Chain B, DNA-directed RNA polymerase alpha chain
Protein Classification
DNA-directed RNA polymerase subunit alpha( domain architecture ID 15176902)
DNA-directed RNA polymerase subunit alpha catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| RpoA | COG0202 | DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]; DNA-directed RNA ... |
20-314 | 9.47e-138 | |||||
DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]; DNA-directed RNA polymerase, alpha subunit/40 kD subunit is part of the Pathway/BioSystem: RNA polymerase : Pssm-ID: 439972 [Multi-domain] Cd Length: 317 Bit Score: 392.50 E-value: 9.47e-138
|
|||||||||
| Name | Accession | Description | Interval | E-value | |||||
| RpoA | COG0202 | DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]; DNA-directed RNA ... |
20-314 | 9.47e-138 | |||||
DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]; DNA-directed RNA polymerase, alpha subunit/40 kD subunit is part of the Pathway/BioSystem: RNA polymerase Pssm-ID: 439972 [Multi-domain] Cd Length: 317 Bit Score: 392.50 E-value: 9.47e-138
|
|||||||||
| PRK05182 | PRK05182 | DNA-directed RNA polymerase subunit alpha; Provisional |
20-314 | 1.60e-137 | |||||
DNA-directed RNA polymerase subunit alpha; Provisional Pssm-ID: 235359 [Multi-domain] Cd Length: 310 Bit Score: 391.38 E-value: 1.60e-137
|
|||||||||
| RNAP_alpha_NTD | cd06928 | N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; The bacterial alpha ... |
20-225 | 3.29e-112 | |||||
N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bacterial RNAP core enzyme consists of four subunits (beta', beta, alpha and omega). All residues in the alpha subunit that is involved in dimerization or in the interaction with other subunits are located within alphaNTD. Pssm-ID: 132904 [Multi-domain] Cd Length: 215 Bit Score: 323.65 E-value: 3.29e-112
|
|||||||||
| rpoA | TIGR02027 | DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type; This family ... |
20-314 | 1.72e-107 | |||||
DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type; This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins. [Transcription, DNA-dependent RNA polymerase] Pssm-ID: 273934 [Multi-domain] Cd Length: 297 Bit Score: 314.98 E-value: 1.72e-107
|
|||||||||
| RPOLD | smart00662 | RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain |
21-225 | 3.20e-72 | |||||
RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain Pssm-ID: 214766 [Multi-domain] Cd Length: 224 Bit Score: 222.49 E-value: 3.20e-72
|
|||||||||
| RNA_pol_L | pfam01193 | RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 ... |
27-221 | 1.30e-62 | |||||
RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 dimerize to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerization domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some of the alpha subunits also contain iron-sulphur binding domains (pfam00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Pssm-ID: 460104 [Multi-domain] Cd Length: 191 Bit Score: 196.86 E-value: 1.30e-62
|
|||||||||
| Name | Accession | Description | Interval | E-value | |||||
| RpoA | COG0202 | DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]; DNA-directed RNA ... |
20-314 | 9.47e-138 | |||||
DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]; DNA-directed RNA polymerase, alpha subunit/40 kD subunit is part of the Pathway/BioSystem: RNA polymerase Pssm-ID: 439972 [Multi-domain] Cd Length: 317 Bit Score: 392.50 E-value: 9.47e-138
|
|||||||||
| PRK05182 | PRK05182 | DNA-directed RNA polymerase subunit alpha; Provisional |
20-314 | 1.60e-137 | |||||
DNA-directed RNA polymerase subunit alpha; Provisional Pssm-ID: 235359 [Multi-domain] Cd Length: 310 Bit Score: 391.38 E-value: 1.60e-137
|
|||||||||
| RNAP_alpha_NTD | cd06928 | N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; The bacterial alpha ... |
20-225 | 3.29e-112 | |||||
N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bacterial RNAP core enzyme consists of four subunits (beta', beta, alpha and omega). All residues in the alpha subunit that is involved in dimerization or in the interaction with other subunits are located within alphaNTD. Pssm-ID: 132904 [Multi-domain] Cd Length: 215 Bit Score: 323.65 E-value: 3.29e-112
|
|||||||||
| rpoA | TIGR02027 | DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type; This family ... |
20-314 | 1.72e-107 | |||||
DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type; This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins. [Transcription, DNA-dependent RNA polymerase] Pssm-ID: 273934 [Multi-domain] Cd Length: 297 Bit Score: 314.98 E-value: 1.72e-107
|
|||||||||
| RPOLD | smart00662 | RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain |
21-225 | 3.20e-72 | |||||
RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain Pssm-ID: 214766 [Multi-domain] Cd Length: 224 Bit Score: 222.49 E-value: 3.20e-72
|
|||||||||
| rpoA | CHL00013 | RNA polymerase alpha subunit |
20-315 | 1.19e-66 | |||||
RNA polymerase alpha subunit Pssm-ID: 214333 [Multi-domain] Cd Length: 327 Bit Score: 211.75 E-value: 1.19e-66
|
|||||||||
| RNA_pol_L | pfam01193 | RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 ... |
27-221 | 1.30e-62 | |||||
RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 dimerize to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerization domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some of the alpha subunits also contain iron-sulphur binding domains (pfam00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Pssm-ID: 460104 [Multi-domain] Cd Length: 191 Bit Score: 196.86 E-value: 1.30e-62
|
|||||||||
| RNA_pol_A_bac | pfam01000 | RNA polymerase Rpb3/RpoA insert domain; Members of this family include: alpha subunit from ... |
56-172 | 3.01e-47 | |||||
RNA polymerase Rpb3/RpoA insert domain; Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal Pssm-ID: 425983 Cd Length: 117 Bit Score: 154.72 E-value: 3.01e-47
|
|||||||||
| RNAP_RPB11_RPB3 | cd00460 | RPB11 and RPB3 subunits of RNA polymerase; The eukaryotic RPB11 and RPB3 subunits of RNA ... |
172-225 | 5.07e-16 | |||||
RPB11 and RPB3 subunits of RNA polymerase; The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts. Pssm-ID: 132901 Cd Length: 86 Bit Score: 72.07 E-value: 5.07e-16
|
|||||||||
| RNA_pol_A_CTD | pfam03118 | Bacterial RNA polymerase, alpha chain C terminal domain; The alpha subunit of RNA polymerase ... |
262-307 | 1.69e-11 | |||||
Bacterial RNA polymerase, alpha chain C terminal domain; The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal. Pssm-ID: 427148 [Multi-domain] Cd Length: 63 Bit Score: 58.71 E-value: 1.69e-11
|
|||||||||
| RNAP_D | cd07030 | D subunit of Archaeal RNA polymerase; The D subunit of archaeal RNA polymerase (RNAP) is ... |
23-149 | 4.28e-07 | |||||
D subunit of Archaeal RNA polymerase; The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer. Pssm-ID: 132908 [Multi-domain] Cd Length: 259 Bit Score: 50.34 E-value: 4.28e-07
|
|||||||||
| PRK00783 | PRK00783 | DNA-directed RNA polymerase subunit D; Provisional |
30-220 | 6.44e-07 | |||||
DNA-directed RNA polymerase subunit D; Provisional Pssm-ID: 234837 [Multi-domain] Cd Length: 263 Bit Score: 49.88 E-value: 6.44e-07
|
|||||||||
| HHH_5 | pfam14520 | Helix-hairpin-helix domain; |
268-308 | 4.07e-05 | |||||
Helix-hairpin-helix domain; Pssm-ID: 434010 [Multi-domain] Cd Length: 57 Bit Score: 40.55 E-value: 4.07e-05
|
|||||||||
| PRK14906 | PRK14906 | DNA-directed RNA polymerase subunit beta'; |
262-312 | 1.39e-03 | |||||
DNA-directed RNA polymerase subunit beta'; Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 40.63 E-value: 1.39e-03
|
|||||||||
| RNAP_RPB3_like | cd07028 | RPB3 subunit of RNA polymerase; The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well ... |
22-218 | 2.24e-03 | |||||
RPB3 subunit of RNA polymerase; The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts. Pssm-ID: 132906 [Multi-domain] Cd Length: 212 Bit Score: 38.70 E-value: 2.24e-03
|
|||||||||
| PRK14979 | PRK14979 | DNA-directed RNA polymerase subunit D; Provisional |
34-219 | 8.84e-03 | |||||
DNA-directed RNA polymerase subunit D; Provisional Pssm-ID: 237878 [Multi-domain] Cd Length: 195 Bit Score: 36.75 E-value: 8.84e-03
|
|||||||||
| RNA_pol_L_2 | pfam13656 | RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 ... |
193-227 | 9.71e-03 | |||||
RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 dimerize to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerization domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some of the alpha subunits also contain iron-sulphur binding domains (pfam00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Many of the members of this family carry only the N-terminal region of Rpb11. Pssm-ID: 463947 Cd Length: 75 Bit Score: 34.41 E-value: 9.71e-03
|
|||||||||
| Blast search parameters | ||||
|
