LOCUS       NZ_CP094869             3109 bp    DNA     circular CON 20-APR-2024
DEFINITION  Staphylococcus epidermidis strain C100 plasmid pC100MK4, complete
            sequence.
ACCESSION   NZ_CP094869
VERSION     NZ_CP094869.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN27161489
            Assembly: GCF_022832915.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3109)
  AUTHORS   Kopczyk,M., Mulroney,K., Chakera,A., Ramsay,J.P., Colombi,E.,
            Coombs,G.W. and Mowlaboccus,S.
  TITLE     Sequencing of Staphylococcus epidermidis isolated from peritoneal
            cavity
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3109)
  AUTHORS   Kopczyk,M., Mulroney,K., Chakera,A., Ramsay,J.P., Colombi,E.,
            Coombs,G.W. and Mowlaboccus,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-MAR-2022) School of Pharmacy & Biomedical Sciences,
            Curtin University, Kent street, Bentley, WA 6102, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 10-MAR-2022
            Assembly Method :: Flye v. 2.9-b1774; Racon v. 1.4.15; Pilon v. 1.23
            Assembly Name                     :: C100MK-10-Mar-2022
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 1841.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022832915.1-RS_2024_04_19
            Annotation Date                   :: 04/19/2024 10:05:55
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,423
            CDSs (total)                      :: 2,339
            Genes (coding)                    :: 2,273
            CDSs (with protein)               :: 2,273
            Genes (RNA)                       :: 84
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 61
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 66
            CDSs (without protein)            :: 66
            Pseudo Genes (ambiguous residues) :: 0 of 66
            Pseudo Genes (frameshifted)       :: 38 of 66
            Pseudo Genes (incomplete)         :: 37 of 66
            Pseudo Genes (internal stop)      :: 26 of 66
            Pseudo Genes (multiple problems)  :: 26 of 66
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP094869.1.
            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..3109
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="C100"
                     /isolation_source="pertoneal cavity"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="pC100MK4"
                     /geo_loc_name="Australia: Perth"
                     /lat_lon="31.92851574 S 115.86399442 E"
                     /collection_date="2017-04-19"
                     /collected_by="Harry Perkins Institute of Medical Research"
     gene            1..945
                     /locus_tag="MUG64_RS12025"
                     /old_locus_tag="MUG64_12025"
     CDS             1..945
                     /locus_tag="MUG64_RS12025"
                     /old_locus_tag="MUG64_12025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000277654.1"
                     /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_070585818.1"
                     /translation="MSKNNHANHSNHLQNKDLDNFSKTGYSNSRLSVPIWDTPQPKLSF
                     DSMTIVGNLSRDNAQKLSEFMSIEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADTWD
                     RRNMRVEFNPNKLTHEEMLWLKQNIIDYMEDDGFTRLDLAFDFEDDLSDYYAMTDKSVK
                     KTIFYGRNGKPETKYFGVRDSDRFIRIYNKKQERKDNADVEVMSEHLWRVEIELKRNMV
                     DYWNDCFDDLHILKPDYSTIEKAPDRHTIMALLFDENEWGKLERKKKYRMKKLMTEISP
                     VDLTELMKSTLRENEKQLQKQIEFWQTKSKKLF"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            1749..2366
                     /locus_tag="MUG64_RS12030"
                     /old_locus_tag="MUG64_12030"
     CDS             1749..2366
                     /locus_tag="MUG64_RS12030"
                     /old_locus_tag="MUG64_12030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017465246.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CadD family cadmium resistance transporter"
                     /protein_id="WP_182601119.1"
                     /translation="MIQTIVTAAILYIATALDLLVILLMFFARAKTRKEYRDIYIGQYV
                     GSVALIVISLFFAFVLNYVPEKWILGLLGLIPIYLGIKVAIYGDSDGEERAKKELNEKG
                     LSKLVGTIAIVTIASCGADNIGLFVPYFVTLSVTNLLITLFVFLILIFFLVFAAQKLAN
                     IPGVGEIVEKFGRWIMAVIYIALGLFIIIENDTIQTILGFIF"
                     /name="CadD family cadmium resistance transporter"
     gene            2385..2732
                     /locus_tag="MUG64_RS12035"
                     /old_locus_tag="MUG64_12035"
     CDS             2385..2732
                     /locus_tag="MUG64_RS12035"
                     /old_locus_tag="MUG64_12035"
                     /function="cadmium resistance"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020366422.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003700 - DNA-binding transcription factor activity
                     [Evidence IEA]"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="metalloregulator ArsR/SmtB family transcription
                     factor"
                     /protein_id="WP_010891100.1"
                     /translation="MSYENACDVICVHEDKVNNALSFLEDDKSKKLLNILEKICDEKKL
                     KIILSLIKEDELCVCDISLILKMSVASTSHHLRLLYKNDVLDFYKKGKMAYYFIKDDEI
                     REFFSKNQEGF"
                     /name="metalloregulator ArsR/SmtB family transcription
                     factor"
     Typing          2..945
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.051"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgagtaaaa ataatcacgc aaatcattca aatcacttac aaaataagga tttagataat
       61 ttttctaaaa ccggctactc taatagccgg ttaagtgtac cgatttggga caccccccaa
      121 ccaaaattaa gttttgactc tatgacaatt gttggaaatc tcagtcgtga caatgctcaa
      181 aaactatcag aatttatgag tattgaacca caaattcgac tttgggatat actacaaacg
      241 aaattcaaag ctaaagctct acaagaaaag gtttatattg aatatgacaa agtaaaagca
      301 gatacatggg atagacgtaa tatgcgtgtt gaatttaacc caaataaact tacacatgaa
      361 gagatgcttt ggttaaaaca aaacattatt gactacatgg aagatgacgg ttttacaaga
      421 ctagatttag cttttgattt tgaagatgat ttgagcgatt actacgcaat gactgataaa
      481 tcagttaaga aaactatctt ttatggtcgt aatggtaagc ctgaaacaaa atatttcggt
      541 gtaagagata gtgatagatt tattagaatt tataataaaa aacaagagcg taaagacaat
      601 gcagatgttg aagttatgtc tgaacatttg tggcgtgtag aaattgaatt gaaacgaaat
      661 atggttgatt attggaatga ttgttttgat gatttacata ttttgaaacc agattattca
      721 acaatagaaa aagctccaga ccgtcataca attatggctt tgttatttga tgaaaacgaa
      781 tggggaaaat tagagcgtaa aaagaaatac cgaatgaaaa aattgatgac tgaaatatct
      841 ccagttgatt taacggaatt aatgaaatcg actttaagag aaaatgaaaa acaattacaa
      901 aagcaaatag aattttggca gacaaaaagt aagaagctat tttaaaaatg gctaccattc
      961 ggctcccttt tagctcccaa atagctacat tattaggtag ctatttggga gctatttttg
     1021 attttaggta tccatatggt atccattttt gattttgtgt agctattcgg tagcttttgt
     1081 gtagcctttc gggagtcata taacaatttt tatcgcataa ataggaatcc catttgacac
     1141 tgtcaaatca atattttgca cagaaatggc taccgaatgg ctacatacgg agacatttct
     1201 gtgcaggatt cctcttatgc tctttaaaat acaagagtta cattatacac ctatttttta
     1261 aggttttagc tttttattaa gaagaataac cgagatagaa aaacatattt cgtattctaa
     1321 aagatttaga aaatgaattt taaaatgatt tatcgtctct ctgttgaacg aaaaagtttt
     1381 tagttatttt ttatacgtgg aatgattaaa tgtcctagaa agggcttaaa atgcaaaata
     1441 aaaagactac tcattttttg agtagccggg aatagttttt gatgtattaa atgaaaagga
     1501 gtaatacatt aatcatatca cacgcattta tgccgagaaa atttattgat gttgagaaga
     1561 acccttaact aaacttggag acgaatgtcg gcatagcgtg agctattaag ccgacgattc
     1621 gacaagttta gggattgtta agggttcgga ggctcaacgt caataaagca attggaataa
     1681 agcatctatg attatttaaa aatataagtt acaatacatt caaaaatatt tttgaatgag
     1741 gtgtaattat gattcagact attgtaactg ctgctattct ttatattgcg acagcattag
     1801 acttattagt gattttatta atgttctttg ctagagcaaa gactaggaaa gaatatcgag
     1861 atatttatat tggtcaatat gtaggatctg tggcattaat tgtcataagt ttattctttg
     1921 cctttgtctt aaattatgtt cctgaaaaat ggatattagg attattaggg ttaataccga
     1981 tttatttagg aattaaagtg gctatttatg gtgatagtga cggagaagag agagctaaaa
     2041 aagaattgaa tgaaaaggga ttgtctaaat tagttggtac gattgcaatt gttacgatag
     2101 caagttgtgg tgctgataat attggtttat ttgttcccta ttttgtgaca ttaagtgtta
     2161 ctaatttatt aattactttg tttgtctttt taattttaat tttcttcttg gtatttgctg
     2221 cacaaaaatt agctaatatt ccaggagttg gagaaattgt tgagaaattt ggtcgttgga
     2281 ttatggctgt tatttatata gctttaggtt tatttatcat tatagaaaat gacactattc
     2341 aaacgatttt aggatttata ttttaattta aggtgtgatt tcatatgagt tatgaaaatg
     2401 cttgtgatgt gatctgtgta catgaggata aagttaacaa tgctttaagt tttttagaag
     2461 atgataaatc taagaaatta cttaacattt tagaaaagat ttgtgatgag aagaaattga
     2521 aaattatatt atctttgatt aaagaagatg agttgtgtgt ttgtgatatt tctttaatat
     2581 tgaaaatgag tgttgcttca acttcacatc atttaagact tttatataaa aatgatgtac
     2641 ttgattttta taaaaaggga aagatggcat attattttat taaagacgat gaaataagag
     2701 aatttttctc taaaaatcag gagggttttt gaaacgagtg aaacgagttt cttcttgtct
     2761 tgatactata tagaaataac tcaaataatt aaaataggta taaaacgttg atatgatagt
     2821 gtttcggatg ttttttggcg tgaaagaaaa atttgacata ggtttataaa caccaaaaag
     2881 cttggtcata atagaccaag ctttttgata gtgttatatt aataacaaaa taaaaaaaga
     2941 agtcgctcac gccctgacca aagtttgtga atgcgactta cccaaagaaa aaacactaag
     3001 ttgttttttt atattttgta tatctagata ttaaacgata ttagtttatt cttcaagata
     3061 tatattcggg tgagcgactt cttaaattaa attaaggagt cgatttttt
//
