LOCUS       NZ_CP118804             6013 bp    DNA     linear   CON 15-MAY-2024
DEFINITION  Mammaliicoccus lentus strain 7066 plasmid pML7066-4.
ACCESSION   NZ_CP118804
VERSION     NZ_CP118804.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33407043
            Assembly: GCF_030013965.1
KEYWORDS    RefSeq.
SOURCE      Mammaliicoccus lentus
  ORGANISM  Mammaliicoccus lentus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Mammaliicoccus.
REFERENCE   1  (bases 1 to 6013)
  AUTHORS   Belhout,C., Boyen,F., Vereecke,N., Theuns,S., Taibi,N., Stegger,M.,
            de la Fe-Rodriguez,P.Y., Bouayad,L., Elgroud,R. and Butaye,P.
  TITLE     Prevalence and Molecular Characterization of Methicillin-Resistant
            Staphylococci (MRS) and Mammaliicocci (MRM) in Dromedary Camels from
            Algeria: First Detection of SCCmec-mecC Hybrid in
            Methicillin-Resistant Mammaliicoccus lentus
  JOURNAL   Antibiotics (Basel) 12 (4), 674 (2023)
   PUBMED   37107036
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 6013)
  AUTHORS   Belhout,C., Stegger,M., Vereecke,N., Elgroud,R. and Butaye,P.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-FEB-2023) Department of Pathobiology, Pharmacology and
            Zoological Medicine, Universiteit Gent, Salisburylaan 133, Merelbeke
            9820, Belgium
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Trycycler; minimap2; medaka v. v0.5.3; v2.20;
            v1.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 396x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013965.1-RS_2024_05_15
            Annotation Date                   :: 05/15/2024 04:32:37
            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)                     :: 2,640
            CDSs (total)                      :: 2,559
            Genes (coding)                    :: 2,513
            CDSs (with protein)               :: 2,513
            Genes (RNA)                       :: 81
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 58
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 46
            CDSs (without protein)            :: 46
            Pseudo Genes (ambiguous residues) :: 0 of 46
            Pseudo Genes (frameshifted)       :: 13 of 46
            Pseudo Genes (incomplete)         :: 22 of 46
            Pseudo Genes (internal stop)      :: 15 of 46
            Pseudo Genes (multiple problems)  :: 4 of 46
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP118804.1.
            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/
FEATURES             Location/Qualifiers
     source          1..6013
                     /organism="Mammaliicoccus lentus"
                     /mol_type="genomic DNA"
                     /strain="7066"
                     /isolation_source="Nose"
                     /host="Camelus dromedarius"
                     /db_xref="taxon:42858"
                     /plasmid="pML7066-4"
                     /geo_loc_name="Algeria: M'sila"
                     /collection_date="2021-12-13"
     gene            <1..1380
                     /gene="tet(K)"
                     /locus_tag="PYH60_RS13150"
                     /old_locus_tag="PYH60_13145"
     ARG             2..1377
                     /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            1567..2808
                     /gene="mobV"
                     /locus_tag="PYH60_RS13155"
                     /old_locus_tag="PYH60_13150"
     CDS             1567..2808
                     /gene="mobV"
                     /locus_tag="PYH60_RS13155"
                     /old_locus_tag="PYH60_13150"
                     /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            3335..4381
                     /locus_tag="PYH60_RS13160"
                     /old_locus_tag="PYH60_13155"
     CDS             3335..4381
                     /locus_tag="PYH60_RS13160"
                     /old_locus_tag="PYH60_13155"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032488463.1"
                     /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_282849009.1"
                     /translation="MYKNNHANHSNHLENHDLDNFSKTGYSNSRLDAHTVCISDPKLSF
                     DAMTIVGNLNRDNAQALSKFMSVEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADSWD
                     RRNMRIEFNPNKLTRDEMIWLKQNIISYMEDDGFTRLDLAFDFEDDLSDYYAMSDKAVK
                     KTIFYGRNGKPETKYFGVRDSNRFIRIYNKKQERKDNADAEVMSEHLWRVEIELKRDMV
                     DYWNDCFSDLHILQPDWKTIQRTADRAIVFMLLSDEEEWGKLHRNSRTKYKNLIKEISP
                     KILLKELERVLGRNTFAERVNKLTEDEPKLNGLAGNLDKKMNPELYSEQEQQQEQQKNQ
                     KRDRGMHL"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            4908..5852
                     /locus_tag="PYH60_RS13165"
                     /old_locus_tag="PYH60_13160"
     CDS             4908..5852
                     /locus_tag="PYH60_RS13165"
                     /old_locus_tag="PYH60_13160"
                     /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          3336..4177
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4909..5852
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1568..2805
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttgtttagtt tatataaaaa atttaaaggt ttgttttata gcgttttatt ttggctttgt
       61 attctttcat tttttagtgt attaaatgaa atggttttaa atgtttcttt acctgatatt
      121 gcaaatcatt ttaatactac tcctggaatt acaaactggg taaacactgc atatatgtta
      181 actttttcga taggaacagc agtatatgga aaattatctg attatataaa tataaaaaaa
      241 ttgttaatta ttggtattag tttgagctgt cttggttcat tgattgcttt tattggtcac
      301 aatcactttt ttattttgat ttttggtagg ttagtacaag gagtaggatc tgctgcattc
      361 ccttcactga ttatggtggt tgtagctaga aatattacaa gaaaaaaaca aggcaaagcc
      421 tttggtttta taggatcaat tgtagcttta ggtgaagggt taggtccttc aataggggga
      481 ataatagcac attatattca ttggtcttac ctacttatac ttcctatgat tacaatagta
      541 actatacctt ttcttattaa agtaatggta cctggtaaat caacaaaaaa tacattagat
      601 atcgtaggta ttgttttaat gtctataagt attatatgtt ttatgttatt tacgacaaat
      661 tataattgga cttttttaat actcttcaca atcttttttg tgatttttat taaacatatt
      721 tcaagagttt ctaacccttt tattaatcct aaactaggga aaaacattcc gtttatgctt
      781 ggtttgtttt ctggtgggct aatattttct atagtagctg gttttatatc aatggtgcct
      841 tatatgatga aaactattta tcatgtaaat gtagcgacaa taggtaatag tgttattttt
      901 cctggaacca tgagtgttat tgtttttggt tattttggtg gttttttagt ggatagaaaa
      961 ggatcattat ttgtttttat tttaggatca ttgtctatct ctataagttt tttaactatt
     1021 gcattttttg ttgagtttag tatgtggttg actactttta tgtttatatt tgttatgggc
     1081 ggattatctt ttactaaaac agttatatca aaaatagtat caagtagtct ttctgaagaa
     1141 gaagttgctt ctggaatgag tttgctaaat ttcacaagtt ttttatcaga gggaacaggt
     1201 atagcaattg taggaggttt attgtcacta caattgatta atcgtaaact agttctggaa
     1261 tttataaatt attcttctgg agtgtatagt aatattcttg tagccatggc tatccttatt
     1321 attttatgtt gtcttttgac gattattgta tttaaacgtt ctgaaaagca gtttgaatag
     1381 ttatattata ttttggttta gaactatgag tggctagcat tttgccactc attttttgcg
     1441 ttagcaaaaa caggtttaag cctcgcagag cacacgtatt aacgacttat tgtaaaataa
     1501 gtctagtgtg ttagacttaa actattaaat acacatgaaa cctttgtgct taggagtgat
     1561 ttttatatgt cttattccat tgttagagtt tcaaaagtta aatctggaac aaatacaacg
     1621 ggcatacaaa aacatgttca aagagaaaat aataattatg aaaatgaaga tatagaccat
     1681 agtaaaactt acttaaatta tgatttggta aatgctaata aacagaattt taataacttg
     1741 attgatgaaa aaatcgaaca gaattataca ggcaaaagaa aaattagaac agacgcgatt
     1801 aaacacattg atggtttaat tacatcagac aatgatttct ttgataatca aacgccagaa
     1861 gatacaaagc agttttttga atatgctaaa gagtttttag aacaagaata cggtaaagat
     1921 aatttattat atgcaacagt tcacatggac gaaaaaacac cacatatgca ttatggcgtt
     1981 gttccaataa ctgatgatgg tcgtttaagt gctaaagaag ttgtaggtaa taaaaaagct
     2041 ttaacagcgt ttcaagatag atttaatgag catgttaaac aacgaggata tgatttagaa
     2101 cgtgggcaat caagacaagt aacaaatgct aaacatgagc aaataagtca gtataaacaa
     2161 aaaacagaat atcataagca agaatatgaa cgtgagagcc aaaaaacaga ccatataaag
     2221 caaaagaacg ataaattaat gcaagagtac caaaaatcgt taaatacgct taaaaagcct
     2281 ataaatgttc cgtatgagca agaaactgaa aaagtaggtg gtttatttag caaagaaata
     2341 caagaaactg gaaatgttgt aataagccaa aaagatttca atgaatttca gaaacagata
     2401 aaagctgctc aagatatttc ggaagattac gagtatataa agtctggtag agccttagat
     2461 gataaagata aggaaatacg agagaaagat gatttattaa ataaagcagt tgagcgtatt
     2521 gaaaacgcag acgataattt taaccaactt tacgaaaatg caaagccact taaagagaat
     2581 atagaaatag cgttaaagct tttaaaaatc ttactaaaag agttagaacg agttttagga
     2641 agaaatacct ttgcggaaag agttaataag ttaacagaag atgaaccaaa actaaatggt
     2701 ttagcaggaa acttagataa aaaaatgaat ccagaattat attcagaaca ggaacagcaa
     2761 caagaacaac aaaagaatca aaaacgagat agaggtatgc acttatagaa catgcattta
     2821 tgccgagaaa acttattggt tggaatgggc tatgtgttag ctaacttgtt agcgagttgg
     2881 ttggacttga attgggatta atcccaagaa agtaccaact caacaacaca taaagccctg
     2941 taggttccga ccaataagga aattggaata aagcaataaa aggagttgaa gaaatgaaat
     3001 tcagagaagc ctttgagaat tttataacaa gtaagtatgt acttggtgtt ttagtagttt
     3061 taactgttta ccagataata caaatgctta aataaaaaaa gacttgatct gattagacca
     3121 agtcttttga tagtgttata ttaataacaa aataaaaagg agtcgctcac gccctgacca
     3181 aagtttgtga acgacatcat tcaaagaaaa aaacactgag ttgtttttat aatcttgtat
     3241 atttagatat taaacgatat ttaaatatac atcaagatat atatttgggt gagcgattcc
     3301 ttaaacgaaa ttgagattaa ggagtcgatt ttttatgtat aaaaacaatc atgcaaatca
     3361 ttcaaatcat ttggaaaatc acgatttaga caatttttct aaaaccggct actctaatag
     3421 ccggttggac gcacatactg tgtgcatatc tgatccaaaa ttaagttttg atgcaatgac
     3481 gatcgttgga aatctcaacc gagacaacgc tcaagccctt tctaaattta tgagtgtaga
     3541 gccccaaata agactttggg atattcttca aacaaagttt aaagctaaag cacttcaaga
     3601 aaaagtttat attgaatatg acaaagtgaa agcagatagt tgggatagac gtaatatgcg
     3661 tattgaattt aatccaaaca aacttacacg agatgaaatg atttggttaa aacaaaatat
     3721 aataagctac atggaagatg acggttttac aagattagat ttagcctttg attttgaaga
     3781 tgatttgagt gactactatg caatgtctga taaagcagtt aagaaaacta ttttttatgg
     3841 tcgtaatggt aagccagaaa caaaatattt tggcgtgaga gatagtaata gatttattag
     3901 aatttataat aaaaagcaag aacgtaaaga taatgcagat gctgaagtta tgtctgaaca
     3961 tttatggcgt gtagaaatcg aacttaaaag agatatggtg gattactgga atgattgctt
     4021 tagtgattta catatcttgc aaccagattg gaaaactatc caacgcactg cggatagagc
     4081 aatagttttt atgttattga gtgatgaaga agaatgggga aagcttcaca gaaattctag
     4141 aacaaaatat aagaatttga taaaagaaat ttcgccaaaa atcttactaa aagagttaga
     4201 acgagtttta ggaagaaata cctttgcgga aagagttaat aagttaacag aagatgaacc
     4261 aaaactaaat ggtttagcag gaaacttaga taaaaaaatg aatccagaat tatattcaga
     4321 acaggaacag caacaagaac aacaaaagaa tcaaaaacga gatagaggta tgcacttata
     4381 gaacatgcat ttatgccgag aaaacttatt ggttggaatg ggctatgtgt tagctaactt
     4441 gttagcgagt tggttggact tgaattggga ttaatcccaa gaaagtacca actcaacaac
     4501 acataaagcc ctgtaggttc cgaccaataa ggaaattgga ataaagcaat aaaaggagtt
     4561 gaagaaatga aattcagaga agcctttgag aattttataa caagtaagta tgtacttggt
     4621 gttttagtag ttttaactgt ttaccagata atacaaatgc ttaaataaaa aaagacttga
     4681 tctgattaga ccaagtcttt tgatagtgtt atattaataa caaaataaaa aggagtcgct
     4741 cacgccctga ccaaagtttg tgaacgacat cattcaaaga aaaaaacact gagttgtttt
     4801 tataatcttg tatatttaga tattaaacga tatttaaata tacatcaaga tatatatttg
     4861 ggtgagcgat tccttaaacg aaattgagat taaggagtcg attttttatg tataaaaaca
     4921 atcatgcaaa tcattcaaat catttggaaa atcacgattt agacaatttt tctaaaaccg
     4981 gctactctaa tagccggttg gacgcacata ctgtgtgcat atctgatcca aaattaagtt
     5041 ttgatgcaat gacgatcgtt ggaaatctca accgagacaa cgctcaagcc ctttctaaat
     5101 ttatgagtgt agagccccaa ataagacttt gggatattct tcaaacaaag tttaaagcta
     5161 aagcacttca agaaaaagtt tatattgaat atgacaaagt gaaagcagat agttgggata
     5221 gacgtaatat gcgtattgaa tttaatccaa acaaacttac acgagatgaa atgatttggt
     5281 taaaacaaaa tataataagc tacatggaag atgacggttt tacaagatta gatttagcct
     5341 ttgattttga agatgatttg agtgactact atgcaatgtc tgataaagca gttaagaaaa
     5401 ctatttttta tggtcgtaat ggtaagccag aaacaaaata ttttggcgtg agagatagta
     5461 atagatttat tagaatttat aataaaaagc aagaacgtaa agataatgca gatgctgaag
     5521 ttatgtctga acatttatgg cgtgtagaaa tcgaacttaa aagagatatg gtggattact
     5581 ggaatgattg ctttagtgat ttacatatct tgcaaccaga ttggaaaact atccaacgca
     5641 ctgcggatag agcaatagtt tttatgttat tgagtgatga agaagaatgg ggaaagcttc
     5701 acagaaattc tagaacaaaa tataagaatt tgataaaaga aatttcgcca gtcgatttaa
     5761 cggacttaat gaaatcgact ttaaaagcga acgaaaaaca attgcaaaaa caaatcgatt
     5821 tttggcaaca tgaatttaaa ttttggaaat agtgtacata ttaatattac tgaacaaaaa
     5881 tgatatattt aaactattct aatttaggag gattttttta tgaagtgtct atttaaaaat
     5941 ttggggaatt tatatgaggt gaaagaataa tttaccccta taaactttag tcacctcaag
     6001 taaagaggta aaa
//
