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Conserved domains on  [gi|326578923|gb|ADZ95992|]
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reverse transcriptase, partial [Theope virgilius]

Protein Classification

RNA-directed DNA polymerase( domain architecture ID 10108517)

RNA-directed DNA polymerase catalyzes DNA replication from an RNA template; contains an exonuclease-endonuclease phosphatase (EEP) domain and may be a fragment of a retrovirus-related Pol polyprotein;

CATH:  3.10.10.10
EC:  2.7.7.49
Gene Ontology:  GO:0003964
PubMed:  1698615
SCOP:  4002796

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 36-148 1.99e-36

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: 125.87  E-value: 1.99e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 326578923  36 TALVHPIPKKGDRSDPSNYRPIAITSLFSKIMESVINCQLLKYLEEHqlISDRQYGFRRGRSAGDLLAYLTHKWAQAVES 115
Cdd:cd01650    1 KARIILIPKKGKPSDPKNYRPISLLSVLYKLLEKILANRLRPVLEEN--ILPNQFGFRPGRSTTDAILLLREVIEKAKEK 78

                         90       100       110
                 ....*....|....*....|....*....|...
gi 326578923 116 KGEALTVSLDIAKAFNRVWHKALLAKLpsyGLP 148
Cdd:cd01650   79 KKSLVLVFLDFEKAFDSVDHEFLLKAL---GVR 108
 
Name Accession Description Interval E-value
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 36-148 1.99e-36

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: 125.87  E-value: 1.99e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 326578923  36 TALVHPIPKKGDRSDPSNYRPIAITSLFSKIMESVINCQLLKYLEEHqlISDRQYGFRRGRSAGDLLAYLTHKWAQAVES 115
Cdd:cd01650    1 KARIILIPKKGKPSDPKNYRPISLLSVLYKLLEKILANRLRPVLEEN--ILPNQFGFRPGRSTTDAILLLREVIEKAKEK 78

                         90       100       110
                 ....*....|....*....|....*....|...
gi 326578923 116 KGEALTVSLDIAKAFNRVWHKALLAKLpsyGLP 148
Cdd:cd01650   79 KKSLVLVFLDFEKAFDSVDHEFLLKAL---GVR 108
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 42-154 8.21e-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: 71.56  E-value: 8.21e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 326578923   42 IPKKGDrsdpSNYRPIAITSLFSKIMESVIncqlLKYLEEHQLISDRQYGFRRGRSAgdllaylthkwaqaveSKGEALT 121
Cdd:pfam00078   1 IPKKGK----GKYRPISLLSIDYKALNKII----VKRLKPENLDSPPQPGFRPGLAK----------------LKKAKWF 56

                          90       100       110
                  ....*....|....*....|....*....|...
gi 326578923  122 VSLDIAKAFNRVWHKALLAKLPSYGLPEKLCNW 154
Cdd:pfam00078  57 LKLDLKKAFDQVPLDELDRKLTAFTTPPININW 89
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
41-142 7.82e-04

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


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 39.29  E-value: 7.82e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 326578923  41 PIPKKGDRsdpsnYRPIAITSLFSKIMESVIncqlLKYLEE--HQLISDRQYGFRRGRSAGDLLAYLthkwAQAVESKGE 118
Cdd:COG3344   84 EIPKPDGG-----VRPLGIPTVRDRVVQQAV----KQVLEPifEPDFSDSSYGFRPGRSAHDALKKA----REYINEGYR 150

                         90       100
                 ....*....|....*....|....
gi 326578923 119 ALtVSLDIAKAFNRVWHKALLAKL 142
Cdd:COG3344  151 WV-VDADIKKFFDNVDHDLLMKRL 173
 
Name Accession Description Interval E-value
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 36-148 1.99e-36

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: 125.87  E-value: 1.99e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 326578923  36 TALVHPIPKKGDRSDPSNYRPIAITSLFSKIMESVINCQLLKYLEEHqlISDRQYGFRRGRSAGDLLAYLTHKWAQAVES 115
Cdd:cd01650    1 KARIILIPKKGKPSDPKNYRPISLLSVLYKLLEKILANRLRPVLEEN--ILPNQFGFRPGRSTTDAILLLREVIEKAKEK 78

                         90       100       110
                 ....*....|....*....|....*....|...
gi 326578923 116 KGEALTVSLDIAKAFNRVWHKALLAKLpsyGLP 148
Cdd:cd01650   79 KKSLVLVFLDFEKAFDSVDHEFLLKAL---GVR 108
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 42-154 8.21e-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: 71.56  E-value: 8.21e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 326578923   42 IPKKGDrsdpSNYRPIAITSLFSKIMESVIncqlLKYLEEHQLISDRQYGFRRGRSAgdllaylthkwaqaveSKGEALT 121
Cdd:pfam00078   1 IPKKGK----GKYRPISLLSIDYKALNKII----VKRLKPENLDSPPQPGFRPGLAK----------------LKKAKWF 56

                          90       100       110
                  ....*....|....*....|....*....|...
gi 326578923  122 VSLDIAKAFNRVWHKALLAKLPSYGLPEKLCNW 154
Cdd:pfam00078  57 LKLDLKKAFDQVPLDELDRKLTAFTTPPININW 89
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 42-143 1.30e-06

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: 46.81  E-value: 1.30e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 326578923  42 IPKKGDRSdpsnyRPIAITSLFSKIMESVINcQLL-KYLEEHQliSDRQYGFRRGRSAGDLLAYL------THKWAqave 114
Cdd:cd01651    5 IPKPNGKK-----RPLGIPTVRDRIVQEALK-LVLePIYEPRF--SDCSYGFRPGRSAHDALKAIrrnvkgGYTWV---- 72

                         90       100
                 ....*....|....*....|....*....
gi 326578923 115 skgealtVSLDIAKAFNRVWHKALLAKLP 143
Cdd:cd01651   73 -------IEGDIKGFFDNIDHDLLLKILK 94
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
41-142 7.82e-04

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


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 39.29  E-value: 7.82e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 326578923  41 PIPKKGDRsdpsnYRPIAITSLFSKIMESVIncqlLKYLEE--HQLISDRQYGFRRGRSAGDLLAYLthkwAQAVESKGE 118
Cdd:COG3344   84 EIPKPDGG-----VRPLGIPTVRDRVVQQAV----KQVLEPifEPDFSDSSYGFRPGRSAHDALKKA----REYINEGYR 150

                         90       100
                 ....*....|....*....|....
gi 326578923 119 ALtVSLDIAKAFNRVWHKALLAKL 142
Cdd:COG3344  151 WV-VDADIKKFFDNVDHDLLMKRL 173
 
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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