LOCUS       NZ_CP120104             4433 bp    DNA     circular CON 06-JAN-2024
DEFINITION  Staphylococcus nepalensis strain Dog109 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP120104
VERSION     NZ_CP120104.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33696799
            Assembly: GCF_034030455.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus nepalensis
  ORGANISM  Staphylococcus nepalensis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 4433)
  AUTHORS   Akarsu,H., Liljander,A., Lacasta,A., Ssajjakambwe,P., Brodard,I.,
            Cherbuin,J., Kuhnert,P., Perreten,V., Torres Puig,S., Labroussaa,F.
            and Jores,J.
  TITLE     Canine Staphylococcaceae circulating in a Kenyan animal shelter
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4433)
  AUTHORS   Akarsu,H., Liljander,A., Lacasta,A., Ssajjakambwe,P., Brodard,I.,
            Cherbuin,J., Kuhnert,P., Perreten,V., Torres Puig,S., Labroussaa,F.
            and Jores,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-DEC-2023) Institute of Veterinary Bacteriology,
            University of Bern, Langgassstrasse 122, Bern 3001, Switzerland
  REMARK    Annotation added by database at submitter's request
REFERENCE   3  (bases 1 to 4433)
  AUTHORS   Akarsu,H., Liljander,A., Lacasta,A., Ssajjakambwe,P., Brodard,I.,
            Cherbuin,J., Kuhnert,P., Perreten,V., Torres Puig,S., Labroussaa,F.
            and Jores,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-MAR-2023) Institute of Veterinary Bacteriology,
            University of Bern, Langgassstrasse 122, Bern 3001, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: AUG-2022
            Assembly Method                   :: Flye v. v2.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 544x
            Sequencing Technology             :: PacBio Sequel II
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/06/2024 10:53:02
            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)                     :: 2,829
            CDSs (total)                      :: 2,743
            Genes (coding)                    :: 2,699
            CDSs (with protein)               :: 2,699
            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)              :: 44
            CDSs (without protein)            :: 44
            Pseudo Genes (ambiguous residues) :: 0 of 44
            Pseudo Genes (frameshifted)       :: 27 of 44
            Pseudo Genes (incomplete)         :: 27 of 44
            Pseudo Genes (internal stop)      :: 15 of 44
            Pseudo Genes (multiple problems)  :: 17 of 44
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP120104.1.
            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..4433
                     /organism="Staphylococcus nepalensis"
                     /mol_type="genomic DNA"
                     /strain="Dog109"
                     /isolation_source="nasal swab"
                     /host="Canis lupus familiaris"
                     /db_xref="taxon:214473"
                     /plasmid="unnamed5"
                     /geo_loc_name="Kenya:Nairobi"
                     /lat_lon="1.3345 S 36.7331 E"
                     /collection_date="2015-06-27"
                     /collected_by="Joerg Jores, Anna Lacasta, Anne Liljander,
                     Paul Ssajjakambwe (International Livestock Research
                     Institute, ILRI)"
     gene            50..1429
                     /gene="tet(K)"
                     /locus_tag="P3T86_RS14125"
                     /old_locus_tag="P3T86_14125"
     ARG             51..1426
                     /name="tet(K)"
                     /gene="tet(K)"
                     /gene_name="tetracycline efflux MFS transporter Tet(K)"
                     /tool="amrfinderplus"
                     /drug_class="TETRACYCLINE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            1615..2856
                     /gene="mobV"
                     /locus_tag="P3T86_RS14130"
                     /old_locus_tag="P3T86_14130"
     CDS             1615..2856
                     /gene="mobV"
                     /locus_tag="P3T86_RS14130"
                     /old_locus_tag="P3T86_14130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010889940.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobV family relaxase"
                     /protein_id="WP_000122374.1"
                     /translation="MSYSIVRVSKVKSGTNTTGIQKHVQRENNNYENEDIDHSKTYLNY
                     DLVNANKQNFNNLIDEKIEQNYTGKRKIRTDAIKHIDGLITSDNDFFDNQTPEDTKQFF
                     EYAKEFLEQEYGKDNLLYATVHMDEKTPHMHYGVVPITDDGRLSAKEVVGNKKALTAFQ
                     DRFNEHVKQRGYDLERGQSRQVTNAKHEQISQYKQKTEYHKQEYERESQKTDHIKQKND
                     KLMQEYQKSLNTLKKPINVPYEQETEKVGGLFSKEIQETGNVVISQKDFNEFQKQIKAA
                     QDISEDYEYIKSGRALDDKDKEIREKDDLLNKAVERIENADDNFNQLYENAKPLKENIE
                     IALKLLKILLKELERVLGRNTFAERVNKLTEDEPKLNGLAGNLDKKMNPELYSEQEQQQ
                     EQQKNQKRDRGMHL"
                     /name="mobV"
     gene            3383..4327
                     /locus_tag="P3T86_RS14135"
                     /old_locus_tag="P3T86_14135"
     CDS             3383..4327
                     /locus_tag="P3T86_RS14135"
                     /old_locus_tag="P3T86_14135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000277654.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003916 - DNA topoisomerase activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation factor domain-containing
                     protein"
                     /protein_id="WP_000277654.1"
                     /translation="MYKNNHANHSNHLENHDLDNFSKTGYSNSRLDAHTVCISDPKLSF
                     DAMTIVGNLNRDNAQALSKFMSVEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADSWD
                     RRNMRIEFNPNKLTRDEMIWLKQNIISYMEDDGFTRLDLAFDFEDDLSDYYAMSDKAVK
                     KTIFYGRNGKPETKYFGVRDSNRFIRIYNKKQERKDNADAEVMSEHLWRVEIELKRDMV
                     DYWNDCFSDLHILQPDWKTIQRTADRAIVFMLLSDEEEWGKLHRNSRTKYKNLIKEISP
                     VDLTDLMKSTLKANEKQLQKQIDFWQHEFKFWK"
                     /name="replication initiation factor domain-containing
                     protein"
     Typing          3384..4327
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1616..2853
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gaataattta cccctataaa ctttagtcac ctcaagtaaa gaggtaaaat tgtttagttt
       61 atataaaaaa tttaaaggtt tgttttatag cgttttattt tggctttgta ttctttcatt
      121 ttttagtgta ttaaatgaaa tggttttaaa tgtttcttta cctgatattg caaatcattt
      181 taatactact cctggaatta caaactgggt aaacactgca tatatgttaa ctttttcgat
      241 aggaacagca gtatatggaa aattatctga ttatataaat ataaaaaaat tgttaattat
      301 tggtattagt ttgagctgtc ttggttcatt gattgctttt attggtcaca atcacttttt
      361 tattttgatt tttggtaggt tagtacaagg agtaggatct gctgcattcc cttcactgat
      421 tatggtggtt gtagctagaa atattacaag aaaaaaacaa ggcaaagcct ttggttttat
      481 aggatcaatt gtagctttag gtgaagggtt aggtccttca atagggggaa taatagcaca
      541 ttatattcat tggtcttacc tacttatact tcctatgatt acaatagtaa ctataccttt
      601 tcttattaaa gtaatggtac ctggtaaatc aacaaaaaat acattagata tcgtaggtat
      661 tgttttaatg tctataagta ttatatgttt tatgttattt acgacaaatt ataattggac
      721 ttttttaata ctcttcacaa tcttttttgt gatttttatt aaacatattt caagagtttc
      781 taaccctttt attaatccta aactagggaa aaacattccg tttatgcttg gtttgttttc
      841 tggtgggcta atattttcta tagtagctgg ttttatatca atggtgcctt atatgatgaa
      901 aactatttat catgtaaatg tagcgacaat aggtaatagt gttatttttc ctggaaccat
      961 gagtgttatt gtttttggtt attttggtgg ttttttagtg gatagaaaag gatcattatt
     1021 tgtttttatt ttaggatcat tgtctatctc tataagtttt ttaactattg cattttttgt
     1081 tgagtttagt atgtggttga ctacttttat gtttatattt gttatgggcg gattatcttt
     1141 tactaaaaca gttatatcaa aaatagtatc aagtagtctt tctgaagaag aagttgcttc
     1201 tggaatgagt ttgctaaatt tcacaagttt tttatcagag ggaacaggta tagcaattgt
     1261 aggaggttta ttgtcactac aattgattaa tcgtaaacta gttctggaat ttataaatta
     1321 ttcttctgga gtgtatagta atattcttgt agccatggct atccttatta ttttatgttg
     1381 tcttttgacg attattgtat ttaaacgttc tgaaaagcag tttgaatagt tatattatat
     1441 tttggtttag aactatgagt ggctagcatt ttgccactca ttttttgcgt tagcaaaaac
     1501 aggtttaagc ctcgcagagc acacgtatta acgacttatt aaaaataagt ctagtgtgtt
     1561 agacttaaac tattaaatac acatgaaacc tttgtgctta ggagtgattt ttatatgtct
     1621 tattccattg ttagagtttc aaaagttaaa tctggaacaa atacaacggg catacaaaaa
     1681 catgttcaaa gagaaaataa taattatgaa aatgaagata tagaccatag taaaacttac
     1741 ttaaattatg atttggtaaa tgctaataaa cagaatttta ataacttgat tgatgaaaaa
     1801 atcgaacaga attatacagg caaaagaaaa attagaacag acgcgattaa acacattgat
     1861 ggtttaatta catcagacaa tgatttcttt gataatcaaa cgccagaaga tacaaagcag
     1921 ttttttgaat atgctaaaga gtttttagaa caagaatacg gtaaagataa tttattatat
     1981 gcaacagttc acatggacga aaaaacacca catatgcatt atggcgttgt tccaataact
     2041 gatgatggtc gtttaagtgc taaagaagtt gtaggtaata aaaaagcttt aacagcgttt
     2101 caagatagat ttaatgagca tgttaaacaa cgaggatatg atttagaacg tgggcaatca
     2161 agacaagtaa caaatgctaa acatgagcaa ataagtcagt ataaacaaaa aacagaatat
     2221 cataagcaag aatatgaacg tgagagccaa aaaacagacc atataaagca aaagaacgat
     2281 aaattaatgc aagagtacca aaaatcgtta aatacgctta aaaagcctat aaatgttccg
     2341 tatgagcaag aaactgaaaa agtaggtggt ttatttagca aagaaataca agaaactgga
     2401 aatgttgtaa taagccaaaa agatttcaat gaatttcaga aacagataaa agctgctcaa
     2461 gatatttcgg aagattacga gtatataaag tctggtagag ccttagatga taaagataag
     2521 gaaatacgag agaaagatga tttattaaat aaagcagttg agcgtattga aaacgcagac
     2581 gataatttta accaacttta cgaaaatgca aagccactta aagagaatat agaaatagcg
     2641 ttaaagcttt taaaaatctt actaaaagag ttagaacgag ttttaggaag aaataccttt
     2701 gcggaaagag ttaataagtt aacagaagat gaaccaaaac taaatggttt agcaggaaac
     2761 ttagataaaa aaatgaatcc agaattatat tcagaacagg aacagcaaca agaacaacaa
     2821 aagaatcaaa aacgagatag aggtatgcac ttatagaaca tgcatttatg ccgagaaaac
     2881 ttattggttg gaatgggcta tgtgttagct aacttgttag cgagttggtt ggacttgaat
     2941 tgggattaat cccaagaaag taccaactca acaacacata aagccctgta ggttccgacc
     3001 aataaggaaa ttggaataaa gcaataaaag gagttgaaga aatgaaattc agagaagcct
     3061 ttgagaattt tataacaagt aagtatgtac ttggtgtttt agtagtttta actgtttacc
     3121 agataataca aatgcttaaa taaaaaaaga cttgatctga ttagaccaag tcttttgata
     3181 gtgttatatt aataacaaaa taaaaaggag tcgctcacgc cctgaccaaa gtttgtgaac
     3241 gacatcattc aaagaaaaaa acactgagtt gtttttataa tcttgtatat ttagatatta
     3301 aacgatattt aaatatacat caagatatat atttgggtga gcgattcctt aaacgaaatt
     3361 gagattaagg agtcgatttt ttatgtataa aaacaatcat gcaaatcatt caaatcattt
     3421 ggaaaatcac gatttagaca atttttctaa aaccggctac tctaatagcc ggttggacgc
     3481 acatactgtg tgcatatctg atccaaaatt aagttttgat gcaatgacga tcgttggaaa
     3541 tctcaaccga gacaacgctc aagccctttc taaatttatg agtgtagagc cccaaataag
     3601 actttgggat attcttcaaa caaagtttaa agctaaagca cttcaagaaa aagtttatat
     3661 tgaatatgac aaagtgaaag cagatagttg ggatagacgt aatatgcgta ttgaatttaa
     3721 tccaaacaaa cttacacgag atgaaatgat ttggttaaaa caaaatataa taagctacat
     3781 ggaagatgac ggttttacaa gattagattt agcctttgat tttgaagatg atttgagtga
     3841 ctactatgca atgtctgata aagcagttaa gaaaactatt ttttatggtc gtaatggtaa
     3901 gccagaaaca aaatattttg gcgtgagaga tagtaataga tttattagaa tttataataa
     3961 aaagcaagaa cgtaaagata atgcagatgc tgaagttatg tctgaacatt tatggcgtgt
     4021 agaaatcgaa cttaaaagag atatggtgga ttactggaat gattgcttta gtgatttaca
     4081 tatcttgcaa ccagattgga aaactatcca acgcactgcg gatagagcaa tagtttttat
     4141 gttattgagt gatgaagaag aatggggaaa gcttcacaga aattctagaa caaaatataa
     4201 gaatttgata aaagaaattt cgccagtcga tttaacggac ttaatgaaat cgactttaaa
     4261 agcgaacgaa aaacaattgc aaaaacaaat cgatttttgg caacatgaat ttaaattttg
     4321 gaaatagtgt acatattaat attactgaac aaaaatgata tatttaaact attctaattt
     4381 aggaggattt ttttatgaag tgtctattta aaaatttggg gaatttatat gag
//
