Annotations: 6Z9T

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth f]	SCOP2B Superfamily	RecA-like P-loop NTPases	8057376	3002019	SCOP2B (2022-06-29)
A [auth f]	SCOP2B Superfamily	Rho N-terminal domain-like	8057372	3001774	SCOP2B (2022-06-29)
A [auth f]	SCOP2B Superfamily	Nucleic acid-binding proteins	8057374	3000135	SCOP2B (2022-06-29)
B [auth a]	SCOP2B Superfamily	Nucleic acid-binding proteins	8057374	3000135	SCOP2B (2022-06-29)
B [auth a]	SCOP2B Superfamily	Rho N-terminal domain-like	8057372	3001774	SCOP2B (2022-06-29)
B [auth a]	SCOP2B Superfamily	RecA-like P-loop NTPases	8057376	3002019	SCOP2B (2022-06-29)
C [auth b]	SCOP2B Superfamily	RecA-like P-loop NTPases	8057376	3002019	SCOP2B (2022-06-29)
C [auth b]	SCOP2B Superfamily	Rho N-terminal domain-like	8057372	3001774	SCOP2B (2022-06-29)
C [auth b]	SCOP2B Superfamily	Nucleic acid-binding proteins	8057374	3000135	SCOP2B (2022-06-29)
D [auth c]	SCOP2B Superfamily	Nucleic acid-binding proteins	8057374	3000135	SCOP2B (2022-06-29)
D [auth c]	SCOP2B Superfamily	Rho N-terminal domain-like	8057372	3001774	SCOP2B (2022-06-29)
D [auth c]	SCOP2B Superfamily	RecA-like P-loop NTPases	8057376	3002019	SCOP2B (2022-06-29)
E [auth d]	SCOP2B Superfamily	Nucleic acid-binding proteins	8057374	3000135	SCOP2B (2022-06-29)
E [auth d]	SCOP2B Superfamily	Rho N-terminal domain-like	8057372	3001774	SCOP2B (2022-06-29)
E [auth d]	SCOP2B Superfamily	RecA-like P-loop NTPases	8057376	3002019	SCOP2B (2022-06-29)
F [auth e]	SCOP2B Superfamily	RecA-like P-loop NTPases	8057376	3002019	SCOP2B (2022-06-29)
F [auth e]	SCOP2B Superfamily	Rho N-terminal domain-like	8057372	3001774	SCOP2B (2022-06-29)
F [auth e]	SCOP2B Superfamily	Nucleic acid-binding proteins	8057374	3000135	SCOP2B (2022-06-29)
G [auth A]	SCOP2B Superfamily	Rad51 N-terminal domain-like	8040765	3000529	SCOP2B (2022-06-29)
H [auth U]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8035907	3001655	SCOP2B (2022-06-29)
H [auth U]	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8037279	3001500	SCOP2B (2022-06-29)
I [auth V]	SCOP2B Superfamily	C-terminal domain of RNA polymerase alpha subunit	8042964	3000519	SCOP2B (2022-06-29)
I [auth V]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8035907	3001655	SCOP2B (2022-06-29)
I [auth V]	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8037279	3001500	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth f]	Rho_RNA_bind	e6z9tf3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rho_RNA_bind	ECOD (1.6)
A [auth f]	Rho_N	e6z9tf2	A: alpha arrays	X: LEM/SAP HeH motif-like	H: LEM/SAP HeH motif	T: LEM/SAP HeH motif	F: Rho_N	ECOD (1.6)
A [auth f]	ATP-synt_ab	e6z9tf1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ATP-synt_ab	ECOD (1.6)
B [auth a]	Rho_RNA_bind	e6z9ta2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rho_RNA_bind	ECOD (1.6)
B [auth a]	Rho_N	e6z9ta3	A: alpha arrays	X: LEM/SAP HeH motif-like	H: LEM/SAP HeH motif	T: LEM/SAP HeH motif	F: Rho_N	ECOD (1.6)
B [auth a]	ATP-synt_ab	e6z9ta1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ATP-synt_ab	ECOD (1.6)
C [auth b]	Rho_RNA_bind	e6z9tb2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rho_RNA_bind	ECOD (1.6)
C [auth b]	Rho_N	e6z9tb1	A: alpha arrays	X: LEM/SAP HeH motif-like	H: LEM/SAP HeH motif	T: LEM/SAP HeH motif	F: Rho_N	ECOD (1.6)
C [auth b]	ATP-synt_ab	e6z9tb3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ATP-synt_ab	ECOD (1.6)
D [auth c]	Rho_RNA_bind	e6z9tc3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rho_RNA_bind	ECOD (1.6)
D [auth c]	Rho_N	e6z9tc2	A: alpha arrays	X: LEM/SAP HeH motif-like	H: LEM/SAP HeH motif	T: LEM/SAP HeH motif	F: Rho_N	ECOD (1.6)
D [auth c]	ATP-synt_ab	e6z9tc1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ATP-synt_ab	ECOD (1.6)
E [auth d]	Rho_RNA_bind	e6z9td1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rho_RNA_bind	ECOD (1.6)
E [auth d]	Rho_N	e6z9td2	A: alpha arrays	X: LEM/SAP HeH motif-like	H: LEM/SAP HeH motif	T: LEM/SAP HeH motif	F: Rho_N	ECOD (1.6)
E [auth d]	ATP-synt_ab	e6z9td3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ATP-synt_ab	ECOD (1.6)
F [auth e]	Rho_RNA_bind	e6z9te2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rho_RNA_bind	ECOD (1.6)
F [auth e]	Rho_N	e6z9te1	A: alpha arrays	X: LEM/SAP HeH motif-like	H: LEM/SAP HeH motif	T: LEM/SAP HeH motif	F: Rho_N	ECOD (1.6)
F [auth e]	ATP-synt_ab	e6z9te3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ATP-synt_ab	ECOD (1.6)
G [auth A]	S1_3	e6z9tA5	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_3	ECOD (1.6)
G [auth A]	HHH_5	e6z9tA6	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_5	ECOD (1.6)
G [auth A]	KH_5	e6z9tA1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Prokaryotic type KH domain (KH-domain type II)	F: KH_5	ECOD (1.6)
G [auth A]	nusA	e6z9tA4	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Prokaryotic type KH domain (KH-domain type II)	F: nusA	ECOD (1.6)
G [auth A]	NusA_N	e6z9tA3	A: a+b complex topology	X: Transcription factor NusA, N-terminal domain (From Topology)	H: Transcription factor NusA, N-terminal domain (From Topology)	T: Transcription factor NusA, N-terminal domain	F: NusA_N	ECOD (1.6)
H [auth U]	RNA_pol_L	e6z9tU2	A: a+b two layers	X: DCoH-like	H: RBP11-like subunits of RNA polymerase (From Topology)	T: RBP11-like subunits of RNA polymerase	F: RNA_pol_L	ECOD (1.6)
H [auth U]	RNA_pol_A_bac	e6z9tU1	A: a+b complex topology	X: Ribosomal protein TL5/L25 C-terminal domain-like	H: Insert subdomain of RNA polymerase alpha subunit (From Topology)	T: Insert subdomain of RNA polymerase alpha subunit	F: RNA_pol_A_bac	ECOD (1.6)
I [auth V]	RNA_pol_A_CTD	e6z9tV2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: RNA_pol_A_CTD	ECOD (1.6)
I [auth V]	RNA_pol_L	e6z9tV3	A: a+b two layers	X: DCoH-like	H: RBP11-like subunits of RNA polymerase (From Topology)	T: RBP11-like subunits of RNA polymerase	F: RNA_pol_L	ECOD (1.6)
I [auth V]	RNA_pol_A_bac	e6z9tV1	A: a+b complex topology	X: Ribosomal protein TL5/L25 C-terminal domain-like	H: Insert subdomain of RNA polymerase alpha subunit (From Topology)	T: Insert subdomain of RNA polymerase alpha subunit	F: RNA_pol_A_bac	ECOD (1.6)
J [auth W]	RNA_pol_Rpb6	e6z9tW1	A: alpha arrays	X: RPB6/omega subunit-like (From Homology)	H: RPB6/omega subunit-like	T: RNA polymerase omega subunit	F: RNA_pol_Rpb6	ECOD (1.6)
K [auth X]	RNA_pol_Rpb2_6_3rd	e6z9tX3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb2_6_3rd	ECOD (1.6)
K [auth X]	PRK09603	e6z9tX9	A: a+b two layers	X: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: PRK09603	ECOD (1.6)
K [auth X]	RNA_pol_Rpb2_6_2nd	e6z9tX2	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: RNA_pol_Rpb2_6_2nd	ECOD (1.6)
K [auth X]	RNA_pol_Rpb2_6_1st	e6z9tX5	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: RNA_pol_Rpb2_6_1st	ECOD (1.6)
K [auth X]	RNA_pol_Rpb2_6_2nd_2	e6z9tX6	A: a+b complex topology	X: Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit (From Topology)	H: Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit (From Topology)	T: Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit	F: RNA_pol_Rpb2_6_2nd_2	ECOD (1.6)
K [auth X]	RNA_pol_Rpb2_3	e6z9tX8	A: a+b complex topology	X: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: N-terminal domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_3	ECOD (1.6)
K [auth X]	RNA_pol_Rpb2_1	e6z9tX1	A: a+b complex topology	X: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: insertion domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_1	ECOD (1.6)
K [auth X]	RNA_pol_Rpb2_45	e6z9tX10	A: a+b complex topology	X: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: barrel domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_45	ECOD (1.6)
K [auth X]	RNA_pol_Rpb2_7	e6z9tX7	A: a+b complex topology	X: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: C-terminal domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_7	ECOD (1.6)
L [auth Y]	RNA_pol_Rpb1_2	e6z9tY4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb1_2	ECOD (1.6)
L [auth Y]	PRK00566_2nd	e6z9tY1	A: a+b two layers	X: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: PRK00566_2nd	ECOD (1.6)
L [auth Y]	PRK14844	e6z9tY7	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: PRK14844	ECOD (1.6)
L [auth Y]	RNA_pol_Rpb1_5_1st	e6z9tY2	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: RNA_pol_Rpb1_5_1st	ECOD (1.6)
L [auth Y]	PRK00566_3rd,RNA_pol_Rpb1_5_3rd	e6z9tY3	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: PRK00566_3rd,RNA_pol_Rpb1_5_3rd	ECOD (1.6)
L [auth Y]	RNA_pol_Rpb1_1	e6z9tY5	A: a+b complex topology	X: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)	H: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)	T: N-terminal domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_1	ECOD (1.6)
L [auth Y]	RNA_pol_Rpb1_5_3rd	e6z9tY9	A: a+b complex topology	X: central helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: central helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: central helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_5_3rd	ECOD (1.6)
L [auth Y]	RNA_pol_Rpb1_4	e6z9tY8	A: a+b complex topology	X: second helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: second helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: second helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_4	ECOD (1.6)
L [auth Y]	RNA_pol_Rpb1_3	e6z9tY6	A: a+b complex topology	X: first helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: first helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: first helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_3	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G [auth A]	PF00006	ATP synthase alpha/beta family, nucleotide-binding domain (ATP-synt_ab)	ATP synthase alpha/beta family, nucleotide-binding domain	This entry includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho.	Domain
G [auth A]	PF07498	Rho termination factor, N-terminal domain (Rho_N)	Rho termination factor, N-terminal domain	The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [1]. This domain is found to the N- ...	The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [1]. This domain is found to the N-terminus of the RNA binding domain (Pfam:PF07497).	Domain
G [auth A]	PF13184	NusA-like KH domain (KH_5)	NusA-like KH domain		Domain
G [auth A]	PF07497	Rho termination factor, RNA-binding domain (Rho_RNA_bind)	Rho termination factor, RNA-binding domain	The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [1].	Domain
G [auth A]	PF08529	NusA N-terminal domain (NusA_N)	NusA N-terminal domain	This domain represents the RNA polymerase binding domain of NusA.	Domain
G [auth A]	PF14520	Helix-hairpin-helix domain (HHH_5)	Helix-hairpin-helix domain		Domain
G [auth A]	PF00575	S1 RNA binding domain (S1)	S1 RNA binding domain	The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.	Domain
H [auth U], I [auth V]	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
H [auth U], I [auth V]	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
H [auth U], I [auth V]	PF03118	Bacterial RNA polymerase, alpha chain C terminal domain (RNA_pol_A_CTD)	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. T ...	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 [2].	Domain
J [auth W]	PF01192	RNA polymerase Rpb6 (RNA_pol_Rpb6)	RNA polymerase Rpb6	-	Family
K [auth X]	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
K [auth X]	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
K [auth X]	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
K [auth X]	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
K [auth X]	PF04563	RNA polymerase beta subunit (RNA_pol_Rpb2_1)	RNA polymerase beta subunit	-	Family
K [auth X]	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
L [auth Y]	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
L [auth Y]	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
L [auth Y]	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
L [auth Y]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], F [auth e]	Transcription termination factor Rho	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity ATP-dependent activity, acting on RNA pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides RNA binding nucleic acid binding identical protein binding protein binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression DNA-templated transcription termination 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 RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression DNA-templated transcription termination 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 membrane intracellular anatomical structure cytoplasm cytosol
G [auth A]	Transcription termination/antitermination protein NusA	protein binding binding protein domain specific binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding RNA polymerase binding bacterial-type RNA polymerase core enzyme binding RNA polymerase core enzyme binding enzyme binding transcription regulator activity DNA-binding transcription factor activity RNA binding protein binding binding protein domain specific binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding RNA polymerase binding bacterial-type RNA polymerase core enzyme binding RNA polymerase core enzyme binding enzyme binding transcription regulator activity DNA-binding transcription factor activity RNA binding nucleic acid binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis 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 cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis 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 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 negative regulation of metabolic process primary metabolic 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 positive regulation of biological process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of gene expression negative regulation of biosynthetic process ribosome biogenesis ribonucleoprotein complex biogenesis regulation of DNA-templated transcription elongation DNA-templated transcription elongation	membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen cytoplasm cytosol
H [auth U], I [auth V]	DNA-directed RNA polymerase subunit alpha	DNA binding binding nucleic acid binding 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 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 negative regulation of metabolic process primary metabolic 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 positive regulation of biological process RNA 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 positive regulation of gene expression negative regulation of biosynthetic process cellular 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 bacterial-type flagellum assembly membraneless organelle 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 transferase complex, transferring phosphorus-containing groups cellular anatomical structure 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 transferase complex, transferring phosphorus-containing groups cellular anatomical structure 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
J [auth W]	DNA-directed RNA polymerase subunit omega	RNA polymerase binding protein binding binding bacterial-type RNA polymerase core enzyme binding RNA polymerase core enzyme binding enzyme binding DNA binding nucleic acid 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 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 negative regulation of metabolic process primary metabolic 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 positive regulation of biological process RNA 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 positive regulation of gene expression negative regulation of biosynthetic process cellular 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 bacterial-type flagellum assembly membraneless organelle 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 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 transferase complex, transferring phosphorus-containing groups cellular anatomical structure 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 transferase complex, transferring phosphorus-containing groups cellular anatomical structure 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
K [auth X]	DNA-directed RNA polymerase subunit beta	ribonucleoside binding binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding DNA binding nucleic acid 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 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 negative regulation of metabolic process primary metabolic 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 positive regulation of biological process RNA 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 positive regulation of gene expression negative regulation of biosynthetic process cellular 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 bacterial-type flagellum assembly membraneless organelle 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 transferase complex, transferring phosphorus-containing groups cellular anatomical structure 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 transferase complex, transferring phosphorus-containing groups cellular anatomical structure 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
L [auth Y]	DNA-directed RNA polymerase subunit beta'	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding 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 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 negative regulation of metabolic process primary metabolic 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 positive regulation of biological process RNA 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 positive regulation of gene expression negative regulation of biosynthetic process cellular 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 bacterial-type flagellum assembly membraneless organelle 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 transferase complex, transferring phosphorus-containing groups cellular anatomical structure 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 transferase complex, transferring phosphorus-containing groups cellular anatomical structure 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
M [auth L]	template strand	-	-	-
N [auth K]	non template strand	-	-	-
O [auth R]	rut RNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], F [auth e]	IPR011129	Cold-shock domain	Domain
A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], F [auth e]	IPR004665	Transcription termination factor Rho	Family
A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], F [auth e]	IPR000194	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain	Domain
A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], F [auth e]	IPR003593	AAA+ ATPase domain	Domain
A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], F [auth e]	IPR036269	Rho termination factor, N-terminal domain superfamily	Homologous Superfamily
A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], F [auth e]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], F [auth e]	IPR011112	Rho termination factor-like, N-terminal	Domain
A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], F [auth e]	IPR011113	Rho termination factor, RNA-binding domain	Domain
A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], F [auth e]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], F [auth e]	IPR041703	Transcription termination factor Rho, ATP binding domain	Domain
G [auth A]	IPR025249	KH domain, NusA-like	Domain
G [auth A]	IPR036555	NusA, N-terminal domain superfamily	Homologous Superfamily
G [auth A]	IPR003029	S1 domain	Domain
G [auth A]	IPR013735	Transcription factor NusA, N-terminal	Domain
G [auth A]	IPR030842	Transcription termination/antitermination protein NusA, bacterial	Family
G [auth A]	IPR010213	Transcription termination factor NusA	Domain
G [auth A]	IPR009019	K homology domain superfamily, prokaryotic type	Homologous Superfamily
G [auth A]	IPR010214	Transcription termination factor NusA, C-terminal duplication	Repeat
G [auth A]	IPR015946	K homology domain-like, alpha/beta	Homologous Superfamily
G [auth A]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
G [auth A]	IPR010995	DNA repair Rad51/transcription factor NusA, alpha-helical	Homologous Superfamily
H [auth U], I [auth V]	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
H [auth U], I [auth V]	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
H [auth U], I [auth V]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
H [auth U], I [auth V]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
H [auth U], I [auth V]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
H [auth U], I [auth V]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
J [auth W]	IPR003716	DNA-directed RNA polymerase, omega subunit	Family
J [auth W]	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
J [auth W]	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
K [auth X]	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
K [auth X]	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
K [auth X]	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
K [auth X]	IPR007642	RNA polymerase Rpb2, domain 2	Domain
K [auth X]	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
K [auth X]	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
K [auth X]	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
K [auth X]	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
K [auth X]	IPR007645	RNA polymerase Rpb2, domain 3	Domain
K [auth X]	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
K [auth X]	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
K [auth X]	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
K [auth X]	IPR007641	RNA polymerase Rpb2, domain 7	Domain
L [auth Y]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
L [auth Y]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
L [auth Y]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
L [auth Y]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
L [auth Y]	IPR006592	RNA polymerase, N-terminal	Domain
L [auth Y]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
L [auth Y]	IPR012754	DNA-directed RNA polymerase, subunit beta-prime, bacterial type	Family
L [auth Y]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
L [auth Y]	IPR000722	RNA polymerase, alpha subunit	Domain
L [auth Y]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
L [auth Y]	IPR007080	RNA polymerase Rpb1, domain 1	Domain