Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
BSCOP2B SuperfamilyRBP11-like subunits of RNA polymerase8035907 3001655 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyInsert subdomain of RNA polymerase alpha subunit8037279 3001500 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyRBP11-like subunits of RNA polymerase8035907 3001655 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyRBP11-like subunits of RNA polymerase8035907 3001655 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyInsert subdomain of RNA polymerase alpha subunit8037279 3001500 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyC-terminal domain of RNA polymerase alpha subunit8042964 3000519 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyRBP11-like subunits of RNA polymerase8035907 3001655 SCOP2B (2022-06-29)
FSCOP2B SuperfamilySigma2 domain of RNA polymerase sigma factors8038503 3001393 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyWinged helix DNA-binding domain8002723 3000034 SCOP2B (2022-06-29)
GSCOP2B SuperfamilycAMP-binding domain-like8002726 3000084 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyWinged helix DNA-binding domain8002723 3000034 SCOP2B (2022-06-29)
HSCOP2B SuperfamilycAMP-binding domain-like8002726 3000084 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
BPF01193e3iydB4 A: a+b two layersX: DCoH-likeH: RBP11-like subunits of RNA polymerase (From Topology)T: RBP11-like subunits of RNA polymeraseF: PF01193ECOD (1.6)
BPF01000e3iydB3 A: a+b complex topologyX: Ribosomal protein TL5/L25 C-terminal domain-likeH: Insert subdomain of RNA polymerase alpha subunit (From Topology)T: Insert subdomain of RNA polymerase alpha subunitF: PF01000ECOD (1.6)
APF03118e3iydA2 A: alpha arraysX: HhH/H2THH: SAM/DNA-glycosylaseT: SAM domain-likeF: PF03118ECOD (1.6)
APF01193e3iydA3 A: a+b two layersX: DCoH-likeH: RBP11-like subunits of RNA polymerase (From Topology)T: RBP11-like subunits of RNA polymeraseF: PF01193ECOD (1.6)
APF01000e3iydA1 A: a+b complex topologyX: Ribosomal protein TL5/L25 C-terminal domain-likeH: Insert subdomain of RNA polymerase alpha subunit (From Topology)T: Insert subdomain of RNA polymerase alpha subunitF: PF01000ECOD (1.6)
CPF00562e3iydC6 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: PF00562ECOD (1.6)
CPF00562e3iydC5 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Single hybrid motifF: PF00562ECOD (1.6)
CPF04563,PF04565e3iydC8 A: a+b complex topologyX: 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-polymeraseF: PF04563,PF04565ECOD (1.6)
CPF04561e3iydC14 A: a+b complex topologyX: 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-polymeraseF: PF04561ECOD (1.6)
CPF10385e3iydC9 A: a+b complex topologyX: 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-polymeraseF: PF10385ECOD (1.6)
CPF00562,PF04560e3iydC11 A: a+b complex topologyX: 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-polymeraseF: PF00562,PF04560ECOD (1.6)
EPF01192e3iydE1 A: alpha arraysX: RPB6/omega subunit-like (From Homology)H: RPB6/omega subunit-likeT: RNA polymerase omega subunitF: PF01192ECOD (1.6)
FPF04539e3iydF2 A: alpha arraysX: HTHH: HTHT: tri-helicalF: PF04539ECOD (1.6)
FPF04545e3iydF1 A: alpha arraysX: HTHH: HTHT: tri-helicalF: PF04545ECOD (1.6)
FPF04542,PF04546e3iydF3 A: alpha complex topologyX: Sigma2 domain-likeH: Sigma2 domain of RNA polymerase sigma factors (From Topology)T: Sigma2 domain of RNA polymerase sigma factorsF: PF04542,PF04546ECOD (1.6)
GPF00027e3iydG1 A: beta sandwichesX: jelly-rollH: Double-stranded beta-helix (From Topology)T: Double-stranded beta-helixF: PF00027ECOD (1.6)
GPF13545e3iydG2 A: alpha arraysX: HTHH: HTHT: wingedF: PF13545ECOD (1.6)
HPF00027e3iydH1 A: beta sandwichesX: jelly-rollH: Double-stranded beta-helix (From Topology)T: Double-stranded beta-helixF: PF00027ECOD (1.6)
HPF13545e3iydH2 A: alpha arraysX: HTHH: HTHT: wingedF: PF13545ECOD (1.6)

AMR Gene: CARD Annotation CARD Database Homepage

ChainsAccessionShort NameDescriptionProvenance Source (Version)
G, H
ARO:3000518CRPCRP is a global regulator that represses MdtEF multidrug efflux pump expression.CARD (3.2.9)

AMR Gene Family: CARD Annotation CARD Database Homepage

ChainsAccessionGene FamilyDrug Class Resistance MachanismProvenance Source (Version)
G, H
ARO:0010004resistance-nodulation-cell division (RND) antibiotic efflux pumpmacrolide antibiotic, fluoroquinolone antibiotic, penamantibiotic effluxCARD (3.2.9)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B
PF01193RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L)RNA polymerase Rpb3/Rpb11 dimerisation domainThe 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
A, B
PF01000RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac)RNA polymerase Rpb3/RpoA insert domainMembers of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaealDomain
A, B
PF03118Bacterial RNA polymerase, alpha chain C terminal domain (RNA_pol_A_CTD)Bacterial RNA polymerase, alpha chain C terminal domainThe 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
PF04561RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2)RNA polymerase Rpb2, domain 2RNA 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
PF10385RNA polymerase beta subunit external 1 domain (RNA_pol_Rpb2_45)RNA polymerase beta subunit external 1 domainRNA 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
PF04560RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7)RNA polymerase Rpb2, domain 7RNA 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
PF04565RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3)RNA polymerase Rpb2, domain 3RNA 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
PF04563RNA polymerase beta subunit (RNA_pol_Rpb2_1)RNA polymerase beta subunit- Family
PF00562RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6)RNA polymerase Rpb2, domain 6RNA 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
PF00623RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)RNA polymerase Rpb1, domain 2RNA 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
PF05000RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)RNA polymerase Rpb1, domain 4RNA 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
PF04983RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)RNA polymerase Rpb1, domain 3RNA 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
PF04998RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)RNA polymerase Rpb1, domain 5RNA 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
PF04997RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1)RNA polymerase Rpb1, domain 1RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp 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 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [1,2].
Domain
PF01192RNA polymerase Rpb6 (RNA_pol_Rpb6)RNA polymerase Rpb6- Family
PF04539Sigma-70 region 3 (Sigma70_r3)Sigma-70 region 3- Family
PF00140Sigma-70 factor, region 1.2 (Sigma70_r1_2)Sigma-70 factor, region 1.2- Family
PF04542Sigma-70 region 2 (Sigma70_r2)Sigma-70 region 2Region 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
PF04545Sigma-70, region 4 (Sigma70_r4)Sigma-70, region 4Region 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
PF04546Sigma-70, non-essential region (Sigma70_ner)Sigma-70, non-essential regionThe 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
G, H
PF13545Crp-like helix-turn-helix domain (HTH_Crp_2)Crp-like helix-turn-helix domainThis family represents a crp-like helix-turn-helix domain that is likely to bind DNA.Domain
G, H
PF00027Cyclic nucleotide-binding domain (cNMP_binding)Cyclic nucleotide-binding domainThis domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B
DNA-directed RNA polymerase subunit alpha
DNA-directed RNA polymerase subunit beta
DNA-directed RNA polymerase subunit beta
DNA-directed RNA polymerase subunit omega
RNA polymerase sigma factor rpoD
G, H
Catabolite gene activator
DNA (98-MER)---
DNA (98-MER)---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B
IPR011773DNA-directed RNA polymerase, alpha subunitFamily
A, B
IPR011260RNA polymerase, alpha subunit, C-terminalDomain
A, B
IPR011263DNA-directed RNA polymerase, RpoA/D/Rpb3-typeDomain
A, B
IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
A, B
IPR011262DNA-directed RNA polymerase, insert domainDomain
A, B
IPR036643DNA-directed RNA polymerase, insert domain superfamilyHomologous Superfamily
IPR007120DNA-directed RNA polymerase, subunit 2, hybrid-binding domainDomain
IPR007121RNA polymerase, beta subunit, conserved siteConserved Site
IPR014724RNA polymerase Rpb2, OB-foldHomologous Superfamily
IPR007642RNA polymerase Rpb2, domain 2Domain
IPR015712DNA-directed RNA polymerase, subunit 2Family
IPR037033DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamilyHomologous Superfamily
IPR042107DNA-directed RNA polymerase, beta subunit, external 1 domain superfamilyHomologous Superfamily
IPR037034RNA polymerase Rpb2, domain 2 superfamilyHomologous Superfamily
IPR007645RNA polymerase Rpb2, domain 3Domain
IPR019462DNA-directed RNA polymerase, beta subunit, external 1 domainDomain
IPR010243DNA-directed RNA polymerase beta subunit, bacterial-typeFamily
IPR007644RNA polymerase, beta subunit, protrusionDomain
IPR007641RNA polymerase Rpb2, domain 7Domain
IPR007081RNA polymerase Rpb1, domain 5Domain
IPR045867DNA-directed RNA polymerase, subunit beta-primeFamily
IPR007083RNA polymerase Rpb1, domain 4Domain
IPR044893RNA polymerase Rpb1, clamp domain superfamilyHomologous Superfamily
IPR006592RNA polymerase, N-terminalDomain
IPR007066RNA polymerase Rpb1, domain 3Domain
IPR012754DNA-directed RNA polymerase, subunit beta-prime, bacterial typeFamily
IPR042102RNA polymerase Rpb1, domain 3 superfamilyHomologous Superfamily
IPR000722RNA polymerase, alpha subunitDomain
IPR038120RNA polymerase Rpb1, funnel domain superfamilyHomologous Superfamily
IPR007080RNA polymerase Rpb1, domain 1Domain
IPR006110RNA polymerase, subunit omega/Rpo6/RPB6Family
IPR036161RPB6/omega subunit-like superfamilyHomologous Superfamily
IPR003716DNA-directed RNA polymerase, omega subunitFamily
IPR007627RNA polymerase sigma-70 region 2Domain
IPR007127RNA polymerase sigma factor 70, region 1.1Domain
IPR000943RNA polymerase sigma-70Domain
IPR013325RNA polymerase sigma factor, region 2Homologous Superfamily
IPR013324RNA polymerase sigma factor, region 3/4-likeHomologous Superfamily
IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
IPR012760RNA polymerase sigma factor RpoD, C-terminalDomain
IPR014284RNA polymerase sigma-70 like domainDomain
IPR009042RNA polymerase sigma-70 region 1.2Domain
IPR007630RNA polymerase sigma-70 region 4Domain
IPR007624RNA polymerase sigma-70 region 3Domain
IPR007631RNA polymerase sigma factor 70, non-essential domainDomain
IPR028630RNA polymerase sigma factor RpoDFamily
IPR042189Sigma-70 factor, region 1.1 superfamilyHomologous Superfamily
G, H
IPR000595Cyclic nucleotide-binding domainDomain
G, H
IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
G, H
IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
G, H
IPR012318Crp-type HTH domainDomain
G, H
IPR014710RmlC-like jelly roll foldHomologous Superfamily
G, H
IPR018488Cyclic nucleotide-binding, conserved siteConserved Site
G, H
IPR018335Transcription regulator HTH, Crp-type, conserved siteConserved Site
G, H
IPR018490Cyclic nucleotide-binding domain superfamilyHomologous Superfamily