NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2151141547|gb|UFA27390|]
View 

polymerase protein [Hepatitis B virus]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
DNA_pol_viral_N super family cl02825
DNA polymerase (viral) N-terminal domain;
4-341 1.10e-168

DNA polymerase (viral) N-terminal domain;


The actual alignment was detected with superfamily member pfam00242:

Pssm-ID: 365972  Cd Length: 401  Bit Score: 494.01  E-value: 1.10e-168
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547   4 SYQHFRRLLLLDDEAGPLEEE--LPRLA----------DEGLNRRV---------AEDLNLGNLNVSIPWTHKVGNFTGL 62
Cdd:pfam00242   1 AEKHFRELELLDDEAGPLEEEklKPQLAmgedvqspgkDEGLHPNVraplshvvrAADIDLGNLGNKIPAKHHLGKFSGL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547  63 YSSTVPVFNPHWKTPSFPNIHLHQDIIKKCEQFVGPLTINEKRRLQLIMPARFYPNVTKYLPLDKGIKPYYPEHLVNHYF 142
Cdd:pfam00242  81 YQMKGCTFNPDWKTPDFPDIHFDEDIINECQQYVGPLTVNEKRNLKLIMPAKFWPKLIKYFPLDAGIKAKYPDNAMNHEA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 143 QTRHYLHTLWKAGILYKRETTRSASFCGSPYSWEQELQH-----------GAESFHQQSSGILS----RPPVGS------ 201
Cdd:pfam00242 161 ITGHYLHRLWEAGILYKRESKHLASFCGKPYNWEQELQHgrlvfqhqtpdGDESFCSKINGIAEnrrrRAPAGPcsrphd 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 202 -----SLQSKHRKSRLGLQSQQGHLARRQQGRSWSIRAGTHPTARRPFGVEPS-----GSGHTTNLASKSASCLYQSPVR 271
Cdd:pfam00242 241 serdcNMVGQIKNNRLGIQPQQGSCANGGGGKHGSITGRLACTGGKPFGTDPSyssrdASAHIDNRARSKSSCGFQSASR 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 272 KAAYPSVS-----------TFEKHSSSGHAVELHNLSPNSARSQSERPIFPCWWLQFRNSKPCSDYCLSHIVNLLEDWGP 340
Cdd:pfam00242 321 KKATGNHHhcsyvtnsveaTSKGQSSPGHAVELHNIPPSFARDQSEGPIFSCWWLEFRASKACDDYCLTHIVNLLEDSGP 400


                  .
gi 2151141547 341 C 341
Cdd:pfam00242 401 C 401
DNA_pol_viral_C super family cl02843
DNA polymerase (viral) C-terminal domain;
590-822 1.53e-132

DNA polymerase (viral) C-terminal domain;


The actual alignment was detected with superfamily member pfam00336:

Pssm-ID: 366036  Cd Length: 241  Bit Score: 394.83  E-value: 1.53e-132
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 590 GCYGSLPQDHIIQKIKECFRKLPVNRPIDWKVCQRIVGLLGFAAPFTQCGYPALMPLYACIQSKQAFTFSPTYKAFLCKQ 669
Cdd:pfam00336   1 DQKFMKIEEHIVIELKQCFKKIKIGAPIDWKCCQRFVGHLGFAAPFTKCGIEALKPLYAAIQNKQAFSFSPAYKAFLCKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 670 YLNLYPVA-RQRPG--LCQVFADATPTGWGLVMGHQRMRG-----TFSAPLPIHTAELLAACFARSRSGANILGTDNSVV 741
Cdd:pfam00336  81 TLGLCKLAiRPKSGvpLCQVAADATPTGGGLAIGHRRIRGgsavfAFSAPLDIHIAELLAACFAKIMIGAKCIGSDNSFV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 742 LSRKYTSFPWLLGCAANWILRGTSFVYVPSALNPADDPSRGRLGLSRPLLRLPFRPTTGRTSLYADSPSVPSHLPDRVHF 821
Cdd:pfam00336 161 CHKKYQSFPWHFACAAKQILRGIQFVFVPSALNPADDPSRGRLGDWRALLHLPFRPTTGRTSLYAVSPSKAIHIPDRLCF 240


                  .
gi 2151141547 822 A 822
Cdd:pfam00336 241 A 241
ps-ssRNAv_RdRp-like super family cl40470
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 505-589 7.44e-10

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: 59.60  E-value: 7.44e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 505 PMGVGLSPFLLAQFTSAICSVVRRAFPHCLAFSYMDDVVLGAKTVQHLESLYTAVTNFLLSLGIHLNPNKTKRwGYSLHF 584
Cdd:cd01645   130 PQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQK-EPPFQY 208


                  ....*
gi 2151141547 585 MGYVI 589
Cdd:cd01645   209 LGYEL 213
 
Name Accession Description Interval E-value
DNA_pol_viral_N pfam00242
DNA polymerase (viral) N-terminal domain;
4-341 1.10e-168

DNA polymerase (viral) N-terminal domain;


Pssm-ID: 365972  Cd Length: 401  Bit Score: 494.01  E-value: 1.10e-168
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547   4 SYQHFRRLLLLDDEAGPLEEE--LPRLA----------DEGLNRRV---------AEDLNLGNLNVSIPWTHKVGNFTGL 62
Cdd:pfam00242   1 AEKHFRELELLDDEAGPLEEEklKPQLAmgedvqspgkDEGLHPNVraplshvvrAADIDLGNLGNKIPAKHHLGKFSGL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547  63 YSSTVPVFNPHWKTPSFPNIHLHQDIIKKCEQFVGPLTINEKRRLQLIMPARFYPNVTKYLPLDKGIKPYYPEHLVNHYF 142
Cdd:pfam00242  81 YQMKGCTFNPDWKTPDFPDIHFDEDIINECQQYVGPLTVNEKRNLKLIMPAKFWPKLIKYFPLDAGIKAKYPDNAMNHEA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 143 QTRHYLHTLWKAGILYKRETTRSASFCGSPYSWEQELQH-----------GAESFHQQSSGILS----RPPVGS------ 201
Cdd:pfam00242 161 ITGHYLHRLWEAGILYKRESKHLASFCGKPYNWEQELQHgrlvfqhqtpdGDESFCSKINGIAEnrrrRAPAGPcsrphd 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 202 -----SLQSKHRKSRLGLQSQQGHLARRQQGRSWSIRAGTHPTARRPFGVEPS-----GSGHTTNLASKSASCLYQSPVR 271
Cdd:pfam00242 241 serdcNMVGQIKNNRLGIQPQQGSCANGGGGKHGSITGRLACTGGKPFGTDPSyssrdASAHIDNRARSKSSCGFQSASR 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 272 KAAYPSVS-----------TFEKHSSSGHAVELHNLSPNSARSQSERPIFPCWWLQFRNSKPCSDYCLSHIVNLLEDWGP 340
Cdd:pfam00242 321 KKATGNHHhcsyvtnsveaTSKGQSSPGHAVELHNIPPSFARDQSEGPIFSCWWLEFRASKACDDYCLTHIVNLLEDSGP 400


                  .
gi 2151141547 341 C 341
Cdd:pfam00242 401 C 401
DNA_pol_viral_C pfam00336
DNA polymerase (viral) C-terminal domain;
590-822 1.53e-132

DNA polymerase (viral) C-terminal domain;


Pssm-ID: 366036  Cd Length: 241  Bit Score: 394.83  E-value: 1.53e-132
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 590 GCYGSLPQDHIIQKIKECFRKLPVNRPIDWKVCQRIVGLLGFAAPFTQCGYPALMPLYACIQSKQAFTFSPTYKAFLCKQ 669
Cdd:pfam00336   1 DQKFMKIEEHIVIELKQCFKKIKIGAPIDWKCCQRFVGHLGFAAPFTKCGIEALKPLYAAIQNKQAFSFSPAYKAFLCKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 670 YLNLYPVA-RQRPG--LCQVFADATPTGWGLVMGHQRMRG-----TFSAPLPIHTAELLAACFARSRSGANILGTDNSVV 741
Cdd:pfam00336  81 TLGLCKLAiRPKSGvpLCQVAADATPTGGGLAIGHRRIRGgsavfAFSAPLDIHIAELLAACFAKIMIGAKCIGSDNSFV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 742 LSRKYTSFPWLLGCAANWILRGTSFVYVPSALNPADDPSRGRLGLSRPLLRLPFRPTTGRTSLYADSPSVPSHLPDRVHF 821
Cdd:pfam00336 161 CHKKYQSFPWHFACAAKQILRGIQFVFVPSALNPADDPSRGRLGDWRALLHLPFRPTTGRTSLYAVSPSKAIHIPDRLCF 240


                  .
gi 2151141547 822 A 822
Cdd:pfam00336 241 A 241
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 505-589 7.44e-10

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: 59.60  E-value: 7.44e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 505 PMGVGLSPFLLAQFTSAICSVVRRAFPHCLAFSYMDDVVLGAKTVQHLESLYTAVTNFLLSLGIHLNPNKTKRwGYSLHF 584
Cdd:cd01645   130 PQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQK-EPPFQY 208


                  ....*
gi 2151141547 585 MGYVI 589
Cdd:cd01645   209 LGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 444-589 6.62e-09

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: 56.54  E-value: 6.62e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 444 SRYVARLSSNSRIFNHQHGTMQNLHDCCSKQLYVSL-----------------LLLYQTFGRKLHLYSHP--IILGFRKI 504
Cdd:pfam00078  24 KIIVKRLKPENLDSPPQPGFRPGLAKLKKAKWFLKLdlkkafdqvpldeldrkLTAFTTPPININWNGELsgGRYEWKGL 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 505 PMGVGLSPFLLAQFTSAICSVVRRAFPHCLAfSYMDDVVLGAKTVQHLESLYTAVTNFLLSLGIHLNPNKTK--RWGYSL 582
Cdd:pfam00078 104 PQGLVLSPALFQLFMNELLRPLRKRAGLTLV-RYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQffLKSKEV 182


                  ....*..
gi 2151141547 583 HFMGYVI 589
Cdd:pfam00078 183 KYLGVTL 189
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 685-781 8.88e-04

DIRS1 family of RNase HI in long-term repeat retroelements; 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. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. The structural features of DIRS1-group elements are different from typical LTR elements. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260007  Cd Length: 120  Bit Score: 39.96  E-value: 8.88e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 685 QVFADATPTGWGLVMGHQRMRGTFS---APLPIHTAELLAA-----CFARSRSGANIL-GTDNSVVLS----RKYTSFPW 751
Cdd:cd09275     1 VLFTDASLSGWGAYLLNSRAHGPWSadeRNKHINLLELKAVllalqHFAAELKNRKILiRTDNTTAVAyinkQGGTSSPP 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2151141547 752 LLGCA---ANWIL-RGTSF--VYVPSALN-PADDPSR 781
Cdd:cd09275    81 LLALArqiLLWCEqRNIWLraSHIPGVLNtEADRLSR 117
 
Name Accession Description Interval E-value
DNA_pol_viral_N pfam00242
DNA polymerase (viral) N-terminal domain;
4-341 1.10e-168

DNA polymerase (viral) N-terminal domain;


Pssm-ID: 365972  Cd Length: 401  Bit Score: 494.01  E-value: 1.10e-168
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547   4 SYQHFRRLLLLDDEAGPLEEE--LPRLA----------DEGLNRRV---------AEDLNLGNLNVSIPWTHKVGNFTGL 62
Cdd:pfam00242   1 AEKHFRELELLDDEAGPLEEEklKPQLAmgedvqspgkDEGLHPNVraplshvvrAADIDLGNLGNKIPAKHHLGKFSGL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547  63 YSSTVPVFNPHWKTPSFPNIHLHQDIIKKCEQFVGPLTINEKRRLQLIMPARFYPNVTKYLPLDKGIKPYYPEHLVNHYF 142
Cdd:pfam00242  81 YQMKGCTFNPDWKTPDFPDIHFDEDIINECQQYVGPLTVNEKRNLKLIMPAKFWPKLIKYFPLDAGIKAKYPDNAMNHEA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 143 QTRHYLHTLWKAGILYKRETTRSASFCGSPYSWEQELQH-----------GAESFHQQSSGILS----RPPVGS------ 201
Cdd:pfam00242 161 ITGHYLHRLWEAGILYKRESKHLASFCGKPYNWEQELQHgrlvfqhqtpdGDESFCSKINGIAEnrrrRAPAGPcsrphd 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 202 -----SLQSKHRKSRLGLQSQQGHLARRQQGRSWSIRAGTHPTARRPFGVEPS-----GSGHTTNLASKSASCLYQSPVR 271
Cdd:pfam00242 241 serdcNMVGQIKNNRLGIQPQQGSCANGGGGKHGSITGRLACTGGKPFGTDPSyssrdASAHIDNRARSKSSCGFQSASR 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 272 KAAYPSVS-----------TFEKHSSSGHAVELHNLSPNSARSQSERPIFPCWWLQFRNSKPCSDYCLSHIVNLLEDWGP 340
Cdd:pfam00242 321 KKATGNHHhcsyvtnsveaTSKGQSSPGHAVELHNIPPSFARDQSEGPIFSCWWLEFRASKACDDYCLTHIVNLLEDSGP 400


                  .
gi 2151141547 341 C 341
Cdd:pfam00242 401 C 401
DNA_pol_viral_C pfam00336
DNA polymerase (viral) C-terminal domain;
590-822 1.53e-132

DNA polymerase (viral) C-terminal domain;


Pssm-ID: 366036  Cd Length: 241  Bit Score: 394.83  E-value: 1.53e-132
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 590 GCYGSLPQDHIIQKIKECFRKLPVNRPIDWKVCQRIVGLLGFAAPFTQCGYPALMPLYACIQSKQAFTFSPTYKAFLCKQ 669
Cdd:pfam00336   1 DQKFMKIEEHIVIELKQCFKKIKIGAPIDWKCCQRFVGHLGFAAPFTKCGIEALKPLYAAIQNKQAFSFSPAYKAFLCKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 670 YLNLYPVA-RQRPG--LCQVFADATPTGWGLVMGHQRMRG-----TFSAPLPIHTAELLAACFARSRSGANILGTDNSVV 741
Cdd:pfam00336  81 TLGLCKLAiRPKSGvpLCQVAADATPTGGGLAIGHRRIRGgsavfAFSAPLDIHIAELLAACFAKIMIGAKCIGSDNSFV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 742 LSRKYTSFPWLLGCAANWILRGTSFVYVPSALNPADDPSRGRLGLSRPLLRLPFRPTTGRTSLYADSPSVPSHLPDRVHF 821
Cdd:pfam00336 161 CHKKYQSFPWHFACAAKQILRGIQFVFVPSALNPADDPSRGRLGDWRALLHLPFRPTTGRTSLYAVSPSKAIHIPDRLCF 240


                  .
gi 2151141547 822 A 822
Cdd:pfam00336 241 A 241
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 505-589 7.44e-10

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: 59.60  E-value: 7.44e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 505 PMGVGLSPFLLAQFTSAICSVVRRAFPHCLAFSYMDDVVLGAKTVQHLESLYTAVTNFLLSLGIHLNPNKTKRwGYSLHF 584
Cdd:cd01645   130 PQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQK-EPPFQY 208


                  ....*
gi 2151141547 585 MGYVI 589
Cdd:cd01645   209 LGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 444-589 6.62e-09

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: 56.54  E-value: 6.62e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 444 SRYVARLSSNSRIFNHQHGTMQNLHDCCSKQLYVSL-----------------LLLYQTFGRKLHLYSHP--IILGFRKI 504
Cdd:pfam00078  24 KIIVKRLKPENLDSPPQPGFRPGLAKLKKAKWFLKLdlkkafdqvpldeldrkLTAFTTPPININWNGELsgGRYEWKGL 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 505 PMGVGLSPFLLAQFTSAICSVVRRAFPHCLAfSYMDDVVLGAKTVQHLESLYTAVTNFLLSLGIHLNPNKTK--RWGYSL 582
Cdd:pfam00078 104 PQGLVLSPALFQLFMNELLRPLRKRAGLTLV-RYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQffLKSKEV 182


                  ....*..
gi 2151141547 583 HFMGYVI 589
Cdd:pfam00078 183 KYLGVTL 189
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 526-605 3.24e-05

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: 45.01  E-value: 3.24e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 526 VRRAFPHCLAFSYMDDVVLGAKTVQHLESLYTAVTNFLLSLGIHLNPNKTK-----RWGYSLHFMGYVIgcYGSLPQDHI 600
Cdd:cd01646    76 LKSKLKGVDYVRYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEilplpEGTASKDFLGYRF--SPILLIKSS 153


                  ....*
gi 2151141547 601 IQKIK 605
Cdd:cd01646   154 ERKMS 158
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 503-589 4.61e-05

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: 43.11  E-value: 4.61e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 503 KIPMGVGLSPfLLAQFTSA-ICSVVRRAFPHCLAFSYMDDVVLGAKTVQHLESLyTAVTNFLLSLGIHLNPNKTK--RWG 579
Cdd:cd00304    11 PLPQGSPLSP-ALANLYMEkLEAPILKQLLDITLIRYVDDLVVIAKSEQQAVKK-RELEEFLARLGLNLSDEKTQftEKE 88

                          90
                  ....*....|
gi 2151141547 580 YSLHFMGYVI 589
Cdd:cd00304    89 KKFKFLGILV 98
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 685-781 8.88e-04

DIRS1 family of RNase HI in long-term repeat retroelements; 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. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. The structural features of DIRS1-group elements are different from typical LTR elements. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260007  Cd Length: 120  Bit Score: 39.96  E-value: 8.88e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 685 QVFADATPTGWGLVMGHQRMRGTFS---APLPIHTAELLAA-----CFARSRSGANIL-GTDNSVVLS----RKYTSFPW 751
Cdd:cd09275     1 VLFTDASLSGWGAYLLNSRAHGPWSadeRNKHINLLELKAVllalqHFAAELKNRKILiRTDNTTAVAyinkQGGTSSPP 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2151141547 752 LLGCA---ANWIL-RGTSF--VYVPSALN-PADDPSR 781
Cdd:cd09275    81 LLALArqiLLWCEqRNIWLraSHIPGVLNtEADRLSR 117
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 501-589 1.13e-03

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: 40.66  E-value: 1.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 501 FRKIPMGVGLSPfllAQFTSAICSVVRRAFPHClAFSYMDDVVLGAKTVQ-HLESLyTAVTNFLLSLGIHLNPNKTKRWG 579
Cdd:cd01647    93 YTRMPFGLKNAP---ATFQRLMNKILGDLLGDF-VEVYLDDILVYSKTEEeHLEHL-REVLERLREAGLKLNPEKCEFGV 167

                          90
                  ....*....|
gi 2151141547 580 YSLHFMGYVI 589
Cdd:cd01647   168 PEVEFLGHIV 177
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 443-576 3.43e-03

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: 39.97  E-value: 3.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 443 LSRYVA-RLSS--NSRIFNHQHGTMQNlhDCCSKQLYVSLLLLYQTFGRKLHLY-------------SHPII---LGfrk 503
Cdd:cd01650    32 LEKILAnRLRPvlEENILPNQFGFRPG--RSTTDAILLLREVIEKAKEKKKSLVlvfldfekafdsvDHEFLlkaLG--- 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151141547 504 IPMGVGLSPFLLAQFTSAI------CSVVRRAFPHCLAFSYMDDVVLGAKTVQH-LESLYTAVTNFLLSLGIHLNPNKTK 576
Cdd:cd01650   107 VRQGDPLSPLLFNLALDDLlrllnkEEEIKLGGPGITHLAYADDIVLFSEGKSRkLQELLQRLQEWSKESGLKINPSKSK 186
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 538-589 8.23e-03

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: 38.72  E-value: 8.23e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2151141547 538 YMDDVVLGAKTVQHLESLYTAVTNFLLSLGIHLNPNKTKR---WGYSLHFMGYVI 589
Cdd:cd01651   172 YADDFVIGVRGPKEAEEIKELIREFLEELGLELNPEKTRIthfKSEGFDFLGFTF 226
 
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