LOCUS       CP030375                3120 bp    DNA     circular BCT 10-OCT-2019
DEFINITION  Staphylococcus aureus strain ER04041.3 plasmid unnamed1, complete
            sequence.
ACCESSION   CP030375
VERSION     CP030375.1
DBLINK      BioProject: PRJNA470993
            BioSample: SAMN09484038
KEYWORDS    .
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3120)
  AUTHORS   Sullivan,M.J., Altman,D.R., Chacko,K., Cliferri,B., Webster,E.,
            Deikus,G., Lewis,M., Khan,Z., Beckford,C., Rendo,A., Samaroo,F.,
            Sebra,R., Karam-Howlin,R., Southwick,K., Adams,E., Ying,L.,
            Kornblum,J., Factor,S., Danesh Yazdi,M., Dingle,T., Hamula,C.,
            Bashir,A., Schadt,E., Kasarskis,A., Patel,G., Wallach,F., Gibbs,K.
            and van Bakel,H.
  TITLE     Whole genome sequencing to identify and define MRSA outbreaks
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3120)
  AUTHORS   Sullivan,M.J., Altman,D.R., Chacko,K., Cliferri,B., Webster,E.,
            Deikus,G., Lewis,M., Khan,Z., Beckford,C., Rendo,A., Samaroo,F.,
            Sebra,R., Karam-Howlin,R., Southwick,K., Adams,E., Ying,L.,
            Kornblum,J., Factor,S., Danesh Yazdi,M., Dingle,T., Hamula,C.,
            Bashir,A., Schadt,E., Kasarskis,A., Patel,G., Wallach,F., Gibbs,K.
            and van Bakel,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-JUN-2018) Genetics and Genomic Sciences, Icahn School
            of Medicine, One Gustave L. Levy Place Box 1498, New York, NY 10029,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 2.2.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 290.279747031x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/29/2018 21:25:02
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            Annotation Method :: Best-placed reference protein set; GeneMarkS+
            Annotation Software revision      :: 4.5
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 3,129
            CDS (total)                       :: 3,047
            Genes (coding)                    :: 2,953
            CDS (coding)                      :: 2,953
            Genes (RNA)                       :: 82
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 59
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 94
            Pseudo Genes (ambiguous residues) :: 0 of 94
            Pseudo Genes (frameshifted)       :: 55 of 94
            Pseudo Genes (incomplete)         :: 37 of 94
            Pseudo Genes (internal stop)      :: 23 of 94
            Pseudo Genes (multiple problems)  :: 19 of 94
            ##Genome-Annotation-Data-END##
            Annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (released 2013). Information about the Pipeline can be
            found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
FEATURES             Location/Qualifiers
     source          1..3120
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="ER04041.3"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="unnamed1"
                     /geo_loc_name="USA:New York City"
                     /lat_lon="40.7903114 N 73.9528738 W"
                     /collection_date="2015"
                     /collected_by="Mount Sinai Hospital"
     gene            complement(9..199)
                     /locus_tag="DQV57_00005"
                     /pseudo=""
     CDS             complement(9..199)
                     /locus_tag="DQV57_00005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001791934.1"
                     /note="frameshifted; 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            582..770
                     /locus_tag="DQV57_00010"
     CDS             582..770
                     /locus_tag="DQV57_00010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001030810.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QFJ24412.1"
                     /translation="MNKNTVLDEGYVIATILNVFFLLGLIFISHLENLYILIPYVILMG
                     INAIYLVVKVMNFKKNN"
                     /name="hypothetical protein"
     gene            complement(1095..1676)
                     /locus_tag="DQV57_00015"
     CDS             complement(1095..1676)
                     /locus_tag="DQV57_00015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000991705.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QFJ24413.1"
                     /translation="MNAIQNSISLRKILVVSLSILTILSMVLDFNFKEAQAQNKNNIAD
                     KNVETLNEKEIEKELKYIYGKIIILDKDGTAKDVNLENAKSRYGYVPEGFQKLKNDIEN
                     KKKTSSISPRAVGGNYKNSGDCFYSEVLNSYGELLTGNIITAVFEDVKAKNLKGVAKKL
                     AKIGIKGNLAGIAATMVSKDVQCNLKYGLL"
                     /name="hypothetical protein"
     gene            2128..3114
                     /locus_tag="DQV57_00020"
     CDS             2128..3114
                     /locus_tag="DQV57_00020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020368559.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="QFJ24414.1"
                     /translation="MQYNTTRSITENQDNKTLKDMTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNILEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQKVI
                     EKVIKEKPKARWLFLTLSTKNAIDGDTLEQSLKHLTKAFDRLSRYKKVKQNLVGFMRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQEEWVNLWQRALQVDYRPVANVKAI
                     KPNRKGDKDIESAIKETSKYSVKSSDFLTDDDEKNQEIVSDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDVEDGNLINASDEDKTTDEEEKAHSITAIWNFESKIII"
                     /name="protein rep"
     Typing          73..236
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.398"
                     /coverage="100.0"
                     /evalue="4.05e-79"
     Typing          2129..3120
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.799"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 agtgttgact aatgtctttt ttgttgattt tttataaaaa agtactgtct tatttttgtg
       61 acaaatgctg tatgtagtgt cacaaaaata agacaaacgc aatatattgt gtcacaaaaa
      121 taagacagta cagctttgta tgatatcact ttaaaatacc ttaaaaccct ggaatttctg
      181 gctttgccag acctatcatt tttgaatgat agcaaattct ccttatgctc ttacggagtt
      241 tttagagaaa aattaaaaat tctcgatttt tgataaaaaa cgccctgcag gaatttagaa
      301 aaacatgtgg aagttttaaa ggattttatg ctaattttta atttgcatgt aaatgggcag
      361 tgttaaaaaa ttagtcactg gttttgctga aatttttgtt tgtgaaatta ccatatattt
      421 atttggctca tatttgcgtt ttaagagctt gtatatattt ttaagttaaa aacctatatg
      481 atacccctaa acctttaaaa taccccttaa aactcaaaat aaaggtattt ataatttgag
      541 taagtcttgt gataaagttt tttaaaaaag gagtgtttat tttgaataaa aacacagtgt
      601 tagatgaagg ttacgttata gcaactattt taaatgtttt ctttttactt ggattaattt
      661 ttatatctca tttggaaaat ttatatatat taattccgta tgttattttg atgggaataa
      721 atgctattta tttggttgtt aaggttatga atttcaaaaa gaataattag aatatttgag
      781 gggattttga aacgagtttc ttcttgtttt cacactgttt ttttattcct attggtgttg
      841 ttgcttactt tttgtttttc tataaagatg atgcttttga cgagatggaa gaaaaatatg
      901 attatcatga agataataaa aaatagacga cgcatttatg ccgagaaaat ttattgatgt
      961 tgagaagaac ccttaactaa acttgcagac gaatgtcggc atagcgtgag ctattaagcc
     1021 gaccattcga caagttttgg gattgttaag gttccgaggc tcaacgtcaa taaagcaatt
     1081 ggaataaata gtatctaaag taacccgtat ttaagattac attgtacatc cttcgaaacc
     1141 atagtagctg cgattccagc taggtttcct tttatcccaa ttttagctaa tttttttgct
     1201 acgcccttta agtttttggc tttaacatct tcaaaaactg ctgtgattat gtttccagtt
     1261 aaaagttctc catatgagtt taaaacttca gaatagaaac agtcaccgct atttttgtag
     1321 ttcccaccaa ctgctctagg tgatattgaa ctagttttct ttttattctc tatgtcgttt
     1381 tttagttttt ggaatccttc aggaacatat ccatatcgag atttggcatt ttctagatta
     1441 acatctttag ctgttccgtc tttatctaaa ataataattt tgccatatat gtattttagt
     1501 tctttttcaa tttctttttc gtttaaagtt tcaacgtttt tatctgcaat gttatttttg
     1561 ttttgggctt gagcttcttt gaaattaaaa tccaagacca ttgaaagtat ggttaaaata
     1621 cttaaagata ctactaaaat ctttcttagt gatatactgt tttgaattgc attcattgta
     1681 aatgccccct tgttttgtta tttaaatgaa ttcaatataa tattaacata taaaaacaaa
     1741 ggagtttaat atgaataagt ttttttactt tttgattatt ttattatctg tatttttaat
     1801 ttttaatttt gttaattcga ttttatttga taatcctttt gactttttag aaagttttat
     1861 ttattcattg gttttcacat taatttattt aggtttagag ggtcataaaa agaagaagga
     1921 ataggttgtt ttttgaaacg agtgtgaacg agtttcttct tgtcttgata ctatatagaa
     1981 ataactcgat tttatatata tagctgtaac tgttgatatt acagtgttta aacgtgtttt
     2041 tgtgcgtgaa aggaaaattt gacaataaaa aaccccagtt atattattaa ggtgtcgaat
     2101 cttaaataat actgggggtc tttttatatg caatataata ctactagaag tataaccgaa
     2161 aatcaagata ataaaacgtt aaaagatatg acgaaaagtg ggaaacaacg cccatggaga
     2221 gaaaagaaaa tagataatgt aagctatgca gatatactag aaattttaaa aatcaaaaag
     2281 gcttttaatg taaaacaatg tggtaatatt ttagaattta agccaactga tgaaggctat
     2341 ttgaagttac ataagacatg gttttgtaaa tcaaaattat gtccggtttg taattggaga
     2401 cgtgctatga aaaatagtta tcaagctcaa aaagtgattg aaaaagtaat taaggaaaag
     2461 ccaaaagcac gttggttgtt tttaacactt tcaacaaaaa atgcgataga tggagatact
     2521 ttagaacaaa gtttgaagca tctaactaaa gcatttgata ggttgagtag atataaaaag
     2581 gttaaacaaa atcttgttgg atttatgcgt tcaacagaag ttaccgttaa taaaaatgac
     2641 ggtagttata atcagcacat gcatgttttg ttatgtgttg aaaatgcata ttttagaaaa
     2701 aaagagaatt atataactca agaagaatgg gttaatttat ggcaaagagc attacaagtt
     2761 gactatcgac ctgttgctaa tgttaaagcg atcaaaccga atagaaaagg cgataaagac
     2821 attgaatcgg caatcaaaga gacctcaaaa tattcggtta aatcatctga ttttttaact
     2881 gatgatgatg aaaaaaatca agaaattgta agtgatttag aaaaaggttt gtatcgaaaa
     2941 cgtatgttaa gttatggtgg attgcttaaa caaaaacata aaattttaaa cttagacgat
     3001 gtcgaagatg gtaatttgat taatgcaagt gatgaagata aaacaacaga cgaagaagaa
     3061 aaagcacatt caattaccgc aatttggaat ttcgaaagca aaattattat ttaagacatt
//
