LOCUS       NZ_CP050768             2986 bp    DNA     circular CON 03-JUN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Indiana strain SI111
            plasmid pSI111-4, complete sequence.
ACCESSION   NZ_CP050768
VERSION     NZ_CP050768.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14450156
            Assembly: GCF_012053145.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Indiana
  ORGANISM  Salmonella enterica subsp. enterica serovar Indiana
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 2986)
  AUTHORS   Chen,Z.
  TITLE     Genomic analyses of multidrug-resistant Salmonella Indiana,
            Typhimurium, and Enteritidis isolates using MinION and MiSeq
            sequencing technologies
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2986)
  AUTHORS   Chen,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-MAR-2020) Joint Institute for Food Safety and Applied
            Nutrition, University of Maryland, 5145 Campus Drive, Patapsco
            Building, Suite 2134, College Park, MD 20742, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Assembly Name                     :: SI111
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 124x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_012053145.1-RS_2024_06_03
            Annotation Date                   :: 06/03/2024 02:25:48
            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)                     :: 4,787
            CDSs (total)                      :: 4,669
            Genes (coding)                    :: 4,503
            CDSs (with protein)               :: 4,503
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 166
            CDSs (without protein)            :: 166
            Pseudo Genes (ambiguous residues) :: 0 of 166
            Pseudo Genes (frameshifted)       :: 61 of 166
            Pseudo Genes (incomplete)         :: 125 of 166
            Pseudo Genes (internal stop)      :: 35 of 166
            Pseudo Genes (multiple problems)  :: 46 of 166
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP050768.1.
            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..2986
                     /organism="Salmonella enterica subsp. enterica serovar
                     Indiana"
                     /mol_type="genomic DNA"
                     /strain="SI111"
                     /serovar="Indiana"
                     /isolation_source="Diarrheal patient"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:286783"
                     /plasmid="pSI111-4"
                     /geo_loc_name="China:Shanghai"
                     /lat_lon="31.23 N 121.47 E"
                     /collection_date="2013-11-13"
                     /collected_by="Shanghai Municipal Center for Disease
                     Control and Prevention"
     gene            1063..1311
                     /locus_tag="HEC81_RS23745"
                     /old_locus_tag="HEC81_23745"
     CDS             1063..1311
                     /locus_tag="HEC81_RS23745"
                     /old_locus_tag="HEC81_23745"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017096688.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_029793011.1"
                     /translation="MKNVRMQFDLPEDRLDELDSLMKKCGISTKKELFNYALTMLEWAV
                     DESESGHEIAAIDRDSKQFYALRMPILKRVNRTSTAN"
                     /name="hypothetical protein"
     gene            1384..1755
                     /locus_tag="HEC81_RS23750"
                     /old_locus_tag="HEC81_23750"
     CDS             1384..1755
                     /locus_tag="HEC81_RS23750"
                     /old_locus_tag="HEC81_23750"
                     /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_024242345.1"
                     /translation="MSDSLDGFTEGDTSKEKQAVKQPKKFFSDVDDSADRRHLRWTKSG
                     VTLAMTILVAVMNWMVISMLYHVVDEELSLIRSGFMQADARTVTTSVYLALIAGTVAEV
                     SALFLIIVKSVFKNNNNDI"
                     /name="hypothetical protein"
     gene            2548..2739
                     /locus_tag="HEC81_RS23755"
                     /old_locus_tag="HEC81_23755"
     CDS             2548..2739
                     /locus_tag="HEC81_RS23755"
                     /old_locus_tag="HEC81_23755"
                     /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="WP_001041614.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(1825..2250)
                     /name="rep_cluster_2374"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.766"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctcactgtat cgttcatgcc tgcatgaacg ggttattctt cctgactaca gaattatatc
       61 gctccttcag ttcatacatc acttttacaa cactccttca gtctgtacat cacttttaca
      121 acacttttgc atcactttta catcatttgt acatcacttt tacatcattc cttcagctca
      181 tacgtcactt ttacgtcagt tccatcctct gtgccatttg tacatccgac ccccttcctg
      241 aacgtgctga aaacggtttt tccggctgtg ccggcaacgc ctcacggcca cgcaataaat
      301 tgcgtccccg ttcaccgttt tcggataaga agaacatcgg aaacaggact taccccggct
      361 gaatggcgtg aatttccgcg ctatgcactt gcgcgcatac tcatgcatgc cgtaaaaaca
      421 gagcctgcgc gtttctggcg ggttttcggg tggtttgttg cctgttttac cggttttccg
      481 tcagaaacgc cctgaggccg ttttagcggt gcgtacaata cttgagttat gttaaatgca
      541 cctaagattt ggatgattgt ttcatctcgt tacaactact gttgtctttt taacctatat
      601 cgttttatac tcgtaatatg ctccaattac actcgacaat ggagatgttt gagtgtaaga
      661 tacaatctgg agcccattac gaggtgtggt gggtaaactg gagatttcac ctgtgagcga
      721 gttaactcaa aactgctcct cgacctccag gaacagtgag gactgcaccg acttcgaaga
      781 actgcctcct aaagagcttt ctttgaagga ttggttctca gtctttactg aggtcgatga
      841 gtaataacca ccatggagga gttttcacaa cctcctccat ggtggggata acctgcttgc
      901 ggagaagaga taaggctaag ccttatccaa attaggagta tcataagtat atgaaactta
      961 atttatttat aggtagagat atataaatac caacggtcct aatggtgaag aatgtgcagc
     1021 atagagtaca aggatgacat gctggcccct cggagattag ttatgaaaaa tgtacgtatg
     1081 caattcgatc tacctgaaga taggttggat gaactcgatt ctttaatgaa gaagtgcggc
     1141 ataagtacta aaaaagagtt gttcaactac gcgttaacaa tgcttgagtg ggctgtggac
     1201 gagtccgaaa gtggtcacga aatcgcagct atcgatagag acagtaagca attttatgct
     1261 ctacgaatgc ctattcttaa gcgagtgaac cgtacatcta ctgcaaatta acttatcact
     1321 tgatgtgtta aggagaaggc cagcttaaac tggccttctt tttttattca agagggtttg
     1381 attgtgtccg atagcctaga tggatttact gaaggcgata cctcaaaaga aaaacaagcg
     1441 gtaaaacaac ccaagaagtt ctttagtgac gtcgacgatt cagcagatag acggcatctg
     1501 agatggacaa aaagtggcgt tactctggct atgacaattt tggttgctgt aatgaactgg
     1561 atggtcataa gcatgctata tcacgtagtt gatgaagagc tttctctgat acgaagtggc
     1621 tttatgcaag cagacgcaag gactgtaact actagtgttt atttggcttt gattgctgga
     1681 acagttgctg aggtatctgc tttatttttg ataattgtaa agtcagtttt taagaacaat
     1741 aacaatgata tatgaagttg attccagtcg ttagatgtag tgtcacacat ggttttgttc
     1801 tgtctgtctt gagatcactc taatcaaaat gtaatctctt gggactgaaa cgaaaaaacc
     1861 acccggcaag gtggtttttt cgaaggttca ttaaccggca agtttctgaa ccgtggtaac
     1921 tggctttcgc agagcacaga aaccgaattc gttttaacag tgtagccgta gtctgcctta
     1981 cacttcaaca cctcaacgct tctttgttct gcgaatctgt tacctgtggc tgctgccatt
     2041 ggcgttttaa cgcgtttttt ccgggttgga ctcaaggtga tagttactgg aaaaaacgca
     2101 gcagtcggac tgaacggggg gttcgtgcat acagtccagc ttggagcgaa ctgccttccc
     2161 ggatctgagt gtcaggcgtg gagtgagaaa acgcggccat aacagcggaa tgacaccggt
     2221 aaaccgaaag gcaggaacag gagagcgcac gagggagcca ccagggggaa acgcctggta
     2281 tctttatagt cctgtcgggt ttcgccacca ctgatttgag cgtccgattc tgtgatgctt
     2341 gtcagggggg cggagcctat ggaaaaacgc cccgccgggg cgttgccttt tagcccttgt
     2401 ccttagcttt cgttatgctt accgttacgt tatctgctta tcttccctcc gctcgccgca
     2461 gactcatgac cgaacggagt gagcgaatga gcgaggaagc ggaaaaccat cagaacgtac
     2521 agtaagcact ttcgcgccgg ggctttcatg aacaaacaac aaaagactgc cgttaacatg
     2581 gctaaattca tccaggatca gtccctgctt cttctggaca ggcttaatga gctggatctg
     2641 gatcatgagg ctgatttctg cgagaaactc catgaggatg cggaacgcct ttaccgaagc
     2701 ctgtcagcgc gcctgaatga gcagcaggac ggtgcgtaat ggctccgttc tgggtattac
     2761 cggagtaata ccggcatcgc cttaattttc attgtcttag cgcttaacat tattaccccg
     2821 gtaataccca gaatccctgt attttttctt ttttatttat ttttcatgca gttgcgatga
     2881 aagtcgcggc tgcgttaggt gtatgaccat tttgaggttg aaaaataatc aaccatggcg
     2941 ggtgatttac gcaggttaag gggagatcgt gacaaaaaaa gcgttc
//
