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Conserved domains on  [gi|2537494622|ref|WP_294073002|]
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MULTISPECIES: reverse transcriptase domain-containing protein [Proteiniphilum]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YkfC super family cl43848
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
2-65 8.87e-25

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


The actual alignment was detected with superfamily member COG3344:

Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 95.53  E-value: 8.87e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2537494622   2 GIPTVVDRVIQQAISQILSPIYEGQFSDNSFGFRPHRSCHKAlsidIQQIMRAILKklpKYCYI 65
Cdd:COG3344    96 GIPTVRDRVVQQAVKQVLEPIFEPDFSDSSYGFRPGRSAHDA----LKKAREYINE---GYRWV 152
 
Name Accession Description Interval E-value
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
2-65 8.87e-25

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


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 95.53  E-value: 8.87e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2537494622   2 GIPTVVDRVIQQAISQILSPIYEGQFSDNSFGFRPHRSCHKAlsidIQQIMRAILKklpKYCYI 65
Cdd:COG3344    96 GIPTVRDRVVQQAVKQVLEPIFEPDFSDSSYGFRPGRSAHDA----LKKAREYINE---GYRWV 152
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 2-44 1.79e-23

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: 91.37  E-value: 1.79e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2537494622   2 GIPTVVDRVIQQAISQILSPIYEGQFSDNSFGFRPHRSCHKAL 44
Cdd:TIGR04416  69 GIPTVRDRVVQQAVKQVLEPIFEPDFSENSYGFRPGRSAHDAI 111
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 2-44 6.99e-20

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: 79.55  E-value: 6.99e-20
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2537494622   2 GIPTVVDRVIQQAISQILSPIYEGQFSDNSFGFRPHRSCHKAL 44
Cdd:cd01651    16 GIPTVRDRIVQEALKLVLEPIYEPRFSDCSYGFRPGRSAHDAL 58
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 2-50 4.06e-04

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: 37.28  E-value: 4.06e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2537494622   2 GIPTVVDRVIQQAISQILSPiyEGQFSDNSFGFRP----HRSCHKALSIDIQQ 50
Cdd:pfam00078  13 SLLSIDYKALNKIIVKRLKP--ENLDSPPQPGFRPglakLKKAKWFLKLDLKK 63
 
Name Accession Description Interval E-value
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
2-65 8.87e-25

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


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 95.53  E-value: 8.87e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2537494622   2 GIPTVVDRVIQQAISQILSPIYEGQFSDNSFGFRPHRSCHKAlsidIQQIMRAILKklpKYCYI 65
Cdd:COG3344    96 GIPTVRDRVVQQAVKQVLEPIFEPDFSDSSYGFRPGRSAHDA----LKKAREYINE---GYRWV 152
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 2-44 1.79e-23

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: 91.37  E-value: 1.79e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2537494622   2 GIPTVVDRVIQQAISQILSPIYEGQFSDNSFGFRPHRSCHKAL 44
Cdd:TIGR04416  69 GIPTVRDRVVQQAVKQVLEPIFEPDFSENSYGFRPGRSAHDAI 111
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 2-44 6.99e-20

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: 79.55  E-value: 6.99e-20
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2537494622   2 GIPTVVDRVIQQAISQILSPIYEGQFSDNSFGFRPHRSCHKAL 44
Cdd:cd01651    16 GIPTVRDRIVQEALKLVLEPIYEPRFSDCSYGFRPGRSAHDAL 58
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 2-50 4.06e-04

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: 37.28  E-value: 4.06e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2537494622   2 GIPTVVDRVIQQAISQILSPiyEGQFSDNSFGFRP----HRSCHKALSIDIQQ 50
Cdd:pfam00078  13 SLLSIDYKALNKIIVKRLKP--ENLDSPPQPGFRPglakLKKAKWFLKLDLKK 63
 
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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