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Conserved domains on  [gi|2660327397|ref|WP_326972866|]
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reverse transcriptase domain-containing protein [Burkholderia sp. 2002721687]

Protein Classification

YkfC family protein( domain architecture ID 11465225)

YkfC family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
47-178 4.06e-65

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


:

Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 206.47  E-value: 4.06e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2660327397  47 DALMERVVERGNMRRAYRRVLRNQGSAGVDGLSVEGLGDWLKMHWPSVKQALLEGRYVPQAVRRADIPKPQGGVRTLGVP 126
Cdd:COG3344    19 TSLLEKILSRENLLEAYKRVKANKGAAGIDGVTVEDFEEYLEENLYDLRERLRSGSYRPQPVRRVEIPKPDGGVRPLGIP 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2660327397 127 SVVDRLIQQALHQVLQPILEPTFSASSYGFRPGKSALDAVRQAQAYVQGGRH 178
Cdd:COG3344    99 TVRDRVVQQAVKQVLEPIFEPDFSDSSYGFRPGRSAHDALKKAREYINEGYR 150
 
Name Accession Description Interval E-value
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
47-178 4.06e-65

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


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 206.47  E-value: 4.06e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2660327397  47 DALMERVVERGNMRRAYRRVLRNQGSAGVDGLSVEGLGDWLKMHWPSVKQALLEGRYVPQAVRRADIPKPQGGVRTLGVP 126
Cdd:COG3344    19 TSLLEKILSRENLLEAYKRVKANKGAAGIDGVTVEDFEEYLEENLYDLRERLRSGSYRPQPVRRVEIPKPDGGVRPLGIP 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2660327397 127 SVVDRLIQQALHQVLQPILEPTFSASSYGFRPGKSALDAVRQAQAYVQGGRH 178
Cdd:COG3344    99 TVRDRVVQQAVKQVLEPIFEPDFSDSSYGFRPGRSAHDALKKAREYINEGYR 150
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 56-178 8.84e-63

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: 198.07  E-value: 8.84e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2660327397  56 RGNMRRAYRRVLRNQGSAGVDGLSVEGLGDWLKMHWPSVKQALLEGRYVPQAVRRADIPKPQGGVRTLGVPSVVDRLIQQ 135
Cdd:TIGR04416   1 KENLLLAYKRVKANKGAAGVDGVTIEDFEEYLEENLYKLWNRLKSGSYRPQPVRRVEIPKPNGKQRPLGIPTVRDRVVQQ 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2660327397 136 ALHQVLQPILEPTFSASSYGFRPGKSALDAVRQAQAYVQGGRH 178
Cdd:TIGR04416  81 AVKQVLEPIFEPDFSENSYGFRPGRSAHDAIAKARKRLNRGYR 123
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 109-178 4.32e-28

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: 104.98  E-value: 4.32e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2660327397 109 RRADIPKPQGGVRTLGVPSVVDRLIQQALHQVLQPILEPTFSASSYGFRPGKSALDAVRQAQAYVQGGRH 178
Cdd:cd01651     1 RRVYIPKPNGKKRPLGIPTVRDRIVQEALKLVLEPIYEPRFSDCSYGFRPGRSAHDALKAIRRNVKGGYT 70
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 113-163 3.02e-07

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: 48.45  E-value: 3.02e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2660327397 113 IPKP-QGGVRTLGVPSVVDRLIQQALHQVLQPilEPTFSASSYGFRPGKSAL 163
Cdd:pfam00078   1 IPKKgKGKYRPISLLSIDYKALNKIIVKRLKP--ENLDSPPQPGFRPGLAKL 50
 
Name Accession Description Interval E-value
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
47-178 4.06e-65

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


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 206.47  E-value: 4.06e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2660327397  47 DALMERVVERGNMRRAYRRVLRNQGSAGVDGLSVEGLGDWLKMHWPSVKQALLEGRYVPQAVRRADIPKPQGGVRTLGVP 126
Cdd:COG3344    19 TSLLEKILSRENLLEAYKRVKANKGAAGIDGVTVEDFEEYLEENLYDLRERLRSGSYRPQPVRRVEIPKPDGGVRPLGIP 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2660327397 127 SVVDRLIQQALHQVLQPILEPTFSASSYGFRPGKSALDAVRQAQAYVQGGRH 178
Cdd:COG3344    99 TVRDRVVQQAVKQVLEPIFEPDFSDSSYGFRPGRSAHDALKKAREYINEGYR 150
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 56-178 8.84e-63

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: 198.07  E-value: 8.84e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2660327397  56 RGNMRRAYRRVLRNQGSAGVDGLSVEGLGDWLKMHWPSVKQALLEGRYVPQAVRRADIPKPQGGVRTLGVPSVVDRLIQQ 135
Cdd:TIGR04416   1 KENLLLAYKRVKANKGAAGVDGVTIEDFEEYLEENLYKLWNRLKSGSYRPQPVRRVEIPKPNGKQRPLGIPTVRDRVVQQ 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2660327397 136 ALHQVLQPILEPTFSASSYGFRPGKSALDAVRQAQAYVQGGRH 178
Cdd:TIGR04416  81 AVKQVLEPIFEPDFSENSYGFRPGRSAHDAIAKARKRLNRGYR 123
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 109-178 4.32e-28

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: 104.98  E-value: 4.32e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2660327397 109 RRADIPKPQGGVRTLGVPSVVDRLIQQALHQVLQPILEPTFSASSYGFRPGKSALDAVRQAQAYVQGGRH 178
Cdd:cd01651     1 RRVYIPKPNGKKRPLGIPTVRDRIVQEALKLVLEPIYEPRFSDCSYGFRPGRSAHDALKAIRRNVKGGYT 70
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 113-163 3.02e-07

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: 48.45  E-value: 3.02e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2660327397 113 IPKP-QGGVRTLGVPSVVDRLIQQALHQVLQPilEPTFSASSYGFRPGKSAL 163
Cdd:pfam00078   1 IPKKgKGKYRPISLLSIDYKALNKIIVKRLKP--ENLDSPPQPGFRPGLAKL 50
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 113-178 3.56e-03

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: 36.89  E-value: 3.56e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2660327397 113 IPKPQGGV-----RTLGVPSVVDRLIQQALHQVLQPILEPTFSASSYGFRPGKSALDAVRQAQAYVQGGRH 178
Cdd:cd01650     7 IPKKGKPSdpknyRPISLLSVLYKLLEKILANRLRPVLEENILPNQFGFRPGRSTTDAILLLREVIEKAKE 77
RT_Bac_retron_II cd03487
RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 115-168 9.17e-03

RT_Bac_retron_II: 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: 239569 [Multi-domain]  Cd Length: 214  Bit Score: 35.63  E-value: 9.17e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2660327397 115 KPQGGVRTLGVPSVVDRLIQQALHQVLQPILEPtfSASSYGFRPGKSALDAVRQ 168
Cdd:cd03487     1 KKNGGFRTIYAPKPELKAIQRKILSNLLSKLPV--HDAAHGFVKGRSIITNAKP 52
 
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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