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Conserved domains on  [gi|359546314|pdb|4A3D|G]
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Chain G, RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7

Protein Classification

DNA-directed RNA polymerase II subunit RPB7( domain architecture ID 1010862)

DNA-directed RNA polymerase II subunit RPB7 is a DNA-dependent RNA polymerase that catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

CATH:  3.30.1490.120|2.40.50.140
EC:  2.7.7.6
Gene Ontology:  GO:0003676|GO:0031369|GO:0006366|GO:0005665|GO:0006352
PubMed:  16327806

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PTZ00162 super family cl36519
DNA-directed RNA polymerase II subunit 7; Provisional
 1-171 6.23e-57

DNA-directed RNA polymerase II subunit 7; Provisional


The actual alignment was detected with superfamily member PTZ00162:

Pssm-ID: 240298 [Multi-domain]  Cd Length: 176  Bit Score: 176.43  E-value: 6.23e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4A3D_G         1 MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIdiQRGRILPTDGSAEFNVKYRAVVFK 80
Cdd:PTZ00162   1 MFFVVELWKNVSLKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHN--EPGRVQDGTGMIVVNVKYQAIVFK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4A3D_G        81 PFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIK--SRIRVKIEGCISQVSSIH 158
Cdd:PTZ00162  79 PFKDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKpnTEVRLRLQGVRYDASNLF 158

                        170
                 ....*....|...
4A3D_G       159 AIGSIKEDYLGAI 171
Cdd:PTZ00162 159 AIATINSDYLGPI 171
 
Name Accession Description Interval E-value
PTZ00162 PTZ00162
DNA-directed RNA polymerase II subunit 7; Provisional
 1-171 6.23e-57

DNA-directed RNA polymerase II subunit 7; Provisional


Pssm-ID: 240298 [Multi-domain]  Cd Length: 176  Bit Score: 176.43  E-value: 6.23e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4A3D_G         1 MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIdiQRGRILPTDGSAEFNVKYRAVVFK 80
Cdd:PTZ00162   1 MFFVVELWKNVSLKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHN--EPGRVQDGTGMIVVNVKYQAIVFK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4A3D_G        81 PFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIK--SRIRVKIEGCISQVSSIH 158
Cdd:PTZ00162  79 PFKDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKpnTEVRLRLQGVRYDASNLF 158

                        170
                 ....*....|...
4A3D_G       159 AIGSIKEDYLGAI 171
Cdd:PTZ00162 159 AIATINSDYLGPI 171
S1_RNAPII_Rpb7 cd04462
S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. ...
 83-169 1.86e-42

S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.


Pssm-ID: 239909 [Multi-domain]  Cd Length: 88  Bit Score: 136.62  E-value: 1.86e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4A3D_G       83 KGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSED-VITIKSRIRVKIEGCISQVSSIHAIG 161
Cdd:cd04462   1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTSNEDiVIKKDTEVRLKIIGTRVDATDIFAIG 80


                ....*...
4A3D_G      162 SIKEDYLG 169
Cdd:cd04462  81 TIKDDYLG 88
rpoE TIGR00448
DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form; This family seems to be ...
 1-148 1.70e-17

DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form; This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 129540 [Multi-domain]  Cd Length: 179  Bit Score: 75.21  E-value: 1.70e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4A3D_G          1 MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVldYDNIDIQRGRILPTDGSAEFNVKYRAVVFK 80
Cdd:TIGR00448   1 MYILSKIADTVRIPPDQFGEDLEEVITHQLNEKFEGRLDKNVGLCITI--YDIEDIGEGKVIPGDGSAYHNVTFRALVFK 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
4A3D_G         81 PFKGEVVDGTVVSCSQHGFEVQVGPMK-VFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIE 148
Cdd:TIGR00448  79 PELGEIVEGEVIEIVEFGAFVSLGPFDgLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIV 147
SHS2_Rpb7-N pfam03876
SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; Rpb7 bind to Rpb4 to form a ...
 8-66 5.22e-13

SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction.


Pssm-ID: 427560 [Multi-domain]  Cd Length: 57  Bit Score: 60.23  E-value: 5.22e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
4A3D_G          8 SLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVldYDNIDIQRGRILPTDG 66
Cdd:pfam03876   1 EDTVRLPPSYLGNPLKGAIEDKLLEKYEGKVDKDLGVVIAV--LDIKEIGEGKILPGDG 57
 
Name Accession Description Interval E-value
PTZ00162 PTZ00162
DNA-directed RNA polymerase II subunit 7; Provisional
 1-171 6.23e-57

DNA-directed RNA polymerase II subunit 7; Provisional


Pssm-ID: 240298 [Multi-domain]  Cd Length: 176  Bit Score: 176.43  E-value: 6.23e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4A3D_G         1 MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIdiQRGRILPTDGSAEFNVKYRAVVFK 80
Cdd:PTZ00162   1 MFFVVELWKNVSLKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHN--EPGRVQDGTGMIVVNVKYQAIVFK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4A3D_G        81 PFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIK--SRIRVKIEGCISQVSSIH 158
Cdd:PTZ00162  79 PFKDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKpnTEVRLRLQGVRYDASNLF 158

                        170
                 ....*....|...
4A3D_G       159 AIGSIKEDYLGAI 171
Cdd:PTZ00162 159 AIATINSDYLGPI 171
S1_RNAPII_Rpb7 cd04462
S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. ...
 83-169 1.86e-42

S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.


Pssm-ID: 239909 [Multi-domain]  Cd Length: 88  Bit Score: 136.62  E-value: 1.86e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4A3D_G       83 KGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSED-VITIKSRIRVKIEGCISQVSSIHAIG 161
Cdd:cd04462   1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTSNEDiVIKKDTEVRLKIIGTRVDATDIFAIG 80


                ....*...
4A3D_G      162 SIKEDYLG 169
Cdd:cd04462  81 TIKDDYLG 88
RNAP_II_Rpb7_N cd04329
RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain. Rpb7 is a subunit of ...
 2-83 2.10e-37

RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain. Rpb7 is a subunit of eukaryotic RNA polymerase (RNAP) II that is homologous to Rpc25 of RNAP III, RpoE of archaeal RNAP, and Rpa43 of eukaryotic RNAP I. Rpb7 heterodimerizes with Rpb4 and this heterodimer binds the 10-subunit core of RNAP II, forming part of the floor of the DNA-binding cleft. Rpb7 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which bind single-stranded RNA. Rpb7 is thought to interact with the nascent RNA strand as it exits the RNAP II complex during transcription elongation. The Rpb7/Rpb4 heterodimer is also thought to serve as an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter.


Pssm-ID: 239821  Cd Length: 80  Bit Score: 123.45  E-value: 2.10e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4A3D_G        2 FFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDniDIQRGRILPTDGSAEFNVKYRAVVFKP 81
Cdd:cd04329   1 FFKIELEHNILLHPSYFGPNLKEYLEQKLLEEVEGTCTGDYGYIIAVTDID--DIGEGKILPGTGSVEFPVKYKAIVFKP 78


                ..
4A3D_G       82 FK 83
Cdd:cd04329  79 FK 80
RNAP_Rpb7_N_like cd00655
RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) ...
 2-83 9.21e-36

RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP. These proteins have, in addition to their N-terminal RNP domain, a C-terminal oligonucleotide-binding (OB) domain. Each of these subunits heterodimerizes with another RNAP subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to Rpa14). The heterodimer is thought to tether the RNAP to a given promoter via its interactions with a promoter-bound transcription factor.The heterodimer is also thought to bind and position nascent RNA as it exits the polymerase complex.


Pssm-ID: 238354  Cd Length: 80  Bit Score: 119.50  E-value: 9.21e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4A3D_G        2 FFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVldYDNIDIQRGRILPTDGSAEFNVKYRAVVFKP 81
Cdd:cd00655   1 FQILEIADLVSVPPKYFGDDCKGVKKCLLQEKGEGDRTPVVGIILAI--KDTKDIPEGAIRPGDGSAYVNVSFRAVVFKP 78


                ..
4A3D_G       82 FK 83
Cdd:cd00655  79 FS 80
rpoE TIGR00448
DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form; This family seems to be ...
 1-148 1.70e-17

DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form; This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 129540 [Multi-domain]  Cd Length: 179  Bit Score: 75.21  E-value: 1.70e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4A3D_G          1 MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVldYDNIDIQRGRILPTDGSAEFNVKYRAVVFK 80
Cdd:TIGR00448   1 MYILSKIADTVRIPPDQFGEDLEEVITHQLNEKFEGRLDKNVGLCITI--YDIEDIGEGKVIPGDGSAYHNVTFRALVFK 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
4A3D_G         81 PFKGEVVDGTVVSCSQHGFEVQVGPMK-VFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIE 148
Cdd:TIGR00448  79 PELGEIVEGEVIEIVEFGAFVSLGPFDgLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIV 147
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 15-147 5.36e-17

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 74.09  E-value: 5.36e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4A3D_G        15 PSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDniDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSC 94
Cdd:PRK08563  15 PEMFGEDLEEAALEVLREKYEGRIDKELGIIVAVLDVK--VIGEGKIVPGDGATYHEVEFDALVFKPELQEVVEGEVVEV 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
4A3D_G        95 SQHGFEVQVGPMKVFVTK-HLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKI 147
Cdd:PRK08563  93 VEFGAFVRIGPVDGLLHIsQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARI 146
SHS2_Rpb7-N pfam03876
SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; Rpb7 bind to Rpb4 to form a ...
 8-66 5.22e-13

SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction.


Pssm-ID: 427560 [Multi-domain]  Cd Length: 57  Bit Score: 60.23  E-value: 5.22e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
4A3D_G          8 SLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVldYDNIDIQRGRILPTDG 66
Cdd:pfam03876   1 EDTVRLPPSYLGNPLKGAIEDKLLEKYEGKVDKDLGVVIAV--LDIKEIGEGKILPGDG 57
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 81-157 3.92e-10

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 53.45  E-value: 3.92e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
4A3D_G         81 PFKGEVVDGTVVSCSQHGFEVQVG-PMKVFVTKHLMPQDLtfnagsnppsYQSSEDVITIKSRIRVKIEGCISQVSSI 157
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGnGVEGFIPISELSDDH----------VEDPDEVIKVGDEVKVKVLKVDKDRRRI 68
RNAP_III_Rpc25_N cd04330
RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain. Rpc25 is a subunit of ...
 46-83 7.96e-09

RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain. Rpc25 is a subunit of eukaryotic RNA polymerase (RNAP) III and is homologous to Rpa43 of eukaryotic RNAP I, Rpb7 of eukaryotic RNAP II, and RpoE of archaeal RNAP. Rpc25 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which are thought to bind single-stranded RNA. Rpc25 heterodimerizes with Rpc17 and plays an important role in transcription initiation. RNAP III transcribes diverse structural and catalytic RNAs including 5S ribosomal RNAs, tRNAs, and a small number of snRNAs involved in RNA and protein synthesis.


Pssm-ID: 239822  Cd Length: 80  Bit Score: 49.90  E-value: 7.96e-09
                        10        20        30
                ....*....|....*....|....*....|....*...
4A3D_G       46 LCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFK 83
Cdd:cd04330  43 LCICLYDILEVEDGYILPGDGASHYKVTFRMVVFRPFV 80
RNAP_E_N cd04331
RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain. RpoE (subunit E) is a subunit of ...
 15-81 2.13e-07

RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain. RpoE (subunit E) is a subunit of the archaeal RNA polymerase (RNAP) that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNAP III, and Rpa43 of eukaryotic RNAP I. RpoE heterodimerizes with RpoF, another RNA polymerase subunit. RpoE has an elongated two-domain structure that includes an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Both domains of RpoE bind single-stranded RNA.


Pssm-ID: 239823  Cd Length: 80  Bit Score: 46.05  E-value: 2.13e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
4A3D_G       15 PSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDniDIQRGRILPTDGSAEFNVKYRAVVFKP 81
Cdd:cd04331  14 PELFGEDLEEAVLEILKEKYEGRLDKDLGKIVSVLDVK--DVGEGKIVHGDGAVYHEVRFDALVFKP 78
 
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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