LOCUS       NZ_CP117186             2525 bp    DNA     circular CON 23-MAR-2024
DEFINITION  Salmonella enterica subsp. enterica strain 123 plasmid p123_2,
            complete sequence.
ACCESSION   NZ_CP117186
VERSION     NZ_CP117186.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33038040
            Assembly: GCF_028596085.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica
  ORGANISM  Salmonella enterica subsp. enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 2525)
  AUTHORS   Bao,D.
  TITLE     Genomic characteristics of a Salmonella enterica isolate
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2525)
  AUTHORS   Bao,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-FEB-2023) Department of Clinical laboratory, Sir Run
            Run Shaw Hospital, School of Medicine, Zhejiang University, 3
            Qingchun East Road, Hangzhou, Zhejiang 310016, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Oxford Nanopore GridION; Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_028596085.1-RS_2024_03_23
            Annotation Date                   :: 03/23/2024 03:23:07
            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)                     :: 5,054
            CDSs (total)                      :: 4,931
            Genes (coding)                    :: 4,804
            CDSs (with protein)               :: 4,804
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 127
            CDSs (without protein)            :: 127
            Pseudo Genes (ambiguous residues) :: 0 of 127
            Pseudo Genes (frameshifted)       :: 39 of 127
            Pseudo Genes (incomplete)         :: 101 of 127
            Pseudo Genes (internal stop)      :: 19 of 127
            Pseudo Genes (multiple problems)  :: 30 of 127
            Pseudo Genes (short protein)      :: 1 of 127
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP117186.1.
            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..2525
                     /organism="Salmonella enterica subsp. enterica"
                     /mol_type="genomic DNA"
                     /strain="123"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:59201"
                     /plasmid="p123_2"
                     /geo_loc_name="China: Sanmen"
                     /collection_date="2019"
                     /collected_by="Danni Bao"
     gene            complement(446..991)
                     /locus_tag="PQ453_RS25230"
                     /old_locus_tag="PQ453_25230"
     CDS             complement(446..991)
                     /locus_tag="PQ453_RS25230"
                     /old_locus_tag="PQ453_25230"
                     /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="SHOCT domain-containing protein"
                     /protein_id="WP_257260733.1"
                     /translation="MRERYLNKISNFDTARIVLFIAIQIISCIFMFWGAIPALIVFFSY
                     LAMRKECNLKPIEKSKVYISVYMLLTAALVLFLFVYKAGMFRRGGDYFPLVFVFILLYV
                     YHLAFHKLWLRTIDENSSIIIENGIFNFNRKNASVGFSRKDVNNIDTLLKLNEARKEGI
                     ISEDEFNKLKKRLNILND"
                     /name="SHOCT domain-containing protein"
     gene            complement(1881..2030)
                     /locus_tag="PQ453_RS25235"
                     /old_locus_tag="PQ453_25235"
     CDS             complement(1881..2030)
                     /locus_tag="PQ453_RS25235"
                     /old_locus_tag="PQ453_25235"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_220537805.1"
                     /translation="MPSEYDEQRGSTDTQLPGEYDLFDLMEKVTEEILHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     Typing          complement(2066..2239)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.714"
                     /coverage="100.0"
                     /evalue="1.2e-79"
     Typing          2..365
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="82.785"
                     /coverage="94.0"
                     /evalue="1.13e-84"
     Typing          2340..2525
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.617"
                     /coverage="86.0"
                     /evalue="1.5500000000000002e-72"
ORIGIN
        1 tgttatggcc gcgtttgtct cattccacgc ctgacactca gttccgggta ggcagttcgc
       61 tccaagctgg actgtatgca cgaacccccc gttcagtccg accgctgcgc cttatccggt
      121 aactatcgtc ttgagtccaa cccggaaaga catgcaaaag caccactggc agcagccact
      181 ggtaattgat ttagaggagt tagtcttgaa gtcatgcgcc ggttaaggct aaactgaaag
      241 gacaagtttt ggtgactgcg ctcctccaag ccagttaccg cggttcaaaa gagcgtcaac
      301 tcttgcgaac cttcgaaaaa ccaccttgcc gggtggtttt ttcgtttgca gggaagaaga
      361 ttacgacgat aaaaaatcaa tgacaagaag atattcaatc ttatcaaaga ttcataagct
      421 tgctttacct ttagttagca aaaaatcagt cgttaagaat atttagtctt ttttttaatt
      481 tattaaactc atcttcactt ataatacctt cttttctagc ctcgtttaat ttaagaagag
      541 tgtcaatgtt atttacatct ttccgactaa atcctacaga tgcattttta cgattaaaat
      601 taaaaatccc gttttcaatt attattgatg agttttcatc tatcgttcgc aaccataatt
      661 tatgaaaagc gagatggtaa acataaagca aaataaaaac aaaaacgaga gggaaataat
      721 caccgcccct tctaaacatg ccagctttat acacgaaaag aaacagcacc aaagcggctg
      781 taagaagcat gtaaacggat atgtaaacct tagacttctc tatcggcttt aaattacatt
      841 ccttcctcat ggctaaatat gagaaaaaaa caatcaaggc aggaatagcc ccccagaaca
      901 taaaaataca agagataatt tgaatggcta taaacaacac tattcttgcc gtatcaaaat
      961 tagatatttt atttaaatac cgttcgcgca taaatcacca ccattcaatc atagttaatt
     1021 aatttaaaat caatcgcctg atattaatat tatttcaaaa aacagaaaag cagtaactaa
     1081 atatggggca tttaccataa caccccttgc gtgcaccgcc tgagaggctc tgagggcgtt
     1141 tctgacggga aaccggtaaa acaggcaaca aaccacccga aaacccgcca gaaacgcgca
     1201 ggctctgttt ttacggcatg catgagtatg cgcgcaagtg catagcgcgg aaattcacac
     1261 cattcagcca ggggaagtcc tgtttccggc attcttccca tccgaaaacg gtgaacgggg
     1321 acgcaattta ttgcgtggcc gtgaagcgtt gccggcgcag ccggaaaacc cgctgtcagc
     1381 acgttcagga aggggggggt gtacaaatgg cacagaggat gaaagtgacg tatgagctga
     1441 aggaatgatg taaaagtgat gtacaaatga tgtaaaagtg atgcaaaagt gttgtaaaag
     1501 tgatgtacag accgaaggag tgttgtaaaa gtgttgtaaa agtgatgtat gaactgaagg
     1561 agcgatgtaa ttctgtagtc aggaagaata acccgttcat gcaggcatga acgatacagt
     1621 gaggaacgct ttttttgtca cgatctcccc ttaacctgcg taaatcaccc tccatggttg
     1681 attatttttc aacctcaaaa tggtcataca ccatacgcaa ccgcgatttt catcgcaatt
     1741 gcatgaatta aaaggtaaaa actgaatttc ccgtttattt atgtaatacg caacgtatta
     1801 caaccacctg taatcatatg aaaataaaga aataagatgt aataccggcg tattaccacg
     1861 tacgcgggca agcgaaaaag ctataacgct tcccggccga caggcggccc agaatccaca
     1921 ggggcatgca ggatctcttc agtaaccttc tccattaaat caaaaaggtc atattcgccg
     1981 ggaagctgcg tatcagtcga accccgttgt tcatcatatt cagatggcat ggggtgatat
     2041 ccagtagcag agaggttgtt agcgggtttc agggcgcagc cctgaaccag tcacgtagcg
     2101 ctagcggagt gtatactggc ttactatgtt ggcactgatg aggatgtcag tgaagtgctt
     2161 catgtggcag gagaaaaaag gctgcaccgg tgcgtcagca gaatatgtga tacaggatat
     2221 attccgcttc ctcgctcact gactcgctac gctcggttgt tcggctgcgg cgagcggtac
     2281 cggcttacaa atggggcgga aatttccggg tagatgccag gagcgaactt aacagggaaa
     2341 cgagaaggcc gcggcgctgc cgtttttcca taggctccgc ccccctgaca agcatcacga
     2401 aatctgacgc tcaaatcagt ggcggcgaaa cccgacagga ctataaagat accaggcgtt
     2461 tccccctggc ggctccctcg tgcgctctcc tgttcctgcc tttcggttta ccggtgtcat
     2521 tccgc
//
