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Conserved domains on  [gi|1373299059|gb|AVT27949|]
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Reverse transcriptase/RNaseH, partial [Lotus badnavirus 1]

Protein Classification

reverse transcriptase family protein( domain architecture ID 10108258)

reverse transcriptase family protein may be an RNA-directed DNA polymerase that catalyzes DNA replication from an RNA template of retrotransposons or retrons

CATH:  3.10.10.10
EC:  2.7.7.-
Gene Ontology:  GO:0016779|GO:0003676
PubMed:  1698615
SCOP:  4002796

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1-80 5.30e-30

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


:

Pssm-ID: 238825  Cd Length: 177  Bit Score: 108.45  E-value: 5.30e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373299059   1 MPFG-KNAPAVFQRKMDNCFKGTEDSIA-VYIDDILVFSQNEDAHVKHLRVLLERCQQNGLILSPTKMAIGQRKIEFLGA 78
Cdd:cd01647    96 MPFGlKNAPATFQRLMNKILGDLLGDFVeVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFLGH 175


                  ..
gi 1373299059  79 II 80
Cdd:cd01647   176 IV 177
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1-80 5.30e-30

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


Pssm-ID: 238825  Cd Length: 177  Bit Score: 108.45  E-value: 5.30e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373299059   1 MPFG-KNAPAVFQRKMDNCFKGTEDSIA-VYIDDILVFSQNEDAHVKHLRVLLERCQQNGLILSPTKMAIGQRKIEFLGA 78
Cdd:cd01647    96 MPFGlKNAPATFQRLMNKILGDLLGDFVeVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFLGH 175


                  ..
gi 1373299059  79 II 80
Cdd:cd01647   176 IV 177
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1-80 1.07e-16

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: 74.26  E-value: 1.07e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373299059   1 MPFG-KNAPAVFQRKMDNCF----KGTEDSIAVYIDDILVFSQNEDAHVKHLRVLLERCQQNGLILSP--TKMAIGQRKI 73
Cdd:pfam00078 103 LPQGlVLSPALFQLFMNELLrplrKRAGLTLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPekTQFFLKSKEV 182


                  ....*..
gi 1373299059  74 EFLGAII 80
Cdd:pfam00078 183 KYLGVTL 189
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1-80 5.30e-30

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


Pssm-ID: 238825  Cd Length: 177  Bit Score: 108.45  E-value: 5.30e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373299059   1 MPFG-KNAPAVFQRKMDNCFKGTEDSIA-VYIDDILVFSQNEDAHVKHLRVLLERCQQNGLILSPTKMAIGQRKIEFLGA 78
Cdd:cd01647    96 MPFGlKNAPATFQRLMNKILGDLLGDFVeVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFLGH 175


                  ..
gi 1373299059  79 II 80
Cdd:cd01647   176 IV 177
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1-80 1.07e-16

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: 74.26  E-value: 1.07e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373299059   1 MPFG-KNAPAVFQRKMDNCF----KGTEDSIAVYIDDILVFSQNEDAHVKHLRVLLERCQQNGLILSP--TKMAIGQRKI 73
Cdd:pfam00078 103 LPQGlVLSPALFQLFMNELLrplrKRAGLTLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPekTQFFLKSKEV 182


                  ....*..
gi 1373299059  74 EFLGAII 80
Cdd:pfam00078 183 KYLGVTL 189
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 1-80 7.94e-06

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: 44.65  E-value: 7.94e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373299059   1 MPFG-KNAPAVF----QRKMDNCFKGTEDSIAV-YIDDILVFSQNEDAHVKHLRVLLERCQQNGLILSPTKMAIGQRKIE 74
Cdd:cd03715   125 LPQGfKNSPTLFhealARDLAPFPLEHEGTILLqYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVK 204


                  ....*.
gi 1373299059  75 FLGAII 80
Cdd:cd03715   205 FLGVVW 210
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 1-80 7.26e-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: 40.03  E-value: 7.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373299059   1 MPFG-KNAPAVFQRKMDNCFKGTEDSIA-----VYIDDILVFSQNEDAHVKhLRVLLERCQQNGLILSPTKM--AIGQRK 72
Cdd:cd00304    12 LPQGsPLSPALANLYMEKLEAPILKQLLditliRYVDDLVVIAKSEQQAVK-KRELEEFLARLGLNLSDEKTqfTEKEKK 90


                  ....*...
gi 1373299059  73 IEFLGAII 80
Cdd:cd00304    91 FKFLGILV 98
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 1-80 2.35e-04

RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.


Pssm-ID: 239684 [Multi-domain]  Cd Length: 119  Bit Score: 39.25  E-value: 2.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373299059   1 MPFG-KNAPAVFQRKMDNCFKGTEDS---IAVYIDDILVFSQNEDAHVKHLRVLLER-CQQNGLILSPTKMAIG-QRKIE 74
Cdd:cd03714    34 LPFGlSLAPRVFTKVVEALLAPLRLLgvrIFSYLDDLLIIASSIKTSEAVLRHLRATlLANLGFTLNLEKSKLGpTQRIT 113


                  ....*.
gi 1373299059  75 FLGAII 80
Cdd:cd03714   114 FLGLEL 119
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 29-78 1.80e-03

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: 37.31  E-value: 1.80e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1373299059  29 YIDDILVFSQNEDAHVKHLRVLLERCQQNGLILSPTK-----MAIGQRKIEFLGA 78
Cdd:cd01646    88 YVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKteilpLPEGTASKDFLGY 142
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 5-65 7.67e-03

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: 35.72  E-value: 7.67e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1373299059   5 KNAPAVFQRKMDNCFKGTEDS-----IAVYIDDILVFSQNEDAHVKHLRVLLERCQQNGLILSPTK 65
Cdd:cd01645   134 KNSPTICQSFVAQALEPFRKQypdivIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEK 199
 
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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