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comparison test-data/ARBH01000003.1.cluster001 @ 4:e78e25d3b4bd draft

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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
comparison
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3:5784e268efca 4:e78e25d3b4bd
1 LOCUS ARBH01000003 3500 bp DNA linear BCT 22-APR-2013 1 LOCUS ARBH01000003 3500 bp DNA linear BCT 22-APR-2013
2 DEFINITION Amycolatopsis balhimycina FH 1894 strain DSM 44591 2 DEFINITION Amycolatopsis balhimycina FH 1894 strain DSM 44591
3 A3CEDRAFT_scaffold1.1_C3, whole genome shotgun sequence. 3 A3CEDRAFT_scaffold1.1_C3, whole genome shotgun sequence.
4 ACCESSION ARBH01000003 4 ACCESSION ARBH01000003
5 VERSION ARBH01000003.1 5 VERSION ARBH01000003.1
6 KEYWORDS . 6 DBLINK BioProject: PRJNA165347
7 BioSample: SAMN02256403
8 KEYWORDS WGS; GSC:MIGS:2.1; IMPROVED_HIGH_QUALITY_DRAFT.
7 SOURCE Amycolatopsis balhimycina FH 1894 9 SOURCE Amycolatopsis balhimycina FH 1894
8 ORGANISM Amycolatopsis balhimycina FH 1894 10 ORGANISM Amycolatopsis balhimycina FH 1894
9 Bacteria; Actinobacteria; Pseudonocardiales; Pseudonocardiaceae; 11 Bacteria; Actinobacteria; Pseudonocardiales; Pseudonocardiaceae;
10 Amycolatopsis. 12 Amycolatopsis.
13 REFERENCE 1 (bases 1 to 3500)
14 AUTHORS Klenk,H.-P., Huntemann,M., Han,J., Chen,A., Kyrpides,N.,
15 Mavromatis,K., Markowitz,V., Palaniappan,K., Ivanova,N.,
16 Schaumberg,A., Pati,A., Liolios,K., Nordberg,H.P., Cantor,M.N.,
17 Hua,S.X. and Woyke,T.
18 TITLE Direct Submission
19 JOURNAL Submitted (16-APR-2013) DOE Joint Genome Institute, 2800 Mitchell
20 Drive, Walnut Creek, CA 94598-1698, USA
21 COMMENT ##MIGS-Data-START##
22 investigation_type :: bacteria_archaea
23 project_name :: Amycolatopsis balhimycina DSM 44591
24 collection_date :: Missing
25 lat_lon :: Missing
26 depth :: Missing
27 alt_elev :: Missing
28 country :: India
29 num_replicons :: Missing
30 ref_biomaterial :: DSM 44591
31 biotic_relationship :: Free living
32 rel_to_oxygen :: Aerobe
33 isol_growth_condt :: Missing
34 assembly :: Velvet v. 1.1.05; ALLPATHS v. r38445; Phrap v. 4.24
35 finishing_strategy :: Missing
36 environment :: Soil
37 trophic_level :: Missing
38 sequencing_meth :: WGS
39 GOLD Stamp ID :: Gi10728
40 Type Strain :: Yes
41 Funding Program :: DOE-CSP 2011
42 Isolation Site :: Soil
43 Cell Shape :: Filament-shaped
44 Motility :: Nonmotile
45 Sporulation :: Sporulating
46 Temperature Range :: Mesophile
47 Gram Staining :: Gram+
48 Diseases :: None
49 ##MIGS-Data-END##
50 ##Genome-Assembly-Data-START##
51 Finishing Goal :: Improved High-Quality Draft
52 Current Finishing Status :: Improved High-Quality Draft
53 Assembly Method :: Velvet v. 1.1.05; ALLPATHS v. r38445; Phrap v.
54 4.24
55 Genome Coverage :: Unknown
56 Sequencing Technology :: Illumina GAii
57 ##Genome-Assembly-Data-END##
58 URL -- http://www.jgi.doe.gov
59 JGI Project ID: 404843
60 Source DNA and Organism available from Hans-Peter Klenk
61 (hpk@dsmz.de)
62 Source DNA available from Hans-Peter Klenk (hpk@dsmz.de)
63 Organism available from Hans-Peter Klenk (hpk@dsmz.de)
64 Contacts: Hans-Peter Klenk (hpk@dsmz.de)
65 Tanja Woyke (microbe@cuba.jgi-psf.org)
66 Whole genome sequencing and draft assembly at JGI-PGF
67 Annotation by JGI-ORNL
68 The JGI and collaborators endorse the principles for the
69 distribution and use of large scale sequencing data adopted by the
70 larger genome sequencing community and urge users of this data to
71 follow them. It is our intention to publish the work of this
72 project in a timely fashion and we welcome collaborative
73 interaction on the project and analysis.
74 (http://www.genome.gov/page.cfm?pageID=10506376)
75 Full annotations are available from IMG.
76 ##antiSMASH-Data-START##
77 Version :: 6.1.0
78 Run date :: 2022-05-03 16:47:32
79 ##antiSMASH-Data-END##
11 FEATURES Location/Qualifiers 80 FEATURES Location/Qualifiers
12 source 1..3500 81 source 1..3500
13 /culture_collection="DSM:44591" 82 /culture_collection="DSM:44591"
14 /db_xref="taxon:1089545" 83 /db_xref="taxon:1089545"
15 /mol_type="genomic DNA" 84 /mol_type="genomic DNA"
16 /organism="Amycolatopsis balhimycina FH 1894" 85 /organism="Amycolatopsis balhimycina FH 1894"
17 /strain="DSM 44591" 86 /strain="DSM 44591"
18 cluster 1..3500 87 CDS complement(170..3134)
19 /contig_edge="True" 88 /ID="input.cds1.1"
20 /cutoff=20000 89 /Name="input.path1.gene1"
21 /extension=20000 90 /Note="initial-exon"
22 /note="Cluster number: 1" 91 /gene="input.path1.gene1"
23 /note="Detection rule(s) for this cluster type: t1pks: 92 /phase="0"
24 ((PKS_KS & PKS_AT) or (ene_KS & PKS_AT) or (mod_KS & 93 /source="GlimmerHMM"
25 PKS_AT) or (hyb_KS & PKS_AT) or (itr_KS & PKS_AT) or 94 /transl_table=1
26 (tra_KS & PKS_AT));" 95 /translation="MPGQVIRRHTPRLQQPEQRHLEGEQRRLGVPRLVEGRGIVVPHHV
27 /note="Monomers prediction: (mal)" 96 PQRTGQVEVPQHRVQRVGEHRVALVQLAAHPGPLAALAGEQERRAAPRHGAPHHAAVRL
28 /note="Structure image: structures/genecluster1.png" 97 VAGQCGQAAPQFVVVLGQQHRTVFEGRPGGGQRVPEHGRRHAVVQGVQHGGGLSAQRCF
29 /product="t1pks" 98 RPAGQRDRHQAGLRLGAGFGGRFRGLLEDGVHVRAAQPEGRDTGPARPAALRPRHAAGR
30 CDS 3..3500 99 QLDRAGAPVDVRGGLVHVQRLGYQPVPQRLHHLDHAGHAGGHLGVADVGLHRAEQQRPF
31 /aSProdPred="mal" 100 PVLAVGGQQGLGLDRVAQRGAGAVALDHVHLGRREPRVGQRLPDHPLLGRAAGRGHAVG
32 /locus_tag="ctg1_1" 101 RAVLVRGRTPDHRQDPVPVALRVGQLLQQHQADALAEGHAVGPVRVGLATAVRGQCALA
33 /note="smCOG: 102 READERPRRRHHAHPAGQRQAALPRPQRLRGQVDGDQRRRAGGVQGDRRALQPEQVGEP
34 SMCOG1001:short-chain_dehydrogenase/reductase_SDR (Score: 103 AGQDAAQRAGDHVAVGVVHRAGHGRGVVLVAGPDEGAGAAAPQRVRVDPGPLERLPRRL
35 64.2; E-value: 2.2e-19);" 104 QQQALLRIHGQCLPRRDAEEARVELGRLVQEAALHRIGLAAGVRVRVVERVGRPVAVGR
36 /sec_met="Type: t1pks" 105 EAGDGVHAAHDQVPQPFRGVRATRVAAGHPDDGDGLAGVHAGHGRCLLDGTRAGDRGGQ
37 /sec_met="Domains detected: PP-binding (E-value: 1.3e-15, 106 EPGQPPRRRVVEHHGGGQGQAGAGGDPVAQVDRGDRVEADVAEGAVLGQRVGRRVAQHG
38 bitscore: 44.0, seeds: 164); PKS_AT (E-value: 8.7e-82, 107 RGLGPDQFQEQVGALGLGQRAQPGGELAAGAGGGRGGGGLGEPPHLRQLVEQQRRPDGG
39 bitscore: 260.9, seeds: 1682); mod_KS (E-value: 9.4e-224, 108 VDRVVPLPVQIGHGQRGLVVVQGPAQTLQRQLRRHEHQAAAHDLLRVDPAEFAVVGPDA
40 bitscore: 729.0, seeds: 217); adh_short (E-value: 7.1e-52, 109 PRQRGGPQPPGAPVGCQRVQVRVAGHVGGVRAGAPQAGGGGVQHERIELVGVEQLVQVA
41 bitscore: 162.1, seeds: 230)" 110 RAHHLGVHGPGERGQVGLGQRVQLDHGGRVHHVPHGPALGPQPRQQGGQRRLVGDVAGH
42 /sec_met="Kind: biosynthetic" 111 RLDGLAQLRQQLPGLRGLGAGAAGQHDVLGALLGQPAGQVRGQGAGAAGDQRGAARGP"
43 /sec_met="NRPS/PKS subtype: Type I Modular PKS" 112 CDS 3249..3404
44 /sec_met="NRPS/PKS Domain: PKS_KR (60-237). E-value: 113 /ID="input.cds2.1"
45 1.4e-53. Score: 173.1; Predicted KR activity: active; 114 /Name="input.path1.gene2"
46 Predicted KR stereochemistry: A2;" 115 /Note="initial-exon"
47 /sec_met="NRPS/PKS Domain: ACP (341-412). E-value: 7.8e-31. 116 /gene="input.path1.gene2"
48 Score: 97.8;" 117 /phase="0"
49 /sec_met="NRPS/PKS Domain: PKS_KS (434-858). E-value: 118 /source="GlimmerHMM"
50 3e-179. Score: 587.9;" 119 /transl_table=1
51 /sec_met="NRPS/PKS Domain: PKS_AT (958-1166). E-value: 120 /translation="MVSVRGSEADVAGHLGEDVAVAAVNGPESVVLAGTEDAVLQAAGR
52 4e-80. Score: 260.9; Substrate specificity predictions: mal 121 LEAAGHK"
53 (PKS signature), mal (Minowa), mal (consensus);"
54 /translation="GGVLALPAELDRRGGDRLAAVLSGATGEDQLAIRAAGVFGRRVVR
55 APAGDRAPARTWTPRGTTLITGGTGTLAPHLARWLAEQGAEHIVLTSRTGAEAPKARQL
56 LAELGETVEAVACDVTDKAALAALLARLRAEGRTVRNVVHTAAVIELHTLAETDLAAFS
57 RTVHAKVVGARNLDELLDTDELDAFVLYSSTAGLWGTGAHAAYVAGNAYLHALAAHRRA
58 RGLRATALSWGIWADDRELGRVDPEQIVRSGLVFMAPELALEGLRRALDDDETALAVAD
59 LDWERYYPVYTAVRPTLLFDELPEVRRLTEAAAATAATGAGGEFAARLRTLPEAERAHL
60 LLELVRAEAAAVLGHASADALPEDRAFRDVGFDSVTAVDLRNRISAGTGLTLPATMVFD
61 HPTPRRLAGFLAATITGSGAVEQAPAVAGVDTGEPVAIIGMACRYPGGANTPERLWDLV
62 VGGVDAISGFPADRNWPTDALYDPDPDAGGKTYSVQGGFLHEAAEFDPGFFGISPREAL
63 SMDPQQRLLLETAWEAFERAGIDPHTLRGSGTGTFIGASYQDYTAAVSGAVDNADGHMI
64 TGSLGSILSGRLSYLFGLEGPAVTLDTACSSSLVAIHLAAQSLRSGESSLALAGGVSVM
65 ATPGAFVGFSRQRALATDGRCKAYSDRADGMTLGEGVGLVLLEKLSDAQRNGHRILAVV
66 RGSATNQDGASNGMTAPSGPSQQRVIRQALANARLSASEVDVIEGHGTGTALGDPIEAQ
67 ALLATYGQDRERPLLLGSVKSNIGHTQMASGVAGVIKVVQALRHGLVPKTLHVDEPSTH
68 VDWSTGSIELPSGSVPWPESGRPRRAGISSFGLSGTNVHTILEQAPEPAAEAGPEPEPG
69 LVPVPLSGRTEAALRAQAATVLDTLDDGVSPAVLGYSLASTRSAFEHRAVLLAEDHDEL
70 RRGLAALAGDQPDGGVVRGTVTRGRTAFLFAGQGSQRAGMGRELYERHPVFADALDAVL
71 GHFDLPRALRDVMWDDDSTALDETGYTQPALFAFEVALFRLLESWGVTPDYLAGHSIGE
72 IAAAHVAGVLSLADACALVAARGALMQALPSGGAMVSVRGSEADVAGHLGEDVAVAAVN
73 GPESVVLAGTEDAVLQAAGRLEAAGHKVRRLRVSHAFHSPLMDPVLAEFATVAQGLTYH
74 "
75 aSDomain 183..713
76 /asDomain_id="nrpspksdomains_ctg1_1_KR1"
77 /database="nrpspksdomains.hmm"
78 /detection="hmmscan"
79 /domain="PKS_KR"
80 /evalue="1.40E-53"
81 /label="ctg1_1_KR1"
82 /locus_tag="ctg1_1"
83 /score="173.1"
84 /specificity="KR activity: active"
85 /specificity="KR stereochemistry: A2"
86 /translation="GTTLITGGTGTLAPHLARWLAEQGAEHIVLTSRTGAEAPKARQLL
87 AELGETVEAVACDVTDKAALAALLARLRAEGRTVRNVVHTAAVIELHTLAETDLAAFSR
88 TVHAKVVGARNLDELLDTDELDAFVLYSSTAGLWGTGAHAAYVAGNAYLHALAAHRRAR
89 GLRATALSWGIWAD"
90 CDS_motif 192..284
91 /aSTool="pksnrpsmotif"
92 /asDomain_id="nrpspksmotif_ctg1_1_0001"
93 /database="abmotifs"
94 /detection="hmmscan"
95 /evalue="3.80E-15"
96 /label="PKSI-KR_m1"
97 /locus_tag="ctg1_1"
98 /motif="PKSI-KR_m1"
99 /note="NRPS/PKS Motif: PKSI-KR_m1 (e-value: 3.8e-15,
100 bit-score: 48.4)"
101 /score="48.4"
102 /translation="LITGGTGTLAPHLARWLAEQGAEHIVLTSRT"
103 CDS_motif 555..665
104 /aSTool="pksnrpsmotif"
105 /asDomain_id="nrpspksmotif_ctg1_1_0002"
106 /database="abmotifs"
107 /detection="hmmscan"
108 /evalue="1.60E-14"
109 /label="PKSI-KR_m4"
110 /locus_tag="ctg1_1"
111 /motif="PKSI-KR_m4"
112 /note="NRPS/PKS Motif: PKSI-KR_m4 (e-value: 1.6e-14,
113 bit-score: 46.4)"
114 /score="46.4"
115 /translation="LDAFVLYSSTAGLWGTGAHAAYVAGNAYLHALAAHRR"
116 aSDomain 1026..1238
117 /asDomain_id="nrpspksdomains_ctg1_1_Xdom01"
118 /database="nrpspksdomains.hmm"
119 /detection="hmmscan"
120 /domain="ACP"
121 /evalue="7.80E-31"
122 /locus_tag="ctg1_1"
123 /score="97.8"
124 /translation="LELVRAEAAAVLGHASADALPEDRAFRDVGFDSVTAVDLRNRISA
125 GTGLTLPATMVFDHPTPRRLAGFLAA"
126 aSDomain 1305..2576
127 /asDomain_id="nrpspksdomains_ctg1_1_Xdom02"
128 /database="nrpspksdomains.hmm"
129 /detection="hmmscan"
130 /domain="PKS_KS"
131 /evalue="3.00E-179"
132 /locus_tag="ctg1_1"
133 /score="587.9"
134 /translation="VAIIGMACRYPGGANTPERLWDLVVGGVDAISGFPADRNWPTDAL
135 YDPDPDAGGKTYSVQGGFLHEAAEFDPGFFGISPREALSMDPQQRLLLETAWEAFERAG
136 IDPHTLRGSGTGTFIGASYQDYTAAVSGAVDNADGHMITGSLGSILSGRLSYLFGLEGP
137 AVTLDTACSSSLVAIHLAAQSLRSGESSLALAGGVSVMATPGAFVGFSRQRALATDGRC
138 KAYSDRADGMTLGEGVGLVLLEKLSDAQRNGHRILAVVRGSATNQDGASNGMTAPSGPS
139 QQRVIRQALANARLSASEVDVIEGHGTGTALGDPIEAQALLATYGQDRERPLLLGSVKS
140 NIGHTQMASGVAGVIKVVQALRHGLVPKTLHVDEPSTHVDWSTGSIELPSGSVPWPESG
141 RPRRAGISSFGLSGTNVHTILEQAP"
142 CDS_motif 1788..1835
143 /aSTool="pksnrpsmotif"
144 /asDomain_id="nrpspksmotif_ctg1_1_0003"
145 /database="abmotifs"
146 /detection="hmmscan"
147 /evalue="2.00E-06"
148 /label="PKSI-KS_m3"
149 /locus_tag="ctg1_1"
150 /motif="PKSI-KS_m3"
151 /note="NRPS/PKS Motif: PKSI-KS_m3 (e-value: 2e-06,
152 bit-score: 19.7)"
153 /score="19.7"
154 /translation="GPAVTLDTACSSSLVA"
155 CDS_motif 2211..2255
156 /aSTool="pksnrpsmotif"
157 /asDomain_id="nrpspksmotif_ctg1_1_0004"
158 /database="abmotifs"
159 /detection="hmmscan"
160 /evalue="1.90E-03"
161 /label="PKSI-KS_m5"
162 /locus_tag="ctg1_1"
163 /motif="PKSI-KS_m5"
164 /note="NRPS/PKS Motif: PKSI-KS_m5 (e-value: 0.0019,
165 bit-score: 10.8)"
166 /score="10.8"
167 /translation="IEGHGTGTALGDPIE"
168 CDS_motif 2310..2354
169 /aSTool="pksnrpsmotif"
170 /asDomain_id="nrpspksmotif_ctg1_1_0005"
171 /database="abmotifs"
172 /detection="hmmscan"
173 /evalue="1.10E-03"
174 /label="PKSI-KS_m6"
175 /locus_tag="ctg1_1"
176 /motif="PKSI-KS_m6"
177 /note="NRPS/PKS Motif: PKSI-KS_m6 (e-value: 0.0011,
178 bit-score: 11.5)"
179 /score="11.5"
180 /translation="GSVKSNIGHTQMASG"
181 CDS_motif 2874..2927
182 /aSTool="pksnrpsmotif"
183 /asDomain_id="nrpspksmotif_ctg1_1_0006"
184 /database="abmotifs"
185 /detection="hmmscan"
186 /evalue="2.30E-06"
187 /label="PKSI-AT-mM_m1"
188 /locus_tag="ctg1_1"
189 /motif="PKSI-AT-mM_m1"
190 /note="NRPS/PKS Motif: PKSI-AT-mM_m1 (e-value: 2.3e-06,
191 bit-score: 19.8)"
192 /score="19.8"
193 /translation="FLFAGQGSQRAGMGRELY"
194 aSDomain 2877..3500
195 /asDomain_id="nrpspksdomains_ctg1_1_AT1"
196 /database="nrpspksdomains.hmm"
197 /detection="hmmscan"
198 /domain="PKS_AT"
199 /evalue="4.00E-80"
200 /label="ctg1_1_AT1"
201 /locus_tag="ctg1_1"
202 /score="260.9"
203 /specificity="PKS signature: mal"
204 /specificity="Minowa: mal"
205 /specificity="consensus: mal"
206 /translation="LFAGQGSQRAGMGRELYERHPVFADALDAVLGHFDLPRALRDVMW
207 DDDSTALDETGYTQPALFAFEVALFRLLESWGVTPDYLAGHSIGEIAAAHVAGVLSLAD
208 ACALVAARGALMQALPSGGAMVSVRGSEADVAGHLGEDVAVAAVNGPESVVLAGTEDAV
209 LQAAGRLEAAGHKVRRLRVSHAFHSPLMDPVLAEFATVAQGLTYH"
210 CDS_motif 3033..3095
211 /aSTool="pksnrpsmotif"
212 /asDomain_id="nrpspksmotif_ctg1_1_0007"
213 /database="abmotifs"
214 /detection="hmmscan"
215 /evalue="3.20E-03"
216 /label="PKSI-AT-mM_m2"
217 /locus_tag="ctg1_1"
218 /motif="PKSI-AT-mM_m2"
219 /note="NRPS/PKS Motif: PKSI-AT-mM_m2 (e-value: 0.0032,
220 bit-score: 10.9)"
221 /score="10.9"
222 /translation="DETGYTQPALFAFEVALFRLL"
223 CDS_motif 3105..3227
224 /aSTool="pksnrpsmotif"
225 /asDomain_id="nrpspksmotif_ctg1_1_0008"
226 /database="abmotifs"
227 /detection="hmmscan"
228 /evalue="2.30E-22"
229 /label="PKSI-AT-M_m3"
230 /locus_tag="ctg1_1"
231 /motif="PKSI-AT-M_m3"
232 /note="NRPS/PKS Motif: PKSI-AT-M_m3 (e-value: 2.3e-22,
233 bit-score: 71.3)"
234 /score="71.3"
235 /translation="GVTPDYLAGHSIGEIAAAHVAGVLSLADACALVAARGALMQ"
236 CDS_motif 3312..3350
237 /aSTool="pksnrpsmotif"
238 /asDomain_id="nrpspksmotif_ctg1_1_0009"
239 /database="abmotifs"
240 /detection="hmmscan"
241 /evalue="4.70E-04"
242 /label="PKSI-AT-M_m5"
243 /locus_tag="ctg1_1"
244 /motif="PKSI-AT-M_m5"
245 /note="NRPS/PKS Motif: PKSI-AT-M_m5 (e-value: 0.00047,
246 bit-score: 13.4)"
247 /score="13.4"
248 /translation="AAVNGPESVVLAG"
249 ORIGIN 122 ORIGIN
250 1 ggggcggcgt gctcgccctg cccgccgagc tggaccgccg cggcggcgac cggctggcgg 123 1 ggggcggcgt gctcgccctg cccgccgagc tggaccgccg cggcggcgac cggctggcgg
251 61 ctgtgctgtc cggcgccacc ggcgaagacc agctggccat ccgcgccgcc ggcgtgttcg 124 61 ctgtgctgtc cggcgccacc ggcgaagacc agctggccat ccgcgccgcc ggcgtgttcg
252 121 gccgccgcgt ggtgcgggcc ccggccggcg accgcgcgcc ggcgcggacc tggaccccgc 125 121 gccgccgcgt ggtgcgggcc ccggccggcg accgcgcgcc ggcgcggacc tggaccccgc
253 181 gcggcaccac gctgatcacc ggcggcaccg gcaccctggc cccgcacctg gcccgctggc 126 181 gcggcaccac gctgatcacc ggcggcaccg gcaccctggc cccgcacctg gcccgctggc