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Conserved domains on  [gi|294352527|gb|ADE66583|]
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reverse transcriptase (plasmid) [Yersinia pestis Z176003]

Protein Classification

reverse transcriptase family protein( domain architecture ID 17)

reverse transcriptase (RT) family protein; RT catalyzes the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes; may be a fragment of a retrovirus-related Pol polyprotein

EC:  2.7.7.49
Gene Ontology:  GO:0003723|GO:0003964

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];
7-144 2.95e-55

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: 179.12  E-value: 2.95e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352527   7 QRKLATWAATDPPRRVERLLRLITQPEWLAEAARITLASKGAhtPGVDGVNKTTLQARLAAELQILRDELLSGCYQPLPA 86
Cdd:COG3344    3 LRRITEKAKPDPGARFTSLLEKILSRENLLEAYKRVKANKGA--AGIDGVTVEDFEEYLEENLYDLRERLRSGSYRPQPV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 294352527  87 RRVYIPKSNGKQRPLGIPTLRDRIVQRAMLMAMEPIWESDFHTLSYGFRPERSVHHAI 144
Cdd:COG3344   81 RRVEIPKPDGGVRPLGIPTVRDRVVQQAVKQVLEPIFEPDFSDSSYGFRPGRSAHDAL 138
 
Name Accession Description Interval E-value
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
7-144 2.95e-55

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


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 179.12  E-value: 2.95e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352527   7 QRKLATWAATDPPRRVERLLRLITQPEWLAEAARITLASKGAhtPGVDGVNKTTLQARLAAELQILRDELLSGCYQPLPA 86
Cdd:COG3344    3 LRRITEKAKPDPGARFTSLLEKILSRENLLEAYKRVKANKGA--AGIDGVTVEDFEEYLEENLYDLRERLRSGSYRPQPV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 294352527  87 RRVYIPKSNGKQRPLGIPTLRDRIVQRAMLMAMEPIWESDFHTLSYGFRPERSVHHAI 144
Cdd:COG3344   81 RRVEIPKPDGGVRPLGIPTVRDRVVQQAVKQVLEPIFEPDFSDSSYGFRPGRSAHDAL 138
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 35-144 1.44e-52

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: 169.95  E-value: 1.44e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352527   35 LAEAARITLASKGAhtPGVDGVNKTTLQARLAAELQILRDELLSGCYQPLPARRVYIPKSNGKQRPLGIPTLRDRIVQRA 114
Cdd:TIGR04416   4 LLLAYKRVKANKGA--AGVDGVTIEDFEEYLEENLYKLWNRLKSGSYRPQPVRRVEIPKPNGKQRPLGIPTVRDRVVQQA 81

                          90       100       110
                  ....*....|....*....|....*....|
gi 294352527  115 MLMAMEPIWESDFHTLSYGFRPERSVHHAI 144
Cdd:TIGR04416  82 VKQVLEPIFEPDFSENSYGFRPGRSAHDAI 111
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 87-144 1.94e-34

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: 120.00  E-value: 1.94e-34
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 294352527  87 RRVYIPKSNGKQRPLGIPTLRDRIVQRAMLMAMEPIWESDFHTLSYGFRPERSVHHAI 144
Cdd:cd01651    1 RRVYIPKPNGKKRPLGIPTVRDRIVQEALKLVLEPIYEPRFSDCSYGFRPGRSAHDAL 58
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 91-136 1.13e-06

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: 46.14  E-value: 1.13e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 294352527   91 IPK-SNGKQRPLGIPTLRDRIVQRAMLMAMEPiwESDFHTLSYGFRP 136
Cdd:pfam00078   1 IPKkGKGKYRPISLLSIDYKALNKIIVKRLKP--ENLDSPPQPGFRP 45
 
Name Accession Description Interval E-value
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
7-144 2.95e-55

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


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 179.12  E-value: 2.95e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352527   7 QRKLATWAATDPPRRVERLLRLITQPEWLAEAARITLASKGAhtPGVDGVNKTTLQARLAAELQILRDELLSGCYQPLPA 86
Cdd:COG3344    3 LRRITEKAKPDPGARFTSLLEKILSRENLLEAYKRVKANKGA--AGIDGVTVEDFEEYLEENLYDLRERLRSGSYRPQPV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 294352527  87 RRVYIPKSNGKQRPLGIPTLRDRIVQRAMLMAMEPIWESDFHTLSYGFRPERSVHHAI 144
Cdd:COG3344   81 RRVEIPKPDGGVRPLGIPTVRDRVVQQAVKQVLEPIFEPDFSDSSYGFRPGRSAHDAL 138
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 35-144 1.44e-52

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: 169.95  E-value: 1.44e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294352527   35 LAEAARITLASKGAhtPGVDGVNKTTLQARLAAELQILRDELLSGCYQPLPARRVYIPKSNGKQRPLGIPTLRDRIVQRA 114
Cdd:TIGR04416   4 LLLAYKRVKANKGA--AGVDGVTIEDFEEYLEENLYKLWNRLKSGSYRPQPVRRVEIPKPNGKQRPLGIPTVRDRVVQQA 81

                          90       100       110
                  ....*....|....*....|....*....|
gi 294352527  115 MLMAMEPIWESDFHTLSYGFRPERSVHHAI 144
Cdd:TIGR04416  82 VKQVLEPIFEPDFSENSYGFRPGRSAHDAI 111
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 87-144 1.94e-34

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: 120.00  E-value: 1.94e-34
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 294352527  87 RRVYIPKSNGKQRPLGIPTLRDRIVQRAMLMAMEPIWESDFHTLSYGFRPERSVHHAI 144
Cdd:cd01651    1 RRVYIPKPNGKKRPLGIPTVRDRIVQEALKLVLEPIYEPRFSDCSYGFRPGRSAHDAL 58
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 91-136 1.13e-06

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: 46.14  E-value: 1.13e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 294352527   91 IPK-SNGKQRPLGIPTLRDRIVQRAMLMAMEPiwESDFHTLSYGFRP 136
Cdd:pfam00078   1 IPKkGKGKYRPISLLSIDYKALNKIIVKRLKP--ENLDSPPQPGFRP 45
RVT_N pfam13655
N-terminal domain of reverse transcriptase; This domain is found at the N-terminus of ...
 20-71 6.54e-03

N-terminal domain of reverse transcriptase; This domain is found at the N-terminus of bacterial reverse transcriptases.


Pssm-ID: 433382  Cd Length: 83  Bit Score: 34.00  E-value: 6.54e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 294352527   20 RRVERLLRLITQpEWLAEA---ARITLASKGAHTPGVDGVNKTTLQARLAAELQI 71
Cdd:pfam13655  30 RKVRRLQKLLTR-SFSAKLlavRRVTQENQGKKTAGVDGVKWLTPKQRLELVLSL 83
 
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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