LOCUS       NZ_CP050738             4715 bp    DNA     circular CON 09-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain ST90
            plasmid pST90-4, complete sequence.
ACCESSION   NZ_CP050738
VERSION     NZ_CP050738.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14450165
            Assembly: GCF_012051625.1
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 4715)
  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  JOURNAL   Unpublished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 4715)
  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                     :: ST90
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 94x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/09/2023 12:00:55
            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)                     :: 5,136
            CDSs (total)                      :: 5,013
            Genes (coding)                    :: 4,845
            CDSs (with protein)               :: 4,845
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 168
            CDSs (without protein)            :: 168
            Pseudo Genes (ambiguous residues) :: 0 of 168
            Pseudo Genes (frameshifted)       :: 59 of 168
            Pseudo Genes (incomplete)         :: 123 of 168
            Pseudo Genes (internal stop)      :: 25 of 168
            Pseudo Genes (multiple problems)  :: 36 of 168
            Pseudo Genes (short protein)      :: 1 of 168
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP050738.1.
            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..4715
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="ST90"
                     /serovar="Typhimurium"
                     /isolation_source="feces"
                     /host="duck"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pST90-4"
                     /geo_loc_name="China:Shanghai"
                     /lat_lon="31.23 N 121.47 E"
                     /collection_date="2012-10-08"
                     /collected_by="Shanghai Municipal Center for Disease
                     Control and Prevention"
     gene            complement(640..834)
                     /locus_tag="HEC90_RS25500"
                     /old_locus_tag="HEC90_25500"
     CDS             complement(640..834)
                     /locus_tag="HEC90_RS25500"
                     /old_locus_tag="HEC90_25500"
                     /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_001041633.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1910..2866
                     /locus_tag="HEC90_RS25505"
                     /old_locus_tag="HEC90_25505"
     CDS             1910..2866
                     /locus_tag="HEC90_RS25505"
                     /old_locus_tag="HEC90_25505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000280763.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000280763.1"
                     /translation="MYLIEEALTSWLLNEYKKPVITKEEISLQIYLFYLKKEYNGERIY
                     QIRKNKAGPNEFEKNILKLLKSGVLSRVESNDKHHAYPHLIGGFYEVFFVKGNDGSPEN
                     DIVCSTYPYGYLSYLSAMDWHNITDKIPKIIHFTTCRSEQWKNKFYHDFQKDNPDIDEA
                     KQFMPRFPRNSEVNGIKIIVTQETNYVEPMKARNSPVRVSSIGKTFMDMTRRPDYCGGE
                     EHVLESFIEHGKKYAPLIIKEVDKLGRHIDKVRVGFILDRIIGVNNKKISEWKQEAGKY
                     RGSSKVLSPKSPFSPYFDEEWFISINVDMVKSYGKRN"
                     /name="hypothetical protein"
     gene            2850..3716
                     /locus_tag="HEC90_RS25510"
                     /old_locus_tag="HEC90_25510"
     CDS             2850..3716
                     /locus_tag="HEC90_RS25510"
                     /old_locus_tag="HEC90_25510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000409995.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nucleotidyl transferase AbiEii/AbiGii toxin
                     family protein"
                     /protein_id="WP_000409995.1"
                     /translation="MEKEINNWIEESGGKYRLMRQAVHIILKSISIEESLNEMMVMKGG
                     TLLGVKHGSDRYTKDIDFSTEKKLSEIDLGDFFNRFNDSMDVAEAELGYGIKCKVQSHK
                     IQPNAQGTFPTVQINIAFCDRSNASAMKRLESNQSPSVINIDFSFNEKTYDFDFLSLDG
                     DDDNDSVKTYSLTDLMAEKYRSVLQQKVRERNREQDIYDINYLLGKYEFSRQDKYKILE
                     SLLKKSEGKQLDNLLNVKGIRDVEIIERSSQRYQDLSSTVKSLPLFEDAYEKVACFYES
                     LPWDIFK"
                     /name="nucleotidyl transferase AbiEii/AbiGii toxin family
                     protein"
     gene            3698..4366
                     /locus_tag="HEC90_RS25515"
                     /old_locus_tag="HEC90_25515"
     CDS             3698..4366
                     /locus_tag="HEC90_RS25515"
                     /old_locus_tag="HEC90_25515"
                     /EC_number="3.1.3.16"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016249761.1"
                     /GO_function="GO:0004722 - protein serine/threonine
                     phosphatase activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="PP2C family serine/threonine-protein phosphatase"
                     /protein_id="WP_223195384.1"
                     /translation="MGYIQMIAFSFSDIGNRCENLDLLSTINCQNDVFGMVIMDGYSCS
                     EWNMKILSGRLDKCVFSGDLNKDIIEPCKSVPVKAAVCFLFKNNTHLHIYNAGDCRVYN
                     KSGVLLTEDNSVAWKRLKENGIDNKKIPHLVCYCPDRNYLTSFVDFCSDEIIFNHSVFD
                     LNDENKEVILCTDGFWEHFNDGTVIDLMKDNPESNLAKFTKNIPGNAENHTVCYVRFPS
                     "
                     /name="PP2C family serine/threonine-protein phosphatase"
     gene            complement(4588..4701)
                     /locus_tag="HEC90_RS25920"
     CDS             complement(4588..4701)
                     /locus_tag="HEC90_RS25920"
                     /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="hypothetical protein"
                     /protein_id="WP_001427893.1"
                     /translation="MHEPPVQPDCCALSGNYRLESNPVRHALTPLAAATGN"
                     /name="hypothetical protein"
     Typing          483..567
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.837"
                     /coverage="100.0"
                     /evalue="1.41e-35"
     Typing          871..969
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          1094..1349
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.899"
                     /coverage="89.0"
                     /evalue="2.61e-118"
     Typing          complement(2..472)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.869"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4593..4715)
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.161"
                     /coverage="100.0"
                     /evalue="5.420000000000001e-47"
ORIGIN
        1 agcgaacgac ctacaccgaa ctgagatacc aacagcgtga gctatgagaa agcgccacgc
       61 ttcccgaagg gagaaaggcg gacaggtatc cggtaagcgg cagggtcgga acaggagagc
      121 gcacgaggga gccaccaggg ggaaacgtct ggtatcttta agtcctgtcg ggtttcgcca
      181 cctctgactt gagcgtcgat ttctgtgatg ctcgtcaggg gggcggagcc tatggaaaaa
      241 cgcctgcggc gcggccttct tcctgttctt ggtcttttgc tcacatgttc tttccggcct
      301 tatcccctga ttctgtggat aaccgtgctg ccgtttttgt gtaagtcagt accgctcgcc
      361 gcagccgaac gaccgagcgt agcgagtcag tgagcgagga agcggtaaag cgcctggacg
      421 cgcattttct ccttacgcat ctgtgcggaa tttcacaccc ggcatggggc acttttcata
      481 caattcgcac tgatgccgca tagttaagtc agtatacact ccgctatcgc tacgtgactg
      541 ggtcagggct tcgccccgac acccgctgac gcgccctggc gggcttgtct gctgccgaaa
      601 acgctcgcgg acaagccgtg agcgcctccg tcagcttcgt tatgttcctg tttcactttc
      661 ggtctcaaag cgaacctgga tgctgttctg gagttcttcc gcgagttcgt gcagtcgttc
      721 gcacatggcc gcctgttcgt cggcatccag agcatccagt ttttcaagca gtgtcaggct
      781 ctggcttttg ataaatcgcg ccatattcag cgcagtttgt tgctgtttgt tcaccttccg
      841 ttgttctccg tcagtaccgg gtgtcgggtg gaccctgacc aggtggtaat tgtaagacgt
      901 tgcgggcgac ggtattacaa ttgcacatcc tgtcctgttt ttttaggacg tatcatggca
      961 cagcatatca actgataaat aatccctgtg cagtgcagcc gctgttgcat aaaatttcgc
     1021 tctgcgtcga gtgtttctta atcaataatt ccgctgatac tccggaaaaa cgcgagtctg
     1081 ttctcatgcc tgaaatgccc acaccccacg caaaaacaag tttttgctga tttttcttta
     1141 taaatagaga gttatgacaa attagttctt cttgctctct ttgtgatatt taaaaaagcg
     1201 gtgtcggcgc ggtgttgtag ctgcgccaac accgcttttt aggggtggta ctgactattt
     1261 tcataaaaaa catcatctta tattaggggt gctgctagcg gcgcggtgtg tttttttaca
     1321 ggacacccct gggggcgctg ctaggggtgt ctgttcagat atgtagcaat gagtcaggga
     1381 ttcacgaact gaaaatgtcc gaaaatgtgt ctcatgggca ctgtatgcgc ccaaaccgat
     1441 cgtcattcac tttcatgcat agctatgcag tgagctgaaa gcgatcctga cgcatttttc
     1501 cggtttaccc cggggagaac atctcttttt gcggtgttcg cggcagaatc gctttcagcg
     1561 cgttttagcg gtgcgcgcaa tgcgacgtta tggtaaatga cgctgaaaaa tgatctttta
     1621 cgctcatcgt ttatgagcaa cagatgtcct aatcatggat ttgaactata accgccgctg
     1681 aattgatcgc atgaggtgtt atgaaaacgg tgatataagt aaactttttc ttgacttcct
     1741 acttattatc ctataaaata aatccttagg atttatttta taggatatca aaaatataaa
     1801 aatggcaaat gcttgtttgt tattattttt ttcttgacaa tcaatctcta atagaatata
     1861 cgtccttagg acgtatattc tattagagac taaaccgaaa aggttgaata tgtatcttat
     1921 cgaagaagcg ctaacgtctt ggttgttgaa tgaatataaa aaaccagtca taaccaaaga
     1981 agaaatctct ttgcagattt acctttttta tttaaaaaaa gaatataatg gtgagaggat
     2041 atatcaaatt agaaagaaca aagcaggacc taatgaattt gaaaaaaata tattaaaatt
     2101 attaaagtca ggggttttat caagagttga aagtaacgat aagcatcatg cttaccccca
     2161 tttaattggc ggtttctatg aggtcttttt tgttaaaggt aacgatggtt ctccggaaaa
     2221 tgatatagtg tgctctacgt atccatatgg atacttatcc tatttatccg ctatggattg
     2281 gcataacatc acagataaaa tacccaagat aatccacttt acgacatgtc gttccgaaca
     2341 gtggaagaat aagttctatc atgattttca aaaggataat cctgatatag acgaagccaa
     2401 acaattcatg cctagatttc caagaaattc tgaggtcaat ggaataaaaa ttatcgttac
     2461 acaagaaaca aattatgttg agccaatgaa ggctcgtaat tcccctgtca gggtatcatc
     2521 tatcggtaag acctttatgg atatgaccag gcggcctgat tactgtggtg gtgaggagca
     2581 tgtattggaa tcatttattg agcacggtaa aaaatatgca cctctgatta taaaggaagt
     2641 cgataagctt ggccgtcata ttgacaaggt aagggttgga ttcattttgg atagaattat
     2701 tggggttaat aataaaaaaa taagcgaatg gaaacaagag gcgggtaaat acagaggtag
     2761 ttcgaaagtg ctatctccaa agagtccatt ctcaccttac tttgatgaag aatggtttat
     2821 ttctattaat gttgatatgg ttaagtctta tggaaaaaga aattaataat tggatcgaag
     2881 agtctggtgg gaagtacagg ttgatgcgcc aggctgtaca tataatactt aaatctattt
     2941 ctatagagga gagtttgaat gaaatgatgg ttatgaaggg agggactctt cttggtgtta
     3001 agcatggtag tgatagatac acaaaggata ttgatttttc taccgaaaaa aaactttctg
     3061 aaattgactt gggggatttt ttcaataggt ttaatgactc aatggatgtt gctgaggctg
     3121 aattgggata tggtattaaa tgtaaagttc aatctcataa aattcaacct aatgcacaag
     3181 gaacatttcc aactgtacag ataaatatag ccttttgcga tcgttctaat gcgtctgcaa
     3241 tgaaaaggct tgaatctaat caatcacctt cagtgataaa tatcgatttt agctttaacg
     3301 aaaaaacgta tgattttgac tttttatcat tagatggtga tgatgacaat gatagcgtaa
     3361 agacctacag cttaactgat ttgatggctg aaaaatatcg atccgttttg caacaaaaag
     3421 ttagagagag aaatcgagag caagatatat atgatatcaa ttatctttta ggtaaatatg
     3481 agttttctcg gcaagataag tataaaatac tggagtctct tttaaaaaag agtgaaggta
     3541 aacaattgga taatctctta aacgttaaag gtataaggga tgtagaaatt atcgagcgtt
     3601 ccagtcagcg atatcaggat ttatcatcca ccgttaaatc attacctctt tttgaagatg
     3661 cttatgaaaa agttgcctgt ttctatgaaa gtcttccgtg ggatatattc aaatgatagc
     3721 gttcagtttt agtgatattg gtaacagatg tgaaaactta gacttattat ctacgataaa
     3781 ttgtcaaaat gatgtgtttg gaatggttat tatggatggg tattcctgct ctgagtggaa
     3841 tatgaaaatt ctctctggta ggttagataa gtgcgtgttt tctggtgatc tgaataaaga
     3901 tattattgaa ccatgcaagt cagttcctgt taaggctgca gtatgtttcc tttttaaaaa
     3961 taatacgcac ctccatatat ataacgcagg agattgccgt gtatataaca aaagtggagt
     4021 ccttctaaca gaggataact cggttgcctg gaaaagatta aaggaaaatg gaatcgataa
     4081 taaaaaaata cctcacctcg tttgttattg cccagacaga aattatctaa catcatttgt
     4141 tgatttctgc tctgatgaga taattttcaa tcattcagtt tttgatttaa atgatgaaaa
     4201 caaagaggtt attttatgta ctgatgggtt ttgggagcat tttaatgatg gtactgttat
     4261 tgacctcatg aaagataacc cagaatctaa cttggctaaa tttactaaaa atatcccggg
     4321 taacgcagag aatcatacgg tttgctacgt tagattccct tcttgatttc gtgttttttg
     4381 aagaagctat tgagatcttc gtgtcatata gataatctct tttctgtaaa agaaaaaaac
     4441 cgcctttgcg gggcggtttt ctcttaggtt caaagagttt gcggctcgaa gaaccaaggt
     4501 aactggctta gaggagcgca gtcaccaaaa cctgttcttt cagtttagcc ttaactggcg
     4561 catgacttca agactaactc ctctaaatca gttaccagtg gctgctgcca gtggcgttaa
     4621 ggcgtgtctt accgggttgg actcaagacg atagttaccg gataaggcgc agcagtcggg
     4681 ctgaacgggg ggttcgtgca cacagcccag cttgg
//
