LOCUS       NZ_CP084482             4722 bp    DNA     circular CON 08-JAN-2024
DEFINITION  Staphylococcus lugdunensis strain RMLUG1 plasmid pRMLUG1_2, complete
            sequence.
ACCESSION   NZ_CP084482
VERSION     NZ_CP084482.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21459164
            Assembly: GCF_026427435.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus lugdunensis
  ORGANISM  Staphylococcus lugdunensis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 4722)
  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  JOURNAL   Unpublished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 4722)
  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                   :: 510.82x
            Sequencing Technology :: Illumina; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/08/2024 05:03:30
            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)                     :: 2,554
            CDSs (total)                      :: 2,471
            Genes (coding)                    :: 2,426
            CDSs (with protein)               :: 2,426
            Genes (RNA)                       :: 83
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 60
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 45
            CDSs (without protein)            :: 45
            Pseudo Genes (ambiguous residues) :: 0 of 45
            Pseudo Genes (frameshifted)       :: 16 of 45
            Pseudo Genes (incomplete)         :: 31 of 45
            Pseudo Genes (internal stop)      :: 11 of 45
            Pseudo Genes (multiple problems)  :: 12 of 45
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP084482.1.
            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..4722
                     /organism="Staphylococcus lugdunensis"
                     /mol_type="genomic DNA"
                     /strain="RMLUG1"
                     /isolation_source="BALF"
                     /host="Homo sapiens"
                     /db_xref="taxon:28035"
                     /plasmid="pRMLUG1_2"
                     /geo_loc_name="China:Fujian"
                     /collection_date="2019-08-05"
     gene            complement(join(4299..4722,1..521))
                     /locus_tag="LFR23_RS12720"
                     /old_locus_tag="LFR23_12725"
     CDS             complement(join(4299..4722,1..521))
                     /locus_tag="LFR23_RS12720"
                     /old_locus_tag="LFR23_12725"
                     /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_267263022.1"
                     /translation="MSKNNHANHSNHLENHDLDNFSKTGYSNSRLNRHTMYTPEPKLSF
                     DAMTIVGNLNKNNAHKLSEFMSIEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADTWD
                     RRNMRVEFNPNKLTHEEILWLKQNVIDYMEDDGFTRLDLAFDFEDDLSNYYAMTDKSVK
                     KTIFYGRDGKPETKYFGVRDSDRFIRIYNKKQERRDNADIEVVSEHLWRVEIELKRGMV
                     DYWNDCFDDLHILQPDWKTIERTSDRAMVFMLLNDEEEWGKLERRTKNKYKQLIKEISP
                     VDLTELMKLTLKANEKQLQKQIDFWQREFRFWK"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            complement(756..962)
                     /locus_tag="LFR23_RS12725"
                     /old_locus_tag="LFR23_12730"
     CDS             complement(756..962)
                     /locus_tag="LFR23_RS12725"
                     /old_locus_tag="LFR23_12730"
                     /inference="COORDINATES: protein motif:HMM:NF024252.4"
                     /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 transcriptional regulator"
                     /protein_id="WP_002502829.1"
                     /translation="MLSKNLKILRIKKDVSQEFLSKKIGVSIQTINKWENDKCLPDAYN
                     LLKLADYYSLSVEELINKEFELV"
                     /name="helix-turn-helix transcriptional regulator"
     gene            1127..1606
                     /locus_tag="LFR23_RS12730"
                     /old_locus_tag="LFR23_12735"
     CDS             1127..1606
                     /locus_tag="LFR23_RS12730"
                     /old_locus_tag="LFR23_12735"
                     /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_002502830.1"
                     /translation="MKKKVITILAGAVLLSPISAALPNNIHTPQINKEASAKSKYKLES
                     VKSKNVSVKQQKKQDKDEAIGNAILSLGIGGIPGYVGKAGSALLTALGLKGSIDQIDKN
                     YAPLTVKKYHYVPKKKASGPSGDMSGYNMGYYVIKVYNQKTGKKVSSKTIPIQRA"
                     /name="hypothetical protein"
     gene            complement(1619..1789)
                     /locus_tag="LFR23_RS12735"
                     /old_locus_tag="LFR23_12740"
     CDS             complement(1619..1789)
                     /locus_tag="LFR23_RS12735"
                     /old_locus_tag="LFR23_12740"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002502831.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002502831.1"
                     /translation="MNISKGFVKAIWFIICVILVIMLGNNYKFVEMFLMVTLGIIGFIL
                     IENFYKKKNGD"
                     /name="hypothetical protein"
     gene            complement(2281..2757)
                     /locus_tag="LFR23_RS12740"
                     /old_locus_tag="LFR23_12745"
     CDS             complement(2281..2757)
                     /locus_tag="LFR23_RS12740"
                     /old_locus_tag="LFR23_12745"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_018113444.1"
                     /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_237625964.1"
                     /translation="MTDQIKRSNTHEIKVNIETDDNLSEFIKQKIDEKFDEKIPNLRTK
                     QTMEQFKWSLMRIEDKQEILDDNIESVHKWATYFKSALMLTLFAVLLISVVATFMGGLF
                     NVLGFDYMYKGLEYQIKHSEGFVAFLWHLGYLIPYLLLATLIWLILALEHKYRY"
                     /name="DUF334 domain-containing protein"
     gene            complement(2783..3634)
                     /locus_tag="LFR23_RS12745"
                     /old_locus_tag="LFR23_12750"
     CDS             complement(2783..3634)
                     /locus_tag="LFR23_RS12745"
                     /old_locus_tag="LFR23_12750"
                     /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_203079345.1"
                     /translation="MATTKLGNTKSASRAINYAEKRAEEKSGLNCDIDYAKSSFKQTRA
                     LYGKENGVQAHTVIQSFKPGEVTPEQCNQLGLELAEKIAPNHQVAVYTHADTNHVHNHI
                     VINSIDLETGKKYQSNKKQREFVKQKNDEVCREHGLSVTERNAAMRYTQAEKGLIEKGK
                     SSWKDEIRDAIEQSQATNFEELERELNQLDITIDRVTNKTITYRHLKENKKVRGKNLGE
                     QFDKGALENEFAFANERREFEQQLSEYEPRESEYRPRDTEKNIKRPKELRVQSRENDFE
                     LE"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(3616..3999)
                     /gene="mobC"
                     /locus_tag="LFR23_RS12750"
                     /old_locus_tag="LFR23_12755"
     CDS             complement(3616..3999)
                     /gene="mobC"
                     /locus_tag="LFR23_RS12750"
                     /old_locus_tag="LFR23_12755"
                     /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"
     Typing          3971..4207
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="82.377"
                     /coverage="100.0"
                     /evalue="1.8e-49"
     Typing          complement(2..455)
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.544"
                     /coverage="86.0"
                     /evalue="0.0"
     Typing          complement(4327..4722)
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.992"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          complement(2787..3634)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.94"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ggtttcccgt cacgaccata aaaaatagtt ttcttaactg atttatcagt cattgcataa
       61 taattactta aatcatcttc aaaatcaaaa gctaaatcta atcttgtaaa accgtcatct
      121 tccatgtagt cgataacgtt ttgttttaac caaagtattt cttcatgcgt aagtttattt
      181 ggattaaatt caacacgcat attacgtcta tcccacgtat ctgcttttac tttgtcatat
      241 tcaatataaa ctttttcttg tagcgcctta gctttaaatt tagtttgaag tatatcccaa
      301 agtcttattt gtggctcaat actcataaat tcagatagtt tgtgagcatt gtttttatta
      361 agatttccaa caatagtcat agcgtcaaaa cttaattttg gttcgggggt gtacatagta
      421 tgtcggttta accggctatt agagtagccg gttttagaaa aattatctaa atcgtgattt
      481 tctaagtgat ttgaatgatt tgcgtgatta tttttactca taaaaaatcg actccttaat
      541 ttaatttaag aagtcgctca cccgaatata tatcttgaag aataaactaa tatcgtttaa
      601 tatctagata tacaaattaa aaaacaaaac atcaaatgtt tttcttttgg ttttgtcgtt
      661 cacaaacttt ggtcggtggg tgagcgactc ctttttattt tgttataaat ataacactgt
      721 ctaaaagctt ggtctaatat gactaagctt ttttgctaaa ctaattcaaa ttctttatta
      781 ataagttctt caacacttaa actataataa tctgctaatt tcaaaagatt ataagcatct
      841 ggcaaacatt tatcattttc ccacttgttt atcgtttgaa tggaaactcc aattttttta
      901 gataaaaatt cttggctaac gtctttttta attcttaata tctttaaatt ctttgataac
      961 actattaaaa attccacctt ttattaattt aatttactta taacttttat aacattaatt
     1021 ttaaaaattg aactgttata cataaattta taaatattta cagttttaat caaatttagg
     1081 taatttaaaa taatgattgt aaatacaata aaaggaggaa atgaaaatga aaaagaaagt
     1141 gataacaata cttgcaggtg ctgtattatt atcacctata agcgcagctt tacctaataa
     1201 tattcatact ccacaaatta acaaagaagc ttcagctaaa tctaaatata aattagaaag
     1261 tgttaaatca aaaaatgtaa gcgtgaaaca acagaaaaag caagataaag acgaagctat
     1321 tggcaatgca atattatcac ttggcatagg aggtatccct ggttatgttg gtaaagcagg
     1381 aagtgcttta ctaacagcac ttggactcaa aggtagcatt gatcaaatag ataaaaatta
     1441 tgctccatta actgttaaaa aataccacta tgtacccaag aagaaagctt caggtccaag
     1501 tggagatatg agcggatata atatgggcta ctacgtaata aaagtataca accaaaaaac
     1561 aggtaaaaaa gtttctagta aaacaatacc tatacaaaga gcataaaaag aacggagatt
     1621 aatctccgtt ctttttttta taaaaatttt ctataagtat aaaacctata atacctaaag
     1681 ttaccattaa aaacatttct acaaatttgt aattatttcc tagcattatt actaaaataa
     1741 cacatattat aaaccaaatc gcctttacaa aaccttttga aatattcata tgtctctcct
     1801 ttaaaagtta tttctagaat ataaccaata aataaaatga taaagataat gctatcaaag
     1861 aacctactac tacctgtaaa tatttttaat taattggaac ataaaagaaa aaatattaat
     1921 tcctttcttt ttttgtcgta ccaataatta acaatacaaa aaataaaaaa tttaataaat
     1981 aaaagagctt ttcccctaaa ggttttccaa taatgttttc attcaatcct ataatcaaac
     2041 aaagtataaa aataacaatg ataatacctg aatatatttt gttttttaat agcataaaat
     2101 taacctttct ttttaatgct ttattccaat tgctttattg acgttgagcc tcggaaccct
     2161 taacaaaccc caaaactgtc gactcgtcgg cctaatagct cacgctatgc cgacattcgt
     2221 cttcaagttt agttaagggt tcttctcaac atcaataaat tttctcggca taaatgcgtg
     2281 ttaatatcta tatttgtgtt ctaaagccaa tataagccat atcagcgtcg ctaatagtaa
     2341 ataaggtatc aagtatccta aatgccataa aaatgctaca aagccttctg agtgctttat
     2401 ttgatattct agccctttat acatgtagtc aaatcctaaa acattgaata aaccacccat
     2461 gaatgtagcg acaacgctaa tcaataaaac ggcaaatagt gtcaacatca acgctgactt
     2521 aaagtaagtc gcccatttgt gaacactttc aatattgtca tcgagtattt cttgtttatc
     2581 ctcaattctc atcaaagacc atttgaattg ttccattgtt tgctttgtac gaagattagg
     2641 tattttttca tcaaatttct catcgatttt ttgtttaata aattcgctta gattatcatc
     2701 tgtctcaata tttactttaa tctcgtgcgt attcgagcgt tttatctgat cggtcattcg
     2761 tgatatatat agcttgtctt catcactcaa gttcaaagtc gttttctcgt gattggactc
     2821 taagttcttt aggacgttta atattttttt ctgtatctct tggtctgtac tcactttctc
     2881 ttggttcgta ttctgataat tgttgctcga attctctccg ttcatttgcg aacgcaaact
     2941 cattttctaa tgccccctta tcgaattgtt cacctaaatt tttacctctc acttttttat
     3001 tttctttcaa gtgtctgtaa gtgattgttt tgtttgtgac acgatcgatt gtgatgtcta
     3061 attggttcaa ctctctctca agctcctcaa aatttgtcgc ttgtgattgt tcaatcgcgt
     3121 ctctaatttc gtctttccaa gagcttttac ctttttcaat taagcctttt tcggcttgag
     3181 tatatcgcat tgctgcgttg cgttcagtta cagacaatcc atgttctcta catacttcat
     3241 catttttttg ttttacgaac tctctttgtt ttttattgct ttgatatttt ttcccagttt
     3301 ctaaatcaat tgaattaatc acaatatgat tgtgtacatg atttgtatct gcgtgcgtat
     3361 agacggctac ttgatgatta ggtgcaatct tttctgccaa ttctaaaccc aattgattac
     3421 attgctctgg cgttacttcg ccaggcttga acgattgaat cactgtatgt gcttgaacac
     3481 cattttcttt gccatataaa gctcgtgttt gcttaaacga tgattttgca taatctatat
     3541 cacaatttaa gccacttttt tcttctgctc gcttttctgc gtaattgatt gctcgacttg
     3601 ccgatttggt attacctaat ttagttgttg ccatatctca tcaagccttt cacgtaactc
     3661 attgatatta tgttctaacg ctatgtaatt gggtgcttca tgttgatgtt tattacaata
     3721 tttagcaatc tgattggcgt ttgcacctaa cttacttaaa tctctagcaa tcgattgtcg
     3781 cgtttcttta tcaaattttg gtgcgactaa tcgactgcct tgtgcctttt tctttacgaa
     3841 agcaggcaca ctcatattta aagtttccgc agattgcctt aactttaaat attcggattc
     3901 gctcacacga aaactaattt gttttggctc cttacggttg ggtttacggt ttcgcccaac
     3961 agtttcgtcg ctagccacaa atgtgttttg ttcgctcatt caatcccacc acgctttctt
     4021 cgaaagtaat gacttaatat aaatctagct tacagggtaa gccagatttt atcaagtcgt
     4081 ttagtggttt ggcaagcgtc gtatattcta gccacttcgt tctgaatata ccggcttgat
     4141 ggggaatatc cccatgcccc ttttgtattt ttgtttgcac aaaaatagtg gctaattgct
     4201 agccactaag ttcaaaacca ttaaagcccc agcaaccaaa aatggtggtt gctatacgtt
     4261 cataaatttt atgatcactt acgtgtataa aatttaattc acttccaaaa tctaaattca
     4321 cgctgccaaa aatcaatctg cttttgcaat tgtttttcgt tcgcttttaa agtcaatttc
     4381 attaattccg ttaaatcaac tggagatatt tctttaatta attgcttata tttattctta
     4441 gtacgtcttt ctaattttcc ccattcttct tcgtcattca acaacataaa aaccattgct
     4501 ctatcagaag tacgttcgat agttttccaa tctggttgta atatatgtaa atcatcaaaa
     4561 caatcgttcc aataatcaac catacctctt tttaattcaa tttctacacg ccatagatgt
     4621 tctgaaacaa cttcaatatc tgcattatcc ctacgttcct gttttttatt ataaattcta
     4681 ataaacctat cactgtcacg aacaccaaaa tattttgttt ct
//
