4YLN,1I3Q,5FLM


Conserved Protein Domain Family
RNA_pol_L

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pfam01193: RNA_pol_L 
Click on image for an interactive view with Cn3D
RNA polymerase Rpb3/Rpb11 dimerization domain
The two eukaryotic subunits Rpb3 and Rpb11 dimerize to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerization domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some of the alpha subunits also contain iron-sulphur binding domains (pfam00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.
Statistics
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PSSM-Id: 334426
View PSSM: pfam01193
Aligned: 466 rows
Threshold Bit Score: 28.2556
Threshold Setting Gi: 503791734
Created: 16-Mar-2017
Updated: 23-May-2017
Structure
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Program:
Drawing:
Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
4YLN_A        36 EPLERGFGHTLGNALRRILLSSMPGCAVTEVEI---------DGVLHEYSTKEG-------------------------- 80  Escherichia coli
WP_011998219  14 RLLAKGYPLAVLNAIRRAALELAPKMAVDFIAVdrndstlfnEVLAHRLAMIPLrseealeryappeac-mectpeeaea 92  Ignicoccus hosp...
WP_014737205  14 RLLVRGVKLHVLNSIRRAILAEVPTMAVDYVVFmenssvfydEYIAHRLGLIPLtsenalgkykp--------peecrea 85  Thermogladius c...
ADM27042      14 EIAISGVPLPLLNALRRYALAKVPTYAVDEVMVvintshmfdEMLAHRIAMIPLrseealerikgldidvcykcgsdsed 93  Ignisphaera agg...
WP_011821708  15 RLYVEGFGLPLVNAIRRAAYSDVPVMAVDVVEVfenntvlydEIIAHRLGLIPLtskealqkyk----------rpeece 84  Hyperthermus bu...
WP_014026602  10 RVLIEGAPLAFVNALRRAAYTMVPVMAIDYVEFidnntvlydEILAHRLGLIPLdsreaiksykkpee--fqescidssg 87  Pyrolobus fumarii
ABK78166      15 SIRLRGVPLQYANALRRICLNGVPVFAVDTVDIventsvladEGLAHRLGLIPLrtdssef----------------knl 78  Cenarchaeum sym...
GAA27694      49 EFDMVHIDCSFANALRRILIAEVPSISIERVYLfqntsvmpdEVLCHRLGLIPLaivprhlifps---------rilpet 119 Clonorchis sine...
XP_018650440  51 EFDMINLDCSFANAVRRILVSEVPSLAIERVYVsqntsimpdEVMCHRLGLIPLavdpkyflfpt---------rkppas 121 Schistosoma man...
EHY64883      21 SFRVNQIEASVLNALRRTIISDTPSIAVHWVYIrenetvmadEILSHRLGLIPIladsstlkni----------vrsevl 90  Nematocida sp. ...
4YLN_A        81 ----VQEDILeILLNL------------KglavrvqgkD----------------------------EVIltlnksgigp 116 Escherichia coli
WP_011998219  93 dkcvVDGKPCyVRLYL------------Dasae-gkqiI-----------------------------VY---------- 120 Ignicoccus hosp...
WP_014737205  86 gekgVFSEDCfVKLEL------------SgegtpggvkT-----------------------------LY---------- 114 Thermogladius c...
ADM27042      94 kppsDVCEKCyVHMFL------------Eavae-dseyT-----------------------------VY---------- 121 Ignisphaera agg...
WP_011821708  85 kaelG-DPSCyVVLRL------------EvetgpreerI-----------------------------VY---------- 112 Hyperthermus bu...
WP_014026602  88 vpkfD-EPGCfATLTL------------EvetgvdevrM-----------------------------VY---------- 115 Pyrolobus fumarii
ABK78166      79 aeidPDDPINrVMLTLdsgeaaetrtvlSs--------------------------------------eLv--------- 111 Cenarchaeum sym...
GAA27694     120 deltEFNPMEhVIFDF------------Kv-------sFkksdlkgcsessgkefisdlnlpsvrssAVY---------- 170 Clonorchis sine...
XP_018650440 122 ddlsGFDPKEhLVYDL------------Cv-------gFthsskdshnkpek---dkddtlpvaqylPVY---------- 169 Schistosoma man...
EHY64883      91 dplaELTDENsIKMEL------------Nvent--tdkV-----------------------------LTv--------- 118 Nematocida sp. ...
4YLN_A       117 vtaadithdgdveivkpQ---------------------------HVICHLTdenasISMRIKVQ------RGRGYvpas 163 Escherichia coli
WP_011998219 121 -----------------Skdlksede-----------dvrpvyenIPVVPLI-----GDQKVKVIayarlgRGREH---- 163 Ignicoccus hosp...
WP_014737205 115 -----------------Agdlvtgdp-----------dvrpvyekIPIVQLL-----ENQRIKLEayarlgRGREH---- 157 Thermogladius c...
ADM27042     122 -----------------Ssdiksede-----------fvkpvygnIPIVILS-----PGQRISLElrarvgRGIEH---- 164 Ignisphaera agg...
WP_011821708 113 -----------------Sgdletsdp-----------dvrpvydnMPIVVMA-----PDQRLRLQayarlgYGREH---- 155 Hyperthermus bu...
WP_014026602 116 -----------------Sgdlqssdp-----------tvkpvypnIPIVLMA-----PGQRLHVRayarlgYGKEH---- 158 Pyrolobus fumarii
ABK78166     112 ----------------sEdssvk-----------------pisdtIPIVELA-----PGQRIKVEayarlgRGTEH---- 149 Cenarchaeum sym...
GAA27694     171 -----------------Sselkwvplpgqee-lfgedqptvvsphILINKLA-----VGDEIEARcvavkgVGRDH---- 223 Clonorchis sine...
XP_018650440 170 -----------------SsdlkwiplagqedhfninnppipvsstILINKLA-----LGDEIEARcvavkgIGRDH---- 223 Schistosoma man...
EHY64883     119 ----------------rSndikivsn-----------tkttlkqnVIITRLA-----PGKRIECKmlavvgTGREH---- 162 Nematocida sp. ...
4YLN_A       164 trihseederpigrllvdACYSPV-------------------------------------------------------- 187 Escherichia coli
WP_011998219 164 ------------------AKWMPAtvsivkpllkgisvkeglcdaecqkecaekcke----afvmkdgkltlkegttlsm 221 Ignicoccus hosp...
WP_014737205 158 ------------------IKWSPAsvashkyiakinidrekcrypgckkcveicpkq---vivekdgtveveearlmdcs 216 Thermogladius c...
ADM27042     165 ------------------IKWSPAtiavtryvadirisedlcnlckkcievcpkn-------vltvyqnriqvkdkyeci 219 Ignisphaera agg...
WP_011821708 156 ------------------AKWMPVsvaahrylpilefnldemsdecirciesgypela-akiremrsgsiavvedvntsg 216 Hyperthermus bu...
WP_014026602 159 ------------------AKWFPVsvaahrylpvlefdpkhekandciecieefapevaeklrnmkekgrieileevrss 220 Pyrolobus fumarii
ABK78166     150 ------------------AKWNSSnvsv---------------------------------------------------- 159 Cenarchaeum sym...
GAA27694     224 ------------------AKFSPVaaayykflpvikllrpiegdearllqrsfahgvi--gidpkteqayilnarldngs 283 Clonorchis sine...
XP_018650440 224 ------------------AKFSPVaaayykfhpiikllrtiegeqaiklqksfasgvi--ginsktgqafvdnarldngs 283 Schistosoma man...
EHY64883     163 ------------------AKWMPTsvcyyrsikklemkdiskameiqkyfrdg------------faiengkpvidedrl 212 Nematocida sp. ...
4YLN_A       188 -------------ERIAynveaarveqrTDLDKLVIEMETNGTID--PEEAIRRAATILAEQL 235 Escherichia coli
WP_011998219 222 vmycieyvcegkgIRPV-----------FEEDTYLFELESDGSLS--ARRTLVEAAKAVVEKL 271 Ignicoccus hospitalis
WP_014737205 217 lcrlcetvcpseaINVS-----------YKEDEYILYFESTGSLT--PKRILIEATRALEDKL 266 Thermogladius cellulolyticus
ADM27042     220 lckqcmyacptkaIDVS-----------YRDNEYILVIESSGALE--PETILRESIGILLNEL 269 Ignisphaera aggregans DSM 17230
WP_011821708 217 lywcvqrrcggkgVKLV-----------YDDKRFILKIESTGALP--PEDIVREAARAIVRKA 266 Hyperthermus butylicus
WP_014026602 221 tllwcvkkrcgdaAKLE-----------FDSNKLILTIESVGQLP--ARDILVLASDAIKRKA 270 Pyrolobus fumarii
ABK78166     160 ----------ltaT--------------DKEDERILTIESTGAMD--PAQLVLEGVTELSRRL 196 Cenarchaeum symbiosum A
GAA27694     284 rehmrhpqfrddaVFVG-----------VDSSHCIFTVESIAPSQrpPARLVRSAIEVMIEKC 335 Clonorchis sinensis
XP_018650440 284 rehmrhpefrddvIFVG-----------MDSSHCIFTVETIAPGSrpPSSLVRCALGVMISKC 335 Schistosoma mansoni
EHY64883     213 lvnmdieknypneIKVR-----------AEPDSFFFEIEAI---AnsPKSILKKGLGILKNKL 261 Nematocida sp. 1 ERTm2
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