LOCUS       NZ_CP007178             3125 bp    DNA     circular CON 03-MAR-2024
DEFINITION  Staphylococcus aureus USA300-ISMMS1 plasmid pUSA02-ISMMS, complete
            sequence.
ACCESSION   NZ_CP007178
VERSION     NZ_CP007178.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03081531
            Assembly: GCF_000568455.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus USA300-ISMMS1
  ORGANISM  Staphylococcus aureus USA300-ISMMS1
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3125)
  AUTHORS   Altman,D.R., Sebra,R., Hand,J., Attie,O., Deikus,G., Carpini,K.W.,
            Patel,G., Rana,M., Arvelakis,A., Grewal,P., Dutta,J., Rose,H.,
            Shopsin,B., Daefler,S., Schadt,E., Kasarskis,A., van Bakel,H.,
            Bashir,A. and Huprikar,S.
  TITLE     Transmission of methicillin-resistant Staphylococcus aureus via
            deceased donor liver transplantation confirmed by whole genome
            sequencing
  JOURNAL   Am J Transplant 14 (11), 2640-2644 (2014)
   PUBMED   25250641
REFERENCE   2  (bases 1 to 3125)
  AUTHORS   Altman,D.R., Sebra,R., Hand,J., Attie,O., Deikus,G., Carpini,K.W.D.,
            Patel,G., Rana,M., Arvelakis,A., Grewal,P., Dutta,J., Rose,H.,
            Shopsin,B., Daefler,S., Schadt,E., Kasarskis,A., van Bakel,H.,
            Bashir,A. and Huprikar,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-FEB-2014) Genetics and Genomic Sciences, Mount Sinai
            School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 1.4
            Genome Coverage                   :: 506x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 03/03/2024 05:41:48
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,992
            CDSs (total)                      :: 2,910
            Genes (coding)                    :: 2,819
            CDSs (with protein)               :: 2,819
            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)              :: 91
            CDSs (without protein)            :: 91
            Pseudo Genes (ambiguous residues) :: 0 of 91
            Pseudo Genes (frameshifted)       :: 48 of 91
            Pseudo Genes (incomplete)         :: 44 of 91
            Pseudo Genes (internal stop)      :: 19 of 91
            Pseudo Genes (multiple problems)  :: 19 of 91
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP007178.1.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..3125
                     /organism="Staphylococcus aureus USA300-ISMMS1"
                     /mol_type="genomic DNA"
                     /strain="USA300-ISMMS1"
                     /db_xref="taxon:1458279"
                     /plasmid="pUSA02-ISMMS"
     gene            452..1033
                     /locus_tag="AZ30_RS15195"
                     /old_locus_tag="AZ30_14360"
     CDS             452..1033
                     /locus_tag="AZ30_RS15195"
                     /old_locus_tag="AZ30_14360"
                     /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="WP_000991705.1"
                     /translation="MNAIQNSISLRKILVVSLSILTILSMVLDFNFKEAQAQNKNNIAD
                     KNVETLNEKEIEKELKYIYGKIIILDKDGTAKDVNLENAKSRYGYVPEGFQKLKNDIEN
                     KKKTSSISPRAVGGNYKNSGDCFYSEVLNSYGELLTGNIITAVFEDVKAKNLKGVAKKL
                     AKIGIKGNLAGIAATMVSKDVQCNLKYGLL"
                     /name="hypothetical protein"
     gene            complement(1359..1547)
                     /locus_tag="AZ30_RS15200"
                     /old_locus_tag="AZ30_14370"
     CDS             complement(1359..1547)
                     /locus_tag="AZ30_RS15200"
                     /old_locus_tag="AZ30_14370"
                     /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="WP_001039248.1"
                     /translation="MNKNTVLDEGYVIATILNVFFLLGLIFISHLENLYILIPYVILMG
                     INAIYLVVKVMNFKKNN"
                     /name="hypothetical protein"
     gene            complement(2130..3125)
                     /locus_tag="AZ30_RS15205"
                     /old_locus_tag="AZ30_14375"
     CDS             complement(2130..3125)
                     /locus_tag="AZ30_RS15205"
                     /old_locus_tag="AZ30_14375"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001199895.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001199892.1"
                     /translation="MQYNTTRSITENQDNKTLKDMTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNILEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQKVI
                     EKVIKEKPKARWLFLTLSTKNAIDGDTLEQSLKHLTKAFDRLSRYKKVKQNLVGFMRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQEEWVNLWQRALQVDYRPVANVKAI
                     KPNRKGDKDIESAIKETSKYSVKSSDFLTDDDEKNQEIVSDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDVEDGNLINASDEDKTTDEEEKAHSITAIWNFEKQNYYLRH"
                     /name="protein rep"
     Typing          complement(1896..2060)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.42e-81"
     Typing          complement(2131..3125)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.9"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ataaaaagac ccccagtatt atttaagatt cgacacctta ataatataac tggggttttt
       61 tattgtcaaa ttttcctttc acgcacaaaa acacgtttaa acactgtaat atcaacagtt
      121 acagctatat atataaaatc gagttatttc tatatagtat caagacaaga agaaactcgt
      181 tcacactcgt ttcaaaaaac aacctattcc ttcttctttt tatgaccctc taaacctaaa
      241 taaattaatg tgaaaaccaa tgaataaata aaactttcta aaaagtcaaa aggattatca
      301 aataaaatcg aattaacaaa attaaaaatt aaaaatacag ataataaaat aatcaaaaag
      361 taaaaaaact tattcatatt aaactccttt gtttttatat gttaatatta tattgaattc
      421 atttaaataa caaaacaagg gggcatttac aatgaatgca attcaaaaca gtatatcact
      481 aagaaagatt ttagtagtat ctttaagtat tttaaccata ctttcaatgg tcttggattt
      541 taatttcaaa gaagctcaag cccaaaacaa aaataacatt gcagataaaa acgttgaaac
      601 tttaaacgaa aaagaaattg aaaaagaact aaaatacata tatggcaaaa ttattatttt
      661 agataaagac ggaacagcta aagatgttaa tctagaaaat gccaaatctc gatatggata
      721 tgttcctgaa ggattccaaa aactaaaaaa cgacatagag aataaaaaga aaactagttc
      781 aatatcacct agagcagttg gtgggaacta caaaaatagc ggtgactgtt tctattctga
      841 agttttaaac tcatatggag aacttttaac tggaaacata atcacagcag tttttgaaga
      901 tgttaaagcc aaaaacttaa agggcgtagc aaaaaaatta gctaaaattg ggataaaagg
      961 aaacctagct ggaatcgcag ctactatggt ttcgaaggat gtacaatgta atcttaaata
     1021 cgggttactt tagatactat ttattccaat tgctttattg acgttgagcc tcggaaccct
     1081 taacaatccc aaaacttgtc gaatggtcgg cttaatagct cacgctatgc cgacattcgt
     1141 ctgcaagttt agttaagggt tcttctcaac atcaataaat tttctcggca taaatgcgtc
     1201 gtctattttt tattatcttc atgataatca tatttttctt ccatctcgtc aaaagcatca
     1261 tctttataga aaaacaaaaa gtaagcaaca acaccaatag gaataaaaaa acagtgtgaa
     1321 aacaagaaga aactcgtttc aaaatcccct caaatattct aattattctt tttgaaattc
     1381 ataaccttaa caaccaaata aatagcattt attcccatca aaataacata cggaattaat
     1441 atatataaat tttccaaatg agatataaaa attaatccaa gtaaaaagaa aacatttaaa
     1501 atagttgcta taacgtaacc ttcatctaac actgtgtttt tattcaaaat aaacactcct
     1561 tttttaaaaa actttatcac aagacttact caaattataa atacctttat tttgagtttt
     1621 aagggggtat tttaaaggtt tagggggtat catataggtt tttaacttaa aaatatatac
     1681 aagctcttaa aacgcaaata tgagccaaat aaatatatgg taatttcaca aacaaaaatt
     1741 tcagcaaaac cagtgactaa ttttttaaca ctgcccattt acatgcaaat taaaaattag
     1801 cataaaatcc tttaaaactt ccacatgttt ttctaaattc ctgcagggcg ttttttatca
     1861 aaaatcgaga atttttaatt tttctctaaa aactccgtaa gagcataagg agaatttgct
     1921 atcattcaaa aatgataggt ctggcaaagc cagaaattcc aggggtttta aggtatttta
     1981 aagtgatatc atacaaagct gtactgtctt atttttgtga cacaatatat tgcgtttgtc
     2041 ttatttttgt gacactacat acagcatttg tcacaaaaat aagacagtac ttttttataa
     2101 aaaatcaaca aaaaagacat tagtcaacac taatgtctta aataataatt ttgcttttcg
     2161 aaattccaaa ttgcggtaat tgaatgtgct ttttcttctt cgtctgttgt tttatcttca
     2221 tcacttgcat taatcaaatt accatcttcg acatcgtcta agtttaaaat tttatgtttt
     2281 tgtttaagca atccaccata acttaacata cgttttcgat acaaaccttt ttctaaatca
     2341 cttacaattt cttgattttt ttcatcatca tcagttaaaa aatcagatga tttaaccgaa
     2401 tattttgagg tctctttgat tgccgattca atgtctttat cgccttttct attcggtttg
     2461 atcgctttaa cattagcaac aggtcgatag tcaacttgta atgctctttg ccataaatta
     2521 acccattctt cttgagttat ataattctct ttttttctaa aatatgcatt ttcaacacat
     2581 aacaaaacat gcatgtgctg attataacta ccgtcatttt tattaacggt aacttctgtt
     2641 gaacgcataa atccaacaag attttgttta acctttttat atctactcaa cctatcaaat
     2701 gctttagtta gatgcttcaa actttgttct aaagtatctc catctatcgc attttttgtt
     2761 gaaagtgtta aaaacaacca acgtgctttt ggcttttcct taattacttt ttcaatcact
     2821 ttttgagctt gataactatt tttcatagca cgtctccaat tacaaaccgg acataatttt
     2881 gatttacaaa accatgtctt atgtaacttc aaatagcctt catcagttgg cttaaattct
     2941 aaaatattac cacattgttt tacattaaaa gcctttttga tttttaaaat ttctagtata
     3001 tctgcatagc ttacattatc tattttcttt tctctccatg ggcgttgttt cccacttttc
     3061 gtcatatctt ttaacgtttt attatcttga ttttcggtta tacttctagt agtattatat
     3121 tgcat
//
