LOCUS       NZ_CP098833             3372 bp    DNA     circular CON 26-JUN-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Indiana strain YZ20MCS14
            plasmid pYUYZMCS14-2, complete sequence.
ACCESSION   NZ_CP098833
VERSION     NZ_CP098833.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28950567
            Assembly: GCF_023848615.1
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   Wang,J.
  TITLE     whole genome of mcr-1 positive Salmonella Indiana YZ20MCS14
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3372)
  AUTHORS   Wang,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-JUN-2022) Key Laboratory of Prevention and Control of
            Biological Hazard Factors (Animal Origin) for Agrifood Safety and
            Quality, Ministry of Agriculture of China, Yangzhou University,
            No.48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/26/2023 02:37:39
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,957
            CDSs (total)                      :: 4,839
            Genes (coding)                    :: 4,654
            CDSs (with protein)               :: 4,654
            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)              :: 185
            CDSs (without protein)            :: 185
            Pseudo Genes (ambiguous residues) :: 0 of 185
            Pseudo Genes (frameshifted)       :: 77 of 185
            Pseudo Genes (incomplete)         :: 128 of 185
            Pseudo Genes (internal stop)      :: 31 of 185
            Pseudo Genes (multiple problems)  :: 43 of 185
            Pseudo Genes (short protein)      :: 1 of 185
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP098833.1.
            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="YZ20MCS14"
                     /serovar="Indiana"
                     /isolation_source="chicken meat"
                     /sub_species="enterica"
                     /db_xref="taxon:286783"
                     /plasmid="pYUYZMCS14-2"
                     /geo_loc_name="China: Yangzhou"
                     /lat_lon="32.15 N 119.01 E"
                     /collection_date="2020"
                     /collected_by="Jiang Yue"
     gene            complement(1094..1327)
                     /locus_tag="NFH10_RS24740"
                     /old_locus_tag="NFH10_24740"
     CDS             complement(1094..1327)
                     /locus_tag="NFH10_RS24740"
                     /old_locus_tag="NFH10_24740"
                     /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(1334..1894)
                     /locus_tag="NFH10_RS24745"
                     /old_locus_tag="NFH10_24745"
     CDS             complement(1334..1894)
                     /locus_tag="NFH10_RS24745"
                     /old_locus_tag="NFH10_24745"
                     /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(<1923..2363)
                     /locus_tag="NFH10_RS24750"
                     /old_locus_tag="NFH10_24750"
                     /pseudo=""
     CDS             complement(<1923..2363)
                     /locus_tag="NFH10_RS24750"
                     /old_locus_tag="NFH10_24750"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /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(2572..2895)
                     /locus_tag="NFH10_RS24755"
                     /old_locus_tag="NFH10_24755"
     CDS             complement(2572..2895)
                     /locus_tag="NFH10_RS24755"
                     /old_locus_tag="NFH10_24755"
                     /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            2959..3150
                     /locus_tag="NFH10_RS24760"
                     /old_locus_tag="NFH10_24760"
     CDS             2959..3150
                     /locus_tag="NFH10_RS24760"
                     /old_locus_tag="NFH10_24760"
                     /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(3232..3311)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.654"
                     /coverage="93.0"
                     /evalue="3.12e-17"
     Typing          complement(1012..2582)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.817"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcgcccgata aacaacacac acgcggacac tggcacaggc gcgtaagtgc acaatgcttg
       61 cctctgtgac tcttccgctt cctcgcccac tcgctcacta cgttcggtcg ctggggctgc
      121 ggcgagcggc gggatcactc tcgttgtgat gcagatccgt tttttttttt gcactggagt
      181 tatcaggagt agcggtgcac atgggatcgt gcgatatgct ggatggtgga aggtcggagg
      241 gaacggcaac aactcacccc tcccagtgaa gggacgggta gtttgccgct ctcgatatgc
      301 cggacggagc caaggccatc gatcacgggg cgcgtcagtg gaagaacccg cgcctgcgtg
      361 acgtatgcgt cttcgccgca ccatctcacc cgtcacgcca ccacataccg ggaactgccg
      421 ccaaggtcta actcaaccaa tctagccgcg ctacatacgg tttttgtggc aactcatcag
      481 gtgtccgctg tcgatgaaac tctctgcgcc ggtagcggaa ctctcacgcg tgcggtcgcc
      541 gtcgtcacag ctcccccaac cgcaaacgat tctcgcaaat acgcaagtat ctgcaaaaac
      601 aggttttttt cggggttcct gggagactgt gctgttgaaa aattcttgaa gaatacagaa
      661 ggttcatgca aactgaatga actggtttct gttgtggatc tcaacagttt ccacaggaac
      721 attgaggagg tcagagacct caatgaaccc gaaacagctc gccttcctgg cgagctgttt
      781 tcgttctact cccgccgacg aaagatcgca agtgcaataa cgagattttt cacgtcttta
      841 cgctcaaaaa gtaaaaaaac catgttttcc cctggctgaa tccccaaaaa cgcgtgaaat
      901 gcgttttcag gatgttgcat agctatgcac aaatacggca cacgatttgt ttcgctcgcc
      961 ccagccgtcg aacgggtcaa aatggcaaga tttcgtcact tccccggtca catctccatt
     1021 gatggcccac tccgaacccg tgccgcgcgt tcctgtacct catgtctgta ccgggcacgc
     1081 tcctgttcat cccttagctg ttgttcgcga taaataaccg actcaagcga tccacttgcc
     1141 cggctaatct ctgcacctgc tgactcaata tcacgacgcg ctcgttcagt atcgcgttgt
     1201 tccgttgcgt aacctcgtgc atcttctgca attccgcgaa ggcgctctcc cactcgttca
     1261 gccgccgcat atagtcctgt tgcaaatgct ctaaggcgtt cagcaaatgc ccttccagtt
     1321 ccgtcatact cgtttactcc ctgaccagcc tcacggcgtt cttgtcgccc accgtccagg
     1381 tgttttcccc tttcaccccg tccggcaaca ccagaaattt cccgttctcg ccattgacga
     1441 acgtcacccc ccaggttttt gcctcgagtt tcgccagcgt gttttcctgc tctctgatag
     1501 tcaggatatt tttcgcaatc ttgctttcct gccactccat cagcccccag caccccagga
     1561 aaatcccgcc cgtgacgctg agcgcggtca gcgccggaaa cagtatccgc cctttgatca
     1621 cccgccagag cagttttttc tgctgccggg acagttcggc ctctgtggtg ctgaactgca
     1681 tgctcacggt ggtgctcagc gtatccagtt gctttttcac ggatgttgta tgttcgctga
     1741 tagcgtctct gattttctgc ctgtttaagc tcagtgcctt gtctacagac tcttcgagct
     1801 tcctgaactc gctgttcagc atgttctcgg tagaagcggc tcgctctttc agtttcttct
     1861 cgaagtctgt tcccatttgt aaaagattgc tcatacagcg ccccctttag cctgagattc
     1921 cgccccccct ccgggtcggc aatactgatg ctgcttttgg ttgtcctcac cacctcaaaa
     1981 cctgccgctg taagcgcctc tgtgacatcc tgacgcgttt ttattgctcc ggcatggtaa
     2041 agagcctcaa gaccccgtgt aatcgcttct gcggcctcct gtttcgcttt tggcagatta
     2101 tttggcgtga caagcgtccg tctgttctcc ggtgcgttcg ggtcacgcag cccgtaatga
     2161 tgattaacca gcgtctgcca ggcatttatc ctcggcctgt ccgcacggtc gtagtacggc
     2221 tggaggcgct taccgctctg tagctccatg ttcgggatga caaaattcag ttcgagccgc
     2281 cccttatcct ggtgttccac ccagagaatg ctgtactggt ctttttcgag accgggcata
     2341 agaacacgct caaagctcgt catcactctt tcgcgttcac ccggtggtag ctccttctcc
     2401 gcgaacgaca gaacgcctga cgtgtatttc ttcgaaaatg gcgtggaatc aatgagttcc
     2461 cgcacttctt ccgggttacc ccggagcacc gttgcgcctt cgcggttacg ctcccgcccc
     2521 agcaggtaat cgaccgggcc acttccaccg cctttccccc tggcatgaaa tttaactatc
     2581 atcccgtacc ccctgttccc tgacagcctg ccgcaactgg cgcaattcac cctcgatggc
     2641 catcagtgcg gccaccacat gaacccggtc aatcgaagac cactggccgc tgttcacctt
     2701 ccgggctgtc tggttcaggt tgttcccgat ggcagccaga tgccgcagca atggcggtgc
     2761 cagtgtcggc agttttcctg tgcgtgcaac cggctccccc agacagaccc gccgcatcca
     2821 ttccgccagt cgtttaccct cgcagcgttc cagtaaccgg gcgtgctcct catcggtaac
     2881 ccgtatcgtg agcatcttct cgcgtttcat cggtatcatt ccccctaaca aatcccccat
     2941 acaaggagcc ttaagaccat gaccaaacag gaaaaaacag cccttaacat ggctcgcttt
     3001 atcagaagcc agacgctaac cctgctggaa aaactcaacg atctggacgc ggacgaacag
     3061 gcagacatct gcgaatcact tcacgaccac gccgacgaac tctaccgcag ttgcctcgca
     3121 cgcttcggcg atgacggtga aagcaactga aacatgcagc tcccggagac gttcacagct
     3181 tgcctgtgag cggatgccgg gagcagacaa gcccgccagg gcgcgtcagt gcgggtgtcg
     3241 gggcgcagcc ctgacccagt cacagagcga tagcgatgtg tatactggct ttcctcattt
     3301 tgcatcggtg cagagtggat gggaagtgca ccatgtcagg agtaaaaagc cgcacagatg
     3361 cgtaaaaaca gc
//
