Mercurial > repos > bgruening > antismash
diff test-data/ARBH01000003.1.cluster001 @ 4:e78e25d3b4bd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit f5f8e44e726c9f2cc57e0f0fe8182a73afa56669
| author | bgruening |
|---|---|
| date | Tue, 31 May 2022 14:04:07 +0000 |
| parents | 5784e268efca |
| children |
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--- a/test-data/ARBH01000003.1.cluster001 Sun Aug 09 10:15:12 2020 -0400 +++ b/test-data/ARBH01000003.1.cluster001 Tue May 31 14:04:07 2022 +0000 @@ -3,11 +3,80 @@ A3CEDRAFT_scaffold1.1_C3, whole genome shotgun sequence. ACCESSION ARBH01000003 VERSION ARBH01000003.1 -KEYWORDS . +DBLINK BioProject: PRJNA165347 + BioSample: SAMN02256403 +KEYWORDS WGS; GSC:MIGS:2.1; IMPROVED_HIGH_QUALITY_DRAFT. SOURCE Amycolatopsis balhimycina FH 1894 ORGANISM Amycolatopsis balhimycina FH 1894 Bacteria; Actinobacteria; Pseudonocardiales; Pseudonocardiaceae; Amycolatopsis. +REFERENCE 1 (bases 1 to 3500) + AUTHORS Klenk,H.-P., Huntemann,M., Han,J., Chen,A., Kyrpides,N., + Mavromatis,K., Markowitz,V., Palaniappan,K., Ivanova,N., + Schaumberg,A., Pati,A., Liolios,K., Nordberg,H.P., Cantor,M.N., + Hua,S.X. and Woyke,T. + TITLE Direct Submission + JOURNAL Submitted (16-APR-2013) DOE Joint Genome Institute, 2800 Mitchell + Drive, Walnut Creek, CA 94598-1698, USA +COMMENT ##MIGS-Data-START## + investigation_type :: bacteria_archaea + project_name :: Amycolatopsis balhimycina DSM 44591 + collection_date :: Missing + lat_lon :: Missing + depth :: Missing + alt_elev :: Missing + country :: India + num_replicons :: Missing + ref_biomaterial :: DSM 44591 + biotic_relationship :: Free living + rel_to_oxygen :: Aerobe + isol_growth_condt :: Missing + assembly :: Velvet v. 1.1.05; ALLPATHS v. r38445; Phrap v. 4.24 + finishing_strategy :: Missing + environment :: Soil + trophic_level :: Missing + sequencing_meth :: WGS + GOLD Stamp ID :: Gi10728 + Type Strain :: Yes + Funding Program :: DOE-CSP 2011 + Isolation Site :: Soil + Cell Shape :: Filament-shaped + Motility :: Nonmotile + Sporulation :: Sporulating + Temperature Range :: Mesophile + Gram Staining :: Gram+ + Diseases :: None + ##MIGS-Data-END## + ##Genome-Assembly-Data-START## + Finishing Goal :: Improved High-Quality Draft + Current Finishing Status :: Improved High-Quality Draft + Assembly Method :: Velvet v. 1.1.05; ALLPATHS v. r38445; Phrap v. + 4.24 + Genome Coverage :: Unknown + Sequencing Technology :: Illumina GAii + ##Genome-Assembly-Data-END## + URL -- http://www.jgi.doe.gov + JGI Project ID: 404843 + Source DNA and Organism available from Hans-Peter Klenk + (hpk@dsmz.de) + Source DNA available from Hans-Peter Klenk (hpk@dsmz.de) + Organism available from Hans-Peter Klenk (hpk@dsmz.de) + Contacts: Hans-Peter Klenk (hpk@dsmz.de) + Tanja Woyke (microbe@cuba.jgi-psf.org) + Whole genome sequencing and draft assembly at JGI-PGF + Annotation by JGI-ORNL + The JGI and collaborators endorse the principles for the + distribution and use of large scale sequencing data adopted by the + larger genome sequencing community and urge users of this data to + follow them. It is our intention to publish the work of this + project in a timely fashion and we welcome collaborative + interaction on the project and analysis. + (http://www.genome.gov/page.cfm?pageID=10506376) + Full annotations are available from IMG. + ##antiSMASH-Data-START## + Version :: 6.1.0 + Run date :: 2022-05-03 16:47:32 + ##antiSMASH-Data-END## FEATURES Location/Qualifiers source 1..3500 /culture_collection="DSM:44591" @@ -15,237 +84,41 @@ /mol_type="genomic DNA" /organism="Amycolatopsis balhimycina FH 1894" /strain="DSM 44591" - cluster 1..3500 - /contig_edge="True" - /cutoff=20000 - /extension=20000 - /note="Cluster number: 1" - /note="Detection rule(s) for this cluster type: t1pks: - ((PKS_KS & PKS_AT) or (ene_KS & PKS_AT) or (mod_KS & - PKS_AT) or (hyb_KS & PKS_AT) or (itr_KS & PKS_AT) or - (tra_KS & PKS_AT));" - /note="Monomers prediction: (mal)" - /note="Structure image: structures/genecluster1.png" - /product="t1pks" - CDS 3..3500 - /aSProdPred="mal" - /locus_tag="ctg1_1" - /note="smCOG: - SMCOG1001:short-chain_dehydrogenase/reductase_SDR (Score: - 64.2; E-value: 2.2e-19);" - /sec_met="Type: t1pks" - /sec_met="Domains detected: PP-binding (E-value: 1.3e-15, - bitscore: 44.0, seeds: 164); PKS_AT (E-value: 8.7e-82, - bitscore: 260.9, seeds: 1682); mod_KS (E-value: 9.4e-224, - bitscore: 729.0, seeds: 217); adh_short (E-value: 7.1e-52, - bitscore: 162.1, seeds: 230)" - /sec_met="Kind: biosynthetic" - /sec_met="NRPS/PKS subtype: Type I Modular PKS" - /sec_met="NRPS/PKS Domain: PKS_KR (60-237). E-value: - 1.4e-53. Score: 173.1; Predicted KR activity: active; - Predicted KR stereochemistry: A2;" - /sec_met="NRPS/PKS Domain: ACP (341-412). E-value: 7.8e-31. - Score: 97.8;" - /sec_met="NRPS/PKS Domain: PKS_KS (434-858). E-value: - 3e-179. Score: 587.9;" - /sec_met="NRPS/PKS Domain: PKS_AT (958-1166). E-value: - 4e-80. Score: 260.9; Substrate specificity predictions: mal - (PKS signature), mal (Minowa), mal (consensus);" - /translation="GGVLALPAELDRRGGDRLAAVLSGATGEDQLAIRAAGVFGRRVVR - APAGDRAPARTWTPRGTTLITGGTGTLAPHLARWLAEQGAEHIVLTSRTGAEAPKARQL - LAELGETVEAVACDVTDKAALAALLARLRAEGRTVRNVVHTAAVIELHTLAETDLAAFS - RTVHAKVVGARNLDELLDTDELDAFVLYSSTAGLWGTGAHAAYVAGNAYLHALAAHRRA - RGLRATALSWGIWADDRELGRVDPEQIVRSGLVFMAPELALEGLRRALDDDETALAVAD - LDWERYYPVYTAVRPTLLFDELPEVRRLTEAAAATAATGAGGEFAARLRTLPEAERAHL - LLELVRAEAAAVLGHASADALPEDRAFRDVGFDSVTAVDLRNRISAGTGLTLPATMVFD - HPTPRRLAGFLAATITGSGAVEQAPAVAGVDTGEPVAIIGMACRYPGGANTPERLWDLV - VGGVDAISGFPADRNWPTDALYDPDPDAGGKTYSVQGGFLHEAAEFDPGFFGISPREAL - SMDPQQRLLLETAWEAFERAGIDPHTLRGSGTGTFIGASYQDYTAAVSGAVDNADGHMI - TGSLGSILSGRLSYLFGLEGPAVTLDTACSSSLVAIHLAAQSLRSGESSLALAGGVSVM - ATPGAFVGFSRQRALATDGRCKAYSDRADGMTLGEGVGLVLLEKLSDAQRNGHRILAVV - RGSATNQDGASNGMTAPSGPSQQRVIRQALANARLSASEVDVIEGHGTGTALGDPIEAQ - ALLATYGQDRERPLLLGSVKSNIGHTQMASGVAGVIKVVQALRHGLVPKTLHVDEPSTH - VDWSTGSIELPSGSVPWPESGRPRRAGISSFGLSGTNVHTILEQAPEPAAEAGPEPEPG - LVPVPLSGRTEAALRAQAATVLDTLDDGVSPAVLGYSLASTRSAFEHRAVLLAEDHDEL - RRGLAALAGDQPDGGVVRGTVTRGRTAFLFAGQGSQRAGMGRELYERHPVFADALDAVL - GHFDLPRALRDVMWDDDSTALDETGYTQPALFAFEVALFRLLESWGVTPDYLAGHSIGE - IAAAHVAGVLSLADACALVAARGALMQALPSGGAMVSVRGSEADVAGHLGEDVAVAAVN - GPESVVLAGTEDAVLQAAGRLEAAGHKVRRLRVSHAFHSPLMDPVLAEFATVAQGLTYH - " - aSDomain 183..713 - /asDomain_id="nrpspksdomains_ctg1_1_KR1" - /database="nrpspksdomains.hmm" - /detection="hmmscan" - /domain="PKS_KR" - /evalue="1.40E-53" - /label="ctg1_1_KR1" - /locus_tag="ctg1_1" - /score="173.1" - /specificity="KR activity: active" - /specificity="KR stereochemistry: A2" - /translation="GTTLITGGTGTLAPHLARWLAEQGAEHIVLTSRTGAEAPKARQLL - AELGETVEAVACDVTDKAALAALLARLRAEGRTVRNVVHTAAVIELHTLAETDLAAFSR - TVHAKVVGARNLDELLDTDELDAFVLYSSTAGLWGTGAHAAYVAGNAYLHALAAHRRAR - GLRATALSWGIWAD" - CDS_motif 192..284 - /aSTool="pksnrpsmotif" - /asDomain_id="nrpspksmotif_ctg1_1_0001" - /database="abmotifs" - /detection="hmmscan" - /evalue="3.80E-15" - /label="PKSI-KR_m1" - /locus_tag="ctg1_1" - /motif="PKSI-KR_m1" - /note="NRPS/PKS Motif: PKSI-KR_m1 (e-value: 3.8e-15, - bit-score: 48.4)" - /score="48.4" - /translation="LITGGTGTLAPHLARWLAEQGAEHIVLTSRT" - CDS_motif 555..665 - /aSTool="pksnrpsmotif" - /asDomain_id="nrpspksmotif_ctg1_1_0002" - /database="abmotifs" - /detection="hmmscan" - /evalue="1.60E-14" - /label="PKSI-KR_m4" - /locus_tag="ctg1_1" - /motif="PKSI-KR_m4" - /note="NRPS/PKS Motif: PKSI-KR_m4 (e-value: 1.6e-14, - bit-score: 46.4)" - /score="46.4" - /translation="LDAFVLYSSTAGLWGTGAHAAYVAGNAYLHALAAHRR" - aSDomain 1026..1238 - /asDomain_id="nrpspksdomains_ctg1_1_Xdom01" - /database="nrpspksdomains.hmm" - /detection="hmmscan" - /domain="ACP" - /evalue="7.80E-31" - /locus_tag="ctg1_1" - /score="97.8" - /translation="LELVRAEAAAVLGHASADALPEDRAFRDVGFDSVTAVDLRNRISA - GTGLTLPATMVFDHPTPRRLAGFLAA" - aSDomain 1305..2576 - /asDomain_id="nrpspksdomains_ctg1_1_Xdom02" - /database="nrpspksdomains.hmm" - /detection="hmmscan" - /domain="PKS_KS" - /evalue="3.00E-179" - /locus_tag="ctg1_1" - /score="587.9" - /translation="VAIIGMACRYPGGANTPERLWDLVVGGVDAISGFPADRNWPTDAL - YDPDPDAGGKTYSVQGGFLHEAAEFDPGFFGISPREALSMDPQQRLLLETAWEAFERAG - IDPHTLRGSGTGTFIGASYQDYTAAVSGAVDNADGHMITGSLGSILSGRLSYLFGLEGP - AVTLDTACSSSLVAIHLAAQSLRSGESSLALAGGVSVMATPGAFVGFSRQRALATDGRC - KAYSDRADGMTLGEGVGLVLLEKLSDAQRNGHRILAVVRGSATNQDGASNGMTAPSGPS - QQRVIRQALANARLSASEVDVIEGHGTGTALGDPIEAQALLATYGQDRERPLLLGSVKS - NIGHTQMASGVAGVIKVVQALRHGLVPKTLHVDEPSTHVDWSTGSIELPSGSVPWPESG - RPRRAGISSFGLSGTNVHTILEQAP" - CDS_motif 1788..1835 - /aSTool="pksnrpsmotif" - /asDomain_id="nrpspksmotif_ctg1_1_0003" - /database="abmotifs" - /detection="hmmscan" - /evalue="2.00E-06" - /label="PKSI-KS_m3" - /locus_tag="ctg1_1" - /motif="PKSI-KS_m3" - /note="NRPS/PKS Motif: PKSI-KS_m3 (e-value: 2e-06, - bit-score: 19.7)" - /score="19.7" - /translation="GPAVTLDTACSSSLVA" - CDS_motif 2211..2255 - /aSTool="pksnrpsmotif" - /asDomain_id="nrpspksmotif_ctg1_1_0004" - /database="abmotifs" - /detection="hmmscan" - /evalue="1.90E-03" - /label="PKSI-KS_m5" - /locus_tag="ctg1_1" - /motif="PKSI-KS_m5" - /note="NRPS/PKS Motif: PKSI-KS_m5 (e-value: 0.0019, - bit-score: 10.8)" - /score="10.8" - /translation="IEGHGTGTALGDPIE" - CDS_motif 2310..2354 - /aSTool="pksnrpsmotif" - /asDomain_id="nrpspksmotif_ctg1_1_0005" - /database="abmotifs" - /detection="hmmscan" - /evalue="1.10E-03" - /label="PKSI-KS_m6" - /locus_tag="ctg1_1" - /motif="PKSI-KS_m6" - /note="NRPS/PKS Motif: PKSI-KS_m6 (e-value: 0.0011, - bit-score: 11.5)" - /score="11.5" - /translation="GSVKSNIGHTQMASG" - CDS_motif 2874..2927 - /aSTool="pksnrpsmotif" - /asDomain_id="nrpspksmotif_ctg1_1_0006" - /database="abmotifs" - /detection="hmmscan" - /evalue="2.30E-06" - /label="PKSI-AT-mM_m1" - /locus_tag="ctg1_1" - /motif="PKSI-AT-mM_m1" - /note="NRPS/PKS Motif: PKSI-AT-mM_m1 (e-value: 2.3e-06, - bit-score: 19.8)" - /score="19.8" - /translation="FLFAGQGSQRAGMGRELY" - aSDomain 2877..3500 - /asDomain_id="nrpspksdomains_ctg1_1_AT1" - /database="nrpspksdomains.hmm" - /detection="hmmscan" - /domain="PKS_AT" - /evalue="4.00E-80" - /label="ctg1_1_AT1" - /locus_tag="ctg1_1" - /score="260.9" - /specificity="PKS signature: mal" - /specificity="Minowa: mal" - /specificity="consensus: mal" - /translation="LFAGQGSQRAGMGRELYERHPVFADALDAVLGHFDLPRALRDVMW - DDDSTALDETGYTQPALFAFEVALFRLLESWGVTPDYLAGHSIGEIAAAHVAGVLSLAD - ACALVAARGALMQALPSGGAMVSVRGSEADVAGHLGEDVAVAAVNGPESVVLAGTEDAV - LQAAGRLEAAGHKVRRLRVSHAFHSPLMDPVLAEFATVAQGLTYH" - CDS_motif 3033..3095 - /aSTool="pksnrpsmotif" - /asDomain_id="nrpspksmotif_ctg1_1_0007" - /database="abmotifs" - /detection="hmmscan" - /evalue="3.20E-03" - /label="PKSI-AT-mM_m2" - /locus_tag="ctg1_1" - /motif="PKSI-AT-mM_m2" - /note="NRPS/PKS Motif: PKSI-AT-mM_m2 (e-value: 0.0032, - bit-score: 10.9)" - /score="10.9" - /translation="DETGYTQPALFAFEVALFRLL" - CDS_motif 3105..3227 - /aSTool="pksnrpsmotif" - /asDomain_id="nrpspksmotif_ctg1_1_0008" - /database="abmotifs" - /detection="hmmscan" - /evalue="2.30E-22" - /label="PKSI-AT-M_m3" - /locus_tag="ctg1_1" - /motif="PKSI-AT-M_m3" - /note="NRPS/PKS Motif: PKSI-AT-M_m3 (e-value: 2.3e-22, - bit-score: 71.3)" - /score="71.3" - /translation="GVTPDYLAGHSIGEIAAAHVAGVLSLADACALVAARGALMQ" - CDS_motif 3312..3350 - /aSTool="pksnrpsmotif" - /asDomain_id="nrpspksmotif_ctg1_1_0009" - /database="abmotifs" - /detection="hmmscan" - /evalue="4.70E-04" - /label="PKSI-AT-M_m5" - /locus_tag="ctg1_1" - /motif="PKSI-AT-M_m5" - /note="NRPS/PKS Motif: PKSI-AT-M_m5 (e-value: 0.00047, - bit-score: 13.4)" - /score="13.4" - /translation="AAVNGPESVVLAG" + CDS complement(170..3134) + /ID="input.cds1.1" + /Name="input.path1.gene1" + /Note="initial-exon" + /gene="input.path1.gene1" + /phase="0" + /source="GlimmerHMM" + /transl_table=1 + /translation="MPGQVIRRHTPRLQQPEQRHLEGEQRRLGVPRLVEGRGIVVPHHV + PQRTGQVEVPQHRVQRVGEHRVALVQLAAHPGPLAALAGEQERRAAPRHGAPHHAAVRL + VAGQCGQAAPQFVVVLGQQHRTVFEGRPGGGQRVPEHGRRHAVVQGVQHGGGLSAQRCF + RPAGQRDRHQAGLRLGAGFGGRFRGLLEDGVHVRAAQPEGRDTGPARPAALRPRHAAGR + QLDRAGAPVDVRGGLVHVQRLGYQPVPQRLHHLDHAGHAGGHLGVADVGLHRAEQQRPF + PVLAVGGQQGLGLDRVAQRGAGAVALDHVHLGRREPRVGQRLPDHPLLGRAAGRGHAVG + RAVLVRGRTPDHRQDPVPVALRVGQLLQQHQADALAEGHAVGPVRVGLATAVRGQCALA + READERPRRRHHAHPAGQRQAALPRPQRLRGQVDGDQRRRAGGVQGDRRALQPEQVGEP + AGQDAAQRAGDHVAVGVVHRAGHGRGVVLVAGPDEGAGAAAPQRVRVDPGPLERLPRRL + QQQALLRIHGQCLPRRDAEEARVELGRLVQEAALHRIGLAAGVRVRVVERVGRPVAVGR + EAGDGVHAAHDQVPQPFRGVRATRVAAGHPDDGDGLAGVHAGHGRCLLDGTRAGDRGGQ + EPGQPPRRRVVEHHGGGQGQAGAGGDPVAQVDRGDRVEADVAEGAVLGQRVGRRVAQHG + RGLGPDQFQEQVGALGLGQRAQPGGELAAGAGGGRGGGGLGEPPHLRQLVEQQRRPDGG + VDRVVPLPVQIGHGQRGLVVVQGPAQTLQRQLRRHEHQAAAHDLLRVDPAEFAVVGPDA + PRQRGGPQPPGAPVGCQRVQVRVAGHVGGVRAGAPQAGGGGVQHERIELVGVEQLVQVA + RAHHLGVHGPGERGQVGLGQRVQLDHGGRVHHVPHGPALGPQPRQQGGQRRLVGDVAGH + RLDGLAQLRQQLPGLRGLGAGAAGQHDVLGALLGQPAGQVRGQGAGAAGDQRGAARGP" + CDS 3249..3404 + /ID="input.cds2.1" + /Name="input.path1.gene2" + /Note="initial-exon" + /gene="input.path1.gene2" + /phase="0" + /source="GlimmerHMM" + /transl_table=1 + /translation="MVSVRGSEADVAGHLGEDVAVAAVNGPESVVLAGTEDAVLQAAGR + LEAAGHK" ORIGIN 1 ggggcggcgt gctcgccctg cccgccgagc tggaccgccg cggcggcgac cggctggcgg 61 ctgtgctgtc cggcgccacc ggcgaagacc agctggccat ccgcgccgcc ggcgtgttcg