LOCUS       CP101358                2468 bp    DNA     circular BCT 15-AUG-2022
DEFINITION  Salmonella enterica strain IndS104 plasmid pIndS104_4, complete
            sequence.
ACCESSION   CP101358
VERSION     CP101358.1
DBLINK      BioProject: PRJNA850394
            BioSample: SAMN29636370
KEYWORDS    .
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 2468)
  AUTHORS   Du,P., Liu,X., Liu,Y., Li,R., Lu,X., Cui,S., Wu,Y., Fanning,S. and
            Bai,L.
  TITLE     Dynamics of Antimicrobial Resistance and Genomic Epidemiology of
            Multidrug-Resistant Salmonella enterica Serovar Indiana ST17 from
            2006 to 2017 in China
  JOURNAL   mSystems, e0025322 (2022) In press
   PUBMED   35861536
  REMARK    Publication Status: Available-Online prior to print
REFERENCE   2  (bases 1 to 2468)
  AUTHORS   Du,P., Liu,X., Liu,Y., Li,R., Lu,X., Cui,S., Wu,Y., Fanning,S. and
            Bai,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-JUL-2022) Institute of Infectious Diseases, Beijing
            Ditan Hospital, Capital Medical University, No.8 jingshundongjie,
            Beijing 100015, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 07/12/2022 21:21:44
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.1
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 4,837
            CDSs (total)                      :: 4,720
            Genes (coding)                    :: 4,560
            CDSs (with protein)               :: 4,560
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 160
            CDSs (without protein)            :: 160
            Pseudo Genes (ambiguous residues) :: 0 of 160
            Pseudo Genes (frameshifted)       :: 58 of 160
            Pseudo Genes (incomplete)         :: 123 of 160
            Pseudo Genes (internal stop)      :: 31 of 160
            Pseudo Genes (multiple problems)  :: 43 of 160
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..2468
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="IndS104"
                     /host="chicken"
                     /db_xref="taxon:28901"
                     /plasmid="pIndS104_4"
                     /geo_loc_name="China:Shanghai"
                     /collection_date="2013"
                     /collected_by="National health commission Key Laboratory of
                     Food Safety Risk Assessment"
     gene            join(2279..2468,1..236)
                     /locus_tag="NMV04_24180"
     CDS             join(2279..2468,1..236)
                     /locus_tag="NMV04_24180"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676030.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="PH domain-containing protein"
                     /protein_id="UUX08078.1"
                     /translation="MGSYVDQSLTRNESVISRAQTSWIPTIIPVIIGILLLPFYGLGLL
                     IIIPVLLRVWSTELALTNQRVIAKVGFIRRNTVELRIDKVESLGIHQGILGRIFNYGSI
                     VIKGTGGTNTPIPNIKAPMQFRSIVNNHIEEMNSKQQ"
                     /name="PH domain-containing protein"
     gene            complement(1110..1301)
                     /locus_tag="NMV04_24185"
     CDS             complement(1110..1301)
                     /locus_tag="NMV04_24185"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /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="UUX08079.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          1481..1838
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.1"
                     /coverage="83.0"
                     /evalue="2.93e-164"
ORIGIN
        1 aaagagtcat cgcaaaagtg ggttttatcc gacgcaatac ggtggaactc cgtattgata
       61 aagttgaaag ccttggcata catcaaggga tactgggacg aatctttaac tatgggtcta
      121 tcgtgattaa aggcactggc ggaaccaaca ctccaattcc aaacatcaag gcgccaatgc
      181 aattcagatc gattgtgaac aatcatatcg aggaaatgaa ttctaagcag cagtagcttc
      241 ctcgtagcat tacaaaaaaa gccctgcggg gctttttttg tacctgccaa tcagctggat
      301 ttaccataac atccgttgcc cgcaccgcct cagaggccct cagggcgttt ctgaggcctc
      361 cggcctgaaa cacacacctt tctgtgccca tatcgagaaa aaacgcccct gatgattctg
      421 gcgcgactgc atggctatgc acggacatac ctggccggga ttttagccgc taaaatccga
      481 tgaacgccct gaaagccacc acgaaccacc ccgataacgg tgaacggatg cgcaatttat
      541 tgcgtggccg tgaggcgttg ccggcacagc cggaaaaacc attttcagca cgtgcaggag
      601 gcccaggaag aggggcggat gtacgaatag ttcagaggtc agatctgacg taaaaatgat
      661 gtaaaagtga cgtaaaagtg atgtactttt gatgtaattc tgttgtacac ccgcgatctg
      721 acgtaaaagt gatgtaattt tgatgtactt ttgatgtaat tctgttgtac acccgcgttc
      781 tggggtaaaa gcagatgcaa ttttgtagtt tatgtgtagt cgctgaaccc atagggtcat
      841 acgagcatga ccctttcccg gaaaaggacg ctttttagcc agaatcatcc ttaacctgcg
      901 gcgccagcac tcgggagtgg tcgttttata tactaaaaaa tgacatacac ctaacgcagc
      961 tgcgattttc atcgcaactt catgaaaaat aaataaaaaa gaaaaaacac agggattctg
     1021 ggtattaccg gggtaataat gttaagcgct aacacaatga aaattaaggc gatgccggta
     1081 ttactccggt aatacccaga acggagccat tacgcaccgt cctgctgctc attcaggcgc
     1141 gctgacaggc ttcggtaaag gcgttccgca tcctcatgga gtttctcgca gaaatcagcc
     1201 tcatgatcca gatccagctc attaagcctg tccagaagaa gcagggactg atcctggatg
     1261 aatttagcca tgttaacggc agtcttttgt tgtttgttca tgaaagcccc ggcgcgaaag
     1321 tgcttactgt acgttcggat ggttttccgc ttcctcgctc attcgctcac tccgttcggt
     1381 catgagtctg cggcgagcgg agggaggata agcagataac gtaacggtaa gcataacgaa
     1441 agctaaggac aagggcgaaa aggccacgcc ccgccggggc gtttttccat aggctccgcc
     1501 cccctgacaa gcatcacgaa aatctgacgc tcaaatcagt ggtggcgaaa cccgacagga
     1561 ctataaagat cccaggcgtt tccccctggt agctccctcg tgcgctctcc tgttcctgcc
     1621 tttcggttta ccggtgtcat tccgctgtta tggccgcgtt tatctcattc cacgcctgac
     1681 actcagttcc gggtaggcag ttcgctccaa gctggactgt atgcacgaac cccccgttca
     1741 gtccgactgc tgcgccttgt ccggtaacta tcatcttgag tccaacccgg aaagacacga
     1801 caaagcgcca ctggcagcag ccactggtaa ctgatttaga ggagttagtc ttgaagttat
     1861 gcgccggtta aggctaaact gaaaggacag atttggttac tgcgctcctc caagccagtt
     1921 accgcggttc aaagagttgg tagctctgag aaccttcgaa aaaccgccct gcaaggcggt
     1981 tttttcgttt ccagagaaag agattacgac gcaacggaca ggatctcaag aagatcatct
     2041 gtgatattcg acagatatgg gataaaggat tgcaacgcca agagtatgtg agacatagca
     2101 gcagccacca ccaccacaga atcaagccag ttgcgtcacg aaaggaaaga accgaactgt
     2161 gcgacggtcg ctacgctctc cgtaaatttt gtatacccac cacggagaca taaagtttct
     2221 attgctgatt cgccttaaaa agggaaaaat cctatttttt ctaaatggat ataaccttat
     2281 gggaagctac gtagaccaat cattaacgag aaatgaatcc gtaatatctc gcgctcaaac
     2341 ctcctggatt ccaacaatca tcccagtaat tatcggaatc ttgttgctgc ctttttacgg
     2401 cttagggtta cttataataa tccctgtgct ccttagagtt tggtcaacgg agcttgcatt
     2461 aactaacc
//
