LOCUS       NZ_CP073901             6455 bp    DNA     circular CON 16-APR-2024
DEFINITION  Staphylococcus epidermidis strain V1949610 plasmid p2V1949610,
            complete sequence.
ACCESSION   NZ_CP073901
VERSION     NZ_CP073901.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18699900
            Assembly: GCF_019330225.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 6455)
  AUTHORS   Papan,C., Schroder,M., Hoffmann,M., Knoll,H., Last,K., Albrecht,F.,
            Geisel,J., Fink,T., Gartner,B.C., Mellmann,A., Volk,T., Berger,F.K.
            and Becker,S.L.
  TITLE     Combined antibiotic stewardship and infection control measures to
            contain the spread of linezolid-resistant Staphylococcus epidermidis
            in an intensive care unit
  JOURNAL   Antimicrob Resist Infect Control 10 (1), 99 (2021)
   PUBMED   34193293
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 6455)
  AUTHORS   Mellmann,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-APR-2021) Inst. Hygiene, University Hospital Muenster,
            Robert-Koch-Str. 41, Muenster 48149, Germany
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. SMRT Link V8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 458x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_019330225.1-RS_2024_04_16
            Annotation Date                   :: 04/16/2024 08:09:37
            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)                     :: 2,679
            CDSs (total)                      :: 2,598
            Genes (coding)                    :: 2,519
            CDSs (with protein)               :: 2,519
            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)              :: 79
            CDSs (without protein)            :: 79
            Pseudo Genes (ambiguous residues) :: 0 of 79
            Pseudo Genes (frameshifted)       :: 40 of 79
            Pseudo Genes (incomplete)         :: 44 of 79
            Pseudo Genes (internal stop)      :: 28 of 79
            Pseudo Genes (multiple problems)  :: 24 of 79
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP073901.1.
            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..6455
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="V1949610"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="p2V1949610"
                     /geo_loc_name="Germany"
                     /collected_by="Institute of Medical Microbiology and
                     Hygiene, Saarland University, Homburg, Germany"
     gene            join(6056..6455,1..245)
                     /locus_tag="KFV25_RS13175"
                     /old_locus_tag="KFV25_13190"
     CDS             join(6056..6455,1..245)
                     /locus_tag="KFV25_RS13175"
                     /old_locus_tag="KFV25_13190"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_063278520.1"
                     /translation="MNMKTINKIVSWFLYIGLPLVVVGLFIWQLDNLEKFFKKYPNAID
                     GATLVFVLITTTLSIIISYKSYKSNIKLFKDNKNEQSYKIQQLLKTETKDSIQKLIGFK
                     SNYKRTQINIFDEIKKLDLENELKNMGTKIKDIREKNIESLIPRDFEKIQDDLELISAI
                     EIQVAYYNTLLELIETQENIRDSLPESAKEQIKQHEETLMYEIDKLIERFK"
                     /name="hypothetical protein"
     gene            524..754
                     /locus_tag="KFV25_RS13180"
                     /old_locus_tag="KFV25_13195"
     CDS             524..754
                     /locus_tag="KFV25_RS13180"
                     /old_locus_tag="KFV25_13195"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_063278521.1"
                     /translation="MPTATKEHKEVMAERNIEIRDRLLKFWRENYEPKFKLISSEIDVS
                     YTNMRRYVNKHHNFGKKNLDKLEKFLIKQGY"
                     /name="hypothetical protein"
     gene            878..2371
                     /locus_tag="KFV25_RS13185"
                     /old_locus_tag="KFV25_13200"
     CDS             878..2371
                     /locus_tag="KFV25_RS13185"
                     /old_locus_tag="KFV25_13200"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_063278522.1"
                     /translation="MAQDNYYSLVQALKKYFVSSKQKHIEQREDGSYRHIPNGLCDNDL
                     VSHIKGIKTVGIFSGEVFTKFLCFDVDTGKSNKAQARNDVLNLRLSLITDFGLSDNNLE
                     VVDSGNKGYHVYLFFDDLIHVSYLKAFYREVLERNNYKPSDIEFRPTHTQGVKLPLGIH
                     RVTGKQCYFVDPSTPKFKRKPLETIHNIKQINTKLFKEKLQLKDLYELQIEDYTYELCK
                     FMKEDEAKLLNGVLNSLDFSTYEVTHAKENIIEMLETNTLVYPDSRNKYTLLIAIYLKG
                     QGYDVEDTIAKINEIMFYSKRQHKDLIQSSEKHIMNETKKIAKYVYRTNITLGGINRDV
                     YLYADELKDVLALRKTHLMKLYTSMLIHAKRHQPLGEKTFYMAYSVMINYGNNSNRSKL
                     KRYLEELQQLNRISIEENHVIDPVMSEIKGHLFSKTNVYSIKKSFNQNSHHKVLIKADE
                     KTVSTTDILIRAYQNNVINYEYIKDNLTRRQFEKFKQAL"
                     /name="hypothetical protein"
     gene            complement(2607..3197)
                     /locus_tag="KFV25_RS13190"
                     /old_locus_tag="KFV25_13205"
     CDS             complement(2607..3197)
                     /locus_tag="KFV25_RS13190"
                     /old_locus_tag="KFV25_13205"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_063279196.1"
                     /translation="MQQPNELSTKNASQFLNISVSSMRLYAKTMESLGYEFKTVENARR
                     FTKYDLQIIYEAMERFKLVGGTMKQSLHYTIVKYEQGQEIADAMPQTTKKNRKVSDELE
                     ALQTNMINEVSNNLKTELVKQYNELSKTIKNSQAQSSEIKYIKADYQTLNDKYNALLDE
                     NKKLKEENKRLHEEMNKLKSKSLWELRKWKKER"
                     /name="hypothetical protein"
     gene            3576..4061
                     /locus_tag="KFV25_RS13195"
                     /old_locus_tag="KFV25_13210"
     CDS             3576..4061
                     /locus_tag="KFV25_RS13195"
                     /old_locus_tag="KFV25_13210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002416577.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_080464618.1"
                     /translation="MEKLKRGAKPKVDYWLTSEGLTLLQGWARKGLSNKQIAQNMGIHQ
                     ATFYKWQNKYSEIYDTIKKGKEVVDYEVENTLLKCALGFEYEETKVNSDGTTIKYIKHV
                     KPNVTAIIFWLKNRKPNEWLEGYQDDSNINYNIDFSDVSTEDLRNCINENGGTYNEN"
                     /name="helix-turn-helix domain-containing protein"
     gene            4051..4221
                     /locus_tag="KFV25_RS13200"
                     /old_locus_tag="KFV25_13215"
     CDS             4051..4221
                     /locus_tag="KFV25_RS13200"
                     /old_locus_tag="KFV25_13215"
                     /inference="COORDINATES: protein motif:HMM:NF024139.4"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_166738018.1"
                     /translation="MRIETYTVNEVAQLLDMNIRTVRKYIKIGEIKASKIGRKYIITSD
                     NVKKFLENKEL"
                     /name="helix-turn-helix domain-containing protein"
     gene            4236..4925
                     /locus_tag="KFV25_RS13205"
                     /old_locus_tag="KFV25_13220"
     CDS             4236..4925
                     /locus_tag="KFV25_RS13205"
                     /old_locus_tag="KFV25_13220"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_063278518.1"
                     /translation="METVETIKKDIEELNKRAKNTIDIDKKKDYIQGIEDIKTKYKDKY
                     TDEALAETINTYKQDKLKGIYDTLNKFDEQSKELGKNIEERILKLEESSKATLEPKTQY
                     DFERYNFLFSKIQNEMMNLFTDKNNNREWQLDEHIKQAKHDYLYANALLNNEGLLINNI
                     RNNKYISNVERDKLKTYVKMNFEAIKKSNVPKEYKEIEGLKNKLRNNKSASSNKKMMFD
                     FMIGKIS"
                     /name="hypothetical protein"
     gene            5122..5739
                     /locus_tag="KFV25_RS13210"
                     /old_locus_tag="KFV25_13225"
     CDS             5122..5739
                     /locus_tag="KFV25_RS13210"
                     /old_locus_tag="KFV25_13225"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_063278519.1"
                     /translation="MKKNRGSKITLVIVFIMLGILIYLSFSNLGSEDNHKSHENSDKKR
                     TDVKKNKKQSSSKDKNKSHENNDRSLKNNNEDTSNSHEYYDDPSLDKQVYEDIKESMTL
                     LNSLTSQDIKEYKVNTQIYNQDKKPNVIITVDLKGKEDYSNSELKYRTEHISSNFTGRN
                     EIEGGFNGYFDKLYIKFKEDGIDVGEAKVKFNDSLNPEVQIK"
                     /name="hypothetical protein"
ORIGIN
        1 taaaagatat tagggaaaag aatatagaaa gtttaatacc aagagatttt gaaaagatac
       61 aagatgattt agaactaata agcgcgattg aaattcaagt tgcttattat aatactttac
      121 ttgaattaat tgaaacacaa gaaaatatta gagattcatt accagaatca gcaaaagaac
      181 aaataaagca acatgaagaa acacttatgt acgaaataga caaacttatc gaacgtttta
      241 aatagtttta ggattattta atagacaaaa agcatctaac cttaattggt caggtgcttt
      301 tttgattgca aacattcaag aacatataaa cgagaatgat aagatgaata cttttgggcg
      361 ttatgtaatc attgatagaa acgacagtat cttatatgta tgtttaacaa ataagaacaa
      421 agcatttatt ttagagtaat aaaataagta ccacaaaaat gttgttttat tattataata
      481 aatgtatcat aaaaacatat tatgtttaag gaggtgtaga acaatgccaa cagcaacaaa
      541 agaacataaa gaagtaatgg cagagcgtaa tattgaaatt cgtgatagat tattaaagtt
      601 ttggcgtgag aattatgagc ctaagtttaa acttatttct tcagagatag acgtaagtta
      661 taccaatatg cgtcgttacg tcaacaaaca tcataatttc ggtaaaaaaa acttagataa
      721 gcttgagaaa ttcttaatta aacaaggtta ttagaagcat tcagataata tatttagcac
      781 agttatataa aaatattatg cttatgtaca aaagataaca ctatgtacta tgtattgata
      841 tctatcttat tattatattt ttacaaagga gtatattatg gcacaagata attattattc
      901 acttgtgcag gctcttaaga agtattttgt cagtagtaaa cagaaacata ttgaacaacg
      961 agaagatggc tcttatagac atatacctaa tggtttatgt gataatgatt tagttagtca
     1021 tattaaaggg attaaaaccg taggtatatt tagtggagaa gtatttacta agtttttatg
     1081 ttttgatgta gatacaggta aatctaataa agcacaggct cgtaatgatg tgttaaacct
     1141 aagactatct ttaataactg attttggact atctgataac aaccttgaag tagttgatag
     1201 tgggaataaa ggttatcatg tttatttatt ttttgacgat cttatacatg ttagttattt
     1261 aaaagcattt tatcgtgaag ttttggaaag aaataactat aaaccttctg atattgaatt
     1321 tagacctaca catacacaag gtgttaaatt acctttaggt attcatagag tgacaggaaa
     1381 gcaatgttat tttgttgatc cttctacacc taaattcaaa agaaaacctt tagaaactat
     1441 tcataatatt aaacagataa atacaaaatt atttaaagag aagttacaac ttaaggactt
     1501 gtacgagtta caaattgaag attatacata tgagctatgt aagtttatga aagaagatga
     1561 ggctaagtta ctcaatggcg tattaaattc attagatttt agtacctatg aagttactca
     1621 tgctaaagaa aacattattg aaatgttaga gactaatact cttgtttatc ctgatagtag
     1681 aaacaaatat acattgttga ttgctatata tttaaagggt caaggttatg atgttgaaga
     1741 tacgatagca aaaatcaatg aaattatgtt ttatagtaaa agacagcata aagatttaat
     1801 acaatcatct gagaaacata ttatgaatga aacaaaaaaa attgctaaat atgtatatag
     1861 aactaatatc acgttaggtg gtataaatag agatgtttat ttatatgctg atgaacttaa
     1921 agatgtatta gctttgagaa agacacattt aatgaaactc tatacatcaa tgttgataca
     1981 tgctaaaagg catcaaccat taggcgaaaa aacgttctat atggcctact cagttatgat
     2041 taattacggt aacaatagca atagaagtaa gctaaagcga taccttgagg aactacaaca
     2101 gctaaataga attagcattg aagaaaacca tgtaattgat ccagttatga gtgagataaa
     2161 aggtcactta tttagtaaaa ccaacgttta tagcataaaa aaaagcttta accaaaactc
     2221 ccatcacaaa gttttaatta aagcagacga aaaaaccgtc agtactactg atatacttat
     2281 aagagcttat cagaataatg ttataaacta tgaatatatt aaagacaatc ttactagacg
     2341 acagtttgag aaattcaaac aagctcttta gtgagtttgt ctttttttaa ttgaatttac
     2401 aatttaaagt ataaatgaaa gaacatatac atgcaataat aaaagcatag cagtaactta
     2461 tcttttttat ttatcttcaa ttcaaattat aacataattt agagagccat attcagcaat
     2521 tatatagttt tagttataaa aaccattcat aaaatttaaa tgctctatat agctctttaa
     2581 atgcctttat atttaattcc actttattag cgttcttttt tccattttct taattcccac
     2641 aagcttttac tttttagctt attcatttct tcatgaagtc ttttattttc ttcttttaac
     2701 ttcttatttt catcaagcaa agcattatat ttatcattta acgtttggta atcagcttta
     2761 atatatttta tttcacttga ttgtgcttgg ctatttttaa tagttttact taattcattg
     2821 tactgtttta ctaattctgt ttttagatta ttactaactt cattgatcat attagtttgt
     2881 aatgcttcta attcatcaga gacttttcta tttttctttg tagtttgtgg catagcgtca
     2941 gcaatttctt gcccttgttc atatttaaca atcgtatagt gtagtgattg tttcattgtt
     3001 cctccaacaa gtttaaaacg ttccattgcc tcataaataa tttgcaaatc gtatttagtg
     3061 aaacgacgtg cattttctac tgttttaaat tcatagccta agctctccat agttttagca
     3121 tataaacgca tagatgacac agatatgttt aaaaattgac ttgcattttt agtgcttaat
     3181 tcatttggtt gttgcatatt ttttacacct aaagcctttc atttaggcat ttataggtaa
     3241 aaggcgacaa taataatatt aagcctttaa tgccttaatg atgggtatta acgctaccta
     3301 taacgccata ttattctctt attaaatagc tatattccta attaaaataa tagcatgaat
     3361 atgtgctgat acacacgcga aacctcactt attgtggtat aatagataca gataaagcct
     3421 tgatataaag ctgtttataa ggttttttct attaatggaa aagtgaagaa aataaagaaa
     3481 aacgagaaaa gatatattga attaaatatt aaattagcca taaggggcaa agaaacaata
     3541 aacccctata aaattcactt ataaggaggt aacttatgga aaaattaaaa agaggtgcaa
     3601 agcctaaagt agattattgg cttacctctg aagggctgac gttattacaa ggttgggcaa
     3661 gaaaaggatt aagcaataaa caaattgctc aaaatatggg cattcatcaa gctacatttt
     3721 ataaatggca aaataaatat agcgaaattt acgacactat aaaaaaagga aaagaagtcg
     3781 tggattatga agtggaaaat acacttttaa aatgtgcatt aggttttgag tatgaagaaa
     3841 caaaagtaaa tagtgatggt actacgataa agtatataaa acacgttaaa cctaatgtaa
     3901 cagctataat attttggttg aagaaccgta agcctaatga atggttagaa ggttatcagg
     3961 acgatagtaa tattaattat aatattgatt tttctgatgt aagcactgag gatttacgta
     4021 actgtatcaa tgaaaacggg ggtacttata atgagaattg aaacatatac agtcaatgaa
     4081 gtagcccagt tgttagatat gaatattaga acagttagaa aatacataaa aattggagaa
     4141 attaaagcca gtaaaatagg acgaaaatat attatcactt cagataatgt taaaaagttt
     4201 cttgaaaaca aagaactata aaaggaggca taaaaatgga aacagtagaa acaattaaaa
     4261 aagatattga ggaattaaat aagcgtgcta aaaatactat tgatattgat aagaaaaaag
     4321 actatataca aggtattgaa gatattaaaa ctaaatacaa agataagtat acagatgaag
     4381 cgttagcaga aacgatcaat acatataaac aagataaatt aaaaggaatt tacgataccc
     4441 ttaataaatt tgatgagcaa tcaaaagaac taggaaaaaa tattgaagaa agaatattaa
     4501 aactagaaga aagttcaaag gcaacactag aaccgaaaac acaatatgac tttgaaagat
     4561 ataatttttt attcagcaaa attcaaaatg aaatgatgaa tttgtttaca gataaaaata
     4621 ataatagaga gtggcaacta gacgagcata taaaacaagc taagcatgat tatttatatg
     4681 ctaatgcttt attaaacaat gagggcttgc tgattaacaa tatacgaaat aataagtaca
     4741 tctcaaatgt tgaacgagac aaactgaaaa cttatgtaaa aatgaatttt gaggcgatca
     4801 aaaaaagcaa tgttcctaaa gagtataaag aaatagaagg gttaaagaat aaacttagaa
     4861 ataataaatc agcttctagt aataaaaaga tgatgtttga ttttatgatt gggaaaatta
     4921 gttaaataag tgctgagata acgatttctg agcattgaaa aacatttaac aggggtattg
     4981 gtttaatggt tgcaacatag agcttacaca tttgaccctt gtagtaattt tttgaagtta
     5041 taattttttg tattttggat attaacaaac gtgctttaac agataaatct taattaaaaa
     5101 tgtagattag cggaggaaaa attgaaaaaa aatagaggtt ctaaaataac gttggttata
     5161 gtatttataa tgttaggtat tttaatatat ttgtcctttt ctaatttagg tagtgaagat
     5221 aatcataaaa gtcatgagaa tagcgataaa aaaaggactg atgtaaaaaa gaataaaaaa
     5281 caaagtagca gtaaagataa aaataaaagt catgagaata atgatagaag tttaaaaaat
     5341 aataacgaag acacttcaaa tagtcacgaa tattacgatg atccaagctt agataaacaa
     5401 gtatatgaag atattaagga atctatgacg ctactaaata gtttaactag tcaagatatt
     5461 aaagagtata aagttaatac tcaaatatat aaccaagata aaaaacctaa tgtgatcatt
     5521 accgttgatt taaaaggtaa agaagactat agcaacagtg aactaaaata tcgtacagaa
     5581 cacatatctt caaactttac tggaagaaat gagatagagg gcggatttaa tggatatttt
     5641 gataaattat atattaaatt taaagaagat ggaattgatg taggtgaagc aaaagtgaaa
     5701 tttaatgatt cgcttaatcc tgaagttcaa ataaaataat aaataaacaa agaaatgata
     5761 tatattgtat aaggtataca tttccactac ctataataca taattatgta aactaaataa
     5821 cttccataaa cattgtattg acgggatcta tagtgttcgt agttacttgt tcaatataca
     5881 taaaatatac aatcgcataa ccacgctgtt tatcgtgttc ggtatacact tataaaatta
     5941 atatttatac attttcgggt accgtcatga gtgattacaa ccaccataaa ataatgtgtt
     6001 aaaaattgta aagttttata taattgatct tgtgaataaa aaaggaataa tgaaaatgaa
     6061 catgaaaaca ataaataaaa ttgtaagttg gtttttgtat atcggtctgc cattagtcgt
     6121 tgtgggctta tttatatggc aattggataa tcttgaaaaa ttctttaaaa aatatcctaa
     6181 tgctatagac ggggctacat tagtgtttgt tttaataaca actactttga gtattatcat
     6241 ttcctataaa tcatacaaat caaatattaa gctatttaaa gataataaaa atgaacaaag
     6301 ttataagata caacaattgt taaaaacaga aacaaaagat tctatacaaa aactaatagg
     6361 tttcaagagt aattataaaa ggacacaaat aaatattttt gatgaaatta aaaagctaga
     6421 tttagaaaat gaattaaaaa acatgggaac aaaga
//
