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Conserved domains on  [gi|108709963|gb|ABF97758|]
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retrotransposon protein, putative, Ty3-gypsy subclass [Oryza sativa Japonica Group]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 510-623 4.71e-57

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: 192.32  E-value: 4.71e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963  510 VYCDASRQGLGCVLMQE-----GHVVAYASRQLRPHEGNYPTHDLELAAVVHALKIWRHYLIGNRCEIYTDHKSLKYIFT 584
Cdd:cd09274     2 LETDASDYGIGAVLSQEdddgkERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLLT 81

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 108709963  585 QSDLNLRQRRWLELIKDYDVGIRYHPGKANVVADALSRK 623
Cdd:cd09274    82 QKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 225-289 2.84e-28

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


The actual alignment was detected with superfamily member pfam08284:

Pssm-ID: 472175  Cd Length: 134  Bit Score: 110.60  E-value: 2.84e-28
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 108709963   225 GEGGTLQYYSPAVPIEIQGIPFPSDLILLDTKNLDVILGMNWLAQFQGVVDCARRTVTLYRGLEQ 289
Cdd:pfam08284   70 GGSVTTNLICPSCPIEIQGISFLADLILLDMKDLDVILGMDWLSKNKANIDCARRTVTLTKEREK 134
transpos_IS481 super family cl41329
IS481 family transposase; null
 706-840 1.94e-10

IS481 family transposase; null


The actual alignment was detected with superfamily member NF033577:

Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 62.99  E-value: 1.94e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963  706 RRVKAEHQRPARLLQplqvpewkwdeigMDfITGLPKT-QGGHDSIWVVVDRLTKVArfipvkttyggnkLAELY----- 779
Cdd:NF033577  118 KVKRYERAHPGELWH-------------ID-IKKLGRIpDVGRLYLHTAIDDHSRFA-------------YAELYpdeta 170

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963  780 ------FARIVSLHGVP-KKIVSDRGSQFTSHF--WKKLQEELGTRLNFSTAYHPQTDGQTERLNQILED 840
Cdd:NF033577  171 etaadfLRRAFAEHGIPiRRVLTDNGSEFRSRAhgFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
CD_CSD super family cl28914
CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this ...
 1038-1071 1.66e-03

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


The actual alignment was detected with superfamily member cd18965:

Pssm-ID: 475127  Cd Length: 53  Bit Score: 37.46  E-value: 1.66e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 108709963 1038 MERRTRNRVIRFCkVQWSNNAEEEATWERESELK 1071
Cdd:cd18965     7 LKKRQFNRKLEYL-VKWHGLPESENTWEREKDIK 39
Retrotran_gag_2 super family cl26047
gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains ...
 1-62 5.10e-03

gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type.


The actual alignment was detected with superfamily member pfam14223:

Pssm-ID: 464108  Cd Length: 130  Bit Score: 38.37  E-value: 5.10e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 108709963     1 MASKLKSMEMEISKGFLVHFIMSSLPQEFSPFTINYNAMKIKWGIDELIAMYVQEEERLKAE 62
Cdd:pfam14223   69 LVNKLSALGVEISDEDLVVKLLRSLPESYENFVTAIESSSDKITLEELISKLLDEEERRKES 130
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 122-137 7.31e-03

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: 34.81  E-value: 7.31e-03
                           10
                   ....*....|....*.
gi 108709963   122 DGCYFCGKSGHRQKDC 137
Cdd:pfam00098    1 GKCYNCGEPGHIARDC 16
ps-ssRNAv_RdRp-like super family cl40470
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 396-415 7.88e-03

conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model.


The actual alignment was detected with superfamily member cd01647:

Pssm-ID: 477363  Cd Length: 177  Bit Score: 38.73  E-value: 7.88e-03
                          10        20
                  ....*....|....*....|
gi 108709963  396 CKLSKCEFWLSEVKFLGHVI 415
Cdd:cd01647   158 LNPEKCEFGVPEVEFLGHIV 177
 
Name Accession Description Interval E-value
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 510-623 4.71e-57

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: 192.32  E-value: 4.71e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963  510 VYCDASRQGLGCVLMQE-----GHVVAYASRQLRPHEGNYPTHDLELAAVVHALKIWRHYLIGNRCEIYTDHKSLKYIFT 584
Cdd:cd09274     2 LETDASDYGIGAVLSQEdddgkERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLLT 81

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 108709963  585 QSDLNLRQRRWLELIKDYDVGIRYHPGKANVVADALSRK 623
Cdd:cd09274    82 QKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 503-601 2.12e-38

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: 138.41  E-value: 2.12e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963   503 DTRKDYLVYCDASRQGLGCVLMQEG-----HVVAYASRQLRPHEGNYPTHDLELAAVVHALKIWRHYLIGNRCEIYTDHK 577
Cdd:pfam17917    1 DPSKPFILETDASDYGIGAVLSQKDedgkeRPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHK 80

                           90       100
                   ....*....|....*....|....
gi 108709963   578 SLKYIFTQSDLNLRQRRWLELIKD 601
Cdd:pfam17917   81 PLKYLFTPKELNGRLARWALFLQE 104
RVP_2 pfam08284
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 225-289 2.84e-28

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


Pssm-ID: 400537  Cd Length: 134  Bit Score: 110.60  E-value: 2.84e-28
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 108709963   225 GEGGTLQYYSPAVPIEIQGIPFPSDLILLDTKNLDVILGMNWLAQFQGVVDCARRTVTLYRGLEQ 289
Cdd:pfam08284   70 GGSVTTNLICPSCPIEIQGISFLADLILLDMKDLDVILGMDWLSKNKANIDCARRTVTLTKEREK 134
transpos_IS481 NF033577
IS481 family transposase; null
 706-840 1.94e-10

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 62.99  E-value: 1.94e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963  706 RRVKAEHQRPARLLQplqvpewkwdeigMDfITGLPKT-QGGHDSIWVVVDRLTKVArfipvkttyggnkLAELY----- 779
Cdd:NF033577  118 KVKRYERAHPGELWH-------------ID-IKKLGRIpDVGRLYLHTAIDDHSRFA-------------YAELYpdeta 170

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963  780 ------FARIVSLHGVP-KKIVSDRGSQFTSHF--WKKLQEELGTRLNFSTAYHPQTDGQTERLNQILED 840
Cdd:NF033577  171 etaadfLRRAFAEHGIPiRRVLTDNGSEFRSRAhgFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 734-825 1.33e-07

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


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 50.39  E-value: 1.33e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963   734 MDFITGLPKTQGGHDSIWVVVDRLTK--VARFIP----VKTTYGGNKLAelyfarIVSLHGVPKKIVSDRGSQFTSHFWK 807
Cdd:pfam00665    7 GDFTYIRIPGGGGKLYLLVIVDDFSReiLAWALSsemdAELVLDALERA------IAFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 108709963   808 KLQEELGTRLNFSTAYHP 825
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 170-268 8.69e-07

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133136  Cd Length: 92  Bit Score: 48.10  E-value: 8.69e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963  170 IDSGATI-----HVANSLQgfaMRRTLRRGERRIRVANGERISTHGDCQRgplgckracpgeggtlqyyspaVPIEIQGI 244
Cdd:cd00303    14 VDSGASVnfiseSLAKKLG---LPPRLLPTPLKVKGANGSSVKTLGVILP----------------------VTIGIGGK 68

                          90       100
                  ....*....|....*....|....
gi 108709963  245 PFPSDLILLDTKNLDVILGMNWLA 268
Cdd:cd00303    69 TFTVDFYVLDLLSYDVILGRPWLE 92
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
780-838 3.79e-05

Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 47.07  E-value: 3.79e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 108709963  780 FARIVSLHGVPKKIV--SDRGSQFTSHFWKKLQEELGTRLNFSTAYHPQTDGQTERLNQIL 838
Cdd:COG2801   197 LEMAIERRGPPKPLIlhSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTL 257
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
506-623 4.46e-05

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 44.45  E-value: 4.46e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963  506 KDYLVYCD-ASRQ-----GLGCVLMQEGHVvayasRQLRPHEGNYPTHDLELAAVVHALKIWRHyLIGNRCEIYTDhkSl 579
Cdd:COG0328     1 KMIEIYTDgACRGnpgpgGWGAVIRYGGEE-----KELSGGLGDTTNNRAELTALIAALEALKE-LGPCEVEIYTD--S- 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 108709963  580 KYI---FTQSDLNLRQRRW------------LELIKDYDVGIRYHPGKA----NVVADALSRK 623
Cdd:COG0328    72 QYVvnqITGWIHGWKKNGWkpvknpdlwqrlDELLARHKVTFEWVKGHAghpgNERADALANK 134
transpos_IS3 NF033516
IS3 family transposase;
782-838 5.04e-05

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 46.79  E-value: 5.04e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 108709963  782 RIVSLHGVPKK--IVSDRGSQFTSHFWKKLQEELGTRLNFSTAYHPQTDGQTERLNQIL 838
Cdd:NF033516  266 MAIEWRGKPEGliLHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTL 324
chromodomain cd18965
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ...
 1038-1071 1.66e-03

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.


Pssm-ID: 349321  Cd Length: 53  Bit Score: 37.46  E-value: 1.66e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 108709963 1038 MERRTRNRVIRFCkVQWSNNAEEEATWERESELK 1071
Cdd:cd18965     7 LKKRQFNRKLEYL-VKWHGLPESENTWEREKDIK 39
Retrotran_gag_2 pfam14223
gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains ...
 1-62 5.10e-03

gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type.


Pssm-ID: 464108  Cd Length: 130  Bit Score: 38.37  E-value: 5.10e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 108709963     1 MASKLKSMEMEISKGFLVHFIMSSLPQEFSPFTINYNAMKIKWGIDELIAMYVQEEERLKAE 62
Cdd:pfam14223   69 LVNKLSALGVEISDEDLVVKLLRSLPESYENFVTAIESSSDKITLEELISKLLDEEERRKES 130
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 122-137 7.31e-03

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: 34.81  E-value: 7.31e-03
                           10
                   ....*....|....*.
gi 108709963   122 DGCYFCGKSGHRQKDC 137
Cdd:pfam00098    1 GKCYNCGEPGHIARDC 16
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 396-415 7.88e-03

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: 38.73  E-value: 7.88e-03
                          10        20
                  ....*....|....*....|
gi 108709963  396 CKLSKCEFWLSEVKFLGHVI 415
Cdd:cd01647   158 LNPEKCEFGVPEVEFLGHIV 177
 
Name Accession Description Interval E-value
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 510-623 4.71e-57

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: 192.32  E-value: 4.71e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963  510 VYCDASRQGLGCVLMQE-----GHVVAYASRQLRPHEGNYPTHDLELAAVVHALKIWRHYLIGNRCEIYTDHKSLKYIFT 584
Cdd:cd09274     2 LETDASDYGIGAVLSQEdddgkERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLLT 81

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 108709963  585 QSDLNLRQRRWLELIKDYDVGIRYHPGKANVVADALSRK 623
Cdd:cd09274    82 QKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 503-601 2.12e-38

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: 138.41  E-value: 2.12e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963   503 DTRKDYLVYCDASRQGLGCVLMQEG-----HVVAYASRQLRPHEGNYPTHDLELAAVVHALKIWRHYLIGNRCEIYTDHK 577
Cdd:pfam17917    1 DPSKPFILETDASDYGIGAVLSQKDedgkeRPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHK 80

                           90       100
                   ....*....|....*....|....
gi 108709963   578 SLKYIFTQSDLNLRQRRWLELIKD 601
Cdd:pfam17917   81 PLKYLFTPKELNGRLARWALFLQE 104
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
478-569 4.08e-36

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 131.85  E-value: 4.08e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963   478 WSPQCEKAFQTLHEKLVSSPVLILPDTRKDYLVYCDASRQGLGCVLMQEG-----HVVAYASRQLRPHEGNYPTHDLELA 552
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDddggeRPIAYASRKLSPAERNYSTTEKELL 80

                           90
                   ....*....|....*..
gi 108709963   553 AVVHALKIWRHYLIGNR 569
Cdd:pfam17919   81 AIVFALKKFRHYLLGRK 97
RVP_2 pfam08284
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 225-289 2.84e-28

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


Pssm-ID: 400537  Cd Length: 134  Bit Score: 110.60  E-value: 2.84e-28
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 108709963   225 GEGGTLQYYSPAVPIEIQGIPFPSDLILLDTKNLDVILGMNWLAQFQGVVDCARRTVTLYRGLEQ 289
Cdd:pfam08284   70 GGSVTTNLICPSCPIEIQGISFLADLILLDMKDLDVILGMDWLSKNKANIDCARRTVTLTKEREK 134
transpos_IS481 NF033577
IS481 family transposase; null
 706-840 1.94e-10

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 62.99  E-value: 1.94e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963  706 RRVKAEHQRPARLLQplqvpewkwdeigMDfITGLPKT-QGGHDSIWVVVDRLTKVArfipvkttyggnkLAELY----- 779
Cdd:NF033577  118 KVKRYERAHPGELWH-------------ID-IKKLGRIpDVGRLYLHTAIDDHSRFA-------------YAELYpdeta 170

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963  780 ------FARIVSLHGVP-KKIVSDRGSQFTSHF--WKKLQEELGTRLNFSTAYHPQTDGQTERLNQILED 840
Cdd:NF033577  171 etaadfLRRAFAEHGIPiRRVLTDNGSEFRSRAhgFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 511-624 5.61e-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: 54.98  E-value: 5.61e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963  511 YCDASRQGLGCVL-MQEGHVVAYAsrqlrpHEGNYPTHDLELAAVVHALKIWRHYLIGNRCEIYTDHKS-LKYIFTQS-- 586
Cdd:cd09275     3 FTDASLSGWGAYLlNSRAHGPWSA------DERNKHINLLELKAVLLALQHFAAELKNRKILIRTDNTTaVAYINKQGgt 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 108709963  587 ---DLNLRQRRWLELIKDYDVGIRYH--PGKANVVADALSRKS 624
Cdd:cd09275    77 sspPLLALARQILLWCEQRNIWLRAShiPGVLNTEADRLSRLG 119
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 510-622 6.40e-08

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: 52.32  E-value: 6.40e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963  510 VYCDASRQ------GLGCVLMQEGHVVaYASRQLRPHEGNyPTHdLELAAVVHALKIWRHYLIgNRCEIYTDHKSL---- 579
Cdd:cd06222     1 INVDGSCRgnpgpaGIGGVLRDHEGGW-LGGFALKIGAPT-ALE-AELLALLLALELALDLGY-LKVIIESDSKYVvdli 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 108709963  580 -KYIFTQSDL-NLRQRRWLELIKDYDVGIRYHPGKANVVADALSR 622
Cdd:cd06222    77 nSGSFKWSPNiLLIEDILLLLSRFWSVKISHVPREGNQVADALAK 121
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 734-825 1.33e-07

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


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 50.39  E-value: 1.33e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963   734 MDFITGLPKTQGGHDSIWVVVDRLTK--VARFIP----VKTTYGGNKLAelyfarIVSLHGVPKKIVSDRGSQFTSHFWK 807
Cdd:pfam00665    7 GDFTYIRIPGGGGKLYLLVIVDDFSReiLAWALSsemdAELVLDALERA------IAFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 108709963   808 KLQEELGTRLNFSTAYHP 825
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 170-268 8.69e-07

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133136  Cd Length: 92  Bit Score: 48.10  E-value: 8.69e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963  170 IDSGATI-----HVANSLQgfaMRRTLRRGERRIRVANGERISTHGDCQRgplgckracpgeggtlqyyspaVPIEIQGI 244
Cdd:cd00303    14 VDSGASVnfiseSLAKKLG---LPPRLLPTPLKVKGANGSSVKTLGVILP----------------------VTIGIGGK 68

                          90       100
                  ....*....|....*....|....
gi 108709963  245 PFPSDLILLDTKNLDVILGMNWLA 268
Cdd:cd00303    69 TFTVDFYVLDLLSYDVILGRPWLE 92
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
780-838 3.79e-05

Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 47.07  E-value: 3.79e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 108709963  780 FARIVSLHGVPKKIV--SDRGSQFTSHFWKKLQEELGTRLNFSTAYHPQTDGQTERLNQIL 838
Cdd:COG2801   197 LEMAIERRGPPKPLIlhSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTL 257
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
506-623 4.46e-05

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 44.45  E-value: 4.46e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108709963  506 KDYLVYCD-ASRQ-----GLGCVLMQEGHVvayasRQLRPHEGNYPTHDLELAAVVHALKIWRHyLIGNRCEIYTDhkSl 579
Cdd:COG0328     1 KMIEIYTDgACRGnpgpgGWGAVIRYGGEE-----KELSGGLGDTTNNRAELTALIAALEALKE-LGPCEVEIYTD--S- 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 108709963  580 KYI---FTQSDLNLRQRRW------------LELIKDYDVGIRYHPGKA----NVVADALSRK 623
Cdd:COG0328    72 QYVvnqITGWIHGWKKNGWkpvknpdlwqrlDELLARHKVTFEWVKGHAghpgNERADALANK 134
transpos_IS3 NF033516
IS3 family transposase;
782-838 5.04e-05

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 46.79  E-value: 5.04e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 108709963  782 RIVSLHGVPKK--IVSDRGSQFTSHFWKKLQEELGTRLNFSTAYHPQTDGQTERLNQIL 838
Cdd:NF033516  266 MAIEWRGKPEGliLHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTL 324
chromodomain cd18965
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ...
 1038-1071 1.66e-03

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.


Pssm-ID: 349321  Cd Length: 53  Bit Score: 37.46  E-value: 1.66e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 108709963 1038 MERRTRNRVIRFCkVQWSNNAEEEATWERESELK 1071
Cdd:cd18965     7 LKKRQFNRKLEYL-VKWHGLPESENTWEREKDIK 39
RP_DDI cd05479
RP_DDI; retropepsin-like domain of DNA damage inducible protein; The family represents the ...
 237-275 1.78e-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: 39.46  E-value: 1.78e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 108709963  237 VPIEIQGIPFPSDLILLDTKNLDVILGMNWLAQFQGVVD 275
Cdd:cd05479    78 AQVKIGNLFLPCSFTVLEDDDVDFLIGLDMLKRHQCVID 116
Retrotran_gag_2 pfam14223
gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains ...
 1-62 5.10e-03

gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type.


Pssm-ID: 464108  Cd Length: 130  Bit Score: 38.37  E-value: 5.10e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 108709963     1 MASKLKSMEMEISKGFLVHFIMSSLPQEFSPFTINYNAMKIKWGIDELIAMYVQEEERLKAE 62
Cdd:pfam14223   69 LVNKLSALGVEISDEDLVVKLLRSLPESYENFVTAIESSSDKITLEELISKLLDEEERRKES 130
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 122-137 7.31e-03

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: 34.81  E-value: 7.31e-03
                           10
                   ....*....|....*.
gi 108709963   122 DGCYFCGKSGHRQKDC 137
Cdd:pfam00098    1 GKCYNCGEPGHIARDC 16
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 396-415 7.88e-03

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: 38.73  E-value: 7.88e-03
                          10        20
                  ....*....|....*....|
gi 108709963  396 CKLSKCEFWLSEVKFLGHVI 415
Cdd:cd01647   158 LNPEKCEFGVPEVEFLGHIV 177
 
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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