LOCUS       NZ_CP066372             2491 bp    DNA     circular CON 03-APR-2024
DEFINITION  Staphylococcus epidermidis strain PH1-28 plasmid pSE4, complete
            sequence.
ACCESSION   NZ_CP066372
VERSION     NZ_CP066372.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16085533
            Assembly: GCF_016406625.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2491)
  AUTHORS   Hilaire,P., Landemaine,L., Contreras,S., Blanquart-Goudezeune,H.,
            Siguier,P., Cornet,F., Chiapello,H., Loux,V., Clavaud,C. and
            Morand,S.C.
  TITLE     Complete Genome Sequence of Staphylococcus epidermidis PH1-28,
            Isolated from the Forehead of a Hyperseborrheic Donor
  JOURNAL   Microbiol Resour Announc 10 (9), e00165-21 (2021)
   PUBMED   33664152
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2491)
  AUTHORS   Morand,S.C., Contreras,S., Hilaire,P., Blanquart-Goudezeune,H. and
            Clavaud,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-DEC-2020) Advanced Research, L'Oreal, 1 Avenue Eugene
            Schueller, Aulnay-Sous-Bois 93600, France
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: NOV-2020
            Assembly Method :: MaSuRCA v. v3.3.0; SPAdes v. v3.10.1; CANU v.
            v2.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 4828.0x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_016406625.1-RS_2024_04_03
            Annotation Date                   :: 04/03/2024 04:47:49
            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)                     :: 2,504
            CDSs (total)                      :: 2,420
            Genes (coding)                    :: 2,334
            CDSs (with protein)               :: 2,334
            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)              :: 86
            CDSs (without protein)            :: 86
            Pseudo Genes (ambiguous residues) :: 0 of 86
            Pseudo Genes (frameshifted)       :: 54 of 86
            Pseudo Genes (incomplete)         :: 39 of 86
            Pseudo Genes (internal stop)      :: 39 of 86
            Pseudo Genes (multiple problems)  :: 35 of 86
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066372.1.
            Bacteria and source DNA available from L'Oreal Advanced Research.
            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..2491
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="PH1-28"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="pSE4"
                     /geo_loc_name="France"
                     /collection_date="2012-06"
     gene            125..313
                     /locus_tag="ICN77_RS00010"
                     /old_locus_tag="ICN77_002488"
     CDS             125..313
                     /locus_tag="ICN77_RS00010"
                     /old_locus_tag="ICN77_002488"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002440614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CsbD family protein"
                     /protein_id="WP_002440614.1"
                     /translation="MSEEKFEQAKGNIKETIGDATDNKDLKAEGKGDKASGKAKEVVDD
                     VKDKANDLIDKVKGDKN"
                     /name="CsbD family protein"
     gene            958..1902
                     /locus_tag="ICN77_RS00015"
                     /old_locus_tag="ICN77_002489"
     CDS             958..1902
                     /locus_tag="ICN77_RS00015"
                     /old_locus_tag="ICN77_002489"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002440612.1"
                     /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_002440612.1"
                     /translation="MSRKEQEIHSKQSTLQEVTNYTSTGYSNSRLGVHSVHPQNPKLSF
                     DAMTIVGNLSRDNAQKLSSFMSIEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADTWD
                     RRNMRVEFNPNKLTHEEMLWLKQNIINYMEDDGFTRIDLAFDFEDDLSNYYAMTDKAVK
                     KTVFYGRDGKPETKYFGVRDSDRFIRIYNKKQERKDNADVEVMSDHLWRVEIELKRDMV
                     DYWNDCFNDLHILKPDWTSPEKLNEQAMVYMLIHEEDKWGELNKRTKYKYKNLIKEISP
                     VDLTELMKSTLRENEKQLQKQIEFWQTKGKKLF"
                     /name="replication initiation factor domain-containing
                     protein"
     Typing          1055..1877
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.204"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 tgtatacatg ggataataca aggtttaatg catgggataa aaaaggatat gatttcactt
       61 ttaaaaaggg tatttgaata atagaattgt attgtagaca ttgattattt aggaggaata
      121 gaaaatgagc gaagaaaaat tcgaacaagc aaaaggaaat atcaaagaga ctattggaga
      181 tgctactgat aataaggatt taaaagcaga aggtaaagga gataaagctt ctggtaaagc
      241 caaagaagta gtagatgatg ttaaagataa agctaatgac ttgattgata aagttaaagg
      301 agataaaaac taaataaaaa ttaaaacgtc ttaagtatta ttatgtagca tacttgggac
      361 gttttttatt taaagtgaat aaaaataaat aataagacac gcatttatgc cgagaaaatt
      421 tattgatgtt gagaagaacc cttaactaaa cttggagacg aatgtcggca tagcgtgagc
      481 tattaagccg accattcgac aagttttggg attgttaagg gttccgaggc tcaacgtcaa
      541 taaagcaatt ggaataaagc aacaaaagga gttgaagaaa atgagtgaga aaactaagaa
      601 aagcattcgt atagcattat cttttgcaca agtagtagta cagtcattta tagtttatta
      661 tgcttacaag caatataaat tatctaaaga aaattaattt ttgattatgt aataagtttt
      721 ggtactaaaa aagacttgat ctgattagac caagcctttt gatagtgtta tattaataaa
      781 caaataaaaa gaagtcgctc acccaccgac caaagtttgt gaacgacaat ccaaaaagaa
      841 aacatgagtt gttttttatg aatttgtata tttaaatact aaacgatatt taaatataca
      901 tcaagataaa tattcgggtg ggcgacttct taaattaaat taaggagtcg attttttatg
      961 agtagaaaag agcaagaaat tcattcaaag caaagcacat tacaagaagt tacaaattac
     1021 acctcaaccg gatactctaa tagccggtta ggagtgcatt ctgtgcaccc acaaaatcct
     1081 aaattaagtt ttgacgctat gacaatagtt ggaaatctca gtcgtgacaa cgctcaaaag
     1141 ctatcgtcat ttatgagtat cgaaccacaa attcgacttt gggatatact acaaacgaaa
     1201 tttaaagcta aagcactgca ggaaaaagtt tatatcgaat acgacaaagt aaaagcagat
     1261 acatgggata gacgtaatat gcgtgttgaa tttaatccga ataaacttac gcatgaagaa
     1321 atgctttggt taaaacaaaa cattatcaac tacatggaag atgacggttt tacaagaata
     1381 gatttagctt ttgattttga agatgattta agtaattatt atgcaatgac tgataaagca
     1441 gttaagaaaa ctgtatttta tggtcgtgac gggaaaccag aaacaaaata ttttggcgtt
     1501 cgtgatagtg atagatttat tagaatttat aacaaaaaac aagaacgtaa agataacgca
     1561 gatgtcgaag ttatgtctga tcacttatgg cgtgtagaaa ttgaacttaa aagagatatg
     1621 gtggattact ggaatgattg ttttaatgat ttacatatct tgaaaccaga ttggacttcg
     1681 ccagaaaaat taaatgaaca agcaatggtt tacatgttaa ttcatgaaga agacaaatgg
     1741 ggagaattga ataaaagaac taaatataaa tataaaaatt taattaaaga aatatctcca
     1801 gttgatttaa cggaattaat gaaatcgact ttaagagaaa atgaaaaaca attacaaaag
     1861 caaatagaat tttggcagac aaaaggtaag aagctatttt aaaaatggct accatttgac
     1921 tcccttttag ctcccaaatg gctccataaa aagggagcta tttgggagct atttttgatt
     1981 ttatgtagcc atttgggagt catttttgat tttgggtagc tattcggtag cttttgtgta
     2041 gtcgttcggg agtcatataa caatttttat cgcataaata ggaatcccat ttgacactgt
     2101 caaatcaata ttttgcacag aaacggctac cgaatggcta catacggaga catttctgtg
     2161 taggattcct cttatgctct tttaaaatat tttaaaatat aaaagttaca ttatacacct
     2221 atttttttca ggttttagct ttttattgag aaggataatt aaaataaaaa aacatatttt
     2281 tttctgaaag tgttgagaaa taaattttaa aatgatttat agcctctctg ttgaacaaaa
     2341 aaagttttta gtcattttta tacgtggaat gattaaatgt cctagaaagg gcttaaaatg
     2401 caaaataaaa agactactca ttttttgagt agtctatctg taggatagtt tttgatattc
     2461 taaatgaaaa ggagtaatac ataaatcatt t
//
