Mercurial > repos > bgruening > antismash
diff test-data/ARBH01000003.1.cluster001 @ 3:5784e268efca draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
| author | bgruening |
|---|---|
| date | Sun, 09 Aug 2020 10:15:12 -0400 |
| parents | 593bb8f5488b |
| children | e78e25d3b4bd |
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--- a/test-data/ARBH01000003.1.cluster001 Sat Feb 10 02:37:49 2018 -0500 +++ b/test-data/ARBH01000003.1.cluster001 Sun Aug 09 10:15:12 2020 -0400 @@ -10,12 +10,15 @@ Amycolatopsis. FEATURES Location/Qualifiers source 1..3500 - /organism="Amycolatopsis balhimycina FH 1894" - /mol_type="genomic DNA" - /strain="DSM 44591" /culture_collection="DSM:44591" /db_xref="taxon:1089545" + /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 & @@ -23,16 +26,31 @@ (tra_KS & PKS_AT));" /note="Monomers prediction: (mal)" /note="Structure image: structures/genecluster1.png" - /cutoff=20000 - /extension=20000 /product="t1pks" - /contig_edge="True" 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);" - /locus_tag="ctg1_1" + /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 @@ -54,81 +72,64 @@ IAAAHVAGVLSLADACALVAARGALMQALPSGGAMVSVRGSEADVAGHLGEDVAVAAVN GPESVVLAGTEDAVLQAAGRLEAAGHKVRRLRVSHAFHSPLMDPVLAEFATVAQGLTYH " - /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);" aSDomain 183..713 - /domain="PKS_KR" - /locus_tag="ctg1_1" + /asDomain_id="nrpspksdomains_ctg1_1_KR1" + /database="nrpspksdomains.hmm" /detection="hmmscan" - /database="nrpspksdomains.hmm" + /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" - /label="ctg1_1_KR1" - /asDomain_id="nrpspksdomains_ctg1_1_KR1" - /specificity="KR activity: active" - /specificity="KR stereochemistry: A2" CDS_motif 192..284 - /note="NRPS/PKS Motif: PKSI-KR_m1 (e-value: 3.8e-15, - bit-score: 48.4)" + /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" - /database="abmotifs" - /evalue="3.80E-15" - /asDomain_id="nrpspksmotif_ctg1_1_0001" - /detection="hmmscan" + /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" - /translation="LITGGTGTLAPHLARWLAEQGAEHIVLTSRT" - /label="PKSI-KR_m1" - CDS_motif 555..665 - /note="NRPS/PKS Motif: PKSI-KR_m4 (e-value: 1.6e-14, - bit-score: 46.4)" + /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" - /database="abmotifs" - /evalue="1.60E-14" - /asDomain_id="nrpspksmotif_ctg1_1_0002" - /detection="hmmscan" + /note="NRPS/PKS Motif: PKSI-KR_m4 (e-value: 1.6e-14, + bit-score: 46.4)" /score="46.4" - /aSTool="pksnrpsmotif" /translation="LDAFVLYSSTAGLWGTGAHAAYVAGNAYLHALAAHRR" - /label="PKSI-KR_m4" aSDomain 1026..1238 + /asDomain_id="nrpspksdomains_ctg1_1_Xdom01" + /database="nrpspksdomains.hmm" + /detection="hmmscan" /domain="ACP" + /evalue="7.80E-31" /locus_tag="ctg1_1" - /detection="hmmscan" - /database="nrpspksdomains.hmm" - /evalue="7.80E-31" /score="97.8" /translation="LELVRAEAAAVLGHASADALPEDRAFRDVGFDSVTAVDLRNRISA GTGLTLPATMVFDHPTPRRLAGFLAA" - /asDomain_id="nrpspksdomains_ctg1_1_Xdom01" 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" - /detection="hmmscan" - /database="nrpspksdomains.hmm" - /evalue="3.00E-179" /score="587.9" /translation="VAIIGMACRYPGGANTPERLWDLVVGGVDAISGFPADRNWPTDAL YDPDPDAGGKTYSVQGGFLHEAAEFDPGFFGISPREALSMDPQQRLLLETAWEAFERAG @@ -138,114 +139,113 @@ QQRVIRQALANARLSASEVDVIEGHGTGTALGDPIEAQALLATYGQDRERPLLLGSVKS NIGHTQMASGVAGVIKVVQALRHGLVPKTLHVDEPSTHVDWSTGSIELPSGSVPWPESG RPRRAGISSFGLSGTNVHTILEQAP" - /asDomain_id="nrpspksdomains_ctg1_1_Xdom02" CDS_motif 1788..1835 - /note="NRPS/PKS Motif: PKSI-KS_m3 (e-value: 2e-06, - bit-score: 19.7)" + /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" - /database="abmotifs" - /evalue="2.00E-06" - /asDomain_id="nrpspksmotif_ctg1_1_0003" - /detection="hmmscan" + /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" - /translation="GPAVTLDTACSSSLVA" - /label="PKSI-KS_m3" - CDS_motif 2211..2255 + /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)" - /locus_tag="ctg1_1" - /motif="PKSI-KS_m5" + /score="10.8" + /translation="IEGHGTGTALGDPIE" + CDS_motif 2310..2354 + /aSTool="pksnrpsmotif" + /asDomain_id="nrpspksmotif_ctg1_1_0005" /database="abmotifs" - /evalue="1.90E-03" - /asDomain_id="nrpspksmotif_ctg1_1_0004" /detection="hmmscan" - /score="10.8" - /aSTool="pksnrpsmotif" - /translation="IEGHGTGTALGDPIE" - /label="PKSI-KS_m5" - CDS_motif 2310..2354 + /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)" - /locus_tag="ctg1_1" - /motif="PKSI-KS_m6" + /score="11.5" + /translation="GSVKSNIGHTQMASG" + CDS_motif 2874..2927 + /aSTool="pksnrpsmotif" + /asDomain_id="nrpspksmotif_ctg1_1_0006" /database="abmotifs" - /evalue="1.10E-03" - /asDomain_id="nrpspksmotif_ctg1_1_0005" /detection="hmmscan" - /score="11.5" - /aSTool="pksnrpsmotif" - /translation="GSVKSNIGHTQMASG" - /label="PKSI-KS_m6" - CDS_motif 2874..2927 - /note="NRPS/PKS Motif: PKSI-AT-mM_m1 (e-value: 2.3e-06, - bit-score: 19.8)" + /evalue="2.30E-06" + /label="PKSI-AT-mM_m1" /locus_tag="ctg1_1" /motif="PKSI-AT-mM_m1" - /database="abmotifs" - /evalue="2.30E-06" - /asDomain_id="nrpspksmotif_ctg1_1_0006" - /detection="hmmscan" + /note="NRPS/PKS Motif: PKSI-AT-mM_m1 (e-value: 2.3e-06, + bit-score: 19.8)" /score="19.8" - /aSTool="pksnrpsmotif" /translation="FLFAGQGSQRAGMGRELY" - /label="PKSI-AT-mM_m1" 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" - /detection="hmmscan" - /database="nrpspksdomains.hmm" - /evalue="4.00E-80" /score="260.9" + /specificity="PKS signature: mal" + /specificity="Minowa: mal" + /specificity="consensus: mal" /translation="LFAGQGSQRAGMGRELYERHPVFADALDAVLGHFDLPRALRDVMW DDDSTALDETGYTQPALFAFEVALFRLLESWGVTPDYLAGHSIGEIAAAHVAGVLSLAD ACALVAARGALMQALPSGGAMVSVRGSEADVAGHLGEDVAVAAVNGPESVVLAGTEDAV LQAAGRLEAAGHKVRRLRVSHAFHSPLMDPVLAEFATVAQGLTYH" - /label="ctg1_1_AT1" - /asDomain_id="nrpspksdomains_ctg1_1_AT1" - /specificity="PKS signature: mal" - /specificity="Minowa: mal" - /specificity="consensus: mal" CDS_motif 3033..3095 - /note="NRPS/PKS Motif: PKSI-AT-mM_m2 (e-value: 0.0032, - bit-score: 10.9)" + /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" - /database="abmotifs" - /evalue="3.20E-03" - /asDomain_id="nrpspksmotif_ctg1_1_0007" - /detection="hmmscan" + /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" - /translation="DETGYTQPALFAFEVALFRLL" - /label="PKSI-AT-mM_m2" - CDS_motif 3105..3227 + /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)" - /locus_tag="ctg1_1" - /motif="PKSI-AT-M_m3" + /score="71.3" + /translation="GVTPDYLAGHSIGEIAAAHVAGVLSLADACALVAARGALMQ" + CDS_motif 3312..3350 + /aSTool="pksnrpsmotif" + /asDomain_id="nrpspksmotif_ctg1_1_0009" /database="abmotifs" - /evalue="2.30E-22" - /asDomain_id="nrpspksmotif_ctg1_1_0008" /detection="hmmscan" - /score="71.3" - /aSTool="pksnrpsmotif" - /translation="GVTPDYLAGHSIGEIAAAHVAGVLSLADACALVAARGALMQ" - /label="PKSI-AT-M_m3" - CDS_motif 3312..3350 + /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)" - /locus_tag="ctg1_1" - /motif="PKSI-AT-M_m5" - /database="abmotifs" - /evalue="4.70E-04" - /asDomain_id="nrpspksmotif_ctg1_1_0009" - /detection="hmmscan" /score="13.4" - /aSTool="pksnrpsmotif" /translation="AAVNGPESVVLAG" - /label="PKSI-AT-M_m5" ORIGIN 1 ggggcggcgt gctcgccctg cccgccgagc tggaccgccg cggcggcgac cggctggcgg 61 ctgtgctgtc cggcgccacc ggcgaagacc agctggccat ccgcgccgcc ggcgtgttcg