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Conserved domains on  [gi|1954090875|gb|QQM16626|]
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RNA polymerase II largest subunit, partial [Usnea stipitata]

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 ...
 1-139 1.03e-23

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: 93.89  E-value: 1.03e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954090875   1 HNCGKILVDESNPA----FADAIRRRDPKKRFDLVWRLCKPKMICETTMALDddapqdktkepkhdhGGCGNIQPEVRRE 76
Cdd:pfam04997  98 KYCSKLLLDPGKPKlfnkDKKRLGLENLKMGAKAILELCKKKDLCEHCGGKN---------------GVCGSQQPVSRKE 162

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1954090875  77 GLRLTGTWKaqkGDEENEgqqpEKKPITPQMALNIFRHISTEDIKRMGLSNDYARPEWMIITV 139
Cdd:pfam04997 163 GLKLKAAIK---KSKEEE----EKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTV 218
 
Name Accession Description Interval E-value
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-139 1.03e-23

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: 93.89  E-value: 1.03e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954090875   1 HNCGKILVDESNPA----FADAIRRRDPKKRFDLVWRLCKPKMICETTMALDddapqdktkepkhdhGGCGNIQPEVRRE 76
Cdd:pfam04997  98 KYCSKLLLDPGKPKlfnkDKKRLGLENLKMGAKAILELCKKKDLCEHCGGKN---------------GVCGSQQPVSRKE 162

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1954090875  77 GLRLTGTWKaqkGDEENEgqqpEKKPITPQMALNIFRHISTEDIKRMGLSNDYARPEWMIITV 139
Cdd:pfam04997 163 GLKLKAAIK---KSKEEE----EKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTV 218
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
 100-139 5.35e-11

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: 59.47  E-value: 5.35e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1954090875 100 KKPITPQMALNIFRHISTEDIKRMGLSNDYARPEWMIITV 139
Cdd:cd02733    93 KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTV 132
PRK08566 PRK08566
DNA-directed RNA polymerase subunit A'; Validated
 2-139 9.19e-05

DNA-directed RNA polymerase subunit A'; Validated


Pssm-ID: 236292 [Multi-domain]  Cd Length: 882  Bit Score: 41.38  E-value: 9.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954090875   2 NCGKILVDESNPA-FADAIRRRdpKKRFDLVWRLCKpkmicettmalddDAPQDKTKEPKHDHggCGNIQPEVRREglRL 80
Cdd:PRK08566  103 ECGRLKLTEEEIEeYLEKLERL--KEWGSLADDLIK-------------EVKKEAAKRMVCPH--CGEKQYKIKFE--KP 163

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1954090875  81 TGTWKAQKGDEENegqqpekkpITPQMALNIFRHISTEDIKRMGLSNDYARPEWMIITV 139
Cdd:PRK08566  164 TTFYEERKEGLVK---------LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTV 213
RNA_pol_rpoA1 TIGR02390
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
 92-139 3.87e-04

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: 39.70  E-value: 3.87e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1954090875  92 ENEGQQPEKkpITPQMALNIFRHISTEDIKRMGLSNDYARPEWMIITV 139
Cdd:TIGR02390 164 EEGKEGDVK--LTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTV 209
 
Name Accession Description Interval E-value
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-139 1.03e-23

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: 93.89  E-value: 1.03e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954090875   1 HNCGKILVDESNPA----FADAIRRRDPKKRFDLVWRLCKPKMICETTMALDddapqdktkepkhdhGGCGNIQPEVRRE 76
Cdd:pfam04997  98 KYCSKLLLDPGKPKlfnkDKKRLGLENLKMGAKAILELCKKKDLCEHCGGKN---------------GVCGSQQPVSRKE 162

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1954090875  77 GLRLTGTWKaqkGDEENEgqqpEKKPITPQMALNIFRHISTEDIKRMGLSNDYARPEWMIITV 139
Cdd:pfam04997 163 GLKLKAAIK---KSKEEE----EKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTV 218
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
 100-139 5.35e-11

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: 59.47  E-value: 5.35e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1954090875 100 KKPITPQMALNIFRHISTEDIKRMGLSNDYARPEWMIITV 139
Cdd:cd02733    93 KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTV 132
RNAP_archeal_A' cd02582
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
 1-139 9.83e-06

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: 44.16  E-value: 9.83e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954090875   1 HNCGKILVDESNPAFADAIRRRDPKKRFDLVWRLckPKMICETTMaldddapqdKTKEPKHdhggCGNIQPEVRREglrl 80
Cdd:cd02582    97 RSCGRILLPEEEIEKYLERIRRLKEKWPELVKRV--IEKVKKKAK---------KRKVCPH----CGAPQYKIKLE---- 157

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1954090875  81 tgtwKAQKGDEENEGqqpEKKPITPQMALNIFRHISTEDIKRMGLSNDYARPEWMIITV 139
Cdd:cd02582   158 ----KPTTFYEEKEE---GEVKLTPSEIRERLEKIPDEDLELLGIDPKTARPEWMVLTV 209
PRK08566 PRK08566
DNA-directed RNA polymerase subunit A'; Validated
 2-139 9.19e-05

DNA-directed RNA polymerase subunit A'; Validated


Pssm-ID: 236292 [Multi-domain]  Cd Length: 882  Bit Score: 41.38  E-value: 9.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954090875   2 NCGKILVDESNPA-FADAIRRRdpKKRFDLVWRLCKpkmicettmalddDAPQDKTKEPKHDHggCGNIQPEVRREglRL 80
Cdd:PRK08566  103 ECGRLKLTEEEIEeYLEKLERL--KEWGSLADDLIK-------------EVKKEAAKRMVCPH--CGEKQYKIKFE--KP 163

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1954090875  81 TGTWKAQKGDEENegqqpekkpITPQMALNIFRHISTEDIKRMGLSNDYARPEWMIITV 139
Cdd:PRK08566  164 TTFYEERKEGLVK---------LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTV 213
RNA_pol_rpoA1 TIGR02390
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
 92-139 3.87e-04

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: 39.70  E-value: 3.87e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1954090875  92 ENEGQQPEKkpITPQMALNIFRHISTEDIKRMGLSNDYARPEWMIITV 139
Cdd:TIGR02390 164 EEGKEGDVK--LTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTV 209
PRK14977 PRK14977
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
 1-139 8.64e-03

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


Pssm-ID: 184940 [Multi-domain]  Cd Length: 1321  Bit Score: 35.77  E-value: 8.64e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954090875    1 HNCGKILVDESNPAFADAIRRR------DPKKRFDlvwrlckPKMICETTMALDDDApqDKTKEPKHdhggCGNIQPEVR 74
Cdd:PRK14977   102 HKCAKLKLPQEDLNVFKLIEEAhaaardIPEKRID-------DEIIEEVRDQVKVYA--KKAKECPH----CGAPQHELE 168

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1954090875   75 REglrltgtwKAQKGDEENEgqqPEKKPITPQMALNIFRHISTEDIKRMGLSNDYARPEWMIITV 139
Cdd:PRK14977   169 FE--------EPTIFIEKTE---IEEHRLLPIEIRDIFEKIIDDDLELIGFDPKKARPEWAVLQA 222
 
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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