8H3V | pdb_00008h3v

Cryo-EM structure of the full transcription activation complex NtcA-NtcB-TAC

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
N [auth X], O [auth Y]	PF13545	Crp-like helix-turn-helix domain (HTH_Crp_2)	Crp-like helix-turn-helix domain	This family represents a crp-like helix-turn-helix domain that is likely to bind DNA.	Domain
N [auth X], O [auth Y]	PF00027	Cyclic nucleotide-binding domain (cNMP_binding)	Cyclic nucleotide-binding domain	This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain
C [auth A]	PF04561	RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2)	RNA polymerase Rpb2, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA po ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain [1]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).	Domain
C [auth A]	PF10385	RNA polymerase beta subunit external 1 domain (RNA_pol_Rpb2_45)	RNA polymerase beta subunit external 1 domain	RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between ...	RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region [1].	Domain
C [auth A]	PF04560	RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7)	RNA polymerase Rpb2, domain 7	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA p ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp [1]. The clamp region (C-terminal) contains a zinc-binding motif [1]. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription [1].	Domain
C [auth A]	PF04565	RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3)	RNA polymerase Rpb2, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site [1].	Domain
C [auth A]	PF04563	RNA polymerase beta subunit (RNA_pol_Rpb2_1)	RNA polymerase beta subunit	-	Family
C [auth A]	PF00562	RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6)	RNA polymerase Rpb2, domain 6	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain [1]. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion[1]. This domain is also involved in binding to Rpb1 and Rpb3 [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).	Domain
D [auth B]	PF05000	RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)	RNA polymerase Rpb1, domain 4	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel do ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2].	Domain
D [auth B]	PF04983	RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)	RNA polymerase Rpb1, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore doma ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2].	Domain
D [auth B]	PF04998	RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)	RNA polymerase Rpb1, domain 5	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontin ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2].	Domain
E [auth C], F [auth D]	PF01193	RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L)	RNA polymerase Rpb3/Rpb11 dimerisation domain	The two eukaryotic subunits Rpb3 and Rpb11 dimerise 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 dimerisation do ...	The two eukaryotic subunits Rpb3 and Rpb11 dimerise 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 dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). 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.	Domain
E [auth C], F [auth D]	PF01000	RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac)	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	Domain
G [auth E]	PF00623	RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)	RNA polymerase Rpb1, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2].	Domain
G [auth E]	PF04983	RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)	RNA polymerase Rpb1, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore doma ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2].	Domain
G [auth E]	PF04997	RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1)	RNA polymerase Rpb1, domain 1	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp dom ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [1,2].	Domain
H [auth F]	PF01192	RNA polymerase Rpb6 (RNA_pol_Rpb6)	RNA polymerase Rpb6	-	Family
I [auth G]	PF04539	Sigma-70 region 3 (Sigma70_r3)	Sigma-70 region 3	-	Family
I [auth G]	PF00140	Sigma-70 factor, region 1.2 (Sigma70_r1_2)	Sigma-70 factor, region 1.2	-	Family
I [auth G]	PF04542	Sigma-70 region 2 (Sigma70_r2)	Sigma-70 region 2	Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA ...	Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [1,2]. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation [1,2].	Domain
I [auth G]	PF04545	Sigma-70, region 4 (Sigma70_r4)	Sigma-70, region 4	Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix fami ...	Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.	Domain
J [auth S], K [auth T], L [auth U], M [auth V]	PF03466	LysR substrate binding domain (LysR_substrate)	LysR substrate binding domain	-	Family
J [auth S], K [auth T], L [auth U], M [auth V]	PF00126	Bacterial regulatory helix-turn-helix protein, lysR family (HTH_1)	Bacterial regulatory helix-turn-helix protein, lysR family		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth 1]	DNA (125-MER)	-	-	-
N [auth X], O [auth Y]	NtcA	DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity	-	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
B [auth 2]	DNA (125-MER)	-	-	-
C [auth A]	DNA-directed RNA polymerase subunit beta	DNA binding binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups ribonucleoside binding nucleoside binding DNA binding binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
D [auth B]	DNA-directed RNA polymerase subunit beta'	DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
E [auth C], F [auth D]	DNA-directed RNA polymerase subunit alpha	DNA binding binding nucleic acid binding protein binding protein dimerization activity DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
G [auth E]	DNA-directed RNA polymerase subunit gamma	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups transition metal ion binding zinc ion binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
H [auth F]	DNA-directed RNA polymerase subunit omega	DNA binding binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
I [auth G]	RNA polymerase sigma factor SigA	DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity sigma factor activity	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm
J [auth S], K [auth T], L [auth U], M [auth V]	NtcB	transcription regulator activity DNA-binding transcription factor activity	-	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
N [auth X], O [auth Y]	IPR050397	Global Transcriptional Regulators in Environmental Response	Family
N [auth X], O [auth Y]	IPR000595	Cyclic nucleotide-binding domain	Domain
N [auth X], O [auth Y]	IPR018335	Transcription regulator HTH, Crp-type, conserved site	Conserved Site
N [auth X], O [auth Y]	IPR018490	Cyclic nucleotide-binding domain superfamily	Homologous Superfamily
N [auth X], O [auth Y]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
N [auth X], O [auth Y]	IPR022299	Transcription regulator, NtcA	Family
N [auth X], O [auth Y]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
N [auth X], O [auth Y]	IPR012318	Crp-type HTH domain	Domain
N [auth X], O [auth Y]	IPR014710	RmlC-like jelly roll fold	Homologous Superfamily
C [auth A]	IPR007642	RNA polymerase Rpb2, domain 2	Domain
C [auth A]	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
C [auth A]	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
C [auth A]	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
C [auth A]	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
C [auth A]	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
C [auth A]	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
C [auth A]	IPR007645	RNA polymerase Rpb2, domain 3	Domain
C [auth A]	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
C [auth A]	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
C [auth A]	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
C [auth A]	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
C [auth A]	IPR007641	RNA polymerase Rpb2, domain 7	Domain
D [auth B]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
D [auth B]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
D [auth B]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
D [auth B]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
D [auth B]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
D [auth B]	IPR012756	DNA-directed RNA polymerase, subunit beta''	Family
D [auth B]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
E [auth C], F [auth D]	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
E [auth C], F [auth D]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
E [auth C], F [auth D]	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
E [auth C], F [auth D]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
E [auth C], F [auth D]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
E [auth C], F [auth D]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
G [auth E]	IPR012755	DNA-directed RNA polymerase, subunit gamma	Family
G [auth E]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
G [auth E]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
G [auth E]	IPR034678	DNA-directed RNA polymerase subunit RpoC1	Family
G [auth E]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
G [auth E]	IPR000722	RNA polymerase, alpha subunit	Domain
G [auth E]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
G [auth E]	IPR006592	RNA polymerase, N-terminal	Domain
G [auth E]	IPR007080	RNA polymerase Rpb1, domain 1	Domain
H [auth F]	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
H [auth F]	IPR003716	DNA-directed RNA polymerase, omega subunit	Family
H [auth F]	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
I [auth G]	IPR007627	RNA polymerase sigma-70 region 2	Domain
I [auth G]	IPR000943	RNA polymerase sigma-70	Domain
I [auth G]	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
I [auth G]	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
I [auth G]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
I [auth G]	IPR012760	RNA polymerase sigma factor RpoD, C-terminal	Domain
I [auth G]	IPR017848	RNA polymerase sigma factor, RpoD/SigA, cyanobacteria	Family
I [auth G]	IPR009042	RNA polymerase sigma-70 region 1.2	Domain
I [auth G]	IPR007630	RNA polymerase sigma-70 region 4	Domain
I [auth G]	IPR014284	RNA polymerase sigma-70-like domain	Domain
I [auth G]	IPR007624	RNA polymerase sigma-70 region 3	Domain
I [auth G]	IPR028630	RNA polymerase sigma factor RpoD	Family
I [auth G]	IPR050239	Sigma-70 factor family, RNA polymerase initiation factors	Family
J [auth S], K [auth T], L [auth U], M [auth V]	IPR050950	HTH-type LysR transcriptional regulators	Family
J [auth S], K [auth T], L [auth U], M [auth V]	IPR005119	LysR, substrate-binding	Domain
J [auth S], K [auth T], L [auth U], M [auth V]	IPR000847	LysR, HTH, N-terminal domain	Domain
J [auth S], K [auth T], L [auth U], M [auth V]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
J [auth S], K [auth T], L [auth U], M [auth V]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily