LOCUS       NZ_AP026681             3428 bp    DNA     circular CON 06-JUN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Oranienburg strain 11548
            plasmid pSO11548-1, complete sequence.
ACCESSION   NZ_AP026681
VERSION     NZ_AP026681.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00280083
            Sequence Read Archive: DRR278176, DRR397993
            Assembly: GCF_027943865.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Oranienburg
  ORGANISM  Salmonella enterica subsp. enterica serovar Oranienburg
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1
  AUTHORS   Ooka,T., Gotoh,Y., Hatanaka,S., Yoshimori,M., Nishitarumizu,K.,
            Kojo,K., Kosakamoto,H., Sameshima,K., Kuroki,Y., Chibana,N., Doi,Y.,
            Yoshino,S., Harada,T., Seto,K., Ikeda,T., Miyanohara,H.,
            Nakayama,K., Gokuden,M., Imuta,N., Kawamura,H., Ogura,Y., Hayashi,T.
            and Nishi,J.
  TITLE     A Salmonella enterica serovar Oranienburg clone caused a cluster of
            bacteremia cases in persons with no recognizable underlying diseases
            in Japan
  JOURNAL   Open Forum Infect Dis ofac695 (2022)
  REMARK    DOI:10.1093/ofid/ofac695 Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3428)
  AUTHORS   Ooka,T., Gotoh,Y., Hatanaka,N., Yoshimori,M., Nishitarumizu,K.,
            Kojo,K., Kosakamoto,H., Sameshima,K., Kuroki,Y., Chibana,N., Doi,Y.,
            Yoshino,S., Harada,T., Seto,K., Ikeda,T., Miyanohara,H.,
            Nakayama,K., Gokuden,M., Kawamura,H., Imuta,N., Ogura,Y., Hayashi,T.
            and Nishi,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-AUG-2022) Contact:Tadasuke Ooka Kagoshima University,
            Department of Microbiology; Sakuragaoka 8-35-1, Kagoshima, Kagoshima
            890-8544, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Coverage                   :: 50x
            Sequencing Technology             :: Illumina MiSeq; Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_027943865.1-RS_2024_06_06
            Annotation Date                   :: 06/06/2024 03:09:59
            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)                     :: 4,556
            CDSs (total)                      :: 4,436
            Genes (coding)                    :: 4,317
            CDSs (with protein)               :: 4,317
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 119
            CDSs (without protein)            :: 119
            Pseudo Genes (ambiguous residues) :: 0 of 119
            Pseudo Genes (frameshifted)       :: 59 of 119
            Pseudo Genes (incomplete)         :: 79 of 119
            Pseudo Genes (internal stop)      :: 26 of 119
            Pseudo Genes (multiple problems)  :: 39 of 119
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP026681.1.
            Annotated by DFAST https://dfast.ddbj.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..3428
                     /organism="Salmonella enterica subsp. enterica serovar
                     Oranienburg"
                     /mol_type="genomic DNA"
                     /strain="11548"
                     /serovar="Oranienburg"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:28147"
                     /plasmid="pSO11548-1"
                     /geo_loc_name="Japan"
                     /collection_date="2018"
     gene            563..>658
                     /locus_tag="QMM99_RS22730"
                     /pseudo=""
     CDS             563..>658
                     /locus_tag="QMM99_RS22730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /name="plasmid mobilization relaxosome protein MobC"
     gene            complement(1223..1411)
                     /locus_tag="QMM99_RS22735"
                     /old_locus_tag="SO02S_43500"
     CDS             complement(1223..1411)
                     /locus_tag="QMM99_RS22735"
                     /old_locus_tag="SO02S_43500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_024157493.1"
                     /translation="MNRQESAVLNIAKFIRAQTLLLLERIDLLDFDDEATDCEQLHEQA
                     EALYRKLSARLESDITA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1603..1866)
                     /locus_tag="QMM99_RS22740"
     CDS             complement(1603..1866)
                     /locus_tag="QMM99_RS22740"
                     /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_138627904.1"
                     /translation="MPLEQAAFLFSGVGGMLLTEMEISNTRNITLIARRLAWINAKRTH
                     IDIPSFAELLFSGQKALFFEQYNYFHSRRYTTAGTSKPPDLP"
                     /name="hypothetical protein"
     gene            complement(2405..3102)
                     /locus_tag="QMM99_RS22745"
     CDS             complement(join(2405..2853,2853..3102))
                     /locus_tag="QMM99_RS22745"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558153.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
                     /protein_id="WP_094106546.1"
                     /translation="MASISIRCPSCSATEGVVRNGKSTAGHQRYLCSHCRKTWQLQFTY
                     TASQPGTHQKIIDMAMNGVGCRASARIMGVGLNTVLRHFKKLRPQSVTSRIQPGSDVIV
                     CAEMDEQWGYVGAKSRQRWLFYAYDRIRRTVVAHVFGERTLATLERLLSLLSAFEVVVW
                     MTDGWPLYESRLKGKLHVISKRYTQRIERHNLNLRQHLARLGRKSLSFSKSVELHDKVI
                     GHYLNIKHYQ"
                     /name="IS1 family transposase"
     Typing          373..457
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.954"
                     /coverage="100.0"
                     /evalue="1.43e-25"
ORIGIN
        1 tcctgccgga gtccggggcg tagacctgag agtcaaggtg cagatatggg tttaatgtcg
       61 ttgaatggta ttaagctggt agtgacattc ctagccagcc ctgctaggat ttgattgcgg
      121 tctgatccga gcaggtatct gcacgaatta gagtactcaa gccctgtgat tctgtcacgg
      181 ggcttttgta catctagagc cagaaaaatc attatcactc agtcagatca ccgcaacgcc
      241 cgccacagct tcatgaccga acgtagtgag cgaatgagcg aggaggcgtc attttcaccg
      301 tccgcccatc attctgctta tgcttcgaag ccgcattttc ctctgccaca tagcccgatt
      361 tctgtcaatt tccgcacagt gttaaaatag ataagccagt atacactccg ctagcgctat
      421 gtgactggtt cagggctgcg ccccgaaacc cgccaaaagc ctgacgcgcc tgcggcttgt
      481 ccaaccccgc gccgaccggg aaagggtttc ccgcccgtca cggcgttatc aggagactgg
      541 tttgtccgag aaacggaaca agatactcac catgtgggtg acggaggatg agtaccggct
      601 actgctggaa cgctgcgggg gtacacagct ttctgcatgg gtgcgcccgt ctgctatgtc
      661 tgttcctcct agttttggtg ggtgcttata tctctgctca atggcataac atgtcactat
      721 taaccgcgat gctaaagcgg gctgtttttc acagtattac cggctcccgt gccggttttt
      781 tttcttaccg gaagggactt cgtgtttatt gatgttctga ttttcggagg gtgtactgat
      841 cgccttgcaa gggacacgat gaggattgta gcccgcgagg aaggaaagac ttacgacgag
      901 gtactttctg acatcaggga aggtggggca gatgagctga cccagataca tttctggcgt
      961 gtcgttagtg cattatatcc cggggcattt aaccgtattg attacctctc tgagtctcgg
     1021 aaataccgtc tctggttatc ctgattttta atctcgtcac tgcttgctta cagttccagt
     1081 ctgtattgtc tgcatttttc tttcatactg agtgcctcac gacccgtaat aaattccgtg
     1141 tccgttcatc cttgagcgac gactggagga tgaagatctc tcaaaagatg atgtggatgc
     1201 catgatgcag gcgacggaaa ggctaagccg ttatgtctga ttccagtcgg gcgctgagct
     1261 tccggtaaag cgcttcggcc tgctcatgca gctgttcgca gtctgtcgct tcgtcatcga
     1321 agtcgagcag gtcaattctt tccagcagga ggagtgtctg ggcgcggata aatttagcta
     1381 tgttgagaac ggcggattcc tggcggttca tgtgtgtttt cctgtgtctt gtgatgattt
     1441 tgatgtgaaa acaggatgcc gtcattctgg tgcatagtca tgcatggcgt taaaatttac
     1501 ctggcacgtt tctggcggct tttcgggtgg tttgttacct gttttaccgt accgccgtca
     1561 gaaacgccct gagggcgcct gaggcggtgc gggcaacgga tgttatggta aatccggtgg
     1621 ctttgacgtg cctgccgttg tgtaccgtcg tgagtgaaaa taattatatt gttcgaagaa
     1681 cagcgctttt tggccggaga aaagcagttc tgcaaacgat ggtatatcga tatgagttct
     1741 tttggcatta atccaggcaa gacgccgggc aataagcgta atattccggg tgttacttat
     1801 ttccatttct gtcaacagca tcccccccac gccggagaat aaaaaagccg cctgttccag
     1861 cggcaagccc tacatcaagg gaaactacgt cttacgattc gttttgaacc gggacgcttt
     1921 gttgctgcga atcactaacc agataatcca cgttttgtga gtgggtttag gttaaggctt
     1981 caatagaaca ataataacgt taagtgatta gggcaacctg tgattgctaa aatgatgaag
     2041 tcttcacatc atttcggtga aggcgatatg tgttacacca cgtattgaga gacctgcatg
     2101 ccctttacag gtgaacggga acgggaatag agcggcgatt tagccagaga tgggtttcat
     2161 aacactgtaa ttcatatcac aattattata actggcggta tttttttaac ctttgcaatt
     2221 cgttttatct gatgtttatg ataattttca aaaagttggc cccctgacat caccgggagc
     2281 caaaaaaaat acaccagtta ttattgtggc tatattattt catgagtaaa caaatatgtc
     2341 aggcgtatat ttgtttactc aaattgcttg ttttttagtc atcgtgatgg gtaatgactc
     2401 caacttactg atagtgtttt atgttcagat aatgcccgat gaccttgtca tgcagctcca
     2461 ccgattttga gaacgacagt gacttccgtc ccagccttgc cagatgttgt ctcagattca
     2521 ggttatgtcg ctcaatgcgc tgcgtatatc gcttgctgat aacgtgcagc tttcccttca
     2581 ggcgtgattc atacagcggc cagccatccg tcatccatac cacgacctca aaggccgaca
     2641 gcaggctcag aagacgctcc agtgtggcca gagtgcgttc accgaagacg tgcgccacaa
     2701 ccgtcctccg tatcctgtca tacgcgtaaa acagccagcg ctgacgtgat ttagcaccga
     2761 cgtagcccca ctgttcgtcc atttcagcgc agacaatcac atcactgccc ggttgtatgc
     2821 gcgaggttac cgactgcggc ctgagttttt taagtgacgt aaaaccgtgt tgaggccaac
     2881 gcccataatg cgtgcactgg cgcgacatcc gacgccattc atggccatat caatgatttt
     2941 ctggtgcgta ccgggctgag aggcggtgta agtgaactgt agttgccatg ttttacggca
     3001 atgagagcag agatagcgct gatgtccggc agtgcttttg ccgttacgca ccacgccttc
     3061 agtagcggag caggaaggac atctgatgga aatggaagcc acgcaagcac cttaaaatca
     3121 ccatcataca ctaaatcagt aagttggcag cattacccgg atttgagagt cgcaaaccca
     3181 tattagggca aagaaagcct aatgcccccg tggtgggtac accagaaaac ggggagcgaa
     3241 gcgaccagca tcaggccgtt cgtatgctgc ttcgattttg tgggtgttgc gccagacctt
     3301 ggcaatcacg cttcaccgca accgctgcct tcactctcac tttatcaggt acgttattgg
     3361 ttaacgtgag accgggtaga gccagcttct ttcccgagct ggtcaggttc ccaccgcttg
     3421 cctgttta
//
