LOCUS       NZ_CP092263             3272 bp    DNA     circular CON 08-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Indiana strain 15
            plasmid unnamed5, complete sequence.
ACCESSION   NZ_CP092263
VERSION     NZ_CP092263.1
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 3272)
  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  JOURNAL   Unpublished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 3272)
  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
            CP092263.1.
            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..3272
                     /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="unnamed5"
                     /geo_loc_name="China:Changzhou"
                     /collection_date="2017-06-08"
     gene            join(3243..3272,1..165)
                     /locus_tag="MF259_RS24385"
                     /old_locus_tag="MF259_24385"
     CDS             join(3243..3272,1..165)
                     /locus_tag="MF259_RS24385"
                     /old_locus_tag="MF259_24385"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041631.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            820..978
                     /locus_tag="MF259_RS24475"
     CDS             820..978
                     /locus_tag="MF259_RS24475"
                     /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_071529495.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDKAPLAAATGNWTRWIEIL
                     RVLEVVA"
                     /name="replication initiation protein"
     gene            1293..2132
                     /locus_tag="MF259_RS24390"
                     /old_locus_tag="MF259_24390"
     CDS             1293..2132
                     /locus_tag="MF259_RS24390"
                     /old_locus_tag="MF259_24390"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000546749.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EcsC family protein"
                     /protein_id="WP_110982636.1"
                     /translation="MHIEEEDLRALERAVELLAQDTITVTLTQLVGTPIDYLMSKLPKG
                     AEKKIYSLVEKSLNKAANAALWSLDNEPNRIASTKTNKFFAALSGAIGGAFGFSALAIE
                     LPVSTTIMLRSIADIARSEGFDLDRIDTKLECLAVFSYGGPSEDDDAVNTAYYATRNLT
                     AEIVQDLSKEISNITVKNAASTQTGKWLASLIEKVATRFGIVITEKMAAQAAPVIGALA
                     GATLNTMFTDYYQDMARGHFIVKRLERKYGDELIKAEYIKISDKLTNQNQRKHLNSN"
                     /name="EcsC family protein"
     Typing          complement(239..323)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="100.0"
                     /evalue="3.06e-32"
     Typing          complement(2729..2984)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.085"
                     /coverage="89.0"
                     /evalue="2.7e-93"
     Typing          complement(3109..3207)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          343..892
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.833"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggcgcgat ttatcaaaag ccagagcctg acactgcttg aaaaactgga tgctctggat
       61 gctgacgaac aggcggccat gtgcgaacga ctgcacgaac tcgcagaaga actccagaac
      121 agcatccaga ttcgctttga ggccgaaagt gaaacaggaa cataacgaag ctgacggagg
      181 cggtcacggc tttcccgtgg gcgttttcgt cagcagacaa gcccgtcagg gcgcgtcagg
      241 gggtttcggg gcgaagccct gaaccagtca cgtagcgata gcggagtgta tactggctta
      301 actatgtagc atcagtacag attataagaa aagagcacca tatgcgatgt gaaataccgc
      361 acagatgcgt aaggagaaaa tgccgcatca ggcgctcttc cgcttcctcg ctcactgact
      421 cgctacgctc ggtcgttcgg ctgcggcgag cggtgccggc tcactcaaag gcggtaatac
      481 ggttatccac agaatcaggg gataaggccg gaaagaacat gtgagcaaaa aggcaaaggg
      541 caacgaaagg ccgcgccgct ggcgtttttc cataggctcc gcccccctga cgagcatcac
      601 aaaaatcgac gctcaagtca gaggtggcga aacccgacag gactataaag ataccaggcg
      661 tttccccctg gaagctccct cgtgcgctct cctgttccga ccctgccgct taccggatac
      721 ctgtccgcct ttctcccttc gggaagcgtg gcgctttctc atagctcacg ctgttggtat
      781 ctcagttcgg tgtaggtcgt tcgctccaag ctgggctgtg tgcacgaacc ccccgttcag
      841 cccgaccgct gcgccttatc cggtaactat cgtcttgagt ccaacccggt aagacacgac
      901 aaagcgccac tggcagcagc cactggtaac tggacaaggt ggattgagat attaagagtt
      961 cttgaagtgg tggcctaact gcggctacac tagaaggaca gtatttggta tctgtgctcc
     1021 accaagccag ttacccggtt aagcagtccc caactgactt aaccttcgac taaaccgcct
     1081 ccccaggcgg ttttttcgtt tactggcagc agattacgcg cagaaaaaaa ggatctcaag
     1141 aggatccttt gatcttttca tcactcctac ttcacggaca acaatgatat cggcatctcg
     1201 cccgttgaat cactgaattc tcccaaggta agatcccaaa acagaccact tacaaaaagt
     1261 aggctacaga ttgattcata agggattttt acatgcatat tgaagaagaa gatctgcgcg
     1321 ctttagaaag agccgtagaa ttattagcac aagatacaat tacagtaaca ctaacccaat
     1381 tagttggaac cccaatagat tacttaatga gtaaacttcc caaaggagca gaaaagaaaa
     1441 tttatagcct agtagaaaaa tctctcaaca aagctgctaa tgcagcctta tggagcctag
     1501 acaatgaacc taaccgaata gcatcaacta agacaaataa gttctttgct gccttatctg
     1561 gagccattgg tggtgctttt ggcttttctg cattagcaat tgagttacca gtttcaacga
     1621 caattatgct tcgttcaatt gcggacatag caagaagtga aggttttgat ctagatagga
     1681 ttgatacaaa actagagtgt ttagcggtgt tttcctacgg aggaccatct gaggacgatg
     1741 atgcagttaa tactgcatac tatgcaacaa ggaatttgac tgctgagatc gtacaagatt
     1801 tatccaaaga aatttctaac attactgtca agaacgctgc ttcaacacaa acaggaaaat
     1861 ggttagcttc gttaatagaa aaagttgcga caagatttgg tatagttatt acagaaaaaa
     1921 tggcagctca agctgctcct gttattggag cactggctgg agccacatta aacacgatgt
     1981 ttaccgacta ttatcaagat atggctcgag gtcattttat tgtcaaaaga cttgagagaa
     2041 aatatggtga tgaattgata aaggctgaat atataaaaat ctcagataaa ctcaccaatc
     2101 agaaccaacg gaagcatttg aacagcaact aacggtttca ctaagtgcat agcaccgtta
     2161 tggccaggtg ctatggaggg tgtcaactca cgaacaatca cacaaacaac aaaattattt
     2221 atgattttat tttaaacatt atattcgcaa caactgcatt aatgaaattg gctttttttg
     2281 aatcaactaa aacagagcca caatttgggc actgactaaa agcattcccc ccatcaacta
     2341 aaacatcgct acatttaggc acagttttac accaatggca tgataaacat ttataggtca
     2401 tagccattct aatcattacc aatttcaact ccacgcacaa aataaatagt taacccagca
     2461 tctacgaata tcaatcatat ttaccataat cccgtattgc gcgcaccgct aaaacgcgct
     2521 gaacgcgatt ctgccgcaaa caccgcaaaa agagatgttt tccccggggt aaaccggaaa
     2581 aatgcgtcag gctcgctttc agctcactgc atagctatgc atgaaagtga atgacgatcg
     2641 gtttgggcgc atacagtgcc catgagacac attttcggac attttcagtt cgtgaatccc
     2701 tgactcattg ctacatatct gaacagacac ccctggcagc gcccccaggg gcgtcctgta
     2761 aaaaaacaca ccgcgcagct agcagcaccc ctaatataag atgatgtttt ttatgaaaat
     2821 agtcagtacc acccctaaaa agcggtgtcg gcgcggtgtt gtagctgcgc caacaccgct
     2881 tttttaaata tcacaaagag agcaagaaga actaatttgt cataactctc tatttataaa
     2941 gaaaaatcag caaaaaattg tttttgcgtg gggtgtgggc atttcaggca tgagaacaga
     3001 ctcgcgtttt tccggagtat cagcggaatt attgattaag aaacactcga cgcagagcga
     3061 aattttatgc aacagcggct gcactgcaca gggattattt atcagttgat atgctgtgcc
     3121 atgatacgtc ctaaagaaac aggacaggat gtgcaattgt aataccgtcg cccgcaacgt
     3181 cttacaatta ccacctgctc agggtccccc cgacacccgg aactgacgga gaacaacgga
     3241 aggtgaacaa acaacaacaa actgcgctga at
//
