LOCUS       NZ_CP092262             3897 bp    DNA     circular CON 08-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Indiana strain 15
            plasmid unnamed4, complete sequence.
ACCESSION   NZ_CP092262
VERSION     NZ_CP092262.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25873476
            Assembly: GCF_022350005.1
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 3897)
  AUTHORS   Chao,G. and Wang,X.
  TITLE     The Large Plasmid Carried Class 1 Integrons Mediated Multidrug
            Resistance of Foodborne Salmonella Indiana
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3897)
  AUTHORS   Chao,G. and Wang,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-FEB-2022) College of Veterinary Medicine, Yangzhou
            University, 88 South University Ave., Yangzhou 225009, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 31-DEC-2019
            Assembly Method                   :: ABySS v. v2.0.2; CANU v. v1.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 423.0x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022350005.1-RS_2024_05_08
            Annotation Date                   :: 05/08/2024 06:41:45
            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)                     :: 4,884
            CDSs (total)                      :: 4,765
            Genes (coding)                    :: 4,603
            CDSs (with protein)               :: 4,603
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 162
            CDSs (without protein)            :: 162
            Pseudo Genes (ambiguous residues) :: 0 of 162
            Pseudo Genes (frameshifted)       :: 63 of 162
            Pseudo Genes (incomplete)         :: 120 of 162
            Pseudo Genes (internal stop)      :: 33 of 162
            Pseudo Genes (multiple problems)  :: 46 of 162
            Pseudo Genes (short protein)      :: 1 of 162
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP092262.1.
            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..3897
                     /organism="Salmonella enterica subsp. enterica serovar
                     Indiana"
                     /mol_type="genomic DNA"
                     /strain="15"
                     /serovar="Indiana"
                     /host="broiler chickens"
                     /sub_species="enterica"
                     /db_xref="taxon:286783"
                     /plasmid="unnamed4"
                     /geo_loc_name="China:Changzhou"
                     /collection_date="2017-06-08"
     gene            1..1032
                     /locus_tag="MF259_RS24365"
                     /old_locus_tag="MF259_24365"
     CDS             1..1032
                     /locus_tag="MF259_RS24365"
                     /old_locus_tag="MF259_24365"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001271372.1"
                     /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_239450412.1"
                     /translation="MSAALQYFEENLPRRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASA
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSKNQADKGKVG
                     GKNSGVVRWTANDDKRRRALDMYILGASTEDIAVAVGVSRWTVRRWMDSSVEWLLSKQI
                     IKI"
                     /name="replication initiation protein"
     gene            complement(1395..1790)
                     /locus_tag="MF259_RS24370"
                     /old_locus_tag="MF259_24370"
     CDS             complement(1395..1790)
                     /locus_tag="MF259_RS24370"
                     /old_locus_tag="MF259_24370"
                     /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_001222910.1"
                     /translation="MRISNIDWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNELQAQENARKQANQKRMEGKTQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELRYPKDNILQKLKAIRLDLETSPDHH"
                     /name="hypothetical protein"
     gene            1970..2923
                     /locus_tag="MF259_RS24375"
                     /old_locus_tag="MF259_24375"
     CDS             1970..2923
                     /locus_tag="MF259_RS24375"
                     /old_locus_tag="MF259_24375"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016235474.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_001360358.1"
                     /translation="MATYHLNVKFGGKGQAGNHADYIERKGEYEKRKDLEYSEHGNMPG
                     WARDNPSHFWQAADQFERANGSTYREIEIALPRELTPDQRIELVQDFVRQVAGERHAYS
                     FAIHNPKASIDGGEQPHAHIMMSQRINDGMERSPEQYFRRYNAKNPERGGAKKDSGNLT
                     PTQQKEQLRTLRASWSALQNEHLARHGHRVRVDHRSLEERGIKRTPERHFGFAASSRLD
                     HAQRREILQNRAQPLEHFLEKAHSVRHQFDAQVQQKELVKTLLQDVARERGHALTARIN
                     KTGEVEFERAPTRTRSNTRGHGMGIRDNSRGYDYER"
                     /name="MobA/MobL family protein"
     gene            2935..3465
                     /locus_tag="MF259_RS24380"
                     /old_locus_tag="MF259_24380"
     CDS             2935..3465
                     /locus_tag="MF259_RS24380"
                     /old_locus_tag="MF259_24380"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000168768.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000168766.1"
                     /translation="MASTEEGLLTLLLSVEHLKNTAIEQQKAVADTLAVARETLRGYRD
                     ISDSVVKQVSDEVRKGVQKTDIAGLMGERMTQDFQRLEETVAKMRANAEALNKDIATIH
                     HNVVKEYNTLNKYSLKWFIGVTVSFLVMFSLLGWFTKTLIDRNYTATEVVYQKIVDIEK
                     KLDKPATGKSRKN"
                     /name="hypothetical protein"
     Typing          2..777
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.941"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          1971..2920
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.685"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgagcgccg cgcttcaata cttcgaagaa aatttacccc gccgtcccta tcacacggat
       61 gatctcgctt tcggccttcg catctccggc aaagggcgtg cgcttcttgc gcggtacatc
      121 cagcagaacc agccacatgc gcagttctgg ctggtttttg acgttgaccg cgagggggca
      181 gcgattgact ggagcgaccg gaacgccccc gcgccgaaca tcaccgttaa aaatcctgtg
      241 aacggacacg ctcacctgct ctatgcactc aatatcgccg tgagaaccgc gcctgatgcg
      301 tcggttaagg cgctgaaata tgccgcagcg gttgaacgtt cgctgtgtga gaaactttgt
      361 gcggatgtga actacagcgg cttgatttgc aaaaatccgt tccacctgga atggctggtg
      421 atggagtggc gcgaggaagc ctataccctc gatgaactgg ctgattatct cgatttgagc
      481 gcctcagcgc gtcgtagcat cgataaacat tatgggatgg ggcgaaactg ccacctgttc
      541 gaaatgacgc gcaaatgggc ttacagggcg attcgtcagg gctggccagc attctcacag
      601 tggcttgatg ccgtgatcca gcgtgtcgaa atgtataacg catcgcttcc cgttccgctt
      661 tcaccggctg aatgtcgggc tattggcaag agcattgcga aatacacgca caggaacttc
      721 acgccggaaa ctttcgcaca gtatgtggct gatacgcaca cgccagaaat tcaggccgca
      781 cgaggtcgca agggcgggaa ggccaattcg tcaaaaaatc aggcggacaa agggaaagtt
      841 ggcgggaaaa acagcggtgt tgtccggtgg acggctaacg atgataaacg tcgtagggcg
      901 cttgatatgt acatcttggg agcgtcaaca gaagatattg cagtggcggt tggtgttagc
      961 cgttggactg ttcgacgctg gatggatagc tctgtagaat ggctactgag taaacaaata
     1021 atcaaaattt aattaacaaa aagaatacat acccccccct gttttgttag ttttttgtta
     1081 attttgggtg cacgaagcaa gcctatatca gataacagcg cctgaacggg ggtttggtgt
     1141 ttttttgcgc ggcgtctccg acccgctccc acacccccaa accaaatacc gaaaccctgc
     1201 aaaccaagcg agtggtggct ccgctcgccg cagccctagc gaccgagccg tcaggctcgc
     1261 gagtgggcga ggaagcggaa gataatcgga agtcacattg agcacttacg cacctatgcc
     1321 agatccgcgc gtagcgcgtc gcgaaatcga aaacattgaa caccggcagg caaacgcacc
     1381 accacgcagc ggaattaatg atgatctggg cttgtttcaa gatcgagcct gattgcctta
     1441 agtttctgta atatattgtc ttttgggtat ctcagttcgc ctgtttttgt gtccactagt
     1501 ccggcctcga tcagtaaccc cgccgcaaga aacaggcggt gattgcgttc ccgtcgttgt
     1561 gttttcccct ccatccgttt ttggttggcc tgtttgcgag cgttctcctg tgcctgtagc
     1621 tcgttttttt ctgcggttgc caggacgtgg agtagtttgc gctcctgttc tgttagtccg
     1681 gcttcgttat cgagcaggtc aatgatctgc ctctgtcgtg cggtctgttc tccgagcttc
     1741 ctgataaagc cgattcgttt cttcaaccag tcgatgttgc tgatgcgcat gtttgggatg
     1801 ctccctggtg ttttttgcgg tgtgttgggg ttgtgcagta tatcgcttgc ggtgggtggg
     1861 tgcagggggg tatcttccgt gctaattcgt aaaattagca ggaagcgcac ttatatgttt
     1921 cttcgccgtt ggctcagaaa catgtgcgct cctgcggagg gctaacaccg tggcaaccta
     1981 tcacctcaat gtaaaatttg gcggcaaggg acaggccgga aaccatgccg attacatcga
     2041 acgcaaaggc gagtacgaga aacgaaaaga tctggaatac tcagagcacg ggaatatgcc
     2101 aggctgggcg cgagataatc cctcccattt ctggcaagcg gctgatcagt ttgaacgtgc
     2161 gaatggttcg acttatcggg agatcgaaat cgccttgccg cgtgaactga caccggatca
     2221 gcgcattgaa ctggtgcagg attttgtgcg tcaggtagct ggagaacggc acgcctatag
     2281 ctttgccatt cacaatccaa aagcgagcat tgacggaggg gaacagcctc atgcgcatat
     2341 catgatgagc cagcgtatta acgatggtat ggaacgttcg ccggaacagt atttccggcg
     2401 ttataacgcc aagaatcccg aacggggagg cgcaaaaaaa gattcaggca atctgacacc
     2461 gactcagcaa aaagagcaat tgcggacgtt acgggcgagc tggtcagcgt tacagaacga
     2521 gcatttagcg cgtcatggtc acagggtgcg cgttgaccat cgctcactgg aagaacgcgg
     2581 aattaaacgc acgccagaac ggcatttcgg atttgccgcc tcatcacggc ttgatcatgc
     2641 gcagcgccgc gaaatcctgc aaaaccgagc gcagccgctc gaacattttc tagagaaagc
     2701 gcattcggtt cgccatcaat ttgatgcaca agttcagcaa aaagagttag ttaaaacgct
     2761 tttacaggac gtcgcacggg agcgagggca cgcgcttacg gcaagaataa ataaaacagg
     2821 tgaagttgaa tttgaacgtg cgccaacgcg gacgcggagt aacacgcgag ggcacggcat
     2881 gggcattcgt gacaactcac gcgggtacga ctacgaacgt taaaagggga ctgtatggcg
     2941 agtacagaag aggggttgct cacgctcttg ttgtccgttg agcatttgaa aaacactgcg
     3001 atagaacaac agaaagcggt tgcagacacg ctggcggtcg caagggaaac actgcggggg
     3061 tatcgggata tttctgacag tgttgtaaaa caggttagcg atgaagtcag aaaaggggta
     3121 cagaaaacgg acattgcggg gctgatgggt gagcgcatga cccaggattt tcagcgtctt
     3181 gaagagactg tggcaaagat gagagccaac gcggaggcgc ttaacaagga cattgcgaca
     3241 attcatcaca atgttgttaa agaatacaac acgctcaata aatacagtct gaaatggttt
     3301 atcggtgtta cggtcagttt tctggtcatg ttctcgttgc ttggctggtt taccaaaacg
     3361 ttgatcgaca ggaactacac cgcgacggag gtcgtgtatc agaaaattgt tgatattgaa
     3421 aagaaactgg acaaaccagc aacagggaag agccggaaaa actgacgcgc ttcgcttgtc
     3481 caacgcctca cgggacgcga aaaaattccg cgtcccgtga ggcgttttct gatgagaaag
     3541 tttgctgttt tgccccgttc gcccttctga acgctcgaaa cagatcgcgc attgctttcg
     3601 tgaatagtta tgcaggctca tgaaaacgat tctgacgcgt ttttctggct ttgcctggtg
     3661 tttccttgtc tttttgcgtt ttttgcgcca gaaagcgatt gagggcgttt taaggggtac
     3721 gtacaacagg agttatggta aatggatcgg gtttgcggga agactcgaca ggttttgtcg
     3781 ttgggggtag tgtaagcgac tgaaaaacaa acgcccctga aattcgtgtc tctccgccaa
     3841 gattgtcacg aagatacagg ggcgtgtggg tcgtaacaca cggaggaatc ctaacac
//
