LOCUS       CP053091                2381 bp    DNA     circular BCT 09-FEB-2021
DEFINITION  Staphylococcus epidermidis strain HD31-1 plasmid pHD31-1_3, complete
            sequence.
ACCESSION   CP053091
VERSION     CP053091.1
DBLINK      BioProject: PRJNA546129
            BioSample: SAMN14732896
KEYWORDS    .
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2381)
  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 2381)
  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                   :: 112x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 05/04/2020 15:51:54
            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)                     :: 2,585
            CDSs (total)                      :: 2,504
            Genes (coding)                    :: 2,428
            CDSs (with protein)               :: 2,428
            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)              :: 76
            CDSs (without protein)            :: 76
            Pseudo Genes (ambiguous residues) :: 0 of 76
            Pseudo Genes (frameshifted)       :: 43 of 76
            Pseudo Genes (incomplete)         :: 35 of 76
            Pseudo Genes (internal stop)      :: 25 of 76
            Pseudo Genes (multiple problems)  :: 21 of 76
            ##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..2381
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="HD31-1"
                     /isolation_source="nose; prosthetic joint infection"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="pHD31-1_3"
                     /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            complement(join(1873..2381,1..490))
                     /locus_tag="HJI00_12915"
     CDS             complement(join(1873..2381,1..490))
                     /locus_tag="HJI00_12915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020368559.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="QRJ24128.1"
                     /translation="MQHNTTRYIDENQDNETLKDMTKSGTQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLYKTWFCKSKLCPVCNWRRSMKNSYQAQKVI
                     EAVVKEKPKARWLFLTLSTKNAIDGETLEQSLKHLTKAFDRLSRYKKVKQNLVGFLRST
                     EVTVNKNDGSYNQHMHVLLCVENSYFKNKANYITQEEWINLWQKALQVDYKPVANIKAI
                     KPNKKGDKDIQAAIKETSKYSVKSSDYLTGNHEKDAEIVQDLEQGLYRKRMLSYGGLLK
                     QKHKLLNLDDAEEGNLIQTSDEEKTTEEEQKAHSITAIWNFEKQNYFLKNL"
                     /name="protein rep"
     gene            complement(709..1128)
                     /locus_tag="HJI00_12920"
     CDS             complement(709..1128)
                     /locus_tag="HJI00_12920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016922374.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="fosfomycin resistance bacillithiol transferase
                     FosB"
                     /protein_id="QRJ24129.1"
                     /translation="MIKGINHITYSVSNIAKSIEFYRDILGADILVEGETSAYFNLGGI
                     WLALNEEKNIPRSEIKYSYTHIAFTISDNDFEDWYIWLKENEVNILEGRDRDIRDKKSI
                     YFTDLDGHKLELHTGSLEDRLSYYKEAKPHMNFYI"
                     /name="fosfomycin resistance bacillithiol transferase FosB"
     gene            complement(1331..1516)
                     /locus_tag="HJI00_12925"
     CDS             complement(1331..1516)
                     /locus_tag="HJI00_12925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020367458.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QRJ24130.1"
                     /translation="MPEKTKLGNSLSFNYFLLLVGVLTFLGYYFLGDSNIMISWLLAMC
                     PITVGIANIGRIKNEK"
                     /name="hypothetical protein"
     ARG             complement(713..1128)
                     /name="fosB"
                     /gene="fosB"
                     /gene_name="fosfomycin resistance bacillithiol transferase
                     FosB"
                     /tool="amrfinderplus"
                     /drug_class="FOSFOMYCIN"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             complement(710..1128)
                     /name="FosB4"
                     /gene="FosB4"
                     /gene_name="fosfomycin thiol transferase"
                     /tool="rgi"
                     /drug_class="phosphonic acid antibiotic"
                     /identity="99.28"
                     /coverage="100.0"
     Typing          complement(63..490)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.203"
                     /coverage="94.0"
                     /evalue="0.0"
     Typing          complement(1874..2381)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.481"
                     /coverage="94.0"
                     /evalue="0.0"
ORIGIN
        1 ctgttgaacg taaaaatcca acaagatttt gcttaacttt tttatatcta ctcaatctat
       61 caaaagcttt tgttaaatgc tttaaacttt gttctaaagt ctcaccatct atcgcatttt
      121 tcgttgaaag tgttaagaat aaccaacgtg cttttggctt ttctttaacc actgcttcaa
      181 tgactttttg agcttgataa ctatttttca ttgaacgcct ccaattacaa accggacata
      241 atttagactt acaaaaccat gttttataaa gttttaaata cccttcatca gtcggcttaa
      301 attctaagac gttaccacat tgcttcacgt taaaagcctt tttaattttt aaaatttcta
      361 gtatatctgc ataacttaca ttgtcgattt tcttttctct ccatgggcgt tgtgtcccac
      421 ttttagtcat atctttcaat gtttcattat cttgattttc gtctatatat cttgtagtat
      481 tatgttgcat ataaaaagac ctccagtaga tgtttattga gtagacgctt taatcatact
      541 actggggttt ttttatgtca aaaatttctt tcaacaacaa aaaaacgcct taaccctcta
      601 ttgacaaggg ataaagcgat aatttaaaaa tcgagttatt tctatatagt atcaagacaa
      661 gaagaaactc gttttcactc gtttcaaaac aaaacacata actttgtttt aaatataaaa
      721 attcatatga ggtttagcct ctttataata actcaatcta tcttctaaac ttcctgtatg
      781 caattctaat ttatgaccat ctaaatcagt gaaatatatt gattttttat ctctaatatc
      841 tctatctcta ccttcaagaa tatttacttc attttctttc aaccagatat accaatcttc
      901 aaaatcatta tctgaaattg taaatgctat atgagtatac gaatatttaa tttcgcttct
      961 aggaatattt ttttcttcgt tcaaagccaa ccatatacca cctaaattaa aataggccga
     1021 ggtctcacct tcaactaaaa tgtcagcccc taaaatatct ctgtaaaatt caattgattt
     1081 agctatatta gaaaccgaat aagtaatatg atttattcct ttaatcatat tctccctccc
     1141 ctttttttaa aattttaaca tagttgcttt attccaattg ctttattgac gttgagcctc
     1201 ggaaccctta acaatcccta aacttgtcga atcgtcggtt taatagctca cgctataccg
     1261 acattcgtct ccaagtttag ttaagggttc ttctcaacat caataaattt tctcggcata
     1321 aatgcataat ctacttttca ttttttattc tacctatatt tgcaattcca acagttattg
     1381 gacacattgc cagtaaccaa ctaatcatga tattagaatc tcctaaaaaa taataaccaa
     1441 gaaaagttaa tacacctaca agtaataaaa aataattaaa agacaatgaa tttcctaatt
     1501 tagttttttc aggcatatct tttttcacgc tccttattct ttgtgctaac aaaatattta
     1561 aagacttaat aaaaattata atgcctttat ttttaatttt aagggggcat tttaaagaat
     1621 taggggttat ttatatagtt tattgcctaa aaacttatat tggctcttaa aacgcaaatg
     1681 agagccaaat aaaaataatt gcttttcaca aacaaaaatt tgagcaaaac cagtgttgaa
     1741 ttttttagac actgcccagt tacatgcaaa tttaaaaatt ggcataaaaa ctgggcaacc
     1801 atgccggttg aacgctatag ttcctgcagg ggcaaaaaag cttaaaaaaa cgctagcttt
     1861 gataagctaa cgttacaaat tttttaagaa ataattttgt ttttcgaaat tccaaatagc
     1921 cgtaattgaa tgggcttttt gttcttcttc agttgttttt tcttcatcgc tcgtttgaat
     1981 taaattacct tcttcggcat cgtctaaatt taaaagttta tgtttttgtt taagcaaacc
     2041 accgtaactt aacatgcgtt ttctgtataa tccttgttcc aaatcttgaa caatttctgc
     2101 gtctttttca tggtttcccg ttaaataatc ggacgactta accgagtatt ttgatgtttc
     2161 tttaattgca gcttgtatat ctttatcgcc ttttttattc ggcttaattg ctttgatatt
     2221 tgcgactggt ttgtaatcaa cttgaagagc tttttgccat aaattgatcc actcttcttg
     2281 cgttatataa ttagctttat tcttaaaata actattttca acacacaata aaacatgcat
     2341 atgttgatta taactgccat catttttatt aacggtcact t
//
