGEYDILVSTTVIEVGIDVPNAnTMIIEDADRFGLSQLHQl 124

                         90
                 ....*....|....*...
gi 6322237  1000 -G-VGRLRDGGLCYLLSR 1015
Cdd:cd18792  125 rGrVGRGKHQSYCYLLYP 142
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 908-1003 2.27e-04

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: 42.88  E-value: 2.27e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237   908 FESEPESKAIVVASTTNEVEELAcswrKYFR-----VVWIHGKLGAAEKVSRTKEFvTDGSMQVLIGTKLVTEGIDIKQL 982
Cdd:cd18787   22 LEKLKPGKAIIFVNTKKRVDRLA----ELLEelgikVAALHGDLSQEERERALKKF-RSGKVRVLVATDVAARGLDIPGV 96

                         90       100
                 ....*....|....*....|.
gi 6322237   983 MMVIMLDNRLNIIELIQGVGR 1003
Cdd:cd18787   97 DHVINYDLPRDAEDYVHRIGR 117
PTZ00424 PTZ00424
helicase 45; Provisional
 908-1003 5.70e-04

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 44.43  E-value: 5.70e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237    908 FESEPESKAIVVASTTNEVEELACSWR-KYFRVVWIHGKLGAAEKVSRTKEFVTdGSMQVLIGTKLVTEGIDIKQLMMVI 986
Cdd:PTZ00424  262 YETLTITQAIIYCNTRRKVDYLTKKMHeRDFTVSCMHGDMDQKDRDLIMREFRS-GSTRVLITTDLLARGIDVQQVSLVI 340

                          90
                  ....*....|....*..
gi 6322237    987 MLDNRLNIIELIQGVGR 1003
Cdd:PTZ00424  341 NYDLPASPENYIHRIGR 357
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
 926-1024 2.53e-03

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 42.44  E-value: 2.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237    926 VEELACSWRKYF---RVVWIHGKLGAAEKVSRTKEFVtDGSMQVLIGTKLVTEGIDIKQL-MMVIMLDNRLNIIELIQ-- 999
Cdd:PRK10917  492 AEETYEELQEAFpelRVGLLHGRMKPAEKDAVMAAFK-AGEIDILVATTVIEVGVDVPNAtVMVIENAERFGLAQLHQlr 570

                          90       100       110
                  ....*....|....*....|....*....|
gi 6322237   1000 G-VGRlrdGGL---CYLLSR-KNSWAARNR 1024
Cdd:PRK10917  571 GrVGR---GAAqsyCVLLYKdPLSETARER 597
PRK10174 PRK10174
hypothetical protein; Provisional
 1556-1609 3.85e-03

hypothetical protein; Provisional


Pssm-ID: 182285  Cd Length: 75  Bit Score: 37.95  E-value: 3.85e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 6322237   1556 MSGRQIKELYFKVWSNLRESKTEVLQYFL---NWDEKKCQEEWEAKDDTVVVEALEK 1609
Cdd:PRK10174    1 MPTQEAKAHHVGEWASLRNTSPEIAEAIFevaGYDEKLAEKIWEEGSDEVLVKAFAK 57
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
909-986 4.06e-03

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 41.67  E-value: 4.06e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322237   909 ESEPESKAIVVASTTNEVEELACSWRKY-FRVVWIHGKLGAAEkvsRTK---EFvTDGSMQVLIGTKLVTEGIDIKQLMM 984
Cdd:COG0513  237 RDEDPERAIVFCNTKRGADRLAEKLQKRgISAAALHGDLSQGQ---RERaldAF-RNGKIRVLVATDVAARGIDIDDVSH 312


                 ..
gi 6322237   985 VI 986
Cdd:COG0513  313 VI 314
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH