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Conserved domains on  [gi|124802663|ref|XP_001347553|]
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DNA-directed RNA polymerase II subunit RPB7, putative [Plasmodium falciparum 3D7]

Protein Classification

RPB7/RPC8 family DNA-directed RNA polymerase subunit( domain architecture ID 11488164)

RPB7/RPC8 family DNA-directed RNA polymerase similar to Dictyostelium discoideum DNA-directed RNA polymerase II subunit Rpb7

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PTZ00162 PTZ00162
DNA-directed RNA polymerase II subunit 7; Provisional
 1-174 4.69e-112

DNA-directed RNA polymerase II subunit 7; Provisional


:

Pssm-ID: 240298 [Multi-domain]  Cd Length: 176  Bit Score: 316.26  E-value: 4.69e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124802663   1 MYFVIEEWKNVIIKPSQLGPRYQQYIEDMLRNSVEGQCSVKYGYVICVIRIIHSEPGRVQDGTGMIVVKVKYQAIVFKPF 80
Cdd:PTZ00162   1 MFFVVELWKNVSLKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124802663  81 KDEVLDAIVTDVNKLGFFAQAGPLKIFISRTAIPKYFEYSEDLHYPCF--SSGDYNIKPQTTVRIKLQGIRYDLSNMFAI 158
Cdd:PTZ00162  81 KDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFVYDSDSAYPCYisSDGQIQIKPNTEVRLRLQGVRYDASNLFAI 160

                        170
                 ....*....|....*.
gi 124802663 159 ATINNEYLGCIESNIL 174
Cdd:PTZ00162 161 ATINSDYLGPIESSIL 176
 
Name Accession Description Interval E-value
PTZ00162 PTZ00162
DNA-directed RNA polymerase II subunit 7; Provisional
 1-174 4.69e-112

DNA-directed RNA polymerase II subunit 7; Provisional


Pssm-ID: 240298 [Multi-domain]  Cd Length: 176  Bit Score: 316.26  E-value: 4.69e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124802663   1 MYFVIEEWKNVIIKPSQLGPRYQQYIEDMLRNSVEGQCSVKYGYVICVIRIIHSEPGRVQDGTGMIVVKVKYQAIVFKPF 80
Cdd:PTZ00162   1 MFFVVELWKNVSLKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124802663  81 KDEVLDAIVTDVNKLGFFAQAGPLKIFISRTAIPKYFEYSEDLHYPCF--SSGDYNIKPQTTVRIKLQGIRYDLSNMFAI 158
Cdd:PTZ00162  81 KDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFVYDSDSAYPCYisSDGQIQIKPNTEVRLRLQGVRYDASNLFAI 160

                        170
                 ....*....|....*.
gi 124802663 159 ATINNEYLGCIESNIL 174
Cdd:PTZ00162 161 ATINSDYLGPIESSIL 176
S1_RNAPII_Rpb7 cd04462
S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. ...
 81-167 3.10e-43

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: 138.93  E-value: 3.10e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124802663  81 KDEVLDAIVTDVNKLGFFAQAGPLKIFISRTAIPKYFEYSEDLHYPCFSS-GDYNIKPQTTVRIKLQGIRYDLSNMFAIA 159
Cdd:cd04462    1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTSnEDIVIKKDTEVRLKIIGTRVDATDIFAIG 80


                 ....*...
gi 124802663 160 TINNEYLG 167
Cdd:cd04462   81 TIKDDYLG 88
SHS2_Rpb7-N pfam03876
SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; Rpb7 bind to Rpb4 to form a ...
 8-64 1.25e-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: 62.15  E-value: 1.25e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 124802663    8 WKNVIIKPSQLGPRYQQYIEDMLRNSVEGQCSVKYGYVICVIRIIHSEPGRVQDGTG 64
Cdd:pfam03876   1 EDTVRLPPSYLGNPLKGAIEDKLLEKYEGKVDKDLGVVIAVLDIKEIGEGKILPGDG 57
 
Name Accession Description Interval E-value
PTZ00162 PTZ00162
DNA-directed RNA polymerase II subunit 7; Provisional
 1-174 4.69e-112

DNA-directed RNA polymerase II subunit 7; Provisional


Pssm-ID: 240298 [Multi-domain]  Cd Length: 176  Bit Score: 316.26  E-value: 4.69e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124802663   1 MYFVIEEWKNVIIKPSQLGPRYQQYIEDMLRNSVEGQCSVKYGYVICVIRIIHSEPGRVQDGTGMIVVKVKYQAIVFKPF 80
Cdd:PTZ00162   1 MFFVVELWKNVSLKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124802663  81 KDEVLDAIVTDVNKLGFFAQAGPLKIFISRTAIPKYFEYSEDLHYPCF--SSGDYNIKPQTTVRIKLQGIRYDLSNMFAI 158
Cdd:PTZ00162  81 KDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFVYDSDSAYPCYisSDGQIQIKPNTEVRLRLQGVRYDASNLFAI 160

                        170
                 ....*....|....*.
gi 124802663 159 ATINNEYLGCIESNIL 174
Cdd:PTZ00162 161 ATINSDYLGPIESSIL 176
S1_RNAPII_Rpb7 cd04462
S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. ...
 81-167 3.10e-43

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: 138.93  E-value: 3.10e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124802663  81 KDEVLDAIVTDVNKLGFFAQAGPLKIFISRTAIPKYFEYSEDLHYPCFSS-GDYNIKPQTTVRIKLQGIRYDLSNMFAIA 159
Cdd:cd04462    1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTSnEDIVIKKDTEVRLKIIGTRVDATDIFAIG 80


                 ....*...
gi 124802663 160 TINNEYLG 167
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 ...
 2-81 3.20e-34

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: 115.74  E-value: 3.20e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124802663   2 YFVIEEWKNVIIKPSQLGPRYQQYIEDMLRNSVEGQCSVKYGYVICVIRIIHSEPGRVQDGTGMIVVKVKYQAIVFKPFK 81
Cdd:cd04329    1 FFKIELEHNILLHPSYFGPNLKEYLEQKLLEEVEGTCTGDYGYIIAVTDIDDIGEGKILPGTGSVEFPVKYKAIVFKPFK 80
RNAP_Rpb7_N_like cd00655
RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) ...
 3-81 2.78e-14

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: 64.41  E-value: 2.78e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124802663   3 FVIEEWKNVI-IKPSQLGPRYQQYIEDMLRNSVEGQCSVKYGYVICVIRIIHSEPGRVQDGTGMIVVKVKYQAIVFKPFK 81
Cdd:cd00655    1 FQILEIADLVsVPPKYFGDDCKGVKKCLLQEKGEGDRTPVVGIILAIKDTKDIPEGAIRPGDGSAYVNVSFRAVVFKPFS 80
SHS2_Rpb7-N pfam03876
SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; Rpb7 bind to Rpb4 to form a ...
 8-64 1.25e-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: 62.15  E-value: 1.25e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 124802663    8 WKNVIIKPSQLGPRYQQYIEDMLRNSVEGQCSVKYGYVICVIRIIHSEPGRVQDGTG 64
Cdd:pfam03876   1 EDTVRLPPSYLGNPLKGAIEDKLLEKYEGKVDKDLGVVIAVLDIKEIGEGKILPGDG 57
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 1-113 7.24e-13

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 63.31  E-value: 7.24e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124802663   1 MYFVIEEWKNVIIKPSQLGPRYQQYIEDMLRNSVEGQCSVKYGYVICVIRIIHSEPGRVQDGTGMIVVKVKYQAIVFKPF 80
Cdd:PRK08563   1 MYKLVKLEDVVRIPPEMFGEDLEEAALEVLREKYEGRIDKELGIIVAVLDVKVIGEGKIVPGDGATYHEVEFDALVFKPE 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 124802663  81 KDEVLDAIVTDVNKLGFFAQAGPLKIFISRTAI 113
Cdd:PRK08563  81 LQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQI 113
RNAP_E_N cd04331
RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain. RpoE (subunit E) is a subunit of ...
 2-79 1.43e-05

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: 41.42  E-value: 1.43e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 124802663   2 YFVIEEWKNVIIKPSQLGPRYQQYIEDMLRNSVEGQCSVKYGYVICVIRIIHSEPGRVQDGTGMIVVKVKYQAIVFKP 79
Cdd:cd04331    1 YKLVELEDVVRVPPELFGEDLEEAVLEILKEKYEGRLDKDLGKIVSVLDVKDVGEGKIVHGDGAVYHEVRFDALVFKP 78
RNAP_III_Rpc25_N cd04330
RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain. Rpc25 is a subunit of ...
 3-81 8.98e-05

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: 39.11  E-value: 8.98e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124802663   3 FVIEEWKNVI-IKPSQLGPRYQQYIEDMLRNSVEGQCSVKYGYVICVIRIIHSEPGRVQDGTGMIVVKVKYQAIVFKPFK 81
Cdd:cd04330    1 FILSEIEDTVrIPPSQFSRPLNDAIEDELNKKYANKVIQNVGLCICLYDILEVEDGYILPGDGASHYKVTFRMVVFRPFV 80
 
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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