Mercurial > repos > iuc > virannot_blast2tsv
diff test-data/otu_s2_rps.tab @ 0:e889010415a1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
| author | iuc |
|---|---|
| date | Mon, 04 Mar 2024 19:55:52 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/otu_s2_rps.tab Mon Mar 04 19:55:52 2024 +0000 @@ -0,0 +1,149 @@ +#query_id query_length cdd_id hit_id evalue startQ endQ frame description superkingdom no rank family genus +"ds2020-328_1" "2975" "pfam00006" "gnl|CDD|376291" "6.25354e-106" "1359" "2033" "-1" "pfam00006, ATP-synt_ab, ATP synthase alpha/beta family, nucleotide-binding domain. This entry includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho." "Bacteria(0.88);Archaea(0.07);Eukaryota(0.05);" "(1.00);" "(0.07);Mycoplasmataceae(0.06);Clostridiaceae(0.04);Spirochaetaceae(0.03);Rhodobacteraceae(0.02);" "Mycoplasma(0.06);(0.03);Clostridium(0.03);Treponema(0.01);Persephonella(0.01);" +"ds2020-328_1" "2975" "pfam00306" "gnl|CDD|366015" "1.33353e-53" "1008" "1340" "-1" "pfam00306, ATP-synt_ab_C, ATP synthase alpha/beta chain, C terminal domain. " "Bacteria(0.94);Eukaryota(0.06);" "(1.00);" "(0.08);Mycoplasmataceae(0.08);Clostridiaceae(0.06);Ruminococcaceae(0.03);Eubacteriaceae(0.02);" "Mycoplasma(0.07);(0.07);Clostridium(0.05);Eubacterium(0.02);Faecalibacterium(0.01);" +"ds2020-328_1" "2975" "pfam02874" "gnl|CDD|367225" "8.80807e-19" "2202" "2405" "-1" "pfam02874, ATP-synt_ab_N, ATP synthase alpha/beta family, beta-barrel domain. This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella." "Bacteria(0.60);Eukaryota(0.28);Archaea(0.13);" "(1.00);" "Spirochaetaceae(0.04);Bacillaceae(0.04);Schizosaccharomycetaceae(0.03);Chlamydomonadaceae(0.03);Sulfolobaceae(0.03);" "Treponema(0.04);Schizosaccharomyces(0.03);Chlamydomonas(0.03);Bacillus(0.03);Thermotoga(0.02);" +"ds2020-328_10" "1434" "pfam17917" "gnl|CDD|375428" "1.68574e-20" "187" "453" "-1" "pfam17917, RT_RNaseH, 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." "unknown" "unknown" "unknown" "unknown" +"ds2020-328_10" "1434" "pfam00078" "gnl|CDD|365856" "1.48081e-05" "920" "1051" "-3" "pfam00078, RVT_1, 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." "Eukaryota(0.62);Viruses(0.23);Bacteria(0.15);" "(0.77);Ortervirales(0.21);Poxviridae(0.02);" "Retroviridae(0.15);Drosophilidae(0.15);Brassicaceae(0.12);Enterobacteriaceae(0.09);Caulimoviridae(0.06);" "Drosophila(0.15);Arabidopsis(0.12);Lentivirus(0.08);Escherichia(0.08);Bombyx(0.05);" +"ds2020-328_101" "454" "pfam14111" "gnl|CDD|372914" "8.33283e-09" "213" "353" "3" "pfam14111, DUF4283, Domain of unknown function (DUF4283). This domain family is found in plants, and is approximately 100 amino acids in length. Considering the very diverse range of other domains it is associated with it is possible that this domain is a binding/guiding region. There are two highly conserved tryptophan residues." "Eukaryota(1.00);" "(1.00);" "Salicaceae(0.35);Brassicaceae(0.27);Poaceae(0.13);Vitaceae(0.08);Solanaceae(0.06);" "Populus(0.35);Brassica(0.13);Arabidopsis(0.11);Brachypodium(0.10);Vitis(0.08);" +"ds2020-328_106" "446" "pfam01348" "gnl|CDD|279664" "1.08017e-09" "40" "303" "-3" "pfam01348, Intron_maturas2, Type II intron maturase. Group II introns use intron-encoded reverse transcriptase, maturase and DNA endonuclease activities for site-specific insertion into DNA. Although this type of intron is self splicing in vitro they require a maturase protein for splicing in vivo. It has been shown that a specific region of the aI2 intron is needed for the maturase function. This region was found to be conserved in group II introns and called domain X." "Eukaryota(1.00);" "(1.00);" "Saccharomycetaceae(0.40);Brassicaceae(0.20);Schizosaccharomycetaceae(0.20);Poaceae(0.20);" "Saccharomyces(0.40);Hordeum(0.20);Schizosaccharomyces(0.20);Baimashania(0.20);" +"ds2020-328_109" "442" "pfam02123" "gnl|CDD|280316" "1.59804e-23" "115" "429" "-2" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_113" "433" "pfam00253" "gnl|CDD|376307" "1.11487e-07" "329" "415" "2" "pfam00253, Ribosomal_S14, Ribosomal protein S14p/S29e. This family includes both ribosomal S14 from prokaryotes and S29 from eukaryotes." "Bacteria(0.75);Eukaryota(0.25);" "(1.00);" "(0.08);Clostridiaceae(0.02);Mycoplasmataceae(0.02);Lactobacillaceae(0.02);Saccharomycetaceae(0.02);" "(0.03);Clostridium(0.02);Lactobacillus(0.02);Mycoplasma(0.02);" +"ds2020-328_115" "426" "pfam00078" "gnl|CDD|365856" "4.24722e-08" "268" "405" "-1" "pfam00078, RVT_1, 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." "Eukaryota(0.62);Viruses(0.23);Bacteria(0.15);" "(0.77);Ortervirales(0.21);Poxviridae(0.02);" "Retroviridae(0.15);Drosophilidae(0.15);Brassicaceae(0.12);Enterobacteriaceae(0.09);Caulimoviridae(0.06);" "Drosophila(0.15);Arabidopsis(0.12);Lentivirus(0.08);Escherichia(0.08);Bombyx(0.05);" +"ds2020-328_115" "426" "pfam17919" "gnl|CDD|375430" "4.69948e-06" "13" "81" "-1" "pfam17919, RT_RNaseH_2, RNase H-like domain found in reverse transcriptase. " "unknown" "unknown" "unknown" "unknown" +"ds2020-328_118" "424" "pfam00665" "gnl|CDD|366234" "6.81632e-21" "93" "413" "3" "pfam00665, rve, 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." "Bacteria(0.76);Viruses(0.14);Eukaryota(0.09);Archaea(0.01);" "(0.86);Ortervirales(0.12);Inoviridae(0.03);" "Retroviridae(0.12);Mycobacteriaceae(0.09);Streptococcaceae(0.08);Enterobacteriaceae(0.06);Burkholderiaceae(0.05);" "Mycobacterium(0.09);Streptomyces(0.05);Escherichia(0.05);Burkholderia(0.04);Sinorhizobium(0.04);" +"ds2020-328_124" no_hit +"ds2020-328_136" "372" "pfam02123" "gnl|CDD|280316" "8.1339e-10" "160" "363" "-1" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_15" "1120" "pfam00146" "gnl|CDD|376297" "8.26121e-18" "936" "1097" "-3" "pfam00146, NADHdh, NADH dehydrogenase. " "Bacteria(0.78);Archaea(0.12);Eukaryota(0.10);" "(1.00);" "(0.04);Peptococcaceae(0.02);Flavobacteriaceae(0.02);Desulfurococcaceae(0.02);Prevotellaceae(0.02);" "(0.02);Prevotella(0.02);Bacteroides(0.01);" +"ds2020-328_153" "353" "pfam01385" "gnl|CDD|366606" "1.33121e-13" "52" "330" "-3" "pfam01385, OrfB_IS605, Probable transposase. This family includes IS891, IS1136 and IS1341. DUF1225, pfam06774, has now been merged into this family." "Bacteria(0.57);Archaea(0.38);Viruses(0.05);" "(0.95);Bicaudaviridae(0.05);" "Sulfolobaceae(0.19);Mycobacteriaceae(0.10);Thermoproteaceae(0.10);Synergistaceae(0.05);Halorubraceae(0.05);" "Caldivirga(0.10);Mycobacterium(0.10);Saccharolobus(0.10);Sulfurisphaera(0.05);Synechocystis(0.05);" +"ds2020-328_154" "351" "pfam00146" "gnl|CDD|376297" "1.33812e-16" "131" "331" "-3" "pfam00146, NADHdh, NADH dehydrogenase. " "Bacteria(0.78);Archaea(0.12);Eukaryota(0.10);" "(1.00);" "(0.04);Peptococcaceae(0.02);Flavobacteriaceae(0.02);Desulfurococcaceae(0.02);Prevotellaceae(0.02);" "(0.02);Prevotella(0.02);Bacteroides(0.01);" +"ds2020-328_170" "343" "pfam02123" "gnl|CDD|280316" "1.56034e-16" "85" "330" "1" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_172" "338" "pfam02123" "gnl|CDD|280316" "9.08289e-09" "87" "305" "-1" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_176" "336" "pfam00361" "gnl|CDD|366050" "7.24395e-08" "101" "256" "-3" "pfam00361, Proton_antipo_M, Proton-conducting membrane transporter. This is a family of membrane transporters that inlcudes some 7 of potentially 14-16 TM regions. In many instances the family forms part of complex I that catalyzes the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction. The family in total represents homologs across the phyla." "Eukaryota(0.54);Bacteria(0.46);" "(1.00);" "Culicidae(0.23);Rhodobacteraceae(0.23);Poaceae(0.15);Enterobacteriaceae(0.15);Phasianidae(0.08);" "Paracoccus(0.23);Anopheles(0.23);Escherichia(0.15);Zea(0.15);Aspergillus(0.08);" +"ds2020-328_177" "335" "pfam00346" "gnl|CDD|366043" "6.6413e-32" "147" "314" "3" "pfam00346, Complex1_49kDa, Respiratory-chain NADH dehydrogenase, 49 Kd subunit. " "Bacteria(0.80);Eukaryota(0.11);Archaea(0.09);" "(1.00);" "(0.06);Rhodobacteraceae(0.02);Acetobacteraceae(0.02);Campylobacteraceae(0.02);Rhodospirillaceae(0.02);" "(0.01);Geobacter(0.01);Campylobacter(0.01);Archaeoglobus(0.01);" +"ds2020-328_188" no_hit +"ds2020-328_193" "321" "pfam03040" "gnl|CDD|367312" "3.21306e-19" "69" "296" "3" "pfam03040, CemA, CemA family. Members of this family are probable integral membrane proteins. Their molecular function is unknown. CemA proteins are found in the inner envelope membrane of chloroplasts but not in the thylakoid membrane. A cyanobacterial member of this family has been implicated in CO2 transport, but is probably not a CO2 transporter itself. They are predicted to be haem-binding however this has not been proven experimentally." "Bacteria(0.77);Eukaryota(0.23);" "(1.00);" "Synechococcaceae(0.17);Aphanothecaceae(0.08);Microcoleaceae(0.06);Chlorellaceae(0.04);Merismopediaceae(0.04);" "Synechococcus(0.13);Oscillatoria(0.04);Physcomitrella(0.04);Microcystis(0.04);Synechocystis(0.04);" +"ds2020-328_196" "318" "pfam02123" "gnl|CDD|280316" "1.94206e-07" "6" "284" "-2" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_197" "318" "pfam03154" "gnl|CDD|367360" "8.39525e-05" "24" "158" "-2" "pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity." "Eukaryota(1.00);" "(1.00);" "Muridae(0.20);Coelacanthidae(0.20);Characidae(0.20);Cyprinidae(0.20);Cichlidae(0.20);" "Rattus(0.20);Danio(0.20);Astyanax(0.20);Oreochromis(0.20);Latimeria(0.20);" +"ds2020-328_199" "316" "pfam13650" "gnl|CDD|379313" "2.17852e-11" "2" "229" "-1" "pfam13650, Asp_protease_2, 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." "Bacteria(0.81);Eukaryota(0.17);Archaea(0.02);" "(1.00);" "Flavobacteriaceae(0.06);Bacteroidaceae(0.06);Rhizobiaceae(0.05);Caulobacteraceae(0.05);Cytophagaceae(0.04);" "Bacteroides(0.06);Geobacter(0.02);Phenylobacterium(0.02);Agrobacterium(0.02);Spirosoma(0.02);" +"ds2020-328_207" "313" "pfam02123" "gnl|CDD|280316" "1.55736e-08" "34" "306" "1" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_210" "311" "pfam00124" "gnl|CDD|365890" "2.92409e-39" "14" "283" "2" "pfam00124, Photo_RC, Photosynthetic reaction centre protein. " "Bacteria(0.95);Eukaryota(0.05);" "(1.00);" "Rhodobacteraceae(0.13);Chromatiaceae(0.13);Ectothiorhodospiraceae(0.08);Synechococcaceae(0.05);(0.05);" "Rhodobacter(0.08);Sphingomonas(0.05);Halorhodospira(0.05);Roseiflexus(0.05);Thioflavicoccus(0.05);" +"ds2020-328_219" "306" "pfam07727" "gnl|CDD|369488" "2.43458e-28" "22" "285" "-1" "pfam07727, RVT_2, 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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model." "Eukaryota(1.00);" "(1.00);" "Debaryomycetaceae(0.83);Saccharomycetaceae(0.17);" "Candida(0.50);Debaryomyces(0.33);Saccharomyces(0.17);" +"ds2020-328_222" "304" "pfam00471" "gnl|CDD|376336" "2.61553e-13" "31" "201" "-2" "pfam00471, Ribosomal_L33, Ribosomal protein L33. " "Bacteria(0.86);Eukaryota(0.14);" "(1.00);" "(0.07);Mycoplasmataceae(0.07);Clostridiaceae(0.06);Bacillaceae(0.03);Lactobacillaceae(0.03);" "Mycoplasma(0.06);Clostridium(0.05);(0.04);Lactobacillus(0.02);Bacillus(0.02);" +"ds2020-328_226" "300" "pfam02123" "gnl|CDD|280316" "5.93549e-06" "76" "276" "-1" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_229" "299" "pfam02123" "gnl|CDD|280316" "2.23217e-17" "58" "276" "1" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_235" "295" "pfam00006" "gnl|CDD|376291" "7.80612e-20" "51" "284" "3" "pfam00006, ATP-synt_ab, ATP synthase alpha/beta family, nucleotide-binding domain. This entry includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho." "Bacteria(0.88);Archaea(0.07);Eukaryota(0.05);" "(1.00);" "(0.07);Mycoplasmataceae(0.06);Clostridiaceae(0.04);Spirochaetaceae(0.03);Rhodobacteraceae(0.02);" "Mycoplasma(0.06);(0.03);Clostridium(0.03);Treponema(0.01);Persephonella(0.01);" +"ds2020-328_241" no_hit +"ds2020-328_244" "292" "pfam01737" "gnl|CDD|366779" "1.98587e-12" "60" "224" "3" "pfam01737, Ycf9, YCF9. This family consists of the hypothetical protein product of the YCF9 gene from chloroplasts and cyanobacteria. These proteins have no known function." "Bacteria(0.76);Eukaryota(0.24);" "(1.00);" "Synechococcaceae(0.15);Prochloraceae(0.09);Phaeodactylaceae(0.06);Bathycoccaceae(0.03);Poaceae(0.03);" "Synechococcus(0.12);Prochlorococcus(0.09);Phaeodactylum(0.06);Stanieria(0.03);Acaryochloris(0.03);" +"ds2020-328_249" "290" "pfam00115" "gnl|CDD|376293" "5.40542e-13" "18" "248" "3" "pfam00115, COX1, Cytochrome C and Quinol oxidase polypeptide I. " "Bacteria(0.87);Archaea(0.09);Eukaryota(0.04);" "(1.00);" "(0.07);Sulfolobaceae(0.03);Flavobacteriaceae(0.03);Bacillaceae(0.02);Burkholderiaceae(0.02);" "(0.03);Methylobacterium(0.01);Hyphomicrobium(0.01);Rhodanobacter(0.01);" +"ds2020-328_251" "288" "pfam02123" "gnl|CDD|280316" "1.42582e-09" "22" "270" "-1" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_26" "872" "pfam01443" "gnl|CDD|366646" "1.90681e-33" "10" "699" "-3" "pfam01443, Viral_helicase1, Viral (Superfamily 1) RNA helicase. Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis." "Viruses(1.00);" "Riboviria(0.99);unclassified viruses(0.01);" "Alphaflexiviridae(0.36);Virgaviridae(0.24);Betaflexiviridae(0.15);Tymoviridae(0.10);Bromoviridae(0.07);" "Potexvirus(0.26);Allexivirus(0.10);Tymovirus(0.08);Carlavirus(0.08);Tobamovirus(0.08);" +"ds2020-328_272" "281" "pfam00253" "gnl|CDD|376307" "1.57301e-14" "125" "256" "2" "pfam00253, Ribosomal_S14, Ribosomal protein S14p/S29e. This family includes both ribosomal S14 from prokaryotes and S29 from eukaryotes." "Bacteria(0.75);Eukaryota(0.25);" "(1.00);" "(0.08);Clostridiaceae(0.02);Mycoplasmataceae(0.02);Lactobacillaceae(0.02);Saccharomycetaceae(0.02);" "(0.03);Clostridium(0.02);Lactobacillus(0.02);Mycoplasma(0.02);" +"ds2020-328_273" "280" "pfam13976" "gnl|CDD|372857" "1.39388e-05" "38" "160" "-1" "pfam13976, gag_pre-integrs, GAG-pre-integrase domain. This domain is found associated with retroviral insertion elements and lies just upstream of the integrase region on the polyproteins." "Eukaryota(1.00);" "(1.00);" "Vitaceae(0.49);Poaceae(0.30);Brassicaceae(0.11);Trichocomaceae(0.02);Fabaceae(0.01);" "Vitis(0.49);Oryza(0.28);Arabidopsis(0.10);Talaromyces(0.02);Zea(0.02);" +"ds2020-328_285" "275" "pfam00954" "gnl|CDD|366384" "3.5917e-06" "91" "264" "-3" "pfam00954, S_locus_glycop, S-locus glycoprotein domain. In Brassicaceae, self-incompatible plants have a self/non-self recognition system. This is sporophytically controlled by multiple alleles at a single locus (S). S-locus glycoproteins, as well as S-receptor kinases, are in linkage with the S-alleles. This region is inferred to be a domain due to it having other domains adjacent to it." "Eukaryota(1.00);" "(1.00);" "Brassicaceae(0.96);Poaceae(0.04);" "Arabidopsis(0.89);Brassica(0.07);Sorghum(0.04);" +"ds2020-328_29" "847" "pfam13456" "gnl|CDD|372609" "2.18686e-07" "176" "397" "2" "pfam13456, RVT_3, Reverse transcriptase-like. This domain is found in plants and appears to be part of a retrotransposon." "Eukaryota(0.85);Bacteria(0.15);" "(1.00);" "Euphorbiaceae(0.30);Brassicaceae(0.22);Poaceae(0.22);Aphanothecaceae(0.11);Peronosporaceae(0.04);" "Ricinus(0.30);Arabidopsis(0.22);Oryza(0.19);Gloeothece(0.07);Synechocystis(0.04);" +"ds2020-328_293" "272" "pfam02123" "gnl|CDD|280316" "4.40145e-17" "17" "259" "-2" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_295" no_hit +"ds2020-328_300" "271" "pfam02392" "gnl|CDD|308156" "2.01502e-45" "15" "239" "-3" "pfam02392, Ycf4, Ycf4. This family consists of hypothetical Ycf4 proteins from various chloroplast genomes. It has been suggested that Ycf4 is involved in the assembly and/or stability of the photosystem I complex in chloroplasts." "Bacteria(0.78);Eukaryota(0.22);" "(1.00);" "Synechococcaceae(0.17);Aphanothecaceae(0.09);Prochloraceae(0.07);Microcoleaceae(0.06);Oscillatoriaceae(0.04);" "Synechococcus(0.13);Prochlorococcus(0.07);Oscillatoria(0.04);Gloeobacter(0.04);Cyanobium(0.02);" +"ds2020-328_303" "271" "pfam02123" "gnl|CDD|280316" "5.58457e-14" "3" "206" "-3" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_309" "270" "pfam07727" "gnl|CDD|369488" "1.02409e-13" "2" "157" "-3" "pfam07727, RVT_2, 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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model." "Eukaryota(1.00);" "(1.00);" "Debaryomycetaceae(0.83);Saccharomycetaceae(0.17);" "Candida(0.50);Debaryomyces(0.33);Saccharomyces(0.17);" +"ds2020-328_312" no_hit +"ds2020-328_319" "268" "pfam00112" "gnl|CDD|365882" "8.20186e-05" "73" "150" "1" "pfam00112, Peptidase_C1, Papain family cysteine protease. " "Eukaryota(0.96);Viruses(0.03);" "(0.97);Baculoviridae(0.03);" "Rhabditidae(0.10);Poaceae(0.07);Fabaceae(0.07);Haemonchidae(0.06);Brassicaceae(0.06);" "Caenorhabditis(0.10);Arabidopsis(0.05);Haemonchus(0.05);Homo(0.04);Entamoeba(0.03);" +"ds2020-328_322" "268" "pfam01425" "gnl|CDD|366635" "5.34115e-12" "33" "248" "3" "pfam01425, Amidase, Amidase. " "Bacteria(0.58);Eukaryota(0.32);Archaea(0.10);" "(1.00);" "Mycobacteriaceae(0.19);Rhabditidae(0.10);Archaeoglobaceae(0.06);Aspergillaceae(0.06);Merismopediaceae(0.06);" "Mycobacterium(0.19);Caenorhabditis(0.10);Synechocystis(0.06);Aspergillus(0.06);Saccharomyces(0.06);" +"ds2020-328_326" "267" "pfam00385" "gnl|CDD|366065" "3.90569e-05" "64" "192" "1" "pfam00385, Chromo, Chromo (CHRromatin Organisation MOdifier) domain. " "Eukaryota(1.00);" "(1.00);" "Hominidae(0.18);Drosophilidae(0.13);Schizosaccharomycetaceae(0.09);Rhabditidae(0.08);Brassicaceae(0.07);" "Homo(0.16);Drosophila(0.13);Schizosaccharomyces(0.09);Caenorhabditis(0.08);Arabidopsis(0.07);" +"ds2020-328_335" "266" "pfam02123" "gnl|CDD|280316" "2.32783e-14" "26" "265" "2" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_361" "260" "pfam00069" "gnl|CDD|365850" "2.38711e-21" "15" "242" "3" "pfam00069, Pkinase, Protein kinase domain. " "Eukaryota(1.00);" "(1.00);" "Saccharomycetaceae(0.31);Hominidae(0.17);Muridae(0.14);Schizosaccharomycetaceae(0.11);Drosophilidae(0.06);" "Saccharomyces(0.31);Homo(0.17);Schizosaccharomyces(0.11);Rattus(0.08);Drosophila(0.06);" +"ds2020-328_364" "259" "pfam02491" "gnl|CDD|376796" "1.8796e-18" "85" "249" "1" "pfam02491, SHS2_FTSA, SHS2 domain inserted in FTSA. FtsA is essential for bacterial cell division, and co-localizes to the septal ring with FtsZ. The SHS2 domain is inserted in to the RNAseH fold of FtsA, and is involved in protein-protein interaction." "Bacteria(1.00);" "(1.00);" "(0.07);Prevotellaceae(0.04);Spirochaetaceae(0.04);Flavobacteriaceae(0.03);Helicobacteraceae(0.02);" "(0.04);Prevotella(0.04);Clostridium(0.02);Helicobacter(0.02);Bacteroides(0.02);" +"ds2020-328_37" "681" "pfam00416" "gnl|CDD|366086" "4.04787e-35" "92" "409" "-3" "pfam00416, Ribosomal_S13, Ribosomal protein S13/S18. This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes." "Eukaryota(0.55);Bacteria(0.27);Archaea(0.18);" "(1.00);" "Brassicaceae(0.18);Muridae(0.09);Poaceae(0.09);Drosophilidae(0.09);Mycobacteriaceae(0.09);" "Arabidopsis(0.18);Geobacillus(0.09);Rattus(0.09);Haloarcula(0.09);Shigella(0.09);" +"ds2020-328_386" "255" "pfam04332" "gnl|CDD|367905" "1.67088e-13" "22" "162" "1" "pfam04332, DUF475, Protein of unknown function (DUF475). Predicted to be an integral membrane protein with multiple membrane spans." "Bacteria(1.00);" "(1.00);" "Mycobacteriaceae(0.29);Sphingomonadaceae(0.14);Streptococcaceae(0.14);Xanthomonadaceae(0.14);Deinococcaceae(0.14);" "Mycobacterium(0.29);Deinococcus(0.14);Streptomyces(0.14);Lactococcus(0.14);Xylella(0.14);" +"ds2020-328_388" "255" "pfam05919" "gnl|CDD|253459" "2.68273e-30" "4" "237" "-1" "pfam05919, Mitovir_RNA_pol, Mitovirus RNA-dependent RNA polymerase. This family consists of several Mitovirus RNA-dependent RNA polymerase proteins. The family also contains fragment matches in the mitochondria of Arabidopsis thaliana." "Viruses(0.90);Eukaryota(0.10);" "Riboviria(0.90);(0.10);" "Narnaviridae(0.90);Ceratobasidiaceae(0.10);" "Mitovirus(0.90);Thanatephorus(0.10);" +"ds2020-328_395" "254" "pfam02123" "gnl|CDD|280316" "3.0801e-11" "25" "240" "-3" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_4" "2545" "pfam00177" "gnl|CDD|365924" "1.11505e-28" "229" "618" "1" "pfam00177, Ribosomal_S7, Ribosomal protein S7p/S5e. This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes." "Bacteria(0.79);Archaea(0.11);Eukaryota(0.10);" "(1.00);" "(0.09);Clostridiaceae(0.04);Mycoplasmataceae(0.03);Spirochaetaceae(0.02);Ruminococcaceae(0.01);" "(0.04);Clostridium(0.04);Mycoplasma(0.03);Treponema(0.01);Desulfovibrio(0.01);" +"ds2020-328_401" "253" "pfam02123" "gnl|CDD|280316" "1.12879e-10" "29" "193" "-1" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_414" "251" "pfam02123" "gnl|CDD|280316" "1.26275e-09" "31" "234" "1" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_415" "251" "pfam01058" "gnl|CDD|376447" "2.16687e-17" "20" "229" "-2" "pfam01058, Oxidored_q6, NADH ubiquinone oxidoreductase, 20 Kd subunit. " "Bacteria(0.70);Archaea(0.30);" "(1.00);" "(0.05);Syntrophobacteraceae(0.04);Aquificaceae(0.04);Methanosarcinaceae(0.04);Thermococcaceae(0.04);" "Methanosarcina(0.04);Syntrophobacter(0.04);Pyrococcus(0.03);Geobacter(0.03);Methanococcus(0.03);" +"ds2020-328_419" "250" "pfam10369" "gnl|CDD|378420" "1.59899e-17" "75" "212" "-3" "pfam10369, ALS_ss_C, Small subunit of acetolactate synthase. ALS_ss_C is the C-terminal half of a family of proteins which are the small subunits of acetolactate synthase. Acetolactate synthase is a tetrameric enzyme, containing probably two large and two small subunits, which catalyzes the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides." "Bacteria(0.90);Archaea(0.06);Eukaryota(0.04);" "(1.00);" "(0.07);Clostridiaceae(0.06);Lachnospiraceae(0.05);Ruminococcaceae(0.03);Peptococcaceae(0.03);" "Clostridium(0.06);(0.05);Eubacterium(0.03);Ruminococcus(0.02);Roseburia(0.02);" +"ds2020-328_43" "644" "pfam00078" "gnl|CDD|365856" "2.15977e-08" "190" "636" "-3" "pfam00078, RVT_1, 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." "Eukaryota(0.62);Viruses(0.23);Bacteria(0.15);" "(0.77);Ortervirales(0.21);Poxviridae(0.02);" "Retroviridae(0.15);Drosophilidae(0.15);Brassicaceae(0.12);Enterobacteriaceae(0.09);Caulimoviridae(0.06);" "Drosophila(0.15);Arabidopsis(0.12);Lentivirus(0.08);Escherichia(0.08);Bombyx(0.05);" +"ds2020-328_430" "248" "pfam00931" "gnl|CDD|366375" "1.82192e-16" "27" "245" "-1" "pfam00931, NB-ARC, NB-ARC domain. " "Eukaryota(1.00);" "(1.00);" "Brassicaceae(0.75);Solanaceae(0.12);Hominidae(0.12);" "Arabidopsis(0.75);Solanum(0.12);Homo(0.12);" +"ds2020-328_431" "247" "pfam01788" "gnl|CDD|366811" "4.75718e-09" "24" "116" "3" "pfam01788, PsbJ, PsbJ. This family consists of the photosystem II reaction centre protein PsbJ from plants and Cyanobacteria. In Synechocystis sp. PCC 6803 PsbJ regulates the number of photosystem II centers in thylakoid membranes, it is a predicted 4kDa protein with one membrane spanning domain." "Bacteria(0.65);Eukaryota(0.35);" "(1.00);" "Microcoleaceae(0.12);Prochloraceae(0.08);Oscillatoriaceae(0.08);Synechococcaceae(0.08);Chroococcaceae(0.08);" "Oscillatoria(0.08);Prochlorococcus(0.08);Synechococcus(0.08);Ectocarpus(0.04);Arenga(0.04);" +"ds2020-328_432" "247" "pfam00116" "gnl|CDD|365885" "2.6628e-32" "16" "159" "1" "pfam00116, COX2, Cytochrome C oxidase subunit II, periplasmic domain. " "Eukaryota(1.00);" "(1.00);" "Saccharomycetaceae(0.09);Sordariaceae(0.09);Phasianidae(0.09);Cercopithecidae(0.09);Schizosaccharomycetaceae(0.09);" "Gallus(0.09);Triticum(0.09);Sus(0.09);Neurospora(0.09);Oryzias(0.09);" +"ds2020-328_452" no_hit +"ds2020-328_457" no_hit +"ds2020-328_462" "244" "pfam02123" "gnl|CDD|280316" "7.52004e-11" "18" "236" "3" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_464" "244" "pfam00421" "gnl|CDD|366090" "1.67641e-26" "57" "242" "-3" "pfam00421, PSII, Photosystem II protein. " "Bacteria(0.79);Eukaryota(0.21);" "(1.00);" "Gloeobacteraceae(0.14);Synechococcaceae(0.14);Prochloraceae(0.14);Acaryochloridaceae(0.14);Nostocaceae(0.07);" "Acaryochloris(0.14);Gloeobacter(0.14);Prochlorococcus(0.14);Synechococcus(0.14);Nostoc(0.07);" +"ds2020-328_47" "623" "pfam00346" "gnl|CDD|366043" "7.39818e-56" "191" "496" "-2" "pfam00346, Complex1_49kDa, Respiratory-chain NADH dehydrogenase, 49 Kd subunit. " "Bacteria(0.80);Eukaryota(0.11);Archaea(0.09);" "(1.00);" "(0.06);Rhodobacteraceae(0.02);Acetobacteraceae(0.02);Campylobacteraceae(0.02);Rhodospirillaceae(0.02);" "(0.01);Geobacter(0.01);Campylobacter(0.01);Archaeoglobus(0.01);" +"ds2020-328_473" "243" "pfam00146" "gnl|CDD|376297" "3.36196e-12" "16" "114" "1" "pfam00146, NADHdh, NADH dehydrogenase. " "Bacteria(0.78);Archaea(0.12);Eukaryota(0.10);" "(1.00);" "(0.04);Peptococcaceae(0.02);Flavobacteriaceae(0.02);Desulfurococcaceae(0.02);Prevotellaceae(0.02);" "(0.02);Prevotella(0.02);Bacteroides(0.01);" +"ds2020-328_476" "243" "pfam02123" "gnl|CDD|280316" "1.20816e-09" "22" "237" "1" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_485" no_hit +"ds2020-328_490" "241" "pfam00016" "gnl|CDD|365810" "1.89423e-13" "2" "121" "2" "pfam00016, RuBisCO_large, Ribulose bisphosphate carboxylase large chain, catalytic domain. The C-terminal domain of RuBisCO large chain is the catalytic domain adopting a TIM barrel fold." "Bacteria(0.89);Eukaryota(0.05);Archaea(0.05);" "(1.00);" "Rhodospirillaceae(0.11);Oceanospirillaceae(0.11);Rhodobacteraceae(0.11);Prochloraceae(0.05);Thalassiosiraceae(0.05);" "Marinomonas(0.11);Magnetospirillum(0.05);Saccharomonospora(0.05);Rhodospirillum(0.05);Paenibacillus(0.05);" +"ds2020-328_491" "241" "pfam02123" "gnl|CDD|280316" "7.45437e-11" "2" "241" "-1" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_497" "240" "pfam01501" "gnl|CDD|279798" "4.58533e-06" "38" "202" "2" "pfam01501, Glyco_transf_8, Glycosyl transferase family 8. This family includes enzymes that transfer sugar residues to donor molecules. Members of this family are involved in lipopolysaccharide biosynthesis and glycogen synthesis. This family includes Lipopolysaccharide galactosyltransferase, lipopolysaccharide glucosyltransferase 1, and glycogenin glucosyltransferase." "Eukaryota(0.62);Bacteria(0.38);" "(1.00);" "Brassicaceae(0.54);Enterobacteriaceae(0.12);Pasteurellaceae(0.12);Helicobacteraceae(0.08);Bacillaceae(0.04);" "Arabidopsis(0.54);Haemophilus(0.08);Salmonella(0.08);Helicobacter(0.08);Bacillus(0.04);" +"ds2020-328_50" "620" "pfam00115" "gnl|CDD|376293" "1.44178e-51" "78" "548" "3" "pfam00115, COX1, Cytochrome C and Quinol oxidase polypeptide I. " "Bacteria(0.87);Archaea(0.09);Eukaryota(0.04);" "(1.00);" "(0.07);Sulfolobaceae(0.03);Flavobacteriaceae(0.03);Bacillaceae(0.02);Burkholderiaceae(0.02);" "(0.03);Methylobacterium(0.01);Hyphomicrobium(0.01);Rhodanobacter(0.01);" +"ds2020-328_517" "237" "pfam00361" "gnl|CDD|366050" "5.54755e-11" "18" "224" "3" "pfam00361, Proton_antipo_M, Proton-conducting membrane transporter. This is a family of membrane transporters that inlcudes some 7 of potentially 14-16 TM regions. In many instances the family forms part of complex I that catalyzes the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction. The family in total represents homologs across the phyla." "Eukaryota(0.54);Bacteria(0.46);" "(1.00);" "Culicidae(0.23);Rhodobacteraceae(0.23);Poaceae(0.15);Enterobacteriaceae(0.15);Phasianidae(0.08);" "Paracoccus(0.23);Anopheles(0.23);Escherichia(0.15);Zea(0.15);Aspergillus(0.08);" +"ds2020-328_52" "598" "pfam00115" "gnl|CDD|376293" "2.60011e-33" "21" "302" "3" "pfam00115, COX1, Cytochrome C and Quinol oxidase polypeptide I. " "Bacteria(0.87);Archaea(0.09);Eukaryota(0.04);" "(1.00);" "(0.07);Sulfolobaceae(0.03);Flavobacteriaceae(0.03);Bacillaceae(0.02);Burkholderiaceae(0.02);" "(0.03);Methylobacterium(0.01);Hyphomicrobium(0.01);Rhodanobacter(0.01);" +"ds2020-328_536" "236" "pfam00453" "gnl|CDD|376335" "3.91827e-17" "51" "188" "3" "pfam00453, Ribosomal_L20, Ribosomal protein L20. " "Bacteria(0.90);Eukaryota(0.10);" "(1.00);" "(0.10);Clostridiaceae(0.05);Mycoplasmataceae(0.03);Spirochaetaceae(0.02);Synergistaceae(0.02);" "(0.06);Clostridium(0.04);Mycoplasma(0.03);Treponema(0.01);" +"ds2020-328_560" "233" "pfam00421" "gnl|CDD|366090" "1.00705e-37" "17" "232" "2" "pfam00421, PSII, Photosystem II protein. " "Bacteria(0.79);Eukaryota(0.21);" "(1.00);" "Gloeobacteraceae(0.14);Synechococcaceae(0.14);Prochloraceae(0.14);Acaryochloridaceae(0.14);Nostocaceae(0.07);" "Acaryochloris(0.14);Gloeobacter(0.14);Prochlorococcus(0.14);Synechococcus(0.14);Nostoc(0.07);" +"ds2020-328_562" "233" "pfam00201" "gnl|CDD|278624" "3.71727e-13" "22" "195" "1" "pfam00201, UDPGT, UDP-glucoronosyl and UDP-glucosyl transferase. " "Eukaryota(1.00);" "(1.00);" "Hominidae(0.46);Muridae(0.31);Leporidae(0.15);Poaceae(0.08);" "Homo(0.46);Rattus(0.31);Oryctolagus(0.15);Zea(0.08);" +"ds2020-328_564" "232" "pfam00119" "gnl|CDD|376294" "2.43866e-07" "4" "201" "-2" "pfam00119, ATP-synt_A, ATP synthase A chain. " "Bacteria(0.92);Eukaryota(0.08);" "(1.00);" "(0.05);Flavobacteriaceae(0.03);Clostridiaceae(0.03);Mycoplasmataceae(0.03);Bacillaceae(0.02);" "(0.03);Clostridium(0.03);Mycoplasma(0.02);Bacteroides(0.02);Prevotella(0.02);" +"ds2020-328_565" "232" "pfam00119" "gnl|CDD|376294" "4.75161e-06" "106" "189" "-2" "pfam00119, ATP-synt_A, ATP synthase A chain. " "Bacteria(0.92);Eukaryota(0.08);" "(1.00);" "(0.05);Flavobacteriaceae(0.03);Clostridiaceae(0.03);Mycoplasmataceae(0.03);Bacillaceae(0.02);" "(0.03);Clostridium(0.03);Mycoplasma(0.02);Bacteroides(0.02);Prevotella(0.02);" +"ds2020-328_568" "232" "pfam00160" "gnl|CDD|365914" "7.47948e-06" "91" "231" "-2" "pfam00160, Pro_isomerase, Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD. The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyze peptidyl-prolyl isomerisation during which the peptide bond preceding proline (the peptidyl-prolyl bond) is stabilized in the cis conformation. Mammalian cyclophilin A (CypA) is a major cellular target for the immunosuppressive drug cyclosporin A (CsA). Other roles for cyclophilins may include chaperone and cell signalling function." "Bacteria(0.57);Eukaryota(0.41);Archaea(0.02);" "(1.00);" "Flavobacteriaceae(0.09);Theileriidae(0.04);Babesiidae(0.04);Cryptococcaceae(0.04);Vibrionaceae(0.04);" "Cryptococcus(0.04);Vibrio(0.04);Gloeobacter(0.04);Babesia(0.04);Theileria(0.04);" +"ds2020-328_579" "230" "pfam09220" "gnl|CDD|370369" "3.32926e-12" "15" "212" "3" "pfam09220, LA-virus_coat, L-A virus, major coat protein. Members of this family form the major coat protein of the Saccharomyces cerevisiae L-A virus." "Eukaryota(1.00);" "(1.00);" "Debaryomycetaceae(1.00);" "Debaryomyces(1.00);" +"ds2020-328_58" "561" "pfam17921" "gnl|CDD|375431" "1.48639e-11" "411" "551" "-2" "pfam17921, Integrase_H2C2, Integrase zinc binding domain. This zinc binding domain is found in a wide variety of integrase proteins." "unknown" "unknown" "unknown" "unknown" +"ds2020-328_594" "229" "pfam02123" "gnl|CDD|280316" "5.55224e-12" "25" "213" "-2" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_597" "229" "pfam00421" "gnl|CDD|366090" "5.55907e-21" "15" "218" "3" "pfam00421, PSII, Photosystem II protein. " "Bacteria(0.79);Eukaryota(0.21);" "(1.00);" "Gloeobacteraceae(0.14);Synechococcaceae(0.14);Prochloraceae(0.14);Acaryochloridaceae(0.14);Nostocaceae(0.07);" "Acaryochloris(0.14);Gloeobacter(0.14);Prochlorococcus(0.14);Synechococcus(0.14);Nostoc(0.07);" +"ds2020-328_600" "229" "pfam05518" "gnl|CDD|253234" "1.13476e-09" "26" "229" "2" "pfam05518, Totivirus_coat, Totivirus coat protein. " "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(1.00);" "Victorivirus(0.57);Leishmaniavirus(0.29);(0.14);" +"ds2020-328_604" "228" "pfam01333" "gnl|CDD|366578" "1.59517e-20" "54" "218" "3" "pfam01333, Apocytochr_F_C, Apocytochrome F, C-terminal. This is a sub-family of cytochrome C. See pfam00034." "Bacteria(0.82);Eukaryota(0.18);" "(1.00);" "Synechococcaceae(0.18);Prochloraceae(0.07);Aphanothecaceae(0.07);Nostocaceae(0.05);Microcoleaceae(0.05);" "Synechococcus(0.14);Prochlorococcus(0.07);Gloeobacter(0.04);Oscillatoria(0.04);Nostoc(0.04);" +"ds2020-328_609" "228" "pfam00006" "gnl|CDD|376291" "1.76934e-18" "20" "211" "2" "pfam00006, ATP-synt_ab, ATP synthase alpha/beta family, nucleotide-binding domain. This entry includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho." "Bacteria(0.88);Archaea(0.07);Eukaryota(0.05);" "(1.00);" "(0.07);Mycoplasmataceae(0.06);Clostridiaceae(0.04);Spirochaetaceae(0.03);Rhodobacteraceae(0.02);" "Mycoplasma(0.06);(0.03);Clostridium(0.03);Treponema(0.01);Persephonella(0.01);" +"ds2020-328_611" "228" "pfam00421" "gnl|CDD|366090" "2.00297e-10" "23" "226" "-3" "pfam00421, PSII, Photosystem II protein. " "Bacteria(0.79);Eukaryota(0.21);" "(1.00);" "Gloeobacteraceae(0.14);Synechococcaceae(0.14);Prochloraceae(0.14);Acaryochloridaceae(0.14);Nostocaceae(0.07);" "Acaryochloris(0.14);Gloeobacter(0.14);Prochlorococcus(0.14);Synechococcus(0.14);Nostoc(0.07);" +"ds2020-328_62" "551" "pfam02123" "gnl|CDD|280316" "7.88589e-16" "4" "294" "1" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_624" "226" "pfam00421" "gnl|CDD|366090" "2.78889e-19" "14" "193" "2" "pfam00421, PSII, Photosystem II protein. " "Bacteria(0.79);Eukaryota(0.21);" "(1.00);" "Gloeobacteraceae(0.14);Synechococcaceae(0.14);Prochloraceae(0.14);Acaryochloridaceae(0.14);Nostocaceae(0.07);" "Acaryochloris(0.14);Gloeobacter(0.14);Prochlorococcus(0.14);Synechococcus(0.14);Nostoc(0.07);" +"ds2020-328_625" "226" "pfam01660" "gnl|CDD|366745" "1.80876e-05" "15" "209" "3" "pfam01660, Vmethyltransf, Viral methyltransferase. This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily." "Viruses(1.00);" "Riboviria(1.00);" "Betaflexiviridae(0.23);Alphaflexiviridae(0.21);Virgaviridae(0.15);Tymoviridae(0.14);Bromoviridae(0.10);" "Potexvirus(0.16);Carlavirus(0.11);Tymovirus(0.08);Tobamovirus(0.07);Alphavirus(0.05);" +"ds2020-328_634" "225" "pfam13041" "gnl|CDD|372443" "6.23279e-08" "54" "185" "-2" "pfam13041, PPR_2, PPR repeat family. This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR." "Eukaryota(1.00);" "(1.00);" "Brassicaceae(0.30);Euphorbiaceae(0.25);Salicaceae(0.16);Funariaceae(0.05);Poaceae(0.04);" "Arabidopsis(0.30);Ricinus(0.25);Populus(0.16);Physcomitrella(0.05);Naegleria(0.03);" +"ds2020-328_641" "225" "pfam04392" "gnl|CDD|367921" "7.39814e-09" "28" "177" "-1" "pfam04392, ABC_sub_bind, ABC transporter substrate binding protein. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins." "Bacteria(1.00);" "(1.00);" "Streptococcaceae(0.33);Phyllobacteriaceae(0.17);Pseudomonadaceae(0.17);Rickettsiaceae(0.17);Aquificaceae(0.17);" "Streptococcus(0.33);Rickettsia(0.17);Pseudomonas(0.17);Mesorhizobium(0.17);Aquifex(0.17);" +"ds2020-328_654" "224" "pfam00223" "gnl|CDD|365957" "8.28468e-21" "41" "205" "-2" "pfam00223, PsaA_PsaB, Photosystem I psaA/psaB protein. " "Bacteria(0.83);Eukaryota(0.17);" "(1.00);" "Prochloraceae(0.28);Synechococcaceae(0.11);Gloeobacteraceae(0.11);Acaryochloridaceae(0.11);Funariaceae(0.06);" "Prochlorococcus(0.28);Acaryochloris(0.11);Gloeobacter(0.11);(0.06);Selaginella(0.06);" +"ds2020-328_657" no_hit +"ds2020-328_659" "223" "pfam01809" "gnl|CDD|376620" "7.3686e-08" "121" "189" "-2" "pfam01809, Haemolytic, Haemolytic domain. This domain has haemolytic activity. It is found in short (73-103 amino acid) proteins and contains three conserved cysteine residues." "Bacteria(0.99);Eukaryota(0.01);" "(1.00);" "Clostridiaceae(0.07);(0.06);Ruminococcaceae(0.03);Flavobacteriaceae(0.02);Eubacteriaceae(0.02);" "Clostridium(0.07);(0.05);Eubacterium(0.02);Ruminococcus(0.02);Lactobacillus(0.01);" +"ds2020-328_66" "532" "pfam09044" "gnl|CDD|370259" "2.02105e-23" "65" "373" "-1" "pfam09044, Kp4, Kp4. Members of this fungal family of toxins specifically inhibit voltage-gated calcium channels in mammalian cells. They adopt an alpha/beta-sandwich structure, comprising a five-stranded antiparallel beta-sheet with two antiparallel alpha-helices lying at approximately 45 degrees to these strands." "Eukaryota(1.00);" "(1.00);" "Hypocreaceae(0.29);Aspergillaceae(0.21);Nectriaceae(0.21);Glomerellaceae(0.14);Clavicipitaceae(0.07);" "Trichoderma(0.29);Aspergillus(0.21);Fusarium(0.21);Colletotrichum(0.14);Metarhizium(0.07);" +"ds2020-328_675" "222" "pfam02468" "gnl|CDD|367094" "3.35789e-17" "22" "123" "1" "pfam02468, PsbN, Photosystem II reaction centre N protein (psbN). This is a family of small proteins encoded on the chloroplast genome. psbN is involved in photosystem II during photosynthesis, but its exact role is unknown." "Bacteria(0.88);Eukaryota(0.12);" "(1.00);" "Synechococcaceae(0.15);Nostocaceae(0.07);Prochloraceae(0.07);Aphanothecaceae(0.07);Microcoleaceae(0.05);" "Synechococcus(0.12);Prochlorococcus(0.07);Cyanobacterium(0.05);(0.03);Trichodesmium(0.03);" +"ds2020-328_677" "222" "pfam00978" "gnl|CDD|250270" "1.73152e-12" "24" "206" "-2" "pfam00978, RdRP_2, RNA dependent RNA polymerase. This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins: 2A protein from bromoviruses putative RNA dependent RNA polymerase from tobamoviruses Non structural polyprotein from togaviruses." "Viruses(1.00);" "Riboviria(1.00);" "Bromoviridae(0.35);Virgaviridae(0.32);Closteroviridae(0.16);Togaviridae(0.10);Betaflexiviridae(0.03);" "Tobamovirus(0.13);Ilarvirus(0.10);Alphavirus(0.10);Cucumovirus(0.10);Bromovirus(0.10);" +"ds2020-328_681" "222" "pfam00562" "gnl|CDD|366167" "2.61251e-09" "26" "145" "-3" "pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, domain 6. RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII)." "Bacteria(0.49);Eukaryota(0.34);Archaea(0.09);Viruses(0.08);" "(0.92);Iridoviridae(0.05);Mimiviridae(0.02);Asfarviridae(0.02);" "Iridoviridae(0.05);Hexamitidae(0.05);Trichomonadidae(0.03);Poaceae(0.03);Cryptosporidiidae(0.03);" "Giardia(0.05);Cryptosporidium(0.03);Trichomonas(0.03);Plasmodium(0.03);Rhodopirellula(0.02);" +"ds2020-328_687" no_hit +"ds2020-328_689" "222" "pfam02670" "gnl|CDD|335036" "5.85343e-14" "34" "135" "1" "pfam02670, DXP_reductoisom, 1-deoxy-D-xylulose 5-phosphate reductoisomerase. This is a family of 1-deoxy-D-xylulose 5-phosphate reductoisomerases. This enzyme catalyzes the formation of 2-C-methyl-D-erythritol 4-phosphate from 1-deoxy-D-xylulose-5-phosphate in the presence of NADPH. This reaction is part of the terpenoid biosynthesis pathway." "Bacteria(0.96);Eukaryota(0.04);" "(1.00);" "Bacillaceae(0.05);Vibrionaceae(0.05);Corynebacteriaceae(0.04);Pasteurellaceae(0.04);Pseudomonadaceae(0.04);" "Bacillus(0.05);Clostridium(0.04);Corynebacterium(0.04);Pseudomonas(0.04);Vibrio(0.04);" +"ds2020-328_69" "528" "pfam01660" "gnl|CDD|366745" "2.23499e-10" "222" "500" "-2" "pfam01660, Vmethyltransf, Viral methyltransferase. This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily." "Viruses(1.00);" "Riboviria(1.00);" "Betaflexiviridae(0.23);Alphaflexiviridae(0.21);Virgaviridae(0.15);Tymoviridae(0.14);Bromoviridae(0.10);" "Potexvirus(0.16);Carlavirus(0.11);Tymovirus(0.08);Tobamovirus(0.07);Alphavirus(0.05);" +"ds2020-328_691" "221" "pfam00329" "gnl|CDD|376317" "1.3793e-18" "81" "197" "-1" "pfam00329, Complex1_30kDa, Respiratory-chain NADH dehydrogenase, 30 Kd subunit. " "Bacteria(0.79);Archaea(0.12);Eukaryota(0.09);" "(1.00);" "(0.05);Peptococcaceae(0.02);Bacteroidaceae(0.02);Desulfurococcaceae(0.02);Rhodobacteraceae(0.01);" "Bacteroides(0.02);(0.02);Prevotella(0.01);Geobacter(0.01);" +"ds2020-328_7" "2116" "pfam01787" "gnl|CDD|366810" "1.27327e-63" "325" "936" "-2" "pfam01787, Ilar_coat, Ilarvirus coat protein. This family consists of various coat proteins from the ilarviruses part of the Bromoviridae, members include apple mosaic virus and prune dwarf virus. The ilarvirus coat protein is required to initiate replication of the viral genome in host plants. Members of the Bromoviridae have a positive stand ssRNA genome with no DNA stage in there replication." "Viruses(1.00);" "Riboviria(1.00);" "Bromoviridae(1.00);" "Ilarvirus(1.00);" +"ds2020-328_7" "2116" "pfam01573" "gnl|CDD|279858" "6.78673e-46" "1134" "1835" "-3" "pfam01573, Bromo_MP, Bromovirus movement protein. " "Viruses(1.00);" "Riboviria(1.00);" "Bromoviridae(1.00);" "Ilarvirus(0.50);Alfamovirus(0.50);" +"ds2020-328_704" "220" "pfam05724" "gnl|CDD|368581" "5.77087e-08" "38" "196" "2" "pfam05724, TPMT, Thiopurine S-methyltransferase (TPMT). This family consists of thiopurine S-methyltransferase proteins from both eukaryotes and prokaryotes. Thiopurine S-methyltransferase (TPMT) is a cytosolic enzyme that catalyzes S-methylation of aromatic and heterocyclic sulfhydryl compounds, including anticancer and immunosuppressive thiopurines." "Bacteria(0.55);Eukaryota(0.45);" "(1.00);" "Pseudomonadaceae(0.27);Brassicaceae(0.18);Muridae(0.09);Vibrionaceae(0.09);Hominidae(0.09);" "Pseudomonas(0.27);Batis(0.09);Ralstonia(0.09);Arabidopsis(0.09);Brassica(0.09);" +"ds2020-328_724" "219" "pfam02123" "gnl|CDD|280316" "1.52156e-13" "35" "199" "-3" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_746" "217" "pfam02123" "gnl|CDD|280316" "4.96199e-13" "13" "210" "-2" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_750" "216" "pfam02123" "gnl|CDD|280316" "7.51118e-17" "8" "214" "-3" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_761" "215" "pfam02123" "gnl|CDD|280316" "4.08427e-09" "37" "198" "-3" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_763" "215" "pfam00201" "gnl|CDD|278624" "6.35685e-07" "113" "193" "-2" "pfam00201, UDPGT, UDP-glucoronosyl and UDP-glucosyl transferase. " "Eukaryota(1.00);" "(1.00);" "Hominidae(0.46);Muridae(0.31);Leporidae(0.15);Poaceae(0.08);" "Homo(0.46);Rattus(0.31);Oryctolagus(0.15);Zea(0.08);" +"ds2020-328_768" "215" "pfam02123" "gnl|CDD|280316" "5.01402e-08" "33" "209" "3" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_775" "214" "pfam00361" "gnl|CDD|366050" "1.62796e-10" "59" "196" "-1" "pfam00361, Proton_antipo_M, Proton-conducting membrane transporter. This is a family of membrane transporters that inlcudes some 7 of potentially 14-16 TM regions. In many instances the family forms part of complex I that catalyzes the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction. The family in total represents homologs across the phyla." "Eukaryota(0.54);Bacteria(0.46);" "(1.00);" "Culicidae(0.23);Rhodobacteraceae(0.23);Poaceae(0.15);Enterobacteriaceae(0.15);Phasianidae(0.08);" "Paracoccus(0.23);Anopheles(0.23);Escherichia(0.15);Zea(0.15);Aspergillus(0.08);" +"ds2020-328_784" "213" "pfam07727" "gnl|CDD|369488" "2.2825e-05" "25" "93" "-1" "pfam07727, RVT_2, 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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model." "Eukaryota(1.00);" "(1.00);" "Debaryomycetaceae(0.83);Saccharomycetaceae(0.17);" "Candida(0.50);Debaryomyces(0.33);Saccharomyces(0.17);" +"ds2020-328_788" "213" "pfam00069" "gnl|CDD|365850" "1.68423e-10" "23" "193" "2" "pfam00069, Pkinase, Protein kinase domain. " "Eukaryota(1.00);" "(1.00);" "Saccharomycetaceae(0.31);Hominidae(0.17);Muridae(0.14);Schizosaccharomycetaceae(0.11);Drosophilidae(0.06);" "Saccharomyces(0.31);Homo(0.17);Schizosaccharomyces(0.11);Rattus(0.08);Drosophila(0.06);" +"ds2020-328_79" "507" "pfam00507" "gnl|CDD|376344" "3.59591e-31" "17" "244" "2" "pfam00507, Oxidored_q4, NADH-ubiquinone/plastoquinone oxidoreductase, chain 3. " "Bacteria(0.80);Eukaryota(0.13);Archaea(0.07);" "(1.00);" "(0.04);Prevotellaceae(0.02);Cytophagaceae(0.02);Sphingobacteriaceae(0.02);Desulfobulbaceae(0.02);" "(0.02);Prevotella(0.02);Bacteroides(0.02);Geobacter(0.01);" +"ds2020-328_79" "507" "pfam00164" "gnl|CDD|333891" "1.13503e-12" "341" "493" "2" "pfam00164, Ribosom_S12_S23, Ribosomal protein S12/S23. This protein is known as S12 in bacteria and archaea and S23 in eukaryotes." "Bacteria(0.45);Eukaryota(0.27);Archaea(0.27);" "(1.00);" "Thermococcaceae(0.09);Micrococcaceae(0.09);Enterobacteriaceae(0.09);Thermaceae(0.09);Muridae(0.09);" "Thermococcus(0.09);Saccharomyces(0.09);Rickettsia(0.09);Synechococcus(0.09);Thermus(0.09);" +"ds2020-328_808" "212" "pfam03822" "gnl|CDD|367678" "6.58628e-13" "73" "189" "-3" "pfam03822, NAF, NAF domain. " "Eukaryota(1.00);" "(1.00);" "Poaceae(0.30);Brassicaceae(0.18);Solanaceae(0.12);Musaceae(0.09);Fabaceae(0.08);" "Solanum(0.11);Musa(0.09);Brassica(0.09);Glycine(0.08);Arabidopsis(0.07);" +"ds2020-328_817" "211" "pfam03732" "gnl|CDD|367628" "2.37772e-05" "26" "208" "2" "pfam03732, Retrotrans_gag, 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." "Eukaryota(1.00);" "(1.00);" "Brassicaceae(0.58);Poaceae(0.29);Tetraodontidae(0.04);Solanaceae(0.02);Plantaginaceae(0.02);" "Arabidopsis(0.58);Oryza(0.18);Sorghum(0.05);Takifugu(0.04);Zea(0.04);" +"ds2020-328_821" "211" "pfam03732" "gnl|CDD|367628" "4.10271e-05" "96" "200" "-3" "pfam03732, Retrotrans_gag, 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." "Eukaryota(1.00);" "(1.00);" "Brassicaceae(0.58);Poaceae(0.29);Tetraodontidae(0.04);Solanaceae(0.02);Plantaginaceae(0.02);" "Arabidopsis(0.58);Oryza(0.18);Sorghum(0.05);Takifugu(0.04);Zea(0.04);" +"ds2020-328_825" no_hit +"ds2020-328_830" "211" "pfam00978" "gnl|CDD|250270" "2.36362e-14" "16" "201" "1" "pfam00978, RdRP_2, RNA dependent RNA polymerase. This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins: 2A protein from bromoviruses putative RNA dependent RNA polymerase from tobamoviruses Non structural polyprotein from togaviruses." "Viruses(1.00);" "Riboviria(1.00);" "Bromoviridae(0.35);Virgaviridae(0.32);Closteroviridae(0.16);Togaviridae(0.10);Betaflexiviridae(0.03);" "Tobamovirus(0.13);Ilarvirus(0.10);Alphavirus(0.10);Cucumovirus(0.10);Bromovirus(0.10);" +"ds2020-328_84" "501" "pfam00284" "gnl|CDD|366000" "1.57316e-21" "211" "324" "-1" "pfam00284, Cytochrom_B559a, Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit. This family is the lumenal portion of cytochrome b559 alpha chain, matches to this family should be accompanied by a match to the pfam00283 family also. The Prosite pattern pattern matches the transmembrane region of the cytochrome b559 alpha and beta subunits." "Bacteria(0.86);Eukaryota(0.14);" "(1.00);" "Synechococcaceae(0.17);Microcoleaceae(0.09);Aphanothecaceae(0.09);Prochloraceae(0.06);Phaeodactylaceae(0.03);" "Synechococcus(0.17);Prochlorococcus(0.06);Stanieria(0.03);Acaryochloris(0.03);Selaginella(0.03);" +"ds2020-328_84" "501" "pfam00283" "gnl|CDD|365999" "1.14937e-08" "346" "432" "-1" "pfam00283, Cytochrom_B559, Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits. " "Bacteria(0.59);Eukaryota(0.41);" "(1.00);" "Synechococcaceae(0.29);Prochloraceae(0.12);Pseudanabaenaceae(0.06);Acaryochloridaceae(0.06);Thalassiosiraceae(0.06);" "Synechococcus(0.29);Prochlorococcus(0.12);Selaginella(0.06);Gloeobacter(0.06);Thalassiosira(0.06);" +"ds2020-328_84" "501" "pfam00283" "gnl|CDD|365999" "2.11473e-07" "100" "186" "-1" "pfam00283, Cytochrom_B559, Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits. " "Bacteria(0.59);Eukaryota(0.41);" "(1.00);" "Synechococcaceae(0.29);Prochloraceae(0.12);Pseudanabaenaceae(0.06);Acaryochloridaceae(0.06);Thalassiosiraceae(0.06);" "Synechococcus(0.29);Prochlorococcus(0.12);Selaginella(0.06);Gloeobacter(0.06);Thalassiosira(0.06);" +"ds2020-328_843" "210" "pfam03514" "gnl|CDD|335361" "1.72129e-13" "26" "130" "2" "pfam03514, GRAS, GRAS domain family. Proteins in the GRAS (GAI, RGA, SCR) family are known as major players in gibberellin (GA) signaling, which regulates various aspects of plant growth and development. Mutation of the SCARECROW (SCR) gene results in a radial pattern defect, loss of a ground tissue layer, in the root. The PAT1 protein is involved in phytochrome A signal transduction. A sequence, structure and evolutionary analysis showed that the GRAS family emerged in bacteria and belongs to the Rossmann-fold, AdoMET (SAM)-dependent methyltransferase superfamily. All bacterial, and a subset of plant GRAS proteins, are predicted to be active and function as small-molecule methylases. Several plant GRAS proteins lack one or more AdoMet (SAM)-binding residues while preserving their substrate-binding residues. Although GRAS proteins are implicated to function as transcriptional factors, the above analysis suggests that they instead might either modify or bind small molecules." "Eukaryota(1.00);" "(1.00);" "Brassicaceae(0.80);Poaceae(0.13);Solanaceae(0.07);" "Arabidopsis(0.80);Oryza(0.07);Solanum(0.07);Zea(0.03);Triticum(0.03);" +"ds2020-328_863" "209" "pfam02123" "gnl|CDD|280316" "7.16978e-05" "38" "181" "2" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_867" "209" "pfam02123" "gnl|CDD|280316" "3.29677e-10" "13" "186" "-3" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_87" "488" "pfam02123" "gnl|CDD|280316" "1.40535e-08" "300" "467" "-1" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_872" "209" "pfam08497" "gnl|CDD|378013" "5.53746e-25" "38" "181" "-2" "pfam08497, Radical_SAM_N, Radical SAM N-terminal. This domain tends to occur to the N-terminus of the pfam04055 domain in hypothetical bacterial proteins." "Bacteria(0.94);Archaea(0.06);" "(1.00);" "Clostridiaceae(0.11);(0.10);Prevotellaceae(0.06);Lachnospiraceae(0.05);Ruminococcaceae(0.04);" "Clostridium(0.11);(0.08);Prevotella(0.05);Eubacterium(0.04);Ruminococcus(0.03);" +"ds2020-328_891" "208" "pfam02123" "gnl|CDD|280316" "2.76435e-10" "31" "150" "1" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_893" "208" "pfam02123" "gnl|CDD|280316" "1.90193e-07" "35" "181" "2" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_9" "1487" "pfam00361" "gnl|CDD|366050" "2.3647e-49" "715" "1476" "-3" "pfam00361, Proton_antipo_M, Proton-conducting membrane transporter. This is a family of membrane transporters that inlcudes some 7 of potentially 14-16 TM regions. In many instances the family forms part of complex I that catalyzes the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction. The family in total represents homologs across the phyla." "Eukaryota(0.54);Bacteria(0.46);" "(1.00);" "Culicidae(0.23);Rhodobacteraceae(0.23);Poaceae(0.15);Enterobacteriaceae(0.15);Phasianidae(0.08);" "Paracoccus(0.23);Anopheles(0.23);Escherichia(0.15);Zea(0.15);Aspergillus(0.08);" +"ds2020-328_90" "476" "pfam01578" "gnl|CDD|307628" "6.70073e-11" "145" "399" "-3" "pfam01578, Cytochrom_C_asm, Cytochrome C assembly protein. This family consists of various proteins involved in cytochrome c assembly from mitochondria and bacteria; CycK from Rhizobium, CcmC from E. coli and Paracoccus denitrificans and orf240 from wheat mitochondria. The members of this family are probably integral membrane proteins with six predicted transmembrane helices. It has been proposed that members of this family comprise a membrane component of an ABC (ATP binding cassette) transporter complex. It is also proposed that this transporter is necessary for transport of some component needed for cytochrome c assembly. One member CycK contains a putative heme-binding motif, orf240 also contains a putative heme-binding motif and is a proposed ABC transporter with c-type heme as its proposed substrate. However it seems unlikely that all members of this family transport heme nor c-type apocytochromes because CcmC in the putative CcmABC transporter transports neither. CcmF forms a working module with CcmH and CcmI, CcmFHI, and itself is unlikely to bind haem directly." "Bacteria(0.56);Eukaryota(0.38);Archaea(0.05);" "(1.00);" "Enterobacteriaceae(0.10);Pasteurellaceae(0.08);Histionidae(0.05);Marchantiaceae(0.05);Archaeoglobaceae(0.05);" "Escherichia(0.08);Reclinomonas(0.05);Archaeoglobus(0.05);Marchantia(0.05);Bradyrhizobium(0.05);" +"ds2020-328_904" no_hit +"ds2020-328_908" "207" "pfam02123" "gnl|CDD|280316" "5.3529e-06" "4" "207" "-1" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_921" no_hit +"ds2020-328_97" "461" "pfam02123" "gnl|CDD|280316" "5.16988e-30" "39" "461" "-1" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_98" "458" "pfam02123" "gnl|CDD|280316" "1.94825e-26" "27" "443" "-1" "pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus." "Viruses(1.00);" "Riboviria(1.00);" "Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);" "Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);" +"ds2020-328_99" "458" "pfam03732" "gnl|CDD|367628" "7.72961e-07" "256" "441" "1" "pfam03732, Retrotrans_gag, 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." "Eukaryota(1.00);" "(1.00);" "Brassicaceae(0.58);Poaceae(0.29);Tetraodontidae(0.04);Solanaceae(0.02);Plantaginaceae(0.02);" "Arabidopsis(0.58);Oryza(0.18);Sorghum(0.05);Takifugu(0.04);Zea(0.04);"