LOCUS       NZ_CP118803             3318 bp    DNA     linear   CON 15-MAY-2024
DEFINITION  Mammaliicoccus lentus strain 7066 plasmid pML7066-3.
ACCESSION   NZ_CP118803
VERSION     NZ_CP118803.1
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 3318)
  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 3318)
  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
            CP118803.1.
            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..3318
                     /organism="Mammaliicoccus lentus"
                     /mol_type="genomic DNA"
                     /strain="7066"
                     /isolation_source="Nose"
                     /host="Camelus dromedarius"
                     /db_xref="taxon:42858"
                     /plasmid="pML7066-3"
                     /geo_loc_name="Algeria: M'sila"
                     /collection_date="2021-12-13"
     gene            1..>804
                     /locus_tag="PYH60_RS13135"
                     /old_locus_tag="PYH60_13130"
                     /pseudo=""
     CDS             1..>804
                     /locus_tag="PYH60_RS13135"
                     /old_locus_tag="PYH60_13130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002405927.1"
                     /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="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation factor domain-containing
                     protein"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            <913..1893
                     /locus_tag="PYH60_RS13140"
                     /old_locus_tag="PYH60_13135"
                     /pseudo=""
     CDS             <913..1893
                     /locus_tag="PYH60_RS13140"
                     /old_locus_tag="PYH60_13135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000492283.1"
                     /GO_function="GO:0022857 - transmembrane transporter
                     activity [Evidence IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="frameshifted; incomplete; partial in the middle of a
                     contig; missing N-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="MFS transporter"
                     /name="MFS transporter"
     gene            2081..>2918
                     /gene="mobV"
                     /locus_tag="PYH60_RS13145"
                     /old_locus_tag="PYH60_13140"
                     /pseudo=""
     CDS             2081..>2918
                     /gene="mobV"
                     /locus_tag="PYH60_RS13145"
                     /old_locus_tag="PYH60_13140"
                     /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="frameshifted; incomplete; partial in the middle of a
                     contig; missing C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="MobV family relaxase"
                     /name="mobV"
     ARG             1289..1893
                     /name="tet(K)"
                     /gene="tet(K)"
                     /gene_name="major facilitator superfamily (MFS) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="tetracycline antibiotic"
                     /identity="96.52"
                     /coverage="43.79"
     Typing          2..756
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.868"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2082..2266
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="92.0"
                     /evalue="1.9e-83"
     Typing          2266..2576
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.231"
                     /coverage="92.0"
                     /evalue="1.9e-83"
ORIGIN
        1 atggcaaaaa taacgaaaaa tgagcaagaa aatttggtga aaaattacac aaaaaaaccg
       61 gcgtactcta atagccggtt aaaccgacat attatgtaca cccccgaacc aaaattacac
      121 tttgatgcta tgacaattgt tgggaatctt aataagaaca atgctcacaa actgtctgaa
      181 tttatgagta ttgcgccaca aattagactt tgggatatat tacaaaccaa atttaaagct
      241 aaggctctac aagaaaaagt ttacatcgaa tatgataaag taaaagcaga tgcgtgggat
      301 agacgtaata tgcgtgttga atttaatcct aataaactta cgcatgaaga aatgctttgg
      361 ttaaaacaaa acatcattga ctacatggaa gatgatggtt ttacaagatt agatttggct
      421 tttgattttg aagacgattt gagcgattat tatgcgatga ctgataaatc agttaagaaa
      481 actatttttt atggtcgtaa cggtaaacca gaaacaaaat attttggtgt tcgtgacagt
      541 gatagattta ttagaattta taataaaaaa caagaacgta aggataatgc agacattgaa
      601 gttatgtctg aacacttatg gcgtgtagaa attgaattaa aaagagatat ggttgattat
      661 tggaacgatt gttttaatga tttacatatt ttgaaaccag attggtctag tttagaaaaa
      721 gtaaaagacc aagcaatgat ttatatgcta attcatgaag aaagtacatg gggtaaatta
      781 gaaagacgta caaaaaataa atacagagtt tttttttttt ttttttttta aaaatgttat
      841 aaattatttt ttcagaaatt gatttaagga cttaatgaaa ttgactttaa aagagaatga
      901 aaaacaattg caaaaaaaca aggcaaagcc tttggtttta taggatcaat tgtagcttta
      961 ggtgaagggt taggtccttc aataggggga ataatagcac attatattca ttggtcttac
     1021 ctacttatac ttcctatgat tacaatagta actatacctt ttcttattaa agtaatggta
     1081 cctggtaaat caacaaaaaa tacattagat atcgtaggta ttgttttaat gtctataagt
     1141 attatatgtt ttatgttatt tacgacaaat tataattgga attttttaat actcttcatt
     1201 caatcttttt tgtgattttt attaaacata tttcaagagt ttcctaaccc ttttattaat
     1261 cctaaactag gaaaaaacat tccgtttatg cttggtttgt tttctagtgg gctaatattt
     1321 tctatagtag ttgattttat atcacttatg tcttatatga tgaaaaccat ttatcatgta
     1381 aatgtagcga caataggtaa tagtgttatt tttcctggaa ccatgagtgt tattgttttt
     1441 ggttattttg gtggtttttt agtggataga aaaggatcat tatttgtttt tattttagga
     1501 tcattgtcta tctctataag ttttttaact attgcatttt ttgttgagtt tagtatgtgg
     1561 ttgactactt ttatgtttat atttgttatg ggcggattat cttttactaa aacagttata
     1621 tcaaaaatag tatcaagtag tctttctgaa gaagaagttg cttctggaat gagtttgcta
     1681 aatttcacaa gttttttatc agagggaaca ggtatagcaa ttgtaggagg tttattgtca
     1741 ctacaattga ttaatcgtaa actagttctg gaatttataa attattcttc tggagtgtat
     1801 agtaatattc ttgtagccat ggctatcctt attattttat gttgtctttt gacgattatt
     1861 gtatttaaat gttctgaaaa gcagtttgaa tagttatatt atattttggt ttagaactat
     1921 gagtggctag catttatgcc actcattttt tgcgttagca aaaacaggtt taagcctcgc
     1981 agagcacacg tattaacgac ttattgtaaa ataagtctag tgtgttagac ttaaactatt
     2041 aaatacacat gaaacctttg tgcttaggag tgatttttat atgtcttatt ccattgttag
     2101 agtttcaaaa gttaaatctg gaacaaatac aacgggcata caaaaacatg ttcaaagaga
     2161 aaataataat tatgaaaatg aagatataga ccatagtaaa acttacttaa attatgattt
     2221 ggtaaatgct aataaacaga attttaataa cttgattgat gaaaaaaatc gaacagaatt
     2281 atacaggcaa aagaaaaatt agaacagacg cgattaaaca cattgatggt ttaattacat
     2341 cagacaatga tttctttgat aatcaaacgc cagaagatac aaagcagttt tttgaatatg
     2401 ctaaagagtt tttagaacaa gaatacggta aagataattt attatatgca acagttcaca
     2461 tggacgaaaa aacaccacat atgcattatg gcgttgttcc aataactgat gatggtcgtt
     2521 taagtgctaa agaagttgta ggtaataaaa aagctttaac agcgtttcaa gatagattta
     2581 atgagcatgt taaacaacga ggatatgatt tagaacgtgg gcaatcaaga caagtaacaa
     2641 atgctaaaca tgagcaaata agtcagtata aacaaaaaac agaatatcat aagcaagaat
     2701 atgaacgtga gagccaaaaa acagaccata taaagcaaaa gaacgataaa ttaatgcaag
     2761 agtaccaaaa atcgttaaat acgcttaaaa agcctataaa tgttccgtat gagcaagaaa
     2821 ctgaaaaagt aggtggttta tttagcaaag aaatacaaga aactggaaat gttgtaataa
     2881 gccaaaaaga tttcaatgaa tttcagaaac agataaaaat tggaataaag caataaagga
     2941 gttgaaagaa atgaaattca gagaagcatt gaacaacttt cttactagca agtatgtatt
     3001 agttttttat agtagcagcg ttggtttttt atctatcata aaataattat gttgtataac
     3061 taaaaaagac ttggatctaa ttaggaacta attagaccaa gccttttgtt agtgttatat
     3121 taataacaaa ataaaaataa gaagtcgttc acgcccctac caaagtttgt gaacgaaatc
     3181 cgaaaagaaa acagtcgatg tttgtttctt aatttgtata tcttgatatt aaacgatttg
     3241 agttaaatct tcaagatata tattcgcaaa tgtaattgga tgagcgactt cttaaacaaa
     3301 attaaggagt cgattttt
//
