LOCUS       NZ_CP101377             5632 bp    DNA     circular CON 31-JUL-2023
DEFINITION  Salmonella enterica strain SC2016091 plasmid pSC2016091-5k, complete
            sequence.
ACCESSION   NZ_CP101377
VERSION     NZ_CP101377.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29630309
            Assembly: GCF_024364925.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5632)
  AUTHORS   Peng,K., Li,R. and Yang,X.
  TITLE     The genomic epidemiology of mcr-positive Salmonella enterica in
            clinical patients from 2014 to 2017 in Sichuan, China and global
            epidemiological features
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5632)
  AUTHORS   Peng,K., Li,R. and Yang,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-JUL-2022) College of Veterinary Medicine, Yangzhou
            University, No. 48, Wenhui East Road, Hanjiang District, Yangzhou,
            Sichuan 225000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Oxford Nanopore MinION; BGISEQ-50
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/31/2023 03:24:46
            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)                     :: 5,058
            CDSs (total)                      :: 4,935
            Genes (coding)                    :: 4,801
            CDSs (with protein)               :: 4,801
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 134
            CDSs (without protein)            :: 134
            Pseudo Genes (ambiguous residues) :: 0 of 134
            Pseudo Genes (frameshifted)       :: 38 of 134
            Pseudo Genes (incomplete)         :: 108 of 134
            Pseudo Genes (internal stop)      :: 18 of 134
            Pseudo Genes (multiple problems)  :: 28 of 134
            Pseudo Genes (short protein)      :: 1 of 134
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP101377.1.
            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..5632
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="SC2016091"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="pSC2016091-5k"
                     /geo_loc_name="China: Chengdu"
                     /lat_lon="30.67 N 104.07 E"
                     /collection_date="2016-07-15"
                     /collected_by="Center for Disease Control and Prevention of
                     Sichuan Province"
     gene            complement(join(4888..5632,1..158))
                     /locus_tag="NMU34_RS24530"
                     /old_locus_tag="NMU34_24530"
     CDS             complement(join(4888..5632,1..158))
                     /locus_tag="NMU34_RS24530"
                     /old_locus_tag="NMU34_24530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009652796.1"
                     /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_057515539.1"
                     /translation="MNNAVLELFNDRLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRAGAAIDWSDRNAPAPTLTITNPENGHAHLLYALETSIRTAPDGKMK
                     PLRYAAAVENALRKKLEADAGYSGLICKNPNHGHWKIAVWQPELYTLDWLADFLDLNAA
                     SDKDIVADYGLGRNCTLFDKTRKWAYRAIRQGWPEYDQWLQACYERASAYNLQFPAPLD
                     EKEVNGIAKSIAKWTEKNFTASSFKEYVINSHRSDIQSKRGRLGGLKSKGGGRPTINSP
                     WEGMGISKSTYYRNIHGKR"
                     /name="replication initiation protein"
     gene            complement(351..635)
                     /gene="nadS"
                     /locus_tag="NMU34_RS24535"
                     /old_locus_tag="NMU34_24535"
     CDS             complement(351..635)
                     /gene="nadS"
                     /locus_tag="NMU34_RS24535"
                     /old_locus_tag="NMU34_24535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000007431.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NadS family protein"
                     /protein_id="WP_001697687.1"
                     /translation="MSFFDELKASLEEAVEIKNGVREPARVTRYELADVKAIRAQLNVS
                     QSEMAKVLGTSLDTIKSWETGRRNPTGLAAKVLATIQANPKFFQELAAH"
                     /name="nadS"
     gene            complement(637..969)
                     /locus_tag="NMU34_RS24540"
                     /old_locus_tag="NMU34_24540"
     CDS             complement(637..969)
                     /locus_tag="NMU34_RS24540"
                     /old_locus_tag="NMU34_24540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015873600.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_000017531.1"
                     /translation="MSHAIEFIETPMFTRQIKQIATDEELRELQKTLIESPDKGDLIQK
                     TGGLRKIRMATGNQGKSGSVRVIYFLATAEVIYLVMAYPKSTKDSLTDAEKAALKTLTQ
                     QLKDEV"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(1131..1355)
                     /locus_tag="NMU34_RS24545"
                     /old_locus_tag="NMU34_24545"
     CDS             complement(1131..1355)
                     /locus_tag="NMU34_RS24545"
                     /old_locus_tag="NMU34_24545"
                     /inference="COORDINATES: protein motif:HMM:NF016769.2"
                     /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_226939304.1"
                     /translation="MEKQLLSALESLQTSYEQQQQAWQDSYSSLQHMFEATSQALTHSD
                     RVCQHLSSQVESLRAQVESLSRNVSRLMR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1425..1910)
                     /locus_tag="NMU34_RS24550"
                     /old_locus_tag="NMU34_24550"
     CDS             complement(1425..1910)
                     /locus_tag="NMU34_RS24550"
                     /old_locus_tag="NMU34_24550"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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_072035998.1"
                     /translation="MSEILNLAKGFEEKSKQQAQDTEQSVKREFARLETSISAELQSSS
                     QSISNAIREQNGRLTGMIRTSVSAAMAWVFLCFALLIGIMGGIIWFQGTIITSRLSEMD
                     SYSQQLANLKAKSGAGVAIYSDDKHRNTYMVVLPKQAHGVETYTSTTDNTVVKYTAK"
                     /name="MbeB family mobilization protein"
     gene            complement(<1957..2379)
                     /locus_tag="NMU34_RS24555"
                     /old_locus_tag="NMU34_24555"
                     /pseudo=""
     CDS             complement(<1957..2379)
                     /locus_tag="NMU34_RS24555"
                     /old_locus_tag="NMU34_24555"
                     /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(2588..2914)
                     /locus_tag="NMU34_RS24560"
                     /old_locus_tag="NMU34_24560"
     CDS             complement(2588..2914)
                     /locus_tag="NMU34_RS24560"
                     /old_locus_tag="NMU34_24560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006674374.1"
                     /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_042927524.1"
                     /translation="MEKRTKEIKIRLTETEHQRLLDRCDRTHLAEWLRQLGLGEHTSRR
                     RRVPDVAPELLRQVSGIGNNLNQIARRLNQTDTLTPSERASLLVVLTSLDRQLGDLLEQ
                     NRDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            complement(3141..4901)
                     /locus_tag="NMU34_RS24565"
                     /old_locus_tag="NMU34_24565"
     CDS             complement(3141..4901)
                     /locus_tag="NMU34_RS24565"
                     /old_locus_tag="NMU34_24565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009652795.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="AIPR family protein"
                     /protein_id="WP_057515538.1"
                     /translation="MARDDFNSDTRTVGLARLANSLEETYGSFINMENTNSKGEARREV
                     LITRCIAAHAVRMYGDELDPGVAAASVCDGSDDGGIDAVYVNPSSKKLILVQSKYIKDG
                     NGSVTIKDFGRFKDACAKVIANDLNSFNDRFLEHKESVTTAITSSSYKCICVFIYSGTQ
                     GLSSEVIGEIDFWEKSQNKALLFRDLESRDEYTILFETPNVTDISTSLSNQSTGAIDIS
                     NVILESYGEITEPYGAIYGTIAARVIHDWWKKYKYALFEKNIRSVLGDSTSVNAGIMST
                     IENSPENFWYYNNGITATYEEVDESIANAGASRKIGIFGFKKLNIINGAQTVSSIGAIF
                     DSIPEEKKDKARVMIRFINAKDPVFLGDVTKYNNTQNRVTGRDFTTQRPEQQKIQREIN
                     FVGGYTYKLLRQEDSGIAASNVIDIDDSLNALICESKKPQLIATLKSNRGRFFDTTEGN
                     LYEQVFNPRNPPSGISVINAVNLYRVCFDVLKDTITKASNSSEDEYSKIPSLLTHGNYV
                     FISILMGKIQPINTVNGIKTYDKNSVSFDTLELAKSIFEYIQSNYPNSYLARFFQNKEK
                     VEQIITHFSS"
                     /name="AIPR family protein"
     Typing          complement(1034..2598)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.743"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cccagccaga acatggcgtg aggctgattg aactggatgt atttcgccag aatggcgcgt
       61 tctttccctg caatgcgtac accaaagtgt aaatcatccg agaagtacgg cttgtgcggt
      121 aagcggtcgt tgaaaagttc gagtactgcg ttattcaatt cgccctgcgc ttatggcggg
      181 ctgttgtctg gcacgtttca tgtgctaata tcctttcaag gtttcgacct ggccctggtt
      241 atcatgtgca tccgccaaga ttgagcatga tttccggggc tttgtttttt ctgttgccgt
      301 taaattacac gcgaacggcc tcgcctgtct aatccttctg tcacaacggc ttagtgcgcc
      361 gccagttcct ggaagaattt cgggttcgcc tggatggttg ccagtacctt cgccgccagt
      421 ccggtcgggt tacggcgtcc ggtttcccag ctcttgatgg tgtcgaggct ggttcccagc
      481 actttcgcca tctcgctctg agatacgttc agctgtgccc tgatggcttt cacgtctgcc
      541 agctcgtaac gggtgacgcg ggcaggctct ctgacgccgt ttttgatttc aacggcttct
      601 tccagcgatg ctttcagctc gtcaaaaaaa ctcatgtcac acctcgtctt tcagttgttg
      661 ggtcagcgtc ttcagcgcgg ctttttccgc gtccgtcagg ctgtctttgg tgcttttcgg
      721 gtaggccatc accagataga tcacctcggc ggtggccaga aagtaaatca ccctcacgct
      781 gccgcttttt ccctggttgc ccgtcgccat cctgattttg cgcagcccgc cggttttctg
      841 aatgagatcg cctttgtccg gcgactcaat cagcgtcttt tgcagctccc tgagttcttc
      901 atccgtggcg atctgtttta tctgacgggt aaacatcggg gtctcgataa actcaatcgc
      961 gtgactcacg gctgtctcct gtttttaacg gagtacatag tacacttaat tctgatttcg
     1021 gaaaagcggt cacatcgagg ggccatagta gcgggtcgtt tttttctgcg gctccggctc
     1081 tggctgctgc tcacgcagct tctcggcgta ggcgcggtcg tgctgcctga tcaacgcatc
     1141 aagcggctga cgttcctgct caagctctcg acctgcgcgc gcaagctctc tacctgactg
     1201 ctcaagtgct gacacacccg gtcgctgtgc gtcagcgcct gtgaggtagc ctcgaacatg
     1261 tgctgcaagc tgctgtagct gtcctgccac gcctgctgct gttgctcgta gcttgtctgt
     1321 aagctctcta aggcgctcag aagctgtttt tccatctcgg tcatggtttt ggtcatcctc
     1381 ggtgttaaaa acgcgctgtg tcgtttcagg gcgctctgac ggggttattt cgccgtgtat
     1441 ttcactacgg tgttgtcggt cgtcgatgta taggtttcca cgccgtgcgc ctgcttcggc
     1501 agcaccacca tgtaggtgtt ccggtgcttg tcgtcgctgt agatcgccac gcccgcgccg
     1561 cttttcgctt tcaggttcgc cagctgctgg ctgtagctgt ccatttcgct caggcgcgag
     1621 gtgatgatcg taccctgaaa ccagattatc ccccccatga tgccgatcag cagggcgaag
     1681 cagaggaata cccacgccat cgccgctgaa acggaggttc tgatcatgcc cgtcagcctg
     1741 ccgttctgct cgcggatagc gttgctgatg ctctgcgagc ttgattgcag ttccgcgctg
     1801 atagacgtct ccagcctcgc gaactcgcgc ttcacgctct gctcggtatc ctgcgcctgc
     1861 tgcttcgatt tctcctcgaa gcccttcgcc aaatttaaaa tctcgctcat aaatcattcc
     1921 tttcagccgg atatttcggc cgccgtccgg atcggcaatg ctgatgctac ttttcgtttc
     1981 ccgcgctacg gtcaggccgt agctttccag ctgcgtcacc acgtcctgcc ggctgcggat
     2041 cacgccctgc tgcatcaggt tcatcaggcc ggcggtgatt ttctctgccg cctgctgttt
     2101 gtcgcggggc agatcgctgg cctgcgtcag cggacggcgg taggtcgggt cattcgggtc
     2161 gcgcagcccc agccggtcgt tggtcagggt ctgccaggcg ttgacgcggg gacggtcggc
     2221 gcggtcaaag tagggttgca ggcgttttcc actctgcaat tcgatgttcg ggatgacaaa
     2281 attcagctca agccgtccct tgtcgcgatg ctctacccac aggcaggcgt actggtcgcg
     2341 gtcgagtccg gtcagcagcg tgtgctccca ttcgtccatc aggcgcgatt tctcggcgtc
     2401 tgcaatgtca ggttcctgga atgaaagcac gccggaagtg taggcgcggg caaagttgca
     2461 gccgtcgatc agctcacgca catgttcagg attgccgcgc agtacgctgg cctgttcgcg
     2521 ctgccggtct tttcccagca ggtaatccac aggaccgctg cccgaacccg caccccgcga
     2581 atgaatttta acgatcacgg ttctgctcca gcaggtcgcc aagctgccga tcaaggctag
     2641 tcagtacgac aagcagcgaa gcacgttcag agggcgtcag ggtgtcagtc tggttcagac
     2701 ggcgggcaat ctggttcagg ttgttaccga ttccgctgac ctgtcgcagc aattcgggcg
     2761 ccacatcggg cacacggcgc ctgcgtgaag tgtgttcacc cagaccaagc tgacgcagcc
     2821 actccgcaag gtgagtccgg tcgcagcgat caagcagtcg ctgatgctcg gtttcggtga
     2881 gccggatttt gatctctttc gttcgctttt ccataggctc cgctgagaga aaattcgcac
     2941 cactgtgaga atttttcgca gtggatgccg ggggtttcgg ggggcggcga gccccctgaa
     3001 ccagtcacag tggcacctcg ttagagggga cgctgtgtgt actggcttag tgtaaggtgc
     3061 agtatataag attatgtggt ggctgcaaaa aaaagccctc tgctagagag ggctgttatc
     3121 tgatataggc ttgtttagtc tcacgatgaa aagtgagtga tgatctgctc tactttttct
     3181 ttgttctgga aaaatctagc cagatagctg ttaggataat tagactggat gtattcaaat
     3241 atgcttttag ctagttcaag agtatcaaaa gagacgctat tcttgtcata ggtttttatg
     3301 ccattaactg tatttatggg ttgtattttc cccattaaaa tactaataaa tacatagtta
     3361 ccatgcgtca gcagtgatgg aattttacta tattcatctt ctgatgagtt agatgcttta
     3421 gtaattgtat cttttaaaac atcgaaacat actctgtata aattaacagc attgataaca
     3481 gaaataccgg atggcggatt tcttgggtta aaaacttgtt cgtaaagatt gccctctgtt
     3541 gtatcaaaaa aacgacctct attagacttc aaagttgcaa taagttgagg tttctttgat
     3601 tcgcaaatta gtgcatttaa tgagtcatct atatcgataa cattagaagc agctatccct
     3661 gaatcttcct gtcgtaagag cttatatgta taacccccaa caaagtttat ttctctctgt
     3721 attttttgct gttcaggtct ttgtgttgtg aaatctctgc cagtaactct attctgagta
     3781 ttgttgtact tagttacgtc acctaaaaaa acaggatctt tcgcatttat aaacctaatc
     3841 atcactcgag ctttgtcttt tttctcctcg ggtatgctat caaatatagc cccaatagag
     3901 cttacagttt gcgccccatt tattatgttt aactttttaa atccgaatat tccaattttc
     3961 cgagatgctc cagcattagc tatgctctca tctacctctt catatgttgc agtaatcccg
     4021 ttgttatagt accaaaagtt ctctgggcta ttttcgatgg tagacatgat ccctgcattt
     4081 actgatgtcg aatcacccaa gacacttctt atatttttct cgaaaagcgc atacttgtat
     4141 tttttccacc aatcatgtat cacccttgca gcaatcgttc cgtagattgc gccgtaaggt
     4201 tcagtgatct caccatacga ctctaatatt acattactta tatctatagc tccggtagat
     4261 tgattgctca agctagtaga tatgtcagta acattaggcg tttcaaatag tattgtatac
     4321 tcatccctag attctaaatc tctaaacaac agcgctttgt tttggctttt ctcccaaaaa
     4381 tcaatctctc caatcacttc tgagcttaac ccttgggttc ctgaataaat aaaaacgcat
     4441 atgcatttat agctactact agtgatagcc gtagtcactg attctttgtg ctctaaaaat
     4501 ctatcattaa atgaattgag atcgttagct ataacttttg cacatgcgtc tttaaaccgt
     4561 ccaaaatctt ttattgttac agaaccattc ccatctttta tatattttga ctgtaccaaa
     4621 ataagttttt tagaacttgg gtttacataa acagcatcaa ttcccccatc atcgctacca
     4681 tcgcaaactg atgcagcagc aactccaggg tcgagttcat caccatacat ccttactgca
     4741 tgcgcagcaa tgcatcttgt gatcagaact tctcttctag cctcaccttt agagttagtg
     4801 ttttccatat taataaaaga accataggtt tcttctaggc tattagctaa ccttgcaagc
     4861 ccaacggttc tagtgtcgct attaaaatca tctcttgcca tgaatattcc tgtaatatgt
     4921 cgatttacta atccccatac cttcccacgg ggagtttatt gttggcctgc cgccaccttt
     4981 gctttttaat ccgcctaaac gacctctttt agattgaata tcgcttctat gagagttaat
     5041 tacgtactct ttaaatgaag atgctgtaaa gtttttttca gtccattttg caatgctttt
     5101 agctatccca ttcacctctt tttcatccag aggtgcaggg aattgcagat tgtaagcact
     5161 tgcgcgttcg tagcaggctt gtagccactg gtcatactcc ggccagccct gacggatggc
     5221 gcggtatgcc catttgcggg ttttgtcgaa cagggtgcag ttacggccta agccgtagtc
     5281 agcaacgatg tctttgtcgc tcgctgcatt caggtcgaga aaatcagcca gccagtccag
     5341 cgtgtagagt tccggctgcc atacggcaat tttccagtgt ccgtggttcg gatttttgca
     5401 gattagtccc gaataccccg catcagcctc taatttttta cgtagcgcat tctccacggc
     5461 agcggcgtag cgcagcggct tcattttccc gtcaggtgcg gtgcgtatcg aggtttccag
     5521 cgcgtacagc aggtgcgcgt gtccgttttc cgggttggtg atggtcagcg tgggcgcggg
     5581 cgcgttgcga tcgctccagt cgatggcggc accggcgcga tcgacgtcga at
//
