LOCUS       CP052945                4363 bp    DNA     circular BCT 09-FEB-2021
DEFINITION  Staphylococcus epidermidis strain HD75-1 plasmid pHD75-1_4, complete
            sequence.
ACCESSION   CP052945
VERSION     CP052945.1
DBLINK      BioProject: PRJNA546129
            BioSample: SAMN14732907
KEYWORDS    .
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 4363)
  AUTHORS   Both,A., Huang,J., Qi,M., Lausmann,C., Weisselberg,S., Buttner,H.,
            Lezius,S., Failla,A.V., Christner,M., Stegger,M., Gehrke,T.,
            Baig,S., Citak,M., Alawi,M., Aepfelbacher,M. and Rohde,H.
  TITLE     Distinct clonal lineages and within-host diversification shape
            invasive Staphylococcus epidermidis populations
  JOURNAL   PLoS Pathog 17 (2), e1009304 (2021)
   PUBMED   33544760
  REMARK    Publication Status: Available-Online prior to print
REFERENCE   2  (bases 1 to 4363)
  AUTHORS   Both,A., Huang,J., Qi,M., Lausmann,C., Weisselberg,S., Buettner,H.,
            Lezius,S., Failla,A.V., Christner,M., Stegger,M., Gehrke,T.,
            Baig,S., Citak,M., Alawi,M., Aepfelbacher,M. and Rohde,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-APR-2020) Institute of Medical Microbiology, Virology
            and Hygiene, University Medical Center Hamburg-Eppendorf,
            Martinistr. 52, Hamburg, Hamburg 20246, Germany
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 146x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/29/2020 14:36:52
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.11
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 2,526
            CDSs (total)                      :: 2,442
            Genes (coding)                    :: 2,393
            CDSs (with protein)               :: 2,393
            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)              :: 49
            CDSs (without protein)            :: 49
            Pseudo Genes (ambiguous residues) :: 0 of 49
            Pseudo Genes (frameshifted)       :: 36 of 49
            Pseudo Genes (incomplete)         :: 19 of 49
            Pseudo Genes (internal stop)      :: 21 of 49
            Pseudo Genes (multiple problems)  :: 19 of 49
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..4363
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="HD75-1"
                     /isolation_source="nose; prosthetic joint infection"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="pHD75-1_4"
                     /geo_loc_name="Germany: Hamburg"
                     /lat_lon="53.33 N 10.1 E"
                     /collection_date="2018"
                     /collected_by="Institute of Medical Microbiology, Virology
                     and Hygiene, University Medical Center Hamburg-Eppendorf"
     gene            join(3945..4363,1..517)
                     /locus_tag="HJI11_12565"
     CDS             join(3945..4363,1..517)
                     /locus_tag="HJI11_12565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002467289.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QRJ01000.1"
                     /translation="MSKENHSNYLQNKDLDNFSKTGYSNSRLSGQTLGKSQPELSFDAM
                     TIVGNLNKTNAKKLSDFMSVEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADTWDRRN
                     MRVEFNPNKLTSEEMLWLKQNIIDYMEDDGFTRLDLAFDFEDDLSDYYAMTDKAVKKTV
                     FYGRNGKPETKYFGVRDSDRFIRIYNKKQERKDNADVEVMSEHLWRVEVELKRDMVDYW
                     NDCFNDLHILKPAWTTLEKINEQAMVYTLLHEESMWGKLSKNTKTKFKKLIREISPIDL
                     TELMKSTLKANEKQLQKQIDFWQREFRFWR"
                     /name="replication initiation protein"
     gene            545..1129
                     /gene="lepB"
                     /locus_tag="HJI11_12570"
     CDS             545..1129
                     /gene="lepB"
                     /locus_tag="HJI11_12570"
                     /EC_number="3.4.21.89"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016898876.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="signal peptidase I"
                     /protein_id="QRJ01001.1"
                     /translation="MKKSIFEWVVSLLIGVVIAILLTTFVGSRYTVKGDSMYPTFKDGE
                     ELIVNKLSVPFHKLNRGDVVIFHATKKRDYIKRLIGKPGDEVKYYKDKLYVNGKYIKEP
                     YLKTNKQTKTTEFLTENFNVSDLKNSNGKNKIPKNKYLVLGDNRLISNDSRRDVGLLDK
                     DKVVGKVFVRLLPLSDFKFDFYSKSFNKVNK"
                     /name="lepB"
     gene            1429..1812
                     /gene="mobC"
                     /locus_tag="HJI11_12575"
     CDS             1429..1812
                     /gene="mobC"
                     /locus_tag="HJI11_12575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000003402.1"
                     /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="QRJ01002.1"
                     /translation="MSEQNNFVASDETVGRNHKPNRKEPKQISFRVSESEYLKLKQSAE
                     TLNMSVPNFVKKKAQGSRLVAPKFDKATRQSIAKDLSKLGANANQIAKYCNQHQYDAPN
                     YPALERNISELRERLDEIWQQLN"
                     /name="mobC"
     gene            1794..2756
                     /locus_tag="HJI11_12580"
     CDS             1794..2756
                     /locus_tag="HJI11_12580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002467288.1"
                     /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="QRJ01003.1"
                     /translation="MATTKLGNTKSASRAINYAEKRAEEKSGLNCDIDYAKSSFKQTRA
                     LYGKENGIQAHTVIQSFKPGEVTPEQCNQLGLELAEKIAPNHQVAIYTHTDKEHVHNHI
                     VINSIDLETGRKYQSNKQQRDLVKQANDDICREHGLSVPERDTAKLRYTQAEKSLIEKD
                     QYSWKDDLREKIEHAKEHTIDFKSFSEYLKESGIEFKVRGKNVSYKPENVNKWVRGKTL
                     GQDYDKGALEYEFERREREEKESERDPVAEYTDQFEVDWDAVEHNAEQLRKTRNRRIEK
                     TKQAHHQVSNRDSRESERTRERPKGHHIEIDRGDEGFSR"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            2725..3186
                     /locus_tag="HJI11_12585"
     CDS             2725..3186
                     /locus_tag="HJI11_12585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015310584.1"
                     /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="QRJ01004.1"
                     /translation="MTGATKDFRDNGVKTHNAFINILKEKLDKVDTDELANIIGRDIYK
                     VRDENERMLQEVQSSHEEYQKRIKLMYRGLGAILLVFMLFALVMTIGSDFMDFIHIDIL
                     QKAIASKIKASEGFMTFIWYIAYGLPYIVAIGGFIYLYEWIRKKFEVFF"
                     /name="DUF334 domain-containing protein"
     gene            3397..3546
                     /locus_tag="HJI11_12590"
     CDS             3397..3546
                     /locus_tag="HJI11_12590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000695367.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QRJ01005.1"
                     /translation="MKIRTFATWTTGGLDKLVNEFCSREDIKVLEIQANSTWLFVTATV
                     IYDD"
                     /name="hypothetical protein"
     Typing          complement(1223..1458)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="82.427"
                     /coverage="100.0"
                     /evalue="3.87e-51"
     Typing          2..511
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.368"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3906..4360
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.421"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          1795..2753
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.062"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agcttttgat tttgaagatg atttaagcga ttactatgca atgactgata aagcagttaa
       61 gaaaactgtt ttttatggtc gtaatggcaa gccagaaaca aaatattttg gcgttcgtga
      121 tagtgataga tttattagaa tttataataa aaaacaagaa cgtaaagata acgcagatgt
      181 cgaagttatg tctgaacatc tatggcgtgt agaagttgaa ttgaaaagag atatggttga
      241 ttattggaat gattgcttta atgatttaca cattttgaaa cctgcgtgga ctactttaga
      301 aaaaattaat gagcaagcta tggtttatac tttgttgcat gaagaaagta tgtggggaaa
      361 gttaagtaag aatactaaga ctaagtttaa aaaattgatt agagaaatat ctccaattga
      421 tttaacagaa ttaatgaaat cgactttaaa agcgaacgaa aaacaattgc aaaagcagat
      481 tgatttttgg cagcgtgaat ttagattttg gcgttagttg aaattttaaa aaaggagtaa
      541 ttttatgaaa aaatcgattt ttgaatgggt tgtatcatta ttaattggag ttgttatagc
      601 aatactttta actacatttg tgggttcaag atatactgtt aaaggagatt caatgtatcc
      661 tacttttaaa gatggcgaag agctaattgt taacaagcta tctgttccat ttcataagct
      721 aaatagagga gatgtggtta tttttcatgc tacaaaaaag agagattata ttaagagatt
      781 gataggtaag cctggcgacg aagttaaata ttataaagat aaattgtacg ttaatggtaa
      841 atatataaaa gaaccttatt taaaaactaa taaacaaaca aaaactacag aatttcttac
      901 tgagaacttt aatgtttcgg atcttaaaaa ttcgaatggt aaaaataaaa ttcctaaaaa
      961 taaatactta gttttaggtg ataaccgatt aattagtaat gatagtagaa gagatgtagg
     1021 tttgttagat aaagataaag tagttggaaa agtctttgtt agactattac cgctaagtga
     1081 ttttaaattt gatttttatt cgaaatcatt taataaagta aataagtagt ttttgtatga
     1141 tcaatcgtaa aatttatgaa tatatagcaa ccacattttt ggttgcttat gttttgattt
     1201 tgaatttggt tttgaactat gagtggctag cattttgcca ctcatttttt gcgttagcaa
     1261 aaacataaag ggtctgggat taatcccagc aagccggtat attcagaacg aagtggctag
     1321 aatatacgac gcttgccaaa ccacaaaatt acttgataaa atctggctta ccctgtaagc
     1381 tagatttata ttaagtaatg actttcgaag aaagcgtggt gggatttgat gagcgaacaa
     1441 aataactttg tggctagcga cgaaactgtt gggcgaaacc ataaacccaa ccgtaaggag
     1501 ccgaaacaaa ttagttttcg tgtgagcgaa tctgaatatt taaagttaaa gcagtctgct
     1561 gaaactttaa atatgagtgt gcctaatttc gttaagaaaa aggcacaggg tagtcgatta
     1621 gtcgcaccta aatttgataa agcaacgcga caatcgatag ccaaagattt aagtaagtta
     1681 ggtgcaaatg cgaatcagat tgccaaatat tgtaatcaac atcaatatga cgcacctaac
     1741 tatccagcgt tagaacgtaa tatcagtgag ttacgtgaaa ggcttgatga gatatggcaa
     1801 caactaaatt aggcaatacc aaatcggcaa gtcgagcaat caattacgca gaaaagcgag
     1861 cagaagaaaa gagtggatta aattgtgata tcgactatgc gaaatcatcg tttaagcaaa
     1921 ctagggcttt atatggcaaa gaaaacggta ttcaagctca tacagttata cagtcattca
     1981 agcctggcga agtaacacca gaacaatgta atcaacttgg cttagaacta gccgaaaaga
     2041 ttgcacctaa tcatcaagtg gcaatctata cgcatacaga taaagagcat gtacacaatc
     2101 atattgtaat taattcaatt gaccttgaaa caggacgcaa atatcaaagt aataaacaac
     2161 aaagagattt ggttaaacaa gccaatgacg atatttgtcg agaacatggt ttgagtgtgc
     2221 cagaacgaga tacggcgaaa ttgagataca cacaagccga aaaatcattg atagagaaag
     2281 accaatattc ttggaaagat gatttgagag aaaaaataga acatgcgaaa gaacatacaa
     2341 tcgattttaa gagcttttca gagtatttaa aggaatcagg tatagaattt aaggtaaggg
     2401 gcaaaaacgt ctcatataag ccggaaaacg taaataaatg ggtacgtggc aaaacccttg
     2461 gacaagatta cgataagggg gcgttagaat atgagtttga aagacgagag agagaagaaa
     2521 aagaatcaga gcgagaccca gtcgcagagt acacagacca attcgaagtc gattgggacg
     2581 cagtcgaaca caacgcagag caacttagaa agacaagaaa tcgaagaatt gaaaaaacaa
     2641 aacaagctca tcatcaagta tctaacagag attcaagaga atcagaacgc acgagagaaa
     2701 gaccaaaagg acatcacatc gaaattgaca ggggcgacga aggattttcg agataatggc
     2761 gtaaagacac ataatgcttt tataaatata ctcaaagaga aattagataa agtcgataca
     2821 gatgagttag ccaatattat aggcagagat atttataagg tgcgtgatga aaacgaacga
     2881 atgctacaag aagtgcaatc atcacatgaa gagtatcaaa aaagaattaa acttatgtat
     2941 cgtggattag gagccatatt attggtattt atgctatttg cgttagttat gactattggc
     3001 agtgatttta tggactttat acacatagat atattacaaa aagcaatagc aagtaaaatt
     3061 aaagcgtctg agggctttat gacatttatt tggtatattg cttatggatt accttatatt
     3121 gttgcgatag gtggttttat ttatctttac gaatggatta gaaaaaaatt cgaagtcttt
     3181 ttctaaggat aagcacgcta ttatgccgag aaaatctatt tgtcgatgag agcccttaat
     3241 tagactaaaa gcggcagcgg tcggatagcg tcaagctatc aaatcgaccg actgcttagc
     3301 tttaggatta ttaaggagcg cagaatcgtc gacaaataga ggaattggaa taaagcagta
     3361 attttggtaa gttagtcaaa aaaaaggtgt gatactttga aaataagaac atttgcaacg
     3421 tggactactg gtggattaga taaattagta aatgaatttt gttcaagaga agatattaaa
     3481 gtattagaaa ttcaagctaa tagcacgtgg ttgtttgtaa ctgctactgt tatatatgat
     3541 gattagtaaa tcataacgag aaaatgagac gtgatttgga ataacatgga gttgataaca
     3601 tgaaattcaa agaagccttt gagaaattca taacaaacaa gtatgtattt ggtgttttgt
     3661 tagtattagt tgtctatcag ctaatactaa tgtttagata aaaaaagact tgatcaaatt
     3721 agaccaagcc ttttgatagt gttatattaa tagcaaaata aaaaaagaag tcgtccaccc
     3781 caatccgacc aaagatttgt gaacgactag ccaaaatata aaacagtcga tgtttttatg
     3841 tttttgtata ttttgatatt aaacgatatt tgattatact tcaacattta catttgatgt
     3901 ttgggtggac gacttcttaa aacaatttaa ggagtcgatt ttttatgagt aaagaaaatc
     3961 attcaaatta cttacaaaat aaggatttag acaatttttc taaaaccggc tactctaata
     4021 gccggttaag tggtcaaact ttgggaaaat ctcaacccga attaagtttt gatgccatga
     4081 caatcgttgg gaatttgaac aaaactaatg ctaaaaagct atctgatttt atgagcgtag
     4141 agccacaaat acgactttgg gatatacttc aaacaaagtt taaagctaaa gcacttcaag
     4201 aaaaagtata tatcgaatat gacaaggtaa aagcagatac ttgggataga cgtaatatgc
     4261 gtgttgaatt taatcctaat aaactcacaa gtgaagaaat gctttggtta aaacaaaata
     4321 ttatcgacta catggaagat gatggtttta caagattaga ttt
//
