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Conserved domains on  [gi|2751359486|ref|WP_353284072|]
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reverse transcriptase domain-containing protein [Wolbachia endosymbiont (group A) of Lypha dubia]

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 ...
 2-156 8.01e-37

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 TIGR04416:

Pssm-ID: 477363 [Multi-domain]  Cd Length: 354  Bit Score: 129.50  E-value: 8.01e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2751359486   2 ANIYLHYVLDLWFEKKFKlrskgyMELVRYADDHLICCEREKDARELLESLKQRLGKFGLEISEDKTRIVKFgkkewqqg 81
Cdd:TIGR04416 191 ANIYLHYLDDEWEKRGYK------VRFVRYADDFVILCRSKEAAERVLEALTKRLEELGLELNPEKTKIVHC-------- 256

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2751359486  82 irekrKTESFNFLGFTHYGTRSRKGRVMVGHKTSKENLSRKLKEIKEWVKKiRNKVHLKDWWSILKAKLTGHYNY 156
Cdd:TIGR04416 257 -----KDGGFDFLGFTFRKRKSKNGKGKLLIKPSKKAVKKFKEKIRELTKR-RRGLSLEELIKKLNPILRGWANY 325
 
Name Accession Description Interval E-value
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 2-156 8.01e-37

group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]


Pssm-ID: 275209 [Multi-domain]  Cd Length: 354  Bit Score: 129.50  E-value: 8.01e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2751359486   2 ANIYLHYVLDLWFEKKFKlrskgyMELVRYADDHLICCEREKDARELLESLKQRLGKFGLEISEDKTRIVKFgkkewqqg 81
Cdd:TIGR04416 191 ANIYLHYLDDEWEKRGYK------VRFVRYADDFVILCRSKEAAERVLEALTKRLEELGLELNPEKTKIVHC-------- 256

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2751359486  82 irekrKTESFNFLGFTHYGTRSRKGRVMVGHKTSKENLSRKLKEIKEWVKKiRNKVHLKDWWSILKAKLTGHYNY 156
Cdd:TIGR04416 257 -----KDGGFDFLGFTFRKRKSKNGKGKLLIKPSKKAVKKFKEKIRELTKR-RRGLSLEELIKKLNPILRGWANY 325
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
2-156 8.50e-27

Retron-type reverse transcriptase [Mobilome: prophages, transposons];


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 104.00  E-value: 8.50e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2751359486   2 ANIYLHYvLDLWFEKKfklrskGYmELVRYADDHLICCEREKDARELLESLKQRLGKFGLEISEDKTRIVKFGKKEWQQG 81
Cdd:COG3344   218 ANIYLHE-LDKELERR------GH-RFVRYADDFVILCRSKRAAERVLESLTERLEKLGLELNPEKTRIVRPGDGFKFLG 289

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2751359486  82 IREKRKT-ESFNFLGFTHYGTRSRKGRVMVGHKTSKEnLSRKLKEIKEWVKKIRNKVHLKDWWSILKAKLTGHYNY 156
Cdd:COG3344   290 FSFRRGKgLGFKFRPRKSKRKKKRKRRRRTRRRSRKR-RRRIRRLLRRLLLGWRRYLLLAELKRLLNALLRGRRRY 364
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 2-98 1.45e-24

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: 94.58  E-value: 1.45e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2751359486   2 ANIYLHYVLDLWFEKKFKLRSKGY-----MELVRYADDHLICCEREKDARELLESLKQRLGKFGLEISEDKTRIVKFgkk 76
Cdd:cd01651   138 ANIYLHELDKFVEEKLKEYYDTSDpkfrrLRYVRYADDFVIGVRGPKEAEEIKELIREFLEELGLELNPEKTRITHF--- 214

                          90       100
                  ....*....|....*....|..
gi 2751359486  77 ewqqgirekrKTESFNFLGFTH 98
Cdd:cd01651   215 ----------KSEGFDFLGFTF 226
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1-97 6.22e-12

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: 60.39  E-value: 6.22e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2751359486   1 MANIYLHYVLDLWfEKKFKLRskgymeLVRYADDHLICCEREKDARELLESLKQRLGKFGLEISEDKTRIVkfgkkewqq 80
Cdd:pfam00078 113 LFQLFMNELLRPL-RKRAGLT------LVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFF--------- 176

                          90
                  ....*....|....*..
gi 2751359486  81 girekRKTESFNFLGFT 97
Cdd:pfam00078 177 -----LKSKEVKYLGVT 188
 
Name Accession Description Interval E-value
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 2-156 8.01e-37

group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]


Pssm-ID: 275209 [Multi-domain]  Cd Length: 354  Bit Score: 129.50  E-value: 8.01e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2751359486   2 ANIYLHYVLDLWFEKKFKlrskgyMELVRYADDHLICCEREKDARELLESLKQRLGKFGLEISEDKTRIVKFgkkewqqg 81
Cdd:TIGR04416 191 ANIYLHYLDDEWEKRGYK------VRFVRYADDFVILCRSKEAAERVLEALTKRLEELGLELNPEKTKIVHC-------- 256

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2751359486  82 irekrKTESFNFLGFTHYGTRSRKGRVMVGHKTSKENLSRKLKEIKEWVKKiRNKVHLKDWWSILKAKLTGHYNY 156
Cdd:TIGR04416 257 -----KDGGFDFLGFTFRKRKSKNGKGKLLIKPSKKAVKKFKEKIRELTKR-RRGLSLEELIKKLNPILRGWANY 325
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
2-156 8.50e-27

Retron-type reverse transcriptase [Mobilome: prophages, transposons];


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 104.00  E-value: 8.50e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2751359486   2 ANIYLHYvLDLWFEKKfklrskGYmELVRYADDHLICCEREKDARELLESLKQRLGKFGLEISEDKTRIVKFGKKEWQQG 81
Cdd:COG3344   218 ANIYLHE-LDKELERR------GH-RFVRYADDFVILCRSKRAAERVLESLTERLEKLGLELNPEKTRIVRPGDGFKFLG 289

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2751359486  82 IREKRKT-ESFNFLGFTHYGTRSRKGRVMVGHKTSKEnLSRKLKEIKEWVKKIRNKVHLKDWWSILKAKLTGHYNY 156
Cdd:COG3344   290 FSFRRGKgLGFKFRPRKSKRKKKRKRRRRTRRRSRKR-RRRIRRLLRRLLLGWRRYLLLAELKRLLNALLRGRRRY 364
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 2-98 1.45e-24

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: 94.58  E-value: 1.45e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2751359486   2 ANIYLHYVLDLWFEKKFKLRSKGY-----MELVRYADDHLICCEREKDARELLESLKQRLGKFGLEISEDKTRIVKFgkk 76
Cdd:cd01651   138 ANIYLHELDKFVEEKLKEYYDTSDpkfrrLRYVRYADDFVIGVRGPKEAEEIKELIREFLEELGLELNPEKTRITHF--- 214

                          90       100
                  ....*....|....*....|..
gi 2751359486  77 ewqqgirekrKTESFNFLGFTH 98
Cdd:cd01651   215 ----------KSEGFDFLGFTF 226
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 2-108 1.43e-12

RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.


Pssm-ID: 238824 [Multi-domain]  Cd Length: 158  Bit Score: 61.58  E-value: 1.43e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2751359486   2 ANIYLHYVlDLWFEKKFKLrsKGYmelVRYADDHLICCEREKDARELLESLKQRLGKFGLEISEDKTRIVKFgkkewqqg 81
Cdd:cd01646    65 ANIYLNDV-DHELKSKLKG--VDY---VRYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEILPL-------- 130

                          90       100
                  ....*....|....*....|....*..
gi 2751359486  82 ireKRKTESFNFLGFTHYGTRSRKGRV 108
Cdd:cd01646   131 ---PEGTASKDFLGYRFSPILLIKSSE 154
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1-97 6.22e-12

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: 60.39  E-value: 6.22e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2751359486   1 MANIYLHYVLDLWfEKKFKLRskgymeLVRYADDHLICCEREKDARELLESLKQRLGKFGLEISEDKTRIVkfgkkewqq 80
Cdd:pfam00078 113 LFQLFMNELLRPL-RKRAGLT------LVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFF--------- 176

                          90
                  ....*....|....*..
gi 2751359486  81 girekRKTESFNFLGFT 97
Cdd:pfam00078 177 -----LKSKEVKYLGVT 188
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 3-97 9.33e-07

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: 46.90  E-value: 9.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2751359486   3 NIYLHYVLDLWFEKKFKLRSKGYMELVRYADDHLICCE-REKDARELLESLKQRLGKFGLEISEDKTRIVKFGKK----- 76
Cdd:cd01650   119 NLALDDLLRLLNKEEEIKLGGPGITHLAYADDIVLFSEgKSRKLQELLQRLQEWSKESGLKINPSKSKVMLIGNKkkrlk 198

                          90       100
                  ....*....|....*....|.
gi 2751359486  77 EWQQGIREKRKTESFNFLGFT 97
Cdd:cd01650   199 DITLNGTPIEAVETFKYLGVT 219
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 2-97 4.30e-05

RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.


Pssm-ID: 238185 [Multi-domain]  Cd Length: 98  Bit Score: 40.41  E-value: 4.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2751359486   2 ANIYLHYvldlwFEKKFKLRSKGyMELVRYADDhLICCEREKDARELLESLKQRLGKFGLEISEDKTrivkfgkkewqqg 81
Cdd:cd00304    23 ANLYMEK-----LEAPILKQLLD-ITLIRYVDD-LVVIAKSEQQAVKKRELEEFLARLGLNLSDEKT------------- 82

                          90
                  ....*....|....*.
gi 2751359486  82 iREKRKTESFNFLGFT 97
Cdd:cd00304    83 -QFTEKEKKFKFLGIL 97
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 28-97 1.32e-04

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.


Pssm-ID: 238823 [Multi-domain]  Cd Length: 213  Bit Score: 40.34  E-value: 1.32e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2751359486  28 LVRYADDHLICCEREKDARELLESLKQRLGKFGLEISEDKtrivkfgkkeWQQGirekrktESFNFLGFT 97
Cdd:cd01645   160 IYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEK----------VQKE-------PPFQYLGYE 212
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 28-80 5.57e-03

RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.


Pssm-ID: 239685 [Multi-domain]  Cd Length: 210  Bit Score: 35.79  E-value: 5.57e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2751359486  28 LVRYADDHLICCEREKDARELLESLKQRLGKFGLEISEDKTRIVkfgKKEWQQ 80
Cdd:cd03715   156 LLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQIC---RAEVKF 205
 
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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