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Conserved domains on  [gi|1063713192|ref|NP_001326806|]
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RNA polymerase Rpb7-like, N-terminal domain-containing protein [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNAP_II_Rpb7_N cd04329
RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain. Rpb7 is a subunit of ...
 2-84 1.71e-24

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: 90.70  E-value: 1.71e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063713192   2 FIKVKLPWDVTIPAEDmdTGLMLQRAIVIRLLEAFSKEKaTKDLGYLITPTILENIGEGKIKEQTGEIQFPVVFNGICFK 81
Cdd:cd04329     1 FFKIELEHNILLHPSY--FGPNLKEYLEQKLLEEVEGTC-TGDYGYIIAVTDIDDIGEGKILPGTGSVEFPVKYKAIVFK 77


                  ...
gi 1063713192  82 MFK 84
Cdd:cd04329    78 PFK 80
PTZ00162 super family cl36519
DNA-directed RNA polymerase II subunit 7; Provisional
 40-174 6.42e-14

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: 65.88  E-value: 6.42e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063713192  40 KATKDLGYLITPTILENIGEGKIKEQTGEIQFPVVFNGICFKMFKGEIVHGVVHKVHKTGVFLKSGPYEiIYLSHMKMPG 119
Cdd:PTZ00162   37 QCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDVNKLGFFAQAGPLK-AFVSRSAIPP 115

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063713192 120 Y-EFIPGENPFFMNQYMSRIQI----GARVRFVVLdtewREAEKDFMALASIDGDNLGPF 174
Cdd:PTZ00162  116 DfVYDSDSAYPCYISSDGQIQIkpntEVRLRLQGV----RYDASNLFAIATINSDYLGPI 171
 
Name Accession Description Interval E-value
RNAP_II_Rpb7_N cd04329
RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain. Rpb7 is a subunit of ...
 2-84 1.71e-24

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: 90.70  E-value: 1.71e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063713192   2 FIKVKLPWDVTIPAEDmdTGLMLQRAIVIRLLEAFSKEKaTKDLGYLITPTILENIGEGKIKEQTGEIQFPVVFNGICFK 81
Cdd:cd04329     1 FFKIELEHNILLHPSY--FGPNLKEYLEQKLLEEVEGTC-TGDYGYIIAVTDIDDIGEGKILPGTGSVEFPVKYKAIVFK 77


                  ...
gi 1063713192  82 MFK 84
Cdd:cd04329    78 PFK 80
rpoE TIGR00448
DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form; This family seems to be ...
 1-146 4.76e-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: 74.44  E-value: 4.76e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063713192   1 MFIKVKLPWDVTIPAEDMdtGLMLQRAIVIRLLEAFSKeKATKDLGYLITPTILENIGEGKIKEQTGEIQFPVVFNGICF 80
Cdd:TIGR00448   1 MYILSKIADTVRIPPDQF--GEDLEEVITHQLNEKFEG-RLDKNVGLCITIYDIEDIGEGKVIPGDGSAYHNVTFRALVF 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1063713192  81 KMFKGEIVHGVVHKVHKTGVFLKSGPYE-IIYLSHMKMPGYEFIPGENPFFMNQYMSRIQIGARVRF 146
Cdd:TIGR00448  78 KPELGEIVEGEVIEIVEFGAFVSLGPFDgLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRA 144
PTZ00162 PTZ00162
DNA-directed RNA polymerase II subunit 7; Provisional
 40-174 6.42e-14

DNA-directed RNA polymerase II subunit 7; Provisional


Pssm-ID: 240298 [Multi-domain]  Cd Length: 176  Bit Score: 65.88  E-value: 6.42e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063713192  40 KATKDLGYLITPTILENIGEGKIKEQTGEIQFPVVFNGICFKMFKGEIVHGVVHKVHKTGVFLKSGPYEiIYLSHMKMPG 119
Cdd:PTZ00162   37 QCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDVNKLGFFAQAGPLK-AFVSRSAIPP 115

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063713192 120 Y-EFIPGENPFFMNQYMSRIQI----GARVRFVVLdtewREAEKDFMALASIDGDNLGPF 174
Cdd:PTZ00162  116 DfVYDSDSAYPCYISSDGQIQIkpntEVRLRLQGV----RYDASNLFAIATINSDYLGPI 171
S1_RNAPII_Rpb7 cd04462
S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. ...
 84-172 4.36e-09

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: 51.11  E-value: 4.36e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063713192  84 KGEIVHGVVHKVHKTGVFLKSGPYEIIYLSHMKMPGYEFIPGENPF-FMNQYMSRIQIGARVRFVVLDTewREAEKDFMA 162
Cdd:cd04462     1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPcFTSNEDIVIKKDTEVRLKIIGT--RVDATDIFA 78

                          90
                  ....*....|
gi 1063713192 163 LASIDGDNLG 172
Cdd:cd04462    79 IGTIKDDYLG 88
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 1-106 8.79e-09

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 52.14  E-value: 8.79e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063713192   1 MFIKVKLPWDVTIPAEDMDTGLmlqRAIVIRLLEAFSKEKATKDLGYLITPTILENIGEGKIKEQTGEIQFPVVFNGICF 80
Cdd:PRK08563    1 MYKLVKLEDVVRIPPEMFGEDL---EEAALEVLREKYEGRIDKELGIIVAVLDVKVIGEGKIVPGDGATYHEVEFDALVF 77

                          90       100
                  ....*....|....*....|....*.
gi 1063713192  81 KMFKGEIVHGVVHKVHKTGVFLKSGP 106
Cdd:PRK08563   78 KPELQEVVEGEVVEVVEFGAFVRIGP 103
SHS2_Rpb7-N pfam03876
SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; Rpb7 bind to Rpb4 to form a ...
 11-67 1.09e-05

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: 40.97  E-value: 1.09e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1063713192  11 VTIPAEDMdtGLMLQRAIVIRLLEAFSkEKATKDLGYLITPTILENIGEGKIKEQTG 67
Cdd:pfam03876   4 VRLPPSYL--GNPLKGAIEDKLLEKYE-GKVDKDLGVVIAVLDIKEIGEGKILPGDG 57
 
Name Accession Description Interval E-value
RNAP_II_Rpb7_N cd04329
RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain. Rpb7 is a subunit of ...
 2-84 1.71e-24

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: 90.70  E-value: 1.71e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063713192   2 FIKVKLPWDVTIPAEDmdTGLMLQRAIVIRLLEAFSKEKaTKDLGYLITPTILENIGEGKIKEQTGEIQFPVVFNGICFK 81
Cdd:cd04329     1 FFKIELEHNILLHPSY--FGPNLKEYLEQKLLEEVEGTC-TGDYGYIIAVTDIDDIGEGKILPGTGSVEFPVKYKAIVFK 77


                  ...
gi 1063713192  82 MFK 84
Cdd:cd04329    78 PFK 80
rpoE TIGR00448
DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form; This family seems to be ...
 1-146 4.76e-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: 74.44  E-value: 4.76e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063713192   1 MFIKVKLPWDVTIPAEDMdtGLMLQRAIVIRLLEAFSKeKATKDLGYLITPTILENIGEGKIKEQTGEIQFPVVFNGICF 80
Cdd:TIGR00448   1 MYILSKIADTVRIPPDQF--GEDLEEVITHQLNEKFEG-RLDKNVGLCITIYDIEDIGEGKVIPGDGSAYHNVTFRALVF 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1063713192  81 KMFKGEIVHGVVHKVHKTGVFLKSGPYE-IIYLSHMKMPGYEFIPGENPFFMNQYMSRIQIGARVRF 146
Cdd:TIGR00448  78 KPELGEIVEGEVIEIVEFGAFVSLGPFDgLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRA 144
PTZ00162 PTZ00162
DNA-directed RNA polymerase II subunit 7; Provisional
 40-174 6.42e-14

DNA-directed RNA polymerase II subunit 7; Provisional


Pssm-ID: 240298 [Multi-domain]  Cd Length: 176  Bit Score: 65.88  E-value: 6.42e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063713192  40 KATKDLGYLITPTILENIGEGKIKEQTGEIQFPVVFNGICFKMFKGEIVHGVVHKVHKTGVFLKSGPYEiIYLSHMKMPG 119
Cdd:PTZ00162   37 QCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDVNKLGFFAQAGPLK-AFVSRSAIPP 115

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063713192 120 Y-EFIPGENPFFMNQYMSRIQI----GARVRFVVLdtewREAEKDFMALASIDGDNLGPF 174
Cdd:PTZ00162  116 DfVYDSDSAYPCYISSDGQIQIkpntEVRLRLQGV----RYDASNLFAIATINSDYLGPI 171
S1_RNAPII_Rpb7 cd04462
S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. ...
 84-172 4.36e-09

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: 51.11  E-value: 4.36e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063713192  84 KGEIVHGVVHKVHKTGVFLKSGPYEIIYLSHMKMPGYEFIPGENPF-FMNQYMSRIQIGARVRFVVLDTewREAEKDFMA 162
Cdd:cd04462     1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPcFTSNEDIVIKKDTEVRLKIIGT--RVDATDIFA 78

                          90
                  ....*....|
gi 1063713192 163 LASIDGDNLG 172
Cdd:cd04462    79 IGTIKDDYLG 88
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 1-106 8.79e-09

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 52.14  E-value: 8.79e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063713192   1 MFIKVKLPWDVTIPAEDMDTGLmlqRAIVIRLLEAFSKEKATKDLGYLITPTILENIGEGKIKEQTGEIQFPVVFNGICF 80
Cdd:PRK08563    1 MYKLVKLEDVVRIPPEMFGEDL---EEAALEVLREKYEGRIDKELGIIVAVLDVKVIGEGKIVPGDGATYHEVEFDALVF 77

                          90       100
                  ....*....|....*....|....*.
gi 1063713192  81 KMFKGEIVHGVVHKVHKTGVFLKSGP 106
Cdd:PRK08563   78 KPELQEVVEGEVVEVVEFGAFVRIGP 103
SHS2_Rpb7-N pfam03876
SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; Rpb7 bind to Rpb4 to form a ...
 11-67 1.09e-05

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: 40.97  E-value: 1.09e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1063713192  11 VTIPAEDMdtGLMLQRAIVIRLLEAFSkEKATKDLGYLITPTILENIGEGKIKEQTG 67
Cdd:pfam03876   4 VRLPPSYL--GNPLKGAIEDKLLEKYE-GKVDKDLGVVIAVLDIKEIGEGKILPGDG 57
RNAP_Rpb7_N_like cd00655
RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) ...
 2-84 3.88e-05

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: 40.14  E-value: 3.88e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063713192   2 FIKVKLPWDVTIPAEDMdtGLMLQRAIVIRLLEAFsKEKATKDLGYLITPTILENIGEGKIKEQTGEIQFPVVFNGICFK 81
Cdd:cd00655     1 FQILEIADLVSVPPKYF--GDDCKGVKKCLLQEKG-EGDRTPVVGIILAIKDTKDIPEGAIRPGDGSAYVNVSFRAVVFK 77


                  ...
gi 1063713192  82 MFK 84
Cdd:cd00655    78 PFS 80
RNAP_E_N cd04331
RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain. RpoE (subunit E) is a subunit of ...
 2-81 2.52e-04

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: 37.96  E-value: 2.52e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063713192   2 FIKVKLPWDVTIPAEDMDTGLMlqrAIVIRLLEAFSKEKATKDLGYLITPTILENIGEGKIKEQTGEIQFPVVFNGICFK 81
Cdd:cd04331     1 YKLVELEDVVRVPPELFGEDLE---EAVLEILKEKYEGRLDKDLGKIVSVLDVKDVGEGKIVHGDGAVYHEVRFDALVFK 77
nusA PRK09202
transcription elongation factor NusA; Validated
 80-150 5.85e-04

transcription elongation factor NusA; Validated


Pssm-ID: 236410 [Multi-domain]  Cd Length: 470  Bit Score: 39.47  E-value: 5.85e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063713192  80 FKMFKGEIVHGVVHKVHKTGVFLKSGPYEIIylshmkMPGYEFIPGENpffmnqymsrIQIGARVRFVVLD 150
Cdd:PRK09202  130 YKDRVGEIITGVVKRVERGNIIVDLGRAEAI------LPRKEQIPREN----------FRPGDRVRAYVYE 184
S1_NusA cd04455
S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like ...
 84-150 5.27e-03

S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.


Pssm-ID: 239902 [Multi-domain]  Cd Length: 67  Bit Score: 33.95  E-value: 5.27e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1063713192  84 KGEIVHGVVHKVHKTGVFLKSGPYEIIylshmkMPGYEFIPGENpffmnqymsrIQIGARVRFVVLD 150
Cdd:cd04455     3 EGEIVTGIVKRVDRGNVIVDLGKVEAI------LPKKEQIPGES----------YRPGDRIKAYVLE 53
 
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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