Mercurial > repos > iuc > virannot_otu
changeset 1:6838c2fd1228 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 48a3a1fa033745898a131f9dca7132947683c02f
| author | iuc |
|---|---|
| date | Sat, 18 May 2024 18:14:42 +0000 |
| parents | c9dac9b2e01c |
| children | |
| files | macros.xml test-data/rps_test.tab virAnnot_otu.xml |
| diffstat | 3 files changed, 13 insertions(+), 7 deletions(-) [+] |
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--- a/macros.xml Mon Mar 04 19:56:40 2024 +0000 +++ b/macros.xml Sat May 18 18:14:42 2024 +0000 @@ -1,4 +1,9 @@ <macros> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">virannot</xref> + </xrefs> + </xml> <xml name="requirements"> <requirements> <requirement type="package" version="1.83">biopython</requirement>
--- a/test-data/rps_test.tab Mon Mar 04 19:56:40 2024 +0000 +++ b/test-data/rps_test.tab Sat May 18 18:14:42 2024 +0000 @@ -1,6 +1,6 @@ #query_id query_length cdd_id hit_id evalue startQ endQ frame description superkingdom ds2020-267_120 339 pfam01333 gnl|CDD|366578 0.000848733 197 325 -3 pfam01333, Apocytochr_F_C, Apocytochrome F, C-terminal. This is a sub-family of cytochrome C. See pfam00034. Eukaryota(19);Bacteria(1) -ds2020-267_374 242 pfam00124 gnl|CDD|365890 5.09126e-07 21 125 3 pfam00124, Photo_RC, Photosynthetic reaction centre protein. Bacteria(9);Eukaryota(6);Viruses(4);unclassified sequences(1) +ds2020-267_374 242 pfam00124 gnl|CDD|365890 5.09126e-07 21 125 3 pfam00124, Photo_RC, Photosynthetic reaction centre protein. Bacteria(10);Eukaryota(5);Viruses(4);unclassified sequences(1) ds2020-267_471 230 pfam00201 gnl|CDD|278624 3.12575e-07 46 210 1 pfam00201, UDPGT, UDP-glucoronosyl and UDP-glucosyl transferase. Eukaryota(20) ds2020-267_710 213 pfam01127 gnl|CDD|366480 0.000723904 46 210 1 pfam01127, Sdh_cyt, Succinate dehydrogenase/Fumarate reductase transmembrane subunit. This family includes a transmembrane protein from both the Succinate dehydrogenase and Fumarate reductase complexes. Bacteria(20) ds2020-267_692 214 pfam00680 gnl|CDD|366242 4.79875e-05 70 180 1 pfam00680, RdRP_1, RNA dependent RNA polymerase. Viruses(20) @@ -11,7 +11,7 @@ ds2020-267_773 210 pfam01641 gnl|CDD|376583 5.23903e-34 16 174 1 pfam01641, SelR, SelR domain. Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterized with respect to structure and function. However, recent studies revealed that MsrA is only specific for methionine-S-sulfoxides. Because oxidized methionines occur in a mixture of R and S isomers in vivo, it was unclear how stereo-specific MsrA could be responsible for the reduction of all protein methionine sulfoxides. It appears that a second methionine sulfoxide reductase, SelR, evolved that is specific for methionine-R-sulfoxides, the activity that is different but complementary to that of MsrA. Thus, these proteins, working together, could reduce both stereoisomers of methionine sulfoxide. This domain is found both in SelR proteins and fused with the peptide methionine sulfoxide reductase enzymatic domain pfam01625. The domain has two conserved cysteine and histidines. The domain binds both selenium and zinc. The final cysteine is found to be replaced by the rare amino acid selenocysteine in some members of the family. This family has methionine-R-sulfoxide reductase activity. Bacteria(18);Archaea(1);unclassified sequences(1) ds2020-267_287 256 pfam00115 gnl|CDD|376293 2.8946e-26 13 237 1 pfam00115, COX1, Cytochrome C and Quinol oxidase polypeptide I. Eukaryota(18);Bacteria(2) ds2020-267_139 320 pfam05860 gnl|CDD|368641 1.34887e-13 167 298 2 pfam05860, Haemagg_act, haemagglutination activity domain. This domain is suggested to be a carbohydrate- dependent haemagglutination activity site. It is found in a range of haemagglutinins and haemolysins. Bacteria(20) -ds2020-267_763 211 pfam00557 gnl|CDD|376349 0.000231782 167 298 2 pfam00557, Peptidase_M24, Metallopeptidase family M24. This family contains metallopeptidases. It also contains non-peptidase homologs such as the N terminal domain of Spt16 which is a histone H3-H4 binding module. Bacteria(18);Archaea(2) +ds2020-267_763 211 pfam00557 gnl|CDD|376349 0.000231782 167 298 2 pfam00557, Peptidase_M24, Metallopeptidase family M24. This family contains metallopeptidases. It also contains non-peptidase homologs such as the N terminal domain of Spt16 which is a histone H3-H4 binding module. Bacteria(17);Archaea(2);unclassified sequences(1) ds2020-267_571 221 pfam00501 gnl|CDD|366135 2.61467e-07 34 201 1 pfam00501, AMP-binding, AMP-binding enzyme. Bacteria(17);Eukaryota(2);unclassified sequences(1) ds2020-267_565 222 pfam03950 gnl|CDD|377172 9.52435e-10 53 184 -3 pfam03950, tRNA-synt_1c_C, tRNA synthetases class I (E and Q), anti-codon binding domain. Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organisms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln). Bacteria(16);Archaea(3);Eukaryota(1) ds2020-267_427 235 pfam03154 gnl|CDD|367360 0.000552392 53 184 -3 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(20) @@ -22,7 +22,7 @@ ds2020-267_278 258 pfam00012 gnl|CDD|365808 4.1355e-19 50 232 2 pfam00012, HSP70, Hsp70 protein. Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region. Bacteria(15);Eukaryota(4);Viruses(1) ds2020-267_364 243 pfam00216 gnl|CDD|365952 1.5507e-10 134 241 -3 pfam00216, Bac_DNA_binding, Bacterial DNA-binding protein. Bacteria(19);unclassified sequences(1) ds2020-267_558 222 pfam03737 gnl|CDD|377116 4.93695e-13 57 179 -2 pfam03737, RraA-like, Aldolase/RraA. Members of this family include regulator of ribonuclease E activity A (RraA) and 4-hydroxy-4-methyl-2-oxoglutarate (HMG)/4-carboxy- 4-hydroxy-2-oxoadipate (CHA) aldolase, also known as RraA-like protein. RraA acts as a trans-acting modulator of RNA turnover, binding essential endonuclease RNase E and inhibiting RNA processing. RraA-like proteins seem to contain aldolase and/or decarboxylase activity either in place of or in addition to the RNase E inhibitor functions. Bacteria(19);unclassified sequences(1) -ds2020-267_218 274 pfam01348 gnl|CDD|279664 1.66328e-05 51 257 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(15);Bacteria(5) +ds2020-267_218 274 pfam01348 gnl|CDD|279664 1.66328e-05 51 257 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(16);Bacteria(4) ds2020-267_363 243 pfam00416 gnl|CDD|366086 2.02528e-05 15 134 -2 pfam00416, Ribosomal_S13, Ribosomal protein S13/S18. This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes. Bacteria(16);Archaea(3);Eukaryota(1) ds2020-267_746 211 pfam01490 gnl|CDD|279788 0.000177299 15 134 -2 pfam01490, Aa_trans, Transmembrane amino acid transporter protein. This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases. Eukaryota(20) ds2020-267_145 315 pfam02626 gnl|CDD|376868 3.97676e-05 140 256 -3 pfam02626, CT_A_B, Carboxyltransferase domain, subdomain A and B. Urea carboxylase (UC) catalyzes a two-step, ATP- and biotin-dependent carboxylation reaction of urea. It is composed of biotin carboxylase (BC), carboxyltransferase (CT), and biotin carboxyl carrier protein (BCCP) domains. The CT domain of UC consists of four subdomains, named A, B, C and D. This domain covers the A and B subdomains of the CT domain. This domain covers the whole length of KipA (kinase A) from Bacillus subtilis. It can also be found in S. cerevisiae urea amidolyase Dur1,2, which is a multifunctional biotin-dependent enzyme with domains for urea carboxylase and allophanate (urea carboxylate) hydrolase activity. Bacteria(19);unclassified sequences(1) @@ -34,10 +34,10 @@ ds2020-267_2 2436 pfam02123 gnl|CDD|280316 2.17343e-21 184 1476 1 pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus. Viruses(19);unclassified sequences(1) ds2020-267_595 219 pfam02123 gnl|CDD|280316 5.90575e-11 13 210 1 pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus. Viruses(19);unclassified sequences(1) ds2020-267_622 217 pfam01370 gnl|CDD|366597 1.5719e-08 50 172 2 pfam01370, Epimerase, NAD dependent epimerase/dehydratase family. This family of proteins utilize NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions. Bacteria(17);unclassified sequences(2);Archaea(1) -ds2020-267_214 276 pfam00070 gnl|CDD|365851 1.70856e-05 135 254 3 pfam00070, Pyr_redox, Pyridine nucleotide-disulphide oxidoreductase. This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain. Eukaryota(12);Bacteria(5);unclassified sequences(2);Archaea(1) +ds2020-267_214 276 pfam00070 gnl|CDD|365851 1.70856e-05 135 254 3 pfam00070, Pyr_redox, Pyridine nucleotide-disulphide oxidoreductase. This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain. Eukaryota(11);Bacteria(6);unclassified sequences(2);Archaea(1) ds2020-267_610 218 pfam17759 gnl|CDD|380005 1.47034e-13 25 195 1 pfam17759, tRNA_synthFbeta, Phenylalanyl tRNA synthetase beta chain CLM domain. This domain corresponds to the catalytic like domain (CLM) in the beta chain of phe tRNA synthetase. Bacteria(17);Archaea(2);unclassified sequences(1) ds2020-267_94 386 pfam01347 gnl|CDD|366585 0.000224462 25 195 1 pfam01347, Vitellogenin_N, Lipoprotein amino terminal region. This family contains regions from: Vitellogenin, Microsomal triglyceride transfer protein and apolipoprotein B-100. These proteins are all involved in lipid transport. This family contains the LV1n chain from lipovitellin, that contains two structural domains. Eukaryota(20) -ds2020-267_323 250 pfam00227 gnl|CDD|365960 5.8155e-09 10 150 -2 pfam00227, Proteasome, Proteasome subunit. The proteasome is a multisubunit structure that degrades proteins. Protein degradation is an essential component of regulation because proteins can become misfolded, damaged, or unnecessary. Proteasomes and their homologs vary greatly in complexity: from HslV (heat shock locus v), which is encoded by 1 gene in bacteria, to the eukaryotic 20S proteasome, which is encoded by more than 14 genes. Recently evidence of two novel groups of bacterial proteasomes was proposed. The first is Anbu, which is sparsely distributed among cyanobacteria and proteobacteria. The second is call beta-proteobacteria proteasome homolog (BPH). Eukaryota(8);Bacteria(7);Archaea(5) +ds2020-267_323 250 pfam00227 gnl|CDD|365960 5.8155e-09 10 150 -2 pfam00227, Proteasome, Proteasome subunit. The proteasome is a multisubunit structure that degrades proteins. Protein degradation is an essential component of regulation because proteins can become misfolded, damaged, or unnecessary. Proteasomes and their homologs vary greatly in complexity: from HslV (heat shock locus v), which is encoded by 1 gene in bacteria, to the eukaryotic 20S proteasome, which is encoded by more than 14 genes. Recently evidence of two novel groups of bacterial proteasomes was proposed. The first is Anbu, which is sparsely distributed among cyanobacteria and proteobacteria. The second is call beta-proteobacteria proteasome homolog (BPH). Eukaryota(8);Bacteria(6);Archaea(6) ds2020-267_168 298 pfam13546 gnl|CDD|379252 0.000766911 10 150 -2 pfam13546, DDE_5, DDE superfamily endonuclease. This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Bacteria(18);unclassified sequences(2) ds2020-267_636 217 pfam13812 gnl|CDD|316342 0.000111468 16 123 -2 pfam13812, PPR_3, Pentatricopeptide repeat domain. This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. In the case of the Arabidopsis protein UniProtKB:Q66GI4, the repeated helices in this N-terminal region, of protein-only RNase P (PRORP) enzymes, form the pentatricopeptide repeat (PPR) domain which enhances pre-tRNA binding affinity. PROPRP enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana. Eukaryota(20) ds2020-267_486 228 pfam17035 gnl|CDD|374956 5.12677e-09 108 203 3 pfam17035, BET, Bromodomain extra-terminal - transcription regulation. The BET, or bromodomain extra-terminal domain, is found on bromodomain proteins that play key roles in development, cancer progression and virus-host pathogenesis. It interacts with NSD3, JMJD6, CHD4, GLTSCR1, and ATAD5 all of which are shown to impart a pTEFb-independent transcriptional activation function on the bromodomain proteins. Eukaryota(20) @@ -82,7 +82,7 @@ ds2020-267_203 281 pfam03040 gnl|CDD|367312 1.76794e-22 121 231 -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. Eukaryota(20) ds2020-267_33 680 pfam04157 gnl|CDD|367847 4.86455e-13 342 494 -1 pfam04157, EAP30, EAP30/Vps36 family. This family includes EAP30 as well as the Vps36 protein. Vps36 is involved in Golgi to endosome trafficking. EAP30 is a subunit of the ELL complex. The ELL is an 80-kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. Eukaryota(17);Archaea(3) ds2020-267_6 1860 pfam02123 gnl|CDD|280316 1.35634e-17 1147 1764 -1 pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus. Viruses(19);unclassified sequences(1) -ds2020-267_555 222 pfam00124 gnl|CDD|365890 7.71427e-08 48 203 3 pfam00124, Photo_RC, Photosynthetic reaction centre protein. Bacteria(9);Eukaryota(6);Viruses(4);unclassified sequences(1) +ds2020-267_555 222 pfam00124 gnl|CDD|365890 7.71427e-08 48 203 3 pfam00124, Photo_RC, Photosynthetic reaction centre protein. Bacteria(10);Eukaryota(5);Viruses(4);unclassified sequences(1) ds2020-267_550 223 pfam05694 gnl|CDD|377548 0.00097637 48 203 3 pfam05694, SBP56, 56kDa selenium binding protein (SBP56). This family consists of several eukaryotic selenium binding proteins as well as three sequences from archaea. The exact function of this protein is unknown although it is thought that SBP56 participates in late stages of intra-Golgi protein transport. The Lotus japonicus homolog of SBP56, LjSBP is thought to have more than one physiological role and can be implicated in controlling the oxidation/reduction status of target proteins, in vesicular Golgi transport. Bacteria(12);Eukaryota(8) ds2020-267_65 462 pfam13406 gnl|CDD|372592 4.82338e-27 145 360 -1 pfam13406, SLT_2, Transglycosylase SLT domain. This family is related to the SLT domain pfam01464. Bacteria(19);unclassified sequences(1) ds2020-267_729 212 pfam01405 gnl|CDD|279713 5.43744e-05 19 99 -3 pfam01405, PsbT, Photosystem II reaction centre T protein. The exact function of this protein is unknown. It probably consists of a single transmembrane spanning helix. The Chlamydomonas reinhardtii psbT protein appears to be (i) a novel photosystem II subunit and (ii) required for maintaining optimal photosystem II activity under adverse growth conditions. Eukaryota(17);Bacteria(3) @@ -102,4 +102,4 @@ ds2020-267_274 258 pfam03713 gnl|CDD|367619 9.45376e-09 24 173 -2 pfam03713, DUF305, Domain of unknown function (DUF305). Domain found in small family of bacterial secreted proteins with no known function. Also found in Paramecium bursaria chlorella virus 1. This domain is short and found in one or two copies. The domain has a conserved HH motif that may be functionally important. This domain belongs to the ferritin superfamily. It contains two sequence similar repeats each of which is composed of two alpha helices. Bacteria(18);unclassified sequences(2) ds2020-267_42 575 pfam00283 gnl|CDD|365999 2.95472e-07 325 411 1 pfam00283, Cytochrom_B559, Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits. Eukaryota(18);Bacteria(2) ds2020-267_283 257 pfam13041 gnl|CDD|372443 3.148e-06 13 114 1 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(20) -ds2020-267_685 214 pfam09334 gnl|CDD|370442 1.80219e-14 16 117 -2 pfam09334, tRNA-synt_1g, tRNA synthetases class I (M). This family includes methionyl tRNA synthetases. Bacteria(17);Archaea(2);unclassified sequences(1) +ds2020-267_685 214 pfam09334 gnl|CDD|370442 1.80219e-14 16 117 -2 pfam09334, tRNA-synt_1g, tRNA synthetases class I (M). This family includes methionyl tRNA synthetases. Bacteria(16);Archaea(3);unclassified sequences(1)