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Conserved domains on  [gi|146291076|sp|Q7LHG5|]
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RecName: Full=Transposon Ty3-I Gag-Pol polyprotein; AltName: Full=Gag3-Pol3; AltName: Full=Transposon Ty3-2 TYA-TYB polyprotein; Contains: RecName: Full=Capsid protein; Short=CA; AltName: Full=p24; Contains: RecName: Full=Spacer peptide p3; Contains: RecName: Full=Nucleocapsid protein p11; Short=NC; Contains: RecName: Full=Ty3 protease; Short=PR; AltName: Full=p16; Contains: RecName: Full=Spacer peptide J; Contains: RecName: Full=Reverse transcriptase/ribonuclease H; Short=RT; Short=RT-RH; AltName: Full=p55; Contains: RecName: Full=Integrase p52; Short=IN; Contains: RecName: Full=Integrase p49; Short=IN

Protein Classification

retropepsin_like and RT_LTR domain-containing protein (domain architecture ID 10265256)

protein containing domains retropepsin_like, RT_LTR, RNase_HI_RT_Ty3, and rve

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
286-462 6.76e-116

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 pfam12384:

Pssm-ID: 325019  Cd Length: 177  Bit Score: 363.96  E-value: 6.76e-116
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076   286 VLTDLELESKDQQTLFIKTLPIVHYIAIPEMDNTAEKTIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYEIYETPPLRFR 365
Cdd:pfam12384    1 VLADLELESKDHKKLFIKSLPIVHYIAIPEMDKTAEKHIKIKNTKIKTLFDSGSPTSFIRRDIVELLKLEIHDTPPLRFR 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076   366 GFVATKSAVTSEAVTIDLKINDLQITLAAYILDNMDYQLLIGNPILRRYPKILHTVLNTRESPDSLKPKTYRSETVNNVR 445
Cdd:pfam12384   81 GFIATESATTSEAVTIDLKIDDLQINLAAYILDKMDYQLLIGNPILRRYPKILHTILNTKECPDALKPKAYHSENVNNVK 160
                          170
                   ....*....|....*..
gi 146291076   446 TYSAGNRGNPRNIKLSF 462
Cdd:pfam12384  161 AKSAGNRGNPRNIKLSF 177
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
649-823 1.67e-83

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: 273.32  E-value: 1.67e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  649 KFIVPSKSPCSSPVVLVPKKDGTFRLCVDYRTLNKATISDPFPLPRIDNLLSRIGNAQIFTTLDLHSGYHQIPMEPKDRY 728
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  729 KTAFVTPSGKYEYTVMPFGLVNAPSTFARYMADTFRDL--RFVNVYLDDILIFSESPEEHWKHLDTVLERLKNENLIVKK 806
Cdd:cd01647    81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlgDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160
                         170
                  ....*....|....*..
gi 146291076  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 5.75e-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: 5.75e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  915 RLTTDASKDGIGAVLEEVDNKNKLvGVVGYFSKSLESAQKNYPAGELELLGIIKALHHFRYMLHGKHFTLRTDHISLLSL 994
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDDDGKE-RPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYL 79
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 146291076  995 QNKNEPARRVQRWLDDLATYDFTLEYLAGPKNVVADAISR 1034
Cdd:cd09274    80 LTQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSR 119
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
1198-1306 7.68e-15

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: 307008  Cd Length: 114  Bit Score: 74.21  E-value: 7.68e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  1198 ISMDFVTGLPPTSNNLNMILVVVDRFSKRAHFIATRKTLDATQLIDLLFRyIFSYHGFPRTITSDRDVRMTADKYQELTK 1277
Cdd:pfam00665    5 WQTDFTYVRVPGGGGKLYLAVAVDDFSREIVAWALSSEMDAELVIDALKR-AIAFRGGPKIIHSDNGSEYTSKAFREFLA 83
                           90       100
                   ....*....|....*....|....*....
gi 146291076  1278 RLGIKSTMSSANHPQTDGQSERTIQTLNR 1306
Cdd:pfam00665   84 HYGITHSFSRPGNPQDNGKVERFNGTLKR 112
Retrotrans_gag super family cl04237
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
70-157 1.08e-03

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: 309014  Cd Length: 97  Bit Score: 40.40  E-value: 1.08e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076    70 HLLNPAAQWANDFVQEQGILEITFDTFIQGLYQHFYKPPDINKIFNAITQLSEAKLGIERLNQRFRKIWDRMPPDFMTEK 149
Cdd:pfam03732    6 SLEGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLENELRSLRQGTESVREYVERFKRLARQLPHHGRDEE 85

                   ....*...
gi 146291076   150 AAIMTYTR 157
Cdd:pfam03732   86 ALISAFLR 93
 
Name Accession Description Interval E-value
Peptidase_A2B pfam12384
Ty3 transposon peptidase; Ty3 is a gypsy-type, retrovirus-like, element found in the budding ...
286-462 6.76e-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: 6.76e-116
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076   286 VLTDLELESKDQQTLFIKTLPIVHYIAIPEMDNTAEKTIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYEIYETPPLRFR 365
Cdd:pfam12384    1 VLADLELESKDHKKLFIKSLPIVHYIAIPEMDKTAEKHIKIKNTKIKTLFDSGSPTSFIRRDIVELLKLEIHDTPPLRFR 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076   366 GFVATKSAVTSEAVTIDLKINDLQITLAAYILDNMDYQLLIGNPILRRYPKILHTVLNTRESPDSLKPKTYRSETVNNVR 445
Cdd:pfam12384   81 GFIATESATTSEAVTIDLKIDDLQINLAAYILDKMDYQLLIGNPILRRYPKILHTILNTKECPDALKPKAYHSENVNNVK 160
                          170
                   ....*....|....*..
gi 146291076   446 TYSAGNRGNPRNIKLSF 462
Cdd:pfam12384  161 AKSAGNRGNPRNIKLSF 177
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
649-823 1.67e-83

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: 273.32  E-value: 1.67e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  649 KFIVPSKSPCSSPVVLVPKKDGTFRLCVDYRTLNKATISDPFPLPRIDNLLSRIGNAQIFTTLDLHSGYHQIPMEPKDRY 728
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  729 KTAFVTPSGKYEYTVMPFGLVNAPSTFARYMADTFRDL--RFVNVYLDDILIFSESPEEHWKHLDTVLERLKNENLIVKK 806
Cdd:cd01647    81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlgDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160
                         170
                  ....*....|....*..
gi 146291076  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 5.75e-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: 5.75e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  915 RLTTDASKDGIGAVLEEVDNKNKLvGVVGYFSKSLESAQKNYPAGELELLGIIKALHHFRYMLHGKHFTLRTDHISLLSL 994
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDDDGKE-RPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYL 79
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 146291076  995 QNKNEPARRVQRWLDDLATYDFTLEYLAGPKNVVADAISR 1034
Cdd:cd09274    80 LTQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSR 119
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
665-823 8.42e-46

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: 306564  Cd Length: 189  Bit Score: 166.32  E-value: 8.42e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076   665 VPKKD-GTFRLC----VDYRTLNKATI-------SDPFPLPRIDNLLSRIGNAQIFTTLDLHSGYHQIPMEPKDRYKTAF 732
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVkrlkpenLDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076   733 VTPS-----------GKYEYTVMPFGLVNAPSTFARYMADTFRDLR-----FVNVYLDDILIFSESPEEHWKHLDTVLER 796
Cdd:pfam00078   81 TTPPininwngelsgGRYEWKGLPQGLVLSPALFQLFMNELLRPLRkraglTLVRYADDILIFSKSEEEHQEALEEVLEW 160
                          170       180
                   ....*....|....*....|....*....
gi 146291076   797 LKNENLIVKKKKCKFA--SEETEFLGYSI 823
Cdd:pfam00078  161 LKESGLKINPEKTQFFlkSKEVKYLGVTL 189
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
323-412 1.95e-15

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: 1.95e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  323 TIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYE-IYETPPLRFRGFVATKSAVTSEAVTIDLKINDLQITLAAYILDNMD 401
Cdd:cd00303     2 KGKINGVPVRALVDSGASVNFISESLAKKLGLPpRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLS 81
                          90
                  ....*....|.
gi 146291076  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 ...
1198-1306 7.68e-15

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: 307008  Cd Length: 114  Bit Score: 74.21  E-value: 7.68e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  1198 ISMDFVTGLPPTSNNLNMILVVVDRFSKRAHFIATRKTLDATQLIDLLFRyIFSYHGFPRTITSDRDVRMTADKYQELTK 1277
Cdd:pfam00665    5 WQTDFTYVRVPGGGGKLYLAVAVDDFSREIVAWALSSEMDAELVIDALKR-AIAFRGGPKIIHSDNGSEYTSKAFREFLA 83
                           90       100
                   ....*....|....*....|....*....
gi 146291076  1278 RLGIKSTMSSANHPQTDGQSERTIQTLNR 1306
Cdd:pfam00665   84 HYGITHSFSRPGNPQDNGKVERFNGTLKR 112
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
70-157 1.08e-03

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: 309014  Cd Length: 97  Bit Score: 40.40  E-value: 1.08e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076    70 HLLNPAAQWANDFVQEQGILEITFDTFIQGLYQHFYKPPDINKIFNAITQLSEAKLGIERLNQRFRKIWDRMPPDFMTEK 149
Cdd:pfam03732    6 SLEGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLENELRSLRQGTESVREYVERFKRLARQLPHHGRDEE 85

                   ....*...
gi 146291076   150 AAIMTYTR 157
Cdd:pfam03732   86 ALISAFLR 93
 
Name Accession Description Interval E-value
Peptidase_A2B pfam12384
Ty3 transposon peptidase; Ty3 is a gypsy-type, retrovirus-like, element found in the budding ...
286-462 6.76e-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: 6.76e-116
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076   286 VLTDLELESKDQQTLFIKTLPIVHYIAIPEMDNTAEKTIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYEIYETPPLRFR 365
Cdd:pfam12384    1 VLADLELESKDHKKLFIKSLPIVHYIAIPEMDKTAEKHIKIKNTKIKTLFDSGSPTSFIRRDIVELLKLEIHDTPPLRFR 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076   366 GFVATKSAVTSEAVTIDLKINDLQITLAAYILDNMDYQLLIGNPILRRYPKILHTVLNTRESPDSLKPKTYRSETVNNVR 445
Cdd:pfam12384   81 GFIATESATTSEAVTIDLKIDDLQINLAAYILDKMDYQLLIGNPILRRYPKILHTILNTKECPDALKPKAYHSENVNNVK 160
                          170
                   ....*....|....*..
gi 146291076   446 TYSAGNRGNPRNIKLSF 462
Cdd:pfam12384  161 AKSAGNRGNPRNIKLSF 177
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
649-823 1.67e-83

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: 273.32  E-value: 1.67e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  649 KFIVPSKSPCSSPVVLVPKKDGTFRLCVDYRTLNKATISDPFPLPRIDNLLSRIGNAQIFTTLDLHSGYHQIPMEPKDRY 728
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  729 KTAFVTPSGKYEYTVMPFGLVNAPSTFARYMADTFRDL--RFVNVYLDDILIFSESPEEHWKHLDTVLERLKNENLIVKK 806
Cdd:cd01647    81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlgDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160
                         170
                  ....*....|....*..
gi 146291076  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 5.75e-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: 5.75e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  915 RLTTDASKDGIGAVLEEVDNKNKLvGVVGYFSKSLESAQKNYPAGELELLGIIKALHHFRYMLHGKHFTLRTDHISLLSL 994
Cdd:cd09274     1 ILETDASDYGIGAVLSQEDDDGKE-RPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYL 79
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 146291076  995 QNKNEPARRVQRWLDDLATYDFTLEYLAGPKNVVADAISR 1034
Cdd:cd09274    80 LTQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSR 119
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
665-823 8.42e-46

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: 306564  Cd Length: 189  Bit Score: 166.32  E-value: 8.42e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076   665 VPKKD-GTFRLC----VDYRTLNKATI-------SDPFPLPRIDNLLSRIGNAQIFTTLDLHSGYHQIPMEPKDRYKTAF 732
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVkrlkpenLDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076   733 VTPS-----------GKYEYTVMPFGLVNAPSTFARYMADTFRDLR-----FVNVYLDDILIFSESPEEHWKHLDTVLER 796
Cdd:pfam00078   81 TTPPininwngelsgGRYEWKGLPQGLVLSPALFQLFMNELLRPLRkraglTLVRYADDILIFSKSEEEHQEALEEVLEW 160
                          170       180
                   ....*....|....*....|....*....
gi 146291076   797 LKNENLIVKKKKCKFA--SEETEFLGYSI 823
Cdd:pfam00078  161 LKESGLKINPEKTQFFlkSKEVKYLGVTL 189
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
622-823 4.29e-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  Cd Length: 210  Bit Score: 118.60  E-value: 4.29e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  622 LPRLQPYHVTEKNEQEINKIVQKLLDNKFIVPSKSPCSSPVVLVPKKDG-TFRLCVDYRTLNKATISDPFPLPRIDNLLS 700
Cdd:cd03715     1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  701 RIGNA-QIFTTLDLHSGYHQIPMEPKDRYKTAFVTPSGKYEYTVMPFGLVNAPSTFARYMAdtfRDLRFVNV-------- 771
Cdd:cd03715    81 LLPPKhQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFHEALA---RDLAPFPLehegtill 157
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 146291076  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 5.01e-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  Cd Length: 213  Bit Score: 106.98  E-value: 5.01e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  623 PRLQPYHVTEKNEQEINKIVQKLLDNKFIVPSKSPCSSPVVLVPKKDGTFRLCVDYRTLNKATIsdPF-------PLPri 695
Cdd:cd01645     2 VWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQ--DMgalqpglPHP-- 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  696 dnllSRIGNAQIFTTLDLHSGYHQIPMEPKDRYKTAF-------VTPSGKYEYTVMPFGLVNAPSTFARYMADTFRDLR- 767
Cdd:cd01645    78 ----AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFtvpsinnKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRk 153
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 146291076  768 -----FVNVYLDDILIFSESPEEHWKHLDTVLERLKNENLIVKKKKCKfASEETEFLGYSI 823
Cdd:cd01645   154 qypdiVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQ-KEPPFQYLGYEL 213
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
323-412 1.95e-15

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: 1.95e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  323 TIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYE-IYETPPLRFRGFVATKSAVTSEAVTIDLKINDLQITLAAYILDNMD 401
Cdd:cd00303     2 KGKINGVPVRALVDSGASVNFISESLAKKLGLPpRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLS 81
                          90
                  ....*....|.
gi 146291076  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 ...
1198-1306 7.68e-15

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: 307008  Cd Length: 114  Bit Score: 74.21  E-value: 7.68e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  1198 ISMDFVTGLPPTSNNLNMILVVVDRFSKRAHFIATRKTLDATQLIDLLFRyIFSYHGFPRTITSDRDVRMTADKYQELTK 1277
Cdd:pfam00665    5 WQTDFTYVRVPGGGGKLYLAVAVDDFSREIVAWALSSEMDAELVIDALKR-AIAFRGGPKIIHSDNGSEYTSKAFREFLA 83
                           90       100
                   ....*....|....*....|....*....
gi 146291076  1278 RLGIKSTMSSANHPQTDGQSERTIQTLNR 1306
Cdd:pfam00665   84 HYGITHSFSRPGNPQDNGKVERFNGTLKR 112
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
711-820 5.24e-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: 5.24e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  711 LDLHSGYHQIPMEPKDRYKTAFVTPSGKYEYTVMPFGLVNAPSTFARYMADTFRDLRFVNV----YLDDILIFSESPeeh 786
Cdd:cd03714     1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLGVrifsYLDDLLIIASSI--- 77
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 146291076  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 3.58e-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: 3.58e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  915 RLTTDASKDGIGAVLEEVDNKnklvgvvGYFSKSlesaQKNYPAGELELLGIIKALHHFRYMLHGKHFTLRTDHISLLSL 994
Cdd:cd09275     1 VLFTDASLSGWGAYLLNSRAH-------GPWSAD----ERNKHINLLELKAVLLALQHFAAELKNRKILIRTDNTTAVAY 69
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 146291076  995 QNK---------NEPARRVQRWLDDLATYdFTLEYLAGPKNVVADAISRA 1035
Cdd:cd09275    70 INKqggtsspplLALARQILLWCEQRNIW-LRASHIPGVLNTEADRLSRL 118
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
323-413 3.13e-04

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


Pssm-ID: 316492  Cd Length: 92  Bit Score: 42.18  E-value: 3.13e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076   323 TIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYEIyetPPLRFRGFVATKS-AVTSEAVTID-LKINDLQIT-LAAYILDN 399
Cdd:pfam13975    2 DVTINGRPVKFLVDTGASVTVISEALAERLGLDR---LVDAYPVTVRTANgTVRAARVRLDsVKIGGIELRnVPAVVLPG 78
                           90
                   ....*....|....
gi 146291076   400 MDYQLLIGNPILRR 413
Cdd:pfam13975   79 DLDDVLLGMDFLKR 92
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
70-157 1.08e-03

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: 309014  Cd Length: 97  Bit Score: 40.40  E-value: 1.08e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076    70 HLLNPAAQWANDFVQEQGILEITFDTFIQGLYQHFYKPPDINKIFNAITQLSEAKLGIERLNQRFRKIWDRMPPDFMTEK 149
Cdd:pfam03732    6 SLEGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLENELRSLRQGTESVREYVERFKRLARQLPHHGRDEE 85

                   ....*...
gi 146291076   150 AAIMTYTR 157
Cdd:pfam03732   86 ALISAFLR 93
RP_DDI cd05479
RP_DDI; retropepsin-like domain of DNA damage inducible protein; The family represents the ...
324-414 4.92e-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: 38.69  E-value: 4.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  324 IKIQNTKVKTLFDSGSPTSFIRRDIVE------LLKYeiyetpplRFRGfVAtKSAVTSEAV----TIDLKINDLQITLA 393
Cdd:cd05479    21 VEINGVPVKAFVDSGAQMTIMSKACAEkcglmrLIDK--------RFQG-IA-KGVGTQKILgrihLAQVKIGNLFLPCS 90
                          90       100
                  ....*....|....*....|.
gi 146291076  394 AYILDNMDYQLLIGNPILRRY 414
Cdd:cd05479    91 FTVLEDDDVDFLIGLDMLKRH 111
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
757-821 7.03e-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: 7.03e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146291076  757 RYMADTFRDLRFVNvYLDDILIFSESPEEHWKHLDTVLERLKNENLIVKKKKCK-----FASEETEFLGY 821
Cdd:cd01646    74 HELKSKLKGVDYVR-YVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEilplpEGTASKDFLGY 142
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.16
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • 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, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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