LOCUS       NZ_CP094863             3110 bp    DNA     circular CON 20-APR-2024
DEFINITION  Staphylococcus epidermidis strain C99 plasmid pC99MK4, complete
            sequence.
ACCESSION   NZ_CP094863
VERSION     NZ_CP094863.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN27160588
            Assembly: GCF_022832895.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3110)
  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  JOURNAL   Unpublished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 3110)
  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                     :: C99MK-9-Mar-2022
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 1552.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022832895.1-RS_2024_04_19
            Annotation Date                   :: 04/19/2024 10:06:15
            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)                     :: 2,425
            CDSs (total)                      :: 2,341
            Genes (coding)                    :: 2,266
            CDSs (with protein)               :: 2,266
            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)              :: 75
            CDSs (without protein)            :: 75
            Pseudo Genes (ambiguous residues) :: 0 of 75
            Pseudo Genes (frameshifted)       :: 48 of 75
            Pseudo Genes (incomplete)         :: 36 of 75
            Pseudo Genes (internal stop)      :: 27 of 75
            Pseudo Genes (multiple problems)  :: 27 of 75
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP094863.1.
            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..3110
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="C99"
                     /isolation_source="pertoneal cavity"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="pC99MK4"
                     /geo_loc_name="Australia: Perth"
                     /lat_lon="31.92851574 S 115.86399442 E"
                     /collection_date="2017-04-14"
                     /collected_by="Harry Perkins Institute of Medical Research"
     gene            1..945
                     /locus_tag="MUB20_RS12030"
                     /old_locus_tag="MUB20_12030"
     CDS             1..945
                     /locus_tag="MUB20_RS12030"
                     /old_locus_tag="MUB20_12030"
                     /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            1750..2367
                     /locus_tag="MUB20_RS12035"
                     /old_locus_tag="MUB20_12035"
     CDS             1750..2367
                     /locus_tag="MUB20_RS12035"
                     /old_locus_tag="MUB20_12035"
                     /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            2386..2733
                     /locus_tag="MUB20_RS12040"
                     /old_locus_tag="MUB20_12040"
     CDS             2386..2733
                     /locus_tag="MUB20_RS12040"
                     /old_locus_tag="MUB20_12040"
                     /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 aaaaaagttt
     1381 ttagttattt tttatacgtg gaatgattaa atgtcctaga aagggcttaa aatgcaaaat
     1441 aaaaagacta ctcatttttt gagtagccgg gaatagtttt tgatgtatta aatgaaaagg
     1501 agtaatacat taatcatatc acacgcattt atgccgagaa aatttattga tgttgagaag
     1561 aacccttaac taaacttgga gacgaatgtc ggcatagcgt gagctattaa gccgacgatt
     1621 cgacaagttt agggattgtt aagggttcgg aggctcaacg tcaataaagc aattggaata
     1681 aagcatctat gattatttaa aaatataagt tacaatacat tcaaaaatat ttttgaatga
     1741 ggtgtaatta tgattcagac tattgtaact gctgctattc tttatattgc gacagcatta
     1801 gacttattag tgattttatt aatgttcttt gctagagcaa agactaggaa agaatatcga
     1861 gatatttata ttggtcaata tgtaggatct gtggcattaa ttgtcataag tttattcttt
     1921 gcctttgtct taaattatgt tcctgaaaaa tggatattag gattattagg gttaataccg
     1981 atttatttag gaattaaagt ggctatttat ggtgatagtg acggagaaga gagagctaaa
     2041 aaagaattga atgaaaaggg attgtctaaa ttagttggta cgattgcaat tgttacgata
     2101 gcaagttgtg gtgctgataa tattggttta tttgttccct attttgtgac attaagtgtt
     2161 actaatttat taattacttt gtttgtcttt ttaattttaa ttttcttctt ggtatttgct
     2221 gcacaaaaat tagctaatat tccaggagtt ggagaaattg ttgagaaatt tggtcgttgg
     2281 attatggctg ttatttatat agctttaggt ttatttatca ttatagaaaa tgacactatt
     2341 caaacgattt taggatttat attttaattt aaggtgtgat ttcatatgag ttatgaaaat
     2401 gcttgtgatg tgatctgtgt acatgaggat aaagttaaca atgctttaag ttttttagaa
     2461 gatgataaat ctaagaaatt acttaacatt ttagaaaaga tttgtgatga gaagaaattg
     2521 aaaattatat tatctttgat taaagaagat gagttgtgtg tttgtgatat ttctttaata
     2581 ttgaaaatga gtgttgcttc aacttcacat catttaagac ttttatataa aaatgatgta
     2641 cttgattttt ataaaaaggg aaagatggca tattatttta ttaaagacga tgaaataaga
     2701 gaatttttct ctaaaaatca ggagggtttt tgaaacgagt gaaacgagtt tcttcttgtc
     2761 ttgatactat atagaaataa ctcaaataat taaaataggt ataaaacgtt gatatgatag
     2821 tgtttcggat gttttttggc gtgaaagaaa aatttgacat aggtttataa acaccaaaaa
     2881 gcttggtcat aatagaccaa gctttttgat agtgttatat taataacaaa ataaaaaaag
     2941 aagtcgctca cgccctgacc aaagtttgtg aatgcgactt acccaaagaa aaaacactaa
     3001 gttgtttttt tatattttgt atatctagat attaaacgat attagtttat tcttcaagat
     3061 atatattcgg gtgagcgact tcttaaatta aattaaggag tcgatttttt
//
