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Conserved domains on  [gi|1315515237|gb|PKU49686|]
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rna-directed dna polymerase from mobile element jockey- hypothetical protein [Limosa lapponica baueri]

Protein Classification

RNA-dependent RNA polymerase family protein( domain architecture ID 1750808)

RNA-dependent RNA polymerase (RdRp) family protein similar to the RdRp catalytic domain of alpha-, beta-, gamma-, delta-coronaviruses, including three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2

EC:  2.7.7.48
Gene Ontology:  GO:0097747
PubMed:  29439438

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ps-ssRNAv_RdRp-like super family cl40470
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 1-134 9.86e-12

conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model.


The actual alignment was detected with superfamily member cd01650:

Pssm-ID: 477363 [Multi-domain]  Cd Length: 220  Bit Score: 59.61  E-value: 9.86e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1315515237   1 MEQILLETLLRHMqnEKVICNSQHGFTKGKSRLTHLVTFYDRVTELVDKGTAADVIYLDLLKAFDTVLHNILVSKserhr 80
Cdd:cd01650    32 LEKILANRLRPVL--EENILPNQFGFRPGRSTTDAILLLREVIEKAKEKKKSLVLVFLDFEKAFDSVDHEFLLKA----- 104

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1315515237  81 ldgwttwwirncidnctqrvavnnstskwkpvmIGISQGLVLGLLLFNIFVSDM 134
Cdd:cd01650   105 ---------------------------------LGVRQGDPLSPLLFNLALDDL 125
 
Name Accession Description Interval E-value
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 1-134 9.86e-12

RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.


Pssm-ID: 238827 [Multi-domain]  Cd Length: 220  Bit Score: 59.61  E-value: 9.86e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1315515237   1 MEQILLETLLRHMqnEKVICNSQHGFTKGKSRLTHLVTFYDRVTELVDKGTAADVIYLDLLKAFDTVLHNILVSKserhr 80
Cdd:cd01650    32 LEKILANRLRPVL--EENILPNQFGFRPGRSTTDAILLLREVIEKAKEKKKSLVLVFLDFEKAFDSVDHEFLLKA----- 104

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1315515237  81 ldgwttwwirncidnctqrvavnnstskwkpvmIGISQGLVLGLLLFNIFVSDM 134
Cdd:cd01650   105 ---------------------------------LGVRQGDPLSPLLFNLALDDL 125
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 9-135 2.54e-07

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 47.30  E-value: 2.54e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1315515237   9 LLRHMQNEKVICNSQHGFTKGKSRLTHLVTFydrvtelvdkgtaadvIYLDLLKAFDTVLHNILVSKSERHRLDGWTTWW 88
Cdd:pfam00078  26 IVKRLKPENLDSPPQPGFRPGLAKLKKAKWF----------------LKLDLKKAFDQVPLDELDRKLTAFTTPPININW 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1315515237  89 IRNCIDNCTQrvavnnstskWKpvmiGISQGLVLGLLLFNIFVSDMD 135
Cdd:pfam00078  90 NGELSGGRYE----------WK----GLPQGLVLSPALFQLFMNELL 122
 
Name Accession Description Interval E-value
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 1-134 9.86e-12

RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.


Pssm-ID: 238827 [Multi-domain]  Cd Length: 220  Bit Score: 59.61  E-value: 9.86e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1315515237   1 MEQILLETLLRHMqnEKVICNSQHGFTKGKSRLTHLVTFYDRVTELVDKGTAADVIYLDLLKAFDTVLHNILVSKserhr 80
Cdd:cd01650    32 LEKILANRLRPVL--EENILPNQFGFRPGRSTTDAILLLREVIEKAKEKKKSLVLVFLDFEKAFDSVDHEFLLKA----- 104

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1315515237  81 ldgwttwwirncidnctqrvavnnstskwkpvmIGISQGLVLGLLLFNIFVSDM 134
Cdd:cd01650   105 ---------------------------------LGVRQGDPLSPLLFNLALDDL 125
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 16-135 1.63e-07

RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).


Pssm-ID: 238828 [Multi-domain]  Cd Length: 226  Bit Score: 48.35  E-value: 1.63e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1315515237  16 EKVICNSQHGFTKGKSRLTHLvtfydRVTELVDKGTAADVIYLDLLKAFDTVLHNILVSKSERHRLDGWTTWWIRNCidn 95
Cdd:cd01651    38 EPRFSDCSYGFRPGRSAHDAL-----KAIRRNVKGGYTWVIEGDIKGFFDNIDHDLLLKILKRRIGDKRVLRLIRKW--- 109

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1315515237  96 ctqRVAVNNSTSKWKPVMIGISQGLVLGLLLFNIFVSDMD 135
Cdd:cd01651   110 ---LKAGVLEDGKLVETEKGTPQGGVISPLLANIYLHELD 146
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 9-135 2.54e-07

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 47.30  E-value: 2.54e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1315515237   9 LLRHMQNEKVICNSQHGFTKGKSRLTHLVTFydrvtelvdkgtaadvIYLDLLKAFDTVLHNILVSKSERHRLDGWTTWW 88
Cdd:pfam00078  26 IVKRLKPENLDSPPQPGFRPGLAKLKKAKWF----------------LKLDLKKAFDQVPLDELDRKLTAFTTPPININW 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1315515237  89 IRNCIDNCTQrvavnnstskWKpvmiGISQGLVLGLLLFNIFVSDMD 135
Cdd:pfam00078  90 NGELSGGRYE----------WK----GLPQGLVLSPALFQLFMNELL 122
 
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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