LOCUS       NZ_AP026682             2495 bp    DNA     circular CON 06-JUN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Oranienburg strain 11548
            plasmid pSO11548-2, complete sequence.
ACCESSION   NZ_AP026682
VERSION     NZ_AP026682.1
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 2495)
  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
            AP026682.1.
            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..2495
                     /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="pSO11548-2"
                     /geo_loc_name="Japan"
                     /collection_date="2018"
     gene            complement(87..278)
                     /locus_tag="QMM99_RS22750"
                     /old_locus_tag="SO02S_43530"
     CDS             complement(87..278)
                     /locus_tag="QMM99_RS22750"
                     /old_locus_tag="SO02S_43530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001046776.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_021243041.1"
                     /translation="MTLSDDERHLLVSVVSVWLRRAGGDAGAMMLDAYRQILSETEPAV
                     RTVMLEFLESVRIHYISS"
                     /name="hypothetical protein"
     gene            1513..1740
                     /locus_tag="QMM99_RS22755"
                     /old_locus_tag="SO02S_43540"
     CDS             1513..1740
                     /locus_tag="QMM99_RS22755"
                     /old_locus_tag="SO02S_43540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010615788.1"
                     /GO_component="GO:0005886 - plasma membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YgdI/YgdR family lipoprotein"
                     /protein_id="WP_021243043.1"
                     /translation="MKKIFVSVFAAAVALSALTGCTRTSYAIHTNDGRTIVSDGKPKES
                     DSGLLGYTDANGVKQQINKTDVKEVSEIPH"
                     /name="YgdI/YgdR family lipoprotein"
     gene            2106..2291
                     /locus_tag="QMM99_RS22760"
                     /old_locus_tag="SO02S_43550"
     CDS             2106..2291
                     /locus_tag="QMM99_RS22760"
                     /old_locus_tag="SO02S_43550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /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_013772937.1"
                     /translation="MTRQESAALNMAKFIRAQTLLLLERLEQMDLDEAAGCCEHLHDQA
                     EALYAMLNAQIGEENA"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(2339..2426)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.86e-39"
     Typing          570..1098
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.598"
                     /coverage="88.0"
                     /evalue="0.0"
ORIGIN
        1 cactcgtcca taacagcatc atggaacgac gaccaccgtc cgtgacggcc gcctcgttta
       61 agtatggaca gaaatacaga aaatgctcag gacgaaatgt aatgaatgcg aacggattca
      121 agaaattcga gcatgacagt ccttacggcc ggttcggttt cagacaaaat ctgccggtat
      181 gcatccagca tcatggctcc ggcatcccct ccggcacgcc gtagccagac cgaaacaacg
      241 gacacaagca ggtgtcgctc atcatcacta agagtcatca gggctccgga agaaaaacca
      301 aacatggctt acctactgtt aacggcaacg cagaagaaag gtttacaggg tagcgggcag
      361 ggatgaaaaa aaaaaaattg cagtcaggcc ggaacggctg ctgaaccggt acaggcgggt
      421 tccgggcgca gcgccggacc agtcacggag cactagcgga gtgtatactg gcttaagatg
      481 tagcatggca gtaacacata gcattaatgc cacataagac aggcgcagaa agtgaaagaa
      541 aacgcgtcag gagaaaatgt gatacagaat atattccgct tcctcgctca ctgactcgct
      601 ccgctcggtc gttcggctgc ggcgagcggg acgggcttac ggatggatca gaaatttcct
      661 gggggatgcc aggaagatac ttaacgaaga aagcataagg ccgcgccaaa gccgtttttc
      721 cataggctcc gcccccctga caagcatcac agaatctgac gctcaaatca gtggtggcga
      781 aacccgatgc ggcttaaaga taccaggcgt ttccccctgg tggctccctc gtgctccccc
      841 gcattcctgc ctttcggttt accggtgtca ctccgctgtt atggccgcgg tttctcattc
      901 cacgcctgac actcagttcc gggaaggcag ttcgctccag gatggactgt atgcacgaac
      961 cccccgttca gtccgaccgc tgcgccttat ccggtaacta tcaacttgag tccaacccgg
     1021 aaagacacga ctaatcgcca ttggcaacgg ccattggcaa acaggatgtg cgagagatgt
     1081 ctcaagagtt cttgaagtgg cggccttagt gaggctacac tgaaaggaca aatttggtga
     1141 catgtctcgc acaagactgt taccacggtt aggggatctg ccaggattac ctaaccttcg
     1201 aaaaaccacc tgccagggtg gttttttcgt ttacagggca agagattacg cgcggaaaaa
     1261 aaggatctca agaagatcct ttataaatta gacatccaac ctcacaaaga ggaatactta
     1321 aatcatcttg gtatatgtat cggccggatt acatctcata taagcctcct ccccgcctga
     1381 caccacactt tgaccatagc acctcgcgcc taactcgata tacagcccac catcaagcct
     1441 cttttcacat aaaaaatgac ctatagttag atggttagtg accaaaactg atatggataa
     1501 aaggagctgg ctttgaaaaa gatttttgtt tcagtgttcg cagcggcagt tgcgctttca
     1561 gccctcaccg gctgcacgcg cacaagctat gccatacaca ccaatgacgg tcgcactatt
     1621 gtcagcgacg gcaaacctaa agaatcagac tcaggcctgc ttggctatac agacgcgaat
     1681 ggtgtcaaac agcagatcaa taaaaccgac gttaaagaag tctccgaaat tccgcactga
     1741 gcatcttctc cgaaaaaggc cgctaatgtg gcctttttct ttacctgtgg ttctccgcca
     1801 aaatcccagc aaattgcatc accaaagcta aaagctttca gggttgtcta aaaagcacaa
     1861 gacataagag gaagtgcggt attttataat caagccccca agaatttacc ataacatccg
     1921 ttgcccgcac cgcctgagac gcgttcagcg cgttcctgac gaaaccatga caaaaaccac
     1981 aacaaaccac cccggaaccc gtcagaaacg cgcctgttaa attttaacgg catgcatgac
     2041 tatgcaccag aatgacgcca tgctcttttc acgcaaaaat catcaccaga cggggaaaat
     2101 caccagtgac cagacaggaa tccgccgccc tcaatatggc caaatttatc cgcgcacaga
     2161 cacttctcct ccttgagcgg ctcgagcaga tggatctgga tgaggctgcc ggctgctgtg
     2221 agcacctgca cgatcaggcc gaagcgcttt acgccatgct gaacgcacag ataggcgagg
     2281 aaaatgcgtg aaaatcggtg aacgggtgcg caattcagtg cgcggccgtg aggcgatggc
     2341 ggggtgtcgg ggcgcagccc tgaccagggt atttgtgatg ccggcgcgtg cgcggtatta
     2401 caaatgcaca tcctgtcccg gaacggacac cgggaaacag caaaaaaaac cgggcggcac
     2461 gcccggaact caatcaagtt agattagatt actct
//
