LOCUS       NZ_CP050782             3372 bp    DNA     circular CON 03-JUN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Indiana strain SI85
            plasmid pSI85-3, complete sequence.
ACCESSION   NZ_CP050782
VERSION     NZ_CP050782.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14450152
            Assembly: GCF_012054045.1
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 3372)
  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  JOURNAL   Unpublished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 3372)
  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                     :: SI85
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 76x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_012054045.1-RS_2024_06_03
            Annotation Date                   :: 06/03/2024 02:49:03
            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)                     :: 4,871
            CDSs (total)                      :: 4,751
            Genes (coding)                    :: 4,584
            CDSs (with protein)               :: 4,584
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 167
            CDSs (without protein)            :: 167
            Pseudo Genes (ambiguous residues) :: 0 of 167
            Pseudo Genes (frameshifted)       :: 63 of 167
            Pseudo Genes (incomplete)         :: 127 of 167
            Pseudo Genes (internal stop)      :: 33 of 167
            Pseudo Genes (multiple problems)  :: 47 of 167
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP050782.1.
            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..3372
                     /organism="Salmonella enterica subsp. enterica serovar
                     Indiana"
                     /mol_type="genomic DNA"
                     /strain="SI85"
                     /serovar="Indiana"
                     /isolation_source="Chicken product"
                     /host="chicken"
                     /sub_species="enterica"
                     /db_xref="taxon:286783"
                     /plasmid="pSI85-3"
                     /geo_loc_name="China:Shanghai"
                     /lat_lon="31.23 N 121.47 E"
                     /collection_date="2012-08-24"
                     /collected_by="Shanghai Municipal Center for Disease
                     Control and Prevention"
     gene            complement(1203..1436)
                     /locus_tag="HEC77_RS24165"
                     /old_locus_tag="HEC77_24165"
     CDS             complement(1203..1436)
                     /locus_tag="HEC77_RS24165"
                     /old_locus_tag="HEC77_24165"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1443..2003)
                     /locus_tag="HEC77_RS24170"
                     /old_locus_tag="HEC77_24170"
     CDS             complement(1443..2003)
                     /locus_tag="HEC77_RS24170"
                     /old_locus_tag="HEC77_24170"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<2035..2691)
                     /locus_tag="HEC77_RS24585"
                     /old_locus_tag="HEC77_24175"
                     /pseudo=""
     CDS             complement(<2035..2691)
                     /locus_tag="HEC77_RS24585"
                     /old_locus_tag="HEC77_24175"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(2681..3004)
                     /locus_tag="HEC77_RS24180"
                     /old_locus_tag="HEC77_24180"
     CDS             complement(2681..3004)
                     /locus_tag="HEC77_RS24180"
                     /old_locus_tag="HEC77_24180"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001696562.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     APPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3068..3259
                     /locus_tag="HEC77_RS24185"
                     /old_locus_tag="HEC77_24185"
     CDS             3068..3259
                     /locus_tag="HEC77_RS24185"
                     /old_locus_tag="HEC77_24185"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(1121..2691)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.817"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agagcgatag cgatgtgtat actggctttc ctcattttgc atcggtgcag agtggatggg
       61 aagtgcacca tgtcaggagt aaaaagccgc acagatgcgt aaaaacagcg cgcccgataa
      121 acaacacaca cgcggacact ggcacaggcg cgtaagtgca caatgcttgc ctctgtgact
      181 cttccgcttc ctcgcccact cgctcactac gttcggtcgc tggggctgcg gcgagcggcg
      241 ggatcactct cgttgtgatg cagatccgtt tttttttttg cactggagtt atcaggagta
      301 gcggtgcaca tgggatcgtg cgatatgctg gatggtggaa ggtcggaggg aacggcaaca
      361 actcacccct cccagtgaag ggacgggtag tttgccgctc tcgatatgcc ggacggagcc
      421 aaggccatcg atcacggggc gcgtcagtgg aagaacccgc gcctgcgtga cgtatgcgtc
      481 ttcgccgcac catctcaccc gtcacgccac cacataccgg gaactgccgc caaggtctaa
      541 ctcaaccaat ctagccgcgc tacatacggt ttttgtggca actcatcagg tgtccgctgt
      601 cgatgaaact ctctgcgccg gtagcggaac tctcacgcgt gcggtcgccg tcgtcacagc
      661 tcccccaacc gcaaacgatt ctcgcaaata cgcaagtatc tgcaaaaaca ggtttttttc
      721 ggggttcctg ggagactgtg ctgttgaaaa attcttgaag aatacagaag gttcatgcaa
      781 actgaatgaa ctggtttctg ttgtggatct caacagtttc cacaggaaca ttgaggaggt
      841 cagagacctc aatgaacccg aaacagctcg ccttcctggc gagctgtttt cgttctactc
      901 ccgccgacga aagatcgcaa gtgcaataac gagatttttc acgtctttac gctcaaaaag
      961 taaaaaaacc atgttttccc ctggctgaat ccccaaaaac gcgtgaaatg cgttttcagg
     1021 atgttgcata gctatgcaca aatacggcac acgatttgtt tcgctcgccc cagccgtcga
     1081 acgggtcaaa atggcaagat ttcgtcactt ccccggtcac atctccattg atggcccact
     1141 ccgaacccgt gccgcgcgtt cctgtacctc atgtctgtac cgggcacgct cctgttcatc
     1201 ccttagctgt tgttcgcgat aaataaccga ctcaagcgat ccacttgccc ggctaatctc
     1261 tgcacctgct gactcaatat cacgacgcgc tcgttcagta tcgcgttgtt ccgttgcgta
     1321 acctcgtgca tcttctgcaa ttccgcgaag gcgctctccc actcgttcag ccgccgcata
     1381 tagtcctgtt gcaaatgctc taaggcgttc agcaaatgcc cttccagttc cgtcatactc
     1441 gtttactccc tgaccagcct cacggcgttc ttgtcgccca ccgtccaggt gttttcccct
     1501 ttcaccccgt ccggcaacac cagaaatttc ccgttctcgc cattgacgaa cgtcaccccc
     1561 caggtttttg cctcgagttt cgccagcgtg ttttcctgct ctctgatagt caggatattt
     1621 ttcgcaatct tgctttcctg ccactccatc agcccccagc accccaggaa aatcccgccc
     1681 gtgacgctga gcgcggtcag cgccggaaac agtatccgcc ctttgatcac ccgccagagc
     1741 agttttttct gctgccggga cagttcggcc tctgtggtgc tgaactgcat gctcacggtg
     1801 gtgctcagcg tatccagttg ctttttcacg gatgttgtat gttcgctgat agcgtctctg
     1861 attttctgcc tgtttaagct cagtgccttg tctacagact cttcgagctt cctgaactcg
     1921 ctgttcagca tgttctcggt agaagcggct cgctctttca gtttcttctc gaagtctgtt
     1981 cccatttgta aaagattgct catacagcgc cccctttagc ctgagattcc gccccccctc
     2041 cgggtcggca atactgatgc tgcttttggt tgtcctcacc acctcaaaac ctgccgctgt
     2101 aagcgcctct gtgacatcct gacgcgtttt tattgctccg gcatggtaaa gagcctcaag
     2161 accccgtgta atcgcttctg cggcctcctg tttcgctttt ggcagattat ttggcgtgac
     2221 aagcgtccgt ctgttctccg gtgcgttcgg gtcacgcagc ccgtaatgat gattaaccag
     2281 cgtctgccag gcatttatcc tcggcctgtc cgcacggtcg tagtacggct ggaggcgctt
     2341 accgctctgt agctccatgt tcgggatgac aaaattcagt tcgagccgcc ccttatcctg
     2401 gtgttccacc cagagaatgc tgtactggtc tttttcgaga ccgggcataa gaacacgctc
     2461 aaagctcgtc atcactcttt cgcgttcacc cggtggtagc tccttctccg cgaacgacag
     2521 aacgcctgac gtgtatttct tcgaaaatgg cgtggaatca atgagttccc gcacttcttc
     2581 cgggttaccc cggagcaccg ttgcgccttc gcggttacgc tcccgcccca gcaggtaatc
     2641 gaccgggcca cttccaccgc ctttccccct ggcatgaaat ttaactatca tcccgtaccc
     2701 cctgttccct gacagcctgc cgcaactggc gcaattcacc ctcgatggcc atcagtgcgg
     2761 ccaccacatg aacccggtca atcgaagacc actggccgct gttcaccttc cgggctgtct
     2821 ggttcaggtt gttcccgatg gcagccagat gccgcagcaa tggcggtgcc agtgtcggca
     2881 gttttcctgt gcgtgcaacc ggctccccca gacagacccg ccgcatccat tccgccagtc
     2941 gtttaccctc gcagcgttcc agtaaccggg cgtgctcctc atcggtaacc cgtatcgtga
     3001 gcatcttctc gcgtttcatc ggtatcattc cccctaacaa atcccccata caaggagcct
     3061 taagaccatg accaaacagg aaaaaacagc ccttaacatg gctcgcttta tcagaagcca
     3121 gacgctaacc ctgctggaaa aactcaacga tctggacgcg gacgaacagg cagacatctg
     3181 cgaatcactt cacgaccacg ccgacgaact ctaccgcagt tgcctcgcac gcttcggcga
     3241 tgacggtgaa agcaactgaa acatgcagct cccggagacg ttcacagctt gcctgtgagc
     3301 ggatgccggg agcagacaag cccgccaggg cgcgtcagtg cgggtgtcgg ggcgcagccc
     3361 tgacccagtc ac
//
