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Conserved domains on  [gi|32425420|gb|AAH15477|]
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HELLS protein, partial [Homo sapiens]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 1000678)

DEAD/DEAH box containing ATP-dependent helicase, similar to ISWI chromatin-remodeling complex ATPases, which are catalytic components of ISW1-type complexes, which act by remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03142 super family cl33647
Probable chromatin-remodeling complex ATPase chain; Provisional
 38-302 1.49e-73

Probable chromatin-remodeling complex ATPase chain; Provisional


The actual alignment was detected with superfamily member PLN03142:

Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 244.71  E-value: 1.49e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420    38 KLQNIMMLLRKCCNHPYLIE--YPIDPvtqeFKIDEELVTNSGKFLILDRMLPELKKRGHKVLLFSQMTSMLDILMDYCH 115
Cdd:PLN03142  433 RLLNIAMQLRKCCNHPYLFQgaEPGPP----YTTGEHLVENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLM 508

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420   116 LRDFNFSRLDGSMSYSEREKNMHSFNTD-PEVFIFLVSTRAGGLGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTK 194
Cdd:PLN03142  509 YRGYQYCRIDGNTGGEDRDASIDAFNKPgSEKFVFLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKK 588

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420   195 PVVVYRLVTANTIDQKIVERAAAKRKLEKLIIHKNHFkggQSGLNLSKNfldpkelmELLKSRDYERE-IKGSREKVISD 273
Cdd:PLN03142  589 EVQVFRFCTEYTIEEKVIERAYKKLALDALVIQQGRL---AEQKTVNKD--------ELLQMVRYGAEmVFSSKDSTITD 657

                         250       260
                  ....*....|....*....|....*....
gi 32425420   274 KDLELLLDRSDlidqmNASGPIKEKMGIF 302
Cdd:PLN03142  658 EDIDRIIAKGE-----EATAELDAKMKKF 681
 
Name Accession Description Interval E-value
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
 38-302 1.49e-73

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 244.71  E-value: 1.49e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420    38 KLQNIMMLLRKCCNHPYLIE--YPIDPvtqeFKIDEELVTNSGKFLILDRMLPELKKRGHKVLLFSQMTSMLDILMDYCH 115
Cdd:PLN03142  433 RLLNIAMQLRKCCNHPYLFQgaEPGPP----YTTGEHLVENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLM 508

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420   116 LRDFNFSRLDGSMSYSEREKNMHSFNTD-PEVFIFLVSTRAGGLGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTK 194
Cdd:PLN03142  509 YRGYQYCRIDGNTGGEDRDASIDAFNKPgSEKFVFLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKK 588

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420   195 PVVVYRLVTANTIDQKIVERAAAKRKLEKLIIHKNHFkggQSGLNLSKNfldpkelmELLKSRDYERE-IKGSREKVISD 273
Cdd:PLN03142  589 EVQVFRFCTEYTIEEKVIERAYKKLALDALVIQQGRL---AEQKTVNKD--------ELLQMVRYGAEmVFSSKDSTITD 657

                         250       260
                  ....*....|....*....|....*....
gi 32425420   274 KDLELLLDRSDlidqmNASGPIKEKMGIF 302
Cdd:PLN03142  658 EDIDRIIAKGE-----EATAELDAKMKKF 681
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 77-202 1.10e-67

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


Pssm-ID: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 207.71  E-value: 1.10e-67
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420  77 SGKFLILDRMLPELKKRGHKVLLFSQMTSMLDILMDYCHLRDFNFSRLDGSMSYSEREKNMHSFNTDPEVFIFLVSTRAG 156
Cdd:cd18793  10 SGKLEALLELLEELREPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDPDIRVFLLSTKAG 89

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 32425420 157 GLGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTKPVVVYRLV 202
Cdd:cd18793  90 GVGLNLTAANRVILYDPWWNPAVEEQAIDRAHRIGQKKPVVVYRLI 135
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 43-226 2.26e-60

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 204.30  E-value: 2.26e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420  43 MMLLRKCCNHPYLIeypidpvtqeFKIDEELVTNSGKFLILDRMLPELKKRGHKVLLFSQMTSMLDILMDYCHLRDFNFS 122
Cdd:COG0553 508 LTRLRQICSHPALL----------LEEGAELSGRSAKLEALLELLEELLAEGEKVLVFSQFTDTLDLLEERLEERGIEYA 577

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420 123 RLDGSMSYSEREKNMHSFNTDPEVFIFLVSTRAGGLGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTKPVVVYRLV 202
Cdd:COG0553 578 YLHGGTSAEERDELVDRFQEGPEAPVFLISLKAGGEGLNLTAADHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLV 657

                       170       180
                ....*....|....*....|....
gi 32425420 203 TANTIDQKIVERAAAKRKLEKLII 226
Cdd:COG0553 658 AEGTIEEKILELLEEKRALAESVL 681
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 78-191 2.04e-31

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: 113.46  E-value: 2.04e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420    78 GKFLILDRMLPelKKRGHKVLLFSQMTSMLDILMdYCHLRDFNFSRLDGSMSYSEREKNMHSFNTDPevFIFLVSTRAGG 157
Cdd:pfam00271   1 EKLEALLELLK--KERGGKVLIFSQTKKTLEAEL-LLEKEGIKVARLHGDLSQEEREEILEDFRKGK--IDVLVATDVAE 75

                          90       100       110
                  ....*....|....*....|....*....|....
gi 32425420   158 LGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIG 191
Cdd:pfam00271  76 RGLDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
HELICc smart00490
helicase superfamily c-terminal domain;
108-191 1.26e-24

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 94.97  E-value: 1.26e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420    108 DILMDYCHLRDFNFSRLDGSMSYSEREKNMHSFNTDPevFIFLVSTRAGGLGINLTAADTVIIYDSDWNPQSDLQAQDRC 187
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGK--IKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78


                   ....
gi 32425420    188 HRIG 191
Cdd:smart00490  79 GRAG 82
DISARM_DrmD_b NF038318
DISARM system SNF2-like helicase DrmD, short form; DrmD, a SNF2-like helicase, is a component ...
 150-221 2.87e-09

DISARM system SNF2-like helicase DrmD, short form; DrmD, a SNF2-like helicase, is a component of class 1 DISARM (Defence Island System Associated with Restriction Modification), which contains a DNA adenine N6 methyltransferase. This HMM describes a distinct form that is somewhat shorter than the majority of DrmD proteins.


Pssm-ID: 468472 [Multi-domain]  Cd Length: 868  Bit Score: 58.16  E-value: 2.87e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 32425420  150 LVSTRAGGLGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTKPVVVYRLV-TANTIDQKIVERAAAKRKL 221
Cdd:NF038318 490 LIVTDAGSEGLNLQFCNTVINYDLPWNPQKIEQRIGRCHRYGQKNDVVAINLLnTQNVADKRVYEILSEKFEL 562
 
Name Accession Description Interval E-value
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
 38-302 1.49e-73

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 244.71  E-value: 1.49e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420    38 KLQNIMMLLRKCCNHPYLIE--YPIDPvtqeFKIDEELVTNSGKFLILDRMLPELKKRGHKVLLFSQMTSMLDILMDYCH 115
Cdd:PLN03142  433 RLLNIAMQLRKCCNHPYLFQgaEPGPP----YTTGEHLVENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLM 508

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420   116 LRDFNFSRLDGSMSYSEREKNMHSFNTD-PEVFIFLVSTRAGGLGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTK 194
Cdd:PLN03142  509 YRGYQYCRIDGNTGGEDRDASIDAFNKPgSEKFVFLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKK 588

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420   195 PVVVYRLVTANTIDQKIVERAAAKRKLEKLIIHKNHFkggQSGLNLSKNfldpkelmELLKSRDYERE-IKGSREKVISD 273
Cdd:PLN03142  589 EVQVFRFCTEYTIEEKVIERAYKKLALDALVIQQGRL---AEQKTVNKD--------ELLQMVRYGAEmVFSSKDSTITD 657

                         250       260
                  ....*....|....*....|....*....
gi 32425420   274 KDLELLLDRSDlidqmNASGPIKEKMGIF 302
Cdd:PLN03142  658 EDIDRIIAKGE-----EATAELDAKMKKF 681
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 77-202 1.10e-67

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


Pssm-ID: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 207.71  E-value: 1.10e-67
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420  77 SGKFLILDRMLPELKKRGHKVLLFSQMTSMLDILMDYCHLRDFNFSRLDGSMSYSEREKNMHSFNTDPEVFIFLVSTRAG 156
Cdd:cd18793  10 SGKLEALLELLEELREPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDPDIRVFLLSTKAG 89

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 32425420 157 GLGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTKPVVVYRLV 202
Cdd:cd18793  90 GVGLNLTAANRVILYDPWWNPAVEEQAIDRAHRIGQKKPVVVYRLI 135
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 43-226 2.26e-60

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 204.30  E-value: 2.26e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420  43 MMLLRKCCNHPYLIeypidpvtqeFKIDEELVTNSGKFLILDRMLPELKKRGHKVLLFSQMTSMLDILMDYCHLRDFNFS 122
Cdd:COG0553 508 LTRLRQICSHPALL----------LEEGAELSGRSAKLEALLELLEELLAEGEKVLVFSQFTDTLDLLEERLEERGIEYA 577

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420 123 RLDGSMSYSEREKNMHSFNTDPEVFIFLVSTRAGGLGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTKPVVVYRLV 202
Cdd:COG0553 578 YLHGGTSAEERDELVDRFQEGPEAPVFLISLKAGGEGLNLTAADHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLV 657

                       170       180
                ....*....|....*....|....
gi 32425420 203 TANTIDQKIVERAAAKRKLEKLII 226
Cdd:COG0553 658 AEGTIEEKILELLEEKRALAESVL 681
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 78-191 2.04e-31

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: 113.46  E-value: 2.04e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420    78 GKFLILDRMLPelKKRGHKVLLFSQMTSMLDILMdYCHLRDFNFSRLDGSMSYSEREKNMHSFNTDPevFIFLVSTRAGG 157
Cdd:pfam00271   1 EKLEALLELLK--KERGGKVLIFSQTKKTLEAEL-LLEKEGIKVARLHGDLSQEEREEILEDFRKGK--IDVLVATDVAE 75

                          90       100       110
                  ....*....|....*....|....*....|....
gi 32425420   158 LGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIG 191
Cdd:pfam00271  76 RGLDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
HELICc smart00490
helicase superfamily c-terminal domain;
108-191 1.26e-24

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 94.97  E-value: 1.26e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420    108 DILMDYCHLRDFNFSRLDGSMSYSEREKNMHSFNTDPevFIFLVSTRAGGLGINLTAADTVIIYDSDWNPQSDLQAQDRC 187
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGK--IKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78


                   ....
gi 32425420    188 HRIG 191
Cdd:smart00490  79 GRAG 82
DISARM_DrmD_b NF038318
DISARM system SNF2-like helicase DrmD, short form; DrmD, a SNF2-like helicase, is a component ...
 150-221 2.87e-09

DISARM system SNF2-like helicase DrmD, short form; DrmD, a SNF2-like helicase, is a component of class 1 DISARM (Defence Island System Associated with Restriction Modification), which contains a DNA adenine N6 methyltransferase. This HMM describes a distinct form that is somewhat shorter than the majority of DrmD proteins.


Pssm-ID: 468472 [Multi-domain]  Cd Length: 868  Bit Score: 58.16  E-value: 2.87e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 32425420  150 LVSTRAGGLGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTKPVVVYRLV-TANTIDQKIVERAAAKRKL 221
Cdd:NF038318 490 LIVTDAGSEGLNLQFCNTVINYDLPWNPQKIEQRIGRCHRYGQKNDVVAINLLnTQNVADKRVYEILSEKFEL 562
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 145-199 8.51e-07

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: 46.16  E-value: 8.51e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 32425420 145 EVFIFLVSTRAGGLGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTKPVVVY 199
Cdd:cd18785  21 SSLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRGGKDEGEVIL 75
HDA2-3 pfam11496
Class II histone deacetylase complex subunits 2 and 3; This family of class II histone ...
 44-209 3.39e-06

Class II histone deacetylase complex subunits 2 and 3; This family of class II histone deacetylase complex subunits HDA2 and HDA3 is found in fungi, The member from S. pombe is referred to as Ccq1 in Swiss:Q10432. These proteins associate with HDA1 to generate the activity of the HDA1 histone deacetylase complex. HDA1 interacts with itself and with the HDA2-HDA3 subcomplex to form a probable tetramer and these interactions are necessary for catalytic activity. The HDA1 histone deacetylase complex is responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. HDA2 and HDA3 have a conserved coiled-coil domain towards their C-terminus.


Pssm-ID: 402894  Cd Length: 281  Bit Score: 47.71  E-value: 3.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420    44 MLLRKCC---NHPYLIEYPIDPVTQEFK-IDEELVTNSGKFLILDRMLPEL----KKRGHKVLLFSQMTSMLDILMDYCH 115
Cdd:pfam11496  52 LCLENLSlvaTHPYLLVDHYMPKSLLLKdEPEKLAYTSGKFLVLNDLVNLLierdRKEPINVAIVARSGKTLDLVEALLL 131

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420   116 LRDFNFSRLDGSMSYSE-REKNMHSFNTDPE-VFIFLVSTR-----AGGLGInlTAADTVIIYDSDWNPQSDLQAQDRCH 188
Cdd:pfam11496 132 GKGLSYKRYSGEMLYGEnKKVSDSGNKKIHStTCHLLSSTGqltndDSLLEN--YKFDLIIAFDSSVDTSSPSVEHLRTQ 209

                         170       180
                  ....*....|....*....|.
gi 32425420   189 RIGQTKPVVVYRLVTANTIDQ 209
Cdd:pfam11496 210 NRRKGNLAPIIRLVVINSIEH 230
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 63-193 4.39e-06

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: 45.19  E-value: 4.39e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32425420  63 VTQEFkideELVTNSGKFLILDRMLPELKKRGhKVLLFSQMTSMLDILMDYCHLRDFNFSRLDGSMSYSEREKNMHSFNT 142
Cdd:cd18787   1 IKQLY----VVVEEEEKKLLLLLLLLEKLKPG-KAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRS 75

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 32425420 143 DpEVFIfLVST----RagglGINLTAADTVIIYDsdwNPQSdlqAQDRCHRIGQT 193
Cdd:cd18787  76 G-KVRV-LVATdvaaR----GLDIPGVDHVINYD---LPRD---AEDYVHRIGRT 118
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 31-56 8.31e-03

SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.


Pssm-ID: 425504 [Multi-domain]  Cd Length: 289  Bit Score: 37.28  E-value: 8.31e-03
                          10        20
                  ....*....|....*....|....*.
gi 32425420    31 VESEVNLKLQNIMMLLRKCCNHPYLI 56
Cdd:pfam00176 264 GGREIKASLLNILMRLRKICNHPGLI 289
 
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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