LOCUS       CP050743                4715 bp    DNA     circular BCT 06-APR-2020
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain ST56
            plasmid pST56-4, complete sequence.
ACCESSION   CP050743
VERSION     CP050743.1
DBLINK      BioProject: PRJNA615288
            BioSample: SAMN14450164
KEYWORDS    .
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  JOURNAL   Unpublished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                     :: ST56
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 113x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 03/31/2020 17:33:49
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.11
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 5,169
            CDSs (total)                      :: 5,043
            Genes (coding)                    :: 4,884
            CDSs (with protein)               :: 4,884
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 159
            CDSs (without protein)            :: 159
            Pseudo Genes (ambiguous residues) :: 0 of 159
            Pseudo Genes (frameshifted)       :: 69 of 159
            Pseudo Genes (incomplete)         :: 92 of 159
            Pseudo Genes (internal stop)      :: 25 of 159
            Pseudo Genes (multiple problems)  :: 25 of 159
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..4715
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="ST56"
                     /serovar="Typhimurium"
                     /isolation_source="Diarrheal patient"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pST56-4"
                     /geo_loc_name="China:Shanghai"
                     /lat_lon="31.23 N 121.47 E"
                     /collection_date="2011-07-21"
                     /collected_by="Shanghai Municipal Center for Disease
                     Control and Prevention"
     gene            370..1326
                     /locus_tag="HEC89_25815"
     CDS             370..1326
                     /locus_tag="HEC89_25815"
                     /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="QIU23334.1"
                     /translation="MYLIEEALTSWLLNEYKKPVITKEEISLQIYLFYLKKEYNGERIY
                     QIRKNKAGPNEFEKNILKLLKSGVLSRVESNDKHHAYPHLIGGFYEVFFVKGNDGSPEN
                     DIVCSTYPYGYLSYLSAMDWHNITDKIPKIIHFTTCRSEQWKNKFYHDFQKDNPDIDEA
                     KQFMPRFPRNSEVNGIKIIVTQETNYVEPMKARNSPVRVSSIGKTFMDMTRRPDYCGGE
                     EHVLESFIEHGKKYAPLIIKEVDKLGRHIDKVRVGFILDRIIGVNNKKISEWKQEAGKY
                     RGSSKVLSPKSPFSPYFDEEWFISINVDMVKSYGKRN"
                     /name="hypothetical protein"
     gene            1310..2176
                     /locus_tag="HEC89_25820"
     CDS             1310..2176
                     /locus_tag="HEC89_25820"
                     /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="QIU23335.1"
                     /translation="MEKEINNWIEESGGKYRLMRQAVHIILKSISIEESLNEMMVMKGG
                     TLLGVKHGSDRYTKDIDFSTEKKLSEIDLGDFFNRFNDSMDVAEAELGYGIKCKVQSHK
                     IQPNAQGTFPTVQINIAFCDRSNASAMKRLESNQSPSVINIDFSFNEKTYDFDFLSLDG
                     DDDNDSVKTYSLTDLMAEKYRSVLQQKVRERNREQDIYDINYLLGKYEFSRQDKYKILE
                     SLLKKSEGKQLDNLLNVKGIRDVEIIERSSQRYQDLSSTVKSLPLFEDAYEKVACFYES
                     LPWNIFK"
                     /name="nucleotidyl transferase AbiEii/AbiGii toxin family
                     protein"
     gene            2173..2826
                     /locus_tag="HEC89_25825"
     CDS             2173..2826
                     /locus_tag="HEC89_25825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016249761.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein phosphatase 2C family protein"
                     /protein_id="QIU23337.1"
                     /translation="MIAFSFSDIGNRCENLDLLSTINCQNDVFGMVIMDGYSCSEWNMK
                     ILSGRLDKCVFSGDLNKDIIEPCKSVPVKAAVCFLFKNNTHLHIYNAGDCRVYNKSGVL
                     LTEDNSVAWKRLKENGIDNKKIPHLVCYCPDRNYLTSFVDFCSDEIIFNHSVFDLNDEN
                     KEVILCTDGFWEHFNDGTVIDLMKDNPESNLAKFTKNIPGNAENHTVCYVRFPS"
                     /name="protein phosphatase 2C family protein"
     gene            complement(3815..4009)
                     /locus_tag="HEC89_25830"
     CDS             complement(3815..4009)
                     /locus_tag="HEC89_25830"
                     /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="QIU23336.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          3660..3742
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          4046..4144
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          4269..4524
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(3090..3647)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.821"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cggcagaatc gcgttcagcg cgttttagcg gtgcgcgtaa tgcgacgtta tggtaaatga
       61 cgctgaaaaa tgatctttta cgctcatcgt ttatgagcaa cagatgtcct aatcatggat
      121 ttgaactata accgccgctg aattgatcgc atgaggtgtt atgaaaacgg tgatataagt
      181 aaactttttc ttgacttcct ccttattatc ctataaaata aatccttagg atttatttta
      241 taggatatca aaaatataaa aatggcaaat gcttgtttgt tattattttt tccttgacaa
      301 tcaatctcta atagaatata cgtccttagg acgtatattc tattagagac taaaccgaaa
      361 aggttgaata tgtatcttat cgaagaagcg ctaacgtctt ggttgttgaa tgaatataaa
      421 aaaccagtca taaccaaaga agaaatctct ttgcagattt acctttttta tttaaaaaaa
      481 gaatataatg gtgagaggat atatcaaatt agaaagaaca aagcaggacc taatgaattt
      541 gaaaaaaata tattaaaatt attaaagtca ggggttttat caagagttga aagtaacgat
      601 aagcatcatg cttaccccca tttaattggc ggtttctatg aggtcttttt tgttaaaggt
      661 aacgatggtt ctccggaaaa tgatatagtg tgctctacgt atccatatgg atacttatcc
      721 tatttatccg ctatggattg gcataacatc acagataaaa tacccaagat aatccacttt
      781 acgacatgtc gttccgaaca gtggaagaat aagttctatc atgattttca aaaggataat
      841 cctgatatag acgaagccaa acaattcatg cctagatttc caagaaattc tgaggtcaat
      901 ggaataaaaa ttatcgttac acaagaaaca aattatgttg agccaatgaa ggctcgtaat
      961 tcccctgtca gggtatcatc tatcggtaag acctttatgg atatgaccag gcggcctgat
     1021 tactgtggtg gtgaggagca tgtattggaa tcatttattg agcacggtaa aaaatatgca
     1081 cctctgatta taaaggaagt cgataagctt ggccgtcata ttgacaaggt aagggttgga
     1141 ttcattttgg atagaattat tggggttaat aataaaaaaa taagcgaatg gaaacaagag
     1201 gcgggtaaat acagaggtag ttcgaaagtg ctatctccaa agagtccatt ctcaccttac
     1261 tttgatgaag aatggtttat ttctattaat gttgatatgg ttaagtctta tggaaaaaga
     1321 aattaataat tggatcgaag agtctggtgg gaagtacagg ttgatgcggc aggctgtaca
     1381 tataatactt aaatctattt ctatagagga gagtttgaat gaaatgatgg ttatgaaggg
     1441 agggactctt cttggtgtta agcatggtag tgatagatac acaaaggata ttgatttttc
     1501 taccgaaaaa aaactttctg aaattgactt gggggatttt ttcaataggt ttaatgactc
     1561 aatggatgtt gctgaggctg aattgggata tggtattaaa tgtaaagttc aatctcataa
     1621 aattcaacct aatgcacaag gaacatttcc aactgtacag ataaatatag ccttttgcga
     1681 tcgttctaat gcgtctgcaa tgaaaaggct tgaatctaat caatcacctt cagtgataaa
     1741 tatcgatttt agctttaacg aaaaaacgta tgattttgac tttttatcat tagatggtga
     1801 tgatgacaat gatagcgtaa agacctacag cttaactgat ttgatggctg aaaaatatcg
     1861 atccgttttg caacaaaaag ttagagagag aaatcgagag caagatatat atgatatcaa
     1921 ttatctttta ggtaaatatg agttttctcg gcaagataag tataaaatac tggagtctct
     1981 tttaaaaaag agtgaaggta aacaattgga taatctctta aacgttaaag gtataaggga
     2041 tgtagaaatt atcgagcgtt ccagtcagcg atatcaggat ttatcatcca ccgttaaatc
     2101 attacctctt tttgaagatg cttatgaaaa agttgcctgt ttctatgaaa gtcttccgtg
     2161 gaatatattc aaatgatagc gttcagtttt agtgatattg gtaacagatg tgaaaactta
     2221 gacttattgt ctacgataaa ttgtcaaaat gatgtgtttg gaatggttat tatggatggg
     2281 tattcctgct ctgagtggaa tatgaaaatt ctctctggta ggttagataa gtgcgtgttt
     2341 tctggtgatc tgaataaaga tattattgaa ccatgcaagt cagttcctgt taaggctgca
     2401 gtatgtttcc tttttaaaaa taatacgcac ctccatatat ataacgcagg agattgccgt
     2461 gtatataaca aaagtggagt ccttctaaca gaggataact cggttgcctg gaaaagatta
     2521 aaggaaaatg gaatcgataa taaaaaaata cctcacctcg tttgttattg cccagacaga
     2581 aattatctaa catcatttgt tgatttctgc tctgatgaga taattttcaa tcattcagtt
     2641 tttgatttaa atgatgaaaa caaagaggtt attttatgta ctgatgggtt ttgggagcat
     2701 tttaatgatg gtactgttat tgacctcatg aaagataacc cagaatctaa cttggctaaa
     2761 tttactaaaa atatcccggg taacgcagag aatcatacgg tttgctacgt tagattccct
     2821 tcttgatttc gtgttttttg aagaagctat tgagatcttc gtgtcatata gataatctct
     2881 tttctgtaaa agaaaaaaac cgcctttgcg gggcggtttt ctcttaggtt caaagagttt
     2941 gcggctcgaa gaaccaaggt aactggcttg gaggagcgca gtcaccaaaa cctgttcttt
     3001 cagtttagcc ttaactggcg catgacttca agactaactc ctctaaatca gttaccagtg
     3061 gctgctgcca gtggcgttaa ggcgtgtctt accgggttgg actcaagacg atagttaccg
     3121 gataaggcgc agcagtcggg ctgaacgggg ggttcgtgca cacagcccag cttggagcga
     3181 acgacctaca ccgaactgag ataccaacag cgtgagctat gagaaagcgc cacgcttccc
     3241 gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg agagcgcacg
     3301 agggagccac cagggggaaa cgtctggtat ctttaagtcc tgtcgggttt cgccacctct
     3361 gacttgagcg tcgatttctg tgatgctcgt caggggggcg gagcctatgg aaaaacgcct
     3421 gcggcgcggc cttcttcctg ctcctggtct tttgctcaca tgttctttcc ggccttatcc
     3481 cctgattctg tggataaccg tgctgccgtt tttgtgtaag tcagtaccgc tcgccgcagc
     3541 cgaacgaccg agcgtagcga gtcagtgagc gaggaagcgg aaaagcgcct ggacgcgcat
     3601 tttctcctta cgcatctgtg cggaatttca cacccggcat ggggcacttt tcatacaatc
     3661 tgcactgatg ccgcatagtt aagccagtat acactccgct atcgctacgt gactgggtca
     3721 gggcttcgcc ccgacacccg ctgacgcgcc ctggcgggct tgtctgctgc cgaaaacgct
     3781 cgcggacaag ccgtgagcgc ctccgtcagc ttcgttatgt tcctgtttca ctttcggtct
     3841 caaagcgaac ctggatgctg ttctggagtt cttccgcgag ttcgtgcagt cgttcgcaca
     3901 tggccgcctg ttcgtcggca tccagagcat ccagtttttc aagcagtgtc aggctctggc
     3961 ttttgataaa tcgcgccata ttcagcgcag tttgttgctg tttgttcacc ttccgttgtt
     4021 ctccgtcagt accgggtgtc gggtggaccc tgaccaggtg gtaattgtaa gacgttgcgg
     4081 gcgacggtat tacaattgca catcctgtcc tgttttttta ggacgtatca tggcacagca
     4141 tatcaactga taaataatcc ctgtgcagtg cagccgctgt tgcataaaat ttcgctctgc
     4201 gtcgagtgtt tcttaatcaa taattccgct gatactccgg aaaaacgcga gtctgttctc
     4261 atgcctgaaa tgcccacacc ccacgcaaaa acaatttttt gctgattttt ctttataaat
     4321 agagagttat gacaaattag ttcttcttgc tctctttgtg atatttaaaa aagcggtgtc
     4381 ggcgcggtgt tgtagctgcg ccaacaccgc tttttagggg tggtactgac tattttcata
     4441 aaaaacatca ttttatatta ggggtgctgc tagcggcgcg gtgtgttttt ttacaggacg
     4501 cccctggggg cgctgctagg ggtgtctgtt cagatatgta gcaatgagtc agggattcac
     4561 gaactgaaaa tgtccgaaaa tgtgtctcat gggcaccgta tgcgcccaaa ccgatcgcca
     4621 ttcactttca tgcatagcta tgcagtgagc tgaaagcgat cctgacgcat ttttccggtt
     4681 ttcgcttggt aaaacatctc tttttgcggt gttcg
//
