LOCUS       NZ_CP061130             2442 bp    DNA     circular CON 09-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain S304
            plasmid pS304_4, complete sequence.
ACCESSION   NZ_CP061130
VERSION     NZ_CP061130.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15962523
            Assembly: GCF_015697825.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella
            typhimurium)
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 2442)
  AUTHORS   Hua,X. and Yu,Y.
  TITLE     Plasmid dynamics of mcr-1-positive Salmonella spp. in a general
            hospital in China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2442)
  AUTHORS   Hua,X. and Yu,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-SEP-2020) Sir Run Run Shaw Hospital, Zhejiang
            University, Qingchundong 3 RD, Hangzhou, Zhejiang 310016, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-JUN-2020
            Assembly Method                   :: other: Unicycler v. 0.4.8
            Assembly Name                     :: S304
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 300x
            Sequencing Technology             :: Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/09/2023 11:57:19
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,200
            CDSs (total)                      :: 5,077
            Genes (coding)                    :: 4,934
            CDSs (with protein)               :: 4,934
            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)              :: 143
            CDSs (without protein)            :: 143
            Pseudo Genes (ambiguous residues) :: 0 of 143
            Pseudo Genes (frameshifted)       :: 41 of 143
            Pseudo Genes (incomplete)         :: 115 of 143
            Pseudo Genes (internal stop)      :: 21 of 143
            Pseudo Genes (multiple problems)  :: 31 of 143
            Pseudo Genes (short protein)      :: 1 of 143
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP061130.1.
            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..2442
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="S304"
                     /serovar="Typhimurium"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pS304_4"
                     /geo_loc_name="China:Hangzhou"
                     /lat_lon="30.2 N 120.2 E"
                     /collection_date="2015-05"
                     /collected_by="Xiaoting Hua"
     gene            join(1979..2442,1..505)
                     /gene="mobV"
                     /locus_tag="IBY93_RS25775"
                     /old_locus_tag="IBY93_25760"
     CDS             join(1979..2442,1..505)
                     /gene="mobV"
                     /locus_tag="IBY93_RS25775"
                     /old_locus_tag="IBY93_25760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000024818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobV family relaxase"
                     /protein_id="WP_000024818.1"
                     /translation="MANYAIMRCKKLTGMGSVASALQHCYRERETPNANAERTPENYCS
                     VSKSTDQAMGRVRELLPEKRRKDAVLAVEYVMTASPEWWKEATPRQQAEFFARSEQWLE
                     KKYGKDRVVAAVVHRDEATPHLSAFVVPLTQDGRLSAKEFIGGRSKMREDQSTYAESVK
                     KLGLERGIEGSRATHQTVQHYYESINRGTRSQVSISPEALEPRVLRKGIFTKDVEDQAA
                     IAKRLSHAVNDGFAGTIAMASQSAQNAKRARELQKTMDAQQKRLQSVTEPFKGLSREQM
                     TEILMMAQRFKQQNQEKEKQQRIEREKQRQTRSRGMGGMER"
                     /name="mobV"
     gene            complement(575..805)
                     /locus_tag="IBY93_RS25780"
                     /old_locus_tag="IBY93_25765"
     CDS             complement(575..805)
                     /locus_tag="IBY93_RS25780"
                     /old_locus_tag="IBY93_25765"
                     /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_124788667.1"
                     /translation="MMNAEDKLFKNVDRLMLHDSLKKNEVLTVWERTFLSSVYSIYRRT
                     SGNKYSTKGLSPKQKNAAFSILKKHNYHLND"
                     /name="hypothetical protein"
     gene            complement(792..1274)
                     /locus_tag="IBY93_RS25785"
                     /old_locus_tag="IBY93_25770"
     CDS             complement(792..1274)
                     /locus_tag="IBY93_RS25785"
                     /old_locus_tag="IBY93_25770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001565850.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_223375251.1"
                     /translation="MNTKKISRLERHTYMDENGEVKQDSKIETFSIPAEPPYVKLYIAD
                     IAMIHGLSKSQNDVLLQLAMLIGWDGFVSVSKTRFEKTIQPRVHIEYQTFKNIIAALVD
                     KQIFFRAGRGELEANPFLFARGDWPSIYERRKKIELKISYDTNGRTVQTKVMDDEC"
                     /name="hypothetical protein"
     Typing          3..502
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.407"
                     /coverage="96.0"
                     /evalue="7.57e-84"
     Typing          1971..2440
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.631"
                     /coverage="96.0"
                     /evalue="3.54e-99"
ORIGIN
        1 gagcacctac gctgaatcag taaaaaaact gggtcttgag cgcggcatcg agggaagccg
       61 cgccacgcat cagacagttc agcactacta cgaatcgata aaccgtggca cccgtagcca
      121 ggtatcgatc tcgccggagg cgctggagcc gcgtgtattg cggaagggca ttttcaccaa
      181 agacgtggaa gatcaggcag ccatagccaa acgtctaagc cacgcagtga acgatggctt
      241 tgcaggaacc atcgctatgg cctctcagag cgcccagaac gcaaaaagag cgcgtgagct
      301 acagaagact atggatgcgc agcagaaacg cctacagagc gtcacagagc cttttaaggg
      361 gctttccaga gagcagatga ccgaaatcct gatgatggct cagcggttta agcagcaaaa
      421 ccaggaaaag gaaaaacagc agcgtattga acgtgaaaaa cagcgacaga cgcgatcgcg
      481 tggcatgggt ggtatggagc gttagttttg atgcgatgca ggatagggct aacgccgcaa
      541 agtgacgtca tttgcggcat tcaccacgaa aaaattaatc attcagatgg taattatgtt
      601 tttttaaaat agaaaaagct gcgtttttct gctttggtga caaaccctta gttgagtatt
      661 tattaccgct agttctacga tatatgctgt aaacactgct taaaaaagta cgctcccaaa
      721 cagtcagaac ctcattcttt tttagtgaat catgcagcat tagcctgtct acatttttaa
      781 aaagtttatc ttcagcattc atcatccatt accttcgtct gcaccgttct tccattggtg
      841 tcataactga tctttaactc aattttcttt cttctttcgt aaattgatgg ccagtctccc
      901 cgtgcaaaaa gaaaggggtt agcttcaagt tccccacgcc ctgcccggaa gaatatttgt
      961 ttatctacaa gagccgcaat tatgttttta aaggtctgat attcaatatg aaccctgggc
     1021 tgtatggttt tttcaaatct agtttttgat acagacacaa acccatccca tccaatcagc
     1081 attgccaatt gtaaaagcac atcattttga gattttgata aaccatgaat catcgcaatg
     1141 tctgcaatgt atagcttgac gtagggaggt tcggctggga tggaaaaggt ctcgatctta
     1201 gagtcttgtt ttacctcacc gttttcatcc atgtatgtat gccgttcaag cctagaaatc
     1261 tttttcgtat tcactccagc cccacgtttc gccatgattt agtactcgca tttaagtact
     1321 aaagagacat acagtcaagt cctttgtatc aagtacgatt agtacttgag gtgagtacga
     1381 ttagtccttg aggtgagtac gattagtact tgaggtgagt acgattggta cttgaggtga
     1441 gtacgattct tcgctctagc ccttggtaca agcgggttcc catatctata tctatatatt
     1501 aagggggaaa ataagggctg aaaaacggca tttttagaca ctgaaaaact gccttttttt
     1561 agcaaggagt gtacgcattt ctatgtacgg ggagtggaaa ttccgcttcc tcgctttggc
     1621 tgttcgttcc tcgtcgcgtt gctcctgcgg tacgcctcag ccaaagctgc ggcgagcggt
     1681 tcctgctctt tcaaagacga tttcattgcc tgatttcgtc aagggcgagc gtagcgagtg
     1741 ccatttaccc ttgacgacac tccggataaa acaggcttgg cagtggtggg gggtggcgcg
     1801 aagcgacgcc ttccacctgc cagaccgccg ttgattttga ccttctggca gcttgctgcc
     1861 cgaacgattt tgcgtagcaa agtctagtga gtacactatc atcttgatag tggcccgccg
     1921 gaggtatcgc aatgcgctcc cccgcctggc tgaatgaatg ccggaatcag gggggaacat
     1981 ggcgaactac gcgataatgc gctgcaaaaa gctgacggga atgggaagcg tggccagcgc
     2041 gttgcagcac tgctaccgag agcgtgagac gccgaacgct aacgctgaac ggacaccaga
     2101 aaactactgc tctgtgtcca aatcaacgga tcaggcaatg gggcgtgtgc gggagctgct
     2161 gccggaaaaa cgccgtaaag atgcggtact ggccgttgaa tacgttatga cagcaagccc
     2221 tgagtggtgg aaagaggcca caccacggca gcaggcggag tttttcgccc gctctgagca
     2281 atggctggag aagaaatacg ggaaggatcg tgttgtggcg gcggtggttc accgggacga
     2341 ggccaccccg cacctgtctg cgttcgtggt gccattgacg caggatggac ggctgtccgc
     2401 gaaagagttt attggcgggc ggtcaaagat gcgtgaagat ca
//
