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Conserved domains on  [gi|1002284869|ref|XP_015646734|]
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DNA-directed RNA polymerase III subunit RPC8 [Oryza sativa Japonica Group]

Protein Classification

RPB7/RPC8 family DNA-directed RNA polymerase subunit( domain architecture ID 10137818)

RPB7/RPC8 family DNA-directed RNA polymerase similar to DNA-directed RNA polymerase III subunit RPC8

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNAP_III_Rpc25_N cd04330
RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain. Rpc25 is a subunit of ...
 2-81 1.70e-39

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: 130.02  E-value: 1.70e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284869   2 FVLSQIEHNLPMPPHLLSRPLVDAIKAELERLFLDKVVANLGLCVSVYDIRSVEGGFIFPGEGCSTYKVSFRLLMFRPFV 81
Cdd:cd04330     1 FILSEIEDTVRIPPSQFSRPLNDAIEDELNKKYANKVIQNVGLCICLYDILEVEDGYILPGDGASHYKVTFRMVVFRPFV 80
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 83-187 2.61e-27

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member pfam08292:

Pssm-ID: 471952  Cd Length: 121  Bit Score: 100.05  E-value: 2.61e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284869  83 EVLVGKISGYDEKGLHVSLDFFSDISIPGHLMQYGTA-RALDGRWMLKTEDGDELYLDLDDEIRFLVSSIKY----PPIP 157
Cdd:pfam08292   1 EILTGKISSCTREGIKVSLGFFDDIFVPPDLLFEPSEfDEEEQAWVWEYDEETELYFDVGEEIRFRVEQEIFvdvkPTSP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1002284869 158 -----------VEQKETDRAFAPMQIIGSIKGDGLGLLAWW 187
Cdd:pfam08292  81 klaeltseslaESEEEIPEKKPPYELIGSCQEDGLGLVSWW 121
 
Name Accession Description Interval E-value
RNAP_III_Rpc25_N cd04330
RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain. Rpc25 is a subunit of ...
 2-81 1.70e-39

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: 130.02  E-value: 1.70e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284869   2 FVLSQIEHNLPMPPHLLSRPLVDAIKAELERLFLDKVVANLGLCVSVYDIRSVEGGFIFPGEGCSTYKVSFRLLMFRPFV 81
Cdd:cd04330     1 FILSEIEDTVRIPPSQFSRPLNDAIEDELNKKYANKVIQNVGLCICLYDILEVEDGYILPGDGASHYKVTFRMVVFRPFV 80
RNA_pol_Rbc25 pfam08292
RNA polymerase III subunit Rpc25; Rpc25 is a strongly conserved subunit of RNA polymerase III ...
 83-187 2.61e-27

RNA polymerase III subunit Rpc25; Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III.


Pssm-ID: 400543  Cd Length: 121  Bit Score: 100.05  E-value: 2.61e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284869  83 EVLVGKISGYDEKGLHVSLDFFSDISIPGHLMQYGTA-RALDGRWMLKTEDGDELYLDLDDEIRFLVSSIKY----PPIP 157
Cdd:pfam08292   1 EILTGKISSCTREGIKVSLGFFDDIFVPPDLLFEPSEfDEEEQAWVWEYDEETELYFDVGEEIRFRVEQEIFvdvkPTSP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1002284869 158 -----------VEQKETDRAFAPMQIIGSIKGDGLGLLAWW 187
Cdd:pfam08292  81 klaeltseslaESEEEIPEKKPPYELIGSCQEDGLGLVSWW 121
SHS2_Rpb7-N pfam03876
SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; Rpb7 bind to Rpb4 to form a ...
 8-64 1.40e-12

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: 59.84  E-value: 1.40e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1002284869   8 EHNLPMPPHLLSRPLVDAIKAELERLFLDKVVANLGLCVSVYDIRSVEGGFIFPGEG 64
Cdd:pfam03876   1 EDTVRLPPSYLGNPLKGAIEDKLLEKYEGKVDKDLGVVIAVLDIKEIGEGKILPGDG 57
PTZ00162 PTZ00162
DNA-directed RNA polymerase II subunit 7; Provisional
 1-182 1.26e-05

DNA-directed RNA polymerase II subunit 7; Provisional


Pssm-ID: 240298 [Multi-domain]  Cd Length: 176  Bit Score: 43.92  E-value: 1.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284869   1 MFVLSQIEHNLPMPPHLLSRPLVDAIKAELERLFLDKVVANLGLCVSVYDIRSVEGGFIFPGEGCSTYKVSFRLLMFRPF 80
Cdd:PTZ00162    1 MFFVVELWKNVSLKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284869  81 VGEVLVGKISGYDEKGLHVSLD----FFSDISIPGHLM-----QYGTARALDGRWMLKTedgdelyldlDDEIRFLVSSI 151
Cdd:PTZ00162   81 KDEVLDAIVTDVNKLGFFAQAGplkaFVSRSAIPPDFVydsdsAYPCYISSDGQIQIKP----------NTEVRLRLQGV 150

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1002284869 152 KYppipveqketdrAFAPMQIIGSIKGDGLG 182
Cdd:PTZ00162  151 RY------------DASNLFAIATINSDYLG 169
 
Name Accession Description Interval E-value
RNAP_III_Rpc25_N cd04330
RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain. Rpc25 is a subunit of ...
 2-81 1.70e-39

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: 130.02  E-value: 1.70e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284869   2 FVLSQIEHNLPMPPHLLSRPLVDAIKAELERLFLDKVVANLGLCVSVYDIRSVEGGFIFPGEGCSTYKVSFRLLMFRPFV 81
Cdd:cd04330     1 FILSEIEDTVRIPPSQFSRPLNDAIEDELNKKYANKVIQNVGLCICLYDILEVEDGYILPGDGASHYKVTFRMVVFRPFV 80
RNA_pol_Rbc25 pfam08292
RNA polymerase III subunit Rpc25; Rpc25 is a strongly conserved subunit of RNA polymerase III ...
 83-187 2.61e-27

RNA polymerase III subunit Rpc25; Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III.


Pssm-ID: 400543  Cd Length: 121  Bit Score: 100.05  E-value: 2.61e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284869  83 EVLVGKISGYDEKGLHVSLDFFSDISIPGHLMQYGTA-RALDGRWMLKTEDGDELYLDLDDEIRFLVSSIKY----PPIP 157
Cdd:pfam08292   1 EILTGKISSCTREGIKVSLGFFDDIFVPPDLLFEPSEfDEEEQAWVWEYDEETELYFDVGEEIRFRVEQEIFvdvkPTSP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1002284869 158 -----------VEQKETDRAFAPMQIIGSIKGDGLGLLAWW 187
Cdd:pfam08292  81 klaeltseslaESEEEIPEKKPPYELIGSCQEDGLGLVSWW 121
RNAP_E_N cd04331
RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain. RpoE (subunit E) is a subunit of ...
 2-79 3.28e-13

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: 62.23  E-value: 3.28e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002284869   2 FVLSQIEHNLPMPPHLLSRPLVDAIKAELERLFLDKVVANLGLCVSVYDIRSVEGGFIFPGEGCSTYKVSFRLLMFRP 79
Cdd:cd04331     1 YKLVELEDVVRVPPELFGEDLEEAVLEILKEKYEGRLDKDLGKIVSVLDVKDVGEGKIVHGDGAVYHEVRFDALVFKP 78
SHS2_Rpb7-N pfam03876
SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; Rpb7 bind to Rpb4 to form a ...
 8-64 1.40e-12

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: 59.84  E-value: 1.40e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1002284869   8 EHNLPMPPHLLSRPLVDAIKAELERLFLDKVVANLGLCVSVYDIRSVEGGFIFPGEG 64
Cdd:pfam03876   1 EDTVRLPPSYLGNPLKGAIEDKLLEKYEGKVDKDLGVVIAVLDIKEIGEGKILPGDG 57
RNAP_Rpb7_N_like cd00655
RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) ...
 2-80 7.84e-11

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: 55.94  E-value: 7.84e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002284869   2 FVLSQIEHNLPMPPHLLSRPLVDAIKAELERLFLDKVVANLGLCVSVYDIRSVEGGFIFPGEGCSTYKVSFRLLMFRPF 80
Cdd:cd00655     1 FQILEIADLVSVPPKYFGDDCKGVKKCLLQEKGEGDRTPVVGIILAIKDTKDIPEGAIRPGDGSAYVNVSFRAVVFKPF 79
PTZ00162 PTZ00162
DNA-directed RNA polymerase II subunit 7; Provisional
 1-182 1.26e-05

DNA-directed RNA polymerase II subunit 7; Provisional


Pssm-ID: 240298 [Multi-domain]  Cd Length: 176  Bit Score: 43.92  E-value: 1.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284869   1 MFVLSQIEHNLPMPPHLLSRPLVDAIKAELERLFLDKVVANLGLCVSVYDIRSVEGGFIFPGEGCSTYKVSFRLLMFRPF 80
Cdd:PTZ00162    1 MFFVVELWKNVSLKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284869  81 VGEVLVGKISGYDEKGLHVSLD----FFSDISIPGHLM-----QYGTARALDGRWMLKTedgdelyldlDDEIRFLVSSI 151
Cdd:PTZ00162   81 KDEVLDAIVTDVNKLGFFAQAGplkaFVSRSAIPPDFVydsdsAYPCYISSDGQIQIKP----------NTEVRLRLQGV 150

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1002284869 152 KYppipveqketdrAFAPMQIIGSIKGDGLG 182
Cdd:PTZ00162  151 RY------------DASNLFAIATINSDYLG 169
RNAP_II_Rpb7_N cd04329
RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain. Rpb7 is a subunit of ...
 2-80 2.47e-05

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: 41.01  E-value: 2.47e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002284869   2 FVLSQIEHNLPMPPHLLSRPLVDAIKAELERLFLDKVVANLGLCVSVYDIRSVEGGFIFPGEGCSTYKVSFRLLMFRPF 80
Cdd:cd04329     1 FFKIELEHNILLHPSYFGPNLKEYLEQKLLEEVEGTCTGDYGYIIAVTDIDDIGEGKILPGTGSVEFPVKYKAIVFKPF 79
 
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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