LOCUS       NZ_CP118986             2361 bp    DNA     circular CON 30-MAR-2024
DEFINITION  Staphylococcus equorum strain DSM 20674 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP118986
VERSION     NZ_CP118986.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33336506
            Assembly: GCF_029024965.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus equorum
  ORGANISM  Staphylococcus equorum
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2361)
  AUTHORS   Romano',A., Ivanovic,I., Segessemann,T., Vazquez Rojo,L., Dreier,M.,
            Sesso,L., Vaccani,M., Schuler,M., Frei,D., Frey,J.E., Ahrens,C.H.,
            Steiner,A. and Graber,H.U.
  TITLE     Elucidation of the Bovine Intramammary Bacteriome and Resistome from
            healthy cows of Swiss dairy farms in the Canton Tessin
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2361)
  AUTHORS   Romano',A., Ivanovic,I., Segessemann,T., Vazquez Rojo,L., Dreier,M.,
            Sesso,L., Vaccani,M., Schuler,M., Frei,D., Frey,J.E., Ahrens,C.H.,
            Steiner,A. and Graber,H.U.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-FEB-2023) Food Microbial Systems, Agroscope,
            Schwarzenburgstrasse 161, Liebefeld 3097, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-MAY-2021
            Assembly Method                   :: Flye v. v2.8.1-b1676
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 5351x
            Sequencing Technology :: Oxford Nanopore + Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_029024965.1-RS_2024_03_30
            Annotation Date                   :: 03/30/2024 07:42:00
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,664
            CDSs (total)                      :: 2,578
            Genes (coding)                    :: 2,548
            CDSs (with protein)               :: 2,548
            Genes (RNA)                       :: 86
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 60
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 30
            CDSs (without protein)            :: 30
            Pseudo Genes (ambiguous residues) :: 0 of 30
            Pseudo Genes (frameshifted)       :: 16 of 30
            Pseudo Genes (incomplete)         :: 11 of 30
            Pseudo Genes (internal stop)      :: 10 of 30
            Pseudo Genes (multiple problems)  :: 6 of 30
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP118986.1.
            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 equorum"
                     /mol_type="genomic DNA"
                     /strain="DSM 20674"
                     /isolation_source="Skin of horse"
                     /host="Horse"
                     /culture_collection="DSM:20674"
                     /type_material="type strain of Staphylococcus equorum"
                     /db_xref="taxon:246432"
                     /plasmid="unnamed4"
                     /collection_date="1984"
     gene            complement(1..486)
                     /gene="lnu(A)"
                     /locus_tag="PYW44_RS13320"
     ARG             complement(5..486)
                     /name="lnu(A)"
                     /gene="lnu(A)"
                     /gene_name="lincosamide nucleotidyltransferase Lnu(A)"
                     /tool="amrfinderplus"
                     /drug_class="LINCOSAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            752..1675
                     /locus_tag="PYW44_RS13325"
     CDS             752..1675
                     /locus_tag="PYW44_RS13325"
                     /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"
     ARG             complement(2..486)
                     /name="lnuA"
                     /gene="lnuA"
                     /gene_name="lincosamide nucleotidyltransferase (LNU)"
                     /tool="rgi"
                     /drug_class="lincosamide antibiotic"
                     /identity="93.79"
                     /coverage="100.0"
     Typing          753..1675
                     /name="rep_cluster_1230"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttatgttatt gattttaaat tttttatatc aaaatggtct ttttctgtta agtcataacc
       61 agaatgaaaa agaagctgag cttcttttga aatacatggt atttttcgac ctttataatt
      121 agtttctgaa aaccattcat tttgaaaaac gtaattgcca ccttctggat ttgcttgagt
      181 aatggaacca tcatcattta aatttatggg atgaatatct aaatatccat attttttatg
      241 tttaagttcc atgcgtgaag gcatccaatc aacttctatt ttatatccta tatcttctaa
      301 tttttgtata actttttgag tgtgttgggc gtcaaaatct atatctatat ctctgtgttc
      361 tctttgttgt tttccagtta atacatctac accccaacct ccatctaacc aataagttac
      421 ttccattttt tcaaataagt ctaaaatata aaataaatcc ttttctgtta cattattaat
      481 tttcatttta tccctcctaa tttaggaatt tgaaacgagt tgaaaacgag tttcttcttg
      541 tcttgataat aagggtaact attacagagt agaatagtta cccttaaagt gttggtatat
      601 ctgggttgaa acacaaaaaa agttgctttt tttagcatac tcatgtagtg ttttaggtgt
      661 ctagtctaaa aacattatga gaaaggagaa aaagcaactt tttttattgt catagtttgt
      721 gaaaactaag ttgtttttta agttatataa catggataag tatactgaga agaaacgaag
      781 aaatcaagta tttcagaaat ttataaagcg acatgtgggg gaaaatcaaa tgacattggt
      841 acgggaatgt aatacctttt tgtcttttgt gacagataag tcgttagaaa aaaataaatt
      901 atataaagca aattcatgta aaaatcgttt ttgtccggtt tgtgcatggc gtaaagcgag
      961 aaaagatgcg ttgggtttat ctttgatgat gcagtatgta caaaaagaac atgaaaaaga
     1021 atttatattt ttaactttaa cgacgcctaa tgtgtctaaa aataaattag aaaatgagat
     1081 taagcattat aatcaatcat ttagacgatt aagtaatcga acaaaattta aaaaggttgt
     1141 taagggttat gtaagaaaat tagaaattac atacaacaaa gagcgggatg attataaccc
     1201 acattttcac gttttaattg cggttaacaa atcttatttc aaagatacta aatcttatat
     1261 tagccaaaaa gaatggttga atttatggcg agatgtgacg ggaatgccag aaattacaca
     1321 agttcatgtc gagaaagtta aggctaataa tgacaaagaa ctttatgaaa tggctaaata
     1381 ttctggtaaa gatagtgatt atttaagtaa tcaaaaagta ttcgacgcgt attatcgttc
     1441 tttaaaaggt aagcaggtat tagtgtattc gggattattt aaagaggcga gaaagttatt
     1501 aaaaaatggc gatttagatt atttaaaaga gattgatcca actgaatata tctatcaaat
     1561 tttttatatt tggaaacaaa aagaatattt agcgagtgaa ttgtatgatt taacagaaca
     1621 agaaaaaaga gaattaaatc atcaaatgat tgatgaaatt gaagaagaaa cataaagtgt
     1681 tggtcttaga ctgacacttt tttattgtta aatatatggt cgcctgcctc tgtgggaact
     1741 ataaaaaatg tatgcaaatt aatttgcatg tagatgggca gtattgaaac taatactgat
     1801 aagttacaac gatattaggt tgattttaaa attgttgaac gtgtccgatt tctacaagct
     1861 aagagtaaat acagaaaagg ctacatttaa ggtacaaaaa gcttacaagt gatttacgat
     1921 ttaaatgtag ttaagttgta tcgttttggt taataaaaat gtagtgttat aacatgcttt
     1981 tatttggctc atatttgcgt tttaagagct tatgtatgtt tttaggtata aaactatatg
     2041 atttacactt aaaactttaa aatacccctt tagaattaaa attaagggca tttaagattt
     2101 aacaaaataa aaaaagccac caataaaatt tggtggcttt ttttattttt ggaagtgaac
     2161 agtgaaaaca aaacagaacg ttaattaaat tataacacgc ttttatgccg agaaaattta
     2221 ttgatcgttg agaagaaccc ttaactaaac ttgtagacga atgtcggcat agcgtgagct
     2281 attaagccga ccattcgaca agttttggga ttgttaaggg ttccgaggct caacgtcaat
     2341 aaagcaattg gaataaagca a
//
