NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|326578921|gb|ADZ95991|]
View 

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 2.14e-38

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: 130.87  E-value: 2.14e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 326578921  36 TALVHPIPKKGDRSDPSNYRPIAITSLFSKIMESVINCQLLKYLEEHqlISDRQYGFRRGRSAGDLLAYLTHKWAQAVES 115
Cdd:cd01650    1 KARIILIPKKGKPSDPKNYRPISLLSVLYKLLEKILANRLRPVLEEN--ILPNQFGFRPGRSTTDAILLLREVIEKAKEK 78

                         90       100       110
                 ....*....|....*....|....*....|...
gi 326578921 116 KGEALAVSLDIAKAFDRVWHKALLAKLpsyGLP 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 2.14e-38

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: 130.87  E-value: 2.14e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 326578921  36 TALVHPIPKKGDRSDPSNYRPIAITSLFSKIMESVINCQLLKYLEEHqlISDRQYGFRRGRSAGDLLAYLTHKWAQAVES 115
Cdd:cd01650    1 KARIILIPKKGKPSDPKNYRPISLLSVLYKLLEKILANRLRPVLEEN--ILPNQFGFRPGRSTTDAILLLREVIEKAKEK 78

                         90       100       110
                 ....*....|....*....|....*....|...
gi 326578921 116 KGEALAVSLDIAKAFDRVWHKALLAKLpsyGLP 148
Cdd:cd01650   79 KKSLVLVFLDFEKAFDSVDHEFLLKAL---GVR 108
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 42-168 1.20e-17

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: 76.19  E-value: 1.20e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 326578921   42 IPKKGDrsdpSNYRPIAITSLFSKIMESVIncqlLKYLEEHQLISDRQYGFRRGRSAgdllaylthkwaqaveSKGEALA 121
Cdd:pfam00078   1 IPKKGK----GKYRPISLLSIDYKALNKII----VKRLKPENLDSPPQPGFRPGLAK----------------LKKAKWF 56

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 326578921  122 VSLDIAKAFDRVWHKALLAKLPSYGLPEKLCNWVTSFLAERSIRVVV 168
Cdd:pfam00078  57 LKLDLKKAFDQVPLDELDRKLTAFTTPPININWNGELSGGRYEWKGL 103
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
41-142 2.25e-05

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


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 43.53  E-value: 2.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 326578921  41 PIPKKGDRsdpsnYRPIAITSLFSKIMESVIncqlLKYLEE--HQLISDRQYGFRRGRSAGDLLAYLthkwAQAVESKGE 118
Cdd:COG3344   84 EIPKPDGG-----VRPLGIPTVRDRVVQQAV----KQVLEPifEPDFSDSSYGFRPGRSAHDALKKA----REYINEGYR 150

                         90       100
                 ....*....|....*....|....
gi 326578921 119 AlAVSLDIAKAFDRVWHKALLAKL 142
Cdd:COG3344  151 W-VVDADIKKFFDNVDHDLLMKRL 173
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 86-142 5.54e-03

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: 36.28  E-value: 5.54e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 326578921   86 SDRQYGFRRGRSAgdllaylthkwAQAVE------SKGEALAVSLDIAKAFDRVWHKALLAKL 142
Cdd:TIGR04416  95 SENSYGFRPGRSA-----------HDAIAkarkrlNRGYRWVVDADIKGFFDNINHDLLMKAV 146
 
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 2.14e-38

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: 130.87  E-value: 2.14e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 326578921  36 TALVHPIPKKGDRSDPSNYRPIAITSLFSKIMESVINCQLLKYLEEHqlISDRQYGFRRGRSAGDLLAYLTHKWAQAVES 115
Cdd:cd01650    1 KARIILIPKKGKPSDPKNYRPISLLSVLYKLLEKILANRLRPVLEEN--ILPNQFGFRPGRSTTDAILLLREVIEKAKEK 78

                         90       100       110
                 ....*....|....*....|....*....|...
gi 326578921 116 KGEALAVSLDIAKAFDRVWHKALLAKLpsyGLP 148
Cdd:cd01650   79 KKSLVLVFLDFEKAFDSVDHEFLLKAL---GVR 108
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 42-168 1.20e-17

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: 76.19  E-value: 1.20e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 326578921   42 IPKKGDrsdpSNYRPIAITSLFSKIMESVIncqlLKYLEEHQLISDRQYGFRRGRSAgdllaylthkwaqaveSKGEALA 121
Cdd:pfam00078   1 IPKKGK----GKYRPISLLSIDYKALNKII----VKRLKPENLDSPPQPGFRPGLAK----------------LKKAKWF 56

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 326578921  122 VSLDIAKAFDRVWHKALLAKLPSYGLPEKLCNWVTSFLAERSIRVVV 168
Cdd:pfam00078  57 LKLDLKKAFDQVPLDELDRKLTAFTTPPININWNGELSGGRYEWKGL 103
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 42-143 1.27e-07

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: 49.51  E-value: 1.27e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 326578921  42 IPKKGDRSdpsnyRPIAITSLFSKIMESVINcQLL-KYLEEHQliSDRQYGFRRGRSAGDLLAYL------THKWaqave 114
Cdd:cd01651    5 IPKPNGKK-----RPLGIPTVRDRIVQEALK-LVLePIYEPRF--SDCSYGFRPGRSAHDALKAIrrnvkgGYTW----- 71

                         90       100
                 ....*....|....*....|....*....
gi 326578921 115 skgealAVSLDIAKAFDRVWHKALLAKLP 143
Cdd:cd01651   72 ------VIEGDIKGFFDNIDHDLLLKILK 94
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
41-142 2.25e-05

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


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 43.53  E-value: 2.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 326578921  41 PIPKKGDRsdpsnYRPIAITSLFSKIMESVIncqlLKYLEE--HQLISDRQYGFRRGRSAGDLLAYLthkwAQAVESKGE 118
Cdd:COG3344   84 EIPKPDGG-----VRPLGIPTVRDRVVQQAV----KQVLEPifEPDFSDSSYGFRPGRSAHDALKKA----REYINEGYR 150

                         90       100
                 ....*....|....*....|....
gi 326578921 119 AlAVSLDIAKAFDRVWHKALLAKL 142
Cdd:COG3344  151 W-VVDADIKKFFDNVDHDLLMKRL 173
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 86-142 5.54e-03

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: 36.28  E-value: 5.54e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 326578921   86 SDRQYGFRRGRSAgdllaylthkwAQAVE------SKGEALAVSLDIAKAFDRVWHKALLAKL 142
Cdd:TIGR04416  95 SENSYGFRPGRSA-----------HDAIAkarkrlNRGYRWVVDADIKGFFDNINHDLLMKAV 146
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH