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Conserved domains on  [gi|1172384876|emb|SJL40791|]
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RT, partial [HIV-1 M:CRF01 BA4]

Protein Classification

reverse transcriptase( domain architecture ID 10254309)

reverse transcriptase (RT) and RT thumb domain-containing protein may catalyze the formation of DNA from an RNA template in reverse transcription

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 ...
 1-194 1.71e-102

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 cd01645:

Pssm-ID: 477363 [Multi-domain]  Cd Length: 213  Bit Score: 298.43  E-value: 1.71e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384876   1 MEEEGKISKIGpeNPYNTPVFAIKRKHGdKWRKLVDFRELNKRTQDFWEIQLGIPHPAGLKKNKSVTVLDVGDAYFSVPL 80
Cdd:cd01645    24 QLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHPAALPKGWPLIVLDLKDCFFSIPL 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384876  81 HEDFRKYTAFTIPSMNNETPGVRYQYNVLPQGWKGSPAIFQASMTKILEPFRAKNPELVICQYMDDLYVASDLEiGQHRA 160
Cdd:cd01645   101 HPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDLE-GQLRE 179

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1172384876 161 KIEKLRAHLLSWGLTTPD*KHQKEPPFRWMGYEL 194
Cdd:cd01645   180 IYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 201-264 1.34e-22

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.


:

Pssm-ID: 429135  Cd Length: 66  Bit Score: 88.53  E-value: 1.34e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1172384876 201 VQPIELPEKDSWTVNDIQKLVGKLNWASQIYA--GIKVKQLCKLLRGAKALTDIVPLTKEAELELE 264
Cdd:pfam06817   1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLGitTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 1-194 1.71e-102

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.


Pssm-ID: 238823 [Multi-domain]  Cd Length: 213  Bit Score: 298.43  E-value: 1.71e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384876   1 MEEEGKISKIGpeNPYNTPVFAIKRKHGdKWRKLVDFRELNKRTQDFWEIQLGIPHPAGLKKNKSVTVLDVGDAYFSVPL 80
Cdd:cd01645    24 QLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHPAALPKGWPLIVLDLKDCFFSIPL 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384876  81 HEDFRKYTAFTIPSMNNETPGVRYQYNVLPQGWKGSPAIFQASMTKILEPFRAKNPELVICQYMDDLYVASDLEiGQHRA 160
Cdd:cd01645   101 HPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDLE-GQLRE 179

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1172384876 161 KIEKLRAHLLSWGLTTPD*KHQKEPPFRWMGYEL 194
Cdd:cd01645   180 IYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 23-194 1.10e-43

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: 147.45  E-value: 1.10e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384876  23 IKRKHGDKWRKL----VDFRELNKRTQD-------FWEIQLGIPHPAG-LKKNKSVTVLDVGDAYFSVPLHEDFRKYTAF 90
Cdd:pfam00078   1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384876  91 TIPSMNN----ETPGVRYQYNVLPQGWKGSPAIFQASMTKILEPFRAKnPELVICQYMDDLYVASDlEIGQHRAKIEKLR 166
Cdd:pfam00078  81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKR-AGLTLVRYADDILIFSK-SEEEHQEALEEVL 158

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1172384876 167 AHLLSWGLTTPD*KHQ---KEPPFRWMGYEL 194
Cdd:pfam00078 159 EWLKESGLKINPEKTQfflKSKEVKYLGVTL 189
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 201-264 1.34e-22

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.


Pssm-ID: 429135  Cd Length: 66  Bit Score: 88.53  E-value: 1.34e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1172384876 201 VQPIELPEKDSWTVNDIQKLVGKLNWASQIYA--GIKVKQLCKLLRGAKALTDIVPLTKEAELELE 264
Cdd:pfam06817   1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLGitTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 1-194 1.71e-102

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.


Pssm-ID: 238823 [Multi-domain]  Cd Length: 213  Bit Score: 298.43  E-value: 1.71e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384876   1 MEEEGKISKIGpeNPYNTPVFAIKRKHGdKWRKLVDFRELNKRTQDFWEIQLGIPHPAGLKKNKSVTVLDVGDAYFSVPL 80
Cdd:cd01645    24 QLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHPAALPKGWPLIVLDLKDCFFSIPL 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384876  81 HEDFRKYTAFTIPSMNNETPGVRYQYNVLPQGWKGSPAIFQASMTKILEPFRAKNPELVICQYMDDLYVASDLEiGQHRA 160
Cdd:cd01645   101 HPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDLE-GQLRE 179

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1172384876 161 KIEKLRAHLLSWGLTTPD*KHQKEPPFRWMGYEL 194
Cdd:cd01645   180 IYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 23-194 1.10e-43

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: 147.45  E-value: 1.10e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384876  23 IKRKHGDKWRKL----VDFRELNKRTQD-------FWEIQLGIPHPAG-LKKNKSVTVLDVGDAYFSVPLHEDFRKYTAF 90
Cdd:pfam00078   1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384876  91 TIPSMNN----ETPGVRYQYNVLPQGWKGSPAIFQASMTKILEPFRAKnPELVICQYMDDLYVASDlEIGQHRAKIEKLR 166
Cdd:pfam00078  81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKR-AGLTLVRYADDILIFSK-SEEEHQEALEEVL 158

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1172384876 167 AHLLSWGLTTPD*KHQ---KEPPFRWMGYEL 194
Cdd:pfam00078 159 EWLKESGLKINPEKTQfflKSKEVKYLGVTL 189
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 15-182 6.93e-29

RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. 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. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.


Pssm-ID: 239685 [Multi-domain]  Cd Length: 210  Bit Score: 109.74  E-value: 6.93e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384876  15 PYNTPVFAIKRKHGDKWRKLVDFRELNKRTQDfweIQLGIPHPAGL-----KKNKSVTVLDVGDAYFSVPLHEDFRKYTA 89
Cdd:cd03715    36 PWNTPILPVKKPGGNDYRMVQDLRLVNQAVLP---IHPAVPNPYTLlsllpPKHQWYTVLDLANAFFSLPLAPDSQPLFA 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384876  90 FTIPsmnnetpGVRYQYNVLPQGWKGSPAIFQASMTKILEPFRAKNPELVICQYMDDLYVASDLEIGQHRAkIEKLRAHL 169
Cdd:cd03715   113 FEWE-------GQQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGTILLQYVDDLLLAADSEEDCLKG-TDALLTHL 184

                         170
                  ....*....|...
gi 1172384876 170 LSWGLTTPD*KHQ 182
Cdd:cd03715   185 GELGYKVSPKKAQ 197
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 15-175 3.67e-27

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


Pssm-ID: 238825  Cd Length: 177  Bit Score: 104.21  E-value: 3.67e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384876  15 PYNTPVFAIKRKHGdKWRKLVDFRELNKRT-QDFWEIqlgiPHPAG----LKKNKSVTVLDVGDAYFSVPLHEDFRKYTA 89
Cdd:cd01647     9 PYASPVVVVKKKDG-KLRLCVDYRKLNKVTiKDRYPL----PTIDElleeLAGAKVFSKLDLRSGYHQIPLAEESRPKTA 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384876  90 FTipsmnneTPGVRYQYNVLPQGWKGSPAIFQASMTKILEPFRAKNpelVICqYMDDLYVASDlEIGQHRAKIEKLRAHL 169
Cdd:cd01647    84 FR-------TPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDF---VEV-YLDDILVYSK-TEEEHLEHLREVLERL 151


                  ....*.
gi 1172384876 170 LSWGLT 175
Cdd:cd01647   152 REAGLK 157
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 201-264 1.34e-22

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.


Pssm-ID: 429135  Cd Length: 66  Bit Score: 88.53  E-value: 1.34e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1172384876 201 VQPIELPEKDSWTVNDIQKLVGKLNWASQIYA--GIKVKQLCKLLRGAKALTDIVPLTKEAELELE 264
Cdd:pfam06817   1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLGitTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 109-194 1.66e-17

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: 75.85  E-value: 1.66e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384876 109 LPQGWKGSPAIFQASMTKILEPFRAKNPELVICQYMDDLYVASDLEigQHRAKIEKLRAHLLSWGLTTPD*KHQ---KEP 185
Cdd:cd00304    12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSE--QQAVKKRELEEFLARLGLNLSDEKTQfteKEK 89


                  ....*....
gi 1172384876 186 PFRWMGYEL 194
Cdd:cd00304    90 KFKFLGILV 98
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 69-194 6.93e-09

RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.


Pssm-ID: 239684 [Multi-domain]  Cd Length: 119  Bit Score: 52.73  E-value: 6.93e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172384876  69 LDVGDAYFSVPLHEDFRKYTAFtIPSmnnetpGVRYQYNVLPQGWKGSPAIFqasmTKILEPFRA--KNPELVICQYMDD 146
Cdd:cd03714     1 VDLKDAYFHIPILPRSRDLLGF-AWQ------GETYQFKALPFGLSLAPRVF----TKVVEALLAplRLLGVRIFSYLDD 69

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1172384876 147 LYVASdlEIGQHRAKIEKLRAHLLSW--GLTTPD*KHQKEPP--FRWMGYEL 194
Cdd:cd03714    70 LLIIA--SSIKTSEAVLRHLRATLLAnlGFTLNLEKSKLGPTqrITFLGLEL 119
 
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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