Mercurial > repos > iuc > virannot_rps2tsv
diff test-data/rps_s2_out.tab @ 3:d1fd5579469d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
| author | iuc |
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| date | Sun, 08 Sep 2024 14:09:07 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rps_s2_out.tab Sun Sep 08 14:09:07 2024 +0000 @@ -0,0 +1,50 @@ +#query_id query_length cdd_id hit_id evalue startQ endQ frame description superkingdom +ds2020-328_1 2975 pfam02874 gnl|CDD|308490 6.56656e-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. cellular organisms(2);Eukaryota(1);Viridiplantae(1) +ds2020-328_15 1120 pfam00146 gnl|CDD|306623 6.73934e-18 936 1097 -3 pfam00146, NADHdh, NADH dehydrogenase. cellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1) +ds2020-328_26 872 pfam01443 gnl|CDD|307550 7.69575e-33 10 696 -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);Riboviria(1);Orthornavirae(1);Kitrinoviricota(1) +ds2020-328_29 847 pfam13456 gnl|CDD|316018 1.2307e-09 176 397 2 pfam13456, RVT_3, Reverse transcriptase-like. This domain is found in plants and appears to be part of a retrotransposon. cellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1) +ds2020-328_37 681 pfam00416 gnl|CDD|306841 7.7464e-31 92 409 -3 pfam00416, Ribosomal_S13, Ribosomal protein S13/S18. This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes. cellular organisms(2);Bacteria(2) +ds2020-328_43 644 pfam00078 gnl|CDD|306564 2.13234e-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. Viruses(1);Riboviria(1);Pararnavirae(1);Artverviricota(1) +ds2020-328_47 623 pfam00346 gnl|CDD|306783 6.5049e-56 191 496 -2 pfam00346, Complex1_49kDa, Respiratory-chain NADH dehydrogenase, 49 Kd subunit. cellular organisms(2);Bacteria(1);Eukaryota(1) +ds2020-328_50 620 pfam00115 gnl|CDD|306596 2.19638e-51 78 548 3 pfam00115, COX1, Cytochrome C and Quinol oxidase polypeptide I. cellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1) +ds2020-328_52 598 pfam00115 gnl|CDD|306596 4.78609e-34 21 302 3 pfam00115, COX1, Cytochrome C and Quinol oxidase polypeptide I. cellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1) +ds2020-328_98 458 pfam02123 gnl|CDD|280316 1.82963e-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);Riboviria(1);Orthornavirae(1);Duplornaviricota(1) +ds2020-328_99 458 pfam03732 gnl|CDD|309014 1.12045e-06 256 441 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. cellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1) +ds2020-328_101 454 pfam14111 gnl|CDD|316622 3.40587e-07 213 353 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. cellular organisms(1);Eukaryota(1);Streptophytina(1);Viridiplantae(1) +ds2020-328_106 446 pfam01348 gnl|CDD|279664 1.01441e-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. cellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1) +ds2020-328_109 442 pfam02123 gnl|CDD|280316 1.50074e-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);Riboviria(1);Orthornavirae(1);Duplornaviricota(1) +ds2020-328_113 433 pfam00253 gnl|CDD|306712 1.66195e-07 329 415 2 pfam00253, Ribosomal_S14, Ribosomal protein S14p/S29e. This family includes both ribosomal S14 from prokaryotes and S29 from eukaryotes. cellular organisms(2);Bacteria(1);Eukaryota(1) +ds2020-328_115 426 pfam00078 gnl|CDD|306564 9.00965e-09 268 405 -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. Viruses(1);Riboviria(1);Pararnavirae(1);Artverviricota(1) +ds2020-328_118 424 pfam00665 gnl|CDD|307008 1.57397e-23 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. cellular organisms(2);Viruses(1) +ds2020-328_124 406 pfam00361 gnl|CDD|306795 9.79473e-05 212 379 2 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. cellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1) +ds2020-328_136 372 pfam02123 gnl|CDD|280316 7.63867e-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);Riboviria(1);Orthornavirae(1);Duplornaviricota(1) +ds2020-328_594 229 pfam02123 gnl|CDD|280316 5.2142e-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);Riboviria(1);Orthornavirae(1);Duplornaviricota(1) +ds2020-328_597 229 pfam00421 gnl|CDD|306845 5.07684e-21 15 218 3 pfam00421, PSII, Photosystem II protein. cellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1) +ds2020-328_600 229 pfam05518 gnl|CDD|253234 1.06567e-09 26 229 2 pfam05518, Totivirus_coat, Totivirus coat protein. Viruses(1);Riboviria(1);Duplornaviricota(1);Orthornavirae(1) +ds2020-328_604 228 pfam01333 gnl|CDD|307480 2.57329e-21 54 218 3 pfam01333, Apocytochr_F_C, Apocytochrome F, C-terminal. This is a sub-family of cytochrome C. See pfam00034. cellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1) +ds2020-328_609 228 pfam00006 gnl|CDD|306512 7.83347e-19 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. cellular organisms(2);Bacteria(2) +ds2020-328_611 228 pfam00421 gnl|CDD|306845 1.91926e-10 23 226 -3 pfam00421, PSII, Photosystem II protein. cellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1) +ds2020-328_624 226 pfam00421 gnl|CDD|306845 4.1109e-19 14 193 2 pfam00421, PSII, Photosystem II protein. cellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1) +ds2020-328_625 226 pfam01660 gnl|CDD|307679 1.36829e-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);Riboviria(1);Orthornavirae(1);Kitrinoviricota(1) +ds2020-328_634 225 pfam13041 gnl|CDD|315669 1.22135e-07 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. cellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1) +ds2020-328_641 225 pfam04392 gnl|CDD|282274 7.01878e-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(2);cellular organisms(1);Terrabacteria group(1) +ds2020-328_654 224 pfam00223 gnl|CDD|306687 7.46218e-21 41 205 -2 pfam00223, PsaA_PsaB, Photosystem I psaA/psaB protein. cellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1) +ds2020-328_657 223 pfam13683 gnl|CDD|316225 0.000987396 41 205 -2 pfam13683, rve_3, Integrase core domain. Bacteria(2);cellular organisms(1);Terrabacteria group(1) +ds2020-328_659 223 pfam01809 gnl|CDD|307773 1.03441e-07 121 189 -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(2);cellular organisms(1);Terrabacteria group(1) +ds2020-328_675 222 pfam02468 gnl|CDD|280606 3.26069e-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. cellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1) +ds2020-328_677 222 pfam00978 gnl|CDD|250270 1.6261e-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);Riboviria(1);Orthornavirae(1);Kitrinoviricota(1) +ds2020-328_681 222 pfam00562 gnl|CDD|306936 2.01964e-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). cellular organisms(2);Eukaryota(1);Viridiplantae(1) +ds2020-328_687 222 pfam00201 gnl|CDD|278624 0.000513014 26 145 -3 pfam00201, UDPGT, UDP-glucoronosyl and UDP-glucosyl transferase. cellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophytina(1) +ds2020-328_689 222 pfam02670 gnl|CDD|308348 4.98265e-14 25 135 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(2);cellular organisms(1);Pseudomonadota(1) +ds2020-328_691 221 pfam00329 gnl|CDD|306769 1.68456e-18 81 197 -1 pfam00329, Complex1_30kDa, Respiratory-chain NADH dehydrogenase, 30 Kd subunit. cellular organisms(2);Bacteria(1);Eukaryota(1) +ds2020-328_704 220 pfam05724 gnl|CDD|310379 3.15883e-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. cellular organisms(2);Bacteria(1);Eukaryota(1) +ds2020-328_724 219 pfam02123 gnl|CDD|280316 1.42892e-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);Riboviria(1);Orthornavirae(1);Duplornaviricota(1) +ds2020-328_746 217 pfam02123 gnl|CDD|280316 4.65988e-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);Riboviria(1);Orthornavirae(1);Duplornaviricota(1) +ds2020-328_750 216 pfam02123 gnl|CDD|280316 7.05387e-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);Riboviria(1);Orthornavirae(1);Duplornaviricota(1) +ds2020-328_761 215 pfam02123 gnl|CDD|280316 3.8356e-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);Riboviria(1);Orthornavirae(1);Duplornaviricota(1) +ds2020-328_763 215 pfam00201 gnl|CDD|278624 5.96981e-07 113 193 -2 pfam00201, UDPGT, UDP-glucoronosyl and UDP-glucosyl transferase. cellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophytina(1) +ds2020-328_768 215 pfam02123 gnl|CDD|280316 4.70874e-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);Riboviria(1);Orthornavirae(1);Duplornaviricota(1) +ds2020-328_775 214 pfam00361 gnl|CDD|306795 1.62395e-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. cellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1) +ds2020-328_825 211 pfam05892 gnl|CDD|283531 0.000183874 59 196 -1 pfam05892, Tricho_coat, Trichovirus coat protein. This family consists of several coat proteins which are specific to the ssRNA positive-strand, no DNA stage viruses such as the Trichovirus and Vitivirus. Viruses(1);Kitrinoviricota(1);Orthornavirae(1);Tymovirales(1) +ds2020-328_826 211 pfam07727 gnl|CDD|311594 9.19953e-05 43 120 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. cellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1) +ds2020-328_830 211 pfam00978 gnl|CDD|250270 2.21971e-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);Riboviria(1);Orthornavirae(1);Kitrinoviricota(1)