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Conserved domains on  [gi|2500376846|ref|YP_010796654|]
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CP, RT, RNaseH and protease polyprotein [Cacao swollen shoot Togo A virus]

Protein Classification

zf-CCHC and RT_LTR domain-containing protein( domain architecture ID 10443361)

protein containing domains zf-CCHC, pepsin_retropepsin_like, RT_LTR, and RNase_H_like

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1350-1536 1.63e-65

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: 219.77  E-value: 1.63e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1350 GVIRPSKSKHRttAFIVesgttidPVTKKTvhGKERMVFNYKRLNDNTEKDQYSLPGIQTILKRVGNKKVFSKFDLKSGF 1429
Cdd:cd01647      1 GIIEPSSSPYA--SPVV-------VVKKKD--GKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGY 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1430 HQVAMAEESIPWTAFWVPQGLYEWLVMPFGLKNAPAVFQRKMDQCFQGT-EDFIAVYIDDILVFSETMEEHAEHIATMLK 1508
Cdd:cd01647     70 HQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlGDFVEVYLDDILVYSKTEEEHLEHLREVLE 149

                          170       180
                   ....*....|....*....|....*...
gi 2500376846 1509 ICQKNGLVLSPSKMSIAQREIEFLGTII 1536
Cdd:cd01647    150 RLREAGLKLNPEKCEFGVPEVEFLGHIV 177
RNase_H_like super family cl14782
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1632-1760 2.62e-19

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


The actual alignment was detected with superfamily member cd09274:

Pssm-ID: 449355 [Multi-domain]  Cd Length: 121  Bit Score: 85.24  E-value: 2.62e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1632 VIESDGCMEGWGGICKwktvKEDSRSTERICAYASGKFSTLK---STIDAEIHALIKALESFKIfYLDKKHLIVRTDCQA 1708
Cdd:cd09274      1 ILETDASDYGIGAVLS----QEDDDGKERPIAFFSRKLTPAErnySTTEKELLAIVWALKKFRH-YLLGRPFTVYTDHKA 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2500376846 1709 IVTFHNKTsgHKPSRI-RWITF-SDYltglgvQVTIEHIEGKENYLADTLSRLV 1760
Cdd:cd09274     76 LKYLLTQK--DLNGRLaRWLLLlSEF------DFEIEYRPGKENVVADALSRLP 121
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 1099-1194 3.85e-05

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 pfam00077:

Pssm-ID: 472175  Cd Length: 101  Bit Score: 44.28  E-value: 3.85e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1099 GKPIKvkAILDTGATTCCTNINSVPKTAIEQNTfLVQFRGINSTQSVDKKLRyGRMTISGHQFRIPYCY-AFPLSLGDei 1177
Cdd:pfam00077   13 GKYFT--ALLDTGADDTVISQNDWPTNWPKQKA-TTNIQGIGGGINVRQSDQ-ILILIGEDKFRGTVSPlILPTCPVN-- 86

                           90
                   ....*....|....*..
gi 2500376846 1178 emILGCNFIRGMYGGLR 1194
Cdd:pfam00077   87 --IIGRDLLQQLGGRLT 101
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 817-834 9.78e-05

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


:

Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 40.97  E-value: 9.78e-05
                           10
                   ....*....|....*...
gi 2500376846  817 CKCYLCGDEGHFARECPN 834
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1350-1536 1.63e-65

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: 219.77  E-value: 1.63e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1350 GVIRPSKSKHRttAFIVesgttidPVTKKTvhGKERMVFNYKRLNDNTEKDQYSLPGIQTILKRVGNKKVFSKFDLKSGF 1429
Cdd:cd01647      1 GIIEPSSSPYA--SPVV-------VVKKKD--GKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGY 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1430 HQVAMAEESIPWTAFWVPQGLYEWLVMPFGLKNAPAVFQRKMDQCFQGT-EDFIAVYIDDILVFSETMEEHAEHIATMLK 1508
Cdd:cd01647     70 HQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlGDFVEVYLDDILVYSKTEEEHLEHLREVLE 149

                          170       180
                   ....*....|....*....|....*...
gi 2500376846 1509 ICQKNGLVLSPSKMSIAQREIEFLGTII 1536
Cdd:cd01647    150 RLREAGLKLNPEKCEFGVPEVEFLGHIV 177
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1377-1536 6.64e-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: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 138.20  E-value: 6.64e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1377 KKTVHGKERMV----FNYKRLNDNTEK-------DQYSLPGIQTILKRVGNKKVFSKFDLKSGFHQVAMAEESIPWTAFW 1445
Cdd:pfam00078    2 PKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFT 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1446 VP-----------QGLYEWLVMPFGLKNAPAVFQRKMDQCFQG----TEDFIAVYIDDILVFSETMEEHAEHIATMLKIC 1510
Cdd:pfam00078   82 TPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPlrkrAGLTLVRYADDILIFSKSEEEHQEALEEVLEWL 161

                          170       180
                   ....*....|....*....|....*...
gi 2500376846 1511 QKNGLVLSPSKMSIA--QREIEFLGTII 1536
Cdd:pfam00078  162 KESGLKINPEKTQFFlkSKEVKYLGVTL 189
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1632-1760 2.62e-19

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


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 85.24  E-value: 2.62e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1632 VIESDGCMEGWGGICKwktvKEDSRSTERICAYASGKFSTLK---STIDAEIHALIKALESFKIfYLDKKHLIVRTDCQA 1708
Cdd:cd09274      1 ILETDASDYGIGAVLS----QEDDDGKERPIAFFSRKLTPAErnySTTEKELLAIVWALKKFRH-YLLGRPFTVYTDHKA 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2500376846 1709 IVTFHNKTsgHKPSRI-RWITF-SDYltglgvQVTIEHIEGKENYLADTLSRLV 1760
Cdd:cd09274     76 LKYLLTQK--DLNGRLaRWLLLlSEF------DFEIEYRPGKENVVADALSRLP 121
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1631-1726 5.68e-09

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 55.21  E-value: 5.68e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1631 TVIESDGCMEGWGGIckwkTVKEDSRSTERICAYASGKFS-TLK--STIDAEIHALIKALESFKIfYLDKKHLIVRTDCQ 1707
Cdd:pfam17917    6 FILETDASDYGIGAV----LSQKDEDGKERPIAYASRKLTpAERnySTTEKELLAIVWALKKFRH-YLLGRKFTVYTDHK 80

                           90       100
                   ....*....|....*....|
gi 2500376846 1708 AIVTFHNKTSGhkPSRI-RW 1726
Cdd:pfam17917   81 PLKYLFTPKEL--NGRLaRW 98
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 1099-1194 3.85e-05

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


Pssm-ID: 425454  Cd Length: 101  Bit Score: 44.28  E-value: 3.85e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1099 GKPIKvkAILDTGATTCCTNINSVPKTAIEQNTfLVQFRGINSTQSVDKKLRyGRMTISGHQFRIPYCY-AFPLSLGDei 1177
Cdd:pfam00077   13 GKYFT--ALLDTGADDTVISQNDWPTNWPKQKA-TTNIQGIGGGINVRQSDQ-ILILIGEDKFRGTVSPlILPTCPVN-- 86

                           90
                   ....*....|....*..
gi 2500376846 1178 emILGCNFIRGMYGGLR 1194
Cdd:pfam00077   87 --IIGRDLLQQLGGRLT 101
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 817-834 9.78e-05

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


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 40.97  E-value: 9.78e-05
                           10
                   ....*....|....*...
gi 2500376846  817 CKCYLCGDEGHFARECPN 834
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
ZnF_C2HC smart00343
zinc finger;
818-834 1.25e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.50  E-value: 1.25e-04
                            10
                    ....*....|....*..
gi 2500376846   818 KCYLCGDEGHFARECPN 834
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 818-837 2.92e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 42.87  E-value: 2.92e-04
                           10        20
                   ....*....|....*....|
gi 2500376846  818 KCYLCGDEGHFARECPNTKR 837
Cdd:PTZ00368   105 ACYNCGGEGHISRDCPNAGK 124
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1350-1536 1.63e-65

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: 219.77  E-value: 1.63e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1350 GVIRPSKSKHRttAFIVesgttidPVTKKTvhGKERMVFNYKRLNDNTEKDQYSLPGIQTILKRVGNKKVFSKFDLKSGF 1429
Cdd:cd01647      1 GIIEPSSSPYA--SPVV-------VVKKKD--GKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGY 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1430 HQVAMAEESIPWTAFWVPQGLYEWLVMPFGLKNAPAVFQRKMDQCFQGT-EDFIAVYIDDILVFSETMEEHAEHIATMLK 1508
Cdd:cd01647     70 HQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlGDFVEVYLDDILVYSKTEEEHLEHLREVLE 149

                          170       180
                   ....*....|....*....|....*...
gi 2500376846 1509 ICQKNGLVLSPSKMSIAQREIEFLGTII 1536
Cdd:cd01647    150 RLREAGLKLNPEKCEFGVPEVEFLGHIV 177
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1377-1536 6.64e-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: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 138.20  E-value: 6.64e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1377 KKTVHGKERMV----FNYKRLNDNTEK-------DQYSLPGIQTILKRVGNKKVFSKFDLKSGFHQVAMAEESIPWTAFW 1445
Cdd:pfam00078    2 PKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFT 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1446 VP-----------QGLYEWLVMPFGLKNAPAVFQRKMDQCFQG----TEDFIAVYIDDILVFSETMEEHAEHIATMLKIC 1510
Cdd:pfam00078   82 TPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPlrkrAGLTLVRYADDILIFSKSEEEHQEALEEVLEWL 161

                          170       180
                   ....*....|....*....|....*...
gi 2500376846 1511 QKNGLVLSPSKMSIA--QREIEFLGTII 1536
Cdd:pfam00078  162 KESGLKINPEKTQFFlkSKEVKYLGVTL 189
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 1342-1536 9.15e-23

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: 98.19  E-value: 9.15e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1342 HVQALLDIGVIRPSKSKHRTTafivesgttIDPVTKKTvhGKE-RMVFNYKRLNDNTEKDQYSLPGIQTILKRVGNK-KV 1419
Cdd:cd03715     20 HIQELLEAGILVPCQSPWNTP---------ILPVKKPG--GNDyRMVQDLRLVNQAVLPIHPAVPNPYTLLSLLPPKhQW 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1420 FSKFDLKSGFHQVAMAEESIPWTAF-WVPQGlYEWLVMPFGLKNAPAVF----QRKMDQCFQGTEDFIAV-YIDDILVFS 1493
Cdd:cd03715     89 YTVLDLANAFFSLPLAPDSQPLFAFeWEGQQ-YTFTRLPQGFKNSPTLFhealARDLAPFPLEHEGTILLqYVDDLLLAA 167

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|...
gi 2500376846 1494 ETMEEHAEHIATMLKICQKNGLVLSPSKMSIAQREIEFLGTII 1536
Cdd:cd03715    168 DSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1632-1760 2.62e-19

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


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 85.24  E-value: 2.62e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1632 VIESDGCMEGWGGICKwktvKEDSRSTERICAYASGKFSTLK---STIDAEIHALIKALESFKIfYLDKKHLIVRTDCQA 1708
Cdd:cd09274      1 ILETDASDYGIGAVLS----QEDDDGKERPIAFFSRKLTPAErnySTTEKELLAIVWALKKFRH-YLLGRPFTVYTDHKA 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2500376846 1709 IVTFHNKTsgHKPSRI-RWITF-SDYltglgvQVTIEHIEGKENYLADTLSRLV 1760
Cdd:cd09274     76 LKYLLTQK--DLNGRLaRWLLLlSEF------DFEIEYRPGKENVVADALSRLP 121
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 1343-1536 9.54e-15

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: 75.01  E-value: 9.54e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1343 VQALLDIGVIRPSKSKHRTTAFIVEsgttidpvtKKTvhGKERMVFNYKRLNDNTEKD---QYSLP---GIQ-----TIL 1411
Cdd:cd01645     21 VTEQLKEGHIEPSTSPWNTPVFVIK---------KKS--GKWRLLHDLRAVNAQTQDMgalQPGLPhpaALPkgwplIVL 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1412 krvgnkkvfskfDLKSGFHQVAMAEESIPWTAFWVP----QG---LYEWLVMPFGLKNAPAVFQRKMDQCFQGTED---- 1480
Cdd:cd01645     90 ------------DLKDCFFSIPLHPDDRERFAFTVPsinnKGpakRYQWKVLPQGMKNSPTICQSFVAQALEPFRKqypd 157

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2500376846 1481 -FIAVYIDDILVFSETMEEHAEHIATMLKICQKNGLVLSPSKMsiaQRE--IEFLGTII 1536
Cdd:cd01645    158 iVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKV---QKEppFQYLGYEL 213
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 1423-1536 1.53e-11

RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.


Pssm-ID: 239684 [Multi-domain]  Cd Length: 119  Bit Score: 63.13  E-value: 1.53e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1423 FDLKSGFHQVAMAEESIPWTAFwVPQGL-YEWLVMPFGLKNAPAVFQRKMDQCFQGTEDF---IAVYIDDILVFSETmEE 1498
Cdd:cd03714      1 VDLKDAYFHIPILPRSRDLLGF-AWQGEtYQFKALPFGLSLAPRVFTKVVEALLAPLRLLgvrIFSYLDDLLIIASS-IK 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2500376846 1499 HAEHIATMLKI--CQKNGLVLSPSKMSIA-QREIEFLGTII 1536
Cdd:cd03714     79 TSEAVLRHLRAtlLANLGFTLNLEKSKLGpTQRITFLGLEL 119
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1631-1726 5.68e-09

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 55.21  E-value: 5.68e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1631 TVIESDGCMEGWGGIckwkTVKEDSRSTERICAYASGKFS-TLK--STIDAEIHALIKALESFKIfYLDKKHLIVRTDCQ 1707
Cdd:pfam17917    6 FILETDASDYGIGAV----LSQKDEDGKERPIAYASRKLTpAERnySTTEKELLAIVWALKKFRH-YLLGRKFTVYTDHK 80

                           90       100
                   ....*....|....*....|
gi 2500376846 1708 AIVTFHNKTSGhkPSRI-RW 1726
Cdd:pfam17917   81 PLKYLFTPKEL--NGRLaRW 98
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 1423-1536 2.34e-06

RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. 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.


Pssm-ID: 238185 [Multi-domain]  Cd Length: 98  Bit Score: 47.73  E-value: 2.34e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1423 FDLKSGFHQVAMaeesipwtafwvpqglyewlvmPFGLKNAPAVFQRKMDQCFQ----GTED-FIAVYIDDILVFSeTME 1497
Cdd:cd00304      1 FDVKSFFTSIPL----------------------PQGSPLSPALANLYMEKLEApilkQLLDiTLIRYVDDLVVIA-KSE 57

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2500376846 1498 EHAEHIATMLKICQKNGLVLSPSKMSIA--QREIEFLGTII 1536
Cdd:cd00304     58 QQAVKKRELEEFLARLGLNLSDEKTQFTekEKKFKFLGILV 98
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1633-1758 1.18e-05

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


Pssm-ID: 259998 [Multi-domain]  Cd Length: 121  Bit Score: 46.54  E-value: 1.18e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1633 IESDGCMEGWGGICKWKTVKEDsRSTERICAYASgkfSTLKSTI-DAEIHALIKALESFKIFYLdkKHLIVRTDCQAIVT 1711
Cdd:cd06222      1 INVDGSCRGNPGPAGIGGVLRD-HEGGWLGGFAL---KIGAPTAlEAELLALLLALELALDLGY--LKVIIESDSKYVVD 74

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2500376846 1712 FHNKTSGHKPSRIRWITFSDYLTGLGVQVTIEHIEGKENYLADTLSR 1758
Cdd:cd06222     75 LINSGSFKWSPNILLIEDILLLLSRFWSVKISHVPREGNQVADALAK 121
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1632-1761 1.85e-05

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


Pssm-ID: 260007  Cd Length: 120  Bit Score: 45.74  E-value: 1.85e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1632 VIESDGCMEGWGGICkwktvkedsrSTERICAYASGKFSTLKSTIdAEIHALIKALESFKiFYLDKKHLIVRTDCQAIVT 1711
Cdd:cd09275      1 VLFTDASLSGWGAYL----------LNSRAHGPWSADERNKHINL-LELKAVLLALQHFA-AELKNRKILIRTDNTTAVA 68

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2500376846 1712 FHNKTSGHKPSRIRWITfSDYLTG---LGVQVTIEHIEGKENYLADTLSRLVF 1761
Cdd:cd09275     69 YINKQGGTSSPPLLALA-RQILLWceqRNIWLRASHIPGVLNTEADRLSRLGL 120
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 1099-1194 3.85e-05

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


Pssm-ID: 425454  Cd Length: 101  Bit Score: 44.28  E-value: 3.85e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1099 GKPIKvkAILDTGATTCCTNINSVPKTAIEQNTfLVQFRGINSTQSVDKKLRyGRMTISGHQFRIPYCY-AFPLSLGDei 1177
Cdd:pfam00077   13 GKYFT--ALLDTGADDTVISQNDWPTNWPKQKA-TTNIQGIGGGINVRQSDQ-ILILIGEDKFRGTVSPlILPTCPVN-- 86

                           90
                   ....*....|....*..
gi 2500376846 1178 emILGCNFIRGMYGGLR 1194
Cdd:pfam00077   87 --IIGRDLLQQLGGRLT 101
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 817-834 9.78e-05

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


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 40.97  E-value: 9.78e-05
                           10
                   ....*....|....*...
gi 2500376846  817 CKCYLCGDEGHFARECPN 834
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
ZnF_C2HC smart00343
zinc finger;
818-834 1.25e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.50  E-value: 1.25e-04
                            10
                    ....*....|....*..
gi 2500376846   818 KCYLCGDEGHFARECPN 834
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 818-837 2.92e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 42.87  E-value: 2.92e-04
                           10        20
                   ....*....|....*....|
gi 2500376846  818 KCYLCGDEGHFARECPNTKR 837
Cdd:PTZ00368   105 ACYNCGGEGHISRDCPNAGK 124
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 818-834 1.64e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.95  E-value: 1.64e-03
                           10
                   ....*....|....*..
gi 2500376846  818 KCYLCGDEGHFARECPN 834
Cdd:PTZ00368    79 SCYNCGQTGHISRECPN 95
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 1375-1519 1.89e-03

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


Pssm-ID: 238822  Cd Length: 213  Bit Score: 41.52  E-value: 1.89e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1375 VTKKTVHGKERMVFN----YK--RLNDNTEKD---QYSLPGIqtILK-RVGnKKVFSKfDLKSGFHQVAMAEESIPWTAF 1444
Cdd:cd01644     10 IKPSKTTTKLRVVFDasarYNgvSLNDMLLKGpdlLNSLFGV--LLRfRQG-KIAVSA-DIEKMFHQVKVRPEDRDVLRF 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1445 -WVPQG------LYEWLVMPFGLKNAPAVFQRKMDQCFQGTEDFIAV-------YIDDILVFSETMEEHAEHIATMLKIC 1510
Cdd:cd01644     86 lWRKDGdepkpiEYRMTVVPFGAASAPFLANRALKQHAEDHPHEAAAkiikrnfYVDDILVSTDTLNEAVNVAKRLIALL 165


                   ....*....
gi 2500376846 1511 QKNGLVLSP 1519
Cdd:cd01644    166 KKGGFNLRK 174
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 819-835 2.92e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.18  E-value: 2.92e-03
                           10
                   ....*....|....*..
gi 2500376846  819 CYLCGDEGHFARECPNT 835
Cdd:PTZ00368    30 CYKCGEPGHLSRECPSA 46
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 1099-1185 4.81e-03

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


Pssm-ID: 433378  Cd Length: 90  Bit Score: 38.03  E-value: 4.81e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2500376846 1099 GKPikVKAILDTGATTCCtnINsvPKTA------IEQNTFLVQFRGINSTQSVDkKLRYGRMTISGHQFRIPYCYAFPls 1172
Cdd:pfam13650    7 GKP--VRFLVDTGASGTV--IS--PSLAerlglkVRGLAYTVRVSTAGGRVSAA-RVRLDSLRLGGLTLENVPALVLD-- 77

                           90
                   ....*....|...
gi 2500376846 1173 LGDEIEMILGCNF 1185
Cdd:pfam13650   78 LGDLIDGLLGMDF 90
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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