LOCUS       NC_011998               3417 bp    DNA     circular CON 11-FEB-2024
DEFINITION  Macrococcoides caseolyticum JCSC5402 plasmid pMCCL4, complete
            sequence.
ACCESSION   NC_011998
VERSION     NC_011998.1
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 3417)
  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
            AP009488.1.
            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..3417
                     /organism="Macrococcoides caseolyticum JCSC5402"
                     /mol_type="genomic DNA"
                     /strain="JCSC5402"
                     /db_xref="taxon:458233"
                     /plasmid="pMCCL4"
     gene            complement(join(3246..3417,1..215))
                     /gene="mobC"
                     /locus_tag="MCCL_RS11830"
     CDS             complement(join(3246..3417,1..215))
                     /gene="mobC"
                     /locus_tag="MCCL_RS11830"
                     /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="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_050742494.1"
                     /translation="MEHNENNGVEIGVKKVKRKAPKQVSFRLTEQEFWKLVGNAEQSNA
                     NSISDYAKKIVLKDGRRSSLVPKIAKEDSLQMVRELNAIGNNLNQIAKWVNSNDRVPMD
                     KEENFINTLERLRREVNEVWQRLS"
                     /name="mobC"
     gene            complement(619..1560)
                     /locus_tag="MCCL_RS11500"
                     /old_locus_tag="MCCL_plsD0001"
     CDS             complement(619..1560)
                     /locus_tag="MCCL_RS11500"
                     /old_locus_tag="MCCL_plsD0001"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017431565.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003916 - DNA topoisomerase 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 factor domain-containing
                     protein"
                     /protein_id="WP_231845611.1"
                     /translation="MQTTTTPLPKINFDRMTIIGDLPLDRVEHMAEFLGNDPYVNLWEK
                     MNNRFKGKALNEKVYIEHDRLKADAWNRRNFRIEFNPNNLSDDEKLWIRENLSSVLENV
                     GFTRLDLAFDFEEDLSDFFVMSDNALKKTVFYGLDGKAETKYFGVRESDRFIRIYNKKQ
                     EQKDNADVEIELENYWRFEIELKRKRVDEWNSNCFNDMHILKPDWTTIEKLNERAIVCM
                     LLTHENEWGKLARHTKYKYRKMIKEISPIDLTDLMRECLKKEESRLQKELDFWLYEKET
                     NFEKYFDFDTSEDLDQIQNRVIAKSKKVRGLE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            complement(2089..3264)
                     /locus_tag="MCCL_RS11505"
                     /old_locus_tag="MCCL_plsD0002"
     CDS             complement(2089..3264)
                     /locus_tag="MCCL_RS11505"
                     /old_locus_tag="MCCL_plsD0002"
                     /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_012655911.1"
                     /translation="MATTKLGNTRVAARSISYAEKKAVVKSSINCDIDNVRASFRAVRE
                     IHGKNDGVQAHTIIQSFKPGEVTAEQANALGRELAERVAKGHQVAIYTHDDTEHIHNHI
                     VINSVADETGKKYQINAKKRHEIKDTNDEICRENGLSIVEKKQEIRKTQAEIELEKKGV
                     VTWKQEIRDVVEVAKEKSKTKEEFIEILKESNINFKETNKTVTYLHSNGQKIRGKRLGN
                     LYDKEEIELSLERNKNRVVEEEKEVKEVKRGGFVAPAQIEEQRKKAFDPILQEQLERFK
                     KKHGIKPNGDFREPLIYREEEQKLAILGAVSKNHSRGHAERMYGSEYGYKVFINEREVA
                     FEGRINSNSLVKFLDQLRASARENNVLDVFERSLDDMRASNKQRQAQQRMR"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     Typing          complement(620..1620)
                     /name="Inc4"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2093..3264)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcctttgcaa ttttaggaac taacgaactt cttctaccat ctttcaaaac tattttcttt
       61 gcataatcag aaattgagtt agcatttgac tgttcagcat tgccaactaa tttccaaaat
      121 tcctgttcag tcaatcgaaa cgaaacttgt ttcggagctt ttcgcttaac tttctttaca
      181 ccaatttcaa caccattgtt ttcattatgt tccataatat caaacactcc tttttaaatt
      241 ttcaatttaa ttttgccaac cgaccaaaaa agtggtcgaa ttgttgtcaa aatacaaagt
      301 cgtaaaaacc gttatactcg taaattttca atttatttat aatatgatac tcacgttgat
      361 acgttcctat tatattataa aatacagtat aacaacaagc gtcgtatatt ctagccactt
      421 cgtgtctaat atacggcttg tcgggggaga ccccgaaccc ctaaaaacca aaaatgacta
      481 gccaaaggct atccattttt aaagtgcagt gaatagccat acgctatcca tctaaagaaa
      541 aaggatagca atatgctatc cttttgtagt ctggagcgac taaaaataaa aataagtgga
      601 tagcttaaag ctaaccactt attcaagacc acgaactttt tttgattttg caatcactcg
      661 attttgaatt tgatccaaat cttctgatgt atcaaaatca aaatatttct caaaattcgt
      721 ttctttttca taaagccaaa aatctaattc tttttgtaat cggctttctt cttttttcaa
      781 acactcacgc attaaatcag ttaaatcaat tggtgaaatc tctttaatca tttttcgata
      841 tttatatttt gtatgtcgtg ctaattttcc ccattcattt tcatgagtca acaacataca
      901 tacaatagca cgctcattta atttttcaat tgttgtccaa tcaggtttta aaatatgcat
      961 atcattaaaa caattactat tccattcatc aacacgtttt ctttttaatt caatttcaaa
     1021 tcgccaataa ttttctaatt caatttctac atcagcatta tctttttgtt cttgtttttt
     1081 attataaatt cgaataaatc tatcgctctc tcttacgcca aagtattttg tttcagcttt
     1141 accatcaaga ccatagaaaa cagttttctt caaagcattg tcactcatca caaaaaaatc
     1201 ggataaatct tcttcaaaat caaaagctaa atctaatcgc gtaaatccta cattttctaa
     1261 aacagaagat aaattttctc taatccataa tttttcatca tctgataaat tattcggatt
     1321 aaattcaatt ctaaaatttc ttctattcca tgcatcagct ttcaatctat catgttctat
     1381 ataaactttt tcattcagtg ctttgccttt aaatctatta ttcatttttt cccaaaggtt
     1441 aacataaggg tcatttccta aaaattctgc catgtgttca actcgatcaa gtggcagatc
     1501 tccaatgata gtcatacggt caaaattgat ttttggtagg ggggtggtcg tagtttgcac
     1561 acctaaccgg ctattagata gggccggctc ccaatttttt tccaattcat tcttattcac
     1621 taaaaaaact ccctttctaa tcacaaaatt tgtaatagaa aaagagccct aaacccactt
     1681 aatcaaattt ctatcttgat aaaaatcatt aaataattta tgatttgggt atagtttaat
     1741 acaaaaacat atttcactga cataactgtt gtgagattat ttttttgtcc ttaaccctcg
     1801 ccgtccaaag caagtgggtt taggactctt tttttattta tttttacttt aacagtttac
     1861 taatagccac tgcaaccgaa ctcaaaaaat aaattgcatt ttttcaacac tctttgcgtt
     1921 tattccaatt tccttttgga gcgagcctct gacacgctga cgctccccca gacccccaag
     1981 agcccatgtt ccgtcgattt gatagctgcc gctaccaaaa tcgccgtgaa cggctctaag
     2041 tgtgttctgg ggggtcttct cctctccaaa agttttctcg gcataaaact acctcattct
     2101 ctgttgtgct tgtctctgct tgtttgaagc cctcatatcg tctaaacttc tttcaaatac
     2161 atctaataca ttattttctc tcgcactcgc tcttaattgg tctaagaact ttacaaggct
     2221 attgctattt attcttccct caaacgctac ttcacgctca ttaataaata ctttatagcc
     2281 atattcagag ccatacattc tttcagcatg acctcttgaa tgattttttg atactgctcc
     2341 taaaatcgct aatttttgtt cttcctcacg ataaatcaaa ggctctctaa aatcgccatt
     2401 cggctttatc ccgtgcttct ttttaaatct ttctaactgt tcttgcaaaa tcggatcaaa
     2461 tgcttttttt ctttgttctt caatctgtgc aggtgcaaca aagccacctc tttttacttc
     2521 tttaacttct ttttcttctt caactacacg atttttattt ctttcaagcg acaattctat
     2581 ttcttctttg tcgtataaat taccaagcct tttacctcgt attttttgac catttgagtg
     2641 taaataagtt actgttttat ttgtttcttt aaaattaata ttagactctt tgagaatttc
     2701 gataaattct tctttggtct ttgatttttc tttcgctact tcaactacat ctctaatctc
     2761 ttgtttccat gtcactacac cttttttctc taactctatt tcagcttgtg tctttctaat
     2821 ctcttgtttt ttttctacaa tcgacaatcc attttctcta caaatttcat cattcgtatc
     2881 ttttatttca tgtcttttct ttgcatttat ctgatatttt tttcccgtct catcagccac
     2941 agaattaatc acaatatgat tatgaatatg ttcagtatca tcatgcgtat aaattgccac
     3001 ctgatgacct ttcgcgacac gttcagctaa ttcacgacct aaagcgttcg cttgttctgc
     3061 tgtcacttct ccaggcttaa atgactgtat aattgtatgt gcttgtacac cgtcattttt
     3121 tccatgaatt tctctgactg ccctaaaaga cgctcttacg ttgtctatat cacaatttat
     3181 actactttta acaactgctt ttttttcagc gtatgaaatt gatcgagcag ctactcttgt
     3241 atttcctagc ttagtcgttg ccatacctca ttcacttctc ttctcaaacg ttctaaagta
     3301 tttataaaat tctcttcttt atccataggc actctatcat ttgaattaac ccatttcgca
     3361 atctgattaa gattatttcc aattgcattt aattctctaa ccatttgtag cgaatct
//
