LOCUS       NZ_CP118780             3048 bp    DNA     linear   CON 15-MAY-2024
DEFINITION  Mammaliicoccus lentus strain 7074 plasmid pML7074-4.
ACCESSION   NZ_CP118780
VERSION     NZ_CP118780.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33407050
            Assembly: GCF_030013925.1
KEYWORDS    RefSeq.
SOURCE      Mammaliicoccus lentus
  ORGANISM  Mammaliicoccus lentus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Mammaliicoccus.
REFERENCE   1  (bases 1 to 3048)
  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 3048)
  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                   :: 324x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013925.1-RS_2024_05_15
            Annotation Date                   :: 05/15/2024 04:35:17
            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)                     :: 2,632
            CDSs (total)                      :: 2,551
            Genes (coding)                    :: 2,509
            CDSs (with protein)               :: 2,509
            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)              :: 42
            CDSs (without protein)            :: 42
            Pseudo Genes (ambiguous residues) :: 0 of 42
            Pseudo Genes (frameshifted)       :: 11 of 42
            Pseudo Genes (incomplete)         :: 18 of 42
            Pseudo Genes (internal stop)      :: 15 of 42
            Pseudo Genes (multiple problems)  :: 2 of 42
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP118780.1.
            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..3048
                     /organism="Mammaliicoccus lentus"
                     /mol_type="genomic DNA"
                     /strain="7074"
                     /isolation_source="Nose"
                     /host="Camelus dromedarius"
                     /db_xref="taxon:42858"
                     /plasmid="pML7074-4"
                     /geo_loc_name="Algeria: Ouargla"
                     /collection_date="2022-06-06"
     gene            <1..1005
                     /locus_tag="PYH61_RS13145"
                     /old_locus_tag="PYH61_13140"
     CDS             <1..1005
                     /locus_tag="PYH61_RS13145"
                     /old_locus_tag="PYH61_13140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020368559.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_078099054.1"
                     /translation="MQYNTTKCIDENQDNKTLKDMTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQKVI
                     EEVVKEKPTARWLFLTLSTKNAIDGDHLEQSLKHMSKAFNKLKMYTKVKKNLVGFLRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQVEWVDLWQKALQVNYRPVANIKAI
                     KPNQKGDKDIQAAIKETSKYSVKSSDFLTDDDEKNQEIVNDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDAEDGNLINTSDEDKTTDEEEKAHSITAIWNFEKQNYYLKDLKR"
                     /name="protein rep"
     gene            2045..2866
                     /locus_tag="PYH61_RS13150"
                     /old_locus_tag="PYH61_13145"
     CDS             2045..2866
                     /locus_tag="PYH61_RS13150"
                     /old_locus_tag="PYH61_13145"
                     /inference="COORDINATES: protein motif:HMM:NF025217.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="putative RNA methyltransferase"
                     /protein_id="WP_049948317.1"
                     /translation="MFFKCSICDEKLKRGYKTLACENNHTFDIAKEGYSNLISGHKKSK
                     YDKKLFIARRELNDSSNLYSILISKIIEIIKKYEIKTKNNVIDVGTGEGYILNEISKTF
                     LGENEFLGIDIAKEGVKKAAKSYKNINWLVADLADIPVMNGNVDFLINVLSPSNYDEFK
                     RVLDKEGKLIKIIPNSDYLKEIRNIVFSNHKNKDYDNSEVIDLFEANFNKIEMIDISYK
                     VKLNKEELNKLLDMTPLTWNLSDVEKEGIIKKNLSEITMSFKVLVGGFKTS"
                     /name="putative RNA methyltransferase"
     Typing          2..1005
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.806"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgcaatata atactactaa atgtatagac gaaaatcaag ataataaaac attaaaagat
       61 atgacgaaaa gtgggaaaca acgcccatgg agagaaaaga agatagataa tgtaagttat
      121 gcagatatac tggaaatctt aaaaattaaa aaggctttta acgtaaaaca atgtggtaac
      181 gtcttagaat tcaagccaac tgatgaaggt tatttgaaat tacataagac atggttttgt
      241 aagtcaaaat tatgcccagt ttgtaattgg aggcgtgcta tgaaaaatag ttatcaagct
      301 caaaaagtga ttgaagaagt ggttaaagaa aagccaactg ctcgttggtt atttcttact
      361 ttatcgacta aaaatgcaat agacggtgac cacttagaac aaagtttaaa acacatgtct
      421 aaggctttta ataaattaaa gatgtataca aaagttaaaa agaatttggt gggtttttta
      481 cgctcaactg aagtaacagt taataaaaat gacggtagtt ataatcaaca tatgcacgtt
      541 ttattgtgtg ttgaaaatgc gtatttcaga aaaaaagaaa actacattac gcaagttgaa
      601 tgggttgatt tatggcaaaa agcattacag gttaattatc gaccagtagc aaatattaaa
      661 gcgatcaaac caaatcaaaa aggcgataaa gatattcaag cagctatcaa agaaacctct
      721 aaatattcag ttaagtcatc tgatttttta actgatgatg acgaaaaaaa tcaagaaatc
      781 gtgaatgatt tggaaaaagg tttataccga aaacgtatgt tgagttatgg tggattgctt
      841 aaacaaaaac ataaaatttt aaatttagac gatgccgaag atggcaattt gattaataca
      901 agtgacgaag ataaaacaac agacgaagaa gaaaaagcac attcaattac ggcaatttgg
      961 aattttgaaa aacaaaatta ttacttaaaa gatttgaaac gttagcttaa aagctagcgt
     1021 tttttttatg tctttttgcc cctgcgggaa ctatagcgtt caaccggcat ggttgcccaa
     1081 ttttcatgtt aatttttaaa tttgcatgta actgggcagt gtttattttt tcttgcccat
     1141 tttgctaact tttaagtttg catataaatg ggcagtgtct aaaaaattcc ccactggtca
     1201 tgaacaaaaa aatgagctaa acaatttaac tttttaagtt atataaattt tagggagttc
     1261 caatcaaatt agaaaaatat ataaaagagc tatatcgttt ttctggctta tgtttaaaaa
     1321 gtacaagtga ttgtatttaa aatgacttta gcaatttaag taatatgtct tttgaataca
     1381 agttaaatgt cagaaagatg tacccttatt ttgctcatat ttgcgtttta agaaatgaat
     1441 atgattatac gtatataaaa ctatataaat ttagagtttg ctctaaatac ccccttaaaa
     1501 ttcaaaataa aggcatttaa aaattaagaa aataaaaaag ctactagcaa aaaactagta
     1561 gcttaaatct tagttaaatt tctatgtagt attaattttt atatctacgc tacaacgtcg
     1621 attctagttc gtgcagtatt aatttttata tctgcgccac aacgccgatt ccttaaaact
     1681 aagataaaaa ttgacgaagg tcgattatgg ttttttacgc gttcttttta gaacgcataa
     1741 gtgcgccctt acgggattta actagattat aacgacgaaa aatagacctg taaagcaata
     1801 acagttgggt ctactttgtc tactgggcag acaagaaaag aacacgcatt tatgccgaga
     1861 aaatttattg atgttgagaa gaacccttaa ctaaacttgc agacgaatgt cggcatagcg
     1921 tgagctatta agccgaccat tcgacaagtt ttgggattgt taagggttcc gaggctcaac
     1981 gtcaataaag caattggaat aaagcaactt tgttatttat aattatttga ttggaggtgt
     2041 gaatatgttt tttaagtgtt ctatatgtga tgaaaaatta aagagaggtt ataaaacttt
     2101 agcatgtgag aataaccata cttttgatat tgcaaaagag ggttattcga atttaatttc
     2161 agggcataaa aaaagtaaat acgataaaaa attgtttatt gctagaagag aattgaatga
     2221 tagtagcaat ttgtattcga tattaatttc aaaaatcata gaaattatta aaaaatatga
     2281 gattaaaact aaaaataatg tgatagatgt tggtactggt gagggttata ttttaaatga
     2341 aattagtaaa acatttcttg gtgaaaatga attcttaggt atagacattg caaaagaagg
     2401 tgtaaaaaaa gcagcaaaat catataaaaa tataaattgg ttggttgctg atctagctga
     2461 tataccagtt atgaatggga atgtagactt tttaattaat gtgcttagcc cttctaatta
     2521 tgatgagttt aaaagagttc tagataaaga ggggaaattg ataaaaataa ttcctaatag
     2581 tgattattta aaagaaataa ggaatatagt ctttagtaat cataaaaata aggattatga
     2641 taattctgag gttatagatt tatttgaagc taattttaat aaaattgaaa tgatagacat
     2701 tagttataag gttaaattaa ataaagaaga attgaataaa ttacttgata tgacgccttt
     2761 aacgtggaat ttaagtgacg tagaaaaaga aggaataatt aagaaaaact taagtgaaat
     2821 tacgatgagt tttaaggttt tggttggtgg ttttaaaacg agttgaaaac gagtttcttc
     2881 ttgtcttgat actatataga aataactcaa agatataaaa agttgcttta tcgttggtat
     2941 gacagtgttt ttatgtattt ttgtgcgtga aagaaaaaat tgacataaaa aagctccagt
     3001 aatatgatta agttacgacg cttaaatcaa tactggaggt ctttttat
//
