LOCUS       NZ_CP014694             2361 bp    DNA     circular CON 05-MAR-2024
DEFINITION  Staphylococcus aureus strain LA-MRSA ST398 isolate E154 plasmid
            plinE154, complete sequence.
ACCESSION   NZ_CP014694
VERSION     NZ_CP014694.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN04276964
            Assembly: GCF_001887075.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2361)
  AUTHORS   Usungo,V., Garneau,P., Harel,J. and Archambault,M.
  TITLE     Staphylococcus aureus subsp. aureus LA-MRSA isolate from poultry in
            Quebec genome sequencing and assembly
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2361)
  AUTHORS   Usungo,V., Garneau,P., Harel,J. and Archambault,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-MAR-2016) Pathologie-Microbiologie, Faculte de
            Medecine Veterinaire - Universite de Montreal, 3200 rue Sicotte,
            Saint-Hyacinthe, Quebec J2S 7C6, Canada
COMMENT     ##Assembly-Data-START##
            Assembly Method                   :: Geneious v. 8.0.5
            Sequencing Technology :: Sanger dideoxy sequencing; PacBio
            ##Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 03/04/2024 14:30:48
            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)                     :: 2,816
            CDSs (total)                      :: 2,734
            Genes (coding)                    :: 2,656
            CDSs (with protein)               :: 2,656
            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)              :: 78
            CDSs (without protein)            :: 78
            Pseudo Genes (ambiguous residues) :: 0 of 78
            Pseudo Genes (frameshifted)       :: 38 of 78
            Pseudo Genes (incomplete)         :: 36 of 78
            Pseudo Genes (internal stop)      :: 24 of 78
            Pseudo Genes (multiple problems)  :: 17 of 78
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP014694.1.
            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..2361
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="LA-MRSA ST398"
                     /isolate="E154"
                     /isolation_source="chicken drumstick"
                     /db_xref="taxon:1280"
                     /plasmid="plinE154"
                     /geo_loc_name="Canada:Quebec"
                     /lat_lon="45.51 N 73.61000000 W"
                     /collection_date="2013-06-30"
                     /collected_by="Jocelyn Bernier-Lachance"
     gene            complement(232..1155)
                     /locus_tag="AS852_RS14705"
                     /old_locus_tag="AS852_14230"
     CDS             complement(232..1155)
                     /locus_tag="AS852_RS14705"
                     /old_locus_tag="AS852_14230"
                     /function="essential for plasmid replication"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002501032.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_011428876.1"
                     /translation="MDKYTEKKRRNQVFQKFIKRHVGENQMTLVRECNTFLSFVTDKSL
                     EKNKLYKANSCKNRFCPVCAWRKARKDALGLSLMMQYVQKEHEKEFIFLTLTTPNVSKN
                     KLENEIKHYNQSFRRLSNRTKFKKVVKGYVRKLEITYNKERDDYNPHFHVLIAVNKSYF
                     KDTKSYISQKEWLNLWRDVTGMPEITQVHVEKVKANNDKELYEMAKYSGKDSDYLSNQK
                     VFDAYYRSLKGKQVLVYSGLFKEARKLLKNGDLDYLKEIDPTEYIYQIFYIWKQKEYLA
                     SELYDLTEQEKRELNHQMIDEIEEET"
                     /name="protein rep"
     gene            1421..1906
                     /gene="lnu(A)"
                     /locus_tag="AS852_RS14710"
                     /old_locus_tag="AS852_14235"
     ARG             1422..1903
                     /name="lnu(A)"
                     /gene="lnu(A)"
                     /gene_name="lincosamide nucleotidyltransferase Lnu(A)"
                     /tool="amrfinderplus"
                     /drug_class="LINCOSAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             1422..1906
                     /name="lnuA"
                     /gene="lnuA"
                     /gene_name="lincosamide nucleotidyltransferase (LNU)"
                     /tool="rgi"
                     /drug_class="lincosamide antibiotic"
                     /identity="93.79"
                     /coverage="100.0"
     Typing          complement(233..1155)
                     /name="rep_cluster_1230"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtaagctttt tgtaccttaa ntgtagcctt ttctgtattt actcttagct tgtagaaatc
       61 ggacacgttc aacaatttta aaatcaacct aatatcgttg taacttatca gtattagttt
      121 caatactgcc catctacatg caaattaatt tgcatacatt ttttatagtt cccacagagg
      181 caggcgacca tatatttaac aataaaaaag tgtcagtcta agaccaacac tttatgtttc
      241 ttcttcaatt tcatcaatca tttgatgatt taattctctt ttttcttgtt ctgttaaatc
      301 atacaattca ctcgctaaat attctttttg tttccaaata taaaaaattt gatagatata
      361 ttcagttgga tcaatctctt ttaaataatc taaatcgcca ttttttaata actttctcgc
      421 ctctttaaat aatcccgaat acactaatac ctgcttacct tttaaagaac gataatacgc
      481 gtcgaatact ttttgattac ttaaataatc actatcttta ccagaatatt tagccatttc
      541 ataaagttct ttgtcattat tagccttaac tttctcgaca tgaacttgtg taatttctgg
      601 cattcccgtc acatctcgcc ataaattcaa ccattctttt tggctaatat aagatttagt
      661 atctttgaaa taagatttgt taaccgcaat taaaacgtga aaatgtgggt tataatcatc
      721 ccgctctttg ttgtatgtaa tttctaattt tcttacataa cccttaacaa cctttttaaa
      781 ttttgttcga ttacttaatc gtctaaatga ttgattataa tgcttaatct cattttctaa
      841 tttattttta gacacattag gcgtcgttaa agttaaaaat ataaattctt tttcatgttc
      901 tttttgtaca tactgcatca tcaaagataa acccaacgca tcttttctcg ctttacgcca
      961 tgcacaaacc ggacaaaaac gatttttaca tgaatttgct ttatataatt tatttttttc
     1021 taacgactta tctgtcacaa aagacaaaaa ggtattacat tcccgtacca atgtcatttg
     1081 attttccccc acatgtcgct ttataaattt ctgaaatact tgatttcttc gtttcttctc
     1141 agtatactta tccatgttat ataacttaaa aaacaactta gttttcacaa actatgacaa
     1201 taaaaaaagt tgctttttct cctttctcat aatgttttta gactagacac ctaaaacact
     1261 acatgagtat gctaaaaaaa gcaacttttt ttgtgtttca acccagatat accaacactt
     1321 taagggtaac tattctactc tgtaatagtt acccttatta tcaagacaag aagaaactcg
     1381 ttttcaactc gtttcaaatt cctaaattag gagggataaa atgaaaatta ataatgtaac
     1441 agaaaaggat ttattttata ttttagactt atttgaaaaa atggaagtaa cttattggtt
     1501 agatggaggt tggggtgtag atgtattaac tggaaaacaa caaagagaac acagagatat
     1561 agatatagat tttgacgccc aacacactca aaaagttata caaaaattag aagatatagg
     1621 atataaaata gaagttgatt ggatgccttc acgcatggaa cttaaacata aaaaatatgg
     1681 atatttagat attcatccca taaatttaaa tgatgatggt tccattactc aagcaaatcc
     1741 agaaggtggc aattacgttt ttcaaaatga atggttttca gaaactaatt ataaaggtcg
     1801 aaaaatacca tgtatttcaa aagaagctca gcttcttttt cattctggtt atgacttaac
     1861 agaaaaagac cattttgata taaaaaattt aaaatcaata acataattgc tttattccaa
     1921 ttgctttatt gacgttgagc ctcggaaccc ttaacaatcc caaaacttgt cgaatggtcg
     1981 gcttaatagc tcacgctatg ccgacattcg tctacaagtt tagttaaggg ttcttctcaa
     2041 cgatcaataa attttctcgg cataaaagcg tgttataatt taattaacgt tctgttttgt
     2101 tttcactgtt cacttccaaa aataaaaaaa gccaccaaat tttattggtg gcttttttta
     2161 ttttgttaaa tcttaaatgc ccttaatttt aattctaaag gggtatttta aagttttaag
     2221 tgtaaatcat atagttttat acctaaaaac atacataagc tcttaaaacg caaatatgag
     2281 ccaaataaaa gcatgttata acactacatt tttattaacc aaaacgatac aacttaacta
     2341 catttaaatc gtaaatcact t
//
