annotate 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

#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)