LOCUS       CP052995                2381 bp    DNA     circular BCT 09-FEB-2021
DEFINITION  Staphylococcus epidermidis strain HD21-2 plasmid pHD21-2_1, complete
            sequence.
ACCESSION   CP052995
VERSION     CP052995.1
DBLINK      BioProject: PRJNA546129
            BioSample: SAMN14734464
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 (27-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                   :: 134x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/29/2020 15:23:15
            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)                     :: 2,649
            CDSs (total)                      :: 2,568
            Genes (coding)                    :: 2,493
            CDSs (with protein)               :: 2,493
            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)              :: 75
            CDSs (without protein)            :: 75
            Pseudo Genes (ambiguous residues) :: 0 of 75
            Pseudo Genes (frameshifted)       :: 41 of 75
            Pseudo Genes (incomplete)         :: 33 of 75
            Pseudo Genes (internal stop)      :: 24 of 75
            Pseudo Genes (multiple problems)  :: 17 of 75
            ##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="HD21-2"
                     /isolation_source="nose; prosthetic joint infection"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282"
                     /plasmid="pHD21-2_1"
                     /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(25..210)
                     /locus_tag="HKH70_13225"
     CDS             complement(25..210)
                     /locus_tag="HKH70_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="QRJ43473.1"
                     /translation="MPEKTKLGNSLSFNYFLLLVGVLTFLGYYFLGDSNIMISWLLAMC
                     PITVGIANIGRIKNEK"
                     /name="hypothetical protein"
     gene            complement(567..1565)
                     /locus_tag="HKH70_13230"
     CDS             complement(567..1565)
                     /locus_tag="HKH70_13230"
                     /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="QRJ43474.1"
                     /translation="MQHNTTRYIDENQDNETLKDMTKSGTQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLYKTWFCKSKLCPVCNWRRSMKNSYQAQKVI
                     EAVVKEKPKARWLFLTLSTKNAIDGETLEQSLKHLTKAFDRLSRYKKVKQNLVGFLRST
                     EVTVNKNDGSYNQHMHVLLCVENSYFKNKANYITQEEWINLWQKALQVDYKPVANIKAI
                     KPNKKGDKDIQAAIKETSKYSVKSSDYLTGNHEKDAEIVQDLEQGLYRKRMLSYGGLLK
                     QKHKLLNLDDAEEGNLIQTSDEEKTTEEEQKAHSITAIWNFEKQNYFLKNL"
                     /name="protein rep"
     gene            complement(1784..2203)
                     /locus_tag="HKH70_13235"
     CDS             complement(1784..2203)
                     /locus_tag="HKH70_13235"
                     /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="QRJ43475.1"
                     /translation="MIKGINHITYSVSNIAKSIEFYRDILGADILVEGETSAYFNLGGI
                     WLALNEEKNIPRSEIKYSYTHIAFTISDNDFEDWYIWLKENEVNILEGRDRDIRDKKSI
                     YFTDLDGHKLELHTGSLEDRLSYYKEAKPHMNFYI"
                     /name="fosfomycin resistance bacillithiol transferase FosB"
     ARG             complement(1788..2203)
                     /name="fosB"
                     /gene="fosB"
                     /gene_name="fosfomycin resistance bacillithiol transferase
                     FosB"
                     /tool="amrfinderplus"
                     /drug_class="FOSFOMYCIN"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             complement(1785..2203)
                     /name="FosB4"
                     /gene="FosB4"
                     /gene_name="fosfomycin thiol transferase"
                     /tool="rgi"
                     /drug_class="phosphonic acid antibiotic"
                     /identity="99.28"
                     /coverage="100.0"
     Typing          complement(568..1565)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.394"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 attttctcgg cataaatgca taatctactt ttcatttttt attctaccta tatttgcaat
       61 tccaacagtt attggacaca ttgccagtaa ccaactaatc atgatattag aatctcctaa
      121 aaaataataa ccaagaaaag ttaatacacc tacaagtaat aaaaaataat taaaagacaa
      181 tgaatttcct aatttagttt tttcaggcat atcttttttc acgctcctta ttctttgtgc
      241 taacaaaata tttaaagact taataaaaat tataatgcct ttatttttaa ttttaagggg
      301 gcattttaaa gaattagggg ttatttatat agtttattgc ctaaaaactt atattggctc
      361 ttaaaacgca aatgagagcc aaataaaaat aattgctttt cacaaacaaa aatttgagca
      421 aaaccagtgt tgaatttttt agacactgcc cagttacatg caaatttaaa aattggcata
      481 aaaactgggc aaccatgccg gttgaacgct atagttcctg caggggcaaa aaagcttaaa
      541 aaaacgctag ctttgataag ctaacgttac aaatttttta agaaataatt ttgtttttcg
      601 aaattccaaa tagccgtaat tgaatgggct ttttgttctt cttcagttgt tttttcttca
      661 tcgctcgttt gaattaaatt accttcttcg gcatcgtcta aatttaaaag tttatgtttt
      721 tgtttaagca aaccaccgta acttaacatg cgttttctgt ataatccttg ttccaaatct
      781 tgaacaattt ctgcgtcttt ttcatggttt cccgttaaat aatcggacga cttaaccgag
      841 tattttgatg tttctttaat tgcagcttgt atatctttat cgcctttttt attcggctta
      901 attgctttga tatttgcgac tggtttgtaa tcaacttgaa gagctttttg ccataaattg
      961 atccactctt cttgcgttat ataattagct ttattcttaa aataactatt ttcaacacac
     1021 aataaaacat gcatatgttg attataactg ccatcatttt tattaacggt cacttctgtt
     1081 gaacgtaaaa atccaacaag attttgctta acttttttat atctactcaa tctatcaaaa
     1141 gcttttgtta aatgctttaa actttgttct aaagtctcac catctatcgc atttttcgtt
     1201 gaaagtgtta agaataacca acgtgctttt ggcttttctt taaccactgc ttcaatgact
     1261 ttttgagctt gataactatt tttcattgaa cgcctccaat tacaaaccgg acataattta
     1321 gacttacaaa accatgtttt ataaagtttt aaataccctt catcagtcgg cttaaattct
     1381 aagacgttac cacattgctt cacgttaaaa gcctttttaa tttttaaaat ttctagtata
     1441 tctgcataac ttacattgtc gattttcttt tctctccatg ggcgttgtgt cccactttta
     1501 gtcatatctt tcaatgtttc attatcttga ttttcgtcta tatatcttgt agtattatgt
     1561 tgcatataaa aagacctcca gtagatgttt attgagtaga cgctttaatc atactactgg
     1621 ggttttttta tgtcaaaaat ttctttcaac aacaaaaaaa cgccttaacc ctctattgac
     1681 aagggataaa gcgataattt aaaaatcgag ttatttctat atagtatcaa gacaagaaga
     1741 aactcgtttt cactcgtttc aaaacaaaac acataacttt gttttaaata taaaaattca
     1801 tatgaggttt agcctcttta taataactca atctatcttc taaacttcct gtatgcaatt
     1861 ctaatttatg accatctaaa tcagtgaaat atattgattt tttatctcta atatctctat
     1921 ctctaccttc aagaatattt acttcatttt ctttcaacca gatataccaa tcttcaaaat
     1981 cattatctga aattgtaaat gctatatgag tatacgaata tttaatttcg cttctaggaa
     2041 tatttttttc ttcgttcaaa gccaaccata taccacctaa attaaaatag gccgaggtct
     2101 caccttcaac taaaatgtca gcccctaaaa tatctctgta aaattcaatt gatttagcta
     2161 tattagaaac cgaataagta atatgattta ttcctttaat catattctcc ctcccctttt
     2221 tttaaaattt taacatagtt gctttattcc aattgcttta ttgacgttga gcctcggaac
     2281 ccttaacaat ccctaaactt gtcgaatcgt cggtttaata gctcacgcta taccgacatt
     2341 cgtctccaag tttagttaag ggttcttctc aacatcaata a
//
