LOCUS       NZ_CP065106             3830 bp    DNA     circular CON 03-SEP-2023
DEFINITION  Salmonella enterica subsp. enterica strain SENT0058 plasmid pS58-4k,
            complete sequence.
ACCESSION   NZ_CP065106
VERSION     NZ_CP065106.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16807077
            Assembly: GCF_031039735.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica
  ORGANISM  Salmonella enterica subsp. enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3830)
  AUTHORS   Huang,T.-W.
  TITLE     Whole-genome sequencing of ceftriaxone-resistant Salmonella enterica
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3830)
  AUTHORS   Huang,T.-W.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-NOV-2020) Department of Microbiology and Immunology,
            School of Medicine, College of Medicine, Taipei Medical University,
            No. 250, Wuxin Street, Taipei 11031, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2020
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 240x
            Sequencing Technology             :: Illumina, Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/01/2023 16:54:13
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,976
            CDSs (total)                      :: 4,863
            Genes (coding)                    :: 4,709
            CDSs (with protein)               :: 4,709
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 77
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 154
            CDSs (without protein)            :: 154
            Pseudo Genes (ambiguous residues) :: 0 of 154
            Pseudo Genes (frameshifted)       :: 70 of 154
            Pseudo Genes (incomplete)         :: 107 of 154
            Pseudo Genes (internal stop)      :: 26 of 154
            Pseudo Genes (multiple problems)  :: 41 of 154
            Pseudo Genes (short protein)      :: 1 of 154
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP065106.1.
            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..3830
                     /organism="Salmonella enterica subsp. enterica"
                     /mol_type="genomic DNA"
                     /strain="SENT0058"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:59201"
                     /plasmid="pS58-4k"
                     /geo_loc_name="Taiwan"
                     /collection_date="2018-11"
     gene            join(3072..3830,1..1146)
                     /locus_tag="I0P33_RS24850"
                     /old_locus_tag="I0P33_24680"
     CDS             join(3072..3830,1..1146)
                     /locus_tag="I0P33_RS24850"
                     /old_locus_tag="I0P33_24680"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003839290.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="methyl-accepting chemotaxis protein"
                     /protein_id="WP_052895204.1"
                     /translation="MSWAYRISMQMKLFIALFPLLLALVWFAGSGIVSRINTEQQMNTI
                     GQLTTLARSAGDVVHQLQSERGMSAGFIGARGQKFRDDLAAQRQLTDKVLATFKRLLTD
                     TNKDLLQGNIAAPLKTFNESIQFLDSTRTAISELTIDSPKASQFYTQTISDVLKFVGGM
                     GHLSTSGSMVNELAAYYSLLNLKEQAGVERALLSNIFSMDRFDDGQFSMFSDVVGQQDA
                     WLTAARSFSTPVQAAELDKSLQSAEATRALELRETAFNKAAEGGFGVNPTDWFNLQTQR
                     IETLQKVENRAVDALQEHAALLAHNARVDWQSFLVISLVALLIAIAFAVMVARSIQQQL
                     NGTLKTIAEMDGDLTRRLDVPGSDELSALNRAYNQAIENIQHIVQEIKSGAVVLRSASS
                     DIAAGNQDLAQRTDEQAASIVETAASMEQISTAITQTADNASEAERLIHSMERDVLEAN
                     RVSNEASQSMAEIRSSSEQISQIVASIDEISFQTNLLALNAAVEAARAGELGKGFAVVA
                     TEVRNLSQRCAREASQIRELINQNMDKIGEGVARVTASGTALKAAAENTGRMKQYVSDI
                     ARAANEQSLGVSQVHQALNQLEQVTQQNAALVSQAASASQMLDGQSEAMSTLVDRFIV"
                     /name="methyl-accepting chemotaxis protein"
     gene            1436..1624
                     /locus_tag="I0P33_RS24855"
                     /old_locus_tag="I0P33_24685"
     CDS             1436..1624
                     /locus_tag="I0P33_RS24855"
                     /old_locus_tag="I0P33_24685"
                     /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_000165998.1"
                     /translation="MTKQESAALNMAKFIRAQSLLLLEKLDVLDLDDEAADCERMHEQA
                     EALYQKLSARFGIQDGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1672..1938)
                     /locus_tag="I0P33_RS24860"
                     /old_locus_tag="I0P33_24690"
     CDS             complement(1672..1938)
                     /locus_tag="I0P33_RS24860"
                     /old_locus_tag="I0P33_24690"
                     /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_223173001.1"
                     /translation="MKRSQLTLIDGCFMFGFSPGELMNLCPDERLLFVRMISAMLRRSG
                     GDAGAVMFEAYRHIVSDTNQARRSYMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            2617..2766
                     /locus_tag="I0P33_RS24865"
     CDS             2617..2766
                     /locus_tag="I0P33_RS24865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001333247.1"
                     /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_077464408.1"
                     /translation="MHEPPVQSDCCAFSGNYRLESNPERHEKSPLAAATGKQDVREMYR
                     EFLK"
                     /name="replication initiation protein"
     Typing          complement(2083..2255)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.954"
                     /coverage="100.0"
                     /evalue="2.04e-62"
     Typing          2180..2764
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.878"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 ctgcgggaga cggcttttaa taaagccgcc gaaggcggat ttggagtcaa cccgactgac
       61 tggtttaacc ttcagaccca gcgtattgaa acgctgcaaa aggtggaaaa tcgcgcggtg
      121 gatgccttgc aggaacatgc tgcgctgctt gcccacaatg cccgtgtcga ctggcagtcc
      181 ttcctggtaa tcagcctggt tgccctactg attgctatcg cctttgcggt gatggtggca
      241 cgcagtatcc agcagcaact gaacggtacg ctgaaaacca tcgcagagat ggacggcgac
      301 ctgacacgtc gtcttgacgt ccccggcagc gacgagctct cagccctgaa ccgtgcctat
      361 aaccaagcga ttgagaatat tcagcatatc gtgcaagaaa ttaagtccgg tgcggtggtg
      421 ttgcgtagcg ccagtagtga tatcgctgcc ggtaatcagg atctggccca gcgtacggat
      481 gaacaggcgg catcgattgt ggaaacggcc gccagcatgg agcagatttc tactgcgatc
      541 acccagaccg ccgataacgc cagcgaggcg gagcgtctga tacattcgat ggagcgggac
      601 gtactggaag ctaatcgcgt ctctaacgag gccagtcaga gcatggcgga aattcgttct
      661 tccagcgagc agatttccca gattgttgcg tcaattgatg agatttcttt ccagaccaac
      721 ttgctggcgc ttaacgccgc cgttgaagcg gcacgtgccg gtgagcttgg caaaggcttt
      781 gcggtagtgg cgacggaggt gcgtaacctt tcccagcgct gtgcacgaga ggccagtcag
      841 atccgtgagc tgattaacca gaatatggat aagattggcg aaggggtagc acgagtcacc
      901 gcgtccggca ccgcgctgaa agcagcggcg gaaaataccg ggcggatgaa acagtacgtg
      961 agcgatattg cccgtgcggc gaatgagcag tcgcttggcg tgtcgcaggt gcatcaggca
     1021 ctgaatcagc tggagcaggt cactcagcaa aacgcagcgc tggtctctca ggcggcgagc
     1081 gccagccaga tgctggacgg ccagtctgaa gcgatgtcca cgctggtcga tcgctttatt
     1141 gtctgatact gccgttcagc atccggtctt gataacttac aatcagaaaa aaccgcctaa
     1201 aaggcggctt ttttatgcct gcaaataact aggatttacc ataacatctg ttgcgtgcac
     1261 cgcctgagag gctctgagag cgtttctgag gactccgacc tgaaacatac acctttctgt
     1321 gcccatatcg agaaaaaacg cccctgatga tttctgcgta cctgcatggc tatgcactca
     1381 agtgaatgaa gtaagatttc agtctgcgat caccataaaa ccgggaaaaa gccgtatgac
     1441 aaaacaggaa tcagccgcac tgaacatggc aaaatttatc cgggcgcagt cgctgctgct
     1501 gctcgaaaaa ctcgacgtgc tcgatcttga tgacgaggca gccgactgtg agcgaatgca
     1561 cgaacaggca gaagcgcttt atcagaagct gagcgcacgc ttcggtatac aggacggcga
     1621 ataaagagac gaaaagaacg ctcacttaga cgaaaagcgt atccagggca actatgtata
     1681 tccaccgtgt acatagtcat gcctgacgct ttcgagcagg tcgagcatgt aggaacgacg
     1741 agcttgattg gtatcggaca caatatggcg atacgcctca aacataacag cacccgcatc
     1801 accgcccgaa cggcgaagca tagcggaaat catccgcaca aagagcagac gttcatcggg
     1861 gcaaaggttc ataagttctc ctggtgaaaa accaaacatg aagcacccat ctattaacgt
     1921 cagctgtgaa cgcttcatta cgcttcatta aaataggtaa acccgggaaa aagatccaaa
     1981 cgttaacatc acaggtaaac agaaacgtcg ggtcgatcgg gaaattcttt cccggacggc
     2041 gcggggttgg gcaagccgca ggcgcgtcag tgcttttagc gggtgtcggg gcgcagccct
     2101 gaaccagtca cgtagcgcta gcggagtgta tactggctta ctatgtaggc acgggtgcgg
     2161 gaatcagtga agtgcttcat gtggcaggag gaaaatgcag cagcagagcg taagcggaat
     2221 atatgagaca ggagatattc cgcttcctcg ctcactgact cgctgcgctc ggtcgttcgg
     2281 ctgcggcgag cggtgcgggc ttacgaatgg ggcggaaatt tcctgggaga tgccaggaag
     2341 aaacttaaca gggaaacgat aaggccgcgg cgaagccgtt tttccatagg ctccgccccc
     2401 ctgacaagca tcacgaaatc tgacgctcaa atcagtggcg gcgaaacccg acaggactat
     2461 aaagatccca ggcgtttccc cctggtagct ccctcgtgcg ctctcctgtt cctacctttc
     2521 ggtttaccgg tgtcattccg ctgttatggc cgcgtttatc tcattccacg cctgacactc
     2581 agttccggga aggcagttcg ctccaagctg gactgtatgc acgaaccccc cgttcagtcc
     2641 gactgctgcg ccttttccgg taactatcgt cttgagtcca acccggaaag acacgaaaaa
     2701 tcgccactgg cagcggccac tggtaaacag gatgtgcgag agatgtatcg agagttcttg
     2761 aagtagtggc ctgactgagg ctacactaga aggacaaatt tggtgacatg tctcgcacaa
     2821 gactgttacc acggttagag aatctgccag gattatctaa ccttcgaaaa accacctgca
     2881 agggtggttt tttcgtttac agagcaagag attacgacga tcgtcaaagg atctcaagaa
     2941 gatcctttat ggattgctac cagcgccact gccgaatgtg gtgcccgttc ccccaacaat
     3001 aaactataaa gtttatgcat gtatctaccg atactcctgc gatccctcaa gaaagtaagg
     3061 aaagtatcga tatgtcatgg gcttatcgta tttcaatgca aatgaagttg tttattgcat
     3121 tattcccgct actgcttgcc ttggtctggt tcgccggttc gggtattgtc agccgtatca
     3181 ataccgaaca gcagatgaac accattggac agctcaccac gctcgcccgc agcgcgggtg
     3241 atgtggtgca tcaactccag agcgaacgtg gaatgagcgc tggatttatc ggcgcgcgcg
     3301 gccaaaagtt tcgcgatgac ttagctgccc agcggcagtt aaccgacaag gtgctggcaa
     3361 catttaagcg gttgctgacc gatacgaata aggatttact ccagggaaat attgccgccc
     3421 ccctgaaaac gtttaatgaa agtattcagt ttctcgactc aacccgtacc gccatcagcg
     3481 aattaactat cgattcacca aaagcgagtc agttctatac ccaaaccatc tctgacgtgc
     3541 tgaagtttgt cggcgggatg gggcatttaa gcacctcagg ctcgatggtg aacgaactgg
     3601 cggcttatta tagtctcttg aatttgaagg agcaggctgg tgtagaacgt gcgctgctgt
     3661 ccaatatctt ctcgatggat cgctttgacg acggccagtt cagcatgttt agcgatgtgg
     3721 taggccagca ggatgcctgg ctgacggcag ctcgcagctt tagcacacct gtgcaggcgg
     3781 ctgagctgga caaatctctt cagtccgctg aagcaactcg tgctcttgaa
//
