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Conserved domains on  [gi|169247244|gb|ACA51513|]
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RNA polymerase II largest subunit, partial [Metschnikowia agaves]

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 ...
 1-226 2.20e-78

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: 237.96  E-value: 2.20e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244    1 HFGHIELAKPVFHIGFISKIKKVCECVCMHCGKLLVDDLNP------LMAQAIhiRDPKKRFNAVWNVCKTKMVCEADTI 74
Cdd:pfam04997  70 HFGHIELAKPVFHIGFFKKTLKILECVCKYCSKLLLDPGKPklfnkdKKRLGL--ENLKMGAKAILELCKKKDLCEHCGG 147

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244   75 NEegqvtsgrGGCGHTQPTVRRDGLKLWGTWKQNKsydenEQPERRLLTPSEILSVFRHISPEDCHKLGFNEDYARPEWM 154
Cdd:pfam04997 148 KN--------GVCGSQQPVSRKEGLKLKAAIKKSK-----EEEEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWM 214

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 169247244  155 LITVLPVPPPPVRPSIAFNDTARGEDDLTFKLADILKANINVQRLEIDGSPQHVISEFEALLQFHVATYMDN 226
Cdd:pfam04997 215 ILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDN 286
 
Name Accession Description Interval E-value
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-226 2.20e-78

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: 237.96  E-value: 2.20e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244    1 HFGHIELAKPVFHIGFISKIKKVCECVCMHCGKLLVDDLNP------LMAQAIhiRDPKKRFNAVWNVCKTKMVCEADTI 74
Cdd:pfam04997  70 HFGHIELAKPVFHIGFFKKTLKILECVCKYCSKLLLDPGKPklfnkdKKRLGL--ENLKMGAKAILELCKKKDLCEHCGG 147

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244   75 NEegqvtsgrGGCGHTQPTVRRDGLKLWGTWKQNKsydenEQPERRLLTPSEILSVFRHISPEDCHKLGFNEDYARPEWM 154
Cdd:pfam04997 148 KN--------GVCGSQQPVSRKEGLKLKAAIKKSK-----EEEEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWM 214

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 169247244  155 LITVLPVPPPPVRPSIAFNDTARGEDDLTFKLADILKANINVQRLEIDGSPQHVISEFEALLQFHVATYMDN 226
Cdd:pfam04997 215 ILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDN 286
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
 1-226 7.38e-54

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: 183.89  E-value: 7.38e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244   1 HFGHIELAKPVFHIGFISKIKKVCECVCmhcgkllvddlnplmaqaihirdpkkrfnavwnvcktkmvceadtineegqv 80
Cdd:cd02733   65 HFGHIELAKPVFHIGFLTKILKILRCVC---------------------------------------------------- 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244  81 tsgrggcghtqptvrrdglklwgtwkqnksydeneqpeRRLLTPSEILSVFRHISPEDCHKLGFNEDYARPEWMLITVLP 160
Cdd:cd02733   93 --------------------------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLP 134

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 169247244 161 VPPPPVRPSIAFNDTARGEDDLTFKLADILKANINVQRLEIDGSPQHVISEFEALLQFHVATYMDN 226
Cdd:cd02733  135 VPPPAVRPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDN 200
RNA_pol_rpoA1 TIGR02390
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
 1-226 5.02e-41

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: 148.71  E-value: 5.02e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244    1 HFGHIELAKPVFHIGFISKIKKVCECVCMHCGKLLVDDlnplmaqaIHIRDPKKRFNAVWNvcKTKMVCE--ADTINEEG 78
Cdd:TIGR02390  69 HFGHIELARPVVHVGFAKEIYKILRATCRKCGRITLTE--------EEIEQYLEKINKLKE--EGGDLAStlIEKIVKEA 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244   79 QVTSGRGGCGHTQPTVRRDglKLWgtwkqnkSYDENEQPERRLLTPSEILSVFRHISPEDCHKLGFNEDYARPEWMLITV 158
Cdd:TIGR02390 139 AKRMKCPHCGEEQKKIKFE--KPT-------YFYEEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTV 209

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 169247244  159 LPVPPPPVRPSIAFNDTARGEDDLTFKLADILKANinvQRLEID---GSPQHVISEFEALLQFHVATYMDN 226
Cdd:TIGR02390 210 LPVPPVTVRPSITLETGERSEDDLTHKLVDIIRIN---QRLKENieaGAPQLIIEDLWELLQYHVATYFDN 277
PRK08566 PRK08566
DNA-directed RNA polymerase subunit A'; Validated
 1-226 5.33e-41

DNA-directed RNA polymerase subunit A'; Validated


Pssm-ID: 236292 [Multi-domain]  Cd Length: 882  Bit Score: 148.47  E-value: 5.33e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244   1 HFGHIELAKPVFHIGFISKIKKVCECVCMHCGKLLVDDLN-----PLMAQAIHIRDPKKRF-NAVWNVCKTKMVCEAdti 74
Cdd:PRK08566  74 HFGHIELARPVIHVGFAKLIYKLLRATCRECGRLKLTEEEieeylEKLERLKEWGSLADDLiKEVKKEAAKRMVCPH--- 150

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244  75 neegqvtsgrggCGHTQPTVRRDglKLWgtwkqnkSYDENEQPERRLLTPSEILSVFRHISPEDCHKLGFNEDYARPEWM 154
Cdd:PRK08566 151 ------------CGEKQYKIKFE--KPT-------TFYEERKEGLVKLTPSDIRERLEKIPDEDLELLGINPEVARPEWM 209

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 169247244 155 LITVLPVPPPPVRPSIAFNDTARGEDDLTFKLADILKANinvQRLE--ID-GSPQHVISEFEALLQFHVATYMDN 226
Cdd:PRK08566 210 VLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRIN---QRLKenIEaGAPQLIIEDLWELLQYHVTTYFDN 281
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
 2-16 3.27e-03

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: 38.22  E-value: 3.27e-03
                          10
                  ....*....|....*
gi 169247244    2 FGHIELAKPVFHIGF 16
Cdd:COG0086    92 MGHIELAMPVFHIWG 106
 
Name Accession Description Interval E-value
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-226 2.20e-78

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: 237.96  E-value: 2.20e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244    1 HFGHIELAKPVFHIGFISKIKKVCECVCMHCGKLLVDDLNP------LMAQAIhiRDPKKRFNAVWNVCKTKMVCEADTI 74
Cdd:pfam04997  70 HFGHIELAKPVFHIGFFKKTLKILECVCKYCSKLLLDPGKPklfnkdKKRLGL--ENLKMGAKAILELCKKKDLCEHCGG 147

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244   75 NEegqvtsgrGGCGHTQPTVRRDGLKLWGTWKQNKsydenEQPERRLLTPSEILSVFRHISPEDCHKLGFNEDYARPEWM 154
Cdd:pfam04997 148 KN--------GVCGSQQPVSRKEGLKLKAAIKKSK-----EEEEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWM 214

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 169247244  155 LITVLPVPPPPVRPSIAFNDTARGEDDLTFKLADILKANINVQRLEIDGSPQHVISEFEALLQFHVATYMDN 226
Cdd:pfam04997 215 ILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDN 286
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
 1-226 7.38e-54

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: 183.89  E-value: 7.38e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244   1 HFGHIELAKPVFHIGFISKIKKVCECVCmhcgkllvddlnplmaqaihirdpkkrfnavwnvcktkmvceadtineegqv 80
Cdd:cd02733   65 HFGHIELAKPVFHIGFLTKILKILRCVC---------------------------------------------------- 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244  81 tsgrggcghtqptvrrdglklwgtwkqnksydeneqpeRRLLTPSEILSVFRHISPEDCHKLGFNEDYARPEWMLITVLP 160
Cdd:cd02733   93 --------------------------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLP 134

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 169247244 161 VPPPPVRPSIAFNDTARGEDDLTFKLADILKANINVQRLEIDGSPQHVISEFEALLQFHVATYMDN 226
Cdd:cd02733  135 VPPPAVRPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDN 200
RNA_pol_rpoA1 TIGR02390
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
 1-226 5.02e-41

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: 148.71  E-value: 5.02e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244    1 HFGHIELAKPVFHIGFISKIKKVCECVCMHCGKLLVDDlnplmaqaIHIRDPKKRFNAVWNvcKTKMVCE--ADTINEEG 78
Cdd:TIGR02390  69 HFGHIELARPVVHVGFAKEIYKILRATCRKCGRITLTE--------EEIEQYLEKINKLKE--EGGDLAStlIEKIVKEA 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244   79 QVTSGRGGCGHTQPTVRRDglKLWgtwkqnkSYDENEQPERRLLTPSEILSVFRHISPEDCHKLGFNEDYARPEWMLITV 158
Cdd:TIGR02390 139 AKRMKCPHCGEEQKKIKFE--KPT-------YFYEEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTV 209

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 169247244  159 LPVPPPPVRPSIAFNDTARGEDDLTFKLADILKANinvQRLEID---GSPQHVISEFEALLQFHVATYMDN 226
Cdd:TIGR02390 210 LPVPPVTVRPSITLETGERSEDDLTHKLVDIIRIN---QRLKENieaGAPQLIIEDLWELLQYHVATYFDN 277
PRK08566 PRK08566
DNA-directed RNA polymerase subunit A'; Validated
 1-226 5.33e-41

DNA-directed RNA polymerase subunit A'; Validated


Pssm-ID: 236292 [Multi-domain]  Cd Length: 882  Bit Score: 148.47  E-value: 5.33e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244   1 HFGHIELAKPVFHIGFISKIKKVCECVCMHCGKLLVDDLN-----PLMAQAIHIRDPKKRF-NAVWNVCKTKMVCEAdti 74
Cdd:PRK08566  74 HFGHIELARPVIHVGFAKLIYKLLRATCRECGRLKLTEEEieeylEKLERLKEWGSLADDLiKEVKKEAAKRMVCPH--- 150

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244  75 neegqvtsgrggCGHTQPTVRRDglKLWgtwkqnkSYDENEQPERRLLTPSEILSVFRHISPEDCHKLGFNEDYARPEWM 154
Cdd:PRK08566 151 ------------CGEKQYKIKFE--KPT-------TFYEERKEGLVKLTPSDIRERLEKIPDEDLELLGINPEVARPEWM 209

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 169247244 155 LITVLPVPPPPVRPSIAFNDTARGEDDLTFKLADILKANinvQRLE--ID-GSPQHVISEFEALLQFHVATYMDN 226
Cdd:PRK08566 210 VLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRIN---QRLKenIEaGAPQLIIEDLWELLQYHVTTYFDN 281
RNAP_archeal_A' cd02582
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
 1-226 6.20e-41

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: 148.16  E-value: 6.20e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244   1 HFGHIELAKPVFHIGFISKIKKVCECVCMHCGKLLVDD------LNPLMAQAIHIRDPKKRF-NAVWNVCKTKMVCEAdt 73
Cdd:cd02582   69 HFGHIELARPVIHVGFAKHIYDLLRATCRSCGRILLPEeeiekyLERIRRLKEKWPELVKRViEKVKKKAKKRKVCPH-- 146

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244  74 ineegqvtsgrggCGHTQPTVRRDglklwgtwKQNKSYDENEQPERRLlTPSEILSVFRHISPEDCHKLGFNEDYARPEW 153
Cdd:cd02582  147 -------------CGAPQYKIKLE--------KPTTFYEEKEEGEVKL-TPSEIRERLEKIPDEDLELLGIDPKTARPEW 204

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 169247244 154 MLITVLPVPPPPVRPSIAFNDTARGEDDLTFKLADILKANinvQRLEID---GSPQHVISEFEALLQFHVATYMDN 226
Cdd:cd02582  205 MVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRIN---QRLKENieaGAPQLIIEDLWDLLQYHVTTYFDN 277
PRK14977 PRK14977
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
 1-226 6.44e-33

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


Pssm-ID: 184940 [Multi-domain]  Cd Length: 1321  Bit Score: 125.52  E-value: 6.44e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244    1 HFGHIELAKPVFHIGFISKIKKVCECVCMHCGKLLV--DDLNPLmaQAIhirdpkKRFNAVWNVCKTKMVCE--ADTINE 76
Cdd:PRK14977   74 HFGHIELAEPVIHIAFIDNIKDLLNSTCHKCAKLKLpqEDLNVF--KLI------EEAHAAARDIPEKRIDDeiIEEVRD 145

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244   77 EGQVTSGRGG-CGHTQPTVRRdgLKLWGTWKqnksYDENEQPERRLLTPSEILSVFRHISPEDCHKLGFNEDYARPEWML 155
Cdd:PRK14977  146 QVKVYAKKAKeCPHCGAPQHE--LEFEEPTI----FIEKTEIEEHRLLPIEIRDIFEKIIDDDLELIGFDPKKARPEWAV 219

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 169247244  156 ITVLPVPPPPVRPSIAFNDTARGEDDLTFKLADILKANINVQRLEIDGSPQHVISEFEALLQFHVATYMDN 226
Cdd:PRK14977  220 LQAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDN 290
RNAP_III_RPC1_N cd02583
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
 1-225 1.01e-22

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: 95.69  E-value: 1.01e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244   1 HFGHIELAKPVFHIGFISKIKKVCECVCMHCGKLLVDD------LNPLMAqaiHIRDPKKR---FNAVWNVCKTKMVCEA 71
Cdd:cd02583   59 HFGYIKLELPVFHIGYFKAIINILQCICKTCSRVLLPEeekrkfLKRLRR---PNLDNLQKkalKKKILEKCKKVRKCPH 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169247244  72 dtineegqvtsgrggCGHTqptvrrdglklwgtwkqNKSYDEneqperrlLTPSEILSVFRHISPEDCHKLGFNEDYARP 151
Cdd:cd02583  136 ---------------CGLL-----------------KKAQED--------LNPLKVLNLFKNIPPEDVELLLMNPLAGRP 175

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 169247244 152 EWMLITVLPVPPPPVRPSIAfNDTARG--EDDLTFKLADILKANINVQRLEIDGSPQHVISEFEALLQFHVATYMD 225
Cdd:cd02583  176 ENLILTRIPVPPLCIRPSVV-MDEKSGtnEDDLTVKLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQCALYIN 250
RNAP_largest_subunit_N cd00399
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
 1-25 1.16e-06

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: 48.58  E-value: 1.16e-06
                         10        20
                 ....*....|....*....|....*
gi 169247244   1 HFGHIELAKPVFHIGFISKIKKVCE 25
Cdd:cd00399   59 HFGHIELAKPVFHVGFIKKVPSFLG 83
RNAP_I_RPA1_N cd01435
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ...
 1-34 1.93e-06

Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the largest subunit of the eukaryotic RNA polymerase I (RNAP I). RNAP I is a multi-subunit protein complex responsible for the synthesis of rRNA precursors. RNAP I consists of at least 14 different subunits, the largest being homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. The yeast member of this family is known as Rpb190. 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. It makes up the head and core of one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between RPA1 and Rpb1 suggests a similar functional and structural role.


Pssm-ID: 259844 [Multi-domain]  Cd Length: 779  Bit Score: 47.95  E-value: 1.93e-06
                         10        20        30
                 ....*....|....*....|....*....|....
gi 169247244   1 HFGHIELAKPVFHIGFISKIKKVCECVCMHCGKL 34
Cdd:cd01435   62 HFGHIELPLPVYNPLFFDLLYKLLRGSCFYCHRF 95
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
 2-16 3.27e-03

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: 38.22  E-value: 3.27e-03
                          10
                  ....*....|....*
gi 169247244    2 FGHIELAKPVFHIGF 16
Cdd:COG0086    92 MGHIELAMPVFHIWG 106
 
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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