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Conserved domains on  [gi|1140176904|ref|NP_001335389|]
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chromodomain-helicase-DNA-binding protein 1-like isoform 4 [Homo sapiens]

Protein Classification

DEAD/DEAH box helicase; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1( domain architecture ID 13327344)

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; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 (SMARCAD1) is a DNA helicase that possesses intrinsic ATP-dependent nucleosome-remodeling activity and is both required for DNA repair and heterochromatin organization

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Macro_Poa1p-like_SNF2 cd03331
macrodomain, Poa1p-like family, SNF2 subfamily; Macrodomains are found in a variety of ...
 435-585 3.08e-95

macrodomain, Poa1p-like family, SNF2 subfamily; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Members of this subfamily contain a C-terminal macrodomain that show similarity to the yeast protein Poa1p, reported to be a phosphatase specific for Appr-1"-p, a tRNA splicing metabolite. In addition, they also contain an SNF2 domain, defined by the presence of seven motifs with sequence similarity to DNA helicases. SNF2 proteins have the capacity to use the energy released by their DNA-dependent ATPase activity to stabilize or perturb protein-DNA interactions and play important roles in transcriptional regulation, maintenance of chromosome integrity and DNA repair.


:

Pssm-ID: 394880  Cd Length: 152  Bit Score: 288.77  E-value: 3.08e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904 435 SLKYVSGDVTHPQA-GAEDALIVHCVDDSGHWGRGGLFTALEKRSAEPRKIYELAGKMKDLSLGGVLLFPVDDKESRNKG 513
Cdd:cd03331     1 DINYVSGDVTHPQTtSTEDAIIVHCVDDSGRWGRGGLFSALSSRSKQPKEQYELAGEMKDLHLGDVHLIPVDDKESRSGG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1140176904 514 QDLLALIVAQHRDRSNVLSGIKMAALEEGLKKIFLAAKKKKASVHLPRIGHATKGFNWYGTERLIRKHLAAR 585
Cdd:cd03331    81 RDYVALIVAQHRDRSNKLSGIKLSALETGLQKIATAAKQRNASVHLPRIGHGTPGFNWYGTERLIRKHLASR 152
PLN03142 super family cl33647
Probable chromatin-remodeling complex ATPase chain; Provisional
 1-418 4.35e-81

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: 275.91  E-value: 4.35e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904    1 MSALQKKYYKAILMKDLDAFeNETAKKVKLQNILSQLRKCVDHPYLFDGVEP-EPFEVGDHLTEASGKLHLLDKLLAFLY 79
Cdd:PLN03142   406 MSQMQKQYYKALLQKDLDVV-NAGGERKRLLNIAMQLRKCCNHPYLFQGAEPgPPYTTGEHLVENSGKMVLLDKLLPKLK 484

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904   80 SGGHRVLLFSQMTQMLDILQDYMDYRGYSYERVDGSVRGEERHLAIKNFGQ--QPIFVFLLSTRAGGVGMNLTAADTVIF 157
Cdd:PLN03142   485 ERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKpgSEKFVFLLSTRAGGLGINLATADIVIL 564

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904  158 VDSDFNPQNDLQAAARAHRIGQNKSVKVIRLIGRDTVEEIVYRKAASKLQLTNMIIEGGHFtlgAQKPAADADlQLSEIL 237
Cdd:PLN03142   565 YDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVIQQGRL---AEQKTVNKD-ELLQMV 640

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904  238 KFGLDKLLASEGSTMDEIDLESIL--GE-------TKDGQWVSDALPAAEGGS---------RDQEEGKNHMYLFEGKDY 299
Cdd:PLN03142   641 RYGAEMVFSSKDSTITDEDIDRIIakGEeataeldAKMKKFTEDAIKFKMDDTaelydfddeDDKDENKLDFKKIVSDNW 720

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904  300 SKEPSKEDRKSFEQLVNLQKTLLEKASQEGRSLRnkgsvlIPGLVEGS------TKRKRVLSPEELEDRQKKRQEAAAKR 373
Cdd:PLN03142   721 IDPPKRERKRNYSESEYFKQAMRQGAPAKPKEPR------IPRMPQLHdfqffnVQRLTELYEKEVRYLMQAHQKGQLKD 794

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1140176904  374 RRLIEEKKRQ-----KEEAEHKKKM-----AWWESNNYQSFCLPSEESEPEDLEN 418
Cdd:PLN03142   795 TIDVAEPEEPgdpltAEEQEEKEQLleegfSTWSRRDFNAFIRACEKYGRNDIKS 849
 
Name Accession Description Interval E-value
Macro_Poa1p-like_SNF2 cd03331
macrodomain, Poa1p-like family, SNF2 subfamily; Macrodomains are found in a variety of ...
 435-585 3.08e-95

macrodomain, Poa1p-like family, SNF2 subfamily; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Members of this subfamily contain a C-terminal macrodomain that show similarity to the yeast protein Poa1p, reported to be a phosphatase specific for Appr-1"-p, a tRNA splicing metabolite. In addition, they also contain an SNF2 domain, defined by the presence of seven motifs with sequence similarity to DNA helicases. SNF2 proteins have the capacity to use the energy released by their DNA-dependent ATPase activity to stabilize or perturb protein-DNA interactions and play important roles in transcriptional regulation, maintenance of chromosome integrity and DNA repair.


Pssm-ID: 394880  Cd Length: 152  Bit Score: 288.77  E-value: 3.08e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904 435 SLKYVSGDVTHPQA-GAEDALIVHCVDDSGHWGRGGLFTALEKRSAEPRKIYELAGKMKDLSLGGVLLFPVDDKESRNKG 513
Cdd:cd03331     1 DINYVSGDVTHPQTtSTEDAIIVHCVDDSGRWGRGGLFSALSSRSKQPKEQYELAGEMKDLHLGDVHLIPVDDKESRSGG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1140176904 514 QDLLALIVAQHRDRSNVLSGIKMAALEEGLKKIFLAAKKKKASVHLPRIGHATKGFNWYGTERLIRKHLAAR 585
Cdd:cd03331    81 RDYVALIVAQHRDRSNKLSGIKLSALETGLQKIATAAKQRNASVHLPRIGHGTPGFNWYGTERLIRKHLASR 152
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
 1-418 4.35e-81

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 275.91  E-value: 4.35e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904    1 MSALQKKYYKAILMKDLDAFeNETAKKVKLQNILSQLRKCVDHPYLFDGVEP-EPFEVGDHLTEASGKLHLLDKLLAFLY 79
Cdd:PLN03142   406 MSQMQKQYYKALLQKDLDVV-NAGGERKRLLNIAMQLRKCCNHPYLFQGAEPgPPYTTGEHLVENSGKMVLLDKLLPKLK 484

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904   80 SGGHRVLLFSQMTQMLDILQDYMDYRGYSYERVDGSVRGEERHLAIKNFGQ--QPIFVFLLSTRAGGVGMNLTAADTVIF 157
Cdd:PLN03142   485 ERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKpgSEKFVFLLSTRAGGLGINLATADIVIL 564

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904  158 VDSDFNPQNDLQAAARAHRIGQNKSVKVIRLIGRDTVEEIVYRKAASKLQLTNMIIEGGHFtlgAQKPAADADlQLSEIL 237
Cdd:PLN03142   565 YDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVIQQGRL---AEQKTVNKD-ELLQMV 640

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904  238 KFGLDKLLASEGSTMDEIDLESIL--GE-------TKDGQWVSDALPAAEGGS---------RDQEEGKNHMYLFEGKDY 299
Cdd:PLN03142   641 RYGAEMVFSSKDSTITDEDIDRIIakGEeataeldAKMKKFTEDAIKFKMDDTaelydfddeDDKDENKLDFKKIVSDNW 720

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904  300 SKEPSKEDRKSFEQLVNLQKTLLEKASQEGRSLRnkgsvlIPGLVEGS------TKRKRVLSPEELEDRQKKRQEAAAKR 373
Cdd:PLN03142   721 IDPPKRERKRNYSESEYFKQAMRQGAPAKPKEPR------IPRMPQLHdfqffnVQRLTELYEKEVRYLMQAHQKGQLKD 794

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1140176904  374 RRLIEEKKRQ-----KEEAEHKKKM-----AWWESNNYQSFCLPSEESEPEDLEN 418
Cdd:PLN03142   795 TIDVAEPEEPgdpltAEEQEEKEQLleegfSTWSRRDFNAFIRACEKYGRNDIKS 849
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 65-189 8.97e-55

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: 182.29  E-value: 8.97e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904  65 SGKLHLLDKLLAFLYSGGHRVLLFSQMTQMLDILQDYMDYRGYSYERVDGSVRGEERHLAIKNFGQQP-IFVFLLSTRAG 143
Cdd:cd18793    10 SGKLEALLELLEELREPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDPdIRVFLLSTKAG 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1140176904 144 GVGMNLTAADTVIFVDSDFNPQNDLQAAARAHRIGQNKSVKVIRLI 189
Cdd:cd18793    90 GVGLNLTAANRVILYDPWWNPAVEEQAIDRAHRIGQKKPVVVYRLI 135
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 1-214 7.70e-48

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 178.11  E-value: 7.70e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904   1 MSALQKKYYKAIL---MKDLDAFENETAKKVKLQnILSQLRKCVDHPYLFDgvepepfEVGDHLTEASGKLHLLDKLLAF 77
Cdd:COG0553   473 LTPEQRALYEAVLeylRRELEGAEGIRRRGLILA-ALTRLRQICSHPALLL-------EEGAELSGRSAKLEALLELLEE 544

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904  78 LYSGGHRVLLFSQMTQMLDILQDYMDYRGYSYERVDGSVRGEERHLAIKNFGQQP-IFVFLLSTRAGGVGMNLTAADTVI 156
Cdd:COG0553   545 LLAEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQEGPeAPVFLISLKAGGEGLNLTAADHVI 624

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1140176904 157 FVDSDFNPQNDLQAAARAHRIGQNKSVKVIRLIGRDTVEEIVYRKAASKLQLTNMIIE 214
Cdd:COG0553   625 HYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGTIEEKILELLEEKRALAESVLG 682
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 66-178 2.28e-23

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: 94.97  E-value: 2.28e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904  66 GKLHLLDKLLAFlySGGHRVLLFSQMTQMLDIlQDYMDYRGYSYERVDGSVRGEERHLAIKNFGQQPIFVfLLSTRAGGV 145
Cdd:pfam00271   1 EKLEALLELLKK--ERGGKVLIFSQTKKTLEA-ELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDV-LVATDVAER 76

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1140176904 146 GMNLTAADTVIFVDSDFNPQNDLQAAARAHRIG 178
Cdd:pfam00271  77 GLDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
HELICc smart00490
helicase superfamily c-terminal domain;
96-178 7.02e-19

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 81.49  E-value: 7.02e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904   96 DILQDYMDYRGYSYERVDGSVRGEERHLAIKNFgQQPIFVFLLSTRAGGVGMNLTAADTVIFVDSDFNPQNDLQAAARAH 175
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKF-NNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAG 79


                   ...
gi 1140176904  176 RIG 178
Cdd:smart00490  80 RAG 82
 
Name Accession Description Interval E-value
Macro_Poa1p-like_SNF2 cd03331
macrodomain, Poa1p-like family, SNF2 subfamily; Macrodomains are found in a variety of ...
 435-585 3.08e-95

macrodomain, Poa1p-like family, SNF2 subfamily; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Members of this subfamily contain a C-terminal macrodomain that show similarity to the yeast protein Poa1p, reported to be a phosphatase specific for Appr-1"-p, a tRNA splicing metabolite. In addition, they also contain an SNF2 domain, defined by the presence of seven motifs with sequence similarity to DNA helicases. SNF2 proteins have the capacity to use the energy released by their DNA-dependent ATPase activity to stabilize or perturb protein-DNA interactions and play important roles in transcriptional regulation, maintenance of chromosome integrity and DNA repair.


Pssm-ID: 394880  Cd Length: 152  Bit Score: 288.77  E-value: 3.08e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904 435 SLKYVSGDVTHPQA-GAEDALIVHCVDDSGHWGRGGLFTALEKRSAEPRKIYELAGKMKDLSLGGVLLFPVDDKESRNKG 513
Cdd:cd03331     1 DINYVSGDVTHPQTtSTEDAIIVHCVDDSGRWGRGGLFSALSSRSKQPKEQYELAGEMKDLHLGDVHLIPVDDKESRSGG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1140176904 514 QDLLALIVAQHRDRSNVLSGIKMAALEEGLKKIFLAAKKKKASVHLPRIGHATKGFNWYGTERLIRKHLAAR 585
Cdd:cd03331    81 RDYVALIVAQHRDRSNKLSGIKLSALETGLQKIATAAKQRNASVHLPRIGHGTPGFNWYGTERLIRKHLASR 152
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
 1-418 4.35e-81

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 275.91  E-value: 4.35e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904    1 MSALQKKYYKAILMKDLDAFeNETAKKVKLQNILSQLRKCVDHPYLFDGVEP-EPFEVGDHLTEASGKLHLLDKLLAFLY 79
Cdd:PLN03142   406 MSQMQKQYYKALLQKDLDVV-NAGGERKRLLNIAMQLRKCCNHPYLFQGAEPgPPYTTGEHLVENSGKMVLLDKLLPKLK 484

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904   80 SGGHRVLLFSQMTQMLDILQDYMDYRGYSYERVDGSVRGEERHLAIKNFGQ--QPIFVFLLSTRAGGVGMNLTAADTVIF 157
Cdd:PLN03142   485 ERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKpgSEKFVFLLSTRAGGLGINLATADIVIL 564

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904  158 VDSDFNPQNDLQAAARAHRIGQNKSVKVIRLIGRDTVEEIVYRKAASKLQLTNMIIEGGHFtlgAQKPAADADlQLSEIL 237
Cdd:PLN03142   565 YDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVIQQGRL---AEQKTVNKD-ELLQMV 640

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904  238 KFGLDKLLASEGSTMDEIDLESIL--GE-------TKDGQWVSDALPAAEGGS---------RDQEEGKNHMYLFEGKDY 299
Cdd:PLN03142   641 RYGAEMVFSSKDSTITDEDIDRIIakGEeataeldAKMKKFTEDAIKFKMDDTaelydfddeDDKDENKLDFKKIVSDNW 720

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904  300 SKEPSKEDRKSFEQLVNLQKTLLEKASQEGRSLRnkgsvlIPGLVEGS------TKRKRVLSPEELEDRQKKRQEAAAKR 373
Cdd:PLN03142   721 IDPPKRERKRNYSESEYFKQAMRQGAPAKPKEPR------IPRMPQLHdfqffnVQRLTELYEKEVRYLMQAHQKGQLKD 794

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1140176904  374 RRLIEEKKRQ-----KEEAEHKKKM-----AWWESNNYQSFCLPSEESEPEDLEN 418
Cdd:PLN03142   795 TIDVAEPEEPgdpltAEEQEEKEQLleegfSTWSRRDFNAFIRACEKYGRNDIKS 849
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 65-189 8.97e-55

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: 182.29  E-value: 8.97e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904  65 SGKLHLLDKLLAFLYSGGHRVLLFSQMTQMLDILQDYMDYRGYSYERVDGSVRGEERHLAIKNFGQQP-IFVFLLSTRAG 143
Cdd:cd18793    10 SGKLEALLELLEELREPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDPdIRVFLLSTKAG 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1140176904 144 GVGMNLTAADTVIFVDSDFNPQNDLQAAARAHRIGQNKSVKVIRLI 189
Cdd:cd18793    90 GVGLNLTAANRVILYDPWWNPAVEEQAIDRAHRIGQKKPVVVYRLI 135
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 1-214 7.70e-48

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 178.11  E-value: 7.70e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904   1 MSALQKKYYKAIL---MKDLDAFENETAKKVKLQnILSQLRKCVDHPYLFDgvepepfEVGDHLTEASGKLHLLDKLLAF 77
Cdd:COG0553   473 LTPEQRALYEAVLeylRRELEGAEGIRRRGLILA-ALTRLRQICSHPALLL-------EEGAELSGRSAKLEALLELLEE 544

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904  78 LYSGGHRVLLFSQMTQMLDILQDYMDYRGYSYERVDGSVRGEERHLAIKNFGQQP-IFVFLLSTRAGGVGMNLTAADTVI 156
Cdd:COG0553   545 LLAEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQEGPeAPVFLISLKAGGEGLNLTAADHVI 624

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1140176904 157 FVDSDFNPQNDLQAAARAHRIGQNKSVKVIRLIGRDTVEEIVYRKAASKLQLTNMIIE 214
Cdd:COG0553   625 HYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGTIEEKILELLEEKRALAESVLG 682
Macro_Poa1p-like cd02901
macrodomain, Poa1p-like family; Macrodomains are found in a variety of proteins with diverse ...
 435-585 3.00e-26

macrodomain, Poa1p-like family; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Members of this family show similarity to the yeast protein Poa1p, reported to be a phosphatase specific for Appr-1"-p, a tRNA splicing metabolite. Poa1p may play a role in tRNA splicing regulation.


Pssm-ID: 394873  Cd Length: 135  Bit Score: 104.26  E-value: 3.00e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904 435 SLKYVSGDVTHPQagaEDALIVHCVDDSGHWGRGGLFTALEK--RSAEPRKIYELAGkmkdlsLGGVLLFPVDDKesrnk 512
Cdd:cd02901     1 KITYVKGDLFACP---ETKSLAHCCNCDGVMGKGIALQFKKKpgRVEELRAQCKKKL------LGGVAVLKRDGV----- 66

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1140176904 513 gQDLLALIVAQHRDRSNvlsgIKMAALEEGLKKIF-LAAKKKKASVHLPRIGHATKGFNWYGTERLIRKHLAAR 585
Cdd:cd02901    67 -KRYIYYLITKKSYGPK----PTYEALRSSLEELReHCRENGVTSVAMPRIGCGLDGLDWEEVEPILKEVFDDR 135
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 66-178 2.28e-23

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: 94.97  E-value: 2.28e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904  66 GKLHLLDKLLAFlySGGHRVLLFSQMTQMLDIlQDYMDYRGYSYERVDGSVRGEERHLAIKNFGQQPIFVfLLSTRAGGV 145
Cdd:pfam00271   1 EKLEALLELLKK--ERGGKVLIFSQTKKTLEA-ELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDV-LVATDVAER 76

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1140176904 146 GMNLTAADTVIFVDSDFNPQNDLQAAARAHRIG 178
Cdd:pfam00271  77 GLDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
HELICc smart00490
helicase superfamily c-terminal domain;
96-178 7.02e-19

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 81.49  E-value: 7.02e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904   96 DILQDYMDYRGYSYERVDGSVRGEERHLAIKNFgQQPIFVFLLSTRAGGVGMNLTAADTVIFVDSDFNPQNDLQAAARAH 175
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKF-NNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAG 79


                   ...
gi 1140176904  176 RIG 178
Cdd:smart00490  80 RAG 82
HDA2-3 pfam11496
Class II histone deacetylase complex subunits 2 and 3; This family of class II histone ...
 29-197 5.58e-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: 48.48  E-value: 5.58e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904  29 KLQNILSQLRKCVDHPYLF-DGVEPEPF---EVGDHLTEASGKLHLLDKLLAFL----YSGGHRVLLFSQMTQMLDILQD 100
Cdd:pfam11496  49 SMTLCLENLSLVATHPYLLvDHYMPKSLllkDEPEKLAYTSGKFLVLNDLVNLLierdRKEPINVAIVARSGKTLDLVEA 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904 101 YMDYRGYSYERVDG-SVRGEERHLAIKNFGQQPIFVFLL------STRAGGVgMNLTAADTVIFVDSDFNPQNDLQAAAR 173
Cdd:pfam11496 129 LLLGKGLSYKRYSGeMLYGENKKVSDSGNKKIHSTTCHLlsstgqLTNDDSL-LENYKFDLIIAFDSSVDTSSPSVEHLR 207

                         170       180
                  ....*....|....*....|....
gi 1140176904 174 AHRIGQNKSVKVIRLIGRDTVEEI 197
Cdd:pfam11496 208 TQNRRKGNLAPIIRLVVINSIEHV 231
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 133-189 6.81e-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: 41.54  E-value: 6.81e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1140176904 133 IFVFLLSTRAGGVGMNLTAADTVIFVDSDFNPQNDLQAAARAHRIGQnKSVKVIRLI 189
Cdd:cd18785    22 SLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRGGK-DEGEVILFV 77
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 282-393 7.01e-05

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 45.88  E-value: 7.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904 282 RDQEEGKNHmylfegKDYSKEPSKEDRKSFEQLvnlQKTLLEKASQEGRSlrnkgsvlipGLVEgsTKRKRVLSPEELED 361
Cdd:pfam17380 466 RQQEEERKR------KKLELEKEKRDRKRAEEQ---RRKILEKELEERKQ----------AMIE--EERKRKLLEKEMEE 524

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1140176904 362 RQKKRQEaaAKRRRLIEEKKRQKEEAEHKKKM 393
Cdd:pfam17380 525 RQKAIYE--EERRREAEEERRKQQEMEERRRI 554
Macro_SF cd02749
macrodomain superfamily; Macrodomains are found in a variety of proteins with diverse cellular ...
 454-580 7.70e-05

macrodomain superfamily; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Macrodomains include the yeast macrodomain Poa1 which is a phosphatase of ADP-ribose-1"-phosphate, a by-product of tRNA splicing. Some macrodomains have ADPr-unrelated binding partners such as the coronavirus SUD-N (N-terminal subdomain) and SUD-M (middle subdomain) of the SARS-unique domain (SUD) which bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). Macrodomains regulate a wide variety of cellular and organismal processes, including DNA damage repair, signal transduction, and immune response.


Pssm-ID: 394871  Cd Length: 121  Bit Score: 42.39  E-value: 7.70e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904 454 LIVHCVDDSGHWGrGGLFTALEKRSAEPRKIYELAGKMKD-LSLGGVLLfpvddkesrNKGQDLLALIVAqHrdrSNVLS 532
Cdd:cd02749     2 AIVNPANNDLYLG-GGVAKAISKKAGGDLQEECEERKKNGyLKVGEVAV---------TKGGNLPARYII-H---VVGPV 67

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1140176904 533 GIKMAALEEGLKKIF-----LAAKKKKASVHLPRIGHATKGFNWYGTERLIRK 580
Cdd:cd02749    68 ASSKKKTYEPLKKCVknclsLADEKGLKSVAFPAIGTGIAGFPPEEAARIMLE 120
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 1-47 1.42e-04

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: 44.21  E-value: 1.42e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1140176904   1 MSALQKKYYKA-ILMKDLDAFENETA---KKVKLQNILSQLRKCVDHPYLF 47
Cdd:pfam00176 239 LSKLQRKLYQTfLLKKDLNAIKTGEGgreIKASLLNILMRLRKICNHPGLI 289
Caldesmon pfam02029
Caldesmon;
301-391 2.00e-03

Caldesmon;


Pssm-ID: 460421 [Multi-domain]  Cd Length: 495  Bit Score: 41.01  E-value: 2.00e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140176904 301 KEPSKEDRKSFEQ-LVNLQKTLLEKASQEGRSLRNKGSVLIPGLVEGSTKRK---RVLSPEEledrQKKRQEAAAKRRRL 376
Cdd:pfam02029 236 REEEAEVFLEAEQkLEELRRRRQEKESEEFEKLRQKQQEAELELEELKKKREerrKLLEEEE----QRRKQEEAERKLRE 311

                          90
                  ....*....|....*
gi 1140176904 377 IEEKKRQKEEAEHKK 391
Cdd:pfam02029 312 EEEKRRMKEEIERRR 326
Selenoprotein_S pfam06936
Selenoprotein S (SelS); This family consists of several mammalian selenoprotein S (SelS) ...
 365-414 2.82e-03

Selenoprotein S (SelS); This family consists of several mammalian selenoprotein S (SelS) sequences. SelS is a plasma membrane protein and is present in a variety of tissues and cell types. Selenoprotein S (SelS) is an intrinsically disordered protein. It formsa selenosulfide bond between cys 174 and Sec 188, that has a redox potential -234 mV. In vitro, SelS is an efficient reductase that depends on the presence of selenocysteine. Due to the high reactivity, SelS also has peroxidase activity that can catalyze the reduction of hydrogen peroxide. It is also resistant to inactivation by hydrogen peroxide which might provide evolutionary advantage compared to cysteine containing peroxidases.


Pssm-ID: 462043 [Multi-domain]  Cd Length: 192  Bit Score: 39.44  E-value: 2.82e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1140176904 365 KRQEA-AAKRRRLIE----------EKKRQKEEAEHKKKMAWWES----NNYQSFCLPSEESEPE 414
Cdd:pfam06936  80 KRQEAlEASRLRMQEeldaqaekfkEKQKQLEEEKRRQKIEMWESmqegKSYKGNAKLAQEETEE 144
CCDC34 pfam13904
Coiled-coil domain-containing protein 3; This family is found in eukaryotes; it has several ...
 347-394 4.82e-03

Coiled-coil domain-containing protein 3; This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known.


Pssm-ID: 464032 [Multi-domain]  Cd Length: 221  Bit Score: 38.92  E-value: 4.82e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1140176904 347 STKRKRVLSPEELEDR-----QKKRQEAAAKRRRLIEEKKRQKEEAEHKKKMA 394
Cdd:pfam13904 128 LAKPERKVSQEEAKEVlqeweRKKLEQQQRKREEEQREQLKKEEEEQERKQLA 180
 
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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