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Conserved domains on  [gi|2716168446|ref|WP_341348909|]
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reverse transcriptase domain-containing protein [Syntrophorhabdus aromaticivorans]

Protein Classification

RNA-dependent RNA polymerase family protein( domain architecture ID 1750808)

RNA-dependent RNA polymerase (RdRp) family protein similar to the RdRp catalytic domain of alpha-, beta-, gamma-, delta-coronaviruses, including three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2

EC:  2.7.7.48
Gene Ontology:  GO:0097747
PubMed:  29439438

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ps-ssRNAv_RdRp-like super family cl40470
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 5-235 7.85e-100

conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model.


The actual alignment was detected with superfamily member TIGR04416:

Pssm-ID: 477363 [Multi-domain]  Cd Length: 354  Bit Score: 297.06  E-value: 7.85e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446   5 RQYVEAGYRCVVDIDLEKFFDTVNHDMLMARVARQVKDKKLLLLIRRYLASDIMHEGVVQAHTEGTPQGSPLSPLLSNIL 84
Cdd:TIGR04416 115 RKRLNRGYRWVVDADIKGFFDNINHDLLMKAVARRISDKRVLRLIRRWLKAGVMEDGEVQETEEGTPQGGVISPLLANIY 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446  85 LDDLDKELERRG--HRFCRYADDCNVYVKSAKAGERVMASLTSFLEkKLRLKVNGKKSAVAAPWV--RKFLGYS----MT 156
Cdd:TIGR04416 195 LHYLDDEWEKRGykVRFVRYADDFVILCRSKEAAERVLEALTKRLE-ELGLELNPEKTKIVHCKDggFDFLGFTfrkrKS 273

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446 157 RQAIPRLKVAP--ESVHRLKGQIKEILRKGRGRAISRVINDLTPVLRGWMEYFRLASVKATFELIDEWIRRKLRCVLWRQ 234
Cdd:TIGR04416 274 KNGKGKLLIKPskKAVKKFKEKIRELTKRRRGLSLEELIKKLNPILRGWANYFGIANSSRTFSKLDHWIRRRLRRWLRKK 353


                  .
gi 2716168446 235 W 235
Cdd:TIGR04416 354 W 354
 
Name Accession Description Interval E-value
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 5-235 7.85e-100

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: 297.06  E-value: 7.85e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446   5 RQYVEAGYRCVVDIDLEKFFDTVNHDMLMARVARQVKDKKLLLLIRRYLASDIMHEGVVQAHTEGTPQGSPLSPLLSNIL 84
Cdd:TIGR04416 115 RKRLNRGYRWVVDADIKGFFDNINHDLLMKAVARRISDKRVLRLIRRWLKAGVMEDGEVQETEEGTPQGGVISPLLANIY 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446  85 LDDLDKELERRG--HRFCRYADDCNVYVKSAKAGERVMASLTSFLEkKLRLKVNGKKSAVAAPWV--RKFLGYS----MT 156
Cdd:TIGR04416 195 LHYLDDEWEKRGykVRFVRYADDFVILCRSKEAAERVLEALTKRLE-ELGLELNPEKTKIVHCKDggFDFLGFTfrkrKS 273

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446 157 RQAIPRLKVAP--ESVHRLKGQIKEILRKGRGRAISRVINDLTPVLRGWMEYFRLASVKATFELIDEWIRRKLRCVLWRQ 234
Cdd:TIGR04416 274 KNGKGKLLIKPskKAVKKFKEKIRELTKRRRGLSLEELIKKLNPILRGWANYFGIANSSRTFSKLDHWIRRRLRRWLRKK 353


                  .
gi 2716168446 235 W 235
Cdd:TIGR04416 354 W 354
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
5-296 1.11e-86

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


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 266.17  E-value: 1.11e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446   5 RQYVEAGYRCVVDIDLEKFFDTVNHDMLMARVARQVKDKKLLLLIRRYLASDIMHEGVVQAHTEGTPQGSPLSPLLSNIL 84
Cdd:COG3344   142 REYINEGYRWVVDADIKKFFDNVDHDLLMKRLRRRIKDKRVLRLIRRWLKAGVMEDGVVEEREEGTPQGGPLSPLLANIY 221

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446  85 LDDLDKELERRGHRFCRYADDCNVYVKSAKAGERVMASLTSFLEkKLRLKVNGKKSAVAAPW-VRKFLGYSMTRQAIPRL 163
Cdd:COG3344   222 LHELDKELERRGHRFVRYADDFVILCRSKRAAERVLESLTERLE-KLGLELNPEKTRIVRPGdGFKFLGFSFRRGKGLGF 300

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446 164 KVAPESVHRLKGQIKEILRKGRGRAISRVINDLTPVLRGWME-YFRLASVKATFELIDEWIRRKLRCVLWRQWKTARTRA 242
Cdd:COG3344   301 KFRPRKSKRKKKRKRRRRTRRRSRKRRRRIRRLLRRLLLGWRrYLLLAELKRLLNALLRGRRRYYRRLWRKRRKKLRRRL 380

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2716168446 243 KRLMERGIEQVRAYTSAFNGHGPWWNAGAQHMNRALPVKWFTQQGLISLLAEQR 296
Cdd:COG3344   381 RLLLLRRARRRRAKRRARGRKRRWRIAASALLSPLLLAHYLLLLLLVLLSRYAL 434
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 5-154 1.15e-49

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: 164.30  E-value: 1.15e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446   5 RQYVEAGYRCVVDIDLEKFFDTVNHDMLMARVARQVKDKKLLLLIRRYLASDIMHEGVVQAHTEGTPQGSPLSPLLSNIL 84
Cdd:cd01651    62 RRNVKGGYTWVIEGDIKGFFDNIDHDLLLKILKRRIGDKRVLRLIRKWLKAGVLEDGKLVETEKGTPQGGVISPLLANIY 141

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446  85 LDDLDKELER-------------RGHRFCRYADDCNVYVKSAKAGERVMASLTSFLEkKLRLKVNGKKSAV--AAPWVRK 149
Cdd:cd01651   142 LHELDKFVEEklkeyydtsdpkfRRLRYVRYADDFVIGVRGPKEAEEIKELIREFLE-ELGLELNPEKTRIthFKSEGFD 220


                  ....*
gi 2716168446 150 FLGYS 154
Cdd:cd01651   221 FLGFT 225
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 10-153 2.06e-26

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: 102.77  E-value: 2.06e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446  10 AGYRCVVDIDLEKFFDTVNHDMLMARVARQVKDKKLLLLIRrylasdimHEGVVQAHTEGTPQGSPLSPLLSNILLDDLD 89
Cdd:pfam00078  51 KKAKWFLKLDLKKAFDQVPLDELDRKLTAFTTPPININWNG--------ELSGGRYEWKGLPQGLVLSPALFQLFMNELL 122

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2716168446  90 KELERR-GHRFCRYADDCNVYVKSAKAGERVMASLTSFLeKKLRLKVNGKKS-AVAAPWVRKFLGY 153
Cdd:pfam00078 123 RPLRKRaGLTLVRYADDILIFSKSEEEHQEALEEVLEWL-KESGLKINPEKTqFFLKSKEVKYLGV 187
 
Name Accession Description Interval E-value
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
 5-235 7.85e-100

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: 297.06  E-value: 7.85e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446   5 RQYVEAGYRCVVDIDLEKFFDTVNHDMLMARVARQVKDKKLLLLIRRYLASDIMHEGVVQAHTEGTPQGSPLSPLLSNIL 84
Cdd:TIGR04416 115 RKRLNRGYRWVVDADIKGFFDNINHDLLMKAVARRISDKRVLRLIRRWLKAGVMEDGEVQETEEGTPQGGVISPLLANIY 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446  85 LDDLDKELERRG--HRFCRYADDCNVYVKSAKAGERVMASLTSFLEkKLRLKVNGKKSAVAAPWV--RKFLGYS----MT 156
Cdd:TIGR04416 195 LHYLDDEWEKRGykVRFVRYADDFVILCRSKEAAERVLEALTKRLE-ELGLELNPEKTKIVHCKDggFDFLGFTfrkrKS 273

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446 157 RQAIPRLKVAP--ESVHRLKGQIKEILRKGRGRAISRVINDLTPVLRGWMEYFRLASVKATFELIDEWIRRKLRCVLWRQ 234
Cdd:TIGR04416 274 KNGKGKLLIKPskKAVKKFKEKIRELTKRRRGLSLEELIKKLNPILRGWANYFGIANSSRTFSKLDHWIRRRLRRWLRKK 353


                  .
gi 2716168446 235 W 235
Cdd:TIGR04416 354 W 354
YkfC COG3344
Retron-type reverse transcriptase [Mobilome: prophages, transposons];
5-296 1.11e-86

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


Pssm-ID: 442573 [Multi-domain]  Cd Length: 434  Bit Score: 266.17  E-value: 1.11e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446   5 RQYVEAGYRCVVDIDLEKFFDTVNHDMLMARVARQVKDKKLLLLIRRYLASDIMHEGVVQAHTEGTPQGSPLSPLLSNIL 84
Cdd:COG3344   142 REYINEGYRWVVDADIKKFFDNVDHDLLMKRLRRRIKDKRVLRLIRRWLKAGVMEDGVVEEREEGTPQGGPLSPLLANIY 221

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446  85 LDDLDKELERRGHRFCRYADDCNVYVKSAKAGERVMASLTSFLEkKLRLKVNGKKSAVAAPW-VRKFLGYSMTRQAIPRL 163
Cdd:COG3344   222 LHELDKELERRGHRFVRYADDFVILCRSKRAAERVLESLTERLE-KLGLELNPEKTRIVRPGdGFKFLGFSFRRGKGLGF 300

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446 164 KVAPESVHRLKGQIKEILRKGRGRAISRVINDLTPVLRGWME-YFRLASVKATFELIDEWIRRKLRCVLWRQWKTARTRA 242
Cdd:COG3344   301 KFRPRKSKRKKKRKRRRRTRRRSRKRRRRIRRLLRRLLLGWRrYLLLAELKRLLNALLRGRRRYYRRLWRKRRKKLRRRL 380

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2716168446 243 KRLMERGIEQVRAYTSAFNGHGPWWNAGAQHMNRALPVKWFTQQGLISLLAEQR 296
Cdd:COG3344   381 RLLLLRRARRRRAKRRARGRKRRWRIAASALLSPLLLAHYLLLLLLVLLSRYAL 434
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 5-154 1.15e-49

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: 164.30  E-value: 1.15e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446   5 RQYVEAGYRCVVDIDLEKFFDTVNHDMLMARVARQVKDKKLLLLIRRYLASDIMHEGVVQAHTEGTPQGSPLSPLLSNIL 84
Cdd:cd01651    62 RRNVKGGYTWVIEGDIKGFFDNIDHDLLLKILKRRIGDKRVLRLIRKWLKAGVLEDGKLVETEKGTPQGGVISPLLANIY 141

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446  85 LDDLDKELER-------------RGHRFCRYADDCNVYVKSAKAGERVMASLTSFLEkKLRLKVNGKKSAV--AAPWVRK 149
Cdd:cd01651   142 LHELDKFVEEklkeyydtsdpkfRRLRYVRYADDFVIGVRGPKEAEEIKELIREFLE-ELGLELNPEKTRIthFKSEGFD 220


                  ....*
gi 2716168446 150 FLGYS 154
Cdd:cd01651   221 FLGFT 225
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 10-153 2.06e-26

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: 102.77  E-value: 2.06e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446  10 AGYRCVVDIDLEKFFDTVNHDMLMARVARQVKDKKLLLLIRrylasdimHEGVVQAHTEGTPQGSPLSPLLSNILLDDLD 89
Cdd:pfam00078  51 KKAKWFLKLDLKKAFDQVPLDELDRKLTAFTTPPININWNG--------ELSGGRYEWKGLPQGLVLSPALFQLFMNELL 122

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2716168446  90 KELERR-GHRFCRYADDCNVYVKSAKAGERVMASLTSFLeKKLRLKVNGKKS-AVAAPWVRKFLGY 153
Cdd:pfam00078 123 RPLRKRaGLTLVRYADDILIFSKSEEEHQEALEEVLEWL-KESGLKINPEKTqFFLKSKEVKYLGV 187
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 19-142 7.84e-20

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: 84.30  E-value: 7.84e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446  19 DLEKFFDTVNHDMLMARVARQVKDKKLLLLIRRYLAS-DIMHEGVVQAHTEGTPQGSPLSPLLSNILLDDLDKELER--R 95
Cdd:cd01646     2 DISNFYDSIYTHSLPWALHGKIKAKQLLKLLRLLGNLlDLLLLSSQYGQTNGLPIGPLTSRFLANIYLNDVDHELKSklK 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2716168446  96 GHRFCRYADDCNVYVKSAKAGERVMASLTSFLeKKLRLKVNGKKSAV 142
Cdd:cd01646    82 GVDYVRYVDDIRIFADSKEEAEEILEELKEFL-AELGLSLNLSKTEI 127
GIIM pfam08388
Group II intron, maturase-specific domain; This region is found mainly in various bacterial ...
 172-241 1.51e-16

Group II intron, maturase-specific domain; This region is found mainly in various bacterial and archaeal species, but a few members of this family are expressed by fungal and chlamydomonal species. It has been implicated in the binding of intron RNA during reverse transcription and splicing.


Pssm-ID: 429966 [Multi-domain]  Cd Length: 80  Bit Score: 73.00  E-value: 1.51e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2716168446 172 RLKGQIKE-ILRKGRGRAISRVINDLTPVLRGWMEYFRLASVKATFELIDEWIRRKLRCVLWRQWKTARTR 241
Cdd:pfam08388   3 RFKRKIRElTLRSHKGLSLEDLIRKLNPIIRGWANYFRHVVSKRTFSKLDHWIRRRLRRWAWRRHKRKKRR 73
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 12-142 1.66e-12

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: 65.39  E-value: 1.66e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446  12 YRCVVDIDLEKFFDTVNHDMLMarvarqvkdKKLlllirrylasdimhegvvqahteGTPQGSPLSPLLSNILLDDLDKE 91
Cdd:cd01650    81 SLVLVFLDFEKAFDSVDHEFLL---------KAL-----------------------GVRQGDPLSPLLFNLALDDLLRL 128

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446  92 LERRGHRFCR--------YADDCNVYVKSAKAG-ERVMASLTSFLeKKLRLKVNGKKSAV 142
Cdd:cd01650   129 LNKEEEIKLGgpgithlaYADDIVLFSEGKSRKlQELLQRLQEWS-KESGLKINPSKSKV 187
RT_Bac_retron_II cd03487
RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 10-149 3.42e-11

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: 61.43  E-value: 3.42e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446  10 AGYRCVVDIDLEKFFDTVNHDMlmarvarqVKDKKLLLLIRRYLASDIM-----HEGVVqahtegtPQGSPLSPLLSNIL 84
Cdd:cd03487    54 CGAKYVLKLDIKDFFPSITFER--------VRGVFRSLGYFSPDVATILaklctYNGHL-------PQGAPTSPALSNLV 118

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2716168446  85 LDDLDKEL----ERRGHRFCRYADDcnVYVKSAKAGERVMASLTSFLEKKLR---LKVNGKKSAVAAPWVRK 149
Cdd:cd03487   119 FRKLDERLsklaKSNGLTYTRYADD--ITFSSNKKLKEALDKLLEIIRSILSeegFKINKSKTRISSKGSRQ 188
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 70-153 1.51e-06

RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.


Pssm-ID: 238185 [Multi-domain]  Cd Length: 98  Bit Score: 45.80  E-value: 1.51e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2716168446  70 TPQGSPLSPLLSNILLDDLDKELERRGH--RFCRYADDcNVYVKSAKAGERVMASLTSFL-EKKLRLKVNGKKSAVAAPW 146
Cdd:cd00304    12 LPQGSPLSPALANLYMEKLEAPILKQLLdiTLIRYVDD-LVVIAKSEQQAVKKRELEEFLaRLGLNLSDEKTQFTEKEKK 90


                  ....*..
gi 2716168446 147 VrKFLGY 153
Cdd:cd00304    91 F-KFLGI 96
TERT cd01648
TERT: Telomerase reverse transcriptase (TERT). Telomerase is a ribonucleoprotein (RNP) that ...
 67-105 2.21e-06

TERT: Telomerase reverse transcriptase (TERT). Telomerase is a ribonucleoprotein (RNP) that synthesizes telomeric DNA repeats. The telomerase RNA subunit provides the template for synthesis of these repeats. The catalytic subunit of RNP is known as telomerase reverse transcriptase (TERT). The reverse transcriptase (RT) domain is located in the C-terminal region of the TERT polypeptide. Single amino acid substitutions in this region lead to telomere shortening and senescence. Telomerase is an enzyme that, in certain cells, maintains the physical ends of chromosomes (telomeres) during replication. In somatic cells, replication of the lagging strand requires the continual presence of an RNA primer approximately 200 nucleotides upstream, which is complementary to the template strand. Since there is a region of DNA less than 200 base pairs from the end of the chromosome where this is not possible, the chromosome is continually shortened. However, a surplus of repetitive DNA at the chromosome ends protects against the erosion of gene-encoding DNA. Telomerase is not normally expressed in somatic cells. It has been suggested that exogenous TERT may extend the lifespan of, or even immortalize, the cell. However, recent studies have shown that telomerase activity can be induced by a number of oncogenes. Conversely, the oncogene c-myc can be activated in human TERT immortalized cells. Sequence comparisons place the telomerase proteins in the RT family but reveal hallmarks that distinguish them from retroviral and retrotransposon relatives.


Pssm-ID: 238826  Cd Length: 119  Bit Score: 45.72  E-value: 2.21e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2716168446  67 TEGTPQGSPLSPLLSNILLDDLDKELERRGHR------FCRYADD 105
Cdd:cd01648    17 KVGIPQGSPLSSLLCSLYYADLENKYLSFLDVidkdslLLRLVDD 61
 
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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