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Conserved domains on  [gi|359372828|gb|AEV42261|]
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hypothetical protein [Beta vulgaris]

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 ...
 486-662 1.21e-94

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: 301.82  E-value: 1.21e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  486 GIIRPSHSAFSSPVLLVKKKDGSWRFCVDYRALNNVTVPDKYPIPVIDELLDELQGSTVFSKLDLKSGYHQILMKKEDVQ 565
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  566 KTAFRTHEGHYEFLVMPFGLTNAPATFQAVMNDVFRPYLRKFVLVFFDDILVYSMGMTQHVEHLKKVLEVLAQNELFANK 645
Cdd:cd01647    81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                         170
                  ....*....|....*..
gi 359372828  646 KKCEFGKQEVAYLGHII 662
Cdd:cd01647   161 EKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 755-869 1.53e-44

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: 156.88  E-value: 1.53e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  755 VIEANASGYGLGVVLLQ-----QGHPIAYFSKVLGVRARAKSIYEKELMAVVLAVLKWRHYLLGRHFVIHSDQQSLKHLL 829
Cdd:cd09274     1 ILETDASDYGIGAVLSQedddgKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 359372828  830 SQREIGPEYQKWVGKLFGYDFEIKYKTGASNRVADGLSRR 869
Cdd:cd09274    81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 932-993 1.61e-15

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: 71.89  E-value: 1.61e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 359372828   932 VPRKvaMTSRLIHEYHATpmGGHSGIFKTYQRLATEWFWKGMKQDVITFIQECAVCQQNKTS 993
Cdd:pfam17921    1 VPKS--LRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 380-469 4.54e-14

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: 68.90  E-value: 4.54e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  380 LRGTIYGEAVIVMIDPGATHNFVSIHTVERLNIP-VSHAKGFEVSLGTGQEVRGTGECLAVPLMVQGVME--NF--Lppp 454
Cdd:cd00303     1 LKGKINGVPVRALVDSGASVNFISESLAKKLGLPpRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFtvDFyvL--- 77

                          90
                  ....*....|....*
gi 359372828  455 PLGNSDVIMGIQWLE 469
Cdd:cd00303    78 DLLSYDVILGRPWLE 92
Retrotrans_gag super family cl46289
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 117-205 1.27e-06

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.


The actual alignment was detected with superfamily member pfam03732:

Pssm-ID: 480629  Cd Length: 97  Bit Score: 48.10  E-value: 1.27e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828   117 AVVALDGEALLWFQWeHRHRPITG---WPEMKAMLLRQFRDTA-LGSLQEQWMNHHQ-EGSVKEYKSRFIELM--APLDN 189
Cdd:pfam03732    3 AVHSLRGAALTWWKS-LVARSIDAfdsWDELKDAFLKRFFPSIrKDLLRNELRSLRQgTESVREYVERFKRLArqLPHHG 81

                           90
                   ....*....|....*.
gi 359372828   190 IPENIAQAQFISKLKE 205
Cdd:pfam03732   82 RDEEALISAFLRGLRP 97
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1010-1106 4.71e-06

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: 46.54  E-value: 4.71e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  1010 IWEdvsMDFVEG-LPKSGGWDSILVVVDRLSKYGHFIGLRHPFSAATVAQVFIKEVVKLHGFPTTIVSDRDKVFMSIFWK 1088
Cdd:pfam00665    4 LWQ---GDFTYIrIPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 359372828  1089 ELFKLQRTLLHRSTAYHP 1106
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
CD_CSD super family cl28914
CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this ...
 1311-1359 5.82e-05

CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this group are chromodomains or chromo shadow domains; these are SH3-fold-beta-barrel domains of the chromo-like superfamily. Chromodomains lack the first strand of the SH3-fold-beta-barrel, this first strand is altered by insertion in the chromo shadow domains. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. Chromodomain-containing proteins include: i) those having an N-terminal chromodomain followed by a related chromo shadow domain, such as Drosophila and human heterochromatin protein Su(var)205 (HP1), and mammalian modifier 1 and 2; ii) those having a single chromodomain, such as Drosophila protein Polycomb (Pc), mammalian modifier 3, human Mi-2 autoantigen, and several yeast and Caenorhabditis elegans proteins of unknown function; iii) those having paired tandem chromodomains, such as mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1; (iv) and elongation factor eEF3, a member of the ATP-binding cassette (ABC) family of proteins, that serves an essential function in the translation cycle of fungi. eEF3 is a soluble factor lacking a transmembrane domain and having two ABC domains arranged in tandem, with a unique chromodomain inserted within the ABC2 domain.


The actual alignment was detected with superfamily member cd18979:

Pssm-ID: 475127  Cd Length: 48  Bit Score: 41.71  E-value: 5.82e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 359372828 1311 PSQVLGIRpnpLNQAAPAEILVQWSDMSADEATWENVQDIHERFPTFHL 1359
Cdd:cd18979     3 PEKVLDIR---QRDKGNKEFLVQWQGLSVEEATWEPYKDLVQQFPDFKL 48
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 486-662 1.21e-94

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: 301.82  E-value: 1.21e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  486 GIIRPSHSAFSSPVLLVKKKDGSWRFCVDYRALNNVTVPDKYPIPVIDELLDELQGSTVFSKLDLKSGYHQILMKKEDVQ 565
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  566 KTAFRTHEGHYEFLVMPFGLTNAPATFQAVMNDVFRPYLRKFVLVFFDDILVYSMGMTQHVEHLKKVLEVLAQNELFANK 645
Cdd:cd01647    81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                         170
                  ....*....|....*..
gi 359372828  646 KKCEFGKQEVAYLGHII 662
Cdd:cd01647   161 EKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 755-869 1.53e-44

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: 156.88  E-value: 1.53e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  755 VIEANASGYGLGVVLLQ-----QGHPIAYFSKVLGVRARAKSIYEKELMAVVLAVLKWRHYLLGRHFVIHSDQQSLKHLL 829
Cdd:cd09274     1 ILETDASDYGIGAVLSQedddgKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 359372828  830 SQREIGPEYQKWVGKLFGYDFEIKYKTGASNRVADGLSRR 869
Cdd:cd09274    81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 502-662 1.38e-41

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: 151.30  E-value: 1.38e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828   502 VKKKD-GSWRFC----VDYRALNNVTVP-------DKYPIPVIDELLDELQGSTVFSKLDLKSGYHQILMKKEDVQKTAF 569
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828   570 RTH-----------EGHYEFLVMPFGLTNAPATFQAVMNDVFRPYLRKF---VLVFFDDILVYSMGMTQHVEHLKKVLEV 635
Cdd:pfam00078   81 TTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRAgltLVRYADDILIFSKSEEEHQEALEEVLEW 160

                          170       180
                   ....*....|....*....|....*....
gi 359372828   636 LAQNELFANKKKCEF--GKQEVAYLGHII 662
Cdd:pfam00078  161 LKESGLKINPEKTQFflKSKEVKYLGVTL 189
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
724-818 4.91e-39

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 140.33  E-value: 4.91e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828   724 WSKEATTAFQLLKEALTTAPVLALPNFELPFVIEANASGYGLGVVLLQQG-----HPIAYFSKVLGVRARAKSIYEKELM 798
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDddggeRPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|
gi 359372828   799 AVVLAVLKWRHYLLGRHFVI 818
Cdd:pfam17919   81 AIVFALKKFRHYLLGRKFTV 100
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 932-993 1.61e-15

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: 71.89  E-value: 1.61e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 359372828   932 VPRKvaMTSRLIHEYHATpmGGHSGIFKTYQRLATEWFWKGMKQDVITFIQECAVCQQNKTS 993
Cdd:pfam17921    1 VPKS--LRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 380-469 4.54e-14

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: 68.90  E-value: 4.54e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  380 LRGTIYGEAVIVMIDPGATHNFVSIHTVERLNIP-VSHAKGFEVSLGTGQEVRGTGECLAVPLMVQGVME--NF--Lppp 454
Cdd:cd00303     1 LKGKINGVPVRALVDSGASVNFISESLAKKLGLPpRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFtvDFyvL--- 77

                          90
                  ....*....|....*
gi 359372828  455 PLGNSDVIMGIQWLE 469
Cdd:cd00303    78 DLLSYDVILGRPWLE 92
RVP_2 pfam08284
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 356-470 3.17e-07

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases.


Pssm-ID: 400537  Cd Length: 134  Bit Score: 50.89  E-value: 3.17e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828   356 AETFVNPEISLNSVMGFSNPKTlklrgtiygeaviVMIDPGATHNFVSIHTVERLNIPVSHAKgFE--VSLGTGQEVRGT 433
Cdd:pfam08284   11 EEAEASPDVIQGTFLVNSIPAT-------------VLFDSGATHSFISHAFVGKLKLPVESLS-NPlcIETPTGGSVTTN 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 359372828   434 GECLAVPLMVQGVmeNF---LPPPPLGNSDVIMGIQWLEK 470
Cdd:pfam08284   77 LICPSCPIEIQGI--SFladLILLDMKDLDVILGMDWLSK 114
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 117-205 1.27e-06

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: 48.10  E-value: 1.27e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828   117 AVVALDGEALLWFQWeHRHRPITG---WPEMKAMLLRQFRDTA-LGSLQEQWMNHHQ-EGSVKEYKSRFIELM--APLDN 189
Cdd:pfam03732    3 AVHSLRGAALTWWKS-LVARSIDAfdsWDELKDAFLKRFFPSIrKDLLRNELRSLRQgTESVREYVERFKRLArqLPHHG 81

                           90
                   ....*....|....*.
gi 359372828   190 IPENIAQAQFISKLKE 205
Cdd:pfam03732   82 RDEEALISAFLRGLRP 97
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1010-1106 4.71e-06

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: 46.54  E-value: 4.71e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  1010 IWEdvsMDFVEG-LPKSGGWDSILVVVDRLSKYGHFIGLRHPFSAATVAQVFIKEVVKLHGFPTTIVSDRDKVFMSIFWK 1088
Cdd:pfam00665    4 LWQ---GDFTYIrIPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 359372828  1089 ELFKLQRTLLHRSTAYHP 1106
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
CD_POL_like cd18979
chromodomain of a Zea maize putative metaviridae (gypsy-type) retrotransposon polyproteins ...
 1311-1359 5.82e-05

chromodomain of a Zea maize putative metaviridae (gypsy-type) retrotransposon polyproteins (Z195D10.9), and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Zea maize Z195D10.9 protein, and other putative TY3/gypsy retrotransposon polyproteins. The pol gene in TY3/gypsy elements generally encodes domains in the following order: an aspartyl protease, a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349335  Cd Length: 48  Bit Score: 41.71  E-value: 5.82e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 359372828 1311 PSQVLGIRpnpLNQAAPAEILVQWSDMSADEATWENVQDIHERFPTFHL 1359
Cdd:cd18979     3 PEKVLDIR---QRDKGNKEFLVQWQGLSVEEATWEPYKDLVQQFPDFKL 48
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 486-662 1.21e-94

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: 301.82  E-value: 1.21e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  486 GIIRPSHSAFSSPVLLVKKKDGSWRFCVDYRALNNVTVPDKYPIPVIDELLDELQGSTVFSKLDLKSGYHQILMKKEDVQ 565
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  566 KTAFRTHEGHYEFLVMPFGLTNAPATFQAVMNDVFRPYLRKFVLVFFDDILVYSMGMTQHVEHLKKVLEVLAQNELFANK 645
Cdd:cd01647    81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                         170
                  ....*....|....*..
gi 359372828  646 KKCEFGKQEVAYLGHII 662
Cdd:cd01647   161 EKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 755-869 1.53e-44

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: 156.88  E-value: 1.53e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  755 VIEANASGYGLGVVLLQ-----QGHPIAYFSKVLGVRARAKSIYEKELMAVVLAVLKWRHYLLGRHFVIHSDQQSLKHLL 829
Cdd:cd09274     1 ILETDASDYGIGAVLSQedddgKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 359372828  830 SQREIGPEYQKWVGKLFGYDFEIKYKTGASNRVADGLSRR 869
Cdd:cd09274    81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 502-662 1.38e-41

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: 151.30  E-value: 1.38e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828   502 VKKKD-GSWRFC----VDYRALNNVTVP-------DKYPIPVIDELLDELQGSTVFSKLDLKSGYHQILMKKEDVQKTAF 569
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828   570 RTH-----------EGHYEFLVMPFGLTNAPATFQAVMNDVFRPYLRKF---VLVFFDDILVYSMGMTQHVEHLKKVLEV 635
Cdd:pfam00078   81 TTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRAgltLVRYADDILIFSKSEEEHQEALEEVLEW 160

                          170       180
                   ....*....|....*....|....*....
gi 359372828   636 LAQNELFANKKKCEF--GKQEVAYLGHII 662
Cdd:pfam00078  161 LKESGLKINPEKTQFflKSKEVKYLGVTL 189
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
724-818 4.91e-39

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 140.33  E-value: 4.91e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828   724 WSKEATTAFQLLKEALTTAPVLALPNFELPFVIEANASGYGLGVVLLQQG-----HPIAYFSKVLGVRARAKSIYEKELM 798
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDddggeRPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|
gi 359372828   799 AVVLAVLKWRHYLLGRHFVI 818
Cdd:pfam17919   81 AIVFALKKFRHYLLGRKFTV 100
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 749-845 2.20e-31

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: 118.77  E-value: 2.20e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828   749 NFELPFVIEANASGYGLGVVLLQQG-----HPIAYFSKVLGVRARAKSIYEKELMAVVLAVLKWRHYLLGRHFVIHSDQQ 823
Cdd:pfam17917    1 DPSKPFILETDASDYGIGAVLSQKDedgkeRPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHK 80

                           90       100
                   ....*....|....*....|..
gi 359372828   824 SLKHLLSQREIGPEYQKWVGKL 845
Cdd:pfam17917   81 PLKYLFTPKELNGRLARWALFL 102
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 484-662 1.49e-24

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: 103.20  E-value: 1.49e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  484 RSGIIRPSHSAFSSPVLLVKKKDG-SWRFCVDYRALNNVTVPDKYPIPVIDELLDELQ-GSTVFSKLDLKSGYHQILMKK 561
Cdd:cd03715    26 EAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLSLLPpKHQWYTVLDLANAFFSLPLAP 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  562 EDVQKTAFRTHEGHYEFLVMPFGLTNAPATF-QAVMNDV--FRPYLRKFVLV-FFDDILVYSMGMTQHVEHLKKVLEVLA 637
Cdd:cd03715   106 DSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFhEALARDLapFPLEHEGTILLqYVDDLLLAADSEEDCLKGTDALLTHLG 185

                         170       180
                  ....*....|....*....|....*
gi 359372828  638 QNELFANKKKCEFGKQEVAYLGHII 662
Cdd:cd03715   186 ELGYKVSPKKAQICRAEVKFLGVVW 210
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 486-662 7.55e-19

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: 86.57  E-value: 7.55e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  486 GIIRPSHSAFSSPVLLVKKKDGSWRFCVDYRALNNVT---------------VPDKYPIPVIdelldelqgstvfsklDL 550
Cdd:cd01645    28 GHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTqdmgalqpglphpaaLPKGWPLIVL----------------DL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  551 KSGYHQILMKKEDVQKTAF-------RTHEGHYEFLVMPFGLTNAPATFQAVMNDVFRPYLRKF----VLVFFDDILVYS 619
Cdd:cd01645    92 KDCFFSIPLHPDDRERFAFtvpsinnKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYpdivIYHYMDDILIAS 171

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 359372828  620 MGMTQHVEHLKKVLEVLAQNELFANKKKCEFGkQEVAYLGHII 662
Cdd:cd01645   172 DLEGQLREIYEELRQTLLRWGLTIPPEKVQKE-PPFQYLGYEL 213
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 932-993 1.61e-15

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: 71.89  E-value: 1.61e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 359372828   932 VPRKvaMTSRLIHEYHATpmGGHSGIFKTYQRLATEWFWKGMKQDVITFIQECAVCQQNKTS 993
Cdd:pfam17921    1 VPKS--LRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 380-469 4.54e-14

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: 68.90  E-value: 4.54e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  380 LRGTIYGEAVIVMIDPGATHNFVSIHTVERLNIP-VSHAKGFEVSLGTGQEVRGTGECLAVPLMVQGVME--NF--Lppp 454
Cdd:cd00303     1 LKGKINGVPVRALVDSGASVNFISESLAKKLGLPpRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFtvDFyvL--- 77

                          90
                  ....*....|....*
gi 359372828  455 PLGNSDVIMGIQWLE 469
Cdd:cd00303    78 DLLSYDVILGRPWLE 92
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 548-659 4.42e-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: 52.73  E-value: 4.42e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  548 LDLKSGYHQILMKKEDVQKTAFRTHEGHYEFLVMPFGLTNAPATFQAVMNDVFRPYLRKFVLVFF--DDILVYSMGMTqh 625
Cdd:cd03714     1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLGVRIFSylDDLLIIASSIK-- 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 359372828  626 veHLKKVLEVLAQNELFA-----NKKKCEFG-KQEVAYLG 659
Cdd:cd03714    79 --TSEAVLRHLRATLLANlgftlNLEKSKLGpTQRITFLG 116
RVP_2 pfam08284
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 356-470 3.17e-07

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases.


Pssm-ID: 400537  Cd Length: 134  Bit Score: 50.89  E-value: 3.17e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828   356 AETFVNPEISLNSVMGFSNPKTlklrgtiygeaviVMIDPGATHNFVSIHTVERLNIPVSHAKgFE--VSLGTGQEVRGT 433
Cdd:pfam08284   11 EEAEASPDVIQGTFLVNSIPAT-------------VLFDSGATHSFISHAFVGKLKLPVESLS-NPlcIETPTGGSVTTN 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 359372828   434 GECLAVPLMVQGVmeNF---LPPPPLGNSDVIMGIQWLEK 470
Cdd:pfam08284   77 LICPSCPIEIQGI--SFladLILLDMKDLDVILGMDWLSK 114
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 117-205 1.27e-06

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: 48.10  E-value: 1.27e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828   117 AVVALDGEALLWFQWeHRHRPITG---WPEMKAMLLRQFRDTA-LGSLQEQWMNHHQ-EGSVKEYKSRFIELM--APLDN 189
Cdd:pfam03732    3 AVHSLRGAALTWWKS-LVARSIDAfdsWDELKDAFLKRFFPSIrKDLLRNELRSLRQgTESVREYVERFKRLArqLPHHG 81

                           90
                   ....*....|....*.
gi 359372828   190 IPENIAQAQFISKLKE 205
Cdd:pfam03732   82 RDEEALISAFLRGLRP 97
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1010-1106 4.71e-06

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: 46.54  E-value: 4.71e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  1010 IWEdvsMDFVEG-LPKSGGWDSILVVVDRLSKYGHFIGLRHPFSAATVAQVFIKEVVKLHGFPTTIVSDRDKVFMSIFWK 1088
Cdd:pfam00665    4 LWQ---GDFTYIrIPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 359372828  1089 ELFKLQRTLLHRSTAYHP 1106
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 755-870 5.23e-05

DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. The structural features of DIRS1-group elements are different from typical LTR elements. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260007  Cd Length: 120  Bit Score: 44.20  E-value: 5.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  755 VIEANASGYGLGVVLL-QQGHpiAYFSKvlgvRARAKSIYEKELMAVVLAVLKWRHYLLGRHFVIHSDQ----QSLKHLL 829
Cdd:cd09275     1 VLFTDASLSGWGAYLLnSRAH--GPWSA----DERNKHINLLELKAVLLALQHFAAELKNRKILIRTDNttavAYINKQG 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 359372828  830 SQREI-GPEYQKWVGKLFGYdFEIKYKT----GASNRVADGLSRRG 870
Cdd:cd09275    75 GTSSPpLLALARQILLWCEQ-RNIWLRAshipGVLNTEADRLSRLG 119
CD_POL_like cd18979
chromodomain of a Zea maize putative metaviridae (gypsy-type) retrotransposon polyproteins ...
 1311-1359 5.82e-05

chromodomain of a Zea maize putative metaviridae (gypsy-type) retrotransposon polyproteins (Z195D10.9), and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Zea maize Z195D10.9 protein, and other putative TY3/gypsy retrotransposon polyproteins. The pol gene in TY3/gypsy elements generally encodes domains in the following order: an aspartyl protease, a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349335  Cd Length: 48  Bit Score: 41.71  E-value: 5.82e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 359372828 1311 PSQVLGIRpnpLNQAAPAEILVQWSDMSADEATWENVQDIHERFPTFHL 1359
Cdd:cd18979     3 PEKVLDIR---QRDKGNKEFLVQWQGLSVEEATWEPYKDLVQQFPDFKL 48
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 549-636 4.73e-03

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


Pssm-ID: 238822  Cd Length: 213  Bit Score: 39.98  E-value: 4.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  549 DLKSGYHQILMKKEDVQKTAF--RTHEG-----HYEFLVMPFGLTNAPATFQAVMNDVFR----PYLRKFVLVFF--DDI 615
Cdd:cd01644    65 DIEKMFHQVKVRPEDRDVLRFlwRKDGDepkpiEYRMTVVPFGAASAPFLANRALKQHAEdhphEAAAKIIKRNFyvDDI 144

                          90       100
                  ....*....|....*....|.
gi 359372828  616 LVYSMGMTQHVEHLKKVLEVL 636
Cdd:cd01644   145 LVSTDTLNEAVNVAKRLIALL 165
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 764-868 9.22e-03

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: 37.68  E-value: 9.22e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359372828  764 GLGVVLLQ-QGHPIAYFSKVLGvrarAKSIYEKELMAVVLAVLKWRHyLLGRHFVIHSDQQSLKHLLSQREIGPE----- 837
Cdd:cd06222    15 GIGGVLRDhEGGWLGGFALKIG----APTALEAELLALLLALELALD-LGYLKVIIESDSKYVVDLINSGSFKWSpnill 89

                          90       100       110
                  ....*....|....*....|....*....|..
gi 359372828  838 -YQKWVGKLFGYDFEIKYKTGASNRVADGLSR 868
Cdd:cd06222    90 iEDILLLLSRFWSVKISHVPREGNQVADALAK 121
 
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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