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comparison test-data/ARBH01000003.1.final @ 1:593bb8f5488b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
author bgruening
date Wed, 07 Feb 2018 06:22:58 -0500
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0:5db064bbb3be 1:593bb8f5488b
1 LOCUS ARBH01000003 3500 bp DNA linear BCT 22-APR-2013
2 DEFINITION Amycolatopsis balhimycina FH 1894 strain DSM 44591
3 A3CEDRAFT_scaffold1.1_C3, whole genome shotgun sequence.
4 ACCESSION ARBH01000003
5 VERSION ARBH01000003.1
6 DBLINK BioProject:PRJNA165347
7 BioSample:SAMN02256403
8 KEYWORDS WGS; GSC:MIGS:2.1; IMPROVED_HIGH_QUALITY_DRAFT.
9 SOURCE Amycolatopsis balhimycina FH 1894
10 ORGANISM Amycolatopsis balhimycina FH 1894
11 Bacteria; Actinobacteria; Pseudonocardiales; Pseudonocardiaceae;
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 URL -- http://www.jgi.doe.gov
22 JGI Project ID: 404843
23 Source DNA and Organism available from Hans-Peter Klenk
24 (hpk@dsmz.de)
25 Source DNA available from Hans-Peter Klenk (hpk@dsmz.de)
26 Organism available from Hans-Peter Klenk (hpk@dsmz.de)
27 Contacts: Hans-Peter Klenk (hpk@dsmz.de)
28 Tanja Woyke (microbe@cuba.jgi-psf.org)
29 Whole genome sequencing and draft assembly at JGI-PGF
30 Annotation by JGI-ORNL
31 The JGI and collaborators endorse the principles for the
32 distribution and use of large scale sequencing data adopted by the
33 larger genome sequencing community and urge users of this data to
34 follow them. It is our intention to publish the work of this
35 project in a timely fashion and we welcome collaborative
36 interaction on the project and analysis.
37 (http://www.genome.gov/page.cfm?pageID=10506376)
38 Full annotations are available from IMG.
39 v. 4.24
40 Phrap v. 4.24
41 FEATURES Location/Qualifiers
42 source 1..3500
43 /culture_collection="DSM:44591"
44 /db_xref="taxon:1089545"
45 /mol_type="genomic DNA"
46 /organism="Amycolatopsis balhimycina FH 1894"
47 /strain="DSM 44591"
48 cluster 1..3500
49 /contig_edge="True"
50 /cutoff=20000
51 /extension=20000
52 /note="Cluster number: 1"
53 /note="Detection rule(s) for this cluster type: t1pks:
54 ((PKS_KS & PKS_AT) or (ene_KS & PKS_AT) or (mod_KS &
55 PKS_AT) or (hyb_KS & PKS_AT) or (itr_KS & PKS_AT) or
56 (tra_KS & PKS_AT));"
57 /note="Monomers prediction: (mal)"
58 /note="Structure image: structures/genecluster1.png"
59 /product="t1pks"
60 CDS 3..3500
61 /aSProdPred="mal"
62 /locus_tag="ctg1_1"
63 /note="smCOG:
64 SMCOG1001:short-chain_dehydrogenase/reductase_SDR (Score:
65 64.2; E-value: 2.2e-19);"
66 /sec_met="Type: t1pks"
67 /sec_met="Domains detected: PP-binding (E-value: 1.3e-15,
68 bitscore: 44.0, seeds: 164); PKS_AT (E-value: 8.7e-82,
69 bitscore: 260.9, seeds: 1682); mod_KS (E-value: 9.4e-224,
70 bitscore: 729.0, seeds: 217); adh_short (E-value: 7.1e-52,
71 bitscore: 162.1, seeds: 230)"
72 /sec_met="Kind: biosynthetic"
73 /sec_met="NRPS/PKS subtype: Type I Modular PKS"
74 /sec_met="NRPS/PKS Domain: PKS_KR (60-237). E-value:
75 1.4e-53. Score: 173.1; Predicted KR activity: active;
76 Predicted KR stereochemistry: A2;"
77 /sec_met="NRPS/PKS Domain: ACP (341-412). E-value: 7.8e-31.
78 Score: 97.8;"
79 /sec_met="NRPS/PKS Domain: PKS_KS (434-858). E-value:
80 3e-179. Score: 587.9;"
81 /sec_met="NRPS/PKS Domain: PKS_AT (958-1166). E-value:
82 4e-80. Score: 260.9; Substrate specificity predictions: mal
83 (PKS signature), mal (Minowa), mal (consensus);"
84 /translation="GGVLALPAELDRRGGDRLAAVLSGATGEDQLAIRAAGVFGRRVVR
85 APAGDRAPARTWTPRGTTLITGGTGTLAPHLARWLAEQGAEHIVLTSRTGAEAPKARQL
86 LAELGETVEAVACDVTDKAALAALLARLRAEGRTVRNVVHTAAVIELHTLAETDLAAFS
87 RTVHAKVVGARNLDELLDTDELDAFVLYSSTAGLWGTGAHAAYVAGNAYLHALAAHRRA
88 RGLRATALSWGIWADDRELGRVDPEQIVRSGLVFMAPELALEGLRRALDDDETALAVAD
89 LDWERYYPVYTAVRPTLLFDELPEVRRLTEAAAATAATGAGGEFAARLRTLPEAERAHL
90 LLELVRAEAAAVLGHASADALPEDRAFRDVGFDSVTAVDLRNRISAGTGLTLPATMVFD
91 HPTPRRLAGFLAATITGSGAVEQAPAVAGVDTGEPVAIIGMACRYPGGANTPERLWDLV
92 VGGVDAISGFPADRNWPTDALYDPDPDAGGKTYSVQGGFLHEAAEFDPGFFGISPREAL
93 SMDPQQRLLLETAWEAFERAGIDPHTLRGSGTGTFIGASYQDYTAAVSGAVDNADGHMI
94 TGSLGSILSGRLSYLFGLEGPAVTLDTACSSSLVAIHLAAQSLRSGESSLALAGGVSVM
95 ATPGAFVGFSRQRALATDGRCKAYSDRADGMTLGEGVGLVLLEKLSDAQRNGHRILAVV
96 RGSATNQDGASNGMTAPSGPSQQRVIRQALANARLSASEVDVIEGHGTGTALGDPIEAQ
97 ALLATYGQDRERPLLLGSVKSNIGHTQMASGVAGVIKVVQALRHGLVPKTLHVDEPSTH
98 VDWSTGSIELPSGSVPWPESGRPRRAGISSFGLSGTNVHTILEQAPEPAAEAGPEPEPG
99 LVPVPLSGRTEAALRAQAATVLDTLDDGVSPAVLGYSLASTRSAFEHRAVLLAEDHDEL
100 RRGLAALAGDQPDGGVVRGTVTRGRTAFLFAGQGSQRAGMGRELYERHPVFADALDAVL
101 GHFDLPRALRDVMWDDDSTALDETGYTQPALFAFEVALFRLLESWGVTPDYLAGHSIGE
102 IAAAHVAGVLSLADACALVAARGALMQALPSGGAMVSVRGSEADVAGHLGEDVAVAAVN
103 GPESVVLAGTEDAVLQAAGRLEAAGHKVRRLRVSHAFHSPLMDPVLAEFATVAQGLTYH
104 "
105 aSDomain 183..713
106 /asDomain_id="nrpspksdomains_ctg1_1_KR1"
107 /database="nrpspksdomains.hmm"
108 /detection="hmmscan"
109 /domain="PKS_KR"
110 /evalue="1.40E-53"
111 /label="ctg1_1_KR1"
112 /locus_tag="ctg1_1"
113 /score="173.1"
114 /specificity="KR activity: active"
115 /specificity="KR stereochemistry: A2"
116 /translation="GTTLITGGTGTLAPHLARWLAEQGAEHIVLTSRTGAEAPKARQLL
117 AELGETVEAVACDVTDKAALAALLARLRAEGRTVRNVVHTAAVIELHTLAETDLAAFSR
118 TVHAKVVGARNLDELLDTDELDAFVLYSSTAGLWGTGAHAAYVAGNAYLHALAAHRRAR
119 GLRATALSWGIWAD"
120 CDS_motif 192..284
121 /aSTool="pksnrpsmotif"
122 /asDomain_id="nrpspksmotif_ctg1_1_0001"
123 /database="abmotifs"
124 /detection="hmmscan"
125 /evalue="3.80E-15"
126 /label="PKSI-KR_m1"
127 /locus_tag="ctg1_1"
128 /motif="PKSI-KR_m1"
129 /note="NRPS/PKS Motif: PKSI-KR_m1 (e-value: 3.8e-15,
130 bit-score: 48.4)"
131 /score="48.4"
132 /translation="LITGGTGTLAPHLARWLAEQGAEHIVLTSRT"
133 CDS_motif 555..665
134 /aSTool="pksnrpsmotif"
135 /asDomain_id="nrpspksmotif_ctg1_1_0002"
136 /database="abmotifs"
137 /detection="hmmscan"
138 /evalue="1.60E-14"
139 /label="PKSI-KR_m4"
140 /locus_tag="ctg1_1"
141 /motif="PKSI-KR_m4"
142 /note="NRPS/PKS Motif: PKSI-KR_m4 (e-value: 1.6e-14,
143 bit-score: 46.4)"
144 /score="46.4"
145 /translation="LDAFVLYSSTAGLWGTGAHAAYVAGNAYLHALAAHRR"
146 aSDomain 1026..1238
147 /asDomain_id="nrpspksdomains_ctg1_1_Xdom01"
148 /database="nrpspksdomains.hmm"
149 /detection="hmmscan"
150 /domain="ACP"
151 /evalue="7.80E-31"
152 /locus_tag="ctg1_1"
153 /score="97.8"
154 /translation="LELVRAEAAAVLGHASADALPEDRAFRDVGFDSVTAVDLRNRISA
155 GTGLTLPATMVFDHPTPRRLAGFLAA"
156 aSDomain 1305..2576
157 /asDomain_id="nrpspksdomains_ctg1_1_Xdom02"
158 /database="nrpspksdomains.hmm"
159 /detection="hmmscan"
160 /domain="PKS_KS"
161 /evalue="3.00E-179"
162 /locus_tag="ctg1_1"
163 /score="587.9"
164 /translation="VAIIGMACRYPGGANTPERLWDLVVGGVDAISGFPADRNWPTDAL
165 YDPDPDAGGKTYSVQGGFLHEAAEFDPGFFGISPREALSMDPQQRLLLETAWEAFERAG
166 IDPHTLRGSGTGTFIGASYQDYTAAVSGAVDNADGHMITGSLGSILSGRLSYLFGLEGP
167 AVTLDTACSSSLVAIHLAAQSLRSGESSLALAGGVSVMATPGAFVGFSRQRALATDGRC
168 KAYSDRADGMTLGEGVGLVLLEKLSDAQRNGHRILAVVRGSATNQDGASNGMTAPSGPS
169 QQRVIRQALANARLSASEVDVIEGHGTGTALGDPIEAQALLATYGQDRERPLLLGSVKS
170 NIGHTQMASGVAGVIKVVQALRHGLVPKTLHVDEPSTHVDWSTGSIELPSGSVPWPESG
171 RPRRAGISSFGLSGTNVHTILEQAP"
172 CDS_motif 1788..1835
173 /aSTool="pksnrpsmotif"
174 /asDomain_id="nrpspksmotif_ctg1_1_0003"
175 /database="abmotifs"
176 /detection="hmmscan"
177 /evalue="2.00E-06"
178 /label="PKSI-KS_m3"
179 /locus_tag="ctg1_1"
180 /motif="PKSI-KS_m3"
181 /note="NRPS/PKS Motif: PKSI-KS_m3 (e-value: 2e-06,
182 bit-score: 19.7)"
183 /score="19.7"
184 /translation="GPAVTLDTACSSSLVA"
185 CDS_motif 2211..2255
186 /aSTool="pksnrpsmotif"
187 /asDomain_id="nrpspksmotif_ctg1_1_0004"
188 /database="abmotifs"
189 /detection="hmmscan"
190 /evalue="1.90E-03"
191 /label="PKSI-KS_m5"
192 /locus_tag="ctg1_1"
193 /motif="PKSI-KS_m5"
194 /note="NRPS/PKS Motif: PKSI-KS_m5 (e-value: 0.0019,
195 bit-score: 10.8)"
196 /score="10.8"
197 /translation="IEGHGTGTALGDPIE"
198 CDS_motif 2310..2354
199 /aSTool="pksnrpsmotif"
200 /asDomain_id="nrpspksmotif_ctg1_1_0005"
201 /database="abmotifs"
202 /detection="hmmscan"
203 /evalue="1.10E-03"
204 /label="PKSI-KS_m6"
205 /locus_tag="ctg1_1"
206 /motif="PKSI-KS_m6"
207 /note="NRPS/PKS Motif: PKSI-KS_m6 (e-value: 0.0011,
208 bit-score: 11.5)"
209 /score="11.5"
210 /translation="GSVKSNIGHTQMASG"
211 CDS_motif 2874..2927
212 /aSTool="pksnrpsmotif"
213 /asDomain_id="nrpspksmotif_ctg1_1_0006"
214 /database="abmotifs"
215 /detection="hmmscan"
216 /evalue="2.30E-06"
217 /label="PKSI-AT-mM_m1"
218 /locus_tag="ctg1_1"
219 /motif="PKSI-AT-mM_m1"
220 /note="NRPS/PKS Motif: PKSI-AT-mM_m1 (e-value: 2.3e-06,
221 bit-score: 19.8)"
222 /score="19.8"
223 /translation="FLFAGQGSQRAGMGRELY"
224 aSDomain 2877..3500
225 /asDomain_id="nrpspksdomains_ctg1_1_AT1"
226 /database="nrpspksdomains.hmm"
227 /detection="hmmscan"
228 /domain="PKS_AT"
229 /evalue="4.00E-80"
230 /label="ctg1_1_AT1"
231 /locus_tag="ctg1_1"
232 /score="260.9"
233 /specificity="PKS signature: mal"
234 /specificity="Minowa: mal"
235 /specificity="consensus: mal"
236 /translation="LFAGQGSQRAGMGRELYERHPVFADALDAVLGHFDLPRALRDVMW
237 DDDSTALDETGYTQPALFAFEVALFRLLESWGVTPDYLAGHSIGEIAAAHVAGVLSLAD
238 ACALVAARGALMQALPSGGAMVSVRGSEADVAGHLGEDVAVAAVNGPESVVLAGTEDAV
239 LQAAGRLEAAGHKVRRLRVSHAFHSPLMDPVLAEFATVAQGLTYH"
240 CDS_motif 3033..3095
241 /aSTool="pksnrpsmotif"
242 /asDomain_id="nrpspksmotif_ctg1_1_0007"
243 /database="abmotifs"
244 /detection="hmmscan"
245 /evalue="3.20E-03"
246 /label="PKSI-AT-mM_m2"
247 /locus_tag="ctg1_1"
248 /motif="PKSI-AT-mM_m2"
249 /note="NRPS/PKS Motif: PKSI-AT-mM_m2 (e-value: 0.0032,
250 bit-score: 10.9)"
251 /score="10.9"
252 /translation="DETGYTQPALFAFEVALFRLL"
253 CDS_motif 3105..3227
254 /aSTool="pksnrpsmotif"
255 /asDomain_id="nrpspksmotif_ctg1_1_0008"
256 /database="abmotifs"
257 /detection="hmmscan"
258 /evalue="2.30E-22"
259 /label="PKSI-AT-M_m3"
260 /locus_tag="ctg1_1"
261 /motif="PKSI-AT-M_m3"
262 /note="NRPS/PKS Motif: PKSI-AT-M_m3 (e-value: 2.3e-22,
263 bit-score: 71.3)"
264 /score="71.3"
265 /translation="GVTPDYLAGHSIGEIAAAHVAGVLSLADACALVAARGALMQ"
266 CDS_motif 3312..3350
267 /aSTool="pksnrpsmotif"
268 /asDomain_id="nrpspksmotif_ctg1_1_0009"
269 /database="abmotifs"
270 /detection="hmmscan"
271 /evalue="4.70E-04"
272 /label="PKSI-AT-M_m5"
273 /locus_tag="ctg1_1"
274 /motif="PKSI-AT-M_m5"
275 /note="NRPS/PKS Motif: PKSI-AT-M_m5 (e-value: 0.00047,
276 bit-score: 13.4)"
277 /score="13.4"
278 /translation="AAVNGPESVVLAG"
279 ORIGIN
280 1 ggggcggcgt gctcgccctg cccgccgagc tggaccgccg cggcggcgac cggctggcgg
281 61 ctgtgctgtc cggcgccacc ggcgaagacc agctggccat ccgcgccgcc ggcgtgttcg
282 121 gccgccgcgt ggtgcgggcc ccggccggcg accgcgcgcc ggcgcggacc tggaccccgc
283 181 gcggcaccac gctgatcacc ggcggcaccg gcaccctggc cccgcacctg gcccgctggc
284 241 tggccgagca gggcgccgag cacatcgtgc tgaccagccg caccggcgcc gaggccccga
285 301 aggcccggca gctgctggcg gagctgggcg agaccgtcga ggcggtggcc tgcgacgtca
286 361 ccgacaaggc ggcgctggcc gccctgctgg cgcggttgcg ggccgagggc cggaccgtgc
287 421 ggaacgtggt gcacacggcc gccgtgatcg agctgcacac gctggccgag accgacctgg
288 481 ccgcgttctc ccggaccgtg cacgccaagg tggtgggcgc gcgcaacctg gacgagctgc
289 541 tcgacaccga cgagctcgat gcgttcgtgc tgtactcctc caccgccggc ctgtggggca
290 601 ccggcgcgca cgccgcctac gtggccggca acgcgtactt gcacgcgctg gcagcccacc
291 661 ggcgcgcccg ggggctgcgg gccaccgcgc tgtcgtgggg catctgggcc gacgaccgcg
292 721 aactcggccg ggtcgacccg gagcagatcg tgcgcagcgg cctggtgttc atggcgccgg
293 781 agctggcgct ggagggtctg cgccgggccc tggacgacga cgagaccgcg ctggccgtgg
294 841 ccgatctgga ctgggagcgg tactacccgg tctacaccgc cgtccggccg acgctgctgt
295 901 tcgacgagct gccggaggtg cggcggctca ccgaggccgc cgccgccacg gccgccaccg
296 961 gcgccggcgg cgagttcgcc gcccggctgc gcacgctgcc cgaggccgag cgcgcccacc
297 1021 tgctcctgga actggtccgg gccgaggccg cggccgtgct gggccacgcg tcggccgacg
298 1081 cgctgcccga ggaccgcgcc ttccgcgacg tcggcttcga ctcggtcacc gcggtcgacc
299 1141 tgcgcaaccg gatctccgcc ggcaccggcc tgaccctgcc cgccaccatg gtgttcgacc
300 1201 acccgacgcc gaggcggctg gccgggttcc tggccgccac gatcaccggc tcgggtgccg
301 1261 tcgagcaggc accggccgtg gccggcgtgg acaccggcga gcccgtcgcc atcatcggga
302 1321 tggcctgccg ctacccgggt ggcgcgaaca ccccggaacg gttgtgggac ctggtcgtgg
303 1381 gcggcgtgga cgccatctcc ggcttcccgg ccgaccgcaa ctggccgacc gacgcgctct
304 1441 acgacccgga cccggacgcc ggcggcaaga cctattcggt gcagggcggc ttcctgcacg
305 1501 aggcggccga gttcgacccg ggcttcttcg gcatctcgcc gcgggaggca ctgtccatgg
306 1561 atccgcagca gcgcctgctg ctggagacgg cgtgggaggc gttcgagcgg gccgggatcg
307 1621 acccgcacac gctgcggggc agcggcaccg gcaccttcat cggggccagc taccaggact
308 1681 acaccgcggc cgtgtccggc gcggtggaca acgccgacgg ccacatgatc accggctcgc
309 1741 tgggcagcat cctgtccggc cggctctcct acctgttcgg gctggagggc ccggcggtca
310 1801 ccctggacac cgcctgctcg tcgtcgctgg tcgccatcca cctggccgcg cagtcgctgc
311 1861 ggtcggggga gagcagcctg gcgctggccg gcggggtgag cgtgatggcg acgccggggg
312 1921 cgttcgtcgg cttctcgcgc cagcgcgcac tggccacgga cggccgttgc aaggcctact
313 1981 cggaccgggc cgacggcatg accctcggcg agggcgtcgg cctggtgctg ctggagaagc
314 2041 tgtccgacgc gcagcgcaac gggcaccgga tcctggcggt ggtccggggt tcggccacga
315 2101 accaggacgg cgcgtccaac ggcatgaccg cgcccagcgg cccgtcccag cagcgggtga
316 2161 tccggcaggc gctggccaac gcgcggctct cggcgtccga ggtggacgtg atcgagggcc
317 2221 acggcaccgg caccgcgctg ggcgacccga tcgaggccca ggccctgctg gccacctacg
318 2281 gccaggaccg ggaacggccg ctgctgctcg gctcggtgaa gtccaacatc ggccacaccc
319 2341 agatggcctc cggcgtggcc ggcgtgatca aggtggtgca ggcgctgcgg cacgggctgg
320 2401 tacccaagac gctgcacgtg gacgagccct ccacgcacgt cgactggagc accggctcga
321 2461 tcgagctgcc gtccggcagc gtgccgtggc cggagagcgg ccggccgcgc cgggccggta
322 2521 tctcgtcctt cgggctgagc ggcacgaacg tgcacaccat cctcgagcag gccccggaac
323 2581 cggccgccga agccggcccc gagccggagc ccggcctggt gccggtcccg ctgtccggcc
324 2641 ggacggaagc agcgctgcgc gctcaggccg ccaccgtgct ggacaccctg gacgacggcg
325 2701 tgtcgccggc cgtgctcggg tactcgctgg cctccacccg gtcggccttc gaacaccgtg
326 2761 cggtgctgct ggccgaggac cacgacgaac tgcggcgcgg cctggccgca ctggccggcg
327 2821 accagccgga cggcggcgtg gtgcggggca ccgtgacgcg gggccgcacg gcgttcctgt
328 2881 tcgccggcca gggcagccag cgggccggga tgggccgcga gctgtacgag cgccacccgg
329 2941 tgttcgccga cgcgctggac gcggtgctgg ggcacttcga cctgccccgt gcgctgcggg
330 3001 acgtgatgtg ggacgacgat tccacggccc tcgacgagac ggggtacacc cagccggcgt
331 3061 tgttcgcctt cgaggtggcg ttgttccggt tgctggagtc gtggggtgtg acgccggatt
332 3121 acctggccgg gcattcgatc ggtgagatcg ccgcggcgca cgtggccgga gtgttgtcgc
333 3181 tggccgatgc ctgtgcgttg gtcgctgcgc ggggtgcgct gatgcaggcg ctgccgtccg
334 3241 gcggggccat ggtttcggtg cgcggctccg aggccgacgt cgccgggcac ctcggcgagg
335 3301 acgtcgccgt cgcggcggtc aacgggcccg agtcggtggt gctggccggg accgaggacg
336 3361 cggtgctcca ggcggccggc cgcctggagg ccgccggcca caaggtccgc cgcctgcggg
337 3421 tcagccacgc cttccactcg cccttgatgg atcccgtgct ggccgagttc gcgacggtgg
338 3481 ctcagggcct gacctaccac
339 //