LOCUS       NZ_AP022931             6404 bp    DNA     circular CON 13-MAR-2024
DEFINITION  Bacillus cereus strain J2 plasmid pJ2_4, complete sequence.
ACCESSION   NZ_AP022931
VERSION     NZ_AP022931.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00203331
            Sequence Read Archive: DRR206371, DRR206395
            Assembly: GCF_021655055.1
KEYWORDS    RefSeq.
SOURCE      Bacillus cereus
  ORGANISM  Bacillus cereus
            Bacteria; Bacillota; Bacilli; Bacillales; Bacillaceae; Bacillus;
            Bacillus cereus group.
REFERENCE   1
  AUTHORS   Furuta,Y., Miyajima,Y., Maehana,S., Tsujinouchi,M. and Higashi,H.
  TITLE     Genomic sequence of Bacillus cereus isolated from bacteremia
            patients in Japan
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6404)
  AUTHORS   Higashi,H. and Furuta,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-MAR-2020) Contact:Hideaki Higashi Hokkaido University,
            Research Center for Zoonosis Control; North 20, West 10, Kita-ku,
            Sapporo, Hokkaido 001-0020, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Canu v. 1.8
            Genome Coverage                   :: 405x
            Sequencing Technology             :: MinION R9.4 Flowcell; MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_021655055.1-RS_2024_03_13
            Annotation Date                   :: 03/13/2024 06:59:32
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 6,035
            CDSs (total)                      :: 5,886
            Genes (coding)                    :: 5,646
            CDSs (with protein)               :: 5,646
            Genes (RNA)                       :: 149
            rRNAs                             :: 13, 13, 13 (5S, 16S, 23S)
            complete rRNAs                    :: 13, 13, 13 (5S, 16S, 23S)
            tRNAs                             :: 105
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 240
            CDSs (without protein)            :: 240
            Pseudo Genes (ambiguous residues) :: 0 of 240
            Pseudo Genes (frameshifted)       :: 132 of 240
            Pseudo Genes (incomplete)         :: 117 of 240
            Pseudo Genes (internal stop)      :: 49 of 240
            Pseudo Genes (multiple problems)  :: 47 of 240
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022931.1.
            Annotated by DFAST v.1.2.5 (https://dfast.nig.ac.jp).
            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..6404
                     /organism="Bacillus cereus"
                     /mol_type="genomic DNA"
                     /strain="J2"
                     /isolation_source="human blood of bacteremia patient"
                     /host="Homo sapiens"
                     /db_xref="taxon:1396"
                     /plasmid="pJ2_4"
                     /geo_loc_name="Japan:Tochigi"
                     /collection_date="2006"
     gene            join(6287..6404,1..164)
                     /locus_tag="L6497_RS29920"
     CDS             join(6287..6404,1..164)
                     /locus_tag="L6497_RS29920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000888627.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_236794095.1"
                     /translation="MLEDKFLESKIENLTNQNVVVFTDDEIIKGVLLDKETGEERLGEV
                     LCKIWGKNFAWFGEGIYIQCEDTITFRDFEEIDNIWSLERKVDYKKLE"
                     /name="hypothetical protein"
     gene            complement(204..332)
                     /locus_tag="L6497_RS30160"
                     /old_locus_tag="BCJMU02_p41"
     CDS             complement(204..332)
                     /locus_tag="L6497_RS30160"
                     /old_locus_tag="BCJMU02_p41"
                     /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_272884642.1"
                     /translation="MFPSFFPSIGQFIKAQPTLSLMTTVIIIQSIIIIKLLKKLDL"
                     /name="hypothetical protein"
     gene            1164..1673
                     /locus_tag="L6497_RS29925"
                     /old_locus_tag="BCJMU02_p42"
     CDS             1164..1673
                     /locus_tag="L6497_RS29925"
                     /old_locus_tag="BCJMU02_p42"
                     /inference="COORDINATES: protein motif:HMM:TIGR01764.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_074544231.1"
                     /translation="MNAKEVAKMLGAHPNTIYKMIKNGEIKAVKQGKSFDIPNIEVNKL
                     MVSKHSIDTNKETEKGAYALIQHFENKMHSEFSRIAIDCYGIAQDFLKMKNEEDIYKRI
                     EMESDIQNGRYFVDLLETVEKYISYKKMCERLKETAEDPLLHESLEEQVAWHNALQVGL
                     GGNDKE"
                     /name="helix-turn-helix domain-containing protein"
     gene            2374..2892
                     /locus_tag="L6497_RS29930"
                     /old_locus_tag="BCJMU02_p43"
     CDS             2374..2892
                     /locus_tag="L6497_RS29930"
                     /old_locus_tag="BCJMU02_p43"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000260421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3967 domain-containing protein"
                     /protein_id="WP_236794097.1"
                     /translation="MVVVYQTTKQAAQTLNINHTTFKKYYGMFERYNGYNFLRDLKGQV
                     MFSEYDLEMFKRLLLVKAEPGRTIEESCRLVGEEFGILDKNQVITDISSENAGYNQAIE
                     ELKELILMQNNKIDELTIKLNEQSNQTKVIETSVGDRDQQLVRLMKEMLEVKRMVAASE
                     KKKWWVFWK"
                     /name="DUF3967 domain-containing protein"
     gene            2999..3289
                     /locus_tag="L6497_RS29935"
                     /old_locus_tag="BCJMU02_p44"
     CDS             2999..3289
                     /locus_tag="L6497_RS29935"
                     /old_locus_tag="BCJMU02_p44"
                     /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_236794098.1"
                     /translation="MTSKKRIQLTLSEESFIKCEELANRYGITPNSFMAFVIGQWLDHN
                     YETNKILAKKVDEALPDMKSIFADPNLASMVKNVLGDDKEFKDSVRKQLSI"
                     /name="hypothetical protein"
     gene            3308..3550
                     /locus_tag="L6497_RS29940"
                     /old_locus_tag="BCJMU02_p45"
     CDS             3308..3550
                     /locus_tag="L6497_RS29940"
                     /old_locus_tag="BCJMU02_p45"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000342926.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_236794086.1"
                     /translation="MNDVLTKILEKLDQLDKKVDTIGSEVREVRKEIQAHRMEIDDNFT
                     KLYKLVEDKEVEIDLLNKRIFKNETTVEKLKRQKH"
                     /name="hypothetical protein"
     gene            3621..3974
                     /locus_tag="L6497_RS29945"
                     /old_locus_tag="BCJMU02_p46"
     CDS             3621..3974
                     /locus_tag="L6497_RS29945"
                     /old_locus_tag="BCJMU02_p46"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001179589.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_236794088.1"
                     /translation="MQNVKEIKKLIRKNPGKYASISTAEDNALEGILLSGFFAKQVMKL
                     ASQSNHISHDFNSNDLKSSDLTLKGVFLFNGTGIDFVFYEGVETIRIYDSPMFEEDSKD
                     MFEYFKEWLHAHS"
                     /name="hypothetical protein"
     gene            4152..4418
                     /locus_tag="L6497_RS29950"
                     /old_locus_tag="BCJMU02_p47"
     CDS             4152..4418
                     /locus_tag="L6497_RS29950"
                     /old_locus_tag="BCJMU02_p47"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000712648.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_236794090.1"
                     /translation="MKEHVKLQFKAENVKGEIEGYSNMPFWNHDLKLEVVLALLNTVDY
                     KDFFESPNYNQLNDYTKQIIEAIEYSLGFDGLYQLVYGDVKKD"
                     /name="hypothetical protein"
     gene            4773..5813
                     /locus_tag="L6497_RS29955"
                     /old_locus_tag="BCJMU02_p48"
     CDS             4773..5813
                     /locus_tag="L6497_RS29955"
                     /old_locus_tag="BCJMU02_p48"
                     /inference="COORDINATES: protein motif:HMM:NF013603.4"
                     /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_236794092.1"
                     /translation="MLLSESFSRLDKHNKAENICNCGSFLKFNICPQGHEKRLSWANFC
                     RVRLCPMCSWRRSLLIAHQVKSIAHEASQQEKLRWLFLTLTVKNCEGENLMDTINHLMK
                     SFHRLSKRKVFNDSSIRGWFRAFEVTRNFHDGSYHPHFHVLLAVKPSYFNGKSKSYMTT
                     TEWGKLWKSCLKVDYDPIVHIRVVKNNRNQEKELKILQNKGIQLSNNGTFELSGAAVAE
                     MAKYSVKSSDYLIYNEYEKKGSKYIPVVESGIDEETTDEVVQTLDEALARRRLIAFGGL
                     MKEVWERLRIEGKMVDAESEEVNLVHVNEDTKCQCSVCGSNMLEELYSWLPEYKNYIKK
                     ENILNT"
                     /name="protein rep"
     gene            complement(6039..6179)
                     /locus_tag="L6497_RS29960"
                     /old_locus_tag="BCJMU02_p49"
     CDS             complement(6039..6179)
                     /locus_tag="L6497_RS29960"
                     /old_locus_tag="BCJMU02_p49"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000130115.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_170869143.1"
                     /translation="MTDKKERVEMRIPQSILKKVDEYKEENGLSTRTATILELIRKGLN
                     K"
                     /name="hypothetical protein"
ORIGIN
        1 agcgtttagg tgaggtttta tgtaaaattt ggggtaagaa ttttgcttgg tttggagaag
       61 gaatatacat acaatgtgaa gatacgataa cgtttcgaga ttttgaagaa attgataata
      121 tttggagtct tgaacgaaaa gtggattata aaaaattaga ataaaaaaag gataccattt
      181 aatgtatcct ttttttattt ttgttataaa tcaagttttt ttagtagttt tataatgata
      241 atactttgaa taatgatgac tgttgtcata agagatagtg taggttgtgc tttaataaat
      301 tgtccaatag atgggaaaaa actaggaaac atatttgtga taattaatac tagtaaactt
      361 actaattcta ttattttttt cattttgtat cattcctttc aattagatat agtcactatc
      421 tggtattagt cactatctgg tatgaagtca tttcaggtat tagttcattt catatacgtc
      481 ccacggagtg gttataaagt gaatcaataa atatgacgca tagaaaagat atttggcaca
      541 tggcaaacat atataattct taaattttat gttttttaga gggcttcaaa acggtataca
      601 acgatctcaa aacggtatac aaatgactgt ttaacggtct caaagcggta tacaagggca
      661 aaaaatgcat cccagaaaaa tagatttaga aactcaatag gcacagccta tttcaccact
      721 ttttttataa agtgggattc ggtttcctta tgctctttta aaaatggtga aaagtgatct
      781 atatattttt ctagacaata tatatttatg tagtttggta tttcaaaaaa tatttacttt
      841 atagtttgaa taggaacgtt ttgagtgtgt aggaaacttt taaaaagagg taagttattt
      901 gatattaaaa agagaatgca ggataaggag atggacacaa atgtgtctat atgtagcagt
      961 caaagcctga tatgatgttt ttttattgtg tttacatttg tgttttaaat ttaaataaga
     1021 tagttaattt gtatctacaa atatatttaa acatcgagaa atcgatgttt ttttgtgttt
     1081 taaatttcat taataataac aattagttac taagttgaaa atatattaac tacgtgttac
     1141 tataaacgaa aggaggttgg aaaatgaatg caaaagaagt agctaaaatg ttaggtgctc
     1201 atccaaatac aatttataaa atgataaaga atggtgaaat taaggctgta aaacaaggta
     1261 agtcttttga tattccaaat atcgaagtta ataaattgat ggtctcaaaa cattctattg
     1321 atacaaataa agaaactgag aaaggagctt atgctttgat ccaacatttt gagaacaaaa
     1381 tgcatagtga gttttcaaga attgctatag attgttatgg gatagcacaa gattttttaa
     1441 aaatgaaaaa tgaagaggat atctataaaa gaatagaaat ggaatcagac atacaaaatg
     1501 gtagatattt tgttgattta ttagaaactg tagaaaaata tattagttat aaaaaaatgt
     1561 gtgagcgttt aaaggaaaca gctgaggatc ctcttcttca tgaatcatta gaagaacaag
     1621 tggcatggca taatgctctt caagtaggat taggaggaaa tgataaagaa tagctagcgt
     1681 atttaaaaat tttatagaaa agatatttta aatgtttttc gcagaattat cgattatgcc
     1741 ctagagattt agttagggtt ggcgagcatt cggccttagg cggatgatcg ccagggatag
     1801 tttaagcgat aaaaggatga aaaatattaa aaagtagtta tctagaggat tattgaatat
     1861 atagttagtc tttattttga gttatagaag atataaccga tataacttaa gttgtaccgg
     1921 tagaaggaat tgaaaaaaat caggaacgat ttaaataatc atcagaacac gcaaaatcac
     1981 ttctgaaagg cttggaatgt gaatcggtag atgggaatag aaagcctgta agaagccgca
     2041 gcaaggcgaa ggagttttat ttagaaaagt tttttgattt gtaaaaagtt ttctaaataa
     2101 aagttgatgt cccggagggt tgctaaaaag aatagtatat caagctatcg cgttctccca
     2161 aacattgttt gggggacacc agctgtaagc gtaaggggtg tgggtcctcc cacgtgggaa
     2221 aatttttgtg tctctttttc taaaaaggac ggttttattt tgtgagagga atacgggacg
     2281 tgaaatttta ttttgtttta taaagtgtat ataaatttat aaaacaagga gttatatcgg
     2341 ttatatcgaa tataactctg tgaggtgatt gtgatggttg ttgtatatca aaccacaaaa
     2401 caggcagcac aaacattaaa tattaatcat acaactttca agaaatatta tgggatgttt
     2461 gagagatata acggatataa ctttttaaga gatttaaaag gacaggttat gtttagtgaa
     2521 tatgatttag aaatgtttaa gaggttatta ttagttaagg cggaaccagg aaggactata
     2581 gaggaatctt gtaggcttgt tggtgaagaa tttggtattt tggataagaa tcaagttata
     2641 acagatatat cttctgaaaa cgcagggtat aatcaggcga ttgaagagtt aaaggaatta
     2701 attttaatgc agaataataa gattgatgaa ttaactatta aattaaatga gcaatcaaat
     2761 caaactaagg taattgaaac aagtgttgga gatagagatc agcaattggt tagattaatg
     2821 aaagaaatgt tggaagtaaa aagaatggtt gcagcaagtg aaaagaaaaa atggtgggta
     2881 ttttggaagt gatttctatt tatcacttta ttttttttgc attttaattt aaaattaact
     2941 cagatgttga ttttatacat ctataaacac attgaatcaa cttgaaaggg tgttttttat
     3001 gacaagtaaa aaaagaattc aattaacttt aagtgaggaa agttttatta aatgtgaaga
     3061 attggctaat cgttatggta ttacacctaa ttcatttatg gcttttgtta ttggtcaatg
     3121 gcttgatcat aattatgaaa caaataaaat attagcaaaa aaagtagatg aggctttacc
     3181 agatatgaaa tctatttttg cagatcctaa tttggcatct atggtgaaaa atgtgttggg
     3241 ggatgataaa gaatttaagg atagtgttag aaaacaatta agtatttagt ttaggaggag
     3301 atataaaatg aatgatgtat taacaaaaat tcttgaaaag ttagatcaac ttgataagaa
     3361 ggtagatacg attgggagtg aagtaaggga agtaagaaaa gaaattcaag cacatcgtat
     3421 ggaaatagat gataacttta caaagttata taagttagtt gaggataaag aggttgagat
     3481 tgatctcttg aataaacgta tatttaaaaa tgaaacaaca gttgaaaaat taaagagaca
     3541 aaaacattag gatttatata taaattaaaa ttatatgtgt gtatttttaa ggaaagaaga
     3601 tatttaagga gaatgatatc ttgcaaaatg ttaaagagat aaagaaatta attaggaaga
     3661 atcctggtaa atatgcgagt atttctacag ccgaagataa tgctttagaa ggaattttat
     3721 tgagtggatt ttttgcaaaa caagttatga aattggcttc tcaatccaat catatttctc
     3781 atgattttaa ttcaaatgat cttaaatctt ctgatctaac tttaaaagga gtttttcttt
     3841 ttaatggtac tggaattgat tttgtttttt atgagggtgt tgagactata aggatttatg
     3901 attcgccaat gtttgaagag gattctaaag atatgtttga gtattttaaa gagtggttac
     3961 atgcacattc ttgatattta ctttagtaaa cgttgtaaga atgtaataaa acatatttaa
     4021 cagtttactg tgtaaatggg cactttgtgg aattgcttag aaagtttgcc ttttatggat
     4081 ttagacataa aagttgaaag attaaagaga gaaagacatt aattcttatt aagaagaggg
     4141 gatttgtttt gatgaaggaa catgtgaaac ttcagtttaa agctgagaat gtaaaagggg
     4201 aaattgaagg ttattctaat atgccttttt ggaatcatga tttgaaatta gaggttgttt
     4261 tagccttatt gaatactgtt gattataagg atttttttga atcaccaaat tataatcaat
     4321 taaatgatta tacaaagcaa ataattgaag ctatagaata tagtttaggg tttgatggat
     4381 tgtatcaatt agtgtatgga gatgtaaaaa aagattgata gaaggagtat ataagtttta
     4441 tttaactagt taatattaat aggagttaga attaagtttt tagtagattt gagtgaacga
     4501 agtgatcgag aatcttcttt acttgatact atagaaacaa ctgacggaat aaaaataacg
     4561 atgagcctta gagccacaag ggttttgttg cttttttagg gtgaacagaa tcatgaatag
     4621 aattgtacat agttgttttt aatattttat tgtatatttt ttcgtttttt gtttttgagg
     4681 aggtaatttg gttgtgtgac agctatgaaa ttctcagaga tatttcaaaa aggggaaagg
     4741 aacgaccctg gattgaacat aaatctaata gtatgttgct tagtgaatct tttagtagat
     4801 tggacaagca taataaggct gaaaatatat gtaattgtgg ttcgtttttg aaatttaata
     4861 tttgccctca gggtcatgaa aaaaggttat cgtgggcaaa tttttgtaga gttagattgt
     4921 gtcctatgtg ttcatggaga cggtcattat taattgctca tcaagtgaaa tcaatagcac
     4981 atgaagcatc tcaacaagaa aagttacgtt ggttatttct taccttaaca gttaaaaatt
     5041 gtgaaggtga gaatttgatg gatacaatta atcatttgat gaagtcattt catcgtttgt
     5101 cgaaacggaa agtttttaat gattcttcta ttcgtgggtg gtttcgagct tttgaagtaa
     5161 ctcgtaattt tcatgatgga agttatcatc ctcattttca tgtattatta gctgttaagc
     5221 caagttattt taatggaaaa tctaaaagtt atatgactac tacagaatgg ggaaagttat
     5281 ggaaatcttg cttaaaagtt gattatgatc caattgtaca tattcgtgta gtaaaaaata
     5341 atcgtaatca agaaaaagag ttgaagattt tacaaaataa aggaattcaa ttgagtaata
     5401 atggtacttt tgaattatct ggtgcggctg tggctgagat ggctaagtac tccgttaaat
     5461 ctagtgatta tttaatttat aatgaatatg aaaaaaaagg ttctaaatat attccagttg
     5521 ttgaaagtgg aattgatgaa gagacaacag atgaagtggt tcaaacttta gatgaagcat
     5581 tagcaaggag acgtttaatt gcttttggtg gattaatgaa agaagtttgg gaacgtttaa
     5641 gaatagaagg taaaatggtt gatgctgaaa gtgaagaagt taatttagtt catgttaatg
     5701 aagatactaa atgtcaatgt agtgtatgtg gatctaatat gttagaggag ctttatagtt
     5761 ggttacctga atataaaaac tacataaaaa aagaaaatat cttaaacact taggacatgg
     5821 ttaagacatt ttcaatcagt agtttgtttg actgttagtt ttatagctaa tatgtattat
     5881 acatgtaatt aataacaagg tctattgatt ttgttattta aaaaagctta tagttattta
     5941 gatttttatt tgattgaaag tctaaattat atggatggaa cttattatag agagattatt
     6001 gtttttagaa gggatataga aattatccct tctatttttt atttatttaa gccttttctt
     6061 ataagttcta gtattgttgc tgttctagta gaaagcccgt tttcttcttt atattcatca
     6121 acttttttta atattgattg tgggattctc atttctacgc gttctttttt atctgtcatt
     6181 attatcacct cttcttgtat tgtacggaaa aatgtcgtat aatacaaatt gtacgggaaa
     6241 ataacgtatt ttttacgtac aaattaaagt taaaggggat tttattatgt tagaagataa
     6301 atttttagaa tctaagattg aaaatttaac taatcaaaat gtagtagttt ttactgatga
     6361 tgagattatt aaaggtgttc ttttagataa ggagactgga gaag
//
