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Conserved domains on  [gi|285812571|tpg|DAA08470.1|]
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TPA: gag-pol fusion protein [Saccharomyces cerevisiae S288c]

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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 ...
649-823 7.74e-84

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 [Multi-domain]  Cd Length: 177  Bit Score: 273.32  E-value: 7.74e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  649 KFIVPSKSPCSSPVVLVPKKDGTFRLCVDYRTLNKATISDPFPLPRIDNLLSRIGNAQIFTTLDLHSGYHQIPMEPKDRY 728
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  729 KTAFVTPSGKYEYTVMPFGLVNAPSTFARYMADTFRDL--RFVNVYLDDILIFSESPEEHWKHLDTVLERLKNENLIVKK 806
Cdd:cd01647    81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlgDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160
                         170
                  ....*....|....*..
gi 285812571  807 KKCKFASEETEFLGYSI 823
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) ...
915-1034 2.46e-47

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  Cd Length: 121  Bit Score: 167.28  E-value: 2.46e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  915 RLTTDASKDGIGAVLEEVDNKNKLvGVVGYFSKSLESAQKNYPAGELELLGIIKALHHFRYMLHGKHFTLRTDHISLLSL 994
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDDDGKE-RPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYL 79
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 285812571  995 QNKNEPARRVQRWLDDLATYDFTLEYLAGPKNVVADAISR 1034
Cdd:cd09274    80 LTQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSR 119
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
323-412 8.10e-16

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: 75.45  E-value: 8.10e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  323 TIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYE-IYETPPLRFRGFVATKSAVTSEAVTIDLKINDLQITLAAYILDNMD 401
Cdd:cd00303     2 KGKINGVPVRALVDSGASVNFISESLAKKLGLPpRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLS 81
                          90
                  ....*....|.
gi 285812571  402 YQLLIGNPILR 412
Cdd:cd00303    82 YDVILGRPWLE 92
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
1198-1308 3.88e-20

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 catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


:

Pssm-ID: 250040  Cd Length: 119  Bit Score: 88.93  E-value: 3.88e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  1198 ISMDFVTGLPPTSNNLNMILVVVDRFSKRAHFIATRKTLDATQLIDLLFRYIFSYHGFPRTITSDRDVRMTADKYQELTK 1277
Cdd:pfam00665    9 WQMDITPIPISSKGGKKYLLVIVDDFSRFVVAYALKSKTDAELVFDLLEAALERRGGKPVTIHSDNGSEFTSKAFQELLK 88
                           90       100       110
                   ....*....|....*....|....*....|.
gi 285812571  1278 RLGIKSTMSSANHPQTDGQSERTIQTLNRLL 1308
Cdd:pfam00665   89 ELGIKHSFSRPGNPQDNGVVERFNRTLKEEL 119
Retrotrans_gag super family cl04237
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
70-157 7.24e-05

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: 252133  Cd Length: 97  Bit Score: 42.71  E-value: 7.24e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571    70 HLLNPAAQWANDFVQEQGILEITFDTFIQGLYQHFYKPPDINKIFNAITQLSEAKLGIERLNQRFRKIWDRMPPDFMTEK 149
Cdd:pfam03732    6 HLEGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLENELRSLRQGTESVREYVERFKRLARQLPHHGFDEE 85

                   ....*...
gi 285812571   150 AAIMTYTR 157
Cdd:pfam03732   86 ALISAFLR 93
zf-H2C2 super family cl07828
His(2)-Cys(2) zinc finger; This domain binds to histone upstream activating sequence (UAS) ...
1138-1172 2.71e-03

His(2)-Cys(2) zinc finger; This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters.


The actual alignment was detected with superfamily member pfam09337:

Pssm-ID: 150113  Cd Length: 39  Bit Score: 37.45  E-value: 2.71e-03
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 285812571  1138 HFGVTVTLAKISPIYYWPKLQHSIIQYIRTCVQCQ 1172
Cdd:pfam09337    5 HAGINKTTSKIAEKYHWKRIKETVARVIRSCPECK 39
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
665-823 1.02e-37

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: 249567 [Multi-domain]  Cd Length: 196  Bit Score: 142.08  E-value: 1.02e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571   665 VPKKD-GTFRLC----VDYRTLNKATIS-------DPFPLPRIDNLLS---RIGNAQIFTTLDLHSGYHQIPMEPKDRYK 729
Cdd:pfam00078    1 IPKKGkGKYRPVslpsVDYKILNKATKKrlepepiFSPPQPGFRPGRSlhdLLKGSKWFLKLDLKKAFDSIPLDPLDRPL 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571   730 TAFVTPS---------------GKYEYTVMPFGLVNAPSTFARYMADTFRDLR------FVNVYLDDILIFSESPEEHWK 788
Cdd:pfam00078   81 TAFGFPGrfirtfsvrvngnpgGRYEWRGLPQGLPLSPLLFNLYMNKLLRPLRkrfpgvTYLRYADDILIFSKSKEELQE 160
                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 285812571   789 HLDTVLERLKNENLIVKKKKCKFA-SEETEFLGYSI 823
Cdd:pfam00078  161 ILEEVLEFLKELGLKLNPEKTKIThSDEVKFLGYVI 196
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
649-823 7.74e-84

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 [Multi-domain]  Cd Length: 177  Bit Score: 273.32  E-value: 7.74e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  649 KFIVPSKSPCSSPVVLVPKKDGTFRLCVDYRTLNKATISDPFPLPRIDNLLSRIGNAQIFTTLDLHSGYHQIPMEPKDRY 728
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  729 KTAFVTPSGKYEYTVMPFGLVNAPSTFARYMADTFRDL--RFVNVYLDDILIFSESPEEHWKHLDTVLERLKNENLIVKK 806
Cdd:cd01647    81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlgDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160
                         170
                  ....*....|....*..
gi 285812571  807 KKCKFASEETEFLGYSI 823
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) ...
915-1034 2.46e-47

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  Cd Length: 121  Bit Score: 167.28  E-value: 2.46e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  915 RLTTDASKDGIGAVLEEVDNKNKLvGVVGYFSKSLESAQKNYPAGELELLGIIKALHHFRYMLHGKHFTLRTDHISLLSL 994
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDDDGKE-RPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYL 79
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 285812571  995 QNKNEPARRVQRWLDDLATYDFTLEYLAGPKNVVADAISR 1034
Cdd:cd09274    80 LTQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSR 119
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
323-412 8.10e-16

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: 75.45  E-value: 8.10e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  323 TIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYE-IYETPPLRFRGFVATKSAVTSEAVTIDLKINDLQITLAAYILDNMD 401
Cdd:cd00303     2 KGKINGVPVRALVDSGASVNFISESLAKKLGLPpRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLS 81
                          90
                  ....*....|.
gi 285812571  402 YQLLIGNPILR 412
Cdd:cd00303    82 YDVILGRPWLE 92
Peptidase_A2B pfam12384
Ty3 transposon peptidase; Ty3 is a gypsy-type, retrovirus-like, element found in the budding ...
286-462 3.07e-116

Ty3 transposon peptidase; Ty3 is a gypsy-type, retrovirus-like, element found in the budding yeast. The Ty3 aspartyl protease is required for processing of the viral polyprotein into its mature species.


Pssm-ID: 152819  Cd Length: 177  Bit Score: 363.96  E-value: 3.07e-116
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571   286 VLTDLELESKDQQTLFIKTLPIVHYIAIPEMDNTAEKTIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYEIYETPPLRFR 365
Cdd:pfam12384    1 VLADLELESKDHKKLFIKSLPIVHYIAIPEMDKTAEKHIKIKNTKIKTLFDSGSPTSFIRRDIVELLKLEIHDTPPLRFR 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571   366 GFVATKSAVTSEAVTIDLKINDLQITLAAYILDNMDYQLLIGNPILRRYPKILHTVLNTRESPDSLKPKTYRSETVNNVR 445
Cdd:pfam12384   81 GFIATESATTSEAVTIDLKIDDLQINLAAYILDKMDYQLLIGNPILRRYPKILHTILNTKECPDALKPKAYHSENVNNVK 160
                          170
                   ....*....|....*..
gi 285812571   446 TYSAGNRGNPRNIKLSF 462
Cdd:pfam12384  161 AKSAGNRGNPRNIKLSF 177
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
1198-1308 3.88e-20

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 catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 250040  Cd Length: 119  Bit Score: 88.93  E-value: 3.88e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  1198 ISMDFVTGLPPTSNNLNMILVVVDRFSKRAHFIATRKTLDATQLIDLLFRYIFSYHGFPRTITSDRDVRMTADKYQELTK 1277
Cdd:pfam00665    9 WQMDITPIPISSKGGKKYLLVIVDDFSRFVVAYALKSKTDAELVFDLLEAALERRGGKPVTIHSDNGSEFTSKAFQELLK 88
                           90       100       110
                   ....*....|....*....|....*....|.
gi 285812571  1278 RLGIKSTMSSANHPQTDGQSERTIQTLNRLL 1308
Cdd:pfam00665   89 ELGIKHSFSRPGNPQDNGVVERFNRTLKEEL 119
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
70-157 7.24e-05

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: 252133  Cd Length: 97  Bit Score: 42.71  E-value: 7.24e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571    70 HLLNPAAQWANDFVQEQGILEITFDTFIQGLYQHFYKPPDINKIFNAITQLSEAKLGIERLNQRFRKIWDRMPPDFMTEK 149
Cdd:pfam03732    6 HLEGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLENELRSLRQGTESVREYVERFKRLARQLPHHGFDEE 85

                   ....*...
gi 285812571   150 AAIMTYTR 157
Cdd:pfam03732   86 ALISAFLR 93
zf-H2C2 pfam09337
His(2)-Cys(2) zinc finger; This domain binds to histone upstream activating sequence (UAS) ...
1138-1172 2.71e-03

His(2)-Cys(2) zinc finger; This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters.


Pssm-ID: 150113  Cd Length: 39  Bit Score: 37.45  E-value: 2.71e-03
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 285812571  1138 HFGVTVTLAKISPIYYWPKLQHSIIQYIRTCVQCQ 1172
Cdd:pfam09337    5 HAGINKTTSKIAEKYHWKRIKETVARVIRSCPECK 39
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
665-823 1.02e-37

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: 249567 [Multi-domain]  Cd Length: 196  Bit Score: 142.08  E-value: 1.02e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571   665 VPKKD-GTFRLC----VDYRTLNKATIS-------DPFPLPRIDNLLS---RIGNAQIFTTLDLHSGYHQIPMEPKDRYK 729
Cdd:pfam00078    1 IPKKGkGKYRPVslpsVDYKILNKATKKrlepepiFSPPQPGFRPGRSlhdLLKGSKWFLKLDLKKAFDSIPLDPLDRPL 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571   730 TAFVTPS---------------GKYEYTVMPFGLVNAPSTFARYMADTFRDLR------FVNVYLDDILIFSESPEEHWK 788
Cdd:pfam00078   81 TAFGFPGrfirtfsvrvngnpgGRYEWRGLPQGLPLSPLLFNLYMNKLLRPLRkrfpgvTYLRYADDILIFSKSKEELQE 160
                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 285812571   789 HLDTVLERLKNENLIVKKKKCKFA-SEETEFLGYSI 823
Cdd:pfam00078  161 ILEEVLEFLKELGLKLNPEKTKIThSDEVKFLGYVI 196
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
764-874 9.18e-03

group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]


Pssm-ID: 275209 [Multi-domain]  Cd Length: 354  Bit Score: 38.59  E-value: 9.18e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571   764 RDLRFVNvYLDDILIFSESPE--EHWKH-LDTVLERLKnenLIVKKKKCK--FASEET-EFLGYSIGIQK---------I 828
Cdd:TIGR04416  207 YKVRFVR-YADDFVILCRSKEaaERVLEaLTKRLEELG---LELNPEKTKivHCKDGGfDFLGFTFRKRKskngkgkllI 282
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 285812571   829 AP----LQHKCAAIRD-------FPTPKTVKQAQRFL-GMINYYRrfIPNCSKIAQPI 874
Cdd:TIGR04416  283 KPskkaVKKFKEKIREltkrrrgLSLEELIKKLNPILrGWANYFG--IANSSRTFSKL 338
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
649-823 7.74e-84

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 [Multi-domain]  Cd Length: 177  Bit Score: 273.32  E-value: 7.74e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  649 KFIVPSKSPCSSPVVLVPKKDGTFRLCVDYRTLNKATISDPFPLPRIDNLLSRIGNAQIFTTLDLHSGYHQIPMEPKDRY 728
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  729 KTAFVTPSGKYEYTVMPFGLVNAPSTFARYMADTFRDL--RFVNVYLDDILIFSESPEEHWKHLDTVLERLKNENLIVKK 806
Cdd:cd01647    81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlgDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160
                         170
                  ....*....|....*..
gi 285812571  807 KKCKFASEETEFLGYSI 823
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) ...
915-1034 2.46e-47

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  Cd Length: 121  Bit Score: 167.28  E-value: 2.46e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  915 RLTTDASKDGIGAVLEEVDNKNKLvGVVGYFSKSLESAQKNYPAGELELLGIIKALHHFRYMLHGKHFTLRTDHISLLSL 994
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDDDGKE-RPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYL 79
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 285812571  995 QNKNEPARRVQRWLDDLATYDFTLEYLAGPKNVVADAISR 1034
Cdd:cd09274    80 LTQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSR 119
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
323-412 8.10e-16

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: 75.45  E-value: 8.10e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  323 TIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYE-IYETPPLRFRGFVATKSAVTSEAVTIDLKINDLQITLAAYILDNMD 401
Cdd:cd00303     2 KGKINGVPVRALVDSGASVNFISESLAKKLGLPpRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLS 81
                          90
                  ....*....|.
gi 285812571  402 YQLLIGNPILR 412
Cdd:cd00303    82 YDVILGRPWLE 92
Peptidase_A2B pfam12384
Ty3 transposon peptidase; Ty3 is a gypsy-type, retrovirus-like, element found in the budding ...
286-462 3.07e-116

Ty3 transposon peptidase; Ty3 is a gypsy-type, retrovirus-like, element found in the budding yeast. The Ty3 aspartyl protease is required for processing of the viral polyprotein into its mature species.


Pssm-ID: 152819  Cd Length: 177  Bit Score: 363.96  E-value: 3.07e-116
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571   286 VLTDLELESKDQQTLFIKTLPIVHYIAIPEMDNTAEKTIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYEIYETPPLRFR 365
Cdd:pfam12384    1 VLADLELESKDHKKLFIKSLPIVHYIAIPEMDKTAEKHIKIKNTKIKTLFDSGSPTSFIRRDIVELLKLEIHDTPPLRFR 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571   366 GFVATKSAVTSEAVTIDLKINDLQITLAAYILDNMDYQLLIGNPILRRYPKILHTVLNTRESPDSLKPKTYRSETVNNVR 445
Cdd:pfam12384   81 GFIATESATTSEAVTIDLKIDDLQINLAAYILDKMDYQLLIGNPILRRYPKILHTILNTKECPDALKPKAYHSENVNNVK 160
                          170
                   ....*....|....*..
gi 285812571   446 TYSAGNRGNPRNIKLSF 462
Cdd:pfam12384  161 AKSAGNRGNPRNIKLSF 177
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
622-823 1.78e-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: 118.60  E-value: 1.78e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  622 LPRLQPYHVTEKNEQEINKIVQKLLDNKFIVPSKSPCSSPVVLVPKKDG-TFRLCVDYRTLNKATISDPFPLPRIDNLLS 700
Cdd:cd03715     1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  701 RIGNA-QIFTTLDLHSGYHQIPMEPKDRYKTAFVTPSGKYEYTVMPFGLVNAPSTFARYMAdtfRDLRFVNV-------- 771
Cdd:cd03715    81 LLPPKhQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFHEALA---RDLAPFPLehegtill 157
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 285812571  772 -YLDDILIFSESPEEHWKHLDTVLERLKNENLIVKKKKCKFASEETEFLGYSI 823
Cdd:cd03715   158 qYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
623-823 2.08e-25

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: 106.98  E-value: 2.08e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  623 PRLQPYHVTEKNEQEINKIVQKLLDNKFIVPSKSPCSSPVVLVPKKDGTFRLCVDYRTLNKATIsdPF-------PLPri 695
Cdd:cd01645     2 VWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQ--DMgalqpglPHP-- 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  696 dnllSRIGNAQIFTTLDLHSGYHQIPMEPKDRYKTAF-------VTPSGKYEYTVMPFGLVNAPSTFARYMADTFRDLR- 767
Cdd:cd01645    78 ----AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFtvpsinnKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRk 153
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 285812571  768 -----FVNVYLDDILIFSESPEEHWKHLDTVLERLKNENLIVKKKKCKfASEETEFLGYSI 823
Cdd:cd01645   154 qypdiVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQ-KEPPFQYLGYEL 213
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
1198-1308 3.88e-20

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 catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 250040  Cd Length: 119  Bit Score: 88.93  E-value: 3.88e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  1198 ISMDFVTGLPPTSNNLNMILVVVDRFSKRAHFIATRKTLDATQLIDLLFRYIFSYHGFPRTITSDRDVRMTADKYQELTK 1277
Cdd:pfam00665    9 WQMDITPIPISSKGGKKYLLVIVDDFSRFVVAYALKSKTDAELVFDLLEAALERRGGKPVTIHSDNGSEFTSKAFQELLK 88
                           90       100       110
                   ....*....|....*....|....*....|.
gi 285812571  1278 RLGIKSTMSSANHPQTDGQSERTIQTLNRLL 1308
Cdd:pfam00665   89 ELGIKHSFSRPGNPQDNGVVERFNRTLKEEL 119
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
711-820 2.18e-10

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  Cd Length: 119  Bit Score: 60.05  E-value: 2.18e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  711 LDLHSGYHQIPMEPKDRYKTAFVTPSGKYEYTVMPFGLVNAPSTFARYMADTFRDLRFVNV----YLDDILIFSESPeeh 786
Cdd:cd03714     1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLGVrifsYLDDLLIIASSI--- 77
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 285812571  787 wKHLDTVLERLK-----NENLIVKKKKCK-FASEETEFLG 820
Cdd:cd03714    78 -KTSEAVLRHLRatllaNLGFTLNLEKSKlGPTQRITFLG 116
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
915-1035 1.49e-09

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: 57.68  E-value: 1.49e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  915 RLTTDASKDGIGAVLEEVDNKnklvgvvGYFSKSlesaQKNYPAGELELLGIIKALHHFRYMLHGKHFTLRTDHISLLSL 994
Cdd:cd09275     1 VLFTDASLSGWGAYLLNSRAH-------GPWSAD----ERNKHINLLELKAVLLALQHFAAELKNRKILIRTDNTTAVAY 69
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 285812571  995 QNK---------NEPARRVQRWLDDLATYdFTLEYLAGPKNVVADAISRA 1035
Cdd:cd09275    70 INKqggtsspplLALARQILLWCEQRNIW-LRASHIPGVLNTEADRLSRL 118
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
70-157 7.24e-05

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: 252133  Cd Length: 97  Bit Score: 42.71  E-value: 7.24e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571    70 HLLNPAAQWANDFVQEQGILEITFDTFIQGLYQHFYKPPDINKIFNAITQLSEAKLGIERLNQRFRKIWDRMPPDFMTEK 149
Cdd:pfam03732    6 HLEGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLENELRSLRQGTESVREYVERFKRLARQLPHHGFDEE 85

                   ....*...
gi 285812571   150 AAIMTYTR 157
Cdd:pfam03732   86 ALISAFLR 93
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
323-410 3.06e-04

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


Pssm-ID: 257959  Cd Length: 89  Bit Score: 40.73  E-value: 3.06e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571   323 TIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYEIYETPPLRFRGfvATKSAVTSEAVTIDLKINDLQIT-LAAYILDNMD 401
Cdd:pfam13650    2 PVTINGKPVRFLLDTGASGTLLSRSLAERLGLKPTKLSTIRVST--ANGTVEAALVRLDSLKIGGITLRnVPAVVLDLGD 79
                           90
                   ....*....|
gi 285812571   402 -YQLLIGNPI 410
Cdd:pfam13650   80 lIDGLLGMDF 89
RP_DDI cd05479
RP_DDI; retropepsin-like domain of DNA damage inducible protein; The family represents the ...
324-414 2.07e-03

RP_DDI; retropepsin-like domain of DNA damage inducible protein; The family represents the retropepsin-like domain of DNA damage inducible protein. DNA damage inducible protein has a retropepsin-like domain and an amino-terminal ubiquitin-like domain and/or a UBA (ubiquitin-associated) domain. This CD represents the retropepsin-like domain of DDI.


Pssm-ID: 133146  Cd Length: 124  Bit Score: 38.30  E-value: 2.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  324 IKIQNTKVKTLFDSGSPTSFIRRDIVE------LLKYeiyetpplRFRGfVAtKSAVTSEAV----TIDLKINDLQITLA 393
Cdd:cd05479    21 VEINGVPVKAFVDSGAQMTIMSKACAEkcglmrLIDK--------RFQG-IA-KGVGTQKILgrihLAQVKIGNLFLPCS 90
                          90       100
                  ....*....|....*....|.
gi 285812571  394 AYILDNMDYQLLIGNPILRRY 414
Cdd:cd05479    91 FTVLEDDDVDFLIGLDMLKRH 111
zf-H2C2 pfam09337
His(2)-Cys(2) zinc finger; This domain binds to histone upstream activating sequence (UAS) ...
1138-1172 2.71e-03

His(2)-Cys(2) zinc finger; This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters.


Pssm-ID: 150113  Cd Length: 39  Bit Score: 37.45  E-value: 2.71e-03
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 285812571  1138 HFGVTVTLAKISPIYYWPKLQHSIIQYIRTCVQCQ 1172
Cdd:pfam09337    5 HAGINKTTSKIAEKYHWKRIKETVARVIRSCPECK 39
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
757-821 2.98e-03

RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.


Pssm-ID: 238824  Cd Length: 158  Bit Score: 38.85  E-value: 2.98e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571  757 RYMADTFRDLRFVNvYLDDILIFSESPEEHWKHLDTVLERLKNENLIVKKKKCK-----FASEETEFLGY 821
Cdd:cd01646    74 HELKSKLKGVDYVR-YVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEilplpEGTASKDFLGY 142
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
665-823 1.02e-37

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: 249567 [Multi-domain]  Cd Length: 196  Bit Score: 142.08  E-value: 1.02e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571   665 VPKKD-GTFRLC----VDYRTLNKATIS-------DPFPLPRIDNLLS---RIGNAQIFTTLDLHSGYHQIPMEPKDRYK 729
Cdd:pfam00078    1 IPKKGkGKYRPVslpsVDYKILNKATKKrlepepiFSPPQPGFRPGRSlhdLLKGSKWFLKLDLKKAFDSIPLDPLDRPL 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571   730 TAFVTPS---------------GKYEYTVMPFGLVNAPSTFARYMADTFRDLR------FVNVYLDDILIFSESPEEHWK 788
Cdd:pfam00078   81 TAFGFPGrfirtfsvrvngnpgGRYEWRGLPQGLPLSPLLFNLYMNKLLRPLRkrfpgvTYLRYADDILIFSKSKEELQE 160
                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 285812571   789 HLDTVLERLKNENLIVKKKKCKFA-SEETEFLGYSI 823
Cdd:pfam00078  161 ILEEVLEFLKELGLKLNPEKTKIThSDEVKFLGYVI 196
group_II_RT_mat TIGR04416
group II intron reverse transcriptase/maturase; Members of this protein family are ...
764-874 9.18e-03

group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]


Pssm-ID: 275209 [Multi-domain]  Cd Length: 354  Bit Score: 38.59  E-value: 9.18e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285812571   764 RDLRFVNvYLDDILIFSESPE--EHWKH-LDTVLERLKnenLIVKKKKCK--FASEET-EFLGYSIGIQK---------I 828
Cdd:TIGR04416  207 YKVRFVR-YADDFVILCRSKEaaERVLEaLTKRLEELG---LELNPEKTKivHCKDGGfDFLGFTFRKRKskngkgkllI 282
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 285812571   829 AP----LQHKCAAIRD-------FPTPKTVKQAQRFL-GMINYYRrfIPNCSKIAQPI 874
Cdd:TIGR04416  283 KPskkaVKKFKEKIREltkrrrgLSLEELIKKLNPILrGWANYFG--IANSSRTFSKL 338
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.14
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A et al. (2009), "CDD: specific functional annotation with the Conserved Domain Database.", Nucleic Acids Res.37(D)205-10.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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