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Conserved domains on  [gi|4432807|gb|AAD20658|]
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putative retroelement pol polyprotein [Arabidopsis thaliana]

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 ...
 686-862 2.97e-93

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: 298.74  E-value: 2.97e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   686 GFIRPSSSPWGAPVLFVKKKDGSFRLCIDYRGLNKVTVKNKYPLPRIDELMDQLGGAQWFSKIDLASGYHQIPIEPTDVR 765
Cdd:cd01647    1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   766 KTAFRTRYDHFEFVVMPFGLTNAPAAFMKMMNGVFRDFLDEFVIIFINDILVYSKSWEAHQEHLRAVLERLREHELFAKL 845
Cdd:cd01647   81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                        170
                 ....*....|....*..
gi 4432807   846 SKCSFWQRSVGFLGHVI 862
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) ...
 956-1070 1.73e-55

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: 188.47  E-value: 1.73e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   956 TVYTDASIVGLGCVLMQKGS-----VIAYASRQLRKHEKNYPTHDLEMAAVVFFLKIWRSYLYGAKVQIYTDHKSLKYIF 1030
Cdd:cd09274    1 ILETDASDYGIGAVLSQEDDdgkerPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 4432807  1031 TQPELNLRQRRWMELVADYNLDIAYHPGKANQVADALSRR 1070
Cdd:cd09274   81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 214-309 1.49e-33

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


:

Pssm-ID: 367628  Cd Length: 97  Bit Score: 125.14  E-value: 1.49e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807     214 DIAVHFLEGDAHNWWLTVEKRRGDEVRSFADFEDEFNKKYFPPEAWDRLECAYLDLVQGNRTVREYDEEFNRLRRYVGRE 293
Cdd:pfam03732    1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHH 80

                           90
                   ....*....|....*.
gi 4432807     294 LEEEQAQLRRFIRGLR 309
Cdd:pfam03732   81 GRDEEALISAFLRGLR 96
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1155-1213 3.51e-17

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: 76.90  E-value: 3.51e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 4432807    1155 NDRALKEEILREAHQSkfSIHPGSNKMYRDLKRYYHWVGMKKDVARWVAKCPTCQLVKA 1213
Cdd:pfam17921    1 VPKSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 522-575 1.81e-12

Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin 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. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family).


The actual alignment was detected with superfamily member pfam08284:

Pssm-ID: 472175  Cd Length: 134  Bit Score: 65.92  E-value: 1.81e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 4432807     522 RGISVVVNGVNMPADLIIVPLKKHDVILGMDWLGKYKAHIDCHRGRIQFERDEG 575
Cdd:pfam08284   80 PSCPIEIQGISFLADLILLDMKDLDVILGMDWLSKNKANIDCARRTVTLTKERE 133
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 398-444 2.94e-10

universal minicircle sequence binding protein (UMSBP); Provisional


The actual alignment was detected with superfamily member PTZ00368:

Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 60.21  E-value: 2.94e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 4432807    398 ACGRCGSKDHAIQSCPKMEPGQskvlgeETRTCFYCGKTGHLKRECP 444
Cdd:PTZ00368   29 PCYKCGEPGHLSRECPSAPGGR------GERSCYNCGKTGHLSRECP 69
transpos_IS481 super family cl41329
IS481 family transposase; null
 1161-1344 8.57e-07

IS481 family transposase; null


The actual alignment was detected with superfamily member NF033577:

Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 52.59  E-value: 8.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   1161 EEILREAHQSKFSIHPGSnkMYRDLKRYyhwvgmkkDVARWVA-KCPTCQLVKAEHQVPSGLLQnlpipewkwdhitMDf 1239
Cdd:NF033577   79 RRIAYELERQGPGVSRST--VHRILRRH--------GLSRLRAlDRKTGKVKRYERAHPGELWH-------------ID- 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   1240 VTGLPTGIKSKHNAVWVVVDRLTKSAHFMAISDKDGAeiIAEKYIDEIVRLHGIPV-SIVSDRDTRFTSKFwKAFQKAL- 1317
Cdd:NF033577  135 IKKLGRIPDVGRLYLHTAIDDHSRFAYAELYPDETAE--TAADFLRRAFAEHGIPIrRVLTDNGSEFRSRA-HGFELALa 211

                         170       180
                  ....*....|....*....|....*....
gi 4432807   1318 --GTRVNLSTAYHPQTDEQSERTIQTLED 1344
Cdd:NF033577  212 elGIEHRRTRPYHPQTNGKVERFHRTLKD 240
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 686-862 2.97e-93

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: 298.74  E-value: 2.97e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   686 GFIRPSSSPWGAPVLFVKKKDGSFRLCIDYRGLNKVTVKNKYPLPRIDELMDQLGGAQWFSKIDLASGYHQIPIEPTDVR 765
Cdd:cd01647    1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   766 KTAFRTRYDHFEFVVMPFGLTNAPAAFMKMMNGVFRDFLDEFVIIFINDILVYSKSWEAHQEHLRAVLERLREHELFAKL 845
Cdd:cd01647   81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                        170
                 ....*....|....*..
gi 4432807   846 SKCSFWQRSVGFLGHVI 862
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) ...
 956-1070 1.73e-55

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: 188.47  E-value: 1.73e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   956 TVYTDASIVGLGCVLMQKGS-----VIAYASRQLRKHEKNYPTHDLEMAAVVFFLKIWRSYLYGAKVQIYTDHKSLKYIF 1030
Cdd:cd09274    1 ILETDASDYGIGAVLSQEDDdgkerPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 4432807  1031 TQPELNLRQRRWMELVADYNLDIAYHPGKANQVADALSRR 1070
Cdd:cd09274   81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 702-862 1.29e-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: 151.69  E-value: 1.29e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807     702 VKKKD-GSFRLC----IDYRGLNKVTVK-------NKYPLPRIDELMDQLGGAQWFSKIDLASGYHQIPIEPTDVRKTAF 769
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807     770 RTR-----------YDHFEFVVMPFGLTNAPAAFMKMMNGVFRDFL---DEFVIIFINDILVYSKSWEAHQEHLRAVLER 835
Cdd:pfam00078   81 TTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRkraGLTLVRYADDILIFSKSEEEHQEALEEVLEW 160

                          170       180
                   ....*....|....*....|....*....
gi 4432807     836 LREHELFAKLSKCSF--WQRSVGFLGHVI 862
Cdd:pfam00078  161 LKESGLKINPEKTQFflKSKEVKYLGVTL 189
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 952-1048 1.85e-39

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: 141.88  E-value: 1.85e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807     952 GEPYTVYTDASIVGLGCVLMQKGS-----VIAYASRQLRKHEKNYPTHDLEMAAVVFFLKIWRSYLYGAKVQIYTDHKSL 1026
Cdd:pfam17917    3 SKPFILETDASDYGIGAVLSQKDEdgkerPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHKPL 82

                           90       100
                   ....*....|....*....|..
gi 4432807    1027 KYIFTQPELNLRQRRWMELVAD 1048
Cdd:pfam17917   83 KYLFTPKELNGRLARWALFLQE 104
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 214-309 1.49e-33

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


Pssm-ID: 367628  Cd Length: 97  Bit Score: 125.14  E-value: 1.49e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807     214 DIAVHFLEGDAHNWWLTVEKRRGDEVRSFADFEDEFNKKYFPPEAWDRLECAYLDLVQGNRTVREYDEEFNRLRRYVGRE 293
Cdd:pfam03732    1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHH 80

                           90
                   ....*....|....*.
gi 4432807     294 LEEEQAQLRRFIRGLR 309
Cdd:pfam03732   81 GRDEEALISAFLRGLR 96
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1155-1213 3.51e-17

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: 76.90  E-value: 3.51e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 4432807    1155 NDRALKEEILREAHQSkfSIHPGSNKMYRDLKRYYHWVGMKKDVARWVAKCPTCQLVKA 1213
Cdd:pfam17921    1 VPKSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
RVP_2 pfam08284
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 522-575 1.81e-12

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: 65.92  E-value: 1.81e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 4432807     522 RGISVVVNGVNMPADLIIVPLKKHDVILGMDWLGKYKAHIDCHRGRIQFERDEG 575
Cdd:pfam08284   80 PSCPIEIQGISFLADLILLDMKDLDVILGMDWLSKNKANIDCARRTVTLTKERE 133
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 398-444 2.94e-10

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 60.21  E-value: 2.94e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 4432807    398 ACGRCGSKDHAIQSCPKMEPGQskvlgeETRTCFYCGKTGHLKRECP 444
Cdd:PTZ00368   29 PCYKCGEPGHLSRECPSAPGGR------GERSCYNCGKTGHLSRECP 69
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 507-554 1.39e-07

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: 50.80  E-value: 1.39e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 4432807   507 VRAAGGQAMYPTGLVRGISVVVNGVNMPADLIIVPLKKHDVILGMDWL 554
Cdd:cd00303   44 VKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLSYDVILGRPWL 91
transpos_IS481 NF033577
IS481 family transposase; null
 1161-1344 8.57e-07

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 52.59  E-value: 8.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   1161 EEILREAHQSKFSIHPGSnkMYRDLKRYyhwvgmkkDVARWVA-KCPTCQLVKAEHQVPSGLLQnlpipewkwdhitMDf 1239
Cdd:NF033577   79 RRIAYELERQGPGVSRST--VHRILRRH--------GLSRLRAlDRKTGKVKRYERAHPGELWH-------------ID- 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   1240 VTGLPTGIKSKHNAVWVVVDRLTKSAHFMAISDKDGAeiIAEKYIDEIVRLHGIPV-SIVSDRDTRFTSKFwKAFQKAL- 1317
Cdd:NF033577  135 IKKLGRIPDVGRLYLHTAIDDHSRFAYAELYPDETAE--TAADFLRRAFAEHGIPIrRVLTDNGSEFRSRA-HGFELALa 211

                         170       180
                  ....*....|....*....|....*....
gi 4432807   1318 --GTRVNLSTAYHPQTDEQSERTIQTLED 1344
Cdd:NF033577  212 elGIEHRRTRPYHPQTNGKVERFHRTLKD 240
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 367-444 3.70e-06

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


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 49.08  E-value: 3.70e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   367 DKVDNTKSDAKTgeCVTCGKN-H-SGTCWKAIgaCGRCGSKDHAIQSCPKmepgqskvlgeeTRTCFYCGKTGHLKRECP 444
Cdd:COG5082   51 EDVSAIREENPV--CFNCGQNgHlRRDCPHSI--CYNCSWDGHRSNHCPK------------PKKCYNCGETGHLSRDCN 114
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1233-1329 6.01e-05

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


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 43.46  E-value: 6.01e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807    1233 DHITMDFVTGlptGIKSKHNAVW--VVVDRLTKSAHFMAISDKDGAEIIAEKYIDEIVRLHGIPVSIVSDRDTRFTSKFW 1310
Cdd:pfam00665    3 QLWQGDFTYI---RIPGGGGKLYllVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAF 79

                           90
                   ....*....|....*....
gi 4432807    1311 KAFQKALGTRVNLSTAYHP 1329
Cdd:pfam00665   80 REFLKDLGIKPSFSRPGNP 98
ZnF_C2HC smart00343
zinc finger;
429-445 8.31e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.89  E-value: 8.31e-05
                            10
                    ....*....|....*..
gi 4432807      429 TCFYCGKTGHLKRECPK 445
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 428-445 1.01e-04

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


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 40.59  E-value: 1.01e-04
                           10
                   ....*....|....*...
gi 4432807     428 RTCFYCGKTGHLKRECPK 445
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 686-862 2.97e-93

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: 298.74  E-value: 2.97e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   686 GFIRPSSSPWGAPVLFVKKKDGSFRLCIDYRGLNKVTVKNKYPLPRIDELMDQLGGAQWFSKIDLASGYHQIPIEPTDVR 765
Cdd:cd01647    1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   766 KTAFRTRYDHFEFVVMPFGLTNAPAAFMKMMNGVFRDFLDEFVIIFINDILVYSKSWEAHQEHLRAVLERLREHELFAKL 845
Cdd:cd01647   81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                        170
                 ....*....|....*..
gi 4432807   846 SKCSFWQRSVGFLGHVI 862
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) ...
 956-1070 1.73e-55

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: 188.47  E-value: 1.73e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   956 TVYTDASIVGLGCVLMQKGS-----VIAYASRQLRKHEKNYPTHDLEMAAVVFFLKIWRSYLYGAKVQIYTDHKSLKYIF 1030
Cdd:cd09274    1 ILETDASDYGIGAVLSQEDDdgkerPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 4432807  1031 TQPELNLRQRRWMELVADYNLDIAYHPGKANQVADALSRR 1070
Cdd:cd09274   81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 702-862 1.29e-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: 151.69  E-value: 1.29e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807     702 VKKKD-GSFRLC----IDYRGLNKVTVK-------NKYPLPRIDELMDQLGGAQWFSKIDLASGYHQIPIEPTDVRKTAF 769
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807     770 RTR-----------YDHFEFVVMPFGLTNAPAAFMKMMNGVFRDFL---DEFVIIFINDILVYSKSWEAHQEHLRAVLER 835
Cdd:pfam00078   81 TTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRkraGLTLVRYADDILIFSKSEEEHQEALEEVLEW 160

                          170       180
                   ....*....|....*....|....*....
gi 4432807     836 LREHELFAKLSKCSF--WQRSVGFLGHVI 862
Cdd:pfam00078  161 LKESGLKINPEKTQFflKSKEVKYLGVTL 189
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 952-1048 1.85e-39

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: 141.88  E-value: 1.85e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807     952 GEPYTVYTDASIVGLGCVLMQKGS-----VIAYASRQLRKHEKNYPTHDLEMAAVVFFLKIWRSYLYGAKVQIYTDHKSL 1026
Cdd:pfam17917    3 SKPFILETDASDYGIGAVLSQKDEdgkerPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHKPL 82

                           90       100
                   ....*....|....*....|..
gi 4432807    1027 KYIFTQPELNLRQRRWMELVAD 1048
Cdd:pfam17917   83 KYLFTPKELNGRLARWALFLQE 104
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
925-1019 8.78e-38

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 137.25  E-value: 8.78e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807     925 WSDECEKSFLELKAMLTNAPVLVLPEEGEPYTVYTDASIVGLGCVLMQKGS-----VIAYASRQLRKHEKNYPTHDLEMA 999
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDdggerPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|
gi 4432807    1000 AVVFFLKIWRSYLYGAKVQI 1019
Cdd:pfam17919   81 AIVFALKKFRHYLLGRKFTV 100
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 214-309 1.49e-33

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


Pssm-ID: 367628  Cd Length: 97  Bit Score: 125.14  E-value: 1.49e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807     214 DIAVHFLEGDAHNWWLTVEKRRGDEVRSFADFEDEFNKKYFPPEAWDRLECAYLDLVQGNRTVREYDEEFNRLRRYVGRE 293
Cdd:pfam03732    1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHH 80

                           90
                   ....*....|....*.
gi 4432807     294 LEEEQAQLRRFIRGLR 309
Cdd:pfam03732   81 GRDEEALISAFLRGLR 96
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 659-862 5.94e-29

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: 115.91  E-value: 5.94e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   659 PISKAPYRMAPAEMAKLKKQLEELLDKGFIRPSSSPWGAPVLFVKKKDG-SFRLCIDYRGLNKVTVKNKYPLPRIDELMD 737
Cdd:cd03715    1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   738 QLGGA-QWFSKIDLASGYHQIPIEPTDVRKTAFRTRYDHFEFVVMPFGLTNAPAAFmkmMNGVFRDfLDEF--------V 808
Cdd:cd03715   81 LLPPKhQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLF---HEALARD-LAPFplehegtiL 156

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 4432807   809 IIFINDILVYSKSWEAHQEHLRAVLERLREHELFAKLSKCSFWQRSVGFLGHVI 862
Cdd:cd03715  157 LQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 675-862 1.06e-22

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.


Pssm-ID: 238823 [Multi-domain]  Cd Length: 213  Bit Score: 98.12  E-value: 1.06e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   675 LKKQLEELLDKGFIRPSSSPWGAPVLFVKKKDGSFRLCIDYRGLNKVTVK---------NKYPLPRIDELMdqlggaqwf 745
Cdd:cd01645   17 LTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDmgalqpglpHPAALPKGWPLI--------- 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   746 sKIDLASGYHQIPIEPTDVRKTAF-------RTRYDHFEFVVMPFGLTNAPAAFMKMMNGVFRDFLDEF----VIIFIND 814
Cdd:cd01645   88 -VLDLKDCFFSIPLHPDDRERFAFtvpsinnKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYpdivIYHYMDD 166

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 4432807   815 ILVYSKSWEAHQEHLRAVLERLREHELFAKLSKcsfWQRS--VGFLGHVI 862
Cdd:cd01645  167 ILIASDLEGQLREIYEELRQTLLRWGLTIPPEK---VQKEppFQYLGYEL 213
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1155-1213 3.51e-17

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: 76.90  E-value: 3.51e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 4432807    1155 NDRALKEEILREAHQSkfSIHPGSNKMYRDLKRYYHWVGMKKDVARWVAKCPTCQLVKA 1213
Cdd:pfam17921    1 VPKSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
RVP_2 pfam08284
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 522-575 1.81e-12

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: 65.92  E-value: 1.81e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 4432807     522 RGISVVVNGVNMPADLIIVPLKKHDVILGMDWLGKYKAHIDCHRGRIQFERDEG 575
Cdd:pfam08284   80 PSCPIEIQGISFLADLILLDMKDLDVILGMDWLSKNKANIDCARRTVTLTKERE 133
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 956-1070 6.25e-11

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: 61.15  E-value: 6.25e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   956 TVYTDASIVGLGCVLmQKGSVIAYASrqlrKHEKNYPTHDLEMAAVVFFLKIWRSYLYGAKVQIYTDHKS-LKYIFTQ-- 1032
Cdd:cd09275    1 VLFTDASLSGWGAYL-LNSRAHGPWS----ADERNKHINLLELKAVLLALQHFAAELKNRKILIRTDNTTaVAYINKQgg 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 4432807  1033 ---PELNLRQRRWMELVADYNLDI-AYH-PGKANQVADALSRR 1070
Cdd:cd09275   76 tssPPLLALARQILLWCEQRNIWLrASHiPGVLNTEADRLSRL 118
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 748-859 7.37e-11

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: 60.82  E-value: 7.37e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   748 IDLASGYHQIPIEPTDVRKTAFRTRYDHFEFVVMPFGLTNAPAAFMKMMNGVFRDFLDEFVIIF--INDILVYSKSwEAH 825
Cdd:cd03714    1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLGVRIFsyLDDLLIIASS-IKT 79

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 4432807   826 QEHLRAVLERLREHELFAKLSKC-SFW--QRSVGFLG 859
Cdd:cd03714   80 SEAVLRHLRATLLANLGFTLNLEkSKLgpTQRITFLG 116
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 398-444 2.94e-10

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 60.21  E-value: 2.94e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 4432807    398 ACGRCGSKDHAIQSCPKMEPGQskvlgeETRTCFYCGKTGHLKRECP 444
Cdd:PTZ00368   29 PCYKCGEPGHLSRECPSAPGGR------GERSCYNCGKTGHLSRECP 69
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 376-458 3.92e-09

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 57.12  E-value: 3.92e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807    376 AKTGECVTCGK-NH-SGTCWKAIG-----ACGRCGSKDHAIQSCPKMEPGQskvlgeETRTCFYCGKTGHLKRECPklta 448
Cdd:PTZ00368   25 AKARPCYKCGEpGHlSRECPSAPGgrgerSCYNCGKTGHLSRECPEAPPGS------GPRSCYNCGQTGHISRECP---- 94

                          90
                  ....*....|
gi 4432807    449 EKQAGQRDNR 458
Cdd:PTZ00368   95 NRAKGGAARR 104
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 371-453 4.11e-09

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 56.74  E-value: 4.11e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807    371 NTKSDAKTGECVTCGK-NH-SGTCWKAIG-----ACGRCGSKDHAIQSCPKMEPGqskvlGEETRTCFYCGKTGHLKREC 443
Cdd:PTZ00368   45 SAPGGRGERSCYNCGKtGHlSRECPEAPPgsgprSCYNCGQTGHISRECPNRAKG-----GAARRACYNCGGEGHISRDC 119

                          90
                  ....*....|
gi 4432807    444 PklTAEKQAG 453
Cdd:PTZ00368  120 P--NAGKRPG 127
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 507-554 1.39e-07

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: 50.80  E-value: 1.39e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 4432807   507 VRAAGGQAMYPTGLVRGISVVVNGVNMPADLIIVPLKKHDVILGMDWL 554
Cdd:cd00303   44 VKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLSYDVILGRPWL 91
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 381-444 1.90e-07

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 52.12  E-value: 1.90e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4432807    381 CVTCG-KNH-SGTC------WKAIGACGRCGSKDHAIQSCPKmEPGQSKvlgeETRTCFYCGKTGHLKRECP 444
Cdd:PTZ00368   80 CYNCGqTGHiSRECpnrakgGAARRACYNCGGEGHISRDCPN-AGKRPG----GDKTCYNCGQTGHLSRDCP 146
transpos_IS481 NF033577
IS481 family transposase; null
 1161-1344 8.57e-07

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 52.59  E-value: 8.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   1161 EEILREAHQSKFSIHPGSnkMYRDLKRYyhwvgmkkDVARWVA-KCPTCQLVKAEHQVPSGLLQnlpipewkwdhitMDf 1239
Cdd:NF033577   79 RRIAYELERQGPGVSRST--VHRILRRH--------GLSRLRAlDRKTGKVKRYERAHPGELWH-------------ID- 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   1240 VTGLPTGIKSKHNAVWVVVDRLTKSAHFMAISDKDGAeiIAEKYIDEIVRLHGIPV-SIVSDRDTRFTSKFwKAFQKAL- 1317
Cdd:NF033577  135 IKKLGRIPDVGRLYLHTAIDDHSRFAYAELYPDETAE--TAADFLRRAFAEHGIPIrRVLTDNGSEFRSRA-HGFELALa 211

                         170       180
                  ....*....|....*....|....*....
gi 4432807   1318 --GTRVNLSTAYHPQTDEQSERTIQTLED 1344
Cdd:NF033577  212 elGIEHRRTRPYHPQTNGKVERFHRTLKD 240
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 367-444 3.70e-06

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


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 49.08  E-value: 3.70e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807   367 DKVDNTKSDAKTgeCVTCGKN-H-SGTCWKAIgaCGRCGSKDHAIQSCPKmepgqskvlgeeTRTCFYCGKTGHLKRECP 444
Cdd:COG5082   51 EDVSAIREENPV--CFNCGQNgHlRRDCPHSI--CYNCSWDGHRSNHCPK------------PKKCYNCGETGHLSRDCN 114
Ty3_capsid pfam19259
Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the ...
 182-365 1.01e-05

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


Pssm-ID: 437091 [Multi-domain]  Cd Length: 197  Bit Score: 48.24  E-value: 1.01e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807     182 FMGSTDPIVADEWRSRLKRNFKSTRCPEDYQRdiaVHF----LEGDAHNWWLTVEKRRGDEVRSFADFEDEFNKKYF-PP 256
Cdd:pfam19259   17 FRGRKDVLKLKSFISEIMLQMSMIFWPNDAER---IVFcarhLTGPAAQWFHDFVQEQGILDATFDTFIKAFKQHFYgKP 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807     257 EAWDRLEcAYLDLVQGNRTVREYDEEFNRLRRYVGRELEEEQAQLRRFIRGLRIEIRNHCLVRTFNSVSELveraamIEE 336
Cdd:pfam19259   94 DINKLFN-DIVNLSEAKLGIERYNSHFNRLWDLLPPDFLSEKAAIMFYIRGLKPETYIIVRLAKPSTLKEA------MEI 166

                          170       180
                   ....*....|....*....|....*....
gi 4432807     337 GIEEERYLNREKAPIRNNQSTKPADKKRK 365
Cdd:pfam19259  167 AYETIPYTERFSPTFTQNSKTVLDADGDT 195
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1233-1329 6.01e-05

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


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 43.46  E-value: 6.01e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4432807    1233 DHITMDFVTGlptGIKSKHNAVW--VVVDRLTKSAHFMAISDKDGAEIIAEKYIDEIVRLHGIPVSIVSDRDTRFTSKFW 1310
Cdd:pfam00665    3 QLWQGDFTYI---RIPGGGGKLYllVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAF 79

                           90
                   ....*....|....*....
gi 4432807    1311 KAFQKALGTRVNLSTAYHP 1329
Cdd:pfam00665   80 REFLKDLGIKPSFSRPGNP 98
ZnF_C2HC smart00343
zinc finger;
429-445 8.31e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.89  E-value: 8.31e-05
                            10
                    ....*....|....*..
gi 4432807      429 TCFYCGKTGHLKRECPK 445
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 428-445 1.01e-04

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


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 40.59  E-value: 1.01e-04
                           10
                   ....*....|....*...
gi 4432807     428 RTCFYCGKTGHLKRECPK 445
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
zf-H2C2 pfam09337
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 1175-1209 6.44e-04

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


Pssm-ID: 430537  Cd Length: 39  Bit Score: 38.85  E-value: 6.44e-04
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 4432807    1175 HPGSNKMYRDLKRYYHWVGMKKDVARWVAKCPTCQ 1209
Cdd:pfam09337    5 HLGINKLTALLARKYHWLGIKETVSEVISSCVACQ 39
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 398-445 9.03e-04

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


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 42.15  E-value: 9.03e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 4432807   398 ACGRCGSKDHAIQSCPKmepgqskvlgeetRTCFYCGKTGHLKRECPK 445
Cdd:COG5082   62 VCFNCGQNGHLRRDCPH-------------SICYNCSWDGHRSNHCPK 96
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 495-556 3.62e-03

gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins.


Pssm-ID: 464060  Cd Length: 92  Bit Score: 38.33  E-value: 3.62e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 4432807     495 GFRKEPNTDYGMVRAAGGQAMYPTGLVRGISV---VVNGVnmpaDLIIVPLKKHDVILGMDWLGK 556
Cdd:pfam13975   32 GLDRLVDAYPVTVRTANGTVRAARVRLDSVKIggiELRNV----PAVVLPGDLDDVLLGMDFLKR 92
 
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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