LOCUS       NZ_CP050733             4593 bp    DNA     circular CON 13-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain ST101
            plasmid pST101-2, complete sequence.
ACCESSION   NZ_CP050733
VERSION     NZ_CP050733.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14450166
            Assembly: GCF_012051385.1
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 4593)
  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  JOURNAL   Unpublished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 4593)
  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                     :: ST101
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 19x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/13/2023 04:24:37
            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)                     :: 5,212
            CDSs (total)                      :: 5,089
            Genes (coding)                    :: 4,921
            CDSs (with protein)               :: 4,921
            Genes (RNA)                       :: 123
            rRNAs                             :: 7, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 168
            CDSs (without protein)            :: 168
            Pseudo Genes (ambiguous residues) :: 0 of 168
            Pseudo Genes (frameshifted)       :: 56 of 168
            Pseudo Genes (incomplete)         :: 126 of 168
            Pseudo Genes (internal stop)      :: 22 of 168
            Pseudo Genes (multiple problems)  :: 34 of 168
            Pseudo Genes (short protein)      :: 1 of 168
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP050733.1.
            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..4593
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="ST101"
                     /serovar="Typhimurium"
                     /isolation_source="Diarrheal patient"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pST101-2"
                     /geo_loc_name="China:Shanghai"
                     /lat_lon="31.23 N 121.47 E"
                     /collection_date="2013-09-12"
                     /collected_by="Shanghai Municipal Center for Disease
                     Control and Prevention"
     gene            complement(join(4422..4593,1..668))
                     /locus_tag="HEC91_RS25865"
                     /old_locus_tag="HEC91_25865"
     CDS             complement(join(4422..4593,1..668))
                     /locus_tag="HEC91_RS25865"
                     /old_locus_tag="HEC91_25865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001354646.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     gene            complement(860..1009)
                     /locus_tag="HEC91_RS26440"
     CDS             complement(860..1009)
                     /locus_tag="HEC91_RS26440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032194431.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPERHVKTPLAAAIGNRLEELVLK
                     LCAG"
                     /name="hypothetical protein"
     gene            complement(1679..1870)
                     /locus_tag="HEC91_RS25880"
                     /old_locus_tag="HEC91_25880"
     CDS             complement(1679..1870)
                     /locus_tag="HEC91_RS25880"
                     /old_locus_tag="HEC91_25880"
                     /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_001677262.1"
                     /translation="MTKQEKTAINMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1933..2256
                     /locus_tag="HEC91_RS25885"
                     /old_locus_tag="HEC91_25885"
     CDS             1933..2256
                     /locus_tag="HEC91_RS25885"
                     /old_locus_tag="HEC91_25885"
                     /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_001677263.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2465..>2899
                     /locus_tag="HEC91_RS26350"
                     /pseudo=""
     CDS             2465..>2899
                     /locus_tag="HEC91_RS26350"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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            2934..3494
                     /locus_tag="HEC91_RS25895"
                     /old_locus_tag="HEC91_25895"
     CDS             2934..3494
                     /locus_tag="HEC91_RS25895"
                     /old_locus_tag="HEC91_25895"
                     /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_000067488.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            3501..3734
                     /locus_tag="HEC91_RS25900"
                     /old_locus_tag="HEC91_25900"
     CDS             3501..3734
                     /locus_tag="HEC91_RS25900"
                     /old_locus_tag="HEC91_25900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_000137388.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          1507..1591
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(938..1496)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.761"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2247..3832
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agtgaaggtt gcattataga tggaaagtat ttgaaaacct cttcatctct gttgaaatta
       61 actaaaaact tgtagtcatc atttataaat ctcaagcata cagcgtcaag cttatcgcct
      121 tttcttatta ttatttcttt ataggaaaga tatttttcag aagataagtc ccacatcaag
      181 cgaaaatctc tctttgcgaa cgagttcgcg tcatcattga aaagagatga tgtgatggct
      241 ttggatagac cttctgtgtt tatctctttg ttggatgggt agtaaatttt attaattgct
      301 ttcattctct caaatgatga atataggtca ttatgccacc ttgttgaaat cactccttta
      361 gttatattct ccttgctaaa attaagccct gtatcaaaaa taaatgcagc catcagtgaa
      421 tatgatatgt tttttattaa ctcagactta aatggttccg ctatggagta gtacagtgat
      481 aaaataacta aaaataaaag gtattgtctt acctttcccg atgagtatat gtaaaggcga
      541 tatttattta ttgatagttt tattttgtat ggaatgatct catttctgtc atatcctctt
      601 cgtggtggag caaaacaaaa gaaacatgca gctattaata aaacaaaaaa gatgaacagt
      661 gtaagcaagt tcggctcctg tgtatgctca ctatgcatga ttgtcttgag atctaacgat
      721 cctgaaggta gtcttgtccg taaacgaaaa aaccgcccag caaggcggct tttcgaaggt
      781 tctcagagca gcaactcttt gaaccaaggt aactggcttg gaggagcaca gccaccaaat
      841 ctgtcctttc agtttagcct taaccggcgc ataacttcaa gactaactcc tctaaacggt
      901 taccaatggc tgctgccagt ggcgttttta cgtgtctttc cgggttggac tcaagacgat
      961 agttaccgga taaggcgcag cggtcgggct gaacgggggg ttcgtgcaca cagcccagct
     1021 tggagcgaac gacctacacc gggccgagat accaacagcg tgagctatga gaaagcgcca
     1081 cgcttcccga agggagaaag gcggacaggt atccggtaag cggcagggtc ggaacaggag
     1141 agcgcacgag ggagcttcca gggggaaacg cctggtatct ttatagtcct gtcgggtttc
     1201 gccacctctg acttgagcat ctgtttttgt gatgctcgtc aggggggcgg agcctatgga
     1261 aaaacgccag cggcgcggcc ttcttcctgt tcctggcctt ttgctcacat gtttcttttg
     1321 gcgttatccc ctgattctgt ggataaccgc atcaccgtct ttgagtgagc tgataccgct
     1381 cgccgcagcc gaacgaccga gcgtagcgag tcagtgagcg aggaagcgga agagcgcctg
     1441 atgcggcatt ttctccttac gcatctgtgc ggtatttcac accgcatatg gtgcactttt
     1501 cttataatcc gcactgatgc cacatagtta agccagtata cactccgcta tcgctacgtg
     1561 actgggtcag ggctgcgccc cgacacccgc taaaacccgc tgacgcgccc tgacgggctt
     1621 gtctgctccc ggcatccgct cacaggcaag ctgtgaacgt ctccgggagc tgcatgtttc
     1681 agttgctttc accgtcatcg ccgaagcgtg cgaggcaact acggtagagt tcgtcggcgt
     1741 ggtcgtgaag tgattcgcag atgtctgcct gttcgtccgc gtccagctcg ttgagttttt
     1801 ccagcagggt cagcgtctgg cttctgataa agcgggccat gttaatggct gttttttcct
     1861 gtttggtcat ggtcttaagg ctccttaata ggggattttt tagggggaat gataccgatg
     1921 aaacgcgaga agatgctcac gatacgggtt agcgatgagg agcacgcccg gttactggaa
     1981 cgctgcgagg gtaaacgact ggcagaatgg atgcggcggg tctgtctggg ggagccggtt
     2041 gcgcgcacag gaaaactgcc gacactatcg ccgccattgc tgcggcatct ggctgccatc
     2101 gggaacaatc tgaaccagac agcccggaag gtgaacagcg gccactggtc ttcgattgac
     2161 cgggttcatg tggtggccgc tctgatggcc atcgagggtg aattgcgcca gttgcggcag
     2221 gctgtcaggg aacagggggg acgggatgat agttaaattt catgccaggg ggaaaggcgg
     2281 tggaagtggc ccggtcgatt acctgctggg gcgggagcgt aaccgcgaag gcgcaacggt
     2341 gctccggggt aacccggaag aaatccggga actcattgat gccacgccat tttcgaagaa
     2401 atacacgtca ggcgttctgt cgttcgcgga gaaggagtta ccgccgggtg aacgcgaaag
     2461 agtgatgacg agctttgagc gtgttcttat gcccggtctc gaaaaagacc agtacagcat
     2521 tctctgggtg gaacaccagg ataaggggcg gctcgaactg aattttgtca ttccgaacat
     2581 ggaactacag agcggtaagc gcctccagcc gtactacgac cgtgcggaca ggccgaggat
     2641 aaatgcctgg cagacgctgg ttaatcatca ttacgggctg cgtgacccga acgcaccgga
     2701 gaacagacgg acgcttgtca caccgaataa tctgccaaaa gcgaaacagg aggccgcaga
     2761 agcgattaca cggggtcttg aggcgcttta ccgtgccgga gcaataaaaa cgcgtcagga
     2821 tgtcactgag gcgctcacag cggcaggttt tgaggtggtg aggacaacca gaagcagtat
     2881 cagtattgcc gacccggagg gggggcggaa tctcaggcta aagggggcgc tgtatgagca
     2941 atcttttaca aatgggaacg gacttcgaga agaaactgaa agagcgagcc gcttctaccg
     3001 agaacatgct gaacagcgag ttcaggaagc tagaagagtc tgtagacaag gcactgagct
     3061 taaacaggca gaaaatcaga gacgctatca gcgaacatac aacatccgtg aaacagcaac
     3121 tggatacgct gagcaccacc gtgagcacgc agctcagcac cacagaggcc gaactgtccc
     3181 ggcagcagaa aaacctgctc tggcaggtga tcaaagggcg ggtactgttt ccggcgctga
     3241 ccgcgctcag cgtcacgggc ggcattttcc tggggtgctg ggggctgatt cagtggcagg
     3301 aaagcaggat tgcgaaaaat atcttgacca tcagagagca ggaaaacacg ctggcgaaac
     3361 tcgaggcaaa aacctggggg gtgacgttcg tcaatggcga gaacgggaaa tttctggtgc
     3421 tgccggacgg ggtgaaaggg gaaaacacct ggacggtggg cgacaagaac gccgtgaggc
     3481 tggtcaggga gtaaacgagt atgacggaac tggaagggca tttgctgaac gccttagagc
     3541 atttgcaaca ggactatatg cggcggctga acgagtggga gagcgccttc gcagaattgc
     3601 agaagatgca cgcggttacg caacagaaca acgcgatact gaacgagcgt gtcgtgaact
     3661 tgagtcagca ggtgcagcta ttagccggac aagtcgaccg cttgagtcgg ttatttatca
     3721 cgaacaacag ataagggatg aacaggagcg tcaggcgcag gagcttgccc ggcgctggca
     3781 tgaagagcag gaacccgaag cgcggatctg gcgtggcccg tcaatgggga tgtgaccggg
     3841 gtaccccctg aaatcgagcc agtttgtggc acgccctacc cggatggcgc caatgttaat
     3901 gtacgtacat tagcattaac aatatccaaa cctccccatt ttgccccgtt cgacggctgg
     3961 aacgtgcgaa actgatcgtc attcagtttc gcgcataact atgcatgagg ttaaaattta
     4021 ccaggcgcga tcgcggcagt ttttcgggtg gtttgttgct gtttttacct gtctgctgcc
     4081 gtgatcgcgc tgaacgcgtt taagcggtac gcgcaatgcg acgttatggt aaatacggag
     4141 tattttaatt gcgggccttt gttgtatatc tctgtcgttt gtccccgggg ggaagcatta
     4201 ctgctaacaa gtcccgtgag aaaactgcgc aatcgtattg cgcaccatga acctattctc
     4261 aaccgcaatc tggaggatga ttttgctacg ataaagagaa ttatcgcgta tcggtgtcag
     4321 cattcattgg agtggatgct gaaaaaccag gtgttactcc ctctacttac acttaaacct
     4381 ctctaaaaat ataagtaagt actatcgagg gctatcatga actatggtgc cctctgagca
     4441 tagctaccca ttacttcttc tatgtcattg aataattcat ttcttaactc taagtattct
     4501 agtaactcca tttctaatga ctctgtcgtg aacttaaatc tagaaggatc tttgattgag
     4561 tttactagtc ttgataacgc tctatatgtt ttg
//
