LOCUS       NC_012003               2968 bp    DNA     circular CON 11-FEB-2024
DEFINITION  Macrococcoides caseolyticum JCSC5402 plasmid pMCCL8, complete
            sequence.
ACCESSION   NC_012003
VERSION     NC_012003.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00060930
            Assembly: GCF_000010585.1
KEYWORDS    RefSeq.
SOURCE      Macrococcoides caseolyticum JCSC5402
  ORGANISM  Macrococcoides caseolyticum JCSC5402
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Macrococcoides.
REFERENCE   1
  AUTHORS   Baba,T., Kuwahara-Arai,K., Uchiyama,I., Takeuchi,F., Ito,T. and
            Hiramatsu,K.
  TITLE     Complete genome sequence of Macrococcus caseolyticus strain
            JCSCS5402, [corrected] reflecting the ancestral genome of the
            human-pathogenic staphylococci
  JOURNAL   J Bacteriol 191 (4), 1180-1190 (2009)
   PUBMED   19074389
  REMARK    Erratum:[J Bacteriol. 2009 May;191(10):3429]
REFERENCE   2  (bases 1 to 2968)
  AUTHORS   Baba,T., Kuwahara-Arai,K., Takeuchi,F. and Hiramatsu,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-JUL-2007) Contact:Tadashi Baba Juntendo University
            School of Medicine, Department of Bacteriology; 2-1-1 Hongo, Bunkyo,
            Tokyo 113-8421, Japan
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/11/2024 01:05:44
            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)                     :: 2,390
            CDSs (total)                      :: 2,323
            Genes (coding)                    :: 2,282
            CDSs (with protein)               :: 2,282
            Genes (RNA)                       :: 67
            rRNAs                             :: 5, 4, 4 (5S, 16S, 23S)
            complete rRNAs                    :: 5, 4, 4 (5S, 16S, 23S)
            tRNAs                             :: 50
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 41
            CDSs (without protein)            :: 41
            Pseudo Genes (ambiguous residues) :: 0 of 41
            Pseudo Genes (frameshifted)       :: 23 of 41
            Pseudo Genes (incomplete)         :: 22 of 41
            Pseudo Genes (internal stop)      :: 2 of 41
            Pseudo Genes (multiple problems)  :: 5 of 41
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP009492.1.
            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..2968
                     /organism="Macrococcoides caseolyticum JCSC5402"
                     /mol_type="genomic DNA"
                     /strain="JCSC5402"
                     /db_xref="taxon:458233"
                     /plasmid="pMCCL8"
     gene            167..1090
                     /locus_tag="MCCL_RS11585"
                     /old_locus_tag="MCCL_plsH0001"
     CDS             167..1090
                     /locus_tag="MCCL_RS11585"
                     /old_locus_tag="MCCL_plsH0001"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002499696.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_041636604.1"
                     /translation="MEKYTEKKKRNQVFQYFIKKFVGEKQMDLIKDCNTFLAFVTDKEQ
                     TKKKLYKNNMCKNRFCPMCAWRKARKDALGLSLMMQYIKQEEKKEFIFLTLTTPNVKAE
                     ELEDEIKKYNLSFGKLVKRKKVKAMMKGYVRKLEITYNKQRDDFNPHFHVLIAVNKSYF
                     TDKRYYISQKEWLEMWRDVTGMPEITQVHVQKIKQNNNKELYEMAKYSGKDSDYLINQK
                     IFDAYYKSLKGKQILVYSGLFKEARKKLKNGELDYLKEIDPTEYLYQIYYIWNQKEYLA
                     SELHELTEEEKRKINHQTISEIEEEK"
                     /name="protein rep"
     gene            2065..2493
                     /locus_tag="MCCL_RS11590"
                     /old_locus_tag="MCCL_plsH0002"
     CDS             2065..2493
                     /locus_tag="MCCL_RS11590"
                     /old_locus_tag="MCCL_plsH0002"
                     /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_012657569.1"
                     /translation="MKVKKIIFIVILLALINMVYSLGAVDVEASTERYVGSTWKYRIDN
                     ASSAKAKHVHFYKKKNGSWDHQLCVYSNGSICDANRNKLPGFSSLPSKVKKAAKADKST
                     GMKNLCACGGRFDGGGSGRNFFAYNLDSKDDDELWKIA"
                     /name="hypothetical protein"
     gene            2478..2915
                     /locus_tag="MCCL_RS11595"
                     /old_locus_tag="MCCL_plsH0003"
     CDS             2478..2915
                     /locus_tag="MCCL_RS11595"
                     /old_locus_tag="MCCL_plsH0003"
                     /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_041636605.1"
                     /translation="MENSLSILTRLLRKENFEFWIVENSDMLNYVTKIFIWREKKILNV
                     LTVTSASKETFLTFEDLIVQIESLVSDLNTKLEVRNLYEFLAFNETDYSEYWDYDEDGE
                     VFVSKREQIESDLIEFIKKNLTDKYSFDYPNLVDETKDYSW"
                     /name="hypothetical protein"
     Typing          204..1090
                     /name="rep_cluster_1294"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          147..1087
                     /name="MOBC"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.815"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tgtctactcc aaaccgttga tattattggc ttaaaacaca aaaaaagttg cattttcata
       61 cctagtaatg tattgtttaa ggtgtctaat ctaaaactat acaggaagga gaaaaagcaa
      121 cttttttgtg ctataaaaaa ctattaagtt gttttatata tctgatatgg aaaagtatac
      181 tgagaaaaag aagagaaatc aagtgtttca gtactttatt aaaaaatttg taggtgaaaa
      241 gcagatggat ctgattaagg actgcaacac atttttagcc tttgtaaccg ataaagagca
      301 gacaaaaaag aaactgtata aaaataatat gtgtaagaat cgtttctgcc cgatgtgtgc
      361 ctggagaaaa gcaagaaaag atgctttggg actgtcgttg atgatgcagt acatcaagca
      421 ggaagagaaa aaagaattta ttttcttaac gttaacgaca ccaaatgtga aagctgaaga
      481 attagaagat gaaataaaaa aatataattt gtcgtttgga aaattagtga aaagaaaaaa
      541 agttaaagcg atgatgaaag gctatgtgag aaaattagaa atcacgtaca ataagcaacg
      601 agatgatttc aacccacatt ttcacgtact gattgcggta aataagtcgt attttacaga
      661 taaacgttat tatatttcac aaaaagaatg gctcgaaatg tggcgagatg tcacaggaat
      721 gccggagatc acacaagtcc atgttcaaaa aattaagcag aataacaaca aagaattata
      781 cgaaatggcg aaatattcgg gtaaagatag cgactatctt atcaatcaaa aaatattcga
      841 cgcatattat aaatctttaa aaggtaaaca gattctagtg tattcaggac tttttaaaga
      901 ggcaagaaag aaactaaaaa atggggaatt agattatctt aaagaaattg atccaactga
      961 atacctttac caaatttatt atatctggaa ccaaaaagag tacctggcaa gtgaacttca
     1021 cgaactgact gaagaagaaa aaagaaaaat caatcatcag acaatcagcg aaatcgaaga
     1081 agaaaaataa aaaaatataa aaatattttg agagttgacc acccacattt gtagtttacg
     1141 gagaacgtgg gtggtcaact ctcaaaattt atttcttaaa aatttatttg ttgttctgat
     1201 gagcgattaa cgattaaaaa agtataatgt aattttttgt cattatactt tttttatacg
     1261 gtcattctac tttcgttata cttttttgcc tctgcgagaa ctatgcaatc aaacggcacg
     1321 tttgcccatt tagaatgcaa attcggaacg attttatgcc aaatttttaa tttgcatgta
     1381 actgggcagt aagtaaaaaa atcagttaat actgattttg aaaagtatat aaaataaaaa
     1441 gttttgtgta ttacatttgt ttatgtatat atcgccatat atacataaaa atatatggtt
     1501 taataacgtt atgtatacag tatgtataca taacgttatg gttttgttat gttatttcaa
     1561 aaaaagtgat gtcacttttt tgatagggta aataactcgg cactgccgag ttcaccacgt
     1621 tttggctctg ccaaaacatc aaagtggtgg cattacccct tatgctcatg ttctgaaaat
     1681 aactagaatg ctcttatttg cctcatattt tgattttaag agcatgtttt tgaataaagt
     1741 attttaaata ctttgagaat taaaacgatc attctacgct caaatttgag ctaatgagat
     1801 aaaaaacgga agtaatctat aaaatttcga ggaactttta tgccgagaaa acttttggag
     1861 aggagaagac cccccagaac acacttagag ccgttcacgg cgattttggt agcggcagct
     1921 atcaaatcga cagaacatgg gctcttgggg gtctggggga gcgtcagcgt gtcagaggct
     1981 cgctccaaaa ggaaattgga ataaaaaata tagtgtttat aggtattttt ttgtatataa
     2041 ttacaaaaaa agggggtaat taatgtgaaa gttaaaaaaa ttatttttat tgtgatttta
     2101 ttagcattaa ttaatatggt ctattcgtta ggagctgtcg atgttgaagc aagtactgaa
     2161 agatatgtag gaagcacttg gaaatataga atcgataatg cttcttcggc caaagctaaa
     2221 catgttcatt tttataaaaa gaagaatgga agttgggatc atcaattatg tgtgtatagc
     2281 aatggtagta tttgtgatgc taatagaaat aaattgccag ggtttagttc attaccatct
     2341 aaagtaaaaa aagcagctaa agcagataag tctacaggaa tgaaaaactt atgtgcttgt
     2401 ggaggtagat ttgatggtgg aggatcgggt agaaatttct ttgcttataa tttagattct
     2461 aaggacgacg atgaattatg gaaaatagct taagtatttt aacgcgatta ttaagaaaag
     2521 agaattttga attttggatt gtagaaaatt cagatatgct taattatgtt acaaaaatat
     2581 ttatttggag agaaaaaaaa atattgaatg tattaacagt tactagtgct tcaaaagaaa
     2641 catttttaac atttgaagat ttaattgttc agatagaaag cttagtttct gatttaaata
     2701 caaaactaga agtaagaaat ttatatgaat ttttagcttt taatgaaact gattatagtg
     2761 aatattggga ttatgatgaa gacggagagg tttttgtttc gaaaagagaa cagatagaat
     2821 cagatcttat tgagtttatt aaaaaaaatc ttactgataa gtattctttt gattatccta
     2881 atctagttga tgaaactaaa gattatagct ggtagaaagt tgtttttttc ttatcttgat
     2941 actataggta attattcacg gcgagtcg
//
