LOCUS       NC_012001               4226 bp    DNA     circular CON 11-FEB-2024
DEFINITION  Macrococcoides caseolyticum JCSC5402 plasmid pMCCL6, complete
            sequence.
ACCESSION   NC_012001
VERSION     NC_012001.1
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 4226)
  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
            AP009490.1.
            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..4226
                     /organism="Macrococcoides caseolyticum JCSC5402"
                     /mol_type="genomic DNA"
                     /strain="JCSC5402"
                     /db_xref="taxon:458233"
                     /plasmid="pMCCL6"
     gene            join(4165..4226,1..64)
                     /locus_tag="MCCL_RS12530"
     CDS             join(4165..4226,1..64)
                     /locus_tag="MCCL_RS12530"
                     /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_269446095.1"
                     /translation="MKTAKKQTANEKRLGTDFSAENVIKLTERQFEKNKAETLCS"
                     /name="hypothetical protein"
     gene            274..663
                     /locus_tag="MCCL_RS11535"
     CDS             274..663
                     /locus_tag="MCCL_RS11535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012657567.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_041636600.1"
                     /translation="MFEERERIRKEKLELIAKKVGLDREGNFKTPVLFVEHADKPVRYT
                     YLSSELKRSERGWSSEIAKENVKFDYYVSPHKKLFSAEYRKENGESLYQTCRKGADRED
                     VSAEFEKAHTKVKQANMSKGRSKSI"
                     /name="hypothetical protein"
     gene            1132..2037
                     /locus_tag="MCCL_RS11540"
                     /old_locus_tag="MCCL_plsF0001"
     CDS             1132..2037
                     /locus_tag="MCCL_RS11540"
                     /old_locus_tag="MCCL_plsF0001"
                     /inference="COORDINATES: protein motif:HMM:NF013235.4"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_012657560.1"
                     /translation="MIDLVKYHNNLNSVVFGKFNANEMNLFFSIISKLKDKGEDTVIFS
                     WNELKDLSRYKPTATQRFVSDLDKTYKKMLELNYGQTFVKKKRLTYSRFVLFTSFHIDC
                     DMNDDGDLDASTGIVAIKINPELRHILNDLEQWTQYSLEEFIKLKSTYSKTIFRLLKQF
                     RTTGYLKLSVEEFREQLDIPNSYRMSHINQKVISVAEKELNAHFKNLKINKIKAKKKGA
                     PVVAIEFRWSPEKTGTFVDYSKKKQPRELTPKWLKNEGQQNRSTDEMSEEELEIEREKL
                     RKELAELENAKQTEIDEYIK"
                     /name="replication initiation protein"
     gene            2140..2514
                     /locus_tag="MCCL_RS11545"
                     /old_locus_tag="MCCL_plsF0002"
     CDS             2140..2514
                     /locus_tag="MCCL_RS11545"
                     /old_locus_tag="MCCL_plsF0002"
                     /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_012657561.1"
                     /translation="MYDKRQELEELEKKRKALLQEIKEKEKEHYKTLLEFYGDDFPRND
                     KKRPISLKQFRENYMLIEKKNYENFKTQDDERRLEAYEKIFGVLRKTADNIDYSQGYPK
                     LPNLSEFTKWVEKFKTKTEI"
                     /name="hypothetical protein"
     gene            3075..3380
                     /locus_tag="MCCL_RS11550"
                     /old_locus_tag="MCCL_plsF0003"
     CDS             3075..3380
                     /locus_tag="MCCL_RS11550"
                     /old_locus_tag="MCCL_plsF0003"
                     /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_012657562.1"
                     /translation="MSEKKKKKSKIISFRANEDEYEVIAGIAKSANMNISEYLKIRALE
                     GNIQQPKVSSEDLRAVVPELTRLTGQIGRIGNNVNQSTKLLSSIGPYGFVSPKNFR"
                     /name="hypothetical protein"
     gene            3447..4196
                     /locus_tag="MCCL_RS11555"
                     /old_locus_tag="MCCL_plsF0004"
     CDS             3447..4196
                     /locus_tag="MCCL_RS11555"
                     /old_locus_tag="MCCL_plsF0004"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_012657563.1"
                     /translation="MAYTKVAPSKSSGASIVYARDGKDNDKDKCVAMSGLNCDPSNAEY
                     EFAVVRRAHNKALKEGEDIQARLIIQSFEGEELSPEEVNEMGYELAENINEKLGGGFQA
                     VVYTHGNTKNLHNHIVFNSVNADTGKKYTMHYEKFEIEKMSDEIVSQRGLNVIEKQKKD
                     ITTNGERKLRENGQYVWKDDLKDRFNRAFDKTLLNVSKNRTENLEEFKKNLSELGVNVK
                     ERYVKKRDTTYFTYVFTDENGKKTDCK"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     Typing          1133..2037
                     /name="rep_cluster_1337"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3448..4184
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.927"
                     /coverage="98.0"
                     /evalue="2.39e-144"
ORIGIN
        1 gaacgtcata aagcttactg aacgtcaatt cgagaaaaat aaggctgaaa ctctttgtag
       61 ttgaaaaaga gacgctagaa acgcccccca gacgccgaaa aacctaaaaa acggactggt
      121 tttgttcctc cagttgagat tgaaagaaac aggatagctg aaataagcca aaataagccc
      181 ctagaagagc aagaaaaaga aaaagagata caaactacca aagacgataa aataacgcta
      241 gaaacgtctc ctaagcccct taaaaatgat tttatgtttg aagaaagaga aagaatcaga
      301 aaagaaaagc ttgaattgat tgctaaaaaa gtcggacttg atagagaggg caactttaaa
      361 acgcctgttt tgtttgttga acatgcagat aaacctgttc gttacactta tctatcaagt
      421 gaacttaaga ggtctgaaag aggttggtcg agtgaaatag caaaagagaa tgtaaagttt
      481 gattattatg tatctcctca caaaaagcta ttttcagcag aatacaggaa agaaaatggt
      541 gaatcattgt atcaaacatg cagaaaaggt gcagacagag aagatgtatc agcagaattt
      601 gaaaaagcac acactaaagt taaacaggcg aatatgtcaa aaggtcgttc aaaatctatt
      661 tagataattt ttcaactact tttgtagttg atccgatttt gacgtttaaa aaattagaag
      721 aaaaatacat gagattttgg gtgtgcctat ttatatatat atttaataat atatttaata
      781 acatatttag gagtctctcg aattttagag ctacaaggga ttgagcctcg ttataaaaac
      841 attttgttgg ttaaagacac ctttttttgt tagtgggtgt ctttaagggg tcactatttt
      901 atatatattt tatatataaa tcttttaaat actcttttag gcacctgttc agacttagag
      961 ccacaagggt tacagaacca ttaggacacc tttttgtctg cattaggaca cctttttgtc
     1021 tgcattagga cacctttttg tctgcattag gacacctttt tgtctgcatt aggacacttt
     1081 tatttttaac gtgtcctaaa taggtgtata atgtttttga ggaggtgcct tatgattgat
     1141 ttagttaagt atcacaacaa cttaaattca gtagtttttg gtaagtttaa cgctaacgaa
     1201 atgaatcttt tctttagcat aattagtaaa ttaaaagata aaggcgaaga tacagtaatc
     1261 ttttcctgga atgaattaaa agatttaagt cgatataaac caactgccac tcaaaggttt
     1321 gttagtgatt tagataaaac ttataaaaaa atgttggaat tgaactatgg tcaaacattc
     1381 gtaaagaaaa aacgcttaac gtactcacgt tttgtattat ttactagttt tcacattgat
     1441 tgtgacatga atgatgacgg agatttagac gcttctactg ggatagtagc tataaaaata
     1501 aacccagaat tacgacatat tttgaacgat ttagagcaat ggactcaata ttcgttagaa
     1561 gaatttatca aactaaaatc tacatattct aaaacaatct ttaggctttt aaaacaattt
     1621 aggacaactg gatatttaaa attatctgtt gaagaattta gagagcaatt agatattcca
     1681 aattcctata gaatgagcca tatcaatcaa aaagtgatat ctgtagctga aaaagaattg
     1741 aacgctcatt tcaaaaactt aaagataaat aaaattaaag caaagaaaaa aggggcgcca
     1801 gtagtggcaa tagagttccg ttggtccccc gaaaaaacag ggacatttgt tgactactct
     1861 aagaaaaaac aaccacgcga attaacacca aagtggttga aaaatgaggg gcaacaaaat
     1921 cgatcaactg atgaaatgtc cgaagaagaa cttgaaatcg aaagagaaaa attaagaaaa
     1981 gagttagctg aactagaaaa tgctaaacag actgaaatag acgaatatat caaataaaac
     2041 ctttgaaacc gggaatttac gtgctgagat tccgatttta agcatgtttt agatgatttc
     2101 aaccaccagt acatcaaaaa acaaatgagg agggtttaca tgtacgataa aagacaagaa
     2161 ctagaagaac ttgagaaaaa gagaaaagca ctgctgcaag aaattaagga gaaagaaaaa
     2221 gagcattaca agactcttct tgaattttac ggagacgatt ttccccgtaa tgataagaaa
     2281 cgtcccattt ctctcaagca gtttagagaa aattatatgc ttattgagaa gaagaactat
     2341 gagaatttta agactcaaga tgatgaacgt cgtctagagg cttacgaaaa gattttcggt
     2401 gttttaagaa agactgcgga taacattgat tattcgcaag gatatcctaa acttccgaac
     2461 ctttcggagt ttacaaaatg ggtcgaaaaa tttaagacga agactgaaat ttaagagaca
     2521 tttagcacac gatcattaag gttgtgtgct ttttttgcgt caaagcagaa agacaaaatc
     2581 agcgtaagta gctgattgaa gttttgacag attgacgcat ccagtaaaac tatttcagac
     2641 gtggcgaaga catttctgta atagttttat ctgcaagaac aagaatattg caacgcaatt
     2701 ttttgttcaa aaggaggggg tggagggggg acgtagttca acctccccac agagacggga
     2761 aatactttgc gaagcaaatg tatacaccga cactgctggt cagatttttg ttcataataa
     2821 atttatgata taattacacc gtaattattc ataaatttat tatgaacaaa aattatgttc
     2881 ttgtgatttt gatatggttt ctgttgttga gaatcagaac gaatagtgat gattaaaaac
     2941 tacagaattt tgtaaaatta gccgactgaa taaggagggt catttacaaa aaagtatcat
     3001 aatcactagg cactaattga acagacagat gagaccgaat agggagcatt tgtctgagaa
     3061 agtaggggct aaagatgagc gagaaaaaaa agaaaaaatc gaagattatt tcgtttcgag
     3121 cgaatgagga cgagtatgaa gtgattgctg gcatcgcaaa gagtgccaac atgaacatca
     3181 gcgagtattt gaagatacgg gcgttggagg gcaacatcca acagcctaaa gtatcttcag
     3241 aagatttaag ggcagttgtt cccgaattga caagattaac aggtcaaatt gggagaatcg
     3301 gaaacaatgt caatcagtca acaaagctat tgagttctat aggtccttac ggttttgtgt
     3361 ctcctaagaa ttttcgttga actgaaagaa gtatttgaaa aatctaacga ggaaatcaca
     3421 gggatcaggg aggaagtgaa agcgatttgg catacactaa agtagcacca tcaaagagtt
     3481 caggggcttc aatcgtctac gcacgtgatg gaaaagacaa cgataaagat aaatgtgttg
     3541 ctatgtcagg tttaaactgt gacccctcta acgctgaata tgagttcgct gtagtcagac
     3601 gggcacataa taaggcactc aaagaggggg aagacataca ggcacgattg attattcagt
     3661 cctttgaggg cgaagaactt tctcccgaag aagttaatga aatgggctat gaacttgctg
     3721 aaaacatcaa cgaaaagctt ggtgggggct ttcaagctgt cgtttataca cacgggaata
     3781 ctaaaaatct tcacaatcac attgttttta actcggtgaa cgctgataca ggtaagaaat
     3841 acaccatgca ttatgaaaag tttgaaatcg agaaaatgag tgatgaaatc gtgtcacagc
     3901 gtggcttgaa cgtgattgaa aagcaaaaaa aagacataac gacaaatggc gaacgaaaat
     3961 tgcgtgagaa tggtcaatac gtttggaaag atgacttaaa agacagattt aatcgtgctt
     4021 tcgataaaac tctgttgaat gtgtcgaaaa ataggactga aaacttagag gagtttaaga
     4081 aaaatctgag tgaacttgga gtaaacgtaa aagaaagata cgttaaaaag cgtgatacga
     4141 cttactttac ctatgttttt actgatgaaa acggcaaaaa aacagactgc aaatgagaaa
     4201 agactaggta ctgactttag tgctga
//
