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Conserved domains on  [gi|1012337756|gb|KYP49023|]
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Retrovirus-related Pol polyprotein from transposon 17.6 [Cajanus cajan]

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 ...
 3-128 6.80e-55

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: 169.70  E-value: 6.80e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012337756   3 ERLAGKSHYYFLDGFSGYFQIHIAPEDQENTTFTCPFGTFAYRRMPFGLCNAPGTFQRCMLSIFSEFLENCIEVFMDDFT 82
Cdd:cd01647    52 EELAGAKVFSKLDLRSGYHQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDIL 131

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1012337756  83 VYGSSFDTCLDSLDRVLNRCIETNLVLNFEKCHFMVEQGIVLGHII 128
Cdd:cd01647   132 VYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFLGHIV 177
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 3-128 6.80e-55

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: 169.70  E-value: 6.80e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012337756   3 ERLAGKSHYYFLDGFSGYFQIHIAPEDQENTTFTCPFGTFAYRRMPFGLCNAPGTFQRCMLSIFSEFLENCIEVFMDDFT 82
Cdd:cd01647    52 EELAGAKVFSKLDLRSGYHQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDIL 131

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1012337756  83 VYGSSFDTCLDSLDRVLNRCIETNLVLNFEKCHFMVEQGIVLGHII 128
Cdd:cd01647   132 VYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFLGHIV 177
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1-128 1.14e-23

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: 90.44  E-value: 1.14e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012337756   1 MHERLAGKSHYYFLDGFSGYFQIHIAPEDQENTTFTCP-----------FGTFAYRRMPFGLCNAPGTFQRCMLSIFSEF 69
Cdd:pfam00078  46 GLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFTTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPL 125

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1012337756  70 L---ENCIEVFMDDFTVYGSSFDTCLDSLDRVLNRCIETNLVLNFEKCHFMVEQGIV--LGHII 128
Cdd:pfam00078 126 RkraGLTLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFFLKSKEVkyLGVTL 189
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 3-128 6.80e-55

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: 169.70  E-value: 6.80e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012337756   3 ERLAGKSHYYFLDGFSGYFQIHIAPEDQENTTFTCPFGTFAYRRMPFGLCNAPGTFQRCMLSIFSEFLENCIEVFMDDFT 82
Cdd:cd01647    52 EELAGAKVFSKLDLRSGYHQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDIL 131

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1012337756  83 VYGSSFDTCLDSLDRVLNRCIETNLVLNFEKCHFMVEQGIVLGHII 128
Cdd:cd01647   132 VYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFLGHIV 177
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1-128 1.14e-23

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: 90.44  E-value: 1.14e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012337756   1 MHERLAGKSHYYFLDGFSGYFQIHIAPEDQENTTFTCP-----------FGTFAYRRMPFGLCNAPGTFQRCMLSIFSEF 69
Cdd:pfam00078  46 GLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFTTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPL 125

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1012337756  70 L---ENCIEVFMDDFTVYGSSFDTCLDSLDRVLNRCIETNLVLNFEKCHFMVEQGIV--LGHII 128
Cdd:pfam00078 126 RkraGLTLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFFLKSKEVkyLGVTL 189
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 18-128 1.28e-06

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: 44.26  E-value: 1.28e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012337756  18 SGYFQIHIAPEDQENTTFTCPFGTFAYRRMPFGLCNAPGTFQRCMLSIFSEFLENCIEVF--MDDFTVYGSSFDTClDSL 95
Cdd:cd03714     5 DAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLGVRIFsyLDDLLIIASSIKTS-EAV 83

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1012337756  96 DRVL--NRCIETNLVLNFEKCHFMVEQGIVLGHII 128
Cdd:cd03714    84 LRHLraTLLANLGFTLNLEKSKLGPTQRITFLGLE 118
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 20-113 5.21e-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: 38.03  E-value: 5.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012337756  20 YFQIHIAPEDQENTTFTCP---FGT----FAYRRMPFGLCNAPGTFQRCMLSIFSEFLEN----CIEVFMDDFTVYGSSF 88
Cdd:cd01645    95 FFSIPLHPDDRERFAFTVPsinNKGpakrYQWKVLPQGMKNSPTICQSFVAQALEPFRKQypdiVIYHYMDDILIASDLE 174

                          90       100
                  ....*....|....*....|....*
gi 1012337756  89 DTCLDSLDRVLNRCIETNLVLNFEK 113
Cdd:cd01645   175 GQLREIYEELRQTLLRWGLTIPPEK 199
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 9-128 1.74e-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: 36.56  E-value: 1.74e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1012337756   9 SHYYFLDGFSGYFQIHIAPEDQENTTFTCPFGTFAYRRMPFGLCNAPGTFQRCMLSIFSEF---LENCIEV-FMDDFTVY 84
Cdd:cd03715    87 QWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFHEALARDLAPFpleHEGTILLqYVDDLLLA 166

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1012337756  85 GSSFDTCLDSLDRVLNRCIETNLVLNFEKCHFMVEQGIVLGHII 128
Cdd:cd03715   167 ADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
 
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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