LOCUS       NC_005007               4679 bp    DNA     circular CON 27-MAR-2024
DEFINITION  Staphylococcus epidermidis ATCC 12228 plasmid pSE-12228-02, complete
            sequence.
ACCESSION   NC_005007
VERSION     NC_005007.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02603126
            Assembly: GCF_000007645.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus epidermidis ATCC 12228
  ORGANISM  Staphylococcus epidermidis ATCC 12228
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 4679)
  AUTHORS   Zhang,Y.Q., Ren,S.X., Li,H.L., Wang,Y.X., Fu,G., Yang,J., Qin,Z.Q.,
            Miao,Y.G., Wang,W.Y., Chen,R.S., Shen,Y., Chen,Z., Yuan,Z.H.,
            Zhao,G.P., Qu,D., Danchin,A. and Wen,Y.M.
  TITLE     Genome-based analysis of virulence genes in a non-biofilm-forming
            Staphylococcus epidermidis strain (ATCC 12228)
  JOURNAL   Mol Microbiol 49 (6), 1577-1593 (2003)
   PUBMED   12950922
REFERENCE   2  (bases 1 to 4679)
  AUTHORS   Zhang,Y., Ren,S., Li,H., Fu,G., Lu,L., Lu,G., Jia,J., Tu,Y., Qin,Z.,
            Chen,Z. and Wen,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-NOV-2002) Chinese National Human Genome Center at
            Shanghai, 250 Bi Bo Road, Shanghai 201203, China
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_000007645.1-RS_2024_03_27
            Annotation Date                   :: 03/27/2024 00:52:58
            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)                     :: 2,440
            CDSs (total)                      :: 2,359
            Genes (coding)                    :: 2,283
            CDSs (with protein)               :: 2,283
            Genes (RNA)                       :: 81
            rRNAs                             :: 6, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 61
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 76
            CDSs (without protein)            :: 76
            Pseudo Genes (ambiguous residues) :: 0 of 76
            Pseudo Genes (frameshifted)       :: 49 of 76
            Pseudo Genes (incomplete)         :: 40 of 76
            Pseudo Genes (internal stop)      :: 25 of 76
            Pseudo Genes (multiple problems)  :: 28 of 76
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AE015931.1.
            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..4679
                     /organism="Staphylococcus epidermidis ATCC 12228"
                     /mol_type="genomic DNA"
                     /strain="ATCC 12228"
                     /db_xref="ATCC:12228"
                     /db_xref="taxon:176280"
                     /plasmid="pSE-12228-02"
     gene            join(4400..4679,1..236)
                     /locus_tag="SE_RS11820"
     CDS             join(4400..4679,1..236)
                     /locus_tag="SE_RS11820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002502825.1"
                     /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_002498954.1"
                     /translation="MNLSDEDKLYISRMTDQIKRSNTHEIKVNIETDDNLSEFIKQKID
                     EKFDEKIPNLRTKQTMEQFKWSLMRIEDKQEILDDNIESVHKWATYFKSALMLTLFAVL
                     LISVVATFMGGLFNVLGFDHMYKGLEYQIKHSEGFVAFLWHLGYLIPYLLLATLIWLIL
                     ALEHKYRY"
                     /name="DUF334 domain-containing protein"
     gene            598..909
                     /locus_tag="SE_RS11825"
                     /old_locus_tag="p201"
                     /old_locus_tag="SE_p201"
     CDS             598..909
                     /locus_tag="SE_RS11825"
                     /old_locus_tag="p201"
                     /old_locus_tag="SE_p201"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002498949.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_011117534.1"
                     /translation="MKLKKVIVTVMFLLVIIFSLNIIIRFQYTESKVRSYLVNIEKKPK
                     KIELKKRIGNLPGYRNYLIEYKEKDTTKYYYYDYKAKQVKGEEQIINGYSKDLKTKSQ"
                     /name="hypothetical protein"
     gene            complement(930..1481)
                     /locus_tag="SE_RS11830"
                     /old_locus_tag="p202"
                     /old_locus_tag="SE_p202"
     CDS             complement(930..1481)
                     /locus_tag="SE_RS11830"
                     /old_locus_tag="p202"
                     /old_locus_tag="SE_p202"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002498950.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YiiX/YebB-like N1pC/P60 family cysteine
                     hydrolase"
                     /protein_id="WP_002498950.1"
                     /translation="MNRNNIFIKILFITSFAMILAIVSNHNQTFALTYKKGDVLTTRST
                     SASGLTGHNGIYIGNGKVLDTPRVHHYPRVMSVKKWIKSYPKTKVTRPKNSSLGNKAAN
                     NAVKYFKGKKIPYKVTPNPKNIKKTYCSEIVWYSYYKAGKQYMIPEHGVWLPPSIVAPY
                     AFVNKQDVKHNGFKFVDNKW"
                     /name="YiiX/YebB-like N1pC/P60 family cysteine hydrolase"
     gene            1769..2689
                     /locus_tag="SE_RS11835"
                     /old_locus_tag="p203"
                     /old_locus_tag="SE_p203"
     CDS             1769..2689
                     /locus_tag="SE_RS11835"
                     /old_locus_tag="p203"
                     /old_locus_tag="SE_p203"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002958488.1"
                     /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_011117535.1"
                     /translation="MSKKNHSNHLRNKDLDNFSKTGYSNSRLNRHTMYTPEPKLSFDAM
                     TIVGNLNKNNAHKLSEFMSIEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADTWDRRN
                     MRVEFNPNKLTHEEMLWLKQNVIDYMEDDGFTRLDLAFDFEDDLSDYYAMTDKSVKKTI
                     FYGRNGKPETKYFGVRDSDRFIRIYNKKQERRDNANIEVVSEHLWRVEIELKRGMVDYW
                     NDCFGDLHILQPDWKTIERTSDRSMVFMLLNDEEEWGKLERRTKNKYKQLIKEISPVDL
                     TELMKLTLKANEKQLQKQIDFWLIK"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            2705..2926
                     /locus_tag="SE_RS11840"
                     /old_locus_tag="p204"
                     /old_locus_tag="SE_p204"
     CDS             2705..2926
                     /locus_tag="SE_RS11840"
                     /old_locus_tag="p204"
                     /old_locus_tag="SE_p204"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002958486.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_011117536.1"
                     /translation="MSDMFEVDREIKNTYLKMSIGKNTCPKCNSIFEVSVFNDDFPNRE
                     NELVSCPYCSSLVGYVRTSGTVRSYKIN"
                     /name="hypothetical protein"
     gene            3197..3580
                     /gene="mobC"
                     /locus_tag="SE_RS11845"
                     /old_locus_tag="p205"
                     /old_locus_tag="SE_p205"
     CDS             3197..3580
                     /gene="mobC"
                     /locus_tag="SE_RS11845"
                     /old_locus_tag="p205"
                     /old_locus_tag="SE_p205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002449121.1"
                     /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_002498952.1"
                     /translation="MSEQNTFVASDETVGRNRKPNRKEPKQISFRVSESEYLKLRQSAE
                     TLNMSVPAFVKKKAQGSRLVAPKFDKETRQSIARDLSKLGANANQIAKYCNKHQHEAPN
                     YIALEHNINELRERLDEIWQQLN"
                     /name="mobC"
     gene            3562..4413
                     /locus_tag="SE_RS11850"
                     /old_locus_tag="p206"
                     /old_locus_tag="SE_p206"
     CDS             3562..4413
                     /locus_tag="SE_RS11850"
                     /old_locus_tag="p206"
                     /old_locus_tag="SE_p206"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011117537.1"
                     /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_011117537.1"
                     /translation="MATTKLGNTKSASRAINYAEKRAEEKSGLNCDIDYAKSSFKQTRA
                     LYGKENGVQAHTVIQSFKPGEVTPEQCNQLGLELAEKIAPNHQVAVYTHADTNHVHNHI
                     VINSIDLETGKKYQSNKKQREFVKQKNDEVCREHGLSVTERNATMRYTQAEKGLIEKDK
                     SSWKDEIRDAIEQSQATNFEELERELNQLDITIDRVTNKTITYRHLKENKKVRGKNLGE
                     QFDKGALENEFAVANERREFEQQLSEYEPRESEYRPRDTEKNIKRPKELRVQSRENDFE
                     LE"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     Typing          complement(2990..3226)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="80.992"
                     /coverage="100.0"
                     /evalue="1.81e-44"
     Typing          1770..2689
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3563..4410
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cagcgttgat gttgacacta tttgccgttt tattgattag cgttgtcgct acattcatgg
       61 gtggtttatt caatgtttta ggatttgacc acatgtataa aggtctagaa tatcaaataa
      121 agcactcaga aggttttgta gcatttttat ggcatttagg atacttgata ccttatttac
      181 tattagcgac gctgatatgg cttatattgg ctttagaaca caaatataga tattaacacg
      241 catttatgcc gagaaaattt attgatgttg agaagaaccc ttaactaaac tgtagcgacg
      301 aatgtcggca tagcgtgagc tattaggccg acgagtcgac agttttgggg tttgttaagg
      361 gttcagaggc tcaacgtcaa taaagcaatt ggaataaagc aaaaatttat acaatttcaa
      421 ataggaggtt ttcatgtgat aaaagagtta tttttaagtg tattgttttt tattgttatt
      481 attttgatct taacgttttc agattatata tttttaaatg atatcaatac tttaaaaaat
      541 atattggcaa caatggctat aacaatattt attatgtgtg ttatagggag ggattaaatg
      601 aaattaaaaa aagtaatagt tactgttatg tttttattag taataatatt ttctttaaat
      661 attattataa gatttcagta tacggaaagt aaggttcgct catatttggt taacattgag
      721 aaaaaaccta aaaaaattga attaaaaaaa agaattggga atttaccagg atataggaat
      781 tatttaatag aatataaaga aaaagatact acgaagtact actattatga ctataaagca
      841 aagcaagtga agggagaaga gcaaataata aatggttatt ctaaagattt aaagactaaa
      901 tctcaataga tttagtcttt attttgtaac taccatttat tatctacgaa tttaaaacca
      961 ttgtgcttaa catcttgttt attaacaaat gcatatgggg ctacaatact tggtggtaac
     1021 caaactccat gctcggggat catatattgt tttccagctt tgtaatagga ataccatact
     1081 atttcgctgc aataggtttt tttgatattt ttaggatttg gtgtaacctt atatggtatt
     1141 tttttgcctt taaaatattt aacggcgttg tttgcagctt tatttcctag actagaattt
     1201 tttggtcgtg ttacttttgt tttaggatag cttttaatcc attttttcac tgacattact
     1261 cttggataat ggtgaactct aggagtgtct agaacttttc cattacctat gtatataccg
     1321 ttatgtcctg taagaccact tgcactagta cttctagttg ttaagacatc acctttttta
     1381 taagtaagag caaaagtttg attgtggtta ctaacaattg caagaatcat agcaaatgat
     1441 gtgataaata aaatttttat gaatatatta tttctattca tatatttcac ctccgtaaat
     1501 tatattacat tttttatata aaaataaaaa gacgtattct taatagacct agatttttta
     1561 tagtgttata ttaatagcaa aataaaaaag aagtcgtcca ccccaaaccg accaaagttt
     1621 acgtgaacga ctagccaaaa tataaaacag tcgatgtttt tatgtttttg tatattttga
     1681 tattaaacga tatttgatta tacttcaaca tttacatttg acgtttgggt ggacgacttc
     1741 ttaaaacaaa ttaaggagtc gattttttat gagtaagaaa aatcattcaa atcacttacg
     1801 aaataaggat ttagataatt tttctaaaac cggctactct aatagccggt taaaccgaca
     1861 tactatgtac acacccgaac caaaattaag ctttgacgct atgactattg ttggaaatct
     1921 taataaaaat aatgctcaca aactatctga atttatgagt attgagccac aaatacgact
     1981 ttgggatata cttcaaacta aatttaaagc taaggcgcta caagaaaaag tttatattga
     2041 atatgacaaa gtaaaagcag atacgtggga tagacgtaat atgcgtgttg aatttaatcc
     2101 aaataaactt acgcatgaag aaatgctttg gttaaaacaa aacgttatcg actacatgga
     2161 agatgacggt tttacaagat tagatttagc ttttgatttt gaagatgatt taagtgatta
     2221 ttatgcaatg actgataaat cagttaagaa aactattttc tatggtcgta atggtaaacc
     2281 agaaacaaaa tattttggtg ttcgtgacag tgataggttt attagaattt ataataaaaa
     2341 acaggaacgt agggataatg caaatattga agttgtttca gaacatctat ggcgtgtaga
     2401 aattgaatta aaaagaggta tggttgatta ttggaacgat tgttttggtg atttacatat
     2461 attacaacca gattggaaaa ctatcgaacg tacttctgat agatcaatgg tttttatgtt
     2521 gttgaatgac gaagaagaat ggggaaaatt agaaagacgt actaagaata aatataagca
     2581 attaattaaa gaaatatctc cagttgattt aacggaatta atgaaattga ctttaaaagc
     2641 gaatgaaaaa caattgcaaa agcagattga tttttggtta attaaataaa aaaggagttt
     2701 taatatgtca gatatgtttg aagtagatag agaaattaaa aatacttatt tgaaaatgag
     2761 tattggaaaa aatacttgtc cgaaatgtaa tagcattttt gaagtttcag tttttaatga
     2821 tgattttccg aatagagaga atgaattagt atcttgtcca tattgttcta gtttagttgg
     2881 ttacgttaga acaagtggaa ctgttagatc ttataaaatt aattaagctt ttaaggatat
     2941 atagcaacca ccatttttgg ttgctggggg tttaatggtc ttgaacttag tggctagcaa
     3001 ttagccacta tttttgtgta aacaaaaata caaaaggggt atggggatat tccccatcaa
     3061 gccggtatat tcagaacgaa gtggctagaa tatacgacgc ttgccaaacc actaaatgac
     3121 ttgataaaat ctggcttacc ctgtaagcta gatttatatt aagtcattac tttcgaagaa
     3181 agcgtggtgg gattaaatga gcgaacaaaa cacatttgtg gctagcgacg aaactgttgg
     3241 gcgaaaccgt aaacccaacc gtaaggagcc aaaacaaatt agttttcgtg tgagcgaatc
     3301 cgaatattta aagttaaggc aatctgcgga aactttaaat atgagtgtgc ctgctttcgt
     3361 aaagaaaaag gcacaaggca gtcgattagt cgcaccaaaa tttgataaag aaacgcgaca
     3421 atcgattgct agagatttaa gtaagttagg tgcaaacgcc aatcagattg ctaaatattg
     3481 taataaacat caacatgaag cacccaatta catagcgtta gaacataata tcaatgagtt
     3541 acgtgaaagg cttgatgaga tatggcaaca actaaattag gtaataccaa atcagcaagt
     3601 cgagcaatca attacgcaga aaagcgagca gaagaaaaaa gtggcttaaa ttgtgatata
     3661 gattatgcaa aatcatcgtt taagcaaaca cgagctttat atggcaaaga gaatggtgtt
     3721 caagcacata cagtgattca atcgttcaag cctggcgagg taacgccaga gcaatgtaat
     3781 caattgggtc tagaattggc agaaaagatt gcacctaatc atcaagtagc cgtctatacg
     3841 cacgcagata caaatcatgt acacaatcat attgtgatta attcaattga tttagaaact
     3901 gggaaaaaat atcaaagcaa taaaaaacaa agagagttcg taaaacaaaa aaatgatgaa
     3961 gtatgtagag aacatggatt gtctgtaact gaacgcaatg caacaatgcg atatactcaa
     4021 gccgaaaaag gcttaattga aaaagataaa agctcttgga aagacgaaat tagagatgcg
     4081 attgaacaat cacaagcgac aaattttgag gagcttgaga gagagttgaa ccaattagac
     4141 atcacaatcg atcgtgtcac aaacaaaaca atcacttaca gacacttgaa agaaaataaa
     4201 aaagtgagag gtaaaaattt aggtgaacaa ttcgataagg gggcattaga aaatgagttt
     4261 gcggtcgcaa atgaacggag agaattcgag caacaattat cagaatacga accgagagaa
     4321 agtgagtaca gaccaagaga tacagaaaaa aatattaaac gtcctaaaga acttagagtc
     4381 caatcacgag aaaacgactt tgaacttgag tgatgaagac aagctatata tatcacgaat
     4441 gaccgatcag ataaaacgct cgaatacgca tgagattaaa gtaaatattg agacagatga
     4501 taatctaagc gaatttatta aacaaaaaat cgatgagaaa tttgatgaaa aaatacctaa
     4561 tcttcgtaca aagcaaacaa tggaacaatt caaatggtct ttgatgagaa ttgaggataa
     4621 acaagaaata ctcgatgaca atattgaaag tgttcacaaa tgggcgactt actttaagt
//
