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Conserved domains on  [gi|1954738841|ref|XP_038722036|]
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uncharacterized protein LOC120014188 [Tripterygium wilfordii]

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 ...
 904-1099 6.56e-79

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: 257.91  E-value: 6.56e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841  904 GVIYPiSDSKWVSPVQVVPKKSGitvvknkddeliptrmttGWRVCIDYRKLNTATRKDHFPLPFIDQMLERLSGHSHYC 983
Cdd:cd01647      1 GIIEP-SSSPYASPVVVVKKKDG------------------KLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFS 61

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841  984 FLDGFSGYNQIPIAPEDQEKTTFTCPFGTFAYRRMPFGLCNAPATFQRCMMAIFSDMVERIIEVFMDDFSVFGSSFDACL 1063
Cdd:cd01647     62 KLDLRSGYHQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHL 141

                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 1954738841 1064 ENLALVLKRCQATNLILNWEKCHFMVRRGIVLGHVV 1099
Cdd:cd01647    142 EHLREVLERLREAGLKLNPEKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1193-1312 1.83e-64

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: 214.28  E-value: 1.83e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1193 ELMCDASDYAVGAVLGQKDGKAS-HVIYYASRTLNDAQLNYSTTEKELLAVVFALEKFRAYLVGSKVIVYTDHAALKYLL 1271
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDDGKeRPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1954738841 1272 NKKDAKPRLIRWILLLQEFDLEIKDKKGSENVVADHLSRIV 1312
Cdd:cd09274     81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1472-1565 4.97e-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: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 75.04  E-value: 4.97e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1472 DVWGIDF-MGPFPPSYGYTYILVAVDYVSKWVEALATRTN-DHRVVLTFLKDMIFTRFGTPRAIISDGGSHFCNKPFEAL 1549
Cdd:pfam00665    3 QLWQGDFtYIRIPGGGGKLYLLVIVDDFSREILAWALSSEmDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFREF 82

                           90
                   ....*....|....*.
gi 1954738841 1550 LKKYNITHKIATPYHP 1565
Cdd:pfam00665   83 LKDLGIKPSFSRPGNP 98
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1394-1451 1.34e-12

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: 64.19  E-value: 1.34e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1954738841 1394 VPEEEQENILRHAHDLacGGHFGAKKTaLKVLQSGFFWPTLFKDAFHFCARCNSCQRS 1451
Cdd:pfam17921    1 VPKSLRKEILKEAHDS--GGHLGIEKT-LARLRRRYWWPGMRKDVKKYVKSCETCQRR 55
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 607-705 1.47e-11

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: 62.35  E-value: 1.47e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841  607 IPITIGSKRHgHAMLDLGASINLMPFSVYKELGIQGM-KKTTVRLELADRSVRYPKGIVEDILVQVDKLILPADFIILDt 685
Cdd:cd00303      1 LKGKINGVPV-RALVDSGASVNFISESLAKKLGLPPRlLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLD- 78

                           90       100
                   ....*....|....*....|
gi 1954738841  686 eesgMNGHDapILLGRPFMA 705
Cdd:cd00303     79 ----LLSYD--VILGRPWLE 92
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 904-1099 6.56e-79

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: 257.91  E-value: 6.56e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841  904 GVIYPiSDSKWVSPVQVVPKKSGitvvknkddeliptrmttGWRVCIDYRKLNTATRKDHFPLPFIDQMLERLSGHSHYC 983
Cdd:cd01647      1 GIIEP-SSSPYASPVVVVKKKDG------------------KLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFS 61

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841  984 FLDGFSGYNQIPIAPEDQEKTTFTCPFGTFAYRRMPFGLCNAPATFQRCMMAIFSDMVERIIEVFMDDFSVFGSSFDACL 1063
Cdd:cd01647     62 KLDLRSGYHQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHL 141

                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 1954738841 1064 ENLALVLKRCQATNLILNWEKCHFMVRRGIVLGHVV 1099
Cdd:cd01647    142 EHLREVLERLREAGLKLNPEKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1193-1312 1.83e-64

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: 214.28  E-value: 1.83e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1193 ELMCDASDYAVGAVLGQKDGKAS-HVIYYASRTLNDAQLNYSTTEKELLAVVFALEKFRAYLVGSKVIVYTDHAALKYLL 1271
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDDGKeRPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1954738841 1272 NKKDAKPRLIRWILLLQEFDLEIKDKKGSENVVADHLSRIV 1312
Cdd:cd09274     81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1187-1289 9.18e-48

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: 165.76  E-value: 9.18e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1187 NWSLPFELMCDASDYAVGAVLGQKD--GKaSHVIYYASRTLNDAQLNYSTTEKELLAVVFALEKFRAYLVGSKVIVYTDH 1264
Cdd:pfam17917    1 DPSKPFILETDASDYGIGAVLSQKDedGK-ERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDH 79

                           90       100
                   ....*....|....*....|....*
gi 1954738841 1265 AALKYLLNKKDAKPRLIRWILLLQE 1289
Cdd:pfam17917   80 KPLKYLFTPKELNGRLARWALFLQE 104
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 938-1099 3.66e-28

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: 113.17  E-value: 3.66e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841  938 IPTRMTTGWRVC----IDYRKLNTATRK-------DHFPLPFIDQMLERLSGHSHYCFLDGFSGYNQIPIAPEDQEKTTF 1006
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1007 TCP-----------FGTFAYRRMPFGLCNAPATFQRCMMAIFSDMVERI---IEVFMDDFSVFGSSFDACLENLALVLKR 1072
Cdd:pfam00078   81 TTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRAgltLVRYADDILIFSKSEEEHQEALEEVLEW 160

                          170       180
                   ....*....|....*....|....*....
gi 1954738841 1073 CQATNLILNWEKCHFMVRRGIV--LGHVV 1099
Cdd:pfam00078  161 LKESGLKINPEKTQFFLKSKEVkyLGVTL 189
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1472-1565 4.97e-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: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 75.04  E-value: 4.97e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1472 DVWGIDF-MGPFPPSYGYTYILVAVDYVSKWVEALATRTN-DHRVVLTFLKDMIFTRFGTPRAIISDGGSHFCNKPFEAL 1549
Cdd:pfam00665    3 QLWQGDFtYIRIPGGGGKLYLLVIVDDFSREILAWALSSEmDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFREF 82

                           90
                   ....*....|....*.
gi 1954738841 1550 LKKYNITHKIATPYHP 1565
Cdd:pfam00665   83 LKDLGIKPSFSRPGNP 98
transpos_IS481 NF033577
IS481 family transposase; null
 1472-1612 5.24e-16

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 80.33  E-value: 5.24e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1472 DVWGIDFM--GPFPPSyGYTYILVAVDYVSKWV--EALATRTndHRVVLTFLKDmIFTRFGTP-RAIISDGGSHFCNK-- 1544
Cdd:NF033577   129 ELWHIDIKklGRIPDV-GRLYLHTAIDDHSRFAyaELYPDET--AETAADFLRR-AFAEHGIPiRRVLTDNGSEFRSRah 204

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1545 PFEALLKKYNITHKIATPYHPQTSGQVEVSNREIKRI-LEKTVNSTRKDwaikLNDALWAYRTAF-----------KTPI 1612
Cdd:NF033577   205 GFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEfAYARPYESLAE----LQAALDEWLHHYnhhrphsalggKTPA 280
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1394-1451 1.34e-12

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: 64.19  E-value: 1.34e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1954738841 1394 VPEEEQENILRHAHDLacGGHFGAKKTaLKVLQSGFFWPTLFKDAFHFCARCNSCQRS 1451
Cdd:pfam17921    1 VPKSLRKEILKEAHDS--GGHLGIEKT-LARLRRRYWWPGMRKDVKKYVKSCETCQRR 55
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 607-705 1.47e-11

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: 62.35  E-value: 1.47e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841  607 IPITIGSKRHgHAMLDLGASINLMPFSVYKELGIQGM-KKTTVRLELADRSVRYPKGIVEDILVQVDKLILPADFIILDt 685
Cdd:cd00303      1 LKGKINGVPV-RALVDSGASVNFISESLAKKLGLPPRlLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLD- 78

                           90       100
                   ....*....|....*....|
gi 1954738841  686 eesgMNGHDapILLGRPFMA 705
Cdd:cd00303     79 ----LLSYD--VILGRPWLE 92
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 607-703 3.01e-04

Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix.


Pssm-ID: 433378  Cd Length: 90  Bit Score: 41.50  E-value: 3.01e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841  607 IPITIGSKRhGHAMLDLGASINLMPFSVYKELGIQGMKKT-TVRLELADRSVRYPKGIVEDIlvQVDKLILPA-DFIILD 684
Cdd:pfam13650    1 VPVTINGKP-VRFLVDTGASGTVISPSLAERLGLKVRGLAyTVRVSTAGGRVSAARVRLDSL--RLGGLTLENvPALVLD 77

                           90
                   ....*....|....*....
gi 1954738841  685 teesgmNGHDAPILLGRPF 703
Cdd:pfam13650   78 ------LGDLIDGLLGMDF 90
transpos_IS21 NF033546
IS21 family transposase;
1490-1580 3.67e-03

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 41.42  E-value: 3.67e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1490 YILVAVDYVSKWVEALATRTNDHRVVLTFLKDMiFTRF-GTPRAIISD-----------GGSHFCNKPFEALLKKYNITH 1557
Cdd:NF033546   139 HVFVAVLGYSRYTYVEATPSESQEDLLDGHQRA-FEFFgGVPREIVYDnlktavdkrdrYEEPRLNPRFAAFAAHYGFEP 217

                           90       100
                   ....*....|....*....|...
gi 1954738841 1558 KIATPYHPQTSGQVEVSNREIKR 1580
Cdd:NF033546   218 RPCRPYRPQEKGKVERAVGYVRR 240
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 904-1099 6.56e-79

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: 257.91  E-value: 6.56e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841  904 GVIYPiSDSKWVSPVQVVPKKSGitvvknkddeliptrmttGWRVCIDYRKLNTATRKDHFPLPFIDQMLERLSGHSHYC 983
Cdd:cd01647      1 GIIEP-SSSPYASPVVVVKKKDG------------------KLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFS 61

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841  984 FLDGFSGYNQIPIAPEDQEKTTFTCPFGTFAYRRMPFGLCNAPATFQRCMMAIFSDMVERIIEVFMDDFSVFGSSFDACL 1063
Cdd:cd01647     62 KLDLRSGYHQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHL 141

                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 1954738841 1064 ENLALVLKRCQATNLILNWEKCHFMVRRGIVLGHVV 1099
Cdd:cd01647    142 EHLREVLERLREAGLKLNPEKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1193-1312 1.83e-64

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: 214.28  E-value: 1.83e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1193 ELMCDASDYAVGAVLGQKDGKAS-HVIYYASRTLNDAQLNYSTTEKELLAVVFALEKFRAYLVGSKVIVYTDHAALKYLL 1271
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDDGKeRPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1954738841 1272 NKKDAKPRLIRWILLLQEFDLEIKDKKGSENVVADHLSRIV 1312
Cdd:cd09274     81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1187-1289 9.18e-48

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: 165.76  E-value: 9.18e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1187 NWSLPFELMCDASDYAVGAVLGQKD--GKaSHVIYYASRTLNDAQLNYSTTEKELLAVVFALEKFRAYLVGSKVIVYTDH 1264
Cdd:pfam17917    1 DPSKPFILETDASDYGIGAVLSQKDedGK-ERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDH 79

                           90       100
                   ....*....|....*....|....*
gi 1954738841 1265 AALKYLLNKKDAKPRLIRWILLLQE 1289
Cdd:pfam17917   80 KPLKYLFTPKELNGRLARWALFLQE 104
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
1162-1260 4.64e-42

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 149.57  E-value: 4.64e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1162 FDKECLAAFNVLKHALTSSPIISTPNWSLPFELMCDASDYAVGAVLGQKDGKAS-HVIYYASRTLNDAQLNYSTTEKELL 1240
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDDGGeRPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|
gi 1954738841 1241 AVVFALEKFRAYLVGSKVIV 1260
Cdd:pfam17919   81 AIVFALKKFRHYLLGRKFTV 100
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 938-1099 3.66e-28

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: 113.17  E-value: 3.66e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841  938 IPTRMTTGWRVC----IDYRKLNTATRK-------DHFPLPFIDQMLERLSGHSHYCFLDGFSGYNQIPIAPEDQEKTTF 1006
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1007 TCP-----------FGTFAYRRMPFGLCNAPATFQRCMMAIFSDMVERI---IEVFMDDFSVFGSSFDACLENLALVLKR 1072
Cdd:pfam00078   81 TTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRAgltLVRYADDILIFSKSEEEHQEALEEVLEW 160

                          170       180
                   ....*....|....*....|....*....
gi 1954738841 1073 CQATNLILNWEKCHFMVRRGIV--LGHVV 1099
Cdd:pfam00078  161 LKESGLKINPEKTQFFLKSKEVkyLGVTL 189
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1472-1565 4.97e-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: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 75.04  E-value: 4.97e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1472 DVWGIDF-MGPFPPSYGYTYILVAVDYVSKWVEALATRTN-DHRVVLTFLKDMIFTRFGTPRAIISDGGSHFCNKPFEAL 1549
Cdd:pfam00665    3 QLWQGDFtYIRIPGGGGKLYLLVIVDDFSREILAWALSSEmDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFREF 82

                           90
                   ....*....|....*.
gi 1954738841 1550 LKKYNITHKIATPYHP 1565
Cdd:pfam00665   83 LKDLGIKPSFSRPGNP 98
transpos_IS481 NF033577
IS481 family transposase; null
 1472-1612 5.24e-16

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 80.33  E-value: 5.24e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1472 DVWGIDFM--GPFPPSyGYTYILVAVDYVSKWV--EALATRTndHRVVLTFLKDmIFTRFGTP-RAIISDGGSHFCNK-- 1544
Cdd:NF033577   129 ELWHIDIKklGRIPDV-GRLYLHTAIDDHSRFAyaELYPDET--AETAADFLRR-AFAEHGIPiRRVLTDNGSEFRSRah 204

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1545 PFEALLKKYNITHKIATPYHPQTSGQVEVSNREIKRI-LEKTVNSTRKDwaikLNDALWAYRTAF-----------KTPI 1612
Cdd:NF033577   205 GFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEfAYARPYESLAE----LQAALDEWLHHYnhhrphsalggKTPA 280
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 900-1084 1.29e-13

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: 71.61  E-value: 1.29e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841  900 LLDVGVIYPiSDSKWVSPVQVVPKKSGITvvknkddeliptrmttgWRVCIDYRKLNTATRKDHFPLPFIDQMLERLS-G 978
Cdd:cd03715     24 LLEAGILVP-CQSPWNTPILPVKKPGGND-----------------YRMVQDLRLVNQAVLPIHPAVPNPYTLLSLLPpK 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841  979 HSHYCFLDGFSGYNQIPIAPEDQEKTTFTCPFGTFAYRRMPFGLCNAPATF----QRCMMAIFSDMVERIIEVFMDDFSV 1054
Cdd:cd03715     86 HQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFhealARDLAPFPLEHEGTILLQYVDDLLL 165

                          170       180       190
                   ....*....|....*....|....*....|
gi 1954738841 1055 FGSSFDACLENLALVLKRCQATNLILNWEK 1084
Cdd:cd03715    166 AADSEEDCLKGTDALLTHLGELGYKVSPKK 195
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1193-1311 2.34e-13

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: 68.46  E-value: 2.34e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1193 ELMCDASDYAVGAVLGqkdGKASHVIYYASrtlndaQLNYSTTEKELLAVVFALEKFRAYLVGSKVIVYTDHA-ALKYLL 1271
Cdd:cd09275      1 VLFTDASLSGWGAYLL---NSRAHGPWSAD------ERNKHINLLELKAVLLALQHFAAELKNRKILIRTDNTtAVAYIN 71

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1954738841 1272 N----KKDAKPRLIRWILLL-QEFDLEIKDK--KGSENVVADHLSRI 1311
Cdd:cd09275     72 KqggtSSPPLLALARQILLWcEQRNIWLRAShiPGVLNTEADRLSRL 118
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1394-1451 1.34e-12

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: 64.19  E-value: 1.34e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1954738841 1394 VPEEEQENILRHAHDLacGGHFGAKKTaLKVLQSGFFWPTLFKDAFHFCARCNSCQRS 1451
Cdd:pfam17921    1 VPKSLRKEILKEAHDS--GGHLGIEKT-LARLRRRYWWPGMRKDVKKYVKSCETCQRR 55
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 607-705 1.47e-11

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: 62.35  E-value: 1.47e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841  607 IPITIGSKRHgHAMLDLGASINLMPFSVYKELGIQGM-KKTTVRLELADRSVRYPKGIVEDILVQVDKLILPADFIILDt 685
Cdd:cd00303      1 LKGKINGVPV-RALVDSGASVNFISESLAKKLGLPPRlLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLD- 78

                           90       100
                   ....*....|....*....|
gi 1954738841  686 eesgMNGHDapILLGRPFMA 705
Cdd:cd00303     79 ----LLSYD--VILGRPWLE 92
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 891-1084 3.88e-09

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: 58.45  E-value: 3.88e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841  891 EVVRAEVLKLLDVGVIYPiSDSKWVSPVQVVPKKSGitvvknkddeliptrmttGWRVCIDYRKLNTATR---------- 960
Cdd:cd01645     15 EALTELVTEQLKEGHIEP-STSPWNTPVFVIKKKSG------------------KWRLLHDLRAVNAQTQdmgalqpglp 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841  961 -----KDHFPLPFIDqmlerLSGhshyCFldgFSgynqIPIAPEDQEKTTFTCP---FGT----FAYRRMPFGLCNAPAT 1028
Cdd:cd01645     76 hpaalPKGWPLIVLD-----LKD----CF---FS----IPLHPDDRERFAFTVPsinNKGpakrYQWKVLPQGMKNSPTI 139

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1029 FQRCMMAIFSDMVER----IIEVFMDDFSVFGSSFDACLENLALVLKRCQATNLILNWEK 1084
Cdd:cd01645    140 CQSFVAQALEPFRKQypdiVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEK 199
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 989-1098 3.26e-08

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: 53.50  E-value: 3.26e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841  989 SGYNQIPIAPEDQEKTTFTCPFGTFAYRRMPFGLCNAPATFQRCMMAIFSDMVERIIEVF--MDDFSVFGSSF---DACL 1063
Cdd:cd03714      5 DAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLGVRIFsyLDDLLIIASSIktsEAVL 84

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1954738841 1064 ENLALVLkrCQATNLILNWEKCHFMVRRGIVLGHV 1098
Cdd:cd03714     85 RHLRATL--LANLGFTLNLEKSKLGPTQRITFLGL 117
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1202-1310 9.23e-05

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.


Pssm-ID: 259998 [Multi-domain]  Cd Length: 121  Bit Score: 43.84  E-value: 9.23e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1202 AVGAVLGQKDGKashviYYASRTLNdaQLNYSTTEKELLAVVFALEKFRAYLVgSKVIVYTDHAALKYLLNKKDAKPR-- 1279
Cdd:cd06222     15 GIGGVLRDHEGG-----WLGGFALK--IGAPTALEAELLALLLALELALDLGY-LKVIIESDSKYVVDLINSGSFKWSpn 86

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1954738841 1280 ---LIRWILLLQEF-DLEIKDKKGSENVVADHLSR 1310
Cdd:cd06222     87 illIEDILLLLSRFwSVKISHVPREGNQVADALAK 121
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 607-703 3.01e-04

Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix.


Pssm-ID: 433378  Cd Length: 90  Bit Score: 41.50  E-value: 3.01e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841  607 IPITIGSKRhGHAMLDLGASINLMPFSVYKELGIQGMKKT-TVRLELADRSVRYPKGIVEDIlvQVDKLILPA-DFIILD 684
Cdd:pfam13650    1 VPVTINGKP-VRFLVDTGASGTVISPSLAERLGLKVRGLAyTVRVSTAGGRVSAARVRLDSL--RLGGLTLENvPALVLD 77

                           90
                   ....*....|....*....
gi 1954738841  685 teesgmNGHDAPILLGRPF 703
Cdd:pfam13650   78 ------LGDLIDGLLGMDF 90
transpos_IS21 NF033546
IS21 family transposase;
1490-1580 3.67e-03

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 41.42  E-value: 3.67e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954738841 1490 YILVAVDYVSKWVEALATRTNDHRVVLTFLKDMiFTRF-GTPRAIISD-----------GGSHFCNKPFEALLKKYNITH 1557
Cdd:NF033546   139 HVFVAVLGYSRYTYVEATPSESQEDLLDGHQRA-FEFFgGVPREIVYDnlktavdkrdrYEEPRLNPRFAAFAAHYGFEP 217

                           90       100
                   ....*....|....*....|...
gi 1954738841 1558 KIATPYHPQTSGQVEVSNREIKR 1580
Cdd:NF033546   218 RPCRPYRPQEKGKVERAVGYVRR 240
 
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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