LOCUS       NZ_CP120158             6274 bp    DNA     circular CON 06-JAN-2024
DEFINITION  Mammaliicoccus lentus strain Dog026 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP120158
VERSION     NZ_CP120158.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33696772
            Assembly: GCF_034042815.1
KEYWORDS    RefSeq.
SOURCE      Mammaliicoccus lentus
  ORGANISM  Mammaliicoccus lentus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Mammaliicoccus.
REFERENCE   1  (bases 1 to 6274)
  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  JOURNAL   Unpublished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 6274)
  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 (19-DEC-2023) Institute of Veterinary Bacteriology,
            University of Bern, Langgassstrasse 122, Bern 3001, Switzerland
  REMARK    Annotation added by database at the request of the submitter
REFERENCE   3  (bases 1 to 6274)
  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                   :: 283x
            Sequencing Technology             :: PacBio Sequel II
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/06/2024 10:51:16
            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)                     :: 2,901
            CDSs (total)                      :: 2,820
            Genes (coding)                    :: 2,796
            CDSs (with protein)               :: 2,796
            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)              :: 24
            CDSs (without protein)            :: 24
            Pseudo Genes (ambiguous residues) :: 0 of 24
            Pseudo Genes (frameshifted)       :: 7 of 24
            Pseudo Genes (incomplete)         :: 16 of 24
            Pseudo Genes (internal stop)      :: 5 of 24
            Pseudo Genes (multiple problems)  :: 3 of 24
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP120158.1.
            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..6274
                     /organism="Mammaliicoccus lentus"
                     /mol_type="genomic DNA"
                     /strain="Dog026"
                     /isolation_source="nasal swab"
                     /host="Canis lupus familiaris"
                     /db_xref="taxon:42858"
                     /plasmid="unnamed3"
                     /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            complement(96..1472)
                     /gene="tet(L)"
                     /locus_tag="P3U54_RS14415"
                     /old_locus_tag="P3U54_14420"
     ARG             complement(100..1472)
                     /name="tet(L)"
                     /gene="tet(L)"
                     /gene_name="tetracycline efflux MFS transporter Tet(L)"
                     /tool="amrfinderplus"
                     /drug_class="TETRACYCLINE"
                     /identity="96.72"
                     /coverage="100.0"
     gene            complement(1672..2655)
                     /locus_tag="P3U54_RS14420"
                     /old_locus_tag="P3U54_14425"
     CDS             complement(1672..2655)
                     /locus_tag="P3U54_RS14420"
                     /old_locus_tag="P3U54_14425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000336291.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_323711120.1"
                     /translation="MCPNSSIYSDEKSRVLVDKTKSGKVRPWREKKIANVDYFELLHIL
                     EFKKAERVKDCAEILEYKQNRETGERKLYRVWFCKSRLCPMCNWRRAMKHGIQSQKVVA
                     EVIKQKPSVRWLFLTLTVKNVYDGEELNKSLSDMAQGFRRMMQYKKINKNLVGFMRATE
                     VTINNKDNSYNQHMHVLVCVEPTYFKNTENYVNQKQWIQFWKKAMKLDYDPNVKVQMIR
                     PKNKYKSDIQSAIDETAKYPVKDTDFMTDDEEKNLKRLSDLEEGLHRKRLISYGGLLKE
                     IHKKLNLDDTEEGDLIHTDDDEKADEDGFSIIAMWNWERKNYFIKE"
                     /name="protein rep"
     gene            complement(2905..4161)
                     /gene="mobV"
                     /locus_tag="P3U54_RS14425"
                     /old_locus_tag="P3U54_14430"
     CDS             complement(2905..4161)
                     /gene="mobV"
                     /locus_tag="P3U54_RS14425"
                     /old_locus_tag="P3U54_14430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001619005.1"
                     /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_323711121.1"
                     /translation="MSYAVCRMQKVKSAGLKGMQFHNQRERKSRTNDDIDHERTRENYD
                     LKNDKNIDYNERVKEIIESQKTGTRKTRKDAVLVNELLVTSDRDFFEQLDPGEQKRFFE
                     ESYKLFSERYGKQNIAYATVHNDEQTPHMHLGVVPMRDGKLQGKNVFNRQELLWLQDKF
                     PEHMKKQGFELKRGERGSDRKHIETAKFKKQTLEKEIDFLEKNLAVKKDEWTAYSDKVK
                     SDLEVPAKRHMKSVEVPTGEKSMFGLGKEIMKTEKKPTKNVVISERDYKNLVTAARDND
                     RLKQHVRNLMSTDMAREYKKLSKEHGQVKEKYSGLVERFNENVNDYNELLEENKSLKSK
                     ISDLKRDVSLIYESTKEFLKERTDGLKAFKNVFKGFVDKVKDKTAQFQEKHDLEPKKNE
                     FEKIHSKELNKEKDRGMEL"
                     /name="mobV"
     gene            complement(4758..5111)
                     /locus_tag="P3U54_RS14430"
                     /old_locus_tag="P3U54_14435"
     CDS             complement(4758..5111)
                     /locus_tag="P3U54_RS14430"
                     /old_locus_tag="P3U54_14435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000085864.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MazG nucleotide pyrophosphohydrolase
                     domain-containing protein"
                     /protein_id="WP_031794976.1"
                     /translation="MGNDKENPKQLTFYELQSYLALKYKEGRTSSALFMKLVEEIGEVA
                     EVLNQLEGRKANTGNASLEKELVDVIHYAVAIASINHIDLTKAIIKKDKQAAIKYNQSP
                     NLEEFLEEEIKVN"
                     /name="MazG nucleotide pyrophosphohydrolase
                     domain-containing protein"
     gene            complement(5244..5429)
                     /locus_tag="P3U54_RS14435"
                     /old_locus_tag="P3U54_14440"
     CDS             complement(5244..5429)
                     /locus_tag="P3U54_RS14435"
                     /old_locus_tag="P3U54_14440"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_031794977.1"
                     /translation="MKRTRLKFSLIVGLVAFILTFLVTFLIESPYPFWASLVVGFLIFE
                     ISYYYFFNKEKRQYDL"
                     /name="hypothetical protein"
     gene            complement(5562..6053)
                     /locus_tag="P3U54_RS14440"
                     /old_locus_tag="P3U54_14445"
     CDS             complement(5562..6053)
                     /locus_tag="P3U54_RS14440"
                     /old_locus_tag="P3U54_14445"
                     /EC_number="1.5.1.3"
                     /function="confers trimethoprim resistance"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016204971.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="trimethoprim-resistant dihydrofolate reductase
                     DfrK"
                     /protein_id="WP_012779617.1"
                     /translation="MKVSLIAAMDKNRVIGKENDIPWRIPEDWEYVKNTTKGYPIILGR
                     KNLESIGRALPGRRNIILTRDKGFSFNGCEIVHSIEDVFELCNSEEEIFIFGGEQIYNL
                     FLPYVEKMYITKIHYEFEGDTFFPEVNYEEWNEVSVTQGITNEKNPYTYYFHIYERKAS
                     "
                     /name="trimethoprim-resistant dihydrofolate reductase DfrK"
     ARG             complement(5566..6053)
                     /name="dfrK"
                     /gene="dfrK"
                     /gene_name="trimethoprim-resistant dihydrofolate reductase
                     DfrK"
                     /tool="amrfinderplus"
                     /drug_class="TRIMETHOPRIM"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             complement(97..1472)
                     /name="tet(45)"
                     /gene="tet(45)"
                     /gene_name="major facilitator superfamily (MFS) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="tetracycline antibiotic"
                     /identity="78.77"
                     /coverage="100.0"
     Typing          complement(1673..2676)
                     /name="rep_cluster_1018"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.9"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2909..4161)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.571"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 caatcgcgcc ctttaatgga acaaaaagat ttgaattcct gttataaaaa aaggatcaat
       61 tttgaactct ctcccaaagt tgatccctta acgatttaga aatccctttg agaatgttta
      121 tatacattca aggtaaccag ccaactaatg acaatgattc ctgaaaaaag taataacaaa
      181 ttactataca gataagttga ctgatcaact tccataggta acaacctttg atcaagtaag
      241 ggtatggata ataaaccacc tacaattgca atacctgttc cctctgataa aaagctggta
      301 aaattaagca aactcattcc ggcaccagct tccttttgtt tcaaactact tgaaacaatt
      361 gttgatataa ctgttttggt gaacgaaaac ccaccaaaaa caaaaactaa tataattgtc
      421 agtaaccatg gtgttacttc taaaaaaaag gcagcaatta aaaagctaac ggaaagaaat
      481 gtaactccaa tggttaacac gtacaatgga ccttttctat caacaagtaa tccaccaatg
      541 taaccgaaga taataacgct cattgttcca gggaaaataa ttacacttcc gatttcggca
      601 gtacttagct ggtgaacatc tttcatcata taaggaacca tagagataaa ccctgctact
      661 gttccaaata taattccccc acaaagaact ccaatcataa aaggtatatt tttccctaat
      721 ccgggatcaa caaaaggatc tgttactttc ctgatatgtt ttacaaatat caggaatgac
      781 agcacgctaa cgataagaaa agaaatgcta tatgatgttg taaacaacat aaaaaataca
      841 atgcctacag acattagtat aattcctttg atatcaaaat gaccttttat ccttacttct
      901 ttctttaata atttcataag aaacggaaca gtgataattg ttatcatagg aatgagtaga
      961 agataggacc aatgaatata atgggctatc attccaccaa tcgctggacc gactccttct
     1021 cccatggcta ctatcgatcc aataagacca aatgctttac ccctattttc ctttggaata
     1081 tagcgcgcaa ctacaaccat tacgagtgct ggaaatgcag ctgcaccagc cccttgaata
     1141 aaacgagcca taataagtaa ggaaaagaaa gaatggccaa caaacccaat taccgacccg
     1201 aaacaattta ttataattcc aaataggagt aaccttttga tgcctaattg atcagatagc
     1261 tttccatata cagctgttcc aatggaaaag gttaacataa aggctgtgtt cacccagttt
     1321 gtactcgcag gtggtttatt aaaatcattt gcaatatcag gtaatgagac gttcaaaacc
     1381 atttcattta atacgctaaa aaaagataaa atgcaaagcc aaattaaaat ttggttgtgt
     1441 cgtaaattcg attgtgaata ggatgtattc acatttcacc ctccaataat gagggcagac
     1501 gtagtttata gggttaatga tacgcttccc tcttttaatt gaaccctgtt acattaatta
     1561 cacttcataa ttaattcctc ctaaacttga ttaaaacatt ttaccacata taaactaagt
     1621 tttaaattca gtatttcatc acttatacaa caatatggcc cgtttgttga actactcttt
     1681 aataaaataa tttttccgtt cccaattcca cattgcaata atagaaaatc catcttcatc
     1741 ggctttttcg tcatcatctg tatgaatcaa atcgccttct tctgtgtcat caaggtttaa
     1801 ttttttatgt atttctttta acaaaccacc ataggagatt aaccttttac ggtgtaaacc
     1861 ttcctccaaa tcagacaaac gtttcaaatt cttttcttca tcatcggtca taaaatccgt
     1921 atcctttaca ggatattttg cagtttcgtc aattgccgat tgtatatccg atttatattt
     1981 atttttcggt cgaatcattt gaacttttac atttggatca tagtctaatt tcattgcctt
     2041 tttccaaaat tgaatccatt gtttttgatt cacgtagttt tctgtattct taaaataagt
     2101 tggttccaca cataccaata catgcatgtg ctgattataa gaattatctt tattatttat
     2161 tgtcacttcc gttgcacgca taaaaccaac aagattttta ttaatttttt tatattgcat
     2221 cattcggcga aatccttgag ccatatctga caaactctta tttaattctt cgccatcata
     2281 aacattttta actgttaatg tgagaaacaa ccaacgaact gatggctttt gtttaataac
     2341 ttcagcaaca accttttgtg actgaatgcc atgtttcatt gctctcctcc agttgcacat
     2401 tggacaaagc ctggatttac aaaaccacac tcgatacaac tttctttcgc ctgtttcacg
     2461 attttgttta tactctaata tttcagcaca atcttttact ctttcagcct ttttaaattc
     2521 aagaatatgc agaagttcaa agtaatcaac attagcgatt ttcttttctc tccatggtct
     2581 cacttttcca ctttttgtct tgtccactaa aacccttgat ttttcatctg aataaatgct
     2641 actattagga cacataatat taaaagaaac ccccatctat ttagttattt gtttggtcac
     2701 ttataacttt aacagatggg gtttttctgt gcaaccaatt ttaagggttt tcaatacttt
     2761 aaaacacata cataccaaca cttcaacgca cctttcagca actaaaataa aaatgacgtt
     2821 atttctatat gtatcaagaa tagaaagaac tggtttttcg ctacgctcaa aaccacgaaa
     2881 aaagcccctt tttacagagg ctttttataa ttccattcca cgatctttct ctttatttaa
     2941 ttctttacta tgaatctttt caaattcgtt ctttttaggt tctaaatcgt gtttttcttg
     3001 gaattgtgct gttttatcct ttaccttgtc tacaaacccc ttaaaaacgt ttttaaaggc
     3061 ttttaagccg tctgtacgtt ccttaaggaa ttccttagtg ctttcataga ttaaactcac
     3121 atcacgcttt aaatcgctta ttttagactt taaagacttg ttttcttcaa gcaactcatt
     3181 ataatcattt acattttcat taaatcgctc tacaagacca ctatattttt ctttaacttg
     3241 cccatgttct ttacttaatt ttttatattc tctcgccata tcagtactca tgagatttct
     3301 aacatgctgt tttaacctat cgttatctct cgcagcagtc actaagtttt tataatcacg
     3361 ctccgatata acaacatttt tggttggttt cttttctgtt ttcattattt cttttcccaa
     3421 accaaacatg gacttttcac ccgttggcac ttcaacactt ttcatgtgtc gtttcgctgg
     3481 tacttctaaa tctgatttaa ctttatcgct ataagcagtc cattcatctt ttttaactgc
     3541 taaatttttt tctagaaaat caatctcttt ttccaaagtt tgttttttaa atttagctgt
     3601 ctcaatatgt ttacggtcag agccacgttc accacgcttc aactcaaaac cctgtttttt
     3661 catatgctcg gggaatttat cttgtagcca taacagttct tgacgattaa acacattttt
     3721 tccttgcagt tttccatcac gcataggcac aacacctaaa tgcatgtgag gggtttgctc
     3781 atcattatga actgttgcat aagcaatatt ttgcttgcca tatcgttcgg aaaataattt
     3841 ataactttcc tcaaaaaatc gtttttgttc tcctggatcc agttgctcaa aaaaatctcg
     3901 gtcagatgtt actagcaact catttacaag aacagcatct ttcctcgttt ttcttgtacc
     3961 tgttttttgt gattcaataa tttctttgac acgttcgttg taatcaatat ttttatcatt
     4021 tttcaaatca taattttcac gtgttcgctc atggtcaata tcatcattcg ttctactttt
     4081 tcgctctctt tgattatgaa attgcatgcc ttttagtcca gctgatttca ctttttgcat
     4141 tctacaaact gcataactca tatgtaaatc gctccttttt aggtggcaca aatgtgaggc
     4201 attttcgctc tttccggcaa ccacttccaa gtaaagtata acacactata ctttatattc
     4261 ataaagtgtg tgctctgcga ggctgtcggc agtgccgacc aaaaccataa aacctttaag
     4321 acctttcttt tttttacgag aaaaaagaaa caaaaaaacc tgccctctgc cacctcagca
     4381 aaggggggtt ttgctctcgt gctcgtttaa aaatcagcaa gggacaggta gtattttttg
     4441 agaagatcac tcaaaaaatc tccaccttta aacccttgcc aatttttatt ttgtccgttt
     4501 tgtctagctt accgaaagcc agactcagca agaataaaat ttttattgtc tttcggtttt
     4561 ctagtgtaac ggacaaaacc actcaaaata aaaaagatac aagagaggtc tctcgtatct
     4621 tttattcagc aatcgcgccc gttaatggaa taactataaa taagttctta accctaaaat
     4681 cacttattta ttattaaact aacgcaccct atagtgcaat aaggaatgtt cctcttcttt
     4741 cataagtatt ttttatgtta atttacttta atttcttctt ctaaaaactc ttctaaattt
     4801 ggagattgat tatatttaat tgcagcttgt ttatccttct taataatggc ctttgttaga
     4861 tcaatatgat ttatgcttgc aatggcaaca gcgtaatgga taacatcaac aagctctttt
     4921 tctaaagaag cattccccgt gtttgccttt cgcccttcta actggtttag tacctctgct
     4981 acctcgccaa tttcttctac tagtttcata aacaaagcag atgaagtgcg tccttctttg
     5041 tattttagtg ctaggtagct ctgtaactca taaaatgtta attgcttcgg attttctttg
     5101 tcatttccca ttttaacacc cctattaatt taaccatcat ccctaacaaa gctgtcatta
     5161 tttgaactct tctgccccgt tagttaaata acgaattgat tatctttcac taacgcaccc
     5221 tattgtttaa tacttttgtt ttatcataaa tcgtactgac gtttctcttt gttaaagaag
     5281 tagtaataac taatttcaaa tattaaaaat cctacaacca gacttgccca aaaaggatac
     5341 ggcgattcaa ttaaaaaagt aactaaaaat gttaagataa acgctactaa accaacaatt
     5401 agggaaaatt ttagacgtgt tcttttcaat ttatacaccc cttttctctt ctatggtcgg
     5461 gactaaattt aaaaatacag attcaaaatt gtactctata ttaatacgat tgacttaaac
     5521 aaaatgtttc aaactttctt ccactaaact gccccgttag ttcaagaagc ttttcgctca
     5581 taaatatgaa aataatatgt ataaggattt ttttcatttg ttattccttg tgtaacagat
     5641 acttcgttcc actcttcata attcacttct ggaaagaatg tatctccttc aaattcgtaa
     5701 tgaatttttg taatgtacat tttctcaaca tatggtagaa acaaattata aatttgttct
     5761 cccccgaaaa tgaaaatttc ctcttcgcta ttacataact caaaaacatc ttctattgaa
     5821 tggacgattt cacaaccatt aaagctgaac cccttatctc ttgtcagaat aatattcctt
     5881 cttccaggta atgctcttcc gattgattca agattcttcc ttcctaatat aattggatat
     5941 ccctttgtag tatttttaac atactcccaa tcctctggga ttctccaagg tatgtcattc
     6001 tctttaccta ttaccctgtt cttatccatc gcagcaatta aagaaacttt catatatcac
     6061 acagccttcc ttaactattt taccgtttaa attcctattc cttgttaagc tatcctgccc
     6121 cgttagttta agtgtaatcc ttcacaatct caattgcatt ataaatatac gtaaatatat
     6181 gtgtttactt tcctcaacaa tatggcccga ttgcagaacg gacgcagatc gcttctcaca
     6241 caatcgcgcc ctttaatgga acaaaaagat ttga
//
