8Y6U

Cryo-EM structure of E.coli transcription initiation complex with transcription factor GcvA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth A]	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8037279	3001500	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8035907	3001655	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8035907	3001655	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8035907	3001655	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8035907	3001655	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8037279	3001500	SCOP2B (2022-06-29)
K [auth I]	SCOP2B Superfamily	C-terminal domain of RNA polymerase alpha subunit	8042964	3000519	SCOP2B (2022-06-29)
J [auth F]	SCOP2B Superfamily	Sigma factor domain-like	8035452	3000953	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth H], B [auth J]	PF03466	LysR substrate binding domain (LysR_substrate)	LysR substrate binding domain	-	Family
A [auth H], B [auth J]	PF00126	Bacterial regulatory helix-turn-helix protein, lysR family (HTH_1)	Bacterial regulatory helix-turn-helix protein, lysR family	-	Domain
E [auth A], F [auth B], K [auth I]	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 A], F [auth B], K [auth I]	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 C]	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
G [auth C]	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
G [auth C]	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
G [auth C]	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
G [auth C]	PF04563	RNA polymerase beta subunit (RNA_pol_Rpb2_1)	RNA polymerase beta subunit	-	Family
G [auth C]	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
H [auth D]	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
H [auth D]	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
H [auth D]	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
H [auth D]	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
I [auth E]	PF01192	RNA polymerase Rpb6 (RNA_pol_Rpb6)	RNA polymerase Rpb6	-	Family
J [auth F]	PF04539	Sigma-70 region 3 (Sigma70_r3)	Sigma-70 region 3	-	Family
J [auth F]	PF00140	Sigma-70 factor, region 1.2 (Sigma70_r1_2)	Sigma-70 factor, region 1.2	-	Family
J [auth F]	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
J [auth F]	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 F]	PF04546	Sigma-70, non-essential region (Sigma70_ner)	Sigma-70, non-essential region	The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H], B [auth J]	Glycine cleavage system transcriptional activator	transcription regulator activity DNA-binding transcription factor activity sequence-specific DNA binding DNA binding binding organic cyclic compound binding nucleic acid binding	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process response to light stimulus response to stimulus response to radiation response to abiotic stimulus response to UV	intracellular anatomical structure cytoplasm cellular anatomical entity
C [auth 1]	Non-template promoter DNA	-	-	-
D [auth 2]	Template promoter DNA	-	-	-
E [auth A], F [auth B], K [auth I]	DNA-directed RNA polymerase subunit alpha	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' 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 protein binding DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' 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 protein binding protein dimerization activity	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly negative regulation of DNA-templated transcription regulation of biological process negative regulation of cellular component organization cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process primary metabolic process negative regulation of cellular biosynthetic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization transcription antitermination cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process DNA-templated transcription termination RNA biosynthetic process cellular component organization nucleic acid biosynthetic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process cellular component organization or biogenesis positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process protein-containing complex organization biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of gene expression negative regulation of biosynthetic process cellular process positive regulation of cellular biosynthetic process regulation of DNA-templated transcription initiation DNA-templated transcription initiation cellular response to stimulus cellular response to stress response to stimulus response to stress cellular response to cell envelope stress organelle assembly cell projection organization non-membrane-bounded organelle assembly bacterial-type flagellum assembly cellular component biogenesis bacterial-type flagellum organization organelle organization cellular component assembly cell projection assembly nitrate assimilation nitrogen cycle metabolic process oxoacid metabolic process small molecule metabolic process organic acid metabolic process nitrate metabolic process reactive nitrogen species metabolic process regulation of DNA-templated transcription elongation DNA-templated transcription elongation cell aggregation biofilm formation aggregation of unicellular organisms submerged biofilm formation cell motility response to heat response to abiotic stimulus response to temperature stimulus bacterial-type flagellum-dependent cell motility archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility	protein-containing complex intracellular anatomical structure catalytic complex transferase complex cellular anatomical entity transferase complex, transferring phosphorus-containing groups cytosolic DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm cytosol intracellular protein-containing complex membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex transferase complex cellular anatomical entity transferase complex, transferring phosphorus-containing groups cytosolic DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm cytosol intracellular protein-containing complex membrane membrane-bounded organelle transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
G [auth C]	DNA-directed RNA polymerase subunit beta	ribonucleoside binding binding organic cyclic compound binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding DNA binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity ribonucleoside binding binding organic cyclic compound binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding DNA binding nucleic acid binding DNA-directed 5'-3' 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	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly negative regulation of DNA-templated transcription regulation of biological process negative regulation of cellular component organization cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process primary metabolic process negative regulation of cellular biosynthetic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization transcription antitermination cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process DNA-templated transcription termination RNA biosynthetic process cellular component organization nucleic acid biosynthetic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process cellular component organization or biogenesis positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process protein-containing complex organization biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of gene expression negative regulation of biosynthetic process cellular process positive regulation of cellular biosynthetic process regulation of DNA-templated transcription initiation DNA-templated transcription initiation response to stimulus response to chemical response to antibiotic cellular response to stimulus cellular response to stress response to stress cellular response to cell envelope stress organelle assembly cell projection organization non-membrane-bounded organelle assembly bacterial-type flagellum assembly cellular component biogenesis bacterial-type flagellum organization organelle organization cellular component assembly cell projection assembly nitrate assimilation nitrogen cycle metabolic process oxoacid metabolic process small molecule metabolic process organic acid metabolic process nitrate metabolic process reactive nitrogen species metabolic process regulation of DNA-templated transcription elongation DNA-templated transcription elongation cell aggregation biofilm formation aggregation of unicellular organisms submerged biofilm formation cell motility response to heat response to abiotic stimulus response to temperature stimulus bacterial-type flagellum-dependent cell motility archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility	protein-containing complex intracellular anatomical structure catalytic complex transferase complex cellular anatomical entity transferase complex, transferring phosphorus-containing groups cytosolic DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm cytosol intracellular protein-containing complex membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex transferase complex cellular anatomical entity transferase complex, transferring phosphorus-containing groups cytosolic DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm cytosol intracellular protein-containing complex membrane membrane-bounded organelle transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
H [auth D]	DNA-directed RNA polymerase subunit beta'	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' 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	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly negative regulation of DNA-templated transcription regulation of biological process negative regulation of cellular component organization cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process primary metabolic process negative regulation of cellular biosynthetic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization transcription antitermination cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process DNA-templated transcription termination RNA biosynthetic process cellular component organization nucleic acid biosynthetic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process cellular component organization or biogenesis positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process protein-containing complex organization biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of gene expression negative regulation of biosynthetic process cellular process positive regulation of cellular biosynthetic process regulation of DNA-templated transcription initiation DNA-templated transcription initiation response to stimulus response to chemical response to antibiotic cellular response to stimulus cellular response to stress response to stress cellular response to cell envelope stress organelle assembly cell projection organization non-membrane-bounded organelle assembly bacterial-type flagellum assembly cellular component biogenesis bacterial-type flagellum organization organelle organization cellular component assembly cell projection assembly nitrate assimilation nitrogen cycle metabolic process oxoacid metabolic process small molecule metabolic process organic acid metabolic process nitrate metabolic process reactive nitrogen species metabolic process regulation of DNA-templated transcription elongation DNA-templated transcription elongation cell aggregation biofilm formation aggregation of unicellular organisms submerged biofilm formation cell motility response to heat response to abiotic stimulus response to temperature stimulus bacterial-type flagellum-dependent cell motility archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility	protein-containing complex intracellular anatomical structure catalytic complex transferase complex cellular anatomical entity transferase complex, transferring phosphorus-containing groups cytosolic DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm cytosol intracellular protein-containing complex membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex transferase complex cellular anatomical entity transferase complex, transferring phosphorus-containing groups cytosolic DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm cytosol intracellular protein-containing complex membrane membrane-bounded organelle transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
I [auth E]	DNA-directed RNA polymerase subunit omega	DNA binding binding organic cyclic compound binding nucleic acid binding RNA polymerase binding protein binding bacterial-type RNA polymerase core enzyme binding RNA polymerase core enzyme binding enzyme binding DNA-directed 5'-3' 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 organic cyclic compound binding nucleic acid binding RNA polymerase binding protein binding bacterial-type RNA polymerase core enzyme binding RNA polymerase core enzyme binding enzyme binding DNA-directed 5'-3' 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	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly negative regulation of DNA-templated transcription regulation of biological process negative regulation of cellular component organization cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process primary metabolic process negative regulation of cellular biosynthetic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization transcription antitermination cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process DNA-templated transcription termination RNA biosynthetic process cellular component organization nucleic acid biosynthetic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process cellular component organization or biogenesis positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process protein-containing complex organization biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of gene expression negative regulation of biosynthetic process cellular process positive regulation of cellular biosynthetic process cellular component biogenesis cellular component assembly protein-containing complex assembly regulation of DNA-templated transcription initiation DNA-templated transcription initiation cellular response to stimulus cellular response to stress response to stimulus response to stress cellular response to cell envelope stress organelle assembly cell projection organization non-membrane-bounded organelle assembly bacterial-type flagellum assembly bacterial-type flagellum organization organelle organization cell projection assembly nitrate assimilation nitrogen cycle metabolic process oxoacid metabolic process small molecule metabolic process organic acid metabolic process nitrate metabolic process reactive nitrogen species metabolic process cell motility regulation of DNA-templated transcription elongation DNA-templated transcription elongation response to heat response to abiotic stimulus response to temperature stimulus cell aggregation biofilm formation aggregation of unicellular organisms submerged biofilm formation bacterial-type flagellum-dependent cell motility archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility	protein-containing complex intracellular anatomical structure catalytic complex transferase complex cellular anatomical entity transferase complex, transferring phosphorus-containing groups cytosolic DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm cytosol intracellular protein-containing complex membrane-bounded organelle transcription elongation factor complex protein-containing complex intracellular anatomical structure catalytic complex transferase complex cellular anatomical entity transferase complex, transferring phosphorus-containing groups cytosolic DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm cytosol intracellular protein-containing complex membrane-bounded organelle transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
J [auth F]	RNA polymerase sigma factor RpoD	DNA binding binding organic cyclic compound binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity sigma factor activity cation binding ion binding metal ion binding small molecule binding	cellular biosynthetic process cellular metabolic 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 cellular biosynthetic process cellular metabolic 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	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth H], B [auth J]	IPR005119	LysR, substrate-binding	Domain
A [auth H], B [auth J]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A [auth H], B [auth J]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A [auth H], B [auth J]	IPR000847	Transcription regulator HTH, LysR	Domain
E [auth A], F [auth B], K [auth I]	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
E [auth A], F [auth B], K [auth I]	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
E [auth A], F [auth B], K [auth I]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
E [auth A], F [auth B], K [auth I]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
E [auth A], F [auth B], K [auth I]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
E [auth A], F [auth B], K [auth I]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
G [auth C]	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
G [auth C]	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
G [auth C]	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
G [auth C]	IPR007642	RNA polymerase Rpb2, domain 2	Domain
G [auth C]	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
G [auth C]	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
G [auth C]	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
G [auth C]	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
G [auth C]	IPR007645	RNA polymerase Rpb2, domain 3	Domain
G [auth C]	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
G [auth C]	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
G [auth C]	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
G [auth C]	IPR007641	RNA polymerase Rpb2, domain 7	Domain
H [auth D]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
H [auth D]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
H [auth D]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
H [auth D]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
H [auth D]	IPR006592	RNA polymerase, N-terminal	Domain
H [auth D]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
H [auth D]	IPR012754	DNA-directed RNA polymerase, subunit beta-prime, bacterial type	Family
H [auth D]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
H [auth D]	IPR000722	RNA polymerase, alpha subunit	Domain
H [auth D]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
H [auth D]	IPR007080	RNA polymerase Rpb1, domain 1	Domain
I [auth E]	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
I [auth E]	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
I [auth E]	IPR003716	DNA-directed RNA polymerase, omega subunit	Family
J [auth F]	IPR007627	RNA polymerase sigma-70 region 2	Domain
J [auth F]	IPR007127	RNA polymerase sigma factor 70, region 1.1	Domain
J [auth F]	IPR000943	RNA polymerase sigma-70	Domain
J [auth F]	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
J [auth F]	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
J [auth F]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
J [auth F]	IPR012760	RNA polymerase sigma factor RpoD, C-terminal	Domain
J [auth F]	IPR009042	RNA polymerase sigma-70 region 1.2	Domain
J [auth F]	IPR007630	RNA polymerase sigma-70 region 4	Domain
J [auth F]	IPR014284	RNA polymerase sigma-70-like domain	Domain
J [auth F]	IPR007624	RNA polymerase sigma-70 region 3	Domain
J [auth F]	IPR007631	RNA polymerase sigma factor 70, non-essential domain	Domain
J [auth F]	IPR028630	RNA polymerase sigma factor RpoD	Family
J [auth F]	IPR042189	Sigma-70 factor, region 1.1 superfamily	Homologous Superfamily
J [auth F]	IPR050239	Sigma-70 factor family, RNA polymerase initiation factors	Family