NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|330443635|ref|NP_012421.2|]
View 

TPA: gag-pol fusion protein [Saccharomyces cerevisiae S288C]

Protein Classification

rve and RVT_2 domain-containing protein (domain architecture ID 10461216)

protein containing domains rve, RVT_2, and RNase_H_like

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
RVT_2 super family cl06662
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1067-1278 4.93e-36

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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


The actual alignment was detected with superfamily member pfam07727:

Pssm-ID: 311594  Cd Length: 246  Bit Score: 140.03  E-value: 4.93e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443635  1067 IVPTNTIFTKKRN-----GIYKARIVCRGDTQSP-----DTYS-VITTESlnhnhIKIFLMIANNRNMFMKTLDINHAFL 1135
Cdd:pfam07727   15 PIGCKWVFKVKRDsdgkvVRYKARLVAKGFTQKEgidydETFSpVARLES-----IRLLLALAAQRGWELHQMDVKSAFL 89
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443635  1136 YAKLEEEIYI---------PHPHDrrcVVKLNKALYGLKQSPKEWNDHLRQYLNGIGLKDNSYTPGLY--QTEDKNLMIA 1204
Cdd:pfam07727   90 NGELEEEVYVkqppgfvvpGKPNK---VCKLKKSLYGLKQAPRAWYSRLDSVLLSLGFKRSKHDHGLFikGKGDGFLIVG 166
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 330443635  1205 VYVDDCVIAASNEQRLDEFINKLKSNFELKITGTLiddvldTDILGMDLVYNKrlGTIDLTLKSFINRMDKKYN 1278
Cdd:pfam07727  167 LYVDDILITGSSEKEINEFKEELSKEFEMKDLGEL------SYFLGIEIKQTP--GGITLSQSKYIKKLLERFG 232
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
369-483 1.80e-16

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: 307008  Cd Length: 114  Bit Score: 79.22  E-value: 1.80e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443635   369 PGSSWCMDIFgPVSSSNADTKRYMLIMVDNNTRYCMTSTHFNK-NAETILAQVRKNIQYVetqfdRKVREINSDRGTEFT 447
Cdd:pfam00665    1 PNELWQTDFT-YVRVPGGGGKLYLAVAVDDFSREIVAWALSSEmDAELVIDALKRAIAFR-----GGPKIIHSDNGSEYT 74
                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 330443635   448 NDQIEEYFISKGIHHILTSTQDHAANGRAERYIRTI 483
Cdd:pfam00665   75 SKAFREFLAHYGITHSFSRPGNPQDNGKVERFNGTL 110
RNase_H_like super family cl14782
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
1386-1523 1.03e-13

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


The actual alignment was detected with superfamily member cd09272:

Pssm-ID: 326352  Cd Length: 140  Bit Score: 71.73  E-value: 1.03e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443635 1386 IAITDASVGSEYD-AQSRIGVILWYGMNIFNVYSNKSTNRCVSSTEAELHAIYEGYADSETLKVTLKELGEGDNNDIVMI 1464
Cdd:cd09272     1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGIPLDGPTTIY 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 330443635 1465 TDSKPAIQGLNRSYQQPKEKFTWIKTEIIKEKIKEKSIKLLKITGKGNIADLLTKPVSA 1523
Cdd:cd09272    81 CDNQSAIALAKNPVFHSRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLPR 139
 
Name Accession Description Interval E-value
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1067-1278 4.93e-36

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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


Pssm-ID: 311594  Cd Length: 246  Bit Score: 140.03  E-value: 4.93e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443635  1067 IVPTNTIFTKKRN-----GIYKARIVCRGDTQSP-----DTYS-VITTESlnhnhIKIFLMIANNRNMFMKTLDINHAFL 1135
Cdd:pfam07727   15 PIGCKWVFKVKRDsdgkvVRYKARLVAKGFTQKEgidydETFSpVARLES-----IRLLLALAAQRGWELHQMDVKSAFL 89
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443635  1136 YAKLEEEIYI---------PHPHDrrcVVKLNKALYGLKQSPKEWNDHLRQYLNGIGLKDNSYTPGLY--QTEDKNLMIA 1204
Cdd:pfam07727   90 NGELEEEVYVkqppgfvvpGKPNK---VCKLKKSLYGLKQAPRAWYSRLDSVLLSLGFKRSKHDHGLFikGKGDGFLIVG 166
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 330443635  1205 VYVDDCVIAASNEQRLDEFINKLKSNFELKITGTLiddvldTDILGMDLVYNKrlGTIDLTLKSFINRMDKKYN 1278
Cdd:pfam07727  167 LYVDDILITGSSEKEINEFKEELSKEFEMKDLGEL------SYFLGIEIKQTP--GGITLSQSKYIKKLLERFG 232
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
369-483 1.80e-16

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: 307008  Cd Length: 114  Bit Score: 79.22  E-value: 1.80e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443635   369 PGSSWCMDIFgPVSSSNADTKRYMLIMVDNNTRYCMTSTHFNK-NAETILAQVRKNIQYVetqfdRKVREINSDRGTEFT 447
Cdd:pfam00665    1 PNELWQTDFT-YVRVPGGGGKLYLAVAVDDFSREIVAWALSSEmDAELVIDALKRAIAFR-----GGPKIIHSDNGSEYT 74
                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 330443635   448 NDQIEEYFISKGIHHILTSTQDHAANGRAERYIRTI 483
Cdd:pfam00665   75 SKAFREFLAHYGITHSFSRPGNPQDNGKVERFNGTL 110
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1386-1523 1.03e-13

Ty1/Copia 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 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 Ty1/Copia family is 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: 260004  Cd Length: 140  Bit Score: 71.73  E-value: 1.03e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443635 1386 IAITDASVGSEYD-AQSRIGVILWYGMNIFNVYSNKSTNRCVSSTEAELHAIYEGYADSETLKVTLKELGEGDNNDIVMI 1464
Cdd:cd09272     1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGIPLDGPTTIY 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 330443635 1465 TDSKPAIQGLNRSYQQPKEKFTWIKTEIIKEKIKEKSIKLLKITGKGNIADLLTKPVSA 1523
Cdd:cd09272    81 CDNQSAIALAKNPVFHSRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLPR 139
 
Name Accession Description Interval E-value
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1067-1278 4.93e-36

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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


Pssm-ID: 311594  Cd Length: 246  Bit Score: 140.03  E-value: 4.93e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443635  1067 IVPTNTIFTKKRN-----GIYKARIVCRGDTQSP-----DTYS-VITTESlnhnhIKIFLMIANNRNMFMKTLDINHAFL 1135
Cdd:pfam07727   15 PIGCKWVFKVKRDsdgkvVRYKARLVAKGFTQKEgidydETFSpVARLES-----IRLLLALAAQRGWELHQMDVKSAFL 89
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443635  1136 YAKLEEEIYI---------PHPHDrrcVVKLNKALYGLKQSPKEWNDHLRQYLNGIGLKDNSYTPGLY--QTEDKNLMIA 1204
Cdd:pfam07727   90 NGELEEEVYVkqppgfvvpGKPNK---VCKLKKSLYGLKQAPRAWYSRLDSVLLSLGFKRSKHDHGLFikGKGDGFLIVG 166
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 330443635  1205 VYVDDCVIAASNEQRLDEFINKLKSNFELKITGTLiddvldTDILGMDLVYNKrlGTIDLTLKSFINRMDKKYN 1278
Cdd:pfam07727  167 LYVDDILITGSSEKEINEFKEELSKEFEMKDLGEL------SYFLGIEIKQTP--GGITLSQSKYIKKLLERFG 232
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
369-483 1.80e-16

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: 307008  Cd Length: 114  Bit Score: 79.22  E-value: 1.80e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443635   369 PGSSWCMDIFgPVSSSNADTKRYMLIMVDNNTRYCMTSTHFNK-NAETILAQVRKNIQYVetqfdRKVREINSDRGTEFT 447
Cdd:pfam00665    1 PNELWQTDFT-YVRVPGGGGKLYLAVAVDDFSREIVAWALSSEmDAELVIDALKRAIAFR-----GGPKIIHSDNGSEYT 74
                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 330443635   448 NDQIEEYFISKGIHHILTSTQDHAANGRAERYIRTI 483
Cdd:pfam00665   75 SKAFREFLAHYGITHSFSRPGNPQDNGKVERFNGTL 110
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1386-1523 1.03e-13

Ty1/Copia 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 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 Ty1/Copia family is 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: 260004  Cd Length: 140  Bit Score: 71.73  E-value: 1.03e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443635 1386 IAITDASVGSEYD-AQSRIGVILWYGMNIFNVYSNKSTNRCVSSTEAELHAIYEGYADSETLKVTLKELGEGDNNDIVMI 1464
Cdd:cd09272     1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGIPLDGPTTIY 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 330443635 1465 TDSKPAIQGLNRSYQQPKEKFTWIKTEIIKEKIKEKSIKLLKITGKGNIADLLTKPVSA 1523
Cdd:cd09272    81 CDNQSAIALAKNPVFHSRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLPR 139
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.16
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH