LOCUS       NC_012002               4061 bp    DNA     circular CON 11-FEB-2024
DEFINITION  Macrococcoides caseolyticum JCSC5402 plasmid pMCCL7, complete
            sequence.
ACCESSION   NC_012002
VERSION     NC_012002.1
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 4061)
  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
            AP009491.1.
            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..4061
                     /organism="Macrococcoides caseolyticum JCSC5402"
                     /mol_type="genomic DNA"
                     /strain="JCSC5402"
                     /db_xref="taxon:458233"
                     /plasmid="pMCCL7"
     gene            complement(219..974)
                     /locus_tag="MCCL_RS11560"
                     /old_locus_tag="MCCL_plsG0001"
     CDS             complement(219..974)
                     /locus_tag="MCCL_RS11560"
                     /old_locus_tag="MCCL_plsG0001"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012657563.1"
                     /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_012657564.1"
                     /translation="MAYTKVAPSKSSGASIVYARDGKDNGKDKCVAMSGLNCDPSNAEY
                     EFAVVRRAHNKALKEGEDIQARLIIQSFEGEELSPEEVNEMGYELAENINEKLGGGFQA
                     VVYTHGNTKNLHNHIVFNSVNADTGKKYTMHYEKFEIEKMNDEIVSQRGLNVIEKQKKD
                     ITTNGERKLRENGQYVWKDDLKDRFNRAFEKTLSNVSENKAENLEEFKKNLNELGVSVK
                     ERYVKKRDTTYFTLMFSTDENRQKTRLAN"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(956..1345)
                     /locus_tag="MCCL_RS11565"
                     /old_locus_tag="MCCL_plsG0002"
     CDS             complement(956..1345)
                     /locus_tag="MCCL_RS11565"
                     /old_locus_tag="MCCL_plsG0002"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012655831.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_012657565.1"
                     /translation="MSEKKKKKSKIISFRVNEDEYEVIAGIAKSANMNVSEYLKIRALE
                     GNIQQPKVSSEDLRAVVPDLTRLTGQIGRIGNNVNQSTKLLRSIGPYGFVSPKNFVELK
                     EVFEKSNEEITGIREEVKAIWHTLK"
                     /name="hypothetical protein"
     gene            complement(1899..2273)
                     /locus_tag="MCCL_RS11570"
                     /old_locus_tag="MCCL_plsG0003"
     CDS             complement(1899..2273)
                     /locus_tag="MCCL_RS11570"
                     /old_locus_tag="MCCL_plsG0003"
                     /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            complement(2376..3257)
                     /locus_tag="MCCL_RS11575"
                     /old_locus_tag="MCCL_plsG0004"
     CDS             complement(2376..3257)
                     /locus_tag="MCCL_RS11575"
                     /old_locus_tag="MCCL_plsG0004"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003010590.1"
                     /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_012657566.1"
                     /translation="MVNETVKYHNDLNTVPMRKWTKEEMDFFFSIISKLKEKGTREIEF
                     DKYQLAELARYTVTHNKRFEETMERLVKNISQIHYIERTSNSLELMNLFSRFKVTWEDD
                     LSDMTLVVKVTEEFNYVINKLQVEFTSWELEEFTSIRSTYAKTMYRLLKQWRTVGKVEY
                     KVDVFKQLLDMPSYYTPSEIDKNVLQPILKELPSFFSNLKIKKIKSNKRGTPVIAYEFT
                     FSPEKTGTFIDYKKKNQPRELTPEWLKNESQTNRSTDAWTEDELEREREKLRKELAELE
                     NAKQTKIDEYLK"
                     /name="replication initiation protein"
     gene            complement(3582..3971)
                     /locus_tag="MCCL_RS11580"
                     /old_locus_tag="MCCL_plsG0005"
     CDS             complement(3582..3971)
                     /locus_tag="MCCL_RS11580"
                     /old_locus_tag="MCCL_plsG0005"
                     /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_148184337.1"
                     /translation="MFEERERIRKEKLETIAKKVGLDREGNFKTPVLFVEHADKPVRYT
                     YLSSELKRSERGWSSEIAKENVKFDYYVSPHKKLFSAEHRKENGESLYQTCRKGADRED
                     VSAEFEKAHTKVKQANMSKGRSKSI"
                     /name="hypothetical protein"
     Typing          complement(2377..3257)
                     /name="rep_cluster_1407"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(223..974)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.602"
                     /coverage="100.0"
                     /evalue="7.06e-158"
ORIGIN
        1 taggggctta ttttggctta tttcagctat cctgtttctt tcaatctcaa ccggaggaac
       61 aaaaccagta tgttttttag gtttttcggc gtctgggggc gtttctagtg tctctttttc
      121 aactacaagg ggttttagcc ttgtttttga tcgaattgtc cgttcagtaa gactctatga
      181 cgttctcagc actaaaaatc agtgccctag tctttttctc aatttgccag tctggttttt
      241 tgccggttct catcagtgga aaacataagg gtaaagtaag ttgtatcgcg tttcttgacg
      301 tatctttcct ttacgctaac accgagttca tttagatttt tcttgaattc ttccaagttt
      361 tcagccttat tttccgacac attcgacagt gttttttcga atgcacgatt aaatctgtcc
      421 tttaagtcat ctttccacac atattgaccg ttttcgcgta attttcgctc tccgttcgtc
      481 gtgatgtctt ttttctgctt ttcaatcacg ttcaagccac gctgtgacac gatttcatca
      541 ttcattttct caatttcaaa tttttcatag tgcatagtat atttcttacc tgtatcagcg
      601 ttcacagagt tgaaaacgat gtgattatga agattttttg tatttccgtg ggtataaaca
      661 acagcttgaa aacccccacc aagtttttcg ttgatgtttt cagcaagttc atagcccatt
      721 tcattaactt cttcgggaga aagttcttcg ccctcaaagg actgaataat caatcgtgcc
      781 tgtatgtctt ccccctcttt gagtgcctta ttatgtgccc gtctgactac agcgaactca
      841 tattcagcgt tagaggggtc gcagtttaaa ccagacatag caacacattt atcttttcca
      901 ttgtcttttc catcacgtgc gtagacgatt gaagcccctg aactctttga tggtgctact
      961 ttagtgtatg ccaaatcgct ttcacttcct ccctgatccc tgtgatttcc tcgttagatt
     1021 tttcaaatac ttctttcagt tcaacgaaat tcttaggaga cacaaaaccg taaggaccta
     1081 tagacctcaa tagctttgtt gactgattga cgttgttgcc aattcgcccg atttgacctg
     1141 ttaaccttgt taaatcggga acaacagccc ttaaatcttc tgaagatact ttcggctgtt
     1201 gaatgttgcc ctccaacgcc cgtatcttca aatactcgct tacgttcatg ttggcactct
     1261 ttgcgatgcc agcaatcact tcgtactcgt cctcattcac tcgaaacgaa ataatcttcg
     1321 attttttctt ttttttctcg ctcactttta gcccctactt tctcagacag atactcccta
     1381 ttcggtctca tctgtctgtt caattagtgc ctagtgatta tgatattttt tgtaaatgac
     1441 cctccctgtt cagtcggcta attttacaaa attctgtagt ttttaatctt cactattcgc
     1501 tcagattctc aacaacagaa acaatcataa tcacaagaac ataatttttg ctctaaattg
     1561 tttcataatt acggtgtaat tatatcataa atttatcatg agcaaaaatc tgaccagcag
     1621 tgtcggtgta tacatttgct tcgcaaagta tttcccgtct ctgtggggag gttgaactac
     1681 gtcccccctc caccccctcc ttttgaacaa aaaattgcgt tgcaatattc ttgttcttgc
     1741 agataaaact attacagaaa tgtcttcgcc acgtctgaaa tagttttact ggatgcgtca
     1801 atctgtcaaa acttcaatca gctacttacg ctgattttgt ctttctgctt tgacgcaaaa
     1861 aaagcacaca accttaatga tcgtgtgcta aatgtctctt aaatttcagt cttcgtctta
     1921 aatttttcga cccattttgt aaactccgaa aggttcggaa gtttaggata tccttgcgaa
     1981 taatcaatgt tatccgcagt ctttcttaaa acaccgaaaa tcttttcgta agcctctaga
     2041 cgacgttcat catcttgagt cttaaaattc tcatagttct tcttctcaat aagcatataa
     2101 ttttctctaa actgcttgag agaaatggga cgtttcttat cattacgggg aaaatcgtct
     2161 ccgtaaaatt caagaagagt cttgtaatgc tctttttctt tctccttaat ttcttgcagc
     2221 agtgcttttc tctttttctc aagttcttct aattcttgtc ttttatcgta catgtaaacc
     2281 ctcctcattt gttttttgat gtactggtgg ttgaaatcat ctaaaacatg cttaaaatcg
     2341 aaatctcagc acataaagac ccgatttcaa atgctttatt taagatattc atcaattttc
     2401 gtttgtttag cattttcaag ttcggctaat tcttttctca gcttctctct ttctctttca
     2461 agttcatctt ctgtccaggc atcagttgat cgatttgtct gactttcatt tttcagccac
     2521 tcgggtgtta attctctagg ttgatttttc tttttgtagt ctataaatgt tcccgtcttt
     2581 tctggactga acgtgaattc atatgcaatt acaggagtac cacgcttatt tgatttgatt
     2641 ttttttattt tgagattaga gaaaaacgaa ggaagttctt ttaaaatggg ttgtaataca
     2701 tttttatcta tctcgctagg cgtgtagtaa ctaggcatat ctaacagttg cttgaaaaca
     2761 tctactttgt attcaacctt tccaactgta cgccattgtt ttaacagtcg atacatcgtt
     2821 tttgcgtagg ttgatcgaat agatgtaaat tcttctaact cccaggaagt gaactctacc
     2881 tgtaacttat taattacata attaaattcc tcagtaactt tgacaacaag tgtcatatcg
     2941 ctcaaatcgt cctcccaggt cactttaaaa cgactaaata aattcataag ttctaaagaa
     3001 ttagaagttc gctctatgta gtgaatttga ctgatgtttt taaccaaacg ttccatcgtc
     3061 tcctcaaaac gtttgttatg agtgacagta taacgtgcca attcagctaa ttgatactta
     3121 tcaaactcaa tttctctcgt acctttttcc tttaactttg aaataatcga gaagaaaaaa
     3181 tccatttctt ccttagtcca cttgcgcata ggcacagtgt tcaaatcgtt atgatattta
     3241 acagtttcat tcaccattat aaagacctcc gttttttatg tctttataat acttcaaaat
     3301 tattataaag acaactaatg cctctttatg accgacattt tgtctttata aaccgacatt
     3361 ctgtctttat aaaccgacat tttgtcttta taaaccgaca ttttgtcttt ataacgcccc
     3421 ttaatccctt gtggctctaa gactcgatta actcctaaat atgttattaa atatattatt
     3481 aaatatatat ataaataggc acgcccaaaa tctcatgtat ttttcctcta aatttttaaa
     3541 actgagcaat cggatcaact gcaaaagtag ttgaaaatta tctaaataga ttttgaacga
     3601 ccttttgaca tattcgcctg tttaacttta gtgtgtgctt tttcaaattc tgctgataca
     3661 tcttctctgt ctgcaccttt tctgcatgtt tgatacaatg attcaccatt ttctttcctg
     3721 tgttctgctg aaaatagctt tttatgagga gatacataat aatcaaactt tacattctct
     3781 tttgctattt cactcgacca acctctttca gacctcttaa gttcacttga tagataagtg
     3841 taacgaacag gtttatctgc atgttcaaca aacaaaacag gcgttttaaa gttgccctct
     3901 ctatcaagtc cgactttttt agcaatcgtt tcaagctttt cttttctaat tctttctctt
     3961 tcttcaaaca taaaatcgct tttaaggggt gtaagagacg tttctagcgt cattttgtcg
     4021 tctttggtag tttgtatctc tttttctttt tcttgctctt c
//
