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Conserved domains on  [gi|1806643730|gb|QHW18740|]
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RNA polymerase II largest subunit, partial [Lecidea cancriformis]

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 ...
 1-92 7.03e-15

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: 67.70  E-value: 7.03e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806643730   1 VGFMTKIKKLLETVCHNCGKILVDESDPR----FRDALRFRDPKKRFDAIWRLCKPKRKCETTAGQEddsldktkepkhd 76
Cdd:pfam04997  83 IGFFKKTLKILECVCKYCSKLLLDPGKPKlfnkDKKRLGLENLKMGAKAILELCKKKDLCEHCGGKN------------- 149

                          90
                  ....*....|....*.
gi 1806643730  77 hGGCGNTHPEVRREGL 92
Cdd:pfam04997 150 -GVCGSQQPVSRKEGL 164
 
Name Accession Description Interval E-value
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-92 7.03e-15

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: 67.70  E-value: 7.03e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806643730   1 VGFMTKIKKLLETVCHNCGKILVDESDPR----FRDALRFRDPKKRFDAIWRLCKPKRKCETTAGQEddsldktkepkhd 76
Cdd:pfam04997  83 IGFFKKTLKILECVCKYCSKLLLDPGKPKlfnkDKKRLGLENLKMGAKAILELCKKKDLCEHCGGKN------------- 149

                          90
                  ....*....|....*.
gi 1806643730  77 hGGCGNTHPEVRREGL 92
Cdd:pfam04997 150 -GVCGSQQPVSRKEGL 164
RNAP_archeal_A' cd02582
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
 1-49 1.38e-04

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: 38.77  E-value: 1.38e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1806643730   1 VGFMTKIKKLLETVCHNCGKILVDESDPRfrdalRFRDPKKRFDAIWRL 49
Cdd:cd02582    82 VGFAKHIYDLLRATCRSCGRILLPEEEIE-----KYLERIRRLKEKWPE 125
PRK14977 PRK14977
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
 1-87 1.54e-04

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


Pssm-ID: 184940 [Multi-domain]  Cd Length: 1321  Bit Score: 38.85  E-value: 1.54e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806643730    1 VGFMTKIKKLLETVCHNCGKILVDESDPRFRDALR-----FRD-PKKRFdaiwrlckPKRKCETTAGQEDDSLDKTKEPK 74
Cdd:PRK14977    87 IAFIDNIKDLLNSTCHKCAKLKLPQEDLNVFKLIEeahaaARDiPEKRI--------DDEIIEEVRDQVKVYAKKAKECP 158

                           90
                   ....*....|...
gi 1806643730   75 HdhggCGNTHPEV 87
Cdd:PRK14977   159 H----CGAPQHEL 167
 
Name Accession Description Interval E-value
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-92 7.03e-15

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: 67.70  E-value: 7.03e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806643730   1 VGFMTKIKKLLETVCHNCGKILVDESDPR----FRDALRFRDPKKRFDAIWRLCKPKRKCETTAGQEddsldktkepkhd 76
Cdd:pfam04997  83 IGFFKKTLKILECVCKYCSKLLLDPGKPKlfnkDKKRLGLENLKMGAKAILELCKKKDLCEHCGGKN------------- 149

                          90
                  ....*....|....*.
gi 1806643730  77 hGGCGNTHPEVRREGL 92
Cdd:pfam04997 150 -GVCGSQQPVSRKEGL 164
RNAP_archeal_A' cd02582
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
 1-49 1.38e-04

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: 38.77  E-value: 1.38e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1806643730   1 VGFMTKIKKLLETVCHNCGKILVDESDPRfrdalRFRDPKKRFDAIWRL 49
Cdd:cd02582    82 VGFAKHIYDLLRATCRSCGRILLPEEEIE-----KYLERIRRLKEKWPE 125
PRK14977 PRK14977
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
 1-87 1.54e-04

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


Pssm-ID: 184940 [Multi-domain]  Cd Length: 1321  Bit Score: 38.85  E-value: 1.54e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806643730    1 VGFMTKIKKLLETVCHNCGKILVDESDPRFRDALR-----FRD-PKKRFdaiwrlckPKRKCETTAGQEDDSLDKTKEPK 74
Cdd:PRK14977    87 IAFIDNIKDLLNSTCHKCAKLKLPQEDLNVFKLIEeahaaARDiPEKRI--------DDEIIEEVRDQVKVYAKKAKECP 158

                           90
                   ....*....|...
gi 1806643730   75 HdhggCGNTHPEV 87
Cdd:PRK14977   159 H----CGAPQHEL 167
 
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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