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Conserved domains on  [gi|558518673|gb|AHA59760|]
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RNA polymerase II largest subunit, partial [Holtermanniella festucosa]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNA_pol_Rpb1_1 super family cl29786
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-216 4.00e-61

RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization 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.


The actual alignment was detected with superfamily member pfam04997:

Pssm-ID: 398595  Cd Length: 320  Bit Score: 193.66  E-value: 4.00e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673    1 VFRQGFMVKVKKILECICVNCGKLKVDMSDPEVNDIARRVKA----QHRLKRIWERAKGVKDCKPDDAPEegadadevvp 76
Cdd:pfam04997  80 VFHIGFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGlenlKMGAKAILELCKKKDLCEHCGGKN---------- 149

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673   77 ghGGCGHKQPDIRKEALKLYANYKLEKDEDADRDakaetdkqlLQPSQVLSILRKIPSNDLLIMGLSEEFARPDWMILTI 156
Cdd:pfam04997 150 --GVCGSQQPVSRKEGLKLKAAIKKSKEEEEKEI---------LNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTV 218

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673  157 LPVPPATVRPSVQQGAGQRSEDDLTHKLFDIIRSSSTVRRLEQEGAPAHIVNEHFDMLQY 216
Cdd:pfam04997 219 LPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQE 278
 
Name Accession Description Interval E-value
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-216 4.00e-61

RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization 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.


Pssm-ID: 398595  Cd Length: 320  Bit Score: 193.66  E-value: 4.00e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673    1 VFRQGFMVKVKKILECICVNCGKLKVDMSDPEVNDIARRVKA----QHRLKRIWERAKGVKDCKPDDAPEegadadevvp 76
Cdd:pfam04997  80 VFHIGFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGlenlKMGAKAILELCKKKDLCEHCGGKN---------- 149

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673   77 ghGGCGHKQPDIRKEALKLYANYKLEKDEDADRDakaetdkqlLQPSQVLSILRKIPSNDLLIMGLSEEFARPDWMILTI 156
Cdd:pfam04997 150 --GVCGSQQPVSRKEGLKLKAAIKKSKEEEEKEI---------LNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTV 218

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673  157 LPVPPATVRPSVQQGAGQRSEDDLTHKLFDIIRSSSTVRRLEQEGAPAHIVNEHFDMLQY 216
Cdd:pfam04997 219 LPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQE 278
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
 117-216 1.65e-44

Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.


Pssm-ID: 259848 [Multi-domain]  Cd Length: 751  Bit Score: 157.70  E-value: 1.65e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673 117 KQLLQPSQVLSILRKIPSNDLLIMGLSEEFARPDWMILTILPVPPATVRPSVQQGAGQRSEDDLTHKLFDIIRSSSTVRR 196
Cdd:cd02733   93 KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPPPAVRPSVVMDGSARSEDDLTHKLADIIKANNQLKR 172

                         90       100
                 ....*....|....*....|
gi 558518673 197 LEQEGAPAHIVNEHFDMLQY 216
Cdd:cd02733  173 QEQNGAPAHIIEEDEQLLQF 192
PRK08566 PRK08566
DNA-directed RNA polymerase subunit A'; Validated
 5-216 1.64e-41

DNA-directed RNA polymerase subunit A'; Validated


Pssm-ID: 236292 [Multi-domain]  Cd Length: 882  Bit Score: 149.62  E-value: 1.64e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673   5 GFMVKVKKILECICVNCGKLKvdMSDPEVNDIARRVKaqhRLKRIWERAKGVKDCKPDDAPEEgadadEVVPgHggCGHK 84
Cdd:PRK08566  88 GFAKLIYKLLRATCRECGRLK--LTEEEIEEYLEKLE---RLKEWGSLADDLIKEVKKEAAKR-----MVCP-H--CGEK 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673  85 QPDIRKEalKLYANYklEKDEDADRDakaetdkqlLQPSQVLSILRKIPSNDLLIMGLSEEFARPDWMILTILPVPPATV 164
Cdd:PRK08566 155 QYKIKFE--KPTTFY--EERKEGLVK---------LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTVLPVPPVTV 221

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 558518673 165 RPSVQQGAGQRSEDDLTHKLFDIIRSSSTVRRLEQEGAPAHIVNEHFDMLQY 216
Cdd:PRK08566 222 RPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQY 273
RNA_pol_rpoA1 TIGR02390
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
 1-216 6.93e-39

DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.


Pssm-ID: 274106 [Multi-domain]  Cd Length: 868  Bit Score: 142.16  E-value: 6.93e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673    1 VFRQGFMVKVKKILECICVNCGKLKVdmsdPEvNDIARRVKAQHRLKRIWERAKgvkDCKPDDAPEEGADADeVVPgHgg 80
Cdd:TIGR02390  79 VVHVGFAKEIYKILRATCRKCGRITL----TE-EEIEQYLEKINKLKEEGGDLA---STLIEKIVKEAAKRM-KCP-H-- 146

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673   81 CGHKQPDIRKEalKLYANYKLEKDEDADrdakaetdkqlLQPSQVLSILRKIPSNDLLIMGLSEEFARPDWMILTILPVP 160
Cdd:TIGR02390 147 CGEEQKKIKFE--KPTYFYEEGKEGDVK-----------LTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTVLPVP 213

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 558518673  161 PATVRPSVQQGAGQRSEDDLTHKLFDIIRSSSTVRRLEQEGAPAHIVNEHFDMLQY 216
Cdd:TIGR02390 214 PVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQY 269
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
 148-215 1.31e-06

DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439856 [Multi-domain]  Cd Length: 1165  Bit Score: 48.23  E-value: 1.31e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 558518673  148 RPDWMILTILPVPPATVRPSVQQGAGQRSEDDLTHKLFDIIRSSSTVRRLEQEGAPAHIVNEHFDMLQ 215
Cdd:COG0086   223 RPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQ 290
 
Name Accession Description Interval E-value
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-216 4.00e-61

RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization 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.


Pssm-ID: 398595  Cd Length: 320  Bit Score: 193.66  E-value: 4.00e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673    1 VFRQGFMVKVKKILECICVNCGKLKVDMSDPEVNDIARRVKA----QHRLKRIWERAKGVKDCKPDDAPEegadadevvp 76
Cdd:pfam04997  80 VFHIGFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGlenlKMGAKAILELCKKKDLCEHCGGKN---------- 149

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673   77 ghGGCGHKQPDIRKEALKLYANYKLEKDEDADRDakaetdkqlLQPSQVLSILRKIPSNDLLIMGLSEEFARPDWMILTI 156
Cdd:pfam04997 150 --GVCGSQQPVSRKEGLKLKAAIKKSKEEEEKEI---------LNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTV 218

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673  157 LPVPPATVRPSVQQGAGQRSEDDLTHKLFDIIRSSSTVRRLEQEGAPAHIVNEHFDMLQY 216
Cdd:pfam04997 219 LPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQE 278
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
 117-216 1.65e-44

Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.


Pssm-ID: 259848 [Multi-domain]  Cd Length: 751  Bit Score: 157.70  E-value: 1.65e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673 117 KQLLQPSQVLSILRKIPSNDLLIMGLSEEFARPDWMILTILPVPPATVRPSVQQGAGQRSEDDLTHKLFDIIRSSSTVRR 196
Cdd:cd02733   93 KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPPPAVRPSVVMDGSARSEDDLTHKLADIIKANNQLKR 172

                         90       100
                 ....*....|....*....|
gi 558518673 197 LEQEGAPAHIVNEHFDMLQY 216
Cdd:cd02733  173 QEQNGAPAHIIEEDEQLLQF 192
PRK08566 PRK08566
DNA-directed RNA polymerase subunit A'; Validated
 5-216 1.64e-41

DNA-directed RNA polymerase subunit A'; Validated


Pssm-ID: 236292 [Multi-domain]  Cd Length: 882  Bit Score: 149.62  E-value: 1.64e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673   5 GFMVKVKKILECICVNCGKLKvdMSDPEVNDIARRVKaqhRLKRIWERAKGVKDCKPDDAPEEgadadEVVPgHggCGHK 84
Cdd:PRK08566  88 GFAKLIYKLLRATCRECGRLK--LTEEEIEEYLEKLE---RLKEWGSLADDLIKEVKKEAAKR-----MVCP-H--CGEK 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673  85 QPDIRKEalKLYANYklEKDEDADRDakaetdkqlLQPSQVLSILRKIPSNDLLIMGLSEEFARPDWMILTILPVPPATV 164
Cdd:PRK08566 155 QYKIKFE--KPTTFY--EERKEGLVK---------LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTVLPVPPVTV 221

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 558518673 165 RPSVQQGAGQRSEDDLTHKLFDIIRSSSTVRRLEQEGAPAHIVNEHFDMLQY 216
Cdd:PRK08566 222 RPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQY 273
RNAP_archeal_A' cd02582
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
 5-216 8.32e-40

A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.


Pssm-ID: 259846 [Multi-domain]  Cd Length: 861  Bit Score: 144.70  E-value: 8.32e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673   5 GFMVKVKKILECICVNCGKLKVdmsdPEvNDIARRVKAQHRLKRIWERAKGvkdcKPDDAPEEGADADEVVPgHggCGHK 84
Cdd:cd02582   83 GFAKHIYDLLRATCRSCGRILL----PE-EEIEKYLERIRRLKEKWPELVK----RVIEKVKKKAKKRKVCP-H--CGAP 150

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673  85 QPDIRKEalKLYaNYKLEKDEDADRdakaetdkqlLQPSQVLSILRKIPSNDLLIMGLSEEFARPDWMILTILPVPPATV 164
Cdd:cd02582  151 QYKIKLE--KPT-TFYEEKEEGEVK----------LTPSEIRERLEKIPDEDLELLGIDPKTARPEWMVLTVLPVPPVTV 217

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 558518673 165 RPSVQQGAGQRSEDDLTHKLFDIIRSSstvRRLEQE---GAPAHIVNEHFDMLQY 216
Cdd:cd02582  218 RPSITLETGERSEDDLTHKLVDIIRIN---QRLKENieaGAPQLIIEDLWDLLQY 269
RNA_pol_rpoA1 TIGR02390
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
 1-216 6.93e-39

DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.


Pssm-ID: 274106 [Multi-domain]  Cd Length: 868  Bit Score: 142.16  E-value: 6.93e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673    1 VFRQGFMVKVKKILECICVNCGKLKVdmsdPEvNDIARRVKAQHRLKRIWERAKgvkDCKPDDAPEEGADADeVVPgHgg 80
Cdd:TIGR02390  79 VVHVGFAKEIYKILRATCRKCGRITL----TE-EEIEQYLEKINKLKEEGGDLA---STLIEKIVKEAAKRM-KCP-H-- 146

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673   81 CGHKQPDIRKEalKLYANYKLEKDEDADrdakaetdkqlLQPSQVLSILRKIPSNDLLIMGLSEEFARPDWMILTILPVP 160
Cdd:TIGR02390 147 CGEEQKKIKFE--KPTYFYEEGKEGDVK-----------LTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTVLPVP 213

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 558518673  161 PATVRPSVQQGAGQRSEDDLTHKLFDIIRSSSTVRRLEQEGAPAHIVNEHFDMLQY 216
Cdd:TIGR02390 214 PVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQY 269
PRK14977 PRK14977
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
 1-216 5.59e-31

bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional


Pssm-ID: 184940 [Multi-domain]  Cd Length: 1321  Bit Score: 119.36  E-value: 5.59e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673    1 VFRQGFMVKVKKILECICVNCGKLKVDMSDPEVNDIARRVKAQHRL---KRIwerakgvkdckPDDAPEEGADADEV-VP 76
Cdd:PRK14977   84 VIHIAFIDNIKDLLNSTCHKCAKLKLPQEDLNVFKLIEEAHAAARDipeKRI-----------DDEIIEEVRDQVKVyAK 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673   77 GHGGCGHKQPDIrkealklyanYKLEKDEDADRDAKAETDKQLLQPSQVLSILRKIPSNDLLIMGLSEEFARPDWMILTI 156
Cdd:PRK14977  153 KAKECPHCGAPQ----------HELEFEEPTIFIEKTEIEEHRLLPIEIRDIFEKIIDDDLELIGFDPKKARPEWAVLQA 222

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673  157 LPVPPATVRPSVQQGAGQRSEDDLTHKLFDIIRSSSTVRRLEQEGAPAHIVNEHFDMLQY 216
Cdd:PRK14977  223 FLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQY 282
RNAP_III_RPC1_N cd02583
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
 1-215 2.36e-24

Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 (C160) subunit forms part of the active site region of RNAP III. RNAP III is one of the three distinct classes of nuclear RNAP in eukaryotes that is responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA genes, and some others. RNAP III is the largest nuclear RNA polymerase with 17 subunits. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site, making up the head and core of the one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between Rpc1 and Rpb1 suggests a similar functional and structural role.


Pssm-ID: 259847 [Multi-domain]  Cd Length: 816  Bit Score: 100.32  E-value: 2.36e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673   1 VFRQGFMVKVKKILECICVNCGKLKVDMSDPEV------NDIARRVKAQHRLKRIWERAKGVKDCKpddapeegadadev 74
Cdd:cd02583   69 VFHIGYFKAIINILQCICKTCSRVLLPEEEKRKflkrlrRPNLDNLQKKALKKKILEKCKKVRKCP-------------- 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673  75 vpgHggCGHKQpdirkealklyanyklekdedadrdaKAETDkqlLQPSQVLSILRKIPSNDLLIMGLSEEFARPDWMIL 154
Cdd:cd02583  135 ---H--CGLLK--------------------------KAQED---LNPLKVLNLFKNIPPEDVELLLMNPLAGRPENLIL 180

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 558518673 155 TILPVPPATVRPSVQQGAGQRS-EDDLTHKLFDIIRSSSTVRRLEQEGAPAHIVNEHFDMLQ 215
Cdd:cd02583  181 TRIPVPPLCIRPSVVMDEKSGTnEDDLTVKLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQ 242
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
148-215 1.65e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 51.08  E-value: 1.65e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 558518673  148 RPDWMILTILPVPPATVRPSVQQGAGQRSEDDLTHKLFDIIRSSSTVRRLEQEGAPAHIVNEHFDMLQ 215
Cdd:PRK09603 1622 RPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQ 1689
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
148-215 2.34e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 50.78  E-value: 2.34e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 558518673  148 RPDWMILTILPVPPATVRPSVQQGAGQRSEDDLTHKLFDIIRSSSTVRRLEQEGAPAHIVNEHFDMLQ 215
Cdd:PRK14844 1665 RPEWMILTTIPILPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQ 1732
rpoC1 PRK02625
DNA-directed RNA polymerase subunit gamma; Provisional
 147-215 3.30e-07

DNA-directed RNA polymerase subunit gamma; Provisional


Pssm-ID: 235055 [Multi-domain]  Cd Length: 627  Bit Score: 50.13  E-value: 3.30e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 558518673 147 ARPDWMILTILPVPPATVRPSVQQGAGQRSEDDLTHKLFDIIRSSSTVRRLEQEGAPAHIVNEHFDMLQ 215
Cdd:PRK02625 240 SRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQ 308
RNAP_beta'_N cd01609
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
 122-215 7.54e-07

Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; Beta' is the largest subunit of bacterial DNA-dependent RNA polymerase (RNAP). This family also includes the eukaryotic plastid-encoded RNAP beta' subunit. Bacterial RNAP is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. Structure studies suggest that RNA polymerase complexes from different organisms share a crab-claw-shaped structure with two "pincers" defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. Beta' contains part of the active site and binds two zinc ions that have a structural role in the formation of the active polymerase.


Pssm-ID: 259845 [Multi-domain]  Cd Length: 659  Bit Score: 49.05  E-value: 7.54e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 558518673 122 PSqVLSILRKIPSNDL--LIMGLSEEF----ARPDWMILTILPVPPATVRPSVQQGAGQRSEDDLTHKLFDIIRSSSTVR 195
Cdd:cd01609  107 PS-RIGLLLDLSPKDLerVIYFVVESFrksgNRPEWMILTVLPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLK 185

                         90       100
                 ....*....|....*....|.
gi 558518673 196 RLEQEGAPAHIV-NEHfDMLQ 215
Cdd:cd01609  186 KLLELGAPEIIVrNEK-RMLQ 205
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
 148-215 1.31e-06

DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439856 [Multi-domain]  Cd Length: 1165  Bit Score: 48.23  E-value: 1.31e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 558518673  148 RPDWMILTILPVPPATVRPSVQQGAGQRSEDDLTHKLFDIIRSSSTVRRLEQEGAPAHIVNEHFDMLQ 215
Cdd:COG0086   223 RPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQ 290
PRK14906 PRK14906
DNA-directed RNA polymerase subunit beta';
148-215 5.48e-06

DNA-directed RNA polymerase subunit beta';


Pssm-ID: 184899 [Multi-domain]  Cd Length: 1460  Bit Score: 46.40  E-value: 5.48e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 558518673  148 RPDWMILTILPVPPATVRPSVQQGAGQRSEDDLTHKLFDIIRSSSTVRRLEQEGAPAHIVNEHFDMLQ 215
Cdd:PRK14906  311 DPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQ 378
RNAP_largest_subunit_N cd00399
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
 145-168 7.50e-05

Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.


Pssm-ID: 259843 [Multi-domain]  Cd Length: 528  Bit Score: 42.80  E-value: 7.50e-05
                         10        20
                 ....*....|....*....|....
gi 558518673 145 EFARPDWMILTILPVPPATVRPSV 168
Cdd:cd00399   80 SFLGPEWMILTCLPVPPPCLRPSV 103
rpoC1 CHL00018
RNA polymerase beta' subunit
 136-180 1.50e-04

RNA polymerase beta' subunit


Pssm-ID: 214336 [Multi-domain]  Cd Length: 663  Bit Score: 42.20  E-value: 1.50e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 558518673 136 DLLI--MGLSEEFAR----PDWMILTILPVPPATVRPSVQQGAGQRSEDDL 180
Cdd:CHL00018 242 DFLVrrIKLAKHFIRtniePEWMVLCLLPVLPPELRPIIQLDGGKLMSSDL 292
PRK00566 PRK00566
DNA-directed RNA polymerase subunit beta'; Provisional
 148-215 6.67e-04

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 234794 [Multi-domain]  Cd Length: 1156  Bit Score: 40.05  E-value: 6.67e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 558518673  148 RPDWMILTILPVPPATVRPSVQQGAGQRSEDDLThklfD-----IIRSSStVRRLEQEGAPAHIVNEHFDMLQ 215
Cdd:PRK00566  223 KPEWMILDVLPVIPPDLRPLVQLDGGRFATSDLN----DlyrrvINRNNR-LKRLLELGAPEIIVRNEKRMLQ 290
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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