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Conserved domains on  [gi|1907087969|ref|XP_036013358|]
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DNA-directed RNA polymerase I subunit RPA43 isoform X1 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RPA43_OB super family cl39351
RPA43 OB domain in RNA Pol I; This is OB domain found in RPA43 proteins (DNA-directed RNA ...
 100-133 1.13e-07

RPA43 OB domain in RNA Pol I; This is OB domain found in RPA43 proteins (DNA-directed RNA polymerase I subunit RPA43, also known as A43) in yeast. Functional analysis of RNA polymerase I show that, subunits A14 and A43 form the heterodimer A14/43, which is distantly related to Rpb4/7 in Pol II and C17/25 in Pol III. Crystal structure analysis show that A43-A14 heterodimer forms the stalk that provides a platform for initiation factors and interacts with newly synthesized RNA.


The actual alignment was detected with superfamily member pfam17875:

Pssm-ID: 465545  Cd Length: 114  Bit Score: 49.29  E-value: 1.13e-07
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1907087969 100 EGTVNKVSSSHIGCLVHGCFNASIPK---PEQMSYEE 133
Cdd:pfam17875   8 EGRINLQSPSHIGLLVYNTFNASIPAahiPKDWKWEF 44
 
Name Accession Description Interval E-value
RPA43_OB pfam17875
RPA43 OB domain in RNA Pol I; This is OB domain found in RPA43 proteins (DNA-directed RNA ...
 100-133 1.13e-07

RPA43 OB domain in RNA Pol I; This is OB domain found in RPA43 proteins (DNA-directed RNA polymerase I subunit RPA43, also known as A43) in yeast. Functional analysis of RNA polymerase I show that, subunits A14 and A43 form the heterodimer A14/43, which is distantly related to Rpb4/7 in Pol II and C17/25 in Pol III. Crystal structure analysis show that A43-A14 heterodimer forms the stalk that provides a platform for initiation factors and interacts with newly synthesized RNA.


Pssm-ID: 465545  Cd Length: 114  Bit Score: 49.29  E-value: 1.13e-07
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1907087969 100 EGTVNKVSSSHIGCLVHGCFNASIPK---PEQMSYEE 133
Cdd:pfam17875   8 EGRINLQSPSHIGLLVYNTFNASIPAahiPKDWKWEF 44
 
Name Accession Description Interval E-value
RPA43_OB pfam17875
RPA43 OB domain in RNA Pol I; This is OB domain found in RPA43 proteins (DNA-directed RNA ...
 100-133 1.13e-07

RPA43 OB domain in RNA Pol I; This is OB domain found in RPA43 proteins (DNA-directed RNA polymerase I subunit RPA43, also known as A43) in yeast. Functional analysis of RNA polymerase I show that, subunits A14 and A43 form the heterodimer A14/43, which is distantly related to Rpb4/7 in Pol II and C17/25 in Pol III. Crystal structure analysis show that A43-A14 heterodimer forms the stalk that provides a platform for initiation factors and interacts with newly synthesized RNA.


Pssm-ID: 465545  Cd Length: 114  Bit Score: 49.29  E-value: 1.13e-07
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1907087969 100 EGTVNKVSSSHIGCLVHGCFNASIPK---PEQMSYEE 133
Cdd:pfam17875   8 EGRINLQSPSHIGLLVYNTFNASIPAahiPKDWKWEF 44
 
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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