LOCUS       NZ_CP068077             2361 bp    DNA     circular CON 06-FEB-2024
DEFINITION  Staphylococcus condimenti strain FDAARGOS_1148 plasmid unnamed4,
            complete sequence.
ACCESSION   NZ_CP068077
VERSION     NZ_CP068077.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357317
            Assembly: GCF_016724565.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus condimenti
  ORGANISM  Staphylococcus condimenti
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2361)
  AUTHORS   Sproer,C., Gronow,S., Severitt,S., Schroder,I., Tallon,L.,
            Sadzewicz,L., Zhao,X., Boylan,J., Ott,S., Bowen,H., Vavikolanu,K.,
            Mehta,A., Aluvathingal,J., Nadendla,S., Lowell,S., Myers,T., Yan,Y.
            and Sichtig,H.
  TITLE     FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS):
            Supporting development and validation of Infectious Disease Dx tests
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2361)
  AUTHORS   Sproer,C., Gronow,S., Severitt,S., Schroder,I., Tallon,L.,
            Sadzewicz,L., Zhao,X., Boylan,J., Ott,S., Bowen,H., Vavikolanu,K.,
            Mehta,A., Aluvathingal,J., Nadendla,S., Lowell,S., Myers,T., Yan,Y.
            and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-JAN-2021) Institute for Genome Sciences, University of
            Maryland School of Medicine, BioPark II, 801 W. Baltimore St., Suite
            619, Baltimore, MD 21201, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: SMRT v. 8.0.0, HGAP v. 4, SPAdes v. 3.11.1
            Genome Coverage                   :: 1434.04x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/06/2024 04:22:18
            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)                     :: 2,595
            CDSs (total)                      :: 2,512
            Genes (coding)                    :: 2,479
            CDSs (with protein)               :: 2,479
            Genes (RNA)                       :: 83
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 61
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 33
            CDSs (without protein)            :: 33
            Pseudo Genes (ambiguous residues) :: 0 of 33
            Pseudo Genes (frameshifted)       :: 14 of 33
            Pseudo Genes (incomplete)         :: 15 of 33
            Pseudo Genes (internal stop)      :: 10 of 33
            Pseudo Genes (multiple problems)  :: 6 of 33
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP068077.1.
            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..2361
                     /organism="Staphylococcus condimenti"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1148"
                     /culture_collection="DSM:11674"
                     /type_material="type strain of Staphylococcus condimenti"
                     /db_xref="taxon:70255"
                     /plasmid="unnamed4"
                     /geo_loc_name="Germany: Braunschweig"
                     /collected_by="DSMZ"
     gene            join(1974..2361,1..536)
                     /locus_tag="I6J05_RS12915"
                     /old_locus_tag="I6J05_12915"
     CDS             join(1974..2361,1..536)
                     /locus_tag="I6J05_RS12915"
                     /old_locus_tag="I6J05_12915"
                     /function="essential for plasmid replication"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002501032.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_011428876.1"
                     /translation="MDKYTEKKRRNQVFQKFIKRHVGENQMTLVRECNTFLSFVTDKSL
                     EKNKLYKANSCKNRFCPVCAWRKARKDALGLSLMMQYVQKEHEKEFIFLTLTTPNVSKN
                     KLENEIKHYNQSFRRLSNRTKFKKVVKGYVRKLEITYNKERDDYNPHFHVLIAVNKSYF
                     KDTKSYISQKEWLNLWRDVTGMPEITQVHVEKVKANNDKELYEMAKYSGKDSDYLSNQK
                     VFDAYYRSLKGKQVLVYSGLFKEARKLLKNGDLDYLKEIDPTEYIYQIFYIWKQKEYLA
                     SELYDLTEQEKRELNHQMIDEIEEET"
                     /name="protein rep"
     gene            complement(1223..1708)
                     /gene="lnu(A)"
                     /locus_tag="I6J05_RS12920"
                     /old_locus_tag="I6J05_12920"
     ARG             complement(1227..1708)
                     /name="lnu(A)"
                     /gene="lnu(A)"
                     /gene_name="lincosamide nucleotidyltransferase Lnu(A)"
                     /tool="amrfinderplus"
                     /drug_class="LINCOSAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             complement(1224..1708)
                     /name="lnuA"
                     /gene="lnuA"
                     /gene_name="lincosamide nucleotidyltransferase (LNU)"
                     /tool="rgi"
                     /drug_class="lincosamide antibiotic"
                     /identity="93.79"
                     /coverage="100.0"
     Typing          2..530
                     /name="rep_cluster_2234"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.934"
                     /coverage="93.0"
                     /evalue="1.69e-149"
     Typing          1975..2361
                     /name="rep_cluster_1230"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4..530
                     /name="MOBC"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="85.227"
                     /coverage="97.0"
                     /evalue="1.93e-101"
ORIGIN
        1 ttaagggtta tgtaagaaaa ttagaaatta catacaacaa agagcgggat gattataacc
       61 cacattttca cgttttaatt gcggttaaca aatcttattt caaagatact aaatcttata
      121 ttagccaaaa agaatggttg aatttatggc gagatgtgac gggaatgcca gaaattacac
      181 aagttcatgt cgagaaagtt aaggctaata atgacaaaga actttatgaa atggctaaat
      241 attctggtaa agatagtgat tatttaagta atcaaaaagt attcgacgcg tattatcgtt
      301 ctttaaaagg taagcaggta ttagtgtatt cgggattatt taaagaggcg agaaagttat
      361 taaaaaatgg cgatttagat tatttaaaag agattgatcc aactgaatat atctatcaaa
      421 ttttttatat ttggaaacaa aaagaatatt tagcgagtga attgtatgat ttaacagaac
      481 aagaaaaaag agaattaaat catcaaatga ttgatgaaat tgaagaagaa acataaagtg
      541 ttggtcttag actgacactt ttttattgtt aaatatatgg tcgcctgcct ctgtgggaac
      601 tataaaaaat gtatgcaaat taatttgcat gtagatgggc agtattgaaa ctaatactga
      661 taagttacaa cgatattagg ttgattttaa aattgttgaa cgtgtccgat ttctacaagc
      721 taagagtaaa tacagaaaag gctacattta aggtacaaaa agcttacaag tgatttacga
      781 tttaaatgta gttaagttgt atcgttttgg ttaataaaaa tgtagtgtta taacatgctt
      841 ttatttggct catatttgcg ttttaagagc ttatgtatgt ttttaggtat aaaactatat
      901 gatttacact taaaacttta aaatacccct ttagaattaa aattaagggc atttaagatt
      961 taacaaaata aaaaaagcca ccaataaaat ttggtggctt tttttatttt tggaagtgaa
     1021 cagtgaaaac aaaacagaac gttaattaaa ttataacacg cttttatgcc gagaaaattt
     1081 attgatcgtt gagaagaacc cttaactaaa cttgtagacg aatgtcggca tagcgtgagc
     1141 tattaagccg accattcgac aagttttggg attgttaagg gttccgaggc tcaacgtcaa
     1201 taaagcaatt ggaataaagc aattatgtta ttgattttaa attttttata tcaaaatggt
     1261 ctttttctgt taagtcataa ccagaatgaa aaagaagctg agcttctttt gaaatacatg
     1321 gtatttttcg acctttataa ttagtttctg aaaaccattc attttgaaaa acgtaattgc
     1381 caccttctgg atttgcttga gtaatggaac catcatcatt taaatttatg ggatgaatat
     1441 ctaaatatcc atatttttta tgtttaagtt ccatgcgtga aggcatccaa tcaacttcta
     1501 ttttatatcc tatatcttct aatttttgta taactttttg agtgtgttgg gcgtcaaaat
     1561 ctatatctat atctctgtgt tctctttgtt gttttccagt taatacatct acaccccaac
     1621 ctccatctaa ccaataagtt acttccattt tttcaaataa gtctaaaata taaaataaat
     1681 ccttttctgt tacattatta attttcattt tatccctcct aatttaggaa tttgaaacga
     1741 gttgaaaacg agtttcttct tgtcttgata ataagggtaa ctattacaga gtagaatagt
     1801 tacccttaaa gtgttggtat atctgggttg aaacacaaaa aaagttgctt tttttagcat
     1861 actcatgtag tgttttaggt gtctagtcta aaaacattat gagaaaggag aaaaagcaac
     1921 tttttttatt gtcatagttt gtgaaaacta agttgttttt taagttatat aacatggata
     1981 agtatactga gaagaaacga agaaatcaag tatttcagaa atttataaag cgacatgtgg
     2041 gggaaaatca aatgacattg gtacgggaat gtaatacctt tttgtctttt gtgacagata
     2101 agtcgttaga aaaaaataaa ttatataaag caaattcatg taaaaatcgt ttttgtccgg
     2161 tttgtgcatg gcgtaaagcg agaaaagatg cgttgggttt atctttgatg atgcagtatg
     2221 tacaaaaaga acatgaaaaa gaatttatat ttttaacttt aacgacgcct aatgtgtcta
     2281 aaaataaatt agaaaatgag attaagcatt ataatcaatc atttagacga ttaagtaatc
     2341 gaacaaaatt taaaaaggtt g
//
