LOCUS       NZ_CP118805             4253 bp    DNA     linear   CON 15-MAY-2024
DEFINITION  Mammaliicoccus lentus strain 7066 plasmid pML7066-5.
ACCESSION   NZ_CP118805
VERSION     NZ_CP118805.1
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 4253)
  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 4253)
  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
            CP118805.1.
            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..4253
                     /organism="Mammaliicoccus lentus"
                     /mol_type="genomic DNA"
                     /strain="7066"
                     /isolation_source="Nose"
                     /host="Camelus dromedarius"
                     /db_xref="taxon:42858"
                     /plasmid="pML7066-5"
                     /geo_loc_name="Algeria: M'sila"
                     /collection_date="2021-12-13"
     gene            1..1497
                     /gene="tet"
                     /locus_tag="PYH60_RS13170"
                     /old_locus_tag="PYH60_13165"
     CDS             1..1497
                     /gene="tet"
                     /locus_tag="PYH60_RS13170"
                     /old_locus_tag="PYH60_13165"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000492283.1"
                     /GO_function="GO:0008493 - tetracycline transmembrane
                     transporter activity [Evidence IEA]; GO:0022857 -
                     transmembrane transporter activity [Evidence IEA]"
                     /GO_process="GO:0015904 - tetracycline transmembrane
                     transport [Evidence IEA]; GO:0055085 - transmembrane
                     transport [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Tet(L)/Tet(K)/Tet(45) family tetracycline efflux
                     MFS transporter"
                     /protein_id="WP_282849010.1"
                     /translation="MIDLLEFIIKKEQERKDNADIEVMSEHLWRVEIELKRDMVDYWND
                     CFNDLHILKPDWSSLEKVKDQAMIYMLIHEESTWGKLERRTKNKYREMLKSISEIDLTD
                     LTVYGKLSDYINIKKLLIIGISLSCLGSLIAFIGHNHFFILIFGRLVQGVGSAAFPSLI
                     MVVVARNITRKKQGKAFGFIGSIVALGEGLGPSIGGIIAHYIHWSYLLILPMITIVTIP
                     FLIKVMVPGKSTKNTLDIVGIVLMSISIICFMLFTTNYNWTFLILFTIFFVIFIKHISR
                     VSNPFINPKLGKNIPFMLGLFSGGLIFSIVAGFISMVPYMMKTIYHVNVATIGNSVIFP
                     GTMSVIVFGYFGGFLVDRKGSLFVFILGSLSISISFLTIAFFVEFSMWLTTFMFIFVMG
                     GLSFTKTVISKIVSSSLSEEEVASGMSLLNFTSFLSEGTGIAIVGGLLSLQLINRKLVL
                     EFINYSSGVYSNILVAMAILIILCCLLTIIVFKRSEKQFE"
                     /name="tet"
     gene            1684..2925
                     /gene="mobV"
                     /locus_tag="PYH60_RS13175"
                     /old_locus_tag="PYH60_13170"
     CDS             1684..2925
                     /gene="mobV"
                     /locus_tag="PYH60_RS13175"
                     /old_locus_tag="PYH60_13170"
                     /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            3716..>4253
                     /locus_tag="PYH60_RS13180"
                     /old_locus_tag="PYH60_13175"
                     /pseudo=""
     CDS             3716..>4253
                     /locus_tag="PYH60_RS13180"
                     /old_locus_tag="PYH60_13175"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002405927.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     ARG             2..1497
                     /name="tet(45)"
                     /gene="tet(45)"
                     /gene_name="major facilitator superfamily (MFS) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="tetracycline antibiotic"
                     /identity="59.38"
                     /coverage="108.73"
     Typing          2..316
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.734"
                     /coverage="84.0"
                     /evalue="4.04e-156"
     Typing          3717..4253
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.814"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1685..2922
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtgatagatt tattagaatt tataataaaa aaagaacaag aacgtaagga taatgcagac
       61 attgaagtta tgtctgaaca cttatggcgt gtagaaattg aattaaaaag agatatggtt
      121 gattattgga acgattgttt taatgattta catattttga aaccagattg gtctagttta
      181 gaaaaagtaa aagaccaagc aatgatttat atgctaattc atgaagaaag tacatggggt
      241 aaattagaaa gacgtacaaa aaataaatac agagaaatgt taaaaagtat ttcagaaatt
      301 gatttaacgg acttaacagt atatggaaaa ttatctgatt atataaatat aaaaaaattg
      361 ttaattattg gtattagttt gagctgtctt ggttcattga ttgcttttat tggtcacaat
      421 cactttttta ttttgatttt tggtaggtta gtacaaggag taggatctgc tgcattccct
      481 tcactgatta tggtggttgt agctagaaat attacaagaa aaaaacaagg caaagccttt
      541 ggttttatag gatcaattgt agctttaggt gaagggttag gtccttcaat agggggaata
      601 atagcacatt atattcattg gtcttaccta cttatacttc ctatgattac aatagtaact
      661 ataccttttc ttattaaagt aatggtacct ggtaaatcaa caaaaaatac attagatatc
      721 gtaggtattg ttttaatgtc tataagtatt atatgtttta tgttatttac gacaaattat
      781 aattggactt ttttaatact cttcacaatc ttttttgtga tttttattaa acatatttca
      841 agagtttcta acccttttat taatcctaaa ctagggaaaa acattccgtt tatgcttggt
      901 ttgttttctg gtgggctaat attttctata gtagctggtt ttatatcaat ggtgccttat
      961 atgatgaaaa ctatttatca tgtaaatgta gcgacaatag gtaatagtgt tatttttcct
     1021 ggaaccatga gtgttattgt ttttggttat tttggtggtt ttttagtgga tagaaaagga
     1081 tcattatttg tttttatttt aggatcattg tctatctcta taagtttttt aactattgca
     1141 ttttttgttg agtttagtat gtggttgact acttttatgt ttatatttgt tatgggcgga
     1201 ttatctttta ctaaaacagt tatatcaaaa atagtatcaa gtagtctttc tgaagaagaa
     1261 gttgcttctg gaatgagttt gctaaatttc acaagttttt tatcagaggg aacaggtata
     1321 gcaattgtag gaggtttatt gtcactacaa ttgattaatc gtaaactagt tctggaattt
     1381 ataaattatt cttctggagt gtatagtaat attcttgtag ccatggctat ccttattatt
     1441 ttatgttgtc ttttgacgat tattgtattt aaacgttctg aaaagcagtt tgaatagtta
     1501 tattatattt tggtttagaa ctatgagtgg ctagcatttt gccactcatt ttttgcgtta
     1561 gcaaaaacag gtttaagcct cgcagagcac acgtattaac gacttattgt aaaataagtc
     1621 tagtgtgtta gacttaaact attaaataca catgaaacct ttgtgcttag gagtgatttt
     1681 tatatgtctt attccattgt tagagtttca aaagttaaat ctggaacaaa tacaacgggc
     1741 atacaaaaac atgttcaaag agaaaataat aattatgaaa atgaagatat agaccatagt
     1801 aaaacttact taaattatga tttggtaaat gctaataaac agaattttaa taacttgatt
     1861 gatgaaaaaa tcgaacagaa ttatacaggc aaaagaaaaa ttagaacaga cgcgattaaa
     1921 cacattgatg gtttaattac atcagacaat gatttctttg ataatcaaac gccagaagat
     1981 acaaagcagt tttttgaata tgctaaagag tttttagaac aagaatacgg taaagataat
     2041 ttattatatg caacagttca catggacgaa aaaacaccac atatgcatta tggcgttgtt
     2101 ccaataactg atgatggtcg tttaagtgct aaagaagttg taggtaataa aaaagcttta
     2161 acagcgtttc aagatagatt taatgagcat gttaaacaac gaggatatga tttagaacgt
     2221 gggcaatcaa gacaagtaac aaatgctaaa catgagcaaa taagtcagta taaacaaaaa
     2281 acagaatatc ataagcaaga atatgaacgt gagagccaaa aaacagacca tataaagcaa
     2341 aagaacgata aattaatgca agagtaccaa aaatcgttaa atacgcttaa aaagcctata
     2401 aatgttccgt atgagcaaga aactgaaaaa gtaggtggtt tatttagcaa agaaatacaa
     2461 gaaactggaa atgttgtaat aagccaaaaa gatttcaatg aatttcagaa acagataaaa
     2521 gctgctcaag atatttcgga agattacgag tatataaagt ctggtagagc cttagatgat
     2581 aaagataagg aaatacgaga gaaagatgat ttattaaata aagcagttga gcgtattgaa
     2641 aacgcagacg ataattttaa ccaactttac gaaaatgcaa agccacttaa agagaatata
     2701 gaaatagcgt taaagctttt aaaaatctta ctaaaagagt tagaacgagt tttaggaaga
     2761 aatacctttg cggaaagagt taataagtta acagaagatg aaccaaaact aaatggttta
     2821 gcaggaaact tagataaaaa aatgaatcca gaattatatt cagaacagga acagcaacaa
     2881 gaacaacaaa agaatcaaaa acgagataga ggtatgcact tatagaacat gcatttatgc
     2941 cgagaaaact tattggttgg aatgggctat gtgttagcta acttgttagc gagttggttg
     3001 gacttgaatt gggattaatc ccaagaaagt accaactcaa caacacataa agccctgtag
     3061 gttccgacca ataaggaaat tggaataaag caataaaagg agttgaagaa atgaaattca
     3121 gagaagcctt tgagaatttt ataacaagta agtatgtact tggtgtttta gtagttttaa
     3181 ctgtttacca gataatacaa atgcttaaat aaaaaaagac ttgatctgat tagaccaagt
     3241 cttttgatag tgttatatta ataacaaaat aaaaaggagt cgctccaact caacaacata
     3301 aagccctgta ggttccgacc aaaaggaaat tggaataaag caataaagga gttgaagaaa
     3361 tgaaattcag agaagcattg aacaactttc ttactagcaa gtatgtatta gttatagtag
     3421 cagcgttggt tatctatcaa ataattatgt tgtataacta aaaaagactt gatctaatta
     3481 ggaactaatt agaccaagcc ttttgttagt gttatattaa taacaaaata aaaataagaa
     3541 gtcgttcacg cccctaccaa agtttgtgaa cgaaatccga aaagaaaaca gtcgatgttt
     3601 gtttcttaat ttgtatatct tgatattaaa cgatttgagt taaatcttca agatatatat
     3661 tcgcaaatgt aattggatga gcgacttctt aaacaaaatt aaggagtcga tttttatggc
     3721 aaaaataacg aaaaatgagc aagaaaattt ggtgaaaaat tacacaaaaa aaccggcgta
     3781 ctctaatagc cggttaaacc gacatattat gtacaccccc gaaccaaaat tacactttga
     3841 tgctatgaca attgttggga atcttaataa gaacaatgct cacaaactgt ctgaatttat
     3901 gagtattgcg ccacaaatta gactttggga tatattacaa accaaattta aagctaaggc
     3961 tctacaagaa aaagtttaca tcgaatatga taaagtaaaa gcagatgcgt gggatagacg
     4021 taatatgcgt gttgaattta atcctaataa acttacgcat gaagaaatgc tttggttaaa
     4081 acaaaacatc attgactaca tggaagatga tggttttaca agattagatt tggcttttga
     4141 ttttgaagac gatttgagcg attattatgc gatgactgat aaatcagtta agaaaactat
     4201 tttttatggt cgtaacggta aaccagaaac aaaatatttt ggtgttcgtg aca
//
