LOCUS       NC_012000               4398 bp    DNA     circular CON 11-FEB-2024
DEFINITION  Macrococcoides caseolyticum JCSC5402 plasmid pMCCL5, complete
            sequence.
ACCESSION   NC_012000
VERSION     NC_012000.1
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 4398)
  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
            AP009489.1.
            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..4398
                     /organism="Macrococcoides caseolyticum JCSC5402"
                     /mol_type="genomic DNA"
                     /strain="JCSC5402"
                     /db_xref="taxon:458233"
                     /plasmid="pMCCL5"
     gene            complement(join(4203..4398,1..653))
                     /gene="str"
                     /locus_tag="MCCL_RS11510"
     CDS             complement(join(4203..4398,1..653))
                     /gene="str"
                     /locus_tag="MCCL_RS11510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001258486.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="streptomycin adenylyltransferase Str"
                     /protein_id="WP_001258486.1"
                     /translation="MRTEKEILNLVSEFAYQRSNVKIIALEGSRTNENIKKDKFQDYDF
                     AFFVSDIEYFTHEESWLSLFGELLFIQKPEDMELFPPDLDYGYSYIMYFKDGIKMDITL
                     INLKDLNRYFSDSDGLVKILVDKDNLVTQEIVPDDSNYWLKKPTEREFYDCCNEFWSVS
                     TYVAKGVFRREILFALDHFNNILRPELLRMISWYIGFNRGFDFSLGKNYKFINKYLTDK
                     EFNMLLATFEMNGYRKTYQSFKLCCELFKYYSNKVSCLGNYNYPNYEKNIENFIRNNYE
                     N"
                     /name="str"
     gene            complement(661..1605)
                     /locus_tag="MCCL_RS11515"
                     /old_locus_tag="MCCL_plsE0001"
     CDS             complement(661..1605)
                     /locus_tag="MCCL_RS11515"
                     /old_locus_tag="MCCL_plsE0001"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011167206.1"
                     /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_011167206.1"
                     /translation="MSKKAEEIQAKQSLEKENSNFSKTGYSNSRLNRHIMYTPEPKLHF
                     DAMTIVGNLNKNNAHKLSEFMSIAPQIRLWDILQTKFKAKALQEKVYIEYDKVKADAWD
                     RRNMRVEFNPNKLTHEEMLWLKQNIIDYMEDDGFTRLDLAFDFEDDLSDYYAMTDKSVK
                     KTIFYGRNGKPETKYFGVRDSDRFIRIYNKKQERKDNADIEVMSEHLWRVEIELKRDMV
                     DYWNDCFNDLHILKPDWSSLEKVKDQAMIYMLIHEESTWGKLERRTKNKYREMLKSISE
                     IDLTDLMKLTLKENEKQLQKQIEFWQREFRFWE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            complement(2166..2621)
                     /locus_tag="MCCL_RS11520"
                     /old_locus_tag="MCCL_plsE0002"
     CDS             complement(2166..2621)
                     /locus_tag="MCCL_RS11520"
                     /old_locus_tag="MCCL_plsE0002"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002485179.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF334 domain-containing protein"
                     /protein_id="WP_000753824.1"
                     /translation="MKKTTEDFQGRGKKVHNDFVRLLQKNLNRVNAEDIEIEVRKDVYG
                     VREEIHSMLREVKQSHEHYQKRQKQLFTGIGAMLLVFMLFALIMTIGRDFMGFLHVDVL
                     QNAIASKIKASEGFISVLWYIAYGLPYILAIGLFIWLYEWIRARFHD"
                     /name="DUF334 domain-containing protein"
     gene            complement(2590..3552)
                     /locus_tag="MCCL_RS11525"
                     /old_locus_tag="MCCL_plsE0003"
     CDS             complement(2590..3552)
                     /locus_tag="MCCL_RS11525"
                     /old_locus_tag="MCCL_plsE0003"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011167204.1"
                     /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_000246202.1"
                     /translation="MATTKLGNTKSASRAINYAEERAEEKSGLNCDVDYAKSYFKQTRA
                     LYGKENGVQAHTVIQSFKPGEVTAKECNEIGLELAKKIAPDYQVAVYTHTDKDHYHNHI
                     IINSVNLETGNKYQSNKEQRDFIKKANDQLCEERGLSVPEKSSEIRYTLAEQNMIDKDK
                     RSWKNDIRMAVEETKDNAVDFEEFNTLLKEKGVEITRVTKNNVTYRHIEEDKKVRGNKL
                     GDSYDKGVIENGFAIEKFRREREEEREYDEYADTFEVDWDAVAENSEDLRKRRIARTEE
                     TKQASNKIYIRDERTTGLERKGIAGNQVEFEKDDGGLSR"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(3534..3932)
                     /gene="mobC"
                     /locus_tag="MCCL_RS11530"
                     /old_locus_tag="MCCL_plsE0004"
     CDS             complement(3534..3932)
                     /gene="mobC"
                     /locus_tag="MCCL_RS11530"
                     /old_locus_tag="MCCL_plsE0004"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002489523.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_001002114.1"
                     /translation="MNEHKDNLASDLSVGGNRKPNRKEPKQISFRVSEQEYSKLKQSAE
                     TLNMTVPNFVKKKAQGSRLVSPKLDKETRQSIAKDLSHLGSNVNQIAKWFNQNKDKATH
                     LPEEKYHDLEKQFDDVKKELHKIWQQLN"
                     /name="mobC"
     Typing          complement(662..1605)
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2594..3552)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tatttgttta taaacttata attctttcct aaactaaaat caaaacccct attaaagcca
       61 atataccaag aaatcattct taataattca ggacgtaaaa tattattgaa atgatctaaa
      121 gcaaataata tttctcttct aaaaacaccc tttgctacat acgttgagac actccaaaac
      181 tcattacagc aatcataaaa ttctcgttct gttggttttt ttaaccaata atttgagtca
      241 tctggaacaa tttcttgagt tactaaatta tctttatcaa ctaaaatttt tacaagacca
      301 tcagaatcac taaaataacg atttaaatct tttaaattaa ttaatgtaat atccattttt
      361 atgccatctt taaaatacat tatataactg taaccataat ctaaatcagg tgggaataat
      421 tccatatctt ctggtttctg tataaacaat aattctccaa ataaacttaa ccaactttct
      481 tcatgtgtga aatactcaat atctgatacg aaaaaagcaa aatcataatc ttgaaactta
      541 tcttttttta tattttcatt agttcttgaa ccctcgagag caataatttt tacattgctt
      601 cgttgataag caaattcaga aactaaattt aaaatttctt tttcagtcct cattgttttt
      661 tcactcccaa aatctaaatt cacgctgcca aaattcaatc tgcttttgca attgtttttc
      721 attctctttt aaagtcaatt tcattaagtc cgttaaatca atttctgaaa tactttttaa
      781 catttctctg tatttatttt ttgtacgtct ttctaattta ccccatgtac tttcttcatg
      841 aattagcata taaatcattg cttggtcttt tactttttct aaactagacc aatctggttt
      901 caaaatatgt aaatcattaa aacaatcgtt ccaataatca accatatctc tttttaattc
      961 aatttctaca cgccataagt gttcagacat aacttcaatg tctgcattat ccttacgttc
     1021 ttgtttttta ttataaattc taataaatct atcactgtca cgaacaccaa aatattttgt
     1081 ttctggttta ccgttacgac cataaaaaat agttttctta actgatttat cagtcatcgc
     1141 ataataatcg ctcaaatcgt cttcaaaatc aaaagccaaa tctaatcttg taaaaccatc
     1201 atcttccatg tagtcaatga tgttttgttt taaccaaagc atttcttcat gcgtaagttt
     1261 attaggatta aattcaacac gcatattacg tctatcccac gcatctgctt ttactttatc
     1321 atattcgatg taaacttttt cttgtagagc cttagcttta aatttggttt gtaatatatc
     1381 ccaaagtcta atttgtggcg caatactcat aaattcagac agtttgtgag cattgttctt
     1441 attaagattc ccaacaattg tcatagcatc aaagtgtaat tttggttcgg gggtgtacat
     1501 aatatgtcgg tttaaccggc tattagagta tccggtttta gaaaaatttg agttttcctt
     1561 ttccaaactt tgttttgcct gaatttcttc tgctttttta ctcataaaaa atcgactcct
     1621 tattttgttt aagaagtcgc tcacccgaat atatatcttg aagaataaac caatatcgtt
     1681 taatatctag atatacaaaa attaagaaaa aaacaccaac tgtttttctt taaggtaagt
     1741 cgcattcaca aactttggtc agggagtgag cgacttcttt ttttgttttt ttatttgcat
     1801 attaatataa cactaacaaa aggcttggtc tattcagact aagtcttttt ttattaggct
     1861 gaatattttt tagaatattt atattgctga taagtgttat aaagtattaa cgcctgcact
     1921 actacttgag caattgatat tgctaaatta atctttttct tcttactcat tttcttcaac
     1981 cccctttgtt gctttattcc aattgcttta tttacattga gcctctgtac ccttaacaaa
     2041 cccaaaactt gtcgaatggt cgggctaata gctcacgcta tgccgacatt cgtctgcaag
     2101 tttagttaag ggtacttctc aatataaata aattttctcg gcataaaagc ctgatcatac
     2161 tttgtttaat catggaatct tgctcttatc cactcataca accaaataaa tagccctata
     2221 gcgagtatat aaggtaaacc ataagcaatg taccataaaa ctgaaataaa gccctcagaa
     2281 gcctttattt tgcttgctat ggcattctgt aatacatcta catgtaaaaa gcccataaaa
     2341 tctctgccaa tcgtcataat caaagcaaaa agcataaaca ctaataacat tgcaccaata
     2401 ccagtaaata attgcttttg tcttttttga taatgttcat gtgattgttt aacttcacgc
     2461 aacatcgaat gaatttcttc tcgaactcca taaacatctt ttcgaacctc tatctcaata
     2521 tcttctgcat tcactcgatt taaattcttt tgtaacaaac gaacaaaatc attatggact
     2581 tttttacctc taccttgaaa gtcctccgtc gtctttttca aactcgactt gattgcctgc
     2641 aattcctttt ctctcaagtc ctgttgttct ttcatctctg atatatattt tattactagc
     2701 ttgttttgtt tcttcagttc ttgcaattct tcgttttcta aggtcttctg aattttctgc
     2761 gactgcgtcc cagtcaactt cgaacgtgtc tgcatattca tcgtattctc gttcttcttc
     2821 tcgttctcgt ctgaatttct cgattgcaaa gccattttca atcactcctt tgtcataaga
     2881 atcgcccaac ttattcccac gtactttttt atcttcttca atgtgtctat acgttacgtt
     2941 gtttttcgtt actctcgtga tttcaacacc tttttctttt agcaaagtat taaattcttc
     3001 aaagtctact gcgttatcct ttgtttcttc aactgccatt cttatatcat ttttccatga
     3061 ccttttatct ttatctatca tgttctgttc tgccaacgta tatctgattt ctgatgactt
     3121 ttctggcaca gataaaccac gttcttcaca taactgatca ttcgcctttt ttataaaatc
     3181 acgttgttct ttgtttgact gatacttgtt gcctgtttct aaatttactg aattaataat
     3241 aatgtgattg tgataatggt ctttgtctgt atgtgtataa actgcaactt gataatctgg
     3301 tgcaattttt ttagctaatt ctaaacctat ctcattacac tctttagctg ttacttcgcc
     3361 aggcttaaaa gattgaatga ctgtatgtgc ttgaacacca ttctctttgc catataacgc
     3421 cctagtttgc ttaaaatatg atttagcata atcaacatca caatttaagc cgcttttttc
     3481 ttctgcacgt tcttctgcgt aattaatggc acgacttgcc gacttcgtat tgcctaattt
     3541 agttgttgcc atatcttatg caactccttt ttcacatcat caaattgctt ttctaaatca
     3601 tgatatttct cttctggtaa atgtgtagcc ttatctttat tttgattaaa ccacttagca
     3661 atctgattca cattactacc caaatgactt aaatctttgg caatcgattg tcgcgtttct
     3721 ttgtctaatt ttggcgacac taatcgactg ccttgtgcct ttttcttaac gaaattaggc
     3781 actgtcatat tcaaagtttc tgccgactgt ttcaactttg aatattcctg ttcactcact
     3841 ctgaaactaa tttgttttgg ctctttgcgg ttgggtttac ggtttccccc aacagacaaa
     3901 tcgctagcca aattatcttt atgttcgttc acaagtccca ccacctttct gacgaaaaat
     3961 attccttttc ataaatatag cttataatat aagctatatt tatgaaaagg aatatagtgg
     4021 tttggcaagc gtcgtatatt ctagccactt cgttctgaat ataccggctt gctgggatta
     4081 atcccagacc ctttatgttt ttgctaacgc aaaaaatgag tggaaaaatg ctagccactc
     4141 atagttcaaa accaaattca aaatcaaaac aaaagcaacc aaaaatgtgg ttgctaataa
     4201 aattaattct cataattatt acgaataaaa ttctcaatat ttttttcgta atttggatag
     4261 ttataatttc ctaaacaact tactttattt gaataatatt taaataattc acaacaaagc
     4321 ttaaaagatt ggtatgtctt tctatatcca ttcatctcaa aagtagctaa aagcatattg
     4381 aattctttat cagttaaa
//
