Mercurial > repos > public-health-bioinformatics > match_plasmid_to_reference

comparison test-data/outdir/reference_plasmid.gbk @ 0:c917ef6807d7 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
author public-health-bioinformatics
date Tue, 12 Nov 2019 22:47:36 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:c917ef6807d7
1 LOCUS JQ739157 6544 bp DNA circular BCT 26-JUL-2016
2 DEFINITION Acinetobacter pittii strain ABCA95 plasmid pABCA95, complete
3 sequence.
4 ACCESSION JQ739157
5 VERSION JQ739157.2
6 KEYWORDS .
7 SOURCE Acinetobacter pittii
8 ORGANISM Acinetobacter pittii
9 Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
10 Moraxellaceae; Acinetobacter; Acinetobacter calcoaceticus/baumannii
11 complex.
12 REFERENCE 1 (bases 1 to 6544)
13 AUTHORS Fu,Y., Du,X., Ji,J., Chen,Y., Jiang,Y. and Yu,Y.
14 TITLE Epidemiological characteristics and genetic structure of blaNDM-1
15 in non-baumannii Acinetobacter spp. in China
16 JOURNAL J. Antimicrob. Chemother. 67 (9), 2114-2122 (2012)
17 PUBMED 22604448
18 REFERENCE 2 (bases 1 to 6544)
19 AUTHORS Fu,Y., Du,X., Ji,J., Chen,Y., Jiang,Y. and Yu,Y.
20 TITLE Direct Submission
21 JOURNAL Submitted (05-MAR-2012) Department of Infectious Diseases, Sir Run
22 Run Shaw Hospital, Affiliated with School of Medicine, Zhejiang
23 University, 3 East Qingchun Road, Hangzhou, Zhejiang 310016, China
24 REFERENCE 3 (bases 1 to 6544)
25 AUTHORS Fu,Y., Du,X., Ji,J., Chen,Y., Jiang,Y. and Yu,Y.
26 TITLE Direct Submission
27 JOURNAL Submitted (12-MAY-2014) Department of Infectious Diseases, Sir Run
28 Run Shaw Hospital, Affiliated with School of Medicine, Zhejiang
29 University, 3 East Qingchun Road, Hangzhou, Zhejiang 310016, China
30 REMARK Sequence update by submitter
31 COMMENT On May 12, 2014 this sequence version replaced JQ739157.1.
32 FEATURES Location/Qualifiers
33 source 1..6544
34 /organism="Acinetobacter pittii"
35 /mol_type="genomic DNA"
36 /strain="ABCA95"
37 /db_xref="taxon:48296"
38 /plasmid="pABCA95"
39 gene 375..1031
40 /gene="aphA6"
41 misc_feature 375..1031
42 /gene="aphA6"
43 /note="similar to aphA6; aminoglycoside
44 3'-phosphotransferase; 5' end of gene is missing"
45 mobile_element 1129..2215
46 /mobile_element_type="insertion sequence:ISAba125"
47 repeat_region 1138..1154
48 /note="IRL"
49 /rpt_type=inverted
50 CDS 1186..2211
51 /codon_start=1
52 /transl_table=11
53 /product="Transposase"
54 /protein_id="AFK73837.1"
55 /translation="MEYIKLSYHHLNFEDRTALMLESRKEGFSARKFAELIKRHPSTI
56 YRELKRNSINDVYQARYASDNTFARRRRGHRKLKIDSILWKFIVEAIRCLWSPQQIAK
57 RLKTFPDLDQTMNVSHTTIYSTIRALPKGELKKDLLSCLRHENKKRKANGEPKKDSIL
58 QDIKTIHERPAEVQERKIPGHWEADLIKGKDNKSSIATLIERNTRLCILATLPDAKAE
59 SVRKALTEALKYLPAELRKTLTYDRGREMSEHKILEEDLGIDVYFCDPHSPWQKGTCE
60 NMNGLIRQYLPKGIDLNQADQHYLNQVAMSLNTRPRKALDWLTPLEKFAQLVDYHMAF
61 ETVAPHV"
62 repeat_region 2190..2206
63 /note="IRL"
64 /rpt_type=inverted
65 gene 2312..3124
66 /gene="blaNDM-1"
67 CDS 2312..3124
68 /gene="blaNDM-1"
69 /codon_start=1
70 /transl_table=11
71 /product="metallo-beta-lactamase"
72 /protein_id="AFK73838.1"
73 /translation="MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQ
74 RFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQIL
75 NWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHS
76 LTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSL
77 GNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"
78 gene 3128..3493
79 /gene="bleo"
80 CDS 3128..3493
81 /gene="bleo"
82 /note="involved in resistance to bleomycin"
83 /codon_start=1
84 /transl_table=11
85 /product="bleomycin resistance protein"
86 /protein_id="AFK73839.1"
87 /translation="MADHVTPNLPSRDFDVTEAFYAKLGFATSWKDRGWMILQRGGLQ
88 LEFFPYPDLDPATSSFGCCLRLDDLDAMVALVNAAGAEEKSTGWPRFKAPQLEASGLR
89 IGYLIDPDCTLVRLIQNPD"
90 gene 3498..4133
91 /gene="trpF"
92 misc_feature 3498..4133
93 /gene="trpF"
94 /note="similar to TrpF; phosphoribosyl anthranilate
95 isomerase; 3' end not present"
96 gene complement(4150..4830)
97 /gene="tat"
98 misc_feature complement(4150..4830)
99 /gene="tat"
100 /note="similar to TAT; twin-arginine translocation pathway
101 signal sequence protein; 5' end of gene is missing."
102 ORIGIN
103 1 aagcttatag cagtgtcaca gatgcgaaaa agcaattaag tgcatatttt gagttttata
104 61 atttgaaacg acctcattcg agtctagaca aaatgacacc aaatgagttt tactatgatc
105 121 agctacccca acaaaacaag gtggcttaac tagagcggaa tatcacttat aaatacgctt
106 181 ttagttgttc aaacaagtgg gaccacctct ctcgcatttg cggggttttt aatgctgaat
107 241 aaaaggaaaa cttgatggaa ttgcccaata ttattcaaca atttattgga aacagcgttt
108 301 tagagccaaa taaaattggt cagtcgccat cggatgttta ttcttttaat cgaaataatg
109 361 aaactttttt tcttaagcga tctagcactt tatatacaga gaccacatac agtgtctctc
110 421 gcgaagcgaa aatgttgagt tggctctctg agaaattaaa ggtgcctgaa ctcatcatga
111 481 cttttcagga tgagcagttt gaattaatga tcactaaagc gatcaatgca aaaccaattt
112 541 cagcgctttt tttaacagac caagaattgc ttgctatcta taaggaggca ctcaatctgt
113 601 taaattcagt tgctattatt gattgtccat ttatttcaaa cattgatcat cggttaaaag
114 661 agtcaaaatt ttttattgat aaccaactcc ttgacgatat agatcaagat gattttgacg
115 721 ctgaattatg gggagaccat agaacttacc taagtctatg gaatgagtta actgagactc
116 781 gtgttgaaga aagattggtt ttttctcatg gcgatatcac ggatagtaat atttttatag
117 841 ataaattcaa tgaaatttac tttttagatc ttggccgtgc tgggttagct gatgaatttg
118 901 tagatatatc ctttgttgaa cgttgcctaa gagaggatgc ctcggaggaa actgctaaaa
119 961 tatttttaaa gcatttaaaa aatgatagac ctgacaaaag gaattatttt ttaaaacttg
120 1021 atgaattgaa ttgattctaa gcattatcta aaaatactta attgtctttt aacgtcgcta
121 1081 aattttaaat aaataagtga agagtgttag tggagccact gatttaaagt tggcagagta
122 1141 aaacttgaag tgcgacataa accacctaat taatttaaag ggtttatgga gtatataaaa
123 1201 ttgtcatacc atcatcttaa ctttgaagat cgtactgcat taatgcttga gtcaagaaaa
124 1261 gaaggctttt cagccagaaa atttgctgaa ctcattaaaa gacatcctag tacgatctat
125 1321 cgtgagctta aaagaaatag catcaatgac gtttatcaag ctcgatatgc ttctgataac
126 1381 accttcgcta gacgtagacg tggtcacaga aaactcaaaa tcgattcaat cctctggaaa
127 1441 tttattgttg aagcgatccg ttgtttatgg tctcctcagc aaatagcaaa gcgtttaaag
128 1501 acatttcctg atttggatca aacaatgaat gtaagccata caacgattta ttcaacgata
129 1561 cgagcattac caaagggtga gttgaaaaaa gacttattat cctgtctacg tcatgaaaat
130 1621 aaaaagcgaa aagctaacgg tgaacctaaa aaagattcta tattacagga tattaaaact
131 1681 attcatgagc gcccagccga agttcaagaa agaaaaatac cgggtcattg ggaagctgat
132 1741 ttaattaaag gtaaagacaa taaaagttcg atagcaacac ttattgaacg aaatacacgg
133 1801 ctctgtatct tggcaacatt acctgatgca aaggcagaat cagtgcgcaa ggctttaact
134 1861 gaagctctga aatatttacc tgcagaactg cgtaaaacgt tgacctatga ccgtggacgt
135 1921 gagatgtcag aacataaaat actcgaagaa gatttaggca tagatgtata tttctgtgac
136 1981 ccacattcac cctggcaaaa aggcacatgc gaaaatatga atggtttaat taggcaatat
137 2041 ttacctaaag ggattgattt aaatcaggca gatcagcatt atttaaatca agttgccatg
138 2101 tcactgaata ctcgtcctag aaaggcgtta gattggctta caccattaga gaaatttgct
139 2161 cagcttgttg attatcatat ggcttttgaa actgtcgcac ctcatgtttg aattcgcccc
140 2221 atatttttgc tacagtgaac caaattaaga tcatctattt actaggcctc gcatttgcgg
141 2281 ggtttttaat gctgaataaa aggaaaactt gatggaattg cccaatatta tgcacccggt
142 2341 cgcgaagctg agcaccgcat tagccgctgc attgatgctg agcgggtgca tgcccggtga
143 2401 aatccgcccg acgattggcc agcaaatgga aactggcgac caacggtttg gcgatctggt
144 2461 tttccgccag ctcgcaccga atgtctggca gcacacttcc tatctcgaca tgccgggttt
145 2521 cggggcagtc gcttccaacg gtttgatcgt cagggatggc ggccgcgtgc tggtggtcga
146 2581 taccgcctgg accgatgacc agaccgccca gatcctcaac tggatcaagc aggagatcaa
147 2641 cctgccggtc gcgctggcgg tggtgactca cgcgcatcag gacaagatgg gcggtatgga
148 2701 cgcgctgcat gcggcgggga ttgcgactta tgccaatgcg ttgtcgaacc agcttgcccc
149 2761 gcaagagggg atggttgcgg cgcaacacag cctgactttc gccgccaatg gctgggtcga
150 2821 accagcaacc gcgcccaact ttggcccgct caaggtattt taccccggcc ccggccacac
151 2881 cagtgacaat atcaccgttg ggatcgacgg caccgacatc gcttttggtg gctgcctgat
152 2941 caaggacagc aaggccaagt cgctcggcaa tctcggtgat gccgacactg agcactacgc
153 3001 cgcgtcagcg cgcgcgtttg gtgcggcgtt ccccaaggcc agcatgatcg tgatgagcca
154 3061 ttccgccccc gatagccgcg ccgcaatcac tcatacggcc cgcatggccg acaagctgcg
155 3121 ctgagccatg gctgaccacg tcacccccaa tctgccatcg cgcgatttcg atgtgacaga
156 3181 ggcgttttat gcgaagctgg gctttgcgac gagttggaag gatcgcggct ggatgatcct
157 3241 gcagcgcggc ggtttgcagc tcgaattctt cccctatcct gacctcgacc cagctacgag
158 3301 ctcgttcggc tgttgcctgc ggttggatga tctcgatgcc atggtggcat tggtgaacgc
159 3361 ggcgggagcc gaggaaaaaa gcaccggctg gccgcgcttc aaagctccgc aactggaggc
160 3421 gagcggcctg aggatcggct acctgatcga tcccgactgc acgctggtgc ggctgatcca
161 3481 gaaccccgac tgaccgcatg cccgcgaaaa tcaagatttg cgggatcagc acacccgagg
162 3541 cgctcgatgc gaccatcgcg gcgcgggcgg actatgccgg gttggtgttc tatccagcgt
163 3601 cgccccgtgc ggttacgtcg aatgtcgcgg gcgctttgac atcgcgcgca gctggccaga
164 3661 tcgccatggt cggtttgttc gtcgatgcgg atgatgctgt catcgccgac gcactggtgg
165 3721 cagccaagct gaacgcgctg cagctgcacg gttcggaatc gcccgaacgc gtggcccagt
166 3781 tgcgcgcgcg gtttggcaag ccggtgtgga aggcgctgcc cgtcgccagc gccagcgatg
167 3841 tcgcacgcgc cgcagcctat gccggggcgg cggacttgat cttgttcgac gccaagaccc
168 3901 ccaaaggcgc gctgcccggc ggcatggggt tggcgttcga ctggtcgctg ctggccggat
169 3961 atcgcggtgc cttgccgtgg gggctggcag gcgggctaaa tccgacgaat gttgccgagg
170 4021 cgattgcgcg caccggagcg ccgctggtcg atacctccag cggcgtcgaa agcgcgccgg
171 4081 gcgtcaagga taccgacaag attaccaatt tcgcctttgc ggtgcgcttg gcctaaatcg
172 4141 cgtcgatcaa taggcgtcgt tcagcgcaaa gatcggcttg cgggtgcgcc actgccctcg
173 4201 ggtgaagtcg ggaaaatcta acgtgcgatt gccctcagca atcgattgtt ccgacagagg
174 4261 cgtgatcgcg ctccaggcca gcgcgtcgta aatgtcgatt ggcatcgggg ccttggcctt
175 4321 cagcgcctcg acaaaagcgt ggatcacgaa ccagtccatc ccgccatgcc cggcccctgc
176 4381 cgccagatcg gcgtagcgtt tccatagcgg gtgatcgtat ttcgcaaacc agccctcggc
177 4441 aggctcccag cggtgcggct gtgggctctt gccctccaga tagatcgact tgttgacgtc
178 4501 catccacagc ccctcggtgc cttgcacccg aaagccgaga gaataggggc gcggcagcga
179 4561 ggtgtcgtgg cacagcatga tcgtttcacc attagtgcag ccgatcatgg tgttgaccac
180 4621 atcacccagt gcgaatttca cctcggcgtt gggatgatcg gcagagccgt tcttgacgac
181 4681 ataatcatgc agcccgcgcg ccttacagcc gaagccgcca gcgcccgctt cgcccggcaa
182 4741 cgcgaccttc agggtgcggg tctgcggcgg gtagcacacg ccggcatcgg cgcagccctg
183 4801 gtacttcacg gtcagggtgg tcgcgctcgc gccggccgcg ggcgtgccgg tgagggtgcc
184 4861 gagcaattcc ttgcggtagg tttcgacgtc gccgaagaat tcgtcgcggt aggccttgcc
185 4921 cttcggcagc gccatggtcg cgccggtgaa ggcggcatcg gccttgaccg aggtgcggtg
186 4981 ccggtacagg taatagccgt cggcgatccg ccagcgcacc tcgatgcggt ccggcgcggt
187 5041 ggcctgcgcg gacaggacga agacctcgtc gaccggcggc agttcgaagt cctgggcgac
188 5101 ggccgaggtc gcgggcagcg caagcagcag ggcgagcccg gccagccagc ggcgcaggcg
189 5161 gatcgtggat gcggtcattg gctcagttta ccggtcggct ctcggcggcc agccattgca
190 5221 ggtattcggg caggccggac gcggcttcga ccgcgagcag ctccgggagt tcgtagggat
191 5281 atagtatttt attaaattct tatgggaaat gacgaatgtt aaattatctt aagagcttta
192 5341 ataatatcaa tacttatttg attttatcga taattctgct gttaatcata atatctctag
193 5401 attatttcta aactgaatga atgtttataa tgagtgattc atattgctat tgaaatcgcc
194 5461 ttctcacttt gaaagaaggc gaggatgagg gacttttatg ttgaattatc attttaaaaa
195 5521 tgccttataa aagaagctta atgtgttttc ttatataggt ttaaacataa ttgttgtata
196 5581 tcttaaatcc aattgatctt aaaattttcc tttatttttt gttatgagtg cgagaaaatt
197 5641 gtcaaaaagg tcaatcagac tgggcgttaa tttgttttgc atactttttc ctatatcgaa
198 5701 ttaaagtcat ataactaaca ccataatctt tagctatttg agtgaaaggg tatgaatcgt
199 5761 ccttattttt aagggtatga attaactctt ttagtttttc ttctgtaatc gcaggcgatc
200 5821 ttcccttgta tttacctttc ttttttttag ctaatttaat tccctctgct tgattctcac
201 5881 taataatacc cctttcaagt tcagctacag cgcctaatac atggagttga aacttatcga
202 5941 acttgtcatc tgaattgggg gtaaagttca ggttattttt gacaatatga acagacactc
203 6001 cttttttatt tagcttttga acaatggtta caaggtcaat caagctacgt gccaatctaa
204 6061 aaacatcatg agcgtacaca atgtccccac tacggacata atcgaacatt tcctgaagtg
205 6121 cagggcgttt ggcagtcttt ccgctaaaat gatcaataaa agttttatct agctcaaagg
206 6181 gtagatcatg gagctgtctt tcagggtttt ggtctttagt ggatacacgg atatacccca
207 6241 ctctttgaaa gggtgtgttt ttaatttgat cttcaatatc taaattttct ttttccataa
208 6301 ccagtataac aaaattagat aacctcaatg ttatatcaca ttagattaac aaaacaaccc
209 6361 tattgttata gggtttttag ggtgtattat tatataacaa tagggtatac cctattgtta
210 6421 tatatcttca ggtataagga aaaataacga tgattaattt taatgatcta agcgaatctg
211 6481 aattattaag gattgcacag actggcatat caaaccgtat aggattgcgt acttcaggac
212 6541 attg
213 //
214