LOCUS       NZ_CP084438             4439 bp    DNA     circular CON 31-MAR-2024
DEFINITION  Staphylococcus lugdunensis strain RMLUG3 plasmid pRMLUG3_1, complete
            sequence.
ACCESSION   NZ_CP084438
VERSION     NZ_CP084438.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21459166
            Assembly: GCF_026427475.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus lugdunensis
  ORGANISM  Staphylococcus lugdunensis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 4439)
  AUTHORS   Fu,S.
  TITLE     The complete genome sequence of Staphylococcus lugdunensis shows the
            characteristics of the staphylococcal cassette chromosome mec and
            lugdunin operon
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4439)
  AUTHORS   Fu,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-SEP-2021) Department of Respiratory and Critical Care
            Medicine, Peking University People's Hospital, No.11 Xizhimen South
            Street, Xicheng District, Beijing, Beijing 100044, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 541.1x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_026427475.1-RS_2024_03_31
            Annotation Date                   :: 03/31/2024 06:43:54
            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)                     :: 2,482
            CDSs (total)                      :: 2,402
            Genes (coding)                    :: 2,371
            CDSs (with protein)               :: 2,371
            Genes (RNA)                       :: 80
            rRNAs                             :: 6, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 60
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 31
            CDSs (without protein)            :: 31
            Pseudo Genes (ambiguous residues) :: 0 of 31
            Pseudo Genes (frameshifted)       :: 9 of 31
            Pseudo Genes (incomplete)         :: 23 of 31
            Pseudo Genes (internal stop)      :: 6 of 31
            Pseudo Genes (multiple problems)  :: 7 of 31
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP084438.1.
            Bacteria and source DNA available from homo sapiens.
            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..4439
                     /organism="Staphylococcus lugdunensis"
                     /mol_type="genomic DNA"
                     /strain="RMLUG3"
                     /isolation_source="wound secretion"
                     /host="Homo sapiens"
                     /db_xref="taxon:28035"
                     /plasmid="pRMLUG3_1"
                     /geo_loc_name="China:Fujian"
                     /collection_date="2017-08-17"
     ARG             4..422
                     /name="tet(K)"
                     /gene="tet(K)"
                     /gene_name="major facilitator superfamily (MFS) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="tetracycline antibiotic"
                     /identity="100.0"
                     /coverage="30.28"
     ARG             3483..4438
                     /name="tet(K)"
                     /gene="tet(K)"
                     /gene_name="major facilitator superfamily (MFS) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="tetracycline antibiotic"
                     /identity="100.0"
                     /coverage="69.5"
     gene            608..1849
                     /gene="mobV"
                     /locus_tag="LE166_RS12395"
                     /old_locus_tag="LE166_12400"
     CDS             608..1849
                     /gene="mobV"
                     /locus_tag="LE166_RS12395"
                     /old_locus_tag="LE166_12400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010889940.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobV family relaxase"
                     /protein_id="WP_000122374.1"
                     /translation="MSYSIVRVSKVKSGTNTTGIQKHVQRENNNYENEDIDHSKTYLNY
                     DLVNANKQNFNNLIDEKIEQNYTGKRKIRTDAIKHIDGLITSDNDFFDNQTPEDTKQFF
                     EYAKEFLEQEYGKDNLLYATVHMDEKTPHMHYGVVPITDDGRLSAKEVVGNKKALTAFQ
                     DRFNEHVKQRGYDLERGQSRQVTNAKHEQISQYKQKTEYHKQEYERESQKTDHIKQKND
                     KLMQEYQKSLNTLKKPINVPYEQETEKVGGLFSKEIQETGNVVISQKDFNEFQKQIKAA
                     QDISEDYEYIKSGRALDDKDKEIREKDDLLNKAVERIENADDNFNQLYENAKPLKENIE
                     IALKLLKILLKELERVLGRNTFAERVNKLTEDEPKLNGLAGNLDKKMNPELYSEQEQQQ
                     EQQKNQKRDRGMHL"
                     /name="mobV"
     gene            2376..3320
                     /locus_tag="LE166_RS12400"
                     /old_locus_tag="LE166_12405"
     CDS             2376..3320
                     /locus_tag="LE166_RS12400"
                     /old_locus_tag="LE166_12405"
                     /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_000277654.1"
                     /translation="MYKNNHANHSNHLENHDLDNFSKTGYSNSRLDAHTVCISDPKLSF
                     DAMTIVGNLNRDNAQALSKFMSVEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADSWD
                     RRNMRIEFNPNKLTRDEMIWLKQNIISYMEDDGFTRLDLAFDFEDDLSDYYAMSDKAVK
                     KTIFYGRNGKPETKYFGVRDSNRFIRIYNKKQERKDNADAEVMSEHLWRVEIELKRDMV
                     DYWNDCFSDLHILQPDWKTIQRTADRAIVFMLLSDEEEWGKLHRNSRTKYKNLIKEISP
                     VDLTDLMKSTLKANEKQLQKQIDFWQHEFKFWK"
                     /name="replication initiation factor domain-containing
                     protein"
     Typing          2377..3320
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          609..1846
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaggatcatt atttgttttt attttaggat cattgtctat ctctataagt tttttaacta
       61 ttgcattttt tgttgagttt agtatgtggt tgactacttt tatgtttata tttgttatgg
      121 gcggattatc ttttactaaa acagttatat caaaaatagt atcaagtagt ctttctgaag
      181 aagaagttgc ttctggaatg agtttgctaa atttcacaag ttttttatca gagggaacag
      241 gtatagcaat tgtaggaggt ttattgtcac tacaattgat taatcgtaaa ctagttctgg
      301 aatttataaa ttattcttct ggagtgtata gtaatattct tgtagccatg gctatcctta
      361 ttattttatg ttgtcttttg acgattattg tatttaaacg ttctgaaaag cagtttgaat
      421 agttatatta tattttggtt tagaactatg agtggctagc attttgccac tcattttttg
      481 cgttagcaaa aacaggttta agcctcgcag agcacacgta ttaacgactt attaaaaata
      541 agtctagtgt gttagactta aactattaaa tacacatgaa acctttgtgc ttaggagtga
      601 tttttatatg tcttattcca ttgttagagt ttcaaaagtt aaatctggaa caaatacaac
      661 gggcatacaa aaacatgttc aaagagaaaa taataattat gaaaatgaag atatagacca
      721 tagtaaaact tacttaaatt atgatttggt aaatgctaat aaacagaatt ttaataactt
      781 gattgatgaa aaaatcgaac agaattatac aggcaaaaga aaaattagaa cagacgcgat
      841 taaacacatt gatggtttaa ttacatcaga caatgatttc tttgataatc aaacgccaga
      901 agatacaaag cagttttttg aatatgctaa agagttttta gaacaagaat acggtaaaga
      961 taatttatta tatgcaacag ttcacatgga cgaaaaaaca ccacatatgc attatggcgt
     1021 tgttccaata actgatgatg gtcgtttaag tgctaaagaa gttgtaggta ataaaaaagc
     1081 tttaacagcg tttcaagata gatttaatga gcatgttaaa caacgaggat atgatttaga
     1141 acgtgggcaa tcaagacaag taacaaatgc taaacatgag caaataagtc agtataaaca
     1201 aaaaacagaa tatcataagc aagaatatga acgtgagagc caaaaaacag accatataaa
     1261 gcaaaagaac gataaattaa tgcaagagta ccaaaaatcg ttaaatacgc ttaaaaagcc
     1321 tataaatgtt ccgtatgagc aagaaactga aaaagtaggt ggtttattta gcaaagaaat
     1381 acaagaaact ggaaatgttg taataagcca aaaagatttc aatgaatttc agaaacagat
     1441 aaaagctgct caagatattt cggaagatta cgagtatata aagtctggta gagccttaga
     1501 tgataaagat aaggaaatac gagagaaaga tgatttatta aataaagcag ttgagcgtat
     1561 tgaaaacgca gacgataatt ttaaccaact ttacgaaaat gcaaagccac ttaaagagaa
     1621 tatagaaata gcgttaaagc ttttaaaaat cttactaaaa gagttagaac gagttttagg
     1681 aagaaatacc tttgcggaaa gagttaataa gttaacagaa gatgaaccaa aactaaatgg
     1741 tttagcagga aacttagata aaaaaatgaa tccagaatta tattcagaac aggaacagca
     1801 acaagaacaa caaaagaatc aaaaacgaga tagaggtatg cacttataga acatgcattt
     1861 atgccgagaa aacttattgg ttggaatggg ctatgtgtta gctaacttgt tagcgagttg
     1921 gttggacttg aattgggatt aatcccaaga aagtaccaac tcaacaacac ataaagccct
     1981 gtaggttccg accaataagg aaattggaat aaagcaataa aaggagttga agaaatgaaa
     2041 ttcagagaag cctttgagaa ttttataaca agtaagtatg tacttggtgt tttagtagtt
     2101 ttaactgttt accagataat acaaatgctt aaataaaaaa agacttgatc tgattagacc
     2161 aagtcttttg atagtgttat attaataaca aaataaaaag gagtcgctca cgccctgacc
     2221 aaagtttgtg aacgacatca ttcaaagaaa aaaacactga gttattttta taatcttgta
     2281 tatttagata ttaaacgata tttaaatata catcaagata tatatttggg tgagcgattc
     2341 cttaaacgaa attgagatta aggagtcgat tttttatgta taaaaacaat catgcaaatc
     2401 attcaaatca tttggaaaat cacgatttag acaatttttc taaaaccggc tactctaata
     2461 gccggttgga cgcacatact gtgtgcatat ctgatccaaa attaagtttt gatgcaatga
     2521 cgatcgttgg aaatctcaac cgagacaacg ctcaagccct ttctaaattt atgagtgtag
     2581 agccccaaat aagactttgg gatattcttc aaacaaagtt taaagctaaa gcacttcaag
     2641 aaaaagttta tattgaatat gacaaagtga aagcagatag ttgggataga cgtaatatgc
     2701 gtattgaatt taatccaaac aaacttacac gagatgaaat gatttggtta aaacaaaata
     2761 taataagcta catggaagat gacggtttta caagattaga tttagccttt gattttgaag
     2821 atgatttgag tgactactat gcaatgtctg ataaagcagt taagaaaact attttttatg
     2881 gtcgtaatgg taagccagaa acaaaatatt ttggcgtgag agatagtaat agatttatta
     2941 gaatttataa taaaaagcaa gaacgtaaag ataatgcaga tgctgaagtt atgtctgaac
     3001 atttatggcg tgtagaaatc gaacttaaaa gagatatggt ggattactgg aatgattgct
     3061 ttagtgattt acatatcttg caaccagatt ggaaaactat ccaacgcact gcggatagag
     3121 caatagtttt tatgttattg agtgatgaag aagaatgggg aaagcttcac agaaattcta
     3181 gaacaaaata taagaatttg ataaaagaaa tttcgccagt cgatttaacg gacttaatga
     3241 aatcgacttt aaaagcgaac gaaaaacaat tgcaaaaaca aatcgatttt tggcaacatg
     3301 aatttaaatt ttggaaatag tgtacatatt aatattactg aacaaaaatg atatatttaa
     3361 actattctaa tttaggagga tttttttatg aagtgtctat ttaaaaattt ggggaattta
     3421 tatgaggtga aagaataatt tacccctata aactttagtc acctcaagta aagaggtaaa
     3481 attgtttagt ttatataaaa aatttaaagg tttgttttat agcgttttat tttggctttg
     3541 tattctttca ttttttagtg tattaaatga aatggtttta aatgtttctt tacctgatat
     3601 tgcaaatcat tttaatacta ctcctggaat tacaaactgg gtaaacactg catatatgtt
     3661 aactttttcg ataggaacag cagtatatgg aaaattatct gattatataa atataaaaaa
     3721 attgttaatt attggtatta gtttgagctg tcttggttca ttgattgctt ttattggtca
     3781 caatcacttt tttattttga tttttggtag gttagtacaa ggagtaggat ctgctgcatt
     3841 cccttcactg attatggtgg ttgtagctag aaatattaca agaaaaaaac aaggcaaagc
     3901 ctttggtttt ataggatcaa ttgtagcttt aggtgaaggg ttaggtcctt caataggggg
     3961 aataatagca cattatattc attggtctta cctacttata cttcctatga ttacaatagt
     4021 aactatacct tttcttatta aagtaatggt acctggtaaa tcaacaaaaa atacattaga
     4081 tatcgtaggt attgttttaa tgtctataag tattatatgt tttatgttat ttacgacaaa
     4141 ttataattgg acttttttaa tactcttcac aatctttttt gtgattttta ttaaacatat
     4201 ttcaagagtt tctaaccctt ttattaatcc taaactaggg aaaaacattc cgtttatgct
     4261 tggtttgttt tctggtgggc taatattttc tatagtagct ggttttatat caatggtgcc
     4321 ttatatgatg aaaactattt atcatgtaaa tgtagcgaca ataggtaata gtgttatttt
     4381 tcctggaacc atgagtgtta ttgtttttgg ttattttggt ggttttttag tggatagaa
//
