LOCUS       CP071275                6343 bp    DNA     circular BCT 08-MAR-2021
DEFINITION  Enterococcus faecium strain AUSMDU00011555 plasmid
            pAUSMDU00011555_04, complete sequence.
ACCESSION   CP071275
VERSION     CP071275.1
DBLINK      BioProject: PRJNA565795
            BioSample: SAMN18082828
KEYWORDS    .
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 6343)
  AUTHORS   Gorrie,C.L., Goncalves da Silva,A., Ingle,D.J., Higgs,C.,
            Seemann,T., Stinear,T.P., Williamson,D.A., Kwong,J.C., Graham,M.L.,
            Sherry,N.L. and Howden,B.P.
  TITLE     Key parameters for genomics-based real-time detection and tracking
            of multidrug-resistant bacteria: a systematic analysis
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6343)
  AUTHORS   Gorrie,C.L., Goncalves da Silva,A., Ingle,D.J., Higgs,C.,
            Seemann,T., Stinear,T.P., Williamson,D.A., Kwong,J.C., Graham,M.L.,
            Sherry,N.L. and Howden,B.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-MAR-2021) University of Melbourne, Microbiological
            Diagnostics Unit, First Floor, Building 248, Parkville, Victoria
            3010, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 19-JUL-2019
            Assembly Method                   :: Unicycler v. 0.4.8beta
            Assembly Name                     :: UOM_Efaec_1.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 74.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 03/02/2021 15:37:01
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 5.1
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 3,207
            CDSs (total)                      :: 3,116
            Genes (coding)                    :: 2,827
            CDSs (with protein)               :: 2,827
            Genes (RNA)                       :: 91
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 69
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 289
            CDSs (without protein)            :: 289
            Pseudo Genes (ambiguous residues) :: 0 of 289
            Pseudo Genes (frameshifted)       :: 205 of 289
            Pseudo Genes (incomplete)         :: 78 of 289
            Pseudo Genes (internal stop)      :: 31 of 289
            Pseudo Genes (multiple problems)  :: 24 of 289
            ##Genome-Annotation-Data-END##
            Bacteria and source DNA available from MDUPHL, 792 Elizabeth
            Street, Melbourne, 3000, Victoria, Australia.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
FEATURES             Location/Qualifiers
     source          1..6343
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="AUSMDU00011555"
                     /isolation_source="Rectal Swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pAUSMDU00011555_04"
                     /geo_loc_name="Australia"
                     /collection_date="2017"
     gene            join(5814..6343,1..25)
                     /locus_tag="J0K77_15995"
                     /pseudo=""
     CDS             join(5814..6343,1..25)
                     /locus_tag="J0K77_15995"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002334266.1"
                     /note="frameshifted; internal stop; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            43..240
                     /locus_tag="J0K77_16000"
     CDS             43..240
                     /locus_tag="J0K77_16000"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QSQ01568.1"
                     /translation="MISKSLKSLKTFTKKNPQIATIRIFIFAIAVAIIVNMLSGGQLYK
                     SGLFLVLILVVLDIIKSKKK"
                     /name="hypothetical protein"
     gene            564..944
                     /locus_tag="J0K77_16005"
     CDS             564..944
                     /locus_tag="J0K77_16005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002348702.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="QSQ01569.1"
                     /translation="MSEQHQNLASDHSKKYTYRSEPKQISFRVSESEFAKLKQSAEALQ
                     MSVPAFVKAKAQNARLVTPKVAPDIAQAIARDLAKAGGNINQIAKWCNTHQHDVAPDDA
                     QRLSENLKIMQKELQKIWQQLK"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            926..1837
                     /locus_tag="J0K77_16010"
                     /pseudo=""
     CDS             926..1837
                     /locus_tag="J0K77_16010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002340563.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            2083..2771
                     /locus_tag="J0K77_16015"
                     /pseudo=""
     CDS             2083..2771
                     /locus_tag="J0K77_16015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298772.1"
                     /note="frameshifted; internal stop; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(2892..2978)
                     /locus_tag="J0K77_16020"
     CDS             complement(2892..2978)
                     /locus_tag="J0K77_16020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017548328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type I toxin-antitoxin system Fst family toxin"
                     /protein_id="QSQ01570.1"
                     /translation="MFERFICPLLVEVCVSLFSYWLNNRNKK"
                     /name="type I toxin-antitoxin system Fst family toxin"
     gene            3675..4607
                     /locus_tag="J0K77_16025"
     CDS             3675..4607
                     /locus_tag="J0K77_16025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002334376.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="RepB family plasmid replication initiator
                     protein"
                     /protein_id="QSQ01565.1"
                     /translation="MANEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMREKGDKTVRL
                     TFDQLKDLSNYKATANNRFINDLEMTYDKLMDLRFGKRSANGLDIDRFVMFSEFKIRGT
                     AKDPYVDIQVYEKALPLLNNLDEWVRYSLQQFNELQSSYAKTMFRLLKQYRTKGFAYFS
                     KEDFHELLDIPKSYWNNQANVDNRVIKPIRQELTAIFKGLSIKKKYGKGRGKPVVGYQF
                     TFKPEIKKADDFNKHAPTKEEQNKALALADKQKEYEEPATTINEKIKQKKRELELLQQI
                     KQLEKEKEALEKQTESALSKKRKKVYYLI"
                     /name="RepB family plasmid replication initiator protein"
     gene            4645..5178
                     /locus_tag="J0K77_16030"
     CDS             4645..5178
                     /locus_tag="J0K77_16030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292473.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF536 domain-containing protein"
                     /protein_id="QSQ01566.1"
                     /translation="MQPQETFTIKELSELFKMSRQAISKHIQKLDSSMIAKNERGYKVV
                     LRSGVLQLARNLGNQMLLDRLHEYEQDNDKNVNIPSKNVVTNKLLDQLREENEFLREQL
                     ALREQNNSHIQKLLDQQQQLTLQANKQIEKLQEKLQLTYTEEAPENDSTTLSEATETID
                     KQIDTEKKWWQLWK"
                     /name="DUF536 domain-containing protein"
     gene            5194..5364
                     /locus_tag="J0K77_16035"
     CDS             5194..5364
                     /locus_tag="J0K77_16035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322958.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QSQ01567.1"
                     /translation="MTRKNLLFGSILLGILGFSPMLLSVINKGNKHGELKLNPNYYNSP
                     NEELFVKETDK"
                     /name="hypothetical protein"
     Typing          3677..4624
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.057"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atctactaga tattcaacgt tataagttaa ggagtgatgt ttttgatatc taaatcatta
       61 aaatcattaa aaacatttac taaaaagaat ccgcaaatag ctactattcg tatttttata
      121 tttgctatag ctgttgctat aattgttaat atgctaagcg gagggcaatt atacaaatct
      181 ggtttatttt tagtgttaat cttagttgtc ttagacataa taaagtctaa aaaaaaataa
      241 atcgatacat tttagaagaa tagggttgtt tgaatattac aaagcaacaa tttcaccttc
      301 ggtgaaataa gcgaaacttt acaaaaagtg gctagcattt gctagccttt ttttgtattg
      361 tggagcgtgg attttgaggg ggattcaagg gggagcttgc gcccctttga caagcggtta
      421 tttgcaccaa atacggaggt atttggctag caaatataga gcttgccaaa cccttttagt
      481 gagttttgta ctcattgtac ctttttaggt acaatggtat tgcgaacgat acgtccgtag
      541 gacgtactga aagggtggga cttatgagcg aacaacatca aaatttggct agcgatcatt
      601 ctaaaaaata tacctatcga tccgagccaa aacaaatcag ttttcgagtg agcgaatccg
      661 aatttgcaaa gctgaagcag tcagctgaag ctttgcaaat gagtgtgccg gctttcgtga
      721 aagccaaggc acaaaacgcg cgtctggtga caccgaaagt ggcgccagac attgcccagg
      781 caatcgcgcg cgatttagcc aaagctggag ggaatatcaa tcaaattgcc aagtggtgca
      841 atacacacca acacgacgtt gctcctgatg atgctcaacg tttatccgaa aacctaaaaa
      901 tcatgcaaaa ggagctacaa aagatatggc aacagttaaa gtaagtcgaa ccacttcatg
      961 tagccgagca atcaattacg cagaaccacg agcaaccgtc aaaacaggaa taaactgtga
     1021 cattgattat gccaaaagtg aaatgaaaca aatacgcacg ctttatggaa aagacgatcg
     1081 tgtacaagca cacttattga ttcagtcctt tcgaccagga gaaattaccg ctgaaaaagc
     1141 caatcaacta ggggcagagt atgcgaaaaa aatagcccct aaccaccaaa tcgcgattta
     1201 cacacataca gacaaagacc atattcataa tcacattgtc attaactccg ttaatcttga
     1261 aactgggaaa aaatttcaag cccatgggca agcattttta aacaaatgtt atgacctaaa
     1321 tgacgagatt tgtcttgaac atgacttaac aatcacggaa cgaggaaaga aaaccgaaaa
     1381 cgaaccatgt ctgaaattaa attaaaagaa aaaatgaacc ggtttggaaa gacgaaattc
     1441 ggtttgcgat tgatcaaaca atgaaaaaca aaaaaactcg aacgtatacc caattttgtg
     1501 attcacttaa aacattcggc attcattgct tgaatcgcgg aaaaaatttt acttacgaat
     1561 tggtccacaa aaagaaaaaa gtacgatcca acaaactagg aaaggattac gaaaaggaga
     1621 cgattttaca tgagctggac agacgagaac gaacctacaa tcaacaacga accaacgagc
     1681 tacgaagagc tcgagctagc attcgcgaaa ctgcagaaga agtacgaaga gaacaacgaa
     1741 ctttacgcct gaacaatcgg aaattagacc gactcgaaga aaccatgaac aacacgttga
     1801 acgaggaaca gaccaccaac aagaattatc gctctaaaac gttaaaagac atcgaaaacg
     1861 aaataaagag acaacgtgcc tttcttgcgc cttataccca agaaaggata caaactacga
     1921 tggattcaca agtcaaaaaa actccaccaa gcgctattag accagcgaaa ccaagaacaa
     1981 aaaaaggctt taattcaacg atcgatggat attcttgccc ccttatgttg cttagtacta
     2041 acattattag ccttttggtt ggtatgggga gaataaacag acatggcatt ctatttaccc
     2101 tatctactca tttctgccag tattttagga attatttggc ttagctataa ggcttatcaa
     2161 acaagatatt cattaaaagg ctctaaaatt cgatttaagc gatttttatt ggtcggggtt
     2221 atatttgcct tatcaatcgt tttaagtggt ttattcggcg ttttagaggg taataaacgt
     2281 gtttcaagaa gcattttatt aggggatatc actcaaaagt atgaagcagc atgtgataaa
     2341 aagaaaaaag agcaagcatt agcacaaaaa aatggaggaa tttaccgctt gttatgagga
     2401 catgaacaat atttttgtgg atcaagagaa acgtttaaca gataaaaaca tgaaaaactc
     2461 actgttttta tcaaaactta ccagaaaaaa cagcaaaaag aggtacaaga aaaatatgag
     2521 caagtaaaaa agacgtgcaa tattttaaag atacgcagac agaagaagct tgttgtaact
     2581 tatttagcga tacaatccct ttttcaacca gtgaacaaga acgaaaagaa cggcaacaat
     2641 cggtcacata cgaacgttat gaaacactgc ttcagcaagc aacaaacata caaaatccaa
     2701 cgaaaaaaga aacggcatta aattatctag aaagtgtcaa ggaatggttg gatcagcaac
     2761 aacaaaattg aatttgatta gcaatcatgt taaactgaac ctgcaaatga tcaaacatta
     2821 gatacacgaa agccccagag aggtcggatt ctctggggct ttttttcagg ttgatgtcgc
     2881 ctttattgat tttacttctt gtttcggtta ttcaaccaat aactgaataa agagacacaa
     2941 acttctacaa gaagggggca aatgaaccgt tcaaacatta gatacacctc cttccagtcg
     3001 caagactgtc ggataggcga caagttatta taccttacaa aataaaatct gtgtggtgtt
     3061 tttaagtatc ccttattttc gggttgttag ggcttgccct gaccgcctgt aaggcgcttt
     3121 aagaacaaga taaggttttt tacccaagac tgtcttaaaa cgacttagac gagctatcag
     3181 aggcttcccc cacctccgtt actgacttgt ttttagcaaa ggagccttta ggcgactgcg
     3241 cagtacaatg tgagagcata gcgatcacac ttttttagcg accgtaggga gcaaggtttt
     3301 gaattggcag ttttgaaaaa tgcgcgaacc tgttggtaga aaaaagaagt ggtttttagg
     3361 cgggaaattt tgtcacccct ttttataatc tctttttaaa ccttttttaa acctctttac
     3421 cgtcggctgt gtccttactc cttcaatgga tacagcgttt tataaactac attttgtctg
     3481 cttttaaact acattttgtc tgcttttaaa ctacattttg tctgctttta aactacattt
     3541 tgtctgcttt taaactacat tttgtctgct tttaaactct ttttttgcac tcacgtatgt
     3601 tataatatgc attatcacag acaaaacgtt gtttataacg tctgtatcca ttgaaggagt
     3661 aaggaggaat atctttggca aatgaaatcg tgaaatacca tcatgaatta aataccattc
     3721 cgttgcggaa atttacacca gttgaaatga atctattttt ctctattgtg tctagaatgc
     3781 gcgaaaaagg cgataaaaca gtccgtctta cttttgacca actaaaagat ttaagtaatt
     3841 ataaagcaac tgctaataat cgtttcatta atgatttaga aatgacttat gataaattaa
     3901 tggatttacg ttttggtaaa agaagtgcta atgggctcga tatagataga ttcgttatgt
     3961 ttagtgagtt taaaatacgt ggaactgcta aagatccata tgtagacata caagtttacg
     4021 aaaaagcttt acctttacta aacaatttag atgagtgggt tcgctattca ctccaacaat
     4081 ttaacgaatt acaaagtagc tatgcaaaga ctatgtttcg attactaaaa caatatcgaa
     4141 ctaaaggttt tgcttatttt tctaaagagg attttcatga actattagat attccaaaaa
     4201 gttactggaa caaccaagca aacgttgata atcgtgttat aaagcctata cgacaggaat
     4261 taactgcaat cttcaaagga ttatcaatca aaaagaaata cggaaaaggg cggggaaaac
     4321 ctgtcgttgg ctatcaattt acgtttaaac cagaaataaa aaaagcagat gattttaata
     4381 aacatgcacc aaccaaagaa gaacaaaata aagcattggc tttagctgat aaacaaaaag
     4441 aatacgaaga acctgctaca acaattaacg aaaaaatcaa acagaagaaa cgagaacttg
     4501 aactcctcca acaaatcaaa caactagaaa aagagaaaga agctcttgaa aaacaaacag
     4561 agtccgcact ttcgaaaaag agaaaaaaag tttattatct gatttagata atttattcca
     4621 gtagcaacct aggaggcaac cagtatgcaa ccacaagaaa cctttacaat aaaggaattg
     4681 tcagaacttt ttaagatgag taggcaagca atatcgaaac atatccaaaa attagattct
     4741 tccatgatag ctaaaaatga gcgtggttat aaggttgtat tgcgttctgg agtattgcaa
     4801 cttgctcgca acttaggcaa ccaaatgttg ctagataggt tgcacgagta cgaacaagac
     4861 aacgataaaa atgttaatat accaagcaaa aacgtggtta caaacaagtt gctagatcag
     4921 ttgcgtgaag aaaatgaatt tttacgagaa caacttgccc tcagagagca aaataattct
     4981 catatacaaa aactactcga ccagcaacaa caactcaccc tacaagccaa caaacaaatc
     5041 gaaaaactgc aagaaaaact acagttgact tatacagaag aagctccaga gaatgactca
     5101 acgactcttt ctgaagcaac agaaacaata gacaaacaaa ttgatactga aaaaaaatgg
     5161 tggcaacttt ggaaataact ggagggaaca ttcatgacaa gaaaaaatct tctattcggt
     5221 tctattttac taggaattct aggattcagt ccgatgttat tgtcagtgat caataaaggg
     5281 aataaacatg gtgaattgaa attgaatcca aattattaca acagtcctaa cgaagaattg
     5341 tttgtaaaag aaacagataa ataataaaaa agactgctct ttcgagcagc cagttaaaaa
     5401 ataatgagtg tttattcttg aaaaagcaac gcgcttatga agcgctacca aaaatttatc
     5461 atattttatt aaaaataaca acccagtaaa aaatgactgg taaaaattca caaagaaacg
     5521 gaaagaagca accgcagaaa atcaagctta aaaagagctt ttgacctaga ccaatcgaaa
     5581 atcacaaagt gagcgcctgt atctattgct acaggcgcta cttggcatag tgtacattat
     5641 gtcaacaaga atttaatata acatattttc ctaatgcatt ctaactatac cacattatca
     5701 aaaatataaa ttatctttac taaataaaat attgacaagc ctataccttt tgttttatga
     5761 ttttcacaaa gaaaacgttt tctatatatt tttctgtatc aggaggaaat tctatgaaaa
     5821 aatttacttt aggggtagct ttgttaacta ttggggcagt tgttttaccg tcaactacta
     5881 tagtttatgc ttcagaaaat tcccaagtgg tatcattaaa cgaaaacaat gctactgaaa
     5941 atgtagttat tgagtacact gaagatggta tggtcgtaac taaatatgag gatggttata
     6001 gtgcggaaga ttttgcaaat tcttcagata tcatgacaag agctgcagtt gcaagatggg
     6061 gcaaaaagga atatacaaat attgctgtaa ccactggagt agctgctaat gctattaatg
     6121 ctgccttttg ggcaggaggg aaagctagca cttctatgtt tggtatccca ggttgggcaa
     6181 ttggtgcttt gttaacattt tgcagaaagt tggactaaaa aggtctcttc tccattcttt
     6241 ttaaagttgc aaaagaatgg gctttttttt ttaaaaatgg taatttttgg attggatttt
     6301 agcaaccaaa ggggatatga tgcagctgga agagttctta gta
//
