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Conserved domains on  [gi|1151099750|ref|WP_078072093|]
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RNA-directed DNA polymerase [Staphylococcus aureus]

Protein Classification

RNA-directed DNA polymerase( domain architecture ID 10108233)

RNA-directed DNA polymerase catalyzes DNA replication from an RNA template of bacterial retrotransposons or retrons

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
1-100 2.16e-21

RT_Bac_retron_I: 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: 238824 [Multi-domain]  Cd Length: 158  Bit Score: 89.70  E-value: 2.16e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1151099750   1 MPTGNILSRIISELYMCYIDSEMENK--GYRYARYVDDISFSFNFEEEKDKFYRDFNKLCMKYELKINDKKTEVNDFPYI 78
Cdd:cd01646    54 LPIGPLTSRFLANIYLNDVDHELKSKlkGVDYVRYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEILPLPEG 133
                          90       100
                  ....*....|....*....|..
gi 1151099750  79 HpQNKDFIFNYFKNYSSNSKDE 100
Cdd:cd01646   134 T-ASKDFLGYRFSPILLIKSSE 154
 
Name Accession Description Interval E-value
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
1-100 2.16e-21

RT_Bac_retron_I: 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: 238824 [Multi-domain]  Cd Length: 158  Bit Score: 89.70  E-value: 2.16e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1151099750   1 MPTGNILSRIISELYMCYIDSEMENK--GYRYARYVDDISFSFNFEEEKDKFYRDFNKLCMKYELKINDKKTEVNDFPYI 78
Cdd:cd01646    54 LPIGPLTSRFLANIYLNDVDHELKSKlkGVDYVRYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEILPLPEG 133
                          90       100
                  ....*....|....*....|..
gi 1151099750  79 HpQNKDFIFNYFKNYSSNSKDE 100
Cdd:cd01646   134 T-ASKDFLGYRFSPILLIKSSE 154
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
2-75 6.10e-08

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


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 54.31  E-value: 6.10e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1151099750   2 PTGNILSRIISELYMCYIDSEMENKGYRYARYVDDISFSFNFEEEKDKFYRDFNKLCMKYELKINDKKTEVNDF 75
Cdd:COG3344   208 PQGGPLSPLLANIYLHELDKELERRGHRFVRYADDFVILCRSKRAAERVLESLTERLEKLGLELNPEKTRIVRP 281
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
2-108 5.06e-05

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: 44.76  E-value: 5.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1151099750   2 PTGNILSRIISELYMCYIDSEMENKGY--RYARYVDDISFSFNFEEEKDKFYRDFNKLCMKYELKINDKKTEVNdfpYIH 79
Cdd:TIGR04416 181 PQGGVISPLLANIYLHYLDDEWEKRGYkvRFVRYADDFVILCRSKEAAERVLEALTKRLEELGLELNPEKTKIV---HCK 257
                          90       100       110
                  ....*....|....*....|....*....|
gi 1151099750  80 PQNKDFI-FNyFKNYSSNSKDETWIIGIKN 108
Cdd:TIGR04416 258 DGGFDFLgFT-FRKRKSKNGKGKLLIKPSK 286
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1-72 3.70e-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: 41.13  E-value: 3.70e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1151099750   1 MPTGNILSRIISELYMCYIDSEMENK-GYRYARYVDDISFSFNFEEEKDKFYRDFNKLCMKYELKINDKKTEV 72
Cdd:pfam00078 103 LPQGLVLSPALFQLFMNELLRPLRKRaGLTLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQF 175
 
Name Accession Description Interval E-value
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
1-100 2.16e-21

RT_Bac_retron_I: 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: 238824 [Multi-domain]  Cd Length: 158  Bit Score: 89.70  E-value: 2.16e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1151099750   1 MPTGNILSRIISELYMCYIDSEMENK--GYRYARYVDDISFSFNFEEEKDKFYRDFNKLCMKYELKINDKKTEVNDFPYI 78
Cdd:cd01646    54 LPIGPLTSRFLANIYLNDVDHELKSKlkGVDYVRYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEILPLPEG 133
                          90       100
                  ....*....|....*....|..
gi 1151099750  79 HpQNKDFIFNYFKNYSSNSKDE 100
Cdd:cd01646   134 T-ASKDFLGYRFSPILLIKSSE 154
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
2-75 6.10e-08

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


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 54.31  E-value: 6.10e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1151099750   2 PTGNILSRIISELYMCYIDSEMENKGYRYARYVDDISFSFNFEEEKDKFYRDFNKLCMKYELKINDKKTEVNDF 75
Cdd:COG3344   208 PQGGPLSPLLANIYLHELDKELERRGHRFVRYADDFVILCRSKRAAERVLESLTERLEKLGLELNPEKTRIVRP 281
RT_Bac_retron_II cd03487
RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
2-72 4.23e-06

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: 47.18  E-value: 4.23e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1151099750   2 PTGNILSRIISELYMCYIDSEM----ENKGYRYARYVDDISFSFNFE--EEKDKFYRDFNKLCMKYELKINDKKTEV 72
Cdd:cd03487   105 PQGAPTSPALSNLVFRKLDERLsklaKSNGLTYTRYADDITFSSNKKlkEALDKLLEIIRSILSEEGFKINKSKTRI 181
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
2-108 5.06e-05

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: 44.76  E-value: 5.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1151099750   2 PTGNILSRIISELYMCYIDSEMENKGY--RYARYVDDISFSFNFEEEKDKFYRDFNKLCMKYELKINDKKTEVNdfpYIH 79
Cdd:TIGR04416 181 PQGGVISPLLANIYLHYLDDEWEKRGYkvRFVRYADDFVILCRSKEAAERVLEALTKRLEELGLELNPEKTKIV---HCK 257
                          90       100       110
                  ....*....|....*....|....*....|
gi 1151099750  80 PQNKDFI-FNyFKNYSSNSKDETWIIGIKN 108
Cdd:TIGR04416 258 DGGFDFLgFT-FRKRKSKNGKGKLLIKPSK 286
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1-72 3.70e-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: 41.13  E-value: 3.70e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1151099750   1 MPTGNILSRIISELYMCYIDSEMENK-GYRYARYVDDISFSFNFEEEKDKFYRDFNKLCMKYELKINDKKTEV 72
Cdd:pfam00078 103 LPQGLVLSPALFQLFMNELLRPLRKRaGLTLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQF 175
 
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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