NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|3377824|gb|AAC28197|]
View 

contains similarity to reverse transcriptases [Arabidopsis thaliana]

Protein Classification

reverse transcriptase family protein; reverse transcriptase/ribonuclease H family protein( domain architecture ID 10108598)

reverse transcriptase family protein may be an RNA-directed DNA polymerase that catalyzes DNA replication from an RNA template of retrotransposons or retrons| reverse transcriptase (RT)/ribonuclease H (RNase H) family protein from retrotransposons catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements, and may be an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 467-689 1.23e-39

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: 146.67  E-value: 1.23e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3377824   467 LIPKIPAPQKVSDYRPIALCSVYYKIIAKLLAKRLQPILHSCISENQSAFVPQRAISDNVLITHEALHYLKNSGalvNCY 546
Cdd:cd01650    6 LIPKKGKPSDPKNYRPISLLSVLYKLLEKILANRLRPVLEENILPNQFGFRPGRSTTDAILLLREVIEKAKEKK---KSL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3377824   547 MAVKTDMSKAYDRLEWDFVkaaLEEMG-----------FhhhfvGWIIEVLSRMclkaqengSLPGIRVAMGCPRVNHLL 615
Cdd:cd01650   83 VLVFLDFEKAFDSVDHEFL---LKALGvrqgdplspllF-----NLALDDLLRL--------LNKEEEIKLGGPGITHLA 146

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 3377824   616 FADDTMFFCRVDPKSCLKLKSILHKYELASGQKINQAK---YSITFSAKTPPAVRERVKQIlliqKEGGQGKYLGLP 689
Cdd:cd01650  147 YADDIVLFSEGKSRKLQELLQRLQEWSKESGLKINPSKskvMLIGNKKKRLKDITLNGTPI----EAVETFKYLGVT 219
RNase_H_like super family cl14782
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 977-1070 3.63e-12

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


The actual alignment was detected with superfamily member pfam13456:

Pssm-ID: 449355 [Multi-domain]  Cd Length: 123  Bit Score: 64.21  E-value: 3.63e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3377824     977 SGNSSASDVGSPLIAETLVTLADVRVACESDIKAISFASDSQIIVKALNQKLQVKELHGILH-DILSLSSSFDACTFTFI 1055
Cdd:pfam13456   29 AGQKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGRSPKQSKLANLLdEIRKLLKRFESVSFEHI 108

                           90
                   ....*....|....*
gi 3377824    1056 NREFNHQADALAKRA 1070
Cdd:pfam13456  109 PREQNRVADTLAKMA 123
 
Name Accession Description Interval E-value
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 467-689 1.23e-39

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: 146.67  E-value: 1.23e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3377824   467 LIPKIPAPQKVSDYRPIALCSVYYKIIAKLLAKRLQPILHSCISENQSAFVPQRAISDNVLITHEALHYLKNSGalvNCY 546
Cdd:cd01650    6 LIPKKGKPSDPKNYRPISLLSVLYKLLEKILANRLRPVLEENILPNQFGFRPGRSTTDAILLLREVIEKAKEKK---KSL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3377824   547 MAVKTDMSKAYDRLEWDFVkaaLEEMG-----------FhhhfvGWIIEVLSRMclkaqengSLPGIRVAMGCPRVNHLL 615
Cdd:cd01650   83 VLVFLDFEKAFDSVDHEFL---LKALGvrqgdplspllF-----NLALDDLLRL--------LNKEEEIKLGGPGITHLA 146

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 3377824   616 FADDTMFFCRVDPKSCLKLKSILHKYELASGQKINQAK---YSITFSAKTPPAVRERVKQIlliqKEGGQGKYLGLP 689
Cdd:cd01650  147 YADDIVLFSEGKSRKLQELLQRLQEWSKESGLKINPSKskvMLIGNKKKRLKDITLNGTPI----EAVETFKYLGVT 219
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 468-662 4.31e-15

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: 74.65  E-value: 4.31e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3377824     468 IPKIPApqkvSDYRPIALCSVYYKIIAKLLAKRLQPilHSCISENQSAFVPQRAisdnvlithealhylknsgALVNCYM 547
Cdd:pfam00078    1 IPKKGK----GKYRPISLLSIDYKALNKIIVKRLKP--ENLDSPPQPGFRPGLA-------------------KLKKAKW 55

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3377824     548 AVKTDMSKAYDRLEWDFVKAALEEMGFHHHFVGWIIEVLSRmclKAQENGsLP-G---------------IRVAMGCPRV 611
Cdd:pfam00078   56 FLKLDLKKAFDQVPLDELDRKLTAFTTPPININWNGELSGG---RYEWKG-LPqGlvlspalfqlfmnelLRPLRKRAGL 131

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 3377824     612 NHLLFADDTMFFCRvDPKSCLKLKSILHKYELASGQKINQAKYSITFSAKT 662
Cdd:pfam00078  132 TLVRYADDILIFSK-SEEEHQEALEEVLEWLKESGLKINPEKTQFFLKSKE 181
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 977-1070 3.63e-12

Reverse transcriptase-like; This domain is found in plants and appears to be part of a retrotransposon.


Pssm-ID: 433223 [Multi-domain]  Cd Length: 123  Bit Score: 64.21  E-value: 3.63e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3377824     977 SGNSSASDVGSPLIAETLVTLADVRVACESDIKAISFASDSQIIVKALNQKLQVKELHGILH-DILSLSSSFDACTFTFI 1055
Cdd:pfam13456   29 AGQKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGRSPKQSKLANLLdEIRKLLKRFESVSFEHI 108

                           90
                   ....*....|....*
gi 3377824    1056 NREFNHQADALAKRA 1070
Cdd:pfam13456  109 PREQNRVADTLAKMA 123
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 990-1071 2.49e-11

RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties.


Pssm-ID: 260011 [Multi-domain]  Cd Length: 128  Bit Score: 62.10  E-value: 2.49e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3377824   990 IAETLVTLADVRVACESDIKAISFASDSQIIVKALNQKLQVKE--LHGILHDILSLSSSFDACTFTFINREFNHQADALA 1067
Cdd:cd09279   44 EAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLNGEYKVKNerLKPLLEKVLELLAKFELVELKWIPREQNKEADALA 123


                 ....
gi 3377824  1068 KRAL 1071
Cdd:cd09279  124 NQAL 127
 
Name Accession Description Interval E-value
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 467-689 1.23e-39

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: 146.67  E-value: 1.23e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3377824   467 LIPKIPAPQKVSDYRPIALCSVYYKIIAKLLAKRLQPILHSCISENQSAFVPQRAISDNVLITHEALHYLKNSGalvNCY 546
Cdd:cd01650    6 LIPKKGKPSDPKNYRPISLLSVLYKLLEKILANRLRPVLEENILPNQFGFRPGRSTTDAILLLREVIEKAKEKK---KSL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3377824   547 MAVKTDMSKAYDRLEWDFVkaaLEEMG-----------FhhhfvGWIIEVLSRMclkaqengSLPGIRVAMGCPRVNHLL 615
Cdd:cd01650   83 VLVFLDFEKAFDSVDHEFL---LKALGvrqgdplspllF-----NLALDDLLRL--------LNKEEEIKLGGPGITHLA 146

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 3377824   616 FADDTMFFCRVDPKSCLKLKSILHKYELASGQKINQAK---YSITFSAKTPPAVRERVKQIlliqKEGGQGKYLGLP 689
Cdd:cd01650  147 YADDIVLFSEGKSRKLQELLQRLQEWSKESGLKINPSKskvMLIGNKKKRLKDITLNGTPI----EAVETFKYLGVT 219
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 468-662 4.31e-15

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: 74.65  E-value: 4.31e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3377824     468 IPKIPApqkvSDYRPIALCSVYYKIIAKLLAKRLQPilHSCISENQSAFVPQRAisdnvlithealhylknsgALVNCYM 547
Cdd:pfam00078    1 IPKKGK----GKYRPISLLSIDYKALNKIIVKRLKP--ENLDSPPQPGFRPGLA-------------------KLKKAKW 55

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3377824     548 AVKTDMSKAYDRLEWDFVKAALEEMGFHHHFVGWIIEVLSRmclKAQENGsLP-G---------------IRVAMGCPRV 611
Cdd:pfam00078   56 FLKLDLKKAFDQVPLDELDRKLTAFTTPPININWNGELSGG---RYEWKG-LPqGlvlspalfqlfmnelLRPLRKRAGL 131

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 3377824     612 NHLLFADDTMFFCRvDPKSCLKLKSILHKYELASGQKINQAKYSITFSAKT 662
Cdd:pfam00078  132 TLVRYADDILIFSK-SEEEHQEALEEVLEWLKESGLKINPEKTQFFLKSKE 181
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 977-1070 3.63e-12

Reverse transcriptase-like; This domain is found in plants and appears to be part of a retrotransposon.


Pssm-ID: 433223 [Multi-domain]  Cd Length: 123  Bit Score: 64.21  E-value: 3.63e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3377824     977 SGNSSASDVGSPLIAETLVTLADVRVACESDIKAISFASDSQIIVKALNQKLQVKELHGILH-DILSLSSSFDACTFTFI 1055
Cdd:pfam13456   29 AGQKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGRSPKQSKLANLLdEIRKLLKRFESVSFEHI 108

                           90
                   ....*....|....*
gi 3377824    1056 NREFNHQADALAKRA 1070
Cdd:pfam13456  109 PREQNRVADTLAKMA 123
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 990-1071 2.49e-11

RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties.


Pssm-ID: 260011 [Multi-domain]  Cd Length: 128  Bit Score: 62.10  E-value: 2.49e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3377824   990 IAETLVTLADVRVACESDIKAISFASDSQIIVKALNQKLQVKE--LHGILHDILSLSSSFDACTFTFINREFNHQADALA 1067
Cdd:cd09279   44 EAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLNGEYKVKNerLKPLLEKVLELLAKFELVELKWIPREQNKEADALA 123


                 ....
gi 3377824  1068 KRAL 1071
Cdd:cd09279  124 NQAL 127
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 942-1068 1.27e-10

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


Pssm-ID: 259998 [Multi-domain]  Cd Length: 121  Bit Score: 60.02  E-value: 1.27e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3377824   942 DVSKQNRLSICSFTAPLHAGSGIWLpsqsdpismeSGNSSASDVGSPLIAETLVTLADVRVACESDIKAISFASDSQIIV 1021
Cdd:cd06222    4 DGSCRGNPGPAGIGGVLRDHEGGWL----------GGFALKIGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVV 73

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 3377824  1022 KALNQKLQVKELHG-ILHDILSLSSSFDACTFTFINREFNHQADALAK 1068
Cdd:cd06222   74 DLINSGSFKWSPNIlLIEDILLLLSRFWSVKISHVPREGNQVADALAK 121
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH