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Conserved domains on  [gi|1215380432|gb|ASK86129|]
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polyprotein, partial [Dioscorea bacilliform virus]

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 ...
 1-72 1.30e-25

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: 96.51  E-value: 1.30e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1215380432   1 AVFQRKMDNCFRGT-EDFIAVYIDDILVFSRSQEEHAQHLKQMLEICRRNGLVLSPTKMKIGTQVVEFLGAVI 72
Cdd:cd01647   105 ATFQRLMNKILGDLlGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFLGHIV 177
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1-72 1.30e-25

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: 96.51  E-value: 1.30e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1215380432   1 AVFQRKMDNCFRGT-EDFIAVYIDDILVFSRSQEEHAQHLKQMLEICRRNGLVLSPTKMKIGTQVVEFLGAVI 72
Cdd:cd01647   105 ATFQRLMNKILGDLlGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFLGHIV 177
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1-69 7.80e-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: 60.78  E-value: 7.80e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1215380432   1 AVFQRKMDNCFRG----TEDFIAVYIDDILVFSRSQEEHAQHLKQMLEICRRNGLVLSPTKMKIGTQV--VEFLG 69
Cdd:pfam00078 112 ALFQLFMNELLRPlrkrAGLTLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFFLKSkeVKYLG 186
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1-72 1.30e-25

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: 96.51  E-value: 1.30e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1215380432   1 AVFQRKMDNCFRGT-EDFIAVYIDDILVFSRSQEEHAQHLKQMLEICRRNGLVLSPTKMKIGTQVVEFLGAVI 72
Cdd:cd01647   105 ATFQRLMNKILGDLlGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFLGHIV 177
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1-69 7.80e-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: 60.78  E-value: 7.80e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1215380432   1 AVFQRKMDNCFRG----TEDFIAVYIDDILVFSRSQEEHAQHLKQMLEICRRNGLVLSPTKMKIGTQV--VEFLG 69
Cdd:pfam00078 112 ALFQLFMNELLRPlrkrAGLTLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFFLKSkeVKYLG 186
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 21-72 2.44e-04

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: 40.02  E-value: 2.44e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1215380432  21 YIDDILVFSRSQEEHAQHLKQMLEICRRNGLVLSPTKMKIGTQVVEFLGAVI 72
Cdd:cd03715   159 YVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 21-83 6.68e-04

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: 38.81  E-value: 6.68e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1215380432  21 YIDDILVFSRSQEEHAQHLKQML-EICRRNGLVLSPTK---MKIGTQVVEFLGAVIGNRKIQLQSHI 83
Cdd:cd01650   147 YADDIVLFSEGKSRKLQELLQRLqEWSKESGLKINPSKskvMLIGNKKKRLKDITLNGTPIEAVETF 213
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 21-72 1.23e-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: 38.03  E-value: 1.23e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1215380432  21 YIDDILVFSRSQEEHAQHLKQMLEICRRNGLVLSPTKMKIGTqVVEFLGAVI 72
Cdd:cd01645   163 YMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEP-PFQYLGYEL 213
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 21-72 6.87e-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: 35.38  E-value: 6.87e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1215380432  21 YIDDILVFSRSQEEHAQHLKQMLEICRRNGLVLSPTKMKI-----GTQVVEFLGAVI 72
Cdd:cd01646    88 YVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEIlplpeGTASKDFLGYRF 144
 
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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