LOCUS       NZ_CP117187             2317 bp    DNA     circular CON 23-MAR-2024
DEFINITION  Salmonella enterica subsp. enterica strain 123 plasmid p123_3,
            complete sequence.
ACCESSION   NZ_CP117187
VERSION     NZ_CP117187.1
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 2317)
  AUTHORS   Bao,D.
  TITLE     Genomic characteristics of a Salmonella enterica isolate
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2317)
  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
            CP117187.1.
            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..2317
                     /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_3"
                     /geo_loc_name="China: Sanmen"
                     /collection_date="2019"
                     /collected_by="Danni Bao"
     gene            760..996
                     /locus_tag="PQ453_RS25240"
                     /old_locus_tag="PQ453_25240"
     CDS             760..996
                     /locus_tag="PQ453_RS25240"
                     /old_locus_tag="PQ453_25240"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676031.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_016947370.1"
                     /translation="MKRLINLTPAEKRFLDDAVAAAERASGKKLNQPNRHIVLNRARAQ
                     IESQRQAERQRSAREEERQQAEFTWSRPRAPRR"
                     /name="hypothetical protein"
     gene            1285..1821
                     /locus_tag="PQ453_RS25245"
                     /old_locus_tag="PQ453_25245"
     CDS             1285..1821
                     /locus_tag="PQ453_RS25245"
                     /old_locus_tag="PQ453_25245"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002069891.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023150440.1"
                     /translation="MKKVYTAIILIVLLCGGVLSANYIFLQRHMNEVLKEDPRNDGISV
                     WVYYKWFVNSSEINYDLRSVSAENSSLDVSRVMLQFAEKVKDYDFSKVYLSYRGKDKFY
                     LKGEYFKTLGQEYGIQNPVYTLRTIPENVYMLNGERAYSVWEGGLLGVMGKQMEDLSDF
                     SKAWYLDDFIKSMSD"
                     /name="hypothetical protein"
     gene            complement(2202..2315)
                     /locus_tag="PQ453_RS25250"
                     /old_locus_tag="PQ453_25250"
     CDS             complement(2202..2315)
                     /locus_tag="PQ453_RS25250"
                     /old_locus_tag="PQ453_25250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_071789001.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPVRHAKAPLAAATGN"
                     /name="replication initiation protein"
     Typing          352..527
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="84.358"
                     /coverage="82.0"
                     /evalue="3.53e-41"
     Typing          complement(2..369)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.591"
                     /coverage="93.0"
                     /evalue="3.72e-134"
     Typing          complement(2203..2315)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.491"
                     /coverage="100.0"
                     /evalue="5.74e-46"
ORIGIN
        1 agtccagctt ggagcgaact gcctacccgg aactgagtgt caggcgtgga atgagataaa
       61 cgcggccata acagcggaat gacaccggta aaccgaaagg caggaacagg agagcgcacg
      121 agggagccac cagggggaaa cgcctgggat ctttaagtcc tgtcgggttt cgccgccact
      181 gatttgagcg tcagattttg tgatgcttgt caggggggcg gagcctatgg aaaaacggca
      241 gcgccgcatc ctttttcggg cccttcttga cctcagcttc atttcgttac ctcgtcattc
      301 gtgagcaggt aacgcccgcc gcagtctcac ggcaggagcg tagcgaccga gtgagcgagg
      361 aggcgtcatt tcaccatcat cagcattttg cacttacgca ccgcagccgc atttttcccc
      421 tgccacatga agcacttccc tgagccacca cgcccaacta acatattaag ccagtataca
      481 ctccgctagc gctacgtgac tggtccggcg ctgcgcccgg aacccgcaaa ttcagaaact
      541 gaaagcggga caagatgtgt ttttggagta ccgccatcat gatgccggca ccaaaacgat
      601 atctcagggc tgcgccccga taccccgcca acgcttcacg gcaccggatt aaaatccgtt
      661 cccgttcacc gtttctcagg gccgttcccg gctgcaggtt cttcatgagg ttcgccgtgt
      721 ctggcagact gtgcagagtt attctgaccg gagaacgcca tgaaacgact gataaacctg
      781 acgcctgccg agaaaagatt tctcgacgat gctgttgccg ccgctgagag agcgtcaggc
      841 aagaagctga atcagcccaa caggcacatt gtccttaaca gggctcgtgc acagatcgaa
      901 tcgcagcgcc aggcagaacg gcagcgatct gcgcgtgagg aggagcggca gcaggcggaa
      961 tttacctggt cgcgtccgcg ggcgccgcgt cgctgattgc cactttcgtc ggttttgtgg
     1021 ggagttcagg gcgaaacagc gtggtattca ctccggtgca tagtcattcg ccaccgtaaa
     1081 actcaccaga gcgattccgg gcggttttct gggggtaaga cgtgctcttt tgtggctgaa
     1141 ggcgcagaaa cgccctgagg ccgttttcgc ggtgcgcgta agaagacgtt atggtaaatc
     1201 gatgcttaat tccttgctaa cttatggcac cttagcttaa aaatctcagg gtaaacttta
     1261 gagcagttga gatggattat agaaatgaaa aaagtatata cagcaatcat attaatagta
     1321 ctcttatgtg gtggtgtttt atctgccaac tacatttttc ttcaaaggca catgaatgag
     1381 gttctgaaag aagatccaag gaatgatggt attagcgttt gggtttatta taagtggttt
     1441 gtaaactctt ccgagattaa ttatgacctt cgttctgttt ctgcagaaaa tagttcactg
     1501 gatgttagta gggtgatgct gcaatttgct gaaaaagtga aagattatga ttttagtaag
     1561 gtttatctta gttacagagg gaaagataag ttttacttaa aaggagagta ttttaaaact
     1621 cttgggcagg aatatggtat tcaaaacccc gtatatacat taagaacaat tccggaaaac
     1681 gtgtatatgt taaatggaga gagagcttat agtgtttggg agggtgggct tctgggtgta
     1741 atgggaaaac agatggaaga tcttagtgat ttctctaagg cttggtactt agatgatttc
     1801 attaaaagca tgagcgatta atttgaagcg atcagtatac attgacgatt agctcacgca
     1861 aatcgctcat tggtcactgg ggtgttttta ctcgtagatg ctttagatgt gtgacctgct
     1921 ccccgtggat tacaaggccg tcatctgata atgcccctaa tgggtcagat ctctaggata
     1981 gtagcaatac agcaaggaac ttcttgagat cctttctgtt gcgtcgtaat ctcttgctct
     2041 gtaaacgaaa aaaccgccca gcaaggcggt tttctcgaag gttctcagag cagcaactct
     2101 ttgaaccgag gtaactggct agttagagga gcgcagtcac caaaactgtt cgtttagttt
     2161 agccttaact ggcgcatgac ttcaagacta tctcctctaa atcagttacc agtggctgct
     2221 gccagtggcg cttttgcatg tcttaccggg ttggactcaa gacgatagtt accggataag
     2281 gcgcagcagt cggactgaac ggggggttcg tgcatac
//
