LOCUS       NZ_CP028191             4397 bp    DNA     circular CON 01-DEC-2023
DEFINITION  Staphylococcus aureus strain CFSAN018749 plasmid pGMI14-005,
            complete sequence.
ACCESSION   NZ_CP028191
VERSION     NZ_CP028191.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN08668672
            Assembly: GCF_003030065.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 4397)
  AUTHORS   Hoffmann,M., Pedersen,S.K., Sanchez,M., Pettengill,J.B. and
            Hendriksen,R.S.
  TITLE     Genome assemblies for Global Microbial Identifier (GMI) Proficiency
            Testing reference strains
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4397)
  AUTHORS   Hoffmann,M., Pedersen,S.K., Sanchez,M., Pettengill,J.B. and
            Hendriksen,R.S.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-MAR-2018) CFSAN-ORS-DM-MMSB, US Food and Drug
            Administration, 5100 Paint Branch Parkway, College Park, MD 20740,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 2.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 160.0x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/01/2023 03:53:37
            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)                     :: 2,901
            CDSs (total)                      :: 2,819
            Genes (coding)                    :: 2,711
            CDSs (with protein)               :: 2,711
            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)              :: 108
            CDSs (without protein)            :: 108
            Pseudo Genes (ambiguous residues) :: 0 of 108
            Pseudo Genes (frameshifted)       :: 58 of 108
            Pseudo Genes (incomplete)         :: 34 of 108
            Pseudo Genes (internal stop)      :: 33 of 108
            Pseudo Genes (multiple problems)  :: 15 of 108
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP028191.1.
            Bacteria and source DNA available from Bacterial culture available
            from Dwayne Roberson, FDA College Park Campus, 5001 Campus Drive,
            College Park, MD 20740.
            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/
            There are 2 base modification files available for this genome.
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..4397
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="CFSAN018749"
                     /isolation_source="tissue and/or biological fluid swine"
                     /db_xref="taxon:1280"
                     /plasmid="pGMI14-005"
                     /geo_loc_name="Denmark"
     gene            join(4280..4397,1..359)
                     /locus_tag="C9J86_RS15050"
                     /old_locus_tag="C9J86_15050"
     CDS             join(4280..4397,1..359)
                     /locus_tag="C9J86_RS15050"
                     /old_locus_tag="C9J86_15050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002485179.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF334 domain-containing protein"
                     /protein_id="WP_165958698.1"
                     /translation="MQAIKSSLKKTTEDFQGRGKKVHNDFVRLLQKNLNRVNAEDIEIE
                     VRKDVYGVREEIHSMLREVKQSHEHYQKRQKQLFTGIGAMLLVFMLFALIMTIGRDFMG
                     FLHVDVLQNAIASKIKASEGFISVLWYIAYGLPYILAIGLFIWLYEWIRARFHD"
                     /name="DUF334 domain-containing protein"
     gene            920..1864
                     /locus_tag="C9J86_RS15055"
                     /old_locus_tag="C9J86_15055"
     CDS             920..1864
                     /locus_tag="C9J86_RS15055"
                     /old_locus_tag="C9J86_15055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011167206.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003916 - DNA topoisomerase activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation factor domain-containing
                     protein"
                     /protein_id="WP_011167206.1"
                     /translation="MSKKAEEIQAKQSLEKENSNFSKTGYSNSRLNRHIMYTPEPKLHF
                     DAMTIVGNLNKNNAHKLSEFMSIAPQIRLWDILQTKFKAKALQEKVYIEYDKVKADAWD
                     RRNMRVEFNPNKLTHEEMLWLKQNIIDYMEDDGFTRLDLAFDFEDDLSDYYAMTDKSVK
                     KTIFYGRNGKPETKYFGVRDSDRFIRIYNKKQERKDNADIEVMSEHLWRVEIELKRDMV
                     DYWNDCFNDLHILKPDWSSLEKVKDQAMIYMLIHEESTWGKLERRTKNKYREMLKSISE
                     IDLTDLMKLTLKENEKQLQKQIEFWQREFRFWE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            1872..2720
                     /gene="str"
                     /locus_tag="C9J86_RS15060"
                     /old_locus_tag="C9J86_15060"
     ARG             1873..2717
                     /name="str"
                     /gene="str"
                     /gene_name="streptomycin adenylyltransferase Str"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            2990..3388
                     /gene="mobC"
                     /locus_tag="C9J86_RS15065"
                     /old_locus_tag="C9J86_15065"
     CDS             2990..3388
                     /gene="mobC"
                     /locus_tag="C9J86_RS15065"
                     /old_locus_tag="C9J86_15065"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002489523.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_001002114.1"
                     /translation="MNEHKDNLASDLSVGGNRKPNRKEPKQISFRVSEQEYSKLKQSAE
                     TLNMTVPNFVKKKAQGSRLVSPKLDKETRQSIAKDLSHLGSNVNQIAKWFNQNKDKATH
                     LPEEKYHDLEKQFDDVKKELHKIWQQLN"
                     /name="mobC"
     gene            3370..4332
                     /locus_tag="C9J86_RS15070"
                     /old_locus_tag="C9J86_15070"
     CDS             3370..4332
                     /locus_tag="C9J86_RS15070"
                     /old_locus_tag="C9J86_15070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011167204.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_000246202.1"
                     /translation="MATTKLGNTKSASRAINYAEERAEEKSGLNCDVDYAKSYFKQTRA
                     LYGKENGVQAHTVIQSFKPGEVTAKECNEIGLELAKKIAPDYQVAVYTHTDKDHYHNHI
                     IINSVNLETGNKYQSNKEQRDFIKKANDQLCEERGLSVPEKSSEIRYTLAEQNMIDKDK
                     RSWKNDIRMAVEETKDNAVDFEEFNTLLKEKGVEITRVTKNNVTYRHIEEDKKVRGNKL
                     GDSYDKGVIENGFAIEKFRREREEEREYDEYADTFEVDWDAVAENSEDLRKRRIARTEE
                     TKQASNKIYIRDERTTGLERKGIAGNQVEFEKDDGGLSR"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     Typing          complement(2785..3019)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="80.0"
                     /coverage="100.0"
                     /evalue="1.4099999999999999e-40"
     Typing          921..1864
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3371..4329
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aagatattga gatagaggtt cgaaaagatg tttatggagt tcgagaagaa attcattcaa
       61 tgttgcgtga agttaaacaa tcacatgaac attatcaaaa aagacaaaag caattattta
      121 ctggtattgg tgcaatgtta ttagtgttta tgctttttgc tttgattatg acgattggca
      181 gagattttat gggcttttta catgtagatg tattacagaa tgccatagca agcaaaataa
      241 aggcttctga gggctttatt tcagttttat ggtacattgc ttatggttta ccttatatac
      301 tcgctatagg gctatttatt tggttgtatg agtggataag agcaagattc catgattaaa
      361 caaagtatga tcaggctttt atgccgagaa aatttattta tattgagaag tacccttaac
      421 taaacttgca gacgaatgtc ggcatagcgt gagctattag cccgaccatt cgacaagttt
      481 tgggtttgtt aagggtacag aggctcaatg taaataaagc aattggaata aagcaacaaa
      541 gggggttgaa gaaaatgagt aagaagaaaa agattaattt agcaatatca attgctcaag
      601 tagtagtgca ggcgttaata ctttataaca cttatcagca atataaatat tctaaaaaat
      661 attcagccta ataaaaaaag acttagtctg aatagaccaa gccttttgtt agtgttatat
      721 taatatgcaa ataaaaaaac aaaaaaagaa gtcgctcact ccctgaccaa agtttgtgaa
      781 tgcgacttac cttaaagaaa aacagttggt gtttttttct taatttttgt atatctagat
      841 attaaacgat attggtttat tcttcaagat atatattcgg gtgagcgact tcttaaacaa
      901 aataaggagt cgatttttta tgagtaaaaa agcagaagaa attcaggcaa aacaaagttt
      961 ggaaaaggaa aactcaaatt tttctaaaac cggatactct aatagccggt taaaccgaca
     1021 tattatgtac acccccgaac caaaattaca ctttgatgct atgacaattg ttgggaatct
     1081 taataagaac aatgctcaca aactgtctga atttatgagt attgcgccac aaattagact
     1141 ttgggatata ttacaaacca aatttaaagc taaggctcta caagaaaaag tttacatcga
     1201 atatgataaa gtaaaagcag atgcgtggga tagacgtaat atgcgtgttg aatttaatcc
     1261 taataaactt acgcatgaag aaatgctttg gttaaaacaa aacatcattg actacatgga
     1321 agatgatggt tttacaagat tagatttggc ttttgatttt gaagacgatt tgagcgatta
     1381 ttatgcgatg actgataaat cagttaagaa aactattttt tatggtcgta acggtaaacc
     1441 agaaacaaaa tattttggtg ttcgtgacag tgatagattt attagaattt ataataaaaa
     1501 acaagaacgt aaggataatg cagacattga agttatgtct gaacacttat ggcgtgtaga
     1561 aattgaatta aaaagagata tggttgatta ttggaacgat tgttttaatg atttacatat
     1621 tttgaaacca gattggtcta gtttagaaaa agtaaaagac caagcaatga tttatatgct
     1681 aattcatgaa gaaagtacat ggggtaaatt agaaagacgt acaaaaaata aatacagaga
     1741 aatgttaaaa agtatttcag aaattgattt aacggactta atgaaattga ctttaaaaga
     1801 gaatgaaaaa caattgcaaa agcagattga attttggcag cgtgaattta gattttggga
     1861 gtgaaaaaac aatgaggact gaaaaagaaa ttttaaattt agtttctgaa tttgcttatc
     1921 aacgaagcaa tgtaaaaatt attgctctcg agggttcaag aactaatgaa aatataaaaa
     1981 aagataagtt tcaagattat gattttgctt ttttcgtatc agatattgag tatttcacac
     2041 atgaagaaag ttggttaagt ttatttggag aattattgtt tatacagaaa ccagaagata
     2101 tggaattatt cccacctgat ttagattatg gttacagtta tataatgtat tttaaagatg
     2161 gcataaaaat ggatattaca ttaattaatt taaaagattt aaatcgttat tttagtgatt
     2221 ctgatggtct tgtaaaaatt ttagttgata aagataattt agtaactcaa gaaattgttc
     2281 cagatgactc aaattattgg ttaaaaaaac caacagaacg agaattttat gattgctgta
     2341 atgagttttg gagtgtctca acgtatgtag caaagggtgt ttttagaaga gaaatattat
     2401 ttgctttaga tcatttcaat aatattttac gtcctgaatt attaagaatg atttcttggt
     2461 atattggctt taataggggt tttgatttta gtttaggaaa gaattataag tttataaaca
     2521 aatatttaac tgataaagaa ttcaatatgc ttttagctac ttttgagatg aatggatata
     2581 gaaagacata ccaatctttt aagctttgtt gtgaattatt taaatattat tcaaataaag
     2641 taagttgttt aggaaattat aactatccaa attacgaaaa aaatattgag aattttattc
     2701 gtaataatta tgagaattaa ttttattagc aaccacattt ttggttgctt ttgttttgat
     2761 tttgaatttg gttttgaact atgagtggct agcattttgc cactcatttt ttgcgttagc
     2821 aaaaacataa agggtctggg attaatccca gcaagccggt atattcagaa cgaagtggct
     2881 agaatatacg acgcttgcca aaccactata ttacttgaga aaatatagat tatattataa
     2941 gctatattta tgaaaaggaa tatttttcgt cagaaaggtg gtgggacttg tgaacgaaca
     3001 taaagataat ttggctagcg atttgtctgt tgggggaaac cgtaaaccca accgcaaaga
     3061 gccaaaacaa attagtttca gagtgagtga acaggaatat tcaaagttga aacagtcggc
     3121 agaaactttg aatatgacag tgcctaattt cgttaagaaa aaggcacaag gcagtcgatt
     3181 agtgtcgcca aaattagaca aagaaacgcg acaatcgatt gccaaagatt taagtcattt
     3241 gggtagtaat gtgaatcaga ttgctaagtg gtttaatcaa aataaagata aggctacaca
     3301 tttaccagaa gagaaatatc atgatttaga aaagcaattt gatgatgtga aaaaggagtt
     3361 gcataagata tggcaacaac taaattaggc aatacgaagt cggcaagtcg tgccattaat
     3421 tacgcagaag aacgtgcaga agaaaaaagc ggcttaaatt gtgatgttga ttatgctaaa
     3481 tcatatttta agcaaactag ggcgttatat ggcaaagaga atggtgttca agcacataca
     3541 gtcattcaat cttttaagcc tggcgaagta acagctaaag agtgtaatga gataggttta
     3601 gaattagcta aaaaaattgc accagattat caagttgcag tttatacaca tacagacaaa
     3661 gaccattatc acaatcacat tattattaat tcagtaaatt tagaaacagg caacaagtat
     3721 cagtcaaaca aagaacaacg tgattttata aaaaaggcga atgatcagtt atgtgaagaa
     3781 cgtggtttat ctgtgccaga aaagtcatca gaaatcagat atacgttggc agaacagaac
     3841 atgatagata aagataaaag gtcatggaaa aatgatataa gaatggcagt tgaagaaaca
     3901 aaggataacg cagtagactt tgaagaattt aatactttgc taaaagaaaa aggtgttgaa
     3961 atcacgagag taacgaaaaa caacgtaacg tatagacaca ttgaagaaga taaaaaagta
     4021 cgtgggaata agttgggcga ttcttatgac aaaggagtga ttgaaaatgg ctttgcaatc
     4081 gagaaattca gacgagaacg agaagaagaa cgagaatacg atgaatatgc agacacgttc
     4141 gaagttgact gggacgcagt cgcagaaaat tcagaagacc ttagaaaacg aagaattgca
     4201 agaactgaag aaacaaaaca agctagtaat aaaatatata tcagagatga aagaacaaca
     4261 ggacttgaga gaaaaggaat tgcaggcaat caagtcgagt ttgaaaaaga cgacggagga
     4321 ctttcaaggt agaggtaaaa aagtccataa tgattttgtt cgtttgttac aaaagaattt
     4381 aaatcgagtg aatgcag
//
