NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2065870543|gb|KAG7636113|]
View 

Retrotransposon gag domain [Arabidopsis thaliana x Arabidopsis arenosa]

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
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 708-822 4.49e-52

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: 178.46  E-value: 4.49e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065870543  708 TVNTDASIVGLGCVLMQKGS-----VIAYASRQLRKHEKNYPTHDLEMASVVFALKIWRSYLYAAKVQIYTDHKSLKYIF 782
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDdgkerPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2065870543  783 TQPELNLRQRRWMELVADYDLDIAYHPGKASQVADALSRR 822
Cdd:cd09274     81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 264-359 9.52e-34

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


:

Pssm-ID: 367628  Cd Length: 97  Bit Score: 125.14  E-value: 9.52e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065870543  264 DIAVHFLEGDAHNWWLSIEKRRGDEVRSFTDFKDEFNKKYFPPEARDRLECAYLDLVQGNRTVHEYDEEFNRLRRYVGRK 343
Cdd:pfam03732    1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHH 80

                           90
                   ....*....|....*.
gi 2065870543  344 LEEEQALVRRFIRGLR 359
Cdd:pfam03732   81 GRDEEALISAFLRGLR 96
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 888-944 1.48e-14

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: 69.20  E-value: 1.48e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2065870543  888 EALKKEILKEAHQSkfSIHPGSNKMYRDLKRYYDWVGMKKEVARWVAKCPACQLVKA 944
Cdd:pfam17921    3 KSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 430-493 9.34e-09

universal minicircle sequence binding protein (UMSBP); Provisional


The actual alignment was detected with superfamily member PTZ00368:

Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 55.58  E-value: 9.34e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2065870543  430 ECVTCGKSHSgtcwkAKGV-CGRCGSKDHAIQSCPRMEPGQskvlgeETRTCFYCGKVGHLKREC 493
Cdd:PTZ00368    15 ECPNSAPAGA-----AKARpCYKCGEPGHLSRECPSAPGGR------GERSCYNCGKTGHLSREC 68
rve super family cl47583
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 964-1060 5.94e-04

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.


The actual alignment was detected with superfamily member pfam00665:

Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 40.38  E-value: 5.94e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065870543  964 DHITMDFVTGlstGIKSKHNTVW--VVVDQLTKSAHFMAISDKDGAKIiAEKYINKIVR-LHGIPVSIVSDRDTRFTSKF 1040
Cdd:pfam00665    3 QLWQGDFTYI---RIPGGGGKLYllVIVDDFSREILAWALSSEMDAEL-VLDALERAIAfRGGVPLIIHSDNGSEYTSKA 78

                           90       100
                   ....*....|....*....|
gi 2065870543 1041 WKAFQKALGTRVNLSTSYHP 1060
Cdd:pfam00665   79 FREFLKDLGIKPSFSRPGNP 98
 
Name Accession Description Interval E-value
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 708-822 4.49e-52

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: 178.46  E-value: 4.49e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065870543  708 TVNTDASIVGLGCVLMQKGS-----VIAYASRQLRKHEKNYPTHDLEMASVVFALKIWRSYLYAAKVQIYTDHKSLKYIF 782
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDdgkerPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2065870543  783 TQPELNLRQRRWMELVADYDLDIAYHPGKASQVADALSRR 822
Cdd:cd09274     81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 704-800 1.57e-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: 136.49  E-value: 1.57e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065870543  704 GEPYTVNTDASIVGLGCVLMQKGS-----VIAYASRQLRKHEKNYPTHDLEMASVVFALKIWRSYLYAAKVQIYTDHKSL 778
Cdd:pfam17917    3 SKPFILETDASDYGIGAVLSQKDEdgkerPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHKPL 82

                           90       100
                   ....*....|....*....|..
gi 2065870543  779 KYIFTQPELNLRQRRWMELVAD 800
Cdd:pfam17917   83 KYLFTPKELNGRLARWALFLQE 104
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 264-359 9.52e-34

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


Pssm-ID: 367628  Cd Length: 97  Bit Score: 125.14  E-value: 9.52e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065870543  264 DIAVHFLEGDAHNWWLSIEKRRGDEVRSFTDFKDEFNKKYFPPEARDRLECAYLDLVQGNRTVHEYDEEFNRLRRYVGRK 343
Cdd:pfam03732    1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHH 80

                           90
                   ....*....|....*.
gi 2065870543  344 LEEEQALVRRFIRGLR 359
Cdd:pfam03732   81 GRDEEALISAFLRGLR 96
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 888-944 1.48e-14

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: 69.20  E-value: 1.48e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2065870543  888 EALKKEILKEAHQSkfSIHPGSNKMYRDLKRYYDWVGMKKEVARWVAKCPACQLVKA 944
Cdd:pfam17921    3 KSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 430-493 9.34e-09

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 55.58  E-value: 9.34e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2065870543  430 ECVTCGKSHSgtcwkAKGV-CGRCGSKDHAIQSCPRMEPGQskvlgeETRTCFYCGKVGHLKREC 493
Cdd:PTZ00368    15 ECPNSAPAGA-----AKARpCYKCGEPGHLSRECPSAPGGR------GERSCYNCGKTGHLSREC 68
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 448-493 7.65e-06

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 47.92  E-value: 7.65e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2065870543  448 VCGRCGSKDHAIQSCP------RMEPGQSKVLGEETRTCFYCGKVGHLKREC 493
Cdd:COG5082     62 VCFNCGQNGHLRRDCPhsicynCSWDGHRSNHCPKPKKCYNCGETGHLSRDC 113
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 964-1060 5.94e-04

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: 40.38  E-value: 5.94e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065870543  964 DHITMDFVTGlstGIKSKHNTVW--VVVDQLTKSAHFMAISDKDGAKIiAEKYINKIVR-LHGIPVSIVSDRDTRFTSKF 1040
Cdd:pfam00665    3 QLWQGDFTYI---RIPGGGGKLYllVIVDDFSREILAWALSSEMDAEL-VLDALERAIAfRGGVPLIIHSDNGSEYTSKA 78

                           90       100
                   ....*....|....*....|
gi 2065870543 1041 WKAFQKALGTRVNLSTSYHP 1060
Cdd:pfam00665   79 FREFLKDLGIKPSFSRPGNP 98
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 478-493 4.72e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 35.58  E-value: 4.72e-03
                           10
                   ....*....|....*.
gi 2065870543  478 RTCFYCGKVGHLKREC 493
Cdd:pfam00098    1 GKCYNCGEPGHIARDC 16
ZnF_C2HC smart00343
zinc finger;
479-495 4.83e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 35.50  E-value: 4.83e-03
                            10
                    ....*....|....*..
gi 2065870543   479 TCFYCGKVGHLKRECHK 495
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
 
Name Accession Description Interval E-value
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 708-822 4.49e-52

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: 178.46  E-value: 4.49e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065870543  708 TVNTDASIVGLGCVLMQKGS-----VIAYASRQLRKHEKNYPTHDLEMASVVFALKIWRSYLYAAKVQIYTDHKSLKYIF 782
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDdgkerPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2065870543  783 TQPELNLRQRRWMELVADYDLDIAYHPGKASQVADALSRR 822
Cdd:cd09274     81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 704-800 1.57e-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: 136.49  E-value: 1.57e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065870543  704 GEPYTVNTDASIVGLGCVLMQKGS-----VIAYASRQLRKHEKNYPTHDLEMASVVFALKIWRSYLYAAKVQIYTDHKSL 778
Cdd:pfam17917    3 SKPFILETDASDYGIGAVLSQKDEdgkerPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHKPL 82

                           90       100
                   ....*....|....*....|..
gi 2065870543  779 KYIFTQPELNLRQRRWMELVAD 800
Cdd:pfam17917   83 KYLFTPKELNGRLARWALFLQE 104
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
677-771 5.60e-36

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 131.85  E-value: 5.60e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065870543  677 WSEECEKSFLELKAMLTNAPVLVLPEEGEPYTVNTDASIVGLGCVLMQKGS-----VIAYASRQLRKHEKNYPTHDLEMA 751
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDdggerPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|
gi 2065870543  752 SVVFALKIWRSYLYAAKVQI 771
Cdd:pfam17919   81 AIVFALKKFRHYLLGRKFTV 100
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 264-359 9.52e-34

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


Pssm-ID: 367628  Cd Length: 97  Bit Score: 125.14  E-value: 9.52e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065870543  264 DIAVHFLEGDAHNWWLSIEKRRGDEVRSFTDFKDEFNKKYFPPEARDRLECAYLDLVQGNRTVHEYDEEFNRLRRYVGRK 343
Cdd:pfam03732    1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHH 80

                           90
                   ....*....|....*.
gi 2065870543  344 LEEEQALVRRFIRGLR 359
Cdd:pfam03732   81 GRDEEALISAFLRGLR 96
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 888-944 1.48e-14

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: 69.20  E-value: 1.48e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2065870543  888 EALKKEILKEAHQSkfSIHPGSNKMYRDLKRYYDWVGMKKEVARWVAKCPACQLVKA 944
Cdd:pfam17921    3 KSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 430-493 9.34e-09

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 55.58  E-value: 9.34e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2065870543  430 ECVTCGKSHSgtcwkAKGV-CGRCGSKDHAIQSCPRMEPGQskvlgeETRTCFYCGKVGHLKREC 493
Cdd:PTZ00368    15 ECPNSAPAGA-----AKARpCYKCGEPGHLSRECPSAPGGR------GERSCYNCGKTGHLSREC 68
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 711-822 1.42e-07

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: 51.52  E-value: 1.42e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065870543  711 TDASIVGLGCVLmQKGSVIAYASrqlrKHEKNYPTHDLEMASVVFALKIWRSYLYAAKVQIYTDHKS-LKYIFTQ----- 784
Cdd:cd09275      4 TDASLSGWGAYL-LNSRAHGPWS----ADERNKHINLLELKAVLLALQHFAAELKNRKILIRTDNTTaVAYINKQggtss 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2065870543  785 PELNLRQRRWMELVADYDLDI-AYH-PGKASQVADALSRR 822
Cdd:cd09275     79 PPLLALARQILLWCEQRNIWLrASHiPGVLNTEADRLSRL 118
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 431-493 1.28e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 49.42  E-value: 1.28e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065870543  431 CVTCGKS-H-SGTCWKAKG-----VCGRCGSKDHAIQSCPRMEPGqskvlGEETRTCFYCGKVGHLKREC 493
Cdd:PTZ00368    55 CYNCGKTgHlSRECPEAPPgsgprSCYNCGQTGHISRECPNRAKG-----GAARRACYNCGGEGHISRDC 119
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 426-493 2.05e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 49.03  E-value: 2.05e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2065870543  426 AKTSECVTCGK-SH-SGTCWKAKG-----VCGRCGSKDHAIQSCPRMEPGQskvlgeETRTCFYCGKVGHLKREC 493
Cdd:PTZ00368    25 AKARPCYKCGEpGHlSRECPSAPGgrgerSCYNCGKTGHLSRECPEAPPGS------GPRSCYNCGQTGHISREC 93
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 448-493 7.65e-06

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 47.92  E-value: 7.65e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2065870543  448 VCGRCGSKDHAIQSCP------RMEPGQSKVLGEETRTCFYCGKVGHLKREC 493
Cdd:COG5082     62 VCFNCGQNGHLRRDCPhsicynCSWDGHRSNHCPKPKKCYNCGETGHLSRDC 113
Ty3_capsid pfam19259
Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the ...
 232-415 7.99e-06

Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the Ty3 transposons of yeast as well as other transposable elements.


Pssm-ID: 437091 [Multi-domain]  Cd Length: 197  Bit Score: 48.24  E-value: 7.99e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065870543  232 FMGNTDPIVADEWRSRLKRNFKSTRCPEDYQRdiaVHF----LEGDAHNWWLSIEKRRGDEVRSFTDFKDEFNKKYF-PP 306
Cdd:pfam19259   17 FRGRKDVLKLKSFISEIMLQMSMIFWPNDAER---IVFcarhLTGPAAQWFHDFVQEQGILDATFDTFIKAFKQHFYgKP 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065870543  307 EARDRLEcAYLDLVQGNRTVHEYDEEFNRLRRYVGRKLEEEQALVRRFIRGLRIEICNHCLVRTFNSVSESveraamIEE 386
Cdd:pfam19259   94 DINKLFN-DIVNLSEAKLGIERYNSHFNRLWDLLPPDFLSEKAAIMFYIRGLKPETYIIVRLAKPSTLKEA------MEI 166

                          170       180
                   ....*....|....*....|....*....
gi 2065870543  387 GIEEERYLNRKKALIRNNQHTKPVDKKRK 415
Cdd:pfam19259  167 AYETIPYTERFSPTFTQNSKTVLDADGDT 195
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 427-493 6.29e-05

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 44.41  E-value: 6.29e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2065870543  427 KTSECVTCG-KSH-SGTC------WKAKGVCGRCGSKDHAIQSCPRmEPGQSKvlgeETRTCFYCGKVGHLKREC 493
Cdd:PTZ00368    76 GPRSCYNCGqTGHiSRECpnrakgGAARRACYNCGGEGHISRDCPN-AGKRPG----GDKTCYNCGQTGHLSRDC 145
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 964-1060 5.94e-04

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: 40.38  E-value: 5.94e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065870543  964 DHITMDFVTGlstGIKSKHNTVW--VVVDQLTKSAHFMAISDKDGAKIiAEKYINKIVR-LHGIPVSIVSDRDTRFTSKF 1040
Cdd:pfam00665    3 QLWQGDFTYI---RIPGGGGKLYllVIVDDFSREILAWALSSEMDAEL-VLDALERAIAfRGGVPLIIHSDNGSEYTSKA 78

                           90       100
                   ....*....|....*....|
gi 2065870543 1041 WKAFQKALGTRVNLSTSYHP 1060
Cdd:pfam00665   79 FREFLKDLGIKPSFSRPGNP 98
zf-H2C2 pfam09337
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 906-940 4.22e-03

H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters.


Pssm-ID: 430537  Cd Length: 39  Bit Score: 36.15  E-value: 4.22e-03
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2065870543  906 HPGSNKMYRDLKRYYDWVGMKKEVARWVAKCPACQ 940
Cdd:pfam09337    5 HLGINKLTALLARKYHWLGIKETVSEVISSCVACQ 39
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 478-493 4.72e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 35.58  E-value: 4.72e-03
                           10
                   ....*....|....*.
gi 2065870543  478 RTCFYCGKVGHLKREC 493
Cdd:pfam00098    1 GKCYNCGEPGHIARDC 16
ZnF_C2HC smart00343
zinc finger;
479-495 4.83e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 35.50  E-value: 4.83e-03
                            10
                    ....*....|....*..
gi 2065870543   479 TCFYCGKVGHLKRECHK 495
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
 
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