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Conserved domains on  [gi|146452990|gb|EDK47246|]
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conserved hypothetical protein [Lodderomyces elongisporus NRRL YB-4239]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 332-509 1.06e-58

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: 199.74  E-value: 1.06e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990  332 GLIRQLgvgESDFNSPVLFVRKKDGSYRMCVDYRLLNLTVVQKQFGMPVVEQLIKEVSGYRYYSTLDMTQSFHQIRLDDE 411
Cdd:cd01647     1 GIIEPS---SSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990  412 TSHVTAFTAFGKKFAYNVLPFGFTNAPAILQETVSQLIQE--IPGCVNYIDDIIVYSNTIEEHRKSLLLLFEAFRRNKFF 489
Cdd:cd01647    78 SRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDllGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLK 157

                         170       180
                  ....*....|....*....|
gi 146452990  490 FKGSKCELGVSKVTFLGHEV 509
Cdd:cd01647   158 LNPEKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 606-727 6.02e-49

Ty3/Gypsy 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. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


:

Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 169.60  E-value: 6.02e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990  606 LEVDASHHAIGAVLKQVHEDKVVGVIEMVSRTLTVAEKNYPIRQKELLLIVFAVKKFRHYILGYETVVYTDHQSLESLFa 685
Cdd:cd09274     2 LETDASDYGIGAVLSQEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL- 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 146452990  686 sNTRPESERIIRWLESLQEVQLKVRYRNGDANVLADVLSRLV 727
Cdd:cd09274    81 -TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 821-876 2.06e-11

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


:

Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 60.34  E-value: 2.06e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 146452990   821 VGKSVARMVLEKVH-SFGHFGITKCYFAIQPYLFVPKLLEVVTDYINSCDHCQRAKA 876
Cdd:pfam17921    1 VPKSLRKEILKEAHdSGGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 120-204 1.42e-09

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


:

Pssm-ID: 133136  Cd Length: 92  Bit Score: 56.19  E-value: 1.42e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990  120 VKGKECMALLDSGSGEDLVLSKFIEG-KIDSLPQDACLCDVIVAFGASRQVTKRVLLEFSINGIHFSRWFMVVPGFTKDM 198
Cdd:cd00303     5 INGVPVRALVDSGASVNFISESLAKKlGLPPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLSYDV 84


                  ....*.
gi 146452990  199 VLGLDF 204
Cdd:cd00303    85 ILGRPW 90
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 898-991 4.67e-05

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


:

Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 43.46  E-value: 4.67e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990   898 IHLDFVTGIPTTPEGYDCILVVVCALTKYCVCIPTRKSTKVVQTAKLLIDEVFSVFGVPHTIKSDKDIQFMNSIMKYVFE 977
Cdd:pfam00665    5 WQGDFTYIRIPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFREFLK 84

                           90
                   ....*....|....
gi 146452990   978 FYQIDFRTTSTNNP 991
Cdd:pfam00665   85 DLGIKPSFSRPGNP 98
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 332-509 1.06e-58

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: 199.74  E-value: 1.06e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990  332 GLIRQLgvgESDFNSPVLFVRKKDGSYRMCVDYRLLNLTVVQKQFGMPVVEQLIKEVSGYRYYSTLDMTQSFHQIRLDDE 411
Cdd:cd01647     1 GIIEPS---SSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990  412 TSHVTAFTAFGKKFAYNVLPFGFTNAPAILQETVSQLIQE--IPGCVNYIDDIIVYSNTIEEHRKSLLLLFEAFRRNKFF 489
Cdd:cd01647    78 SRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDllGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLK 157

                         170       180
                  ....*....|....*....|
gi 146452990  490 FKGSKCELGVSKVTFLGHEV 509
Cdd:cd01647   158 LNPEKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 606-727 6.02e-49

Ty3/Gypsy 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. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 169.60  E-value: 6.02e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990  606 LEVDASHHAIGAVLKQVHEDKVVGVIEMVSRTLTVAEKNYPIRQKELLLIVFAVKKFRHYILGYETVVYTDHQSLESLFa 685
Cdd:cd09274     2 LETDASDYGIGAVLSQEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL- 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 146452990  686 sNTRPESERIIRWLESLQEVQLKVRYRNGDANVLADVLSRLV 727
Cdd:cd09274    81 -TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 604-704 2.05e-37

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 136.10  E-value: 2.05e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990   604 FQLEVDASHHAIGAVLKQVHEDKVVGVIEMVSRTLTVAEKNYPIRQKELLLIVFAVKKFRHYILGYETVVYTDHQSLESL 683
Cdd:pfam17917    6 FILETDASDYGIGAVLSQKDEDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHKPLKYL 85

                           90       100
                   ....*....|....*....|.
gi 146452990   684 FasNTRPESERIIRWLESLQE 704
Cdd:pfam17917   86 F--TPKELNGRLARWALFLQE 104
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 351-509 3.87e-27

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: 109.70  E-value: 3.87e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990   351 VRKKD-GSYRMC----VDYRLLNLTVVQK----------QFGMPvveQLIKEVSGYRYYSTLDMTQSFHQIRLDDETSHV 415
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKRlkpenldsppQPGFR---PGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKL 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990   416 TAFTAF-----------GKKFAYNVLPFGFTNAPAILQETVSQLIQEIPGCVN-----YIDDIIVYSNTIEEHRKSLLLL 479
Cdd:pfam00078   78 TAFTTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRAGltlvrYADDILIFSKSEEEHQEALEEV 157

                          170       180       190
                   ....*....|....*....|....*....|..
gi 146452990   480 FEAFRRNKFFFKGSKCE--LGVSKVTFLGHEV 509
Cdd:pfam00078  158 LEWLKESGLKINPEKTQffLKSKEVKYLGVTL 189
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 821-876 2.06e-11

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 60.34  E-value: 2.06e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 146452990   821 VGKSVARMVLEKVH-SFGHFGITKCYFAIQPYLFVPKLLEVVTDYINSCDHCQRAKA 876
Cdd:pfam17921    1 VPKSLRKEILKEAHdSGGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 120-204 1.42e-09

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133136  Cd Length: 92  Bit Score: 56.19  E-value: 1.42e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990  120 VKGKECMALLDSGSGEDLVLSKFIEG-KIDSLPQDACLCDVIVAFGASRQVTKRVLLEFSINGIHFSRWFMVVPGFTKDM 198
Cdd:cd00303     5 INGVPVRALVDSGASVNFISESLAKKlGLPPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLSYDV 84


                  ....*.
gi 146452990  199 VLGLDF 204
Cdd:cd00303    85 ILGRPW 90
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 898-991 4.67e-05

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 43.46  E-value: 4.67e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990   898 IHLDFVTGIPTTPEGYDCILVVVCALTKYCVCIPTRKSTKVVQTAKLLIDEVFSVFGVPHTIKSDKDIQFMNSIMKYVFE 977
Cdd:pfam00665    5 WQGDFTYIRIPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFREFLK 84

                           90
                   ....*....|....
gi 146452990   978 FYQIDFRTTSTNNP 991
Cdd:pfam00665   85 DLGIKPSFSRPGNP 98
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 332-509 1.06e-58

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: 199.74  E-value: 1.06e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990  332 GLIRQLgvgESDFNSPVLFVRKKDGSYRMCVDYRLLNLTVVQKQFGMPVVEQLIKEVSGYRYYSTLDMTQSFHQIRLDDE 411
Cdd:cd01647     1 GIIEPS---SSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990  412 TSHVTAFTAFGKKFAYNVLPFGFTNAPAILQETVSQLIQE--IPGCVNYIDDIIVYSNTIEEHRKSLLLLFEAFRRNKFF 489
Cdd:cd01647    78 SRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDllGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLK 157

                         170       180
                  ....*....|....*....|
gi 146452990  490 FKGSKCELGVSKVTFLGHEV 509
Cdd:cd01647   158 LNPEKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 606-727 6.02e-49

Ty3/Gypsy 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. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 169.60  E-value: 6.02e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990  606 LEVDASHHAIGAVLKQVHEDKVVGVIEMVSRTLTVAEKNYPIRQKELLLIVFAVKKFRHYILGYETVVYTDHQSLESLFa 685
Cdd:cd09274     2 LETDASDYGIGAVLSQEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL- 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 146452990  686 sNTRPESERIIRWLESLQEVQLKVRYRNGDANVLADVLSRLV 727
Cdd:cd09274    81 -TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 604-704 2.05e-37

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 136.10  E-value: 2.05e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990   604 FQLEVDASHHAIGAVLKQVHEDKVVGVIEMVSRTLTVAEKNYPIRQKELLLIVFAVKKFRHYILGYETVVYTDHQSLESL 683
Cdd:pfam17917    6 FILETDASDYGIGAVLSQKDEDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHKPLKYL 85

                           90       100
                   ....*....|....*....|.
gi 146452990   684 FasNTRPESERIIRWLESLQE 704
Cdd:pfam17917   86 F--TPKELNGRLARWALFLQE 104
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
571-673 7.16e-31

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 117.22  E-value: 7.16e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990   571 FTQVHDKAFNQLKADLVKSDALVKVNYELKpvrFQLEVDASHHAIGAVLKQVHEDKVVGVIEMVSRTLTVAEKNYPIRQK 650
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKP---FILETDASDYGIGAVLSQEDDDGGERPIAYASRKLSPAERNYSTTEK 77

                           90       100
                   ....*....|....*....|...
gi 146452990   651 ELLLIVFAVKKFRHYILGYETVV 673
Cdd:pfam17919   78 ELLAIVFALKKFRHYLLGRKFTV 100
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 309-506 5.26e-28

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: 112.83  E-value: 5.26e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990  309 KQYPLAKPEFEELKSQVRKMLDAGLIRQLgvgESDFNSPVLFVRKKDG-SYRMCVDYRLLNLTVVQKQFGMPVVEQLIKE 387
Cdd:cd03715     5 KQYPLPREAREGITPHIQELLEAGILVPC---QSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLSL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990  388 VS-GYRYYSTLDMTQSFHQIRLDDETSHVTAFTAFGKKFAYNVLPFGFTNAPAILQETVSQLIQEIP----GC--VNYID 460
Cdd:cd03715    82 LPpKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFHEALARDLAPFPleheGTilLQYVD 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 146452990  461 DIIVYSNTIEE----HRKSLLLLFEA-FRRNKFFFKGSKcelgvSKVTFLG 506
Cdd:cd03715   162 DLLLAADSEEDclkgTDALLTHLGELgYKVSPKKAQICR-----AEVKFLG 207
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 351-509 3.87e-27

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: 109.70  E-value: 3.87e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990   351 VRKKD-GSYRMC----VDYRLLNLTVVQK----------QFGMPvveQLIKEVSGYRYYSTLDMTQSFHQIRLDDETSHV 415
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKRlkpenldsppQPGFR---PGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKL 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990   416 TAFTAF-----------GKKFAYNVLPFGFTNAPAILQETVSQLIQEIPGCVN-----YIDDIIVYSNTIEEHRKSLLLL 479
Cdd:pfam00078   78 TAFTTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRAGltlvrYADDILIFSKSEEEHQEALEEV 157

                          170       180       190
                   ....*....|....*....|....*....|..
gi 146452990   480 FEAFRRNKFFFKGSKCE--LGVSKVTFLGHEV 509
Cdd:pfam00078  158 LEWLKESGLKINPEKTQffLKSKEVKYLGVTL 189
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 309-509 1.06e-22

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: 97.74  E-value: 1.06e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990  309 KQYPLAKPEFEELKSQVRKMLDAGlirQLGVGESDFNSPVLFVRKKDGSYRMCVDYRLLNLTVV---QKQFGMPVVEQLI 385
Cdd:cd01645     5 KQWPLTEEKLEALTELVTEQLKEG---HIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQdmgALQPGLPHPAALP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990  386 KevsgyRYYST-LDMTQSFHQIRLDDETSHVTAFT-------AFGKKFAYNVLPFGFTNAPAILQETVSQLIQEIPGC-- 455
Cdd:cd01645    82 K-----GWPLIvLDLKDCFFSIPLHPDDRERFAFTvpsinnkGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQyp 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 146452990  456 ----VNYIDDIIVYSNTIEEHRKSLLLLFEAFRRNKFFFKGSKCELGvSKVTFLGHEV 509
Cdd:cd01645   157 diviYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKE-PPFQYLGYEL 213
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 821-876 2.06e-11

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 60.34  E-value: 2.06e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 146452990   821 VGKSVARMVLEKVH-SFGHFGITKCYFAIQPYLFVPKLLEVVTDYINSCDHCQRAKA 876
Cdd:pfam17921    1 VPKSLRKEILKEAHdSGGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 120-204 1.42e-09

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133136  Cd Length: 92  Bit Score: 56.19  E-value: 1.42e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990  120 VKGKECMALLDSGSGEDLVLSKFIEG-KIDSLPQDACLCDVIVAFGASRQVTKRVLLEFSINGIHFSRWFMVVPGFTKDM 198
Cdd:cd00303     5 INGVPVRALVDSGASVNFISESLAKKlGLPPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLSYDV 84


                  ....*.
gi 146452990  199 VLGLDF 204
Cdd:cd00303    85 ILGRPW 90
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 397-509 2.13e-06

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: 48.11  E-value: 2.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990  397 LDMTQSFHQIRLDDETSHVTAFTAFGKKFAYNVLPFGFTNAPAI----LQETVSQLIQEIPGCVNYIDDIIVYSNTIEEH 472
Cdd:cd03714     1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVftkvVEALLAPLRLLGVRIFSYLDDLLIIASSIKTS 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 146452990  473 RKSLLLLFEAFRRNK-FFFKGSKCELGVSK-VTFLGHEV 509
Cdd:cd03714    81 EAVLRHLRATLLANLgFTLNLEKSKLGPTQrITFLGLEL 119
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 642-728 1.42e-05

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: 45.74  E-value: 1.42e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990  642 EKNYPIRQKELLLIVFAVKKFRHYILGYETVVYTD---------HQSLESLFASNTrpESERIIRWLESlQEVQLKVRYR 712
Cdd:cd09275    28 ERNKHINLLELKAVLLALQHFAAELKNRKILIRTDnttavayinKQGGTSSPPLLA--LARQILLWCEQ-RNIWLRASHI 104

                          90
                  ....*....|....*.
gi 146452990  713 NGDANVLADVLSRLVD 728
Cdd:cd09275   105 PGVLNTEADRLSRLGL 120
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 898-991 4.67e-05

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 43.46  E-value: 4.67e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990   898 IHLDFVTGIPTTPEGYDCILVVVCALTKYCVCIPTRKSTKVVQTAKLLIDEVFSVFGVPHTIKSDKDIQFMNSIMKYVFE 977
Cdd:pfam00665    5 WQGDFTYIRIPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFREFLK 84

                           90
                   ....*....|....
gi 146452990   978 FYQIDFRTTSTNNP 991
Cdd:pfam00665   85 DLGIKPSFSRPGNP 98
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 398-472 1.33e-03

RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.


Pssm-ID: 238822  Cd Length: 213  Bit Score: 41.52  E-value: 1.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146452990  398 DMTQSFHQIRLDDETSHVTAF-------TAFGKKFAYNVLPFGFTNAPAILQETVSQLIQEIPGCVN--------YIDDI 462
Cdd:cd01644    65 DIEKMFHQVKVRPEDRDVLRFlwrkdgdEPKPIEYRMTVVPFGAASAPFLANRALKQHAEDHPHEAAakiikrnfYVDDI 144

                          90
                  ....*....|
gi 146452990  463 IVYSNTIEEH 472
Cdd:cd01644   145 LVSTDTLNEA 154
 
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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