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Conserved domains on  [gi|693267292|gb|AIS25227|]
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RNA polymerase II largest subunit, partial [Wallemia tropicalis]

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 ...
 2-171 1.98e-28

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: 106.99  E-value: 1.98e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693267292    2 NCGRLLADENDPELAKIVRTVPVGKR---RFEAVHAYCTKISICKPDEPNEngedappsqpghGGCGRLQPAIRREALKL 78
Cdd:pfam04997  99 YCSKLLLDPGKPKLFNKDKKRLGLENlkmGAKAILELCKKKDLCEHCGGKN------------GVCGSQQPVSRKEGLKL 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693267292   79 FSvnkQQKHDEEDDtkaqqDKRQLSAAEVYTLFKKIPDSDITLMGLSAEFARPDWMIITVLPVPPPPVRPSIAVDGGAtR 158
Cdd:pfam04997 167 KA---AIKKSKEEE-----EKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGGR-R 237

                         170
                  ....*....|...
gi 693267292  159 SEDDLTYKLADIL 171
Cdd:pfam04997 238 AEDDLTHKLRDII 250
 
Name Accession Description Interval E-value
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 2-171 1.98e-28

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: 106.99  E-value: 1.98e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693267292    2 NCGRLLADENDPELAKIVRTVPVGKR---RFEAVHAYCTKISICKPDEPNEngedappsqpghGGCGRLQPAIRREALKL 78
Cdd:pfam04997  99 YCSKLLLDPGKPKLFNKDKKRLGLENlkmGAKAILELCKKKDLCEHCGGKN------------GVCGSQQPVSRKEGLKL 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693267292   79 FSvnkQQKHDEEDDtkaqqDKRQLSAAEVYTLFKKIPDSDITLMGLSAEFARPDWMIITVLPVPPPPVRPSIAVDGGAtR 158
Cdd:pfam04997 167 KA---AIKKSKEEE-----EKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGGR-R 237

                         170
                  ....*....|...
gi 693267292  159 SEDDLTYKLADIL 171
Cdd:pfam04997 238 AEDDLTHKLRDII 250
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
 99-171 7.43e-21

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: 88.36  E-value: 7.43e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 693267292  99 KRQLSAAEVYTLFKKIPDSDITLMGLSAEFARPDWMIITVLPVPPPPVRPSIAVDGGAtRSEDDLTYKLADIL 171
Cdd:cd02733   93 KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPPPAVRPSVVMDGSA-RSEDDLTHKLADII 164
PRK08566 PRK08566
DNA-directed RNA polymerase subunit A'; Validated
 2-171 1.65e-14

DNA-directed RNA polymerase subunit A'; Validated


Pssm-ID: 236292 [Multi-domain]  Cd Length: 882  Bit Score: 70.27  E-value: 1.65e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693267292   2 NCGRLLADENDPE--LAKIVRTVPVG---KRRFEAVHAYCTKISICkpdepnengedapPSqpghggCGRLQPAIRREal 76
Cdd:PRK08566 103 ECGRLKLTEEEIEeyLEKLERLKEWGslaDDLIKEVKKEAAKRMVC-------------PH------CGEKQYKIKFE-- 161

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693267292  77 KLFSVNKQQKHDEEddtkaqqdkrQLSAAEVYTLFKKIPDSDITLMGLSAEFARPDWMIITVLPVPPPPVRPSIAVDGGa 156
Cdd:PRK08566 162 KPTTFYEERKEGLV----------KLTPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTVLPVPPVTVRPSITLETG- 230

                        170
                 ....*....|....*
gi 693267292 157 TRSEDDLTYKLADIL 171
Cdd:PRK08566 231 QRSEDDLTHKLVDII 245
RNA_pol_rpoA1 TIGR02390
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
 101-171 1.31e-13

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: 67.43  E-value: 1.31e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 693267292  101 QLSAAEVYTLFKKIPDSDITLMGLSAEFARPDWMIITVLPVPPPPVRPSIAVDGGaTRSEDDLTYKLADIL 171
Cdd:TIGR02390 172 KLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTVLPVPPVTVRPSITLETG-ERSEDDLTHKLVDII 241
 
Name Accession Description Interval E-value
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 2-171 1.98e-28

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: 106.99  E-value: 1.98e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693267292    2 NCGRLLADENDPELAKIVRTVPVGKR---RFEAVHAYCTKISICKPDEPNEngedappsqpghGGCGRLQPAIRREALKL 78
Cdd:pfam04997  99 YCSKLLLDPGKPKLFNKDKKRLGLENlkmGAKAILELCKKKDLCEHCGGKN------------GVCGSQQPVSRKEGLKL 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693267292   79 FSvnkQQKHDEEDDtkaqqDKRQLSAAEVYTLFKKIPDSDITLMGLSAEFARPDWMIITVLPVPPPPVRPSIAVDGGAtR 158
Cdd:pfam04997 167 KA---AIKKSKEEE-----EKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGGR-R 237

                         170
                  ....*....|...
gi 693267292  159 SEDDLTYKLADIL 171
Cdd:pfam04997 238 AEDDLTHKLRDII 250
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
 99-171 7.43e-21

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: 88.36  E-value: 7.43e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 693267292  99 KRQLSAAEVYTLFKKIPDSDITLMGLSAEFARPDWMIITVLPVPPPPVRPSIAVDGGAtRSEDDLTYKLADIL 171
Cdd:cd02733   93 KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPPPAVRPSVVMDGSA-RSEDDLTHKLADII 164
PRK08566 PRK08566
DNA-directed RNA polymerase subunit A'; Validated
 2-171 1.65e-14

DNA-directed RNA polymerase subunit A'; Validated


Pssm-ID: 236292 [Multi-domain]  Cd Length: 882  Bit Score: 70.27  E-value: 1.65e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693267292   2 NCGRLLADENDPE--LAKIVRTVPVG---KRRFEAVHAYCTKISICkpdepnengedapPSqpghggCGRLQPAIRREal 76
Cdd:PRK08566 103 ECGRLKLTEEEIEeyLEKLERLKEWGslaDDLIKEVKKEAAKRMVC-------------PH------CGEKQYKIKFE-- 161

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693267292  77 KLFSVNKQQKHDEEddtkaqqdkrQLSAAEVYTLFKKIPDSDITLMGLSAEFARPDWMIITVLPVPPPPVRPSIAVDGGa 156
Cdd:PRK08566 162 KPTTFYEERKEGLV----------KLTPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTVLPVPPVTVRPSITLETG- 230

                        170
                 ....*....|....*
gi 693267292 157 TRSEDDLTYKLADIL 171
Cdd:PRK08566 231 QRSEDDLTHKLVDII 245
RNA_pol_rpoA1 TIGR02390
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
 101-171 1.31e-13

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: 67.43  E-value: 1.31e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 693267292  101 QLSAAEVYTLFKKIPDSDITLMGLSAEFARPDWMIITVLPVPPPPVRPSIAVDGGaTRSEDDLTYKLADIL 171
Cdd:TIGR02390 172 KLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTVLPVPPVTVRPSITLETG-ERSEDDLTHKLVDII 241
RNAP_archeal_A' cd02582
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
 64-171 8.66e-13

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: 65.35  E-value: 8.66e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693267292  64 CGRLQPAIRREalklfsvnKQQKHDEEDDtkaqQDKRQLSAAEVYTLFKKIPDSDITLMGLSAEFARPDWMIITVLPVPP 143
Cdd:cd02582  147 CGAPQYKIKLE--------KPTTFYEEKE----EGEVKLTPSEIRERLEKIPDEDLELLGIDPKTARPEWMVLTVLPVPP 214

                         90       100
                 ....*....|....*....|....*...
gi 693267292 144 PPVRPSIAVDGGaTRSEDDLTYKLADIL 171
Cdd:cd02582  215 VTVRPSITLETG-ERSEDDLTHKLVDII 241
RNAP_III_RPC1_N cd02583
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
 2-171 1.58e-10

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: 58.71  E-value: 1.58e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693267292   2 NCGRLLADENDPE--LAKIVRTV--PVGKRR-FEAVHAYCTKISICkpdePNengedappsqpghggCGRLQpairreal 76
Cdd:cd02583   88 TCSRVLLPEEEKRkfLKRLRRPNldNLQKKAlKKKILEKCKKVRKC----PH---------------CGLLK-------- 140

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693267292  77 klfsvnkqqkhdeeddtKAQQDKRQLsaaEVYTLFKKIPDSDITLMGLSAEFARPDWMIITVLPVPPPPVRPSIAVDGGA 156
Cdd:cd02583  141 -----------------KAQEDLNPL---KVLNLFKNIPPEDVELLLMNPLAGRPENLILTRIPVPPLCIRPSVVMDEKS 200

                        170
                 ....*....|....*
gi 693267292 157 TRSEDDLTYKLADIL 171
Cdd:cd02583  201 GTNEDDLTVKLSEII 215
PRK14977 PRK14977
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
 3-171 4.87e-09

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


Pssm-ID: 184940 [Multi-domain]  Cd Length: 1321  Bit Score: 54.26  E-value: 4.87e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693267292    3 CGRLLADENDPELAKIVrtvpvgkrrfEAVHAYCTKISICK-PDEPNENGEDAPPSQPGHGG----CGRLQPAIRREALK 77
Cdd:PRK14977  104 CAKLKLPQEDLNVFKLI----------EEAHAAARDIPEKRiDDEIIEEVRDQVKVYAKKAKecphCGAPQHELEFEEPT 173

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693267292   78 LFSVnkqqkhdeeddtKAQQDKRQLSAAEVYTLFKKIPDSDITLMGLSAEFARPDWMIITVLPVPPPPVRPSIAVDGGaT 157
Cdd:PRK14977  174 IFIE------------KTEIEEHRLLPIEIRDIFEKIIDDDLELIGFDPKKARPEWAVLQAFLVPPLTARPSIILETG-E 240

                         170
                  ....*....|....
gi 693267292  158 RSEDDLTYKLADIL 171
Cdd:PRK14977  241 RSEDDLTHILVDII 254
 
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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