LOCUS       NZ_CP065657             4679 bp    DNA     circular CON 15-FEB-2024
DEFINITION  Staphylococcus epidermidis strain FDAARGOS_913 plasmid unnamed3,
            complete sequence.
ACCESSION   NZ_CP065657
VERSION     NZ_CP065657.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13450443
            Assembly: GCF_016026915.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 4679)
  AUTHORS   Jackson,S., Kralj,J., Tallon,L., Sadzewicz,L., Zhao,X., Boylan,J.,
            Ott,S., Bowen,H., Vavikolanu,K., Mehta,A., Aluvathingal,J.,
            Nadendla,S., Yan,Y. and Sichtig,H.
  TITLE     FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS):
            Supporting development and validation of Infectious Disease Dx tests
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4679)
  AUTHORS   Jackson,S., Kralj,J., Tallon,L., Sadzewicz,L., Zhao,X., Boylan,J.,
            Ott,S., Bowen,H., Vavikolanu,K., Mehta,A., Aluvathingal,J.,
            Nadendla,S., Yan,Y. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-DEC-2020) Center for Devices and Radiological Health,
            US Food and Drug Administration, 10903 New Hampshire Avenue, Silver
            Spring, MD 20993-0002, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Canu v. 1.7
            Genome Coverage                   :: 2034.24x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/15/2024 04:08:23
            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)                     :: 2,517
            CDSs (total)                      :: 2,433
            Genes (coding)                    :: 2,341
            CDSs (with protein)               :: 2,341
            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)              :: 92
            CDSs (without protein)            :: 92
            Pseudo Genes (ambiguous residues) :: 0 of 92
            Pseudo Genes (frameshifted)       :: 58 of 92
            Pseudo Genes (incomplete)         :: 47 of 92
            Pseudo Genes (internal stop)      :: 30 of 92
            Pseudo Genes (multiple problems)  :: 33 of 92
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP065657.1.
            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"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_913"
                     /culture_collection="ATCC:12228-1"
                     /db_xref="taxon:1282"
                     /plasmid="unnamed3"
                     /collected_by="NIST<ATCC"
     gene            complement(join(3823..4679,1..64))
                     /locus_tag="I6G70_RS11905"
                     /old_locus_tag="I6G70_11905"
     CDS             complement(join(3823..4679,1..64))
                     /locus_tag="I6G70_RS11905"
                     /old_locus_tag="I6G70_11905"
                     /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_197931517.1"
                     /translation="MSKKNHSNHLRNKDLDNFSKTGYSNSRLNRHTMYTPEPKLSFDAM
                     TIVGNLNKNNAHKLSEFMSIEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADTWDRRN
                     MRVEFNPNKLTHEEMLWLKQNVIDYMEDDGFTRLDLAFDFEDDLSDYYAMTDKSVKKTI
                     FYGRNGKPETKYFGVRDSDRFIRIYNKKQERRDNANIEVVSEHLWRVEIELKRGMVDYW
                     NDCFGDLHILQPDWKTIERTSDRSMVFMLLNDEEEWEKLERRTKNKYKQLIKEISPVDL
                     TELMKLTLKANEKQLQKQIDFWLIK"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            352..903
                     /locus_tag="I6G70_RS11910"
                     /old_locus_tag="I6G70_11910"
     CDS             352..903
                     /locus_tag="I6G70_RS11910"
                     /old_locus_tag="I6G70_11910"
                     /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            complement(924..1235)
                     /locus_tag="I6G70_RS11915"
                     /old_locus_tag="I6G70_11915"
     CDS             complement(924..1235)
                     /locus_tag="I6G70_RS11915"
                     /old_locus_tag="I6G70_11915"
                     /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(1597..2112)
                     /locus_tag="I6G70_RS11920"
                     /old_locus_tag="I6G70_11920"
     CDS             complement(1597..2112)
                     /locus_tag="I6G70_RS11920"
                     /old_locus_tag="I6G70_11920"
                     /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            complement(2099..2950)
                     /locus_tag="I6G70_RS11925"
                     /old_locus_tag="I6G70_11925"
     CDS             complement(2099..2950)
                     /locus_tag="I6G70_RS11925"
                     /old_locus_tag="I6G70_11925"
                     /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"
     gene            complement(2932..3315)
                     /gene="mobC"
                     /locus_tag="I6G70_RS11930"
                     /old_locus_tag="I6G70_11930"
     CDS             complement(2932..3315)
                     /gene="mobC"
                     /locus_tag="I6G70_RS11930"
                     /old_locus_tag="I6G70_11930"
                     /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            complement(3586..3807)
                     /locus_tag="I6G70_RS11935"
                     /old_locus_tag="I6G70_11935"
     CDS             complement(3586..3807)
                     /locus_tag="I6G70_RS11935"
                     /old_locus_tag="I6G70_11935"
                     /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"
     Typing          3287..3523
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="80.992"
                     /coverage="100.0"
                     /evalue="1.81e-44"
     Typing          complement(3824..4679)
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.883"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2103..2950)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cggttttaga aaaattatct aaatccttat ttcgtaagtg atttgaatga tttttcttac
       61 tcataaaaaa tcgactcctt aatttgtttt aagaagtcgt ccacccaaac gtcaaatgta
      121 aatgttgaag tataatcaaa tatcgtttaa tatcaaaata tacaaaaaca taaaaacatc
      181 gactgtttta tattttggct agtcgttcac gtaaactttg gtcggtttgg ggtggacgac
      241 ttctttttta ttttgctatt aatataacac tataaaaaat ctaggtctat taagaatacg
      301 tctttttatt tttatataaa aaatgtaata taatttacgg aggtgaaata tatgaataga
      361 aataatatat tcataaaaat tttatttatc acatcatttg ctatgattct tgcaattgtt
      421 agtaaccaca atcaaacttt tgctcttact tataaaaaag gtgatgtctt aacaactaga
      481 agtactagtg caagtggtct tacaggacat aacggtatat acataggtaa tggaaaagtt
      541 ctagacactc ctagagttca ccattatcca agagtaatgt cagtgaaaaa atggattaaa
      601 agctatccta aaacaaaagt aacacgacca aaaaattcta gtctaggaaa taaagctgca
      661 aacaacgccg ttaaatattt taaaggcaaa aaaataccat ataaggttac accaaatcct
      721 aaaaatatca aaaaaaccta ttgcagcgaa atagtatggt attcctatta caaagctgga
      781 aaacaatata tgatccccga gcatggagtt tggttaccac caagtattgt agccccatat
      841 gcatttgtta ataaacaaga tgttaagcac aatggtttta aattcgtaga taataaatgg
      901 tagttacaaa ataaagacta aatctattga gatttagtct ttaaatcttt agaataacca
      961 tttattattt gctcttctcc cttcacttgc tttgctttat agtcataata gtagtacttc
     1021 gtagtatctt tttctttata ttctattaaa taattcctat atcctggtaa attcccaatt
     1081 ctttttttta attcaatttt tttaggtttt ttctcaatgt taaccaaata tgagcgaacc
     1141 ttactttccg tatactgaaa tcttataata atatttaaag aaaatattat tactaataaa
     1201 aacataacag taactattac tttttttaat ttcatttaat ccctccctat aacacacata
     1261 ataaatattg ttatagccat tgttgccaat atatttttta aagtattgat atcatttaaa
     1321 aatatataat ctgaaaacgt taagatcaaa ataataacaa taaaaaacaa tacacttaaa
     1381 aataactctt ttatcacatg aaaacctcct atttgaaatt gtataaattt ttgctttatt
     1441 ccaattgctt tattgacgtt gagcctctga acccttaaca aaccccaaaa ctgtcgactc
     1501 gtcggcctaa tagctcacgc tatgccgaca ttcgtcgcta cagtttagtt aagggttctt
     1561 ctcaacatca ataaattttc tcggcataaa tgcgtgttaa tatctatatt tgtgttctaa
     1621 agccaatata agccatatca gcgtcgctaa tagtaaataa ggtatcaagt atcctaaatg
     1681 ccataaaaat gctacaaaac cttctgagtg ctttatttga tattctagac ctttatacat
     1741 gtggtcaaat cctaaaacat tgaataaacc acccatgaat gtagcgacaa cgctaatcaa
     1801 taaaacggca aatagtgtca acatcaacgc tgacttaaag taagtcgccc atttgtgaac
     1861 actttcaata ttgtcatcga gtatttcttg tttatcctca attctcatca aagaccattt
     1921 gaattgttcc attgtttgct ttgtacgaag attaggtatt ttttcatcaa atttctcatc
     1981 gattttttgt ttaataaatt cgcttagatt atcatctgtc tcaatattta ctttaatctc
     2041 atgcgtattc gagcgtttta tctgatcggt cattcgtgat atatatagct tgtcttcatc
     2101 actcaagttc aaagtcgttt tctcgtgatt ggactctaag ttctttagga cgtttaatat
     2161 ttttttctgt atctcttggt ctgtactcac tttctctcgg ttcgtattct gataattgtt
     2221 gctcgaattc tctccgttca tttgcgaccg caaactcatt ttctaatgcc cccttatcga
     2281 attgttcacc taaattttta cctctcactt ttttattttc tttcaagtgt ctgtaagtga
     2341 ttgttttgtt tgtgacacga tcgattgtga tgtctaattg gttcaactct ctctcaagct
     2401 cctcaaaatt tgtcgcttgt gattgttcaa tcgcatctct aatttcgtct ttccaagagc
     2461 ttttatcttt ttcaattaag cctttttcgg cttgagtata tcgcattgtt gcattgcgtt
     2521 cagttacaga caatccatgt tctctacata cttcatcatt tttttgtttt acgaactctc
     2581 tttgtttttt attgctttga tattttttcc cagtttctaa atcaattgaa ttaatcacaa
     2641 tatgattgtg tacatgattt gtatctgcgt gcgtatagac ggctacttga tgattaggtg
     2701 caatcttttc tgccaattct agacccaatt gattacattg ctctggcgtt acctcgccag
     2761 gcttgaacga ttgaatcact gtatgtgctt gaacaccatt ctctttgcca tataaagctc
     2821 gtgtttgctt aaacgatgat tttgcataat ctatatcaca atttaagcca cttttttctt
     2881 ctgctcgctt ttctgcgtaa ttgattgctc gacttgctga tttggtatta cctaatttag
     2941 ttgttgccat atctcatcaa gcctttcacg taactcattg atattatgtt ctaacgctat
     3001 gtaattgggt gcttcatgtt gatgtttatt acaatattta gcaatctgat tggcgtttgc
     3061 acctaactta cttaaatctc tagcaatcga ttgtcgcgtt tctttatcaa attttggtgc
     3121 gactaatcga ctgccttgtg cctttttctt tacgaaagca ggcacactca tatttaaagt
     3181 ttccgcagat tgccttaact ttaaatattc ggattcgctc acacgaaaac taatttgttt
     3241 tggctcctta cggttgggtt tacggtttcg cccaacagtt tcgtcgctag ccacaaatgt
     3301 gttttgttcg ctcatttaat cccaccacgc tttcttcgaa agtaatgact taatataaat
     3361 ctagcttaca gggtaagcca gattttatca agtcatttag tggtttggca agcgtcgtat
     3421 attctagcca cttcgttctg aatataccgg cttgatgggg aatatcccca tacccctttt
     3481 gtatttttgt ttacacaaaa atagtggcta attgctagcc actaagttca agaccattaa
     3541 acccccagca accaaaaatg gtggttgcta tatatcctta aaagcttaat taattttata
     3601 agatctaaca gttccacttg ttctaacgta accaactaaa ctagaacaat atggacaaga
     3661 tactaattca ttctctctat tcggaaaatc atcattaaaa actgaaactt caaaaatgct
     3721 attacatttc ggacaagtat tttttccaat actcattttc aaataagtat ttttaatttc
     3781 tctatctact tcaaacatat ctgacatatt aaaactcctt ttttatttaa ttaaccaaaa
     3841 atcaatctgc ttttgcaatt gtttttcatt cgcttttaaa gtcaatttca ttaattccgt
     3901 taaatcaact ggagatattt ctttaattaa ttgcttatat ttattcttag tacgtctttc
     3961 taatttttcc cattcttctt cgtcattcaa caacataaaa accattgatc tatcagaagt
     4021 acgttcgata gttttccaat ctggttgtaa tatatgtaaa tcaccaaaac aatcgttcca
     4081 ataatcaacc atacctcttt ttaattcaat ttctacacgc catagatgtt ctgaaacaac
     4141 ttcaatattt gcattatccc tacgttcctg ttttttatta taaattctaa taaacctatc
     4201 actgtcacga acaccaaaat attttgtttc tggtttacca ttacgaccat agaaaatagt
     4261 tttcttaact gatttatcag tcattgcata ataatcactt aaatcatctt caaaatcaaa
     4321 agctaaatct aatcttgtaa aaccgtcatc ttccatgtag tcgataacgt tttgttttaa
     4381 ccaaagcatt tcttcatgcg taagtttatt tggattaaat tcaacacgca tattacgtct
     4441 atcccacgta tctgctttta ctttgtcata ttcaatataa actttttctt gtagcgcctt
     4501 agctttaaat ttagtttgaa gtatatccca aagtcgtatt tgtggctcaa tactcataaa
     4561 ttcagatagt ttgtgagcat tatttttatt aagatttcca acaatagtca tagcgtcaaa
     4621 gcttaatttt ggttcgggtg tgtacatagt atgtcggttt aaccggctat tagagtagc
//
