LOCUS       NZ_AP022955             5049 bp    DNA     circular CON 13-MAR-2024
DEFINITION  Bacillus cereus strain J39 plasmid pJ39_3, complete sequence.
ACCESSION   NZ_AP022955
VERSION     NZ_AP022955.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00203334
            Sequence Read Archive: DRR206374, DRR206398
            Assembly: GCF_021655175.1
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  JOURNAL   Unpublished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 5049)
  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                   :: 506x
            Sequencing Technology             :: MinION R9.4 Flowcell; MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_021655175.1-RS_2024_03_13
            Annotation Date                   :: 03/13/2024 06:50:43
            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)                     :: 5,874
            CDSs (total)                      :: 5,722
            Genes (coding)                    :: 5,455
            CDSs (with protein)               :: 5,455
            Genes (RNA)                       :: 152
            rRNAs                             :: 14, 14, 14 (5S, 16S, 23S)
            complete rRNAs                    :: 14, 14, 14 (5S, 16S, 23S)
            tRNAs                             :: 105
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 267
            CDSs (without protein)            :: 267
            Pseudo Genes (ambiguous residues) :: 0 of 267
            Pseudo Genes (frameshifted)       :: 140 of 267
            Pseudo Genes (incomplete)         :: 134 of 267
            Pseudo Genes (internal stop)      :: 53 of 267
            Pseudo Genes (multiple problems)  :: 54 of 267
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022955.1.
            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..5049
                     /organism="Bacillus cereus"
                     /mol_type="genomic DNA"
                     /strain="J39"
                     /isolation_source="human blood of bacteremia patient"
                     /host="Homo sapiens"
                     /db_xref="taxon:1396"
                     /plasmid="pJ39_3"
                     /geo_loc_name="Japan:Tochigi"
                     /collection_date="2006"
     gene            complement(join(4886..5049,1..175))
                     /locus_tag="L6483_RS29180"
     CDS             complement(join(4886..5049,1..175))
                     /locus_tag="L6483_RS29180"
                     /inference="COORDINATES: protein motif:HMM:NF015807.4"
                     /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="Arc family DNA-binding protein"
                     /protein_id="WP_236796014.1"
                     /translation="MSDNVNFPLRIPRELRDKFKKVSQKTGTSMNSSICQLIAEHIYKM
                     EQLGLKDIEEPNVIQVTPVKEETKAFIKKAIKEADEAKELAETKTKKRLRKSPKKKIGG
                     ETDGSKKD"
                     /name="Arc family DNA-binding protein"
     gene            complement(187..510)
                     /locus_tag="L6483_RS29185"
                     /old_locus_tag="BCJMU39_p31"
     CDS             complement(187..510)
                     /locus_tag="L6483_RS29185"
                     /old_locus_tag="BCJMU39_p31"
                     /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_236796016.1"
                     /translation="MMMNLLSLQQEANSVIQDLNGKDISSMSLIQKANYSNRIVKVRMS
                     LEAYRNTPGVNEFINALDHLRFKLAEVQQQETRQQANKRRAEIIQNGIKETPYPTMPMF
                     LNN"
                     /name="hypothetical protein"
     gene            complement(928..1773)
                     /locus_tag="L6483_RS29190"
                     /old_locus_tag="BCJMU39_p32"
     CDS             complement(928..1773)
                     /locus_tag="L6483_RS29190"
                     /old_locus_tag="BCJMU39_p32"
                     /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="replication initiation factor domain-containing
                     protein"
                     /protein_id="WP_236796018.1"
                     /translation="METDISIDRLTLVGYDTGMIEGYLKYSEYISFVGFSKNYGFRHSY
                     QGIKGELLEIGEKGKVRLDFNPNTANMEQVRDVVSRLKYIYLTRLDIAIDYFGVDLSEV
                     EWTSPKRRKQNLWLDPEGQQETRYIGAPSSERRYRIYNKKLERLEKKEELDPRAVNGQW
                     RVEVQQRFKESNNILDPIDYFTGDLFDIRPYRKVVDLSHIEKPMERIIIAGLMARPSEL
                     KNLSKNARGKYKKMIQEAREKSGVAINPEPIEVYTKEKDLLAEQLTSLFAHCAKSVAQV
                     "
                     /name="replication initiation factor domain-containing
                     protein"
     gene            complement(1976..2698)
                     /locus_tag="L6483_RS29195"
                     /old_locus_tag="BCJMU39_p33"
     CDS             complement(1976..2698)
                     /locus_tag="L6483_RS29195"
                     /old_locus_tag="BCJMU39_p33"
                     /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="helix-turn-helix domain-containing protein"
                     /protein_id="WP_236796021.1"
                     /translation="MKKAFAENYINPVVERFSELDTPNGGFYTSIPQAVQYCWFLDDKE
                     LSVLLALSTYADENGRCKVYQRTLARKVKIKSTTTLRTKLKSLVKKRFILQVNTDGESS
                     IYQIKDYSTNPYILLSEAIEKVEQVAKKKYGVSVSKIAETMDELIASKIDYMAMITKIE
                     ESFNGYDVALKSVQGYVNEALGLEMDISLQTKKPRRERGFKMSKVIKPKQPKRNREFII
                     SEGESEAPVKREGLRLRL"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(2791..2943)
                     /locus_tag="L6483_RS29200"
                     /old_locus_tag="BCJMU39_p34"
     CDS             complement(2791..2943)
                     /locus_tag="L6483_RS29200"
                     /old_locus_tag="BCJMU39_p34"
                     /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_236796023.1"
                     /translation="MPKVVSSKEKMQPKTFKLHPRTIEQIKELAEKKQMTQAEVIDKAL
                     KLLAR"
                     /name="hypothetical protein"
     gene            3812..3958
                     /locus_tag="L6483_RS29205"
                     /old_locus_tag="BCJMU39_p35"
     CDS             3812..3958
                     /locus_tag="L6483_RS29205"
                     /old_locus_tag="BCJMU39_p35"
                     /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_236796009.1"
                     /translation="MKKTKKQAKKQPKKQPKKQMKTAMKIVGITKDVVNFVGNLIRIYT
                     FFF"
                     /name="hypothetical protein"
     gene            complement(3982..4182)
                     /locus_tag="L6483_RS29210"
                     /old_locus_tag="BCJMU39_p36"
     CDS             complement(3982..4182)
                     /locus_tag="L6483_RS29210"
                     /old_locus_tag="BCJMU39_p36"
                     /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_236796011.1"
                     /translation="MDIEAKKEAFVTFLVEKVLFQTFAERTTSLEEKEVYEKFIKLYDQ
                     ELNRLNFELTIASVNRKRANL"
                     /name="hypothetical protein"
     gene            complement(4666..4905)
                     /locus_tag="L6483_RS29215"
                     /old_locus_tag="BCJMU39_p37"
     CDS             complement(4666..4905)
                     /locus_tag="L6483_RS29215"
                     /old_locus_tag="BCJMU39_p37"
                     /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_236796012.1"
                     /translation="MEVKKIKIKPKKIVRNEENHKLEFDKVRLSIEIPISIRDNFKEAV
                     EKNGKTMKEVLEAYMQRYSVKELLTDLKEETIDN"
                     /name="hypothetical protein"
ORIGIN
        1 ttacattagg ttcttctata tccttcaatc ctaattgctc cattttataa atgtgttccg
       61 ctattagttg gcaaattgat gagttcatac tcgtcccagt cttctgtgaa acctttttaa
      121 acttatcccg caattcacga ggtattctca atggaaaatt aacattatcg ctcatatcct
      181 atcctcctaa ttatttagaa acattggcat cgttgggtac ggtgtttctt ttattccatt
      241 ttgaattatt tcagctcttc ttttattagc ctgttgtcgt gtttcctgtt gttgtacttc
      301 agctaactta aatcttaagt ggtccaatgc atttataaat tcatttactc ccggagtatt
      361 tctatatgcc tcaaggctca ttctaacttt cactattcga ttagaataat tagccttctg
      421 gatcaaactc attgaagaaa tatccttacc gtttaaatct tgaatcacac tgttagcttc
      481 ctgttgtaaa cttaacaaat tcatcatcat aatattttcc ctcttttctg ttgtgataat
      541 caatacgact attaaattga ttatcaatat gatagtcatt tataaaaaca tcgtaactct
      601 taaccaaaaa tctgtatact gggttactta aaaaatttaa aatttatttt taaattgtca
      661 ccttacctat ataaaaatta acaaaatcga gagggtgtag gagcgcattt tcagatacag
      721 aacctaataa gcggtgggtg gggtgttttt caaacaatag cctaaataga caactattaa
      781 tcctaaagca cgagctaacg caataaactt aaaggaaata catatattct taacgaatcc
      841 ccttaaaaca aagaaaaaga gaggtgaatt ccctctcttc ttttgctata ctaacattag
      901 atatttactt gttataagtt ttaaagttta cacttgtgct acgctcttag cacagtgggc
      961 gaacaggctt gttagttgct cagctaacaa gtctttttct tttgtataaa cttctattgg
     1021 ttcaggattt atcgctacac cgcttttttc cctagcctct tgtatcatct tcttatactt
     1081 acctctagcg ttcttactaa gattcttaag ttcactaggt cttgccatta atcccgctat
     1141 tataattcgt tccataggct tttctatatg agataaatca accacctttc gatatggtct
     1201 aatatcgaat agatcacctg taaaataatc aatagggtct aatatgttat tggactcttt
     1261 aaaacgttgt tgtacctcaa cacgccactg tccattaact gctctagggt ctaactcttc
     1321 tttcttttct aaccgttcta acttcttgtt ataaatacga taccttctct cacttgatgg
     1381 cgcacctatg tatctcgttt cttgttgccc ttctgggtct aaccataagt tttgttttct
     1441 tcgtttaggg cttgtccact caacctcaga taaatctaca ccaaaataat ctatcgctat
     1501 atctaatcgc gttaaataga tgtatttcag tcgagaaacg acgtctctta cctgctccat
     1561 atttgcggta ttagggttaa aatctaaacg taccttccct ttctcgccta tctcaagcaa
     1621 ttctcctttt atcccttggt atgaatgacg aaaaccataa ttcttagaaa accccacgaa
     1681 tgaaatatat tccgagtatt taagataccc ttctatcatt ccagtatcgt atccaacgag
     1741 agttaggcgg tctatactaa tatctgtttc catcctaaac actcatttcc gttttatttg
     1801 ctatcttagt atgcttcagt aatttctttg atagatatat atattaattt ctttttagta
     1861 ttttatattt agtagtaatc aaattttgat taagaggtac acaaaaattg tgtaaggggt
     1921 aatcaatttt tgactaggta ttcaagtcct ataaggtaat atataattac cttattcaaa
     1981 gtcgtaatct aagaccttcc cgtttcacag gagcttcaga ttcaccctct gaaataataa
     2041 attctctgtt acgtttaggt tgcttaggtt taataacttt actcatctta aaacctcgtt
     2101 cccgtcgagg ttttttcgtt tgtaaagaaa tatccatttc taatcctaaa gcctcattta
     2161 cataaccttg tacagatttt aaagctacat cataaccatt aaaactttcc tctatcttag
     2221 ttatcatagc catataatct atcttactag caattaattc atccatcgtt tcagctattt
     2281 tagatactga aacaccatat ttctttttag ctacctgttc gactttttca atagcctcac
     2341 taagaagaat ataaggattg gtagaataat ctttaatctg ataaatacta gattctccat
     2401 ctgtattaac ctgcaatata aaacgcttct tcactaaact tttcaattta gttcgtaatg
     2461 ttgttgtact tttaatctta actttcctag ctaacgttcg ttgatatacc ttgcaacgtc
     2521 cattttcgtc tgcataggtc gatagtgcta ataatacact taactcttta tcatctaaaa
     2581 accaacagta ttgaactgct tgtggaatgg aagtatagaa accgccattt ggagtatcta
     2641 attcactaaa acgttccaca acaggattaa tataattctc tgcaaatgcc tttttcatta
     2701 cagatcacct tttcctttta attttccctc cttgttatct tgtttgctat gttagtatgc
     2761 tacgttattt gcgatgggat atatattttt ttatcgtgct aataacttta acgccttatc
     2821 aatcacttca gcttgcgtca tttgcttctt ttcagctaat tcctttattt gttcaatcgt
     2881 cctaggatgc aatttaaatg ttttgggttg catcttttcc ttagaactaa ctactttcgg
     2941 cataatatca ctcctcaaca caatgatagg tactccctaa aaacagctta acatcaacga
     3001 ttctatttgt ccacttcaaa aacagtcaaa aaacacataa aaaaatagaa caaactaata
     3061 aggacatttt tttgatcaaa aaagaaagga gaaaacctaa aacaaaaaac attttgatat
     3121 ggtgaatccc tcgaaagagg acgctaaccc gctgttagag aagcgggttt ttcgacgtgt
     3181 cgaacatccc tatagttata aaaaatcaga gcaagaacta gaatacatag ttcttaatca
     3241 tccgaacaaa acccaaactt tttgggagac tattttcaaa tgaaaaatcg ttattgtttt
     3301 gtatagaaag agtaatggca cttttgagct actatttggg ctactaaatt agataccttt
     3361 ttcaatcttt atccaagata cacttttcta tagaggataa tctcgataaa aagacggata
     3421 aatcacggat aaattaagga taaagagaag gataaatact atgaagaaaa gctctaaaat
     3481 ttaactaaga aaagaatcac accaacacga acaatataat gtgcctatct ctttgaagaa
     3541 aaaaactctt aatacaaatc tctcaaaaag tgtcacaaaa catagatgaa aagacgaata
     3601 gaaaactagg aggtgttatt ccattgacaa tccaaattga tatttttact caagttttat
     3661 acatatagca aaccaaaaaa ccttagtatc tgcgcctatg tttataaaag aaattttttt
     3721 gaaaaagaat aaaaaaaata aggatttctc aaaaaacgtc acaagtaata gatagcaaga
     3781 cgaacaacta ctaaataggg ggaattaatt tatgaagaaa actaaaaaac aagcaaaaaa
     3841 acaacctaag aaacaaccta agaaacaaat gaagacagca atgaaaatag tcggaataac
     3901 aaaagacgtg gtcaattttg ttggaaatct aatccgaatt tatacattct tcttctaaac
     3961 aaaaagagct aatctataac attataggtt ggctcttttt ctatttacag atgctattgt
     4021 caattcgaaa tttagtctat ttaattcttg atcatatagc ttaataaact tttcatacac
     4081 ctctttttct tctaaagaag tagtcctttc tgcaaatgtt tgaaatagaa ctttctctac
     4141 aaggaaggtc acaaatgctt ctttcttagc ttctatatcc ataacttact tcctccaata
     4201 agcggaattc aatcattgac aacgagcctc cagtccgtgg gtcataagcc aatgccccac
     4261 tccttcaact cgctaacgct caaacaagga ttggcaagcc ataacaggct accacggaca
     4321 ttctcattgt aaatgaaccg ctacgctttg attccttagt ggtcttccct aatcttcgct
     4381 aatactcgat gaaaaccaat taatttaacc cttaattctt cgccaatcct cgttaaacct
     4441 cgccatttct tccctaaaaa ccgacatacc gtaaaccgca aagactatgc cctcacatga
     4501 atgcctcctg gttcaccact atcttaggaa gaatacttat agttgtttag cgtaaattta
     4561 gcgatatttt tattgatagg tcgtgttttt tctactttta ccaactataa aatttaagcc
     4621 ttaaaaatgt acatgtattc aaggtttaaa cgaggtattc agattctaat tatctattgt
     4681 ttcttctttt aaatccgtta atagctcttt aacactatac ctttgcatat atgcttctaa
     4741 tacttccttc atcgtcttcc cgttcttttc taccgcttct ttaaagttat ctctaataga
     4801 aatagggatt tcaatgctta atcttacctt atcaaattct aatttatgat tttcttcatt
     4861 acgcactatt tttttaggtt tgatcttaat cttttttact tccatctgtt tcaccgccta
     4921 ttttcttctt gggcgacttt cttaatcttt ttttcgtctt agtttcagct aattccttag
     4981 cttcatcagc ttcttttata gccttcttta taaacgcctt tgtttcttct ttaaccggcg
     5041 taacttgaa
//
