LOCUS       CP050744                4073 bp    DNA     circular BCT 06-APR-2020
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain ST56
            plasmid pST56-5, complete sequence.
ACCESSION   CP050744
VERSION     CP050744.1
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 4073)
  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  JOURNAL   Unpublished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 4073)
  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..4073
                     /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="pST56-5"
                     /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            complement(join(2039..4073,1..125))
                     /locus_tag="HEC89_25835"
     CDS             complement(join(2039..4073,1..125))
                     /locus_tag="HEC89_25835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="QIU23338.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAECRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="MobA/MobL family protein"
     gene            313..567
                     /locus_tag="HEC89_25840"
     CDS             313..567
                     /locus_tag="HEC89_25840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091744.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /protein_id="QIU23339.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobilization protein"
     gene            1099..1791
                     /locus_tag="HEC89_25845"
     CDS             1099..1791
                     /locus_tag="HEC89_25845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QIU23340.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(2..126)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1e-58"
     Typing          127..306
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.238"
                     /coverage="100.0"
                     /evalue="2.68e-81"
     Typing          complement(3841..4073)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.863"
                     /coverage="100.0"
                     /evalue="2.0100000000000002e-110"
     Typing          1100..1791
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2043..4072)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.705"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tagtcgtgag tcagtccggt acgctcatca agcatcagtg aaccggaacg ataggcagcg
       61 gaagctacgg cgctgtagcc gctgcttctg gagataattt tcatgctgag atgataaatc
      121 gccatttctg ccgtaatgcc tttttgtagt tttctttcag ccccgcaggg cgcacacaat
      181 cgaaacggag tggagattgt ataagtgcgc actttgtgca ctttgtgatt tgtcgtgcat
      241 tatgccagct cagtttttaa actaccagtg acgcgctaaa atgcgatttt tcatcgcgca
      301 cggagttaca tcatgagcag aacgctcgaa cagaagattg ctgatgctga ggcgagatta
      361 cagcgcctga aggcgaagag ccggagcctg gacacagcgc agaaggttgt tgtgggtgca
      421 gcattgctgg caaaggtcag aaagccggag gaggtgcagt tgcgtgcctg gttactccag
      481 ttcctgaagg cagaggtgac acgacaggct gatgtgacgc gcatactgcc gctgattaac
      541 gagctggagg cgctgccagg acagtgattg tatcgtccgc tcgccgcagc cccagcgacc
      601 gagcgttagc gagcgagtgg gcgaggaagc ggaagtgaat ccgtcgccag gttgagcaca
      661 tacgcacggt ttttcggtag gtgatatgcg ctgaacccgc atgaatactg gatttccaca
      721 gggttggaag gggagtattc ggaacttgca atcctgcttt cttgcaacac attgttttta
      781 ttggtttttt gttttcagcg ccccaagtta tccacaggct cgccgttaag tttttagatc
      841 ttgtttttaa gatcttgttt ttaatacttg ttttagggtc aaaattcatt aataaaatca
      901 atatgttata gcggtatatg tggaggaatt taaggtaaag gtggagggat ttaaggtgtt
      961 taggtggagg aatttaaggt aaaggtggag gaatttaagg tgttattcac agaaatgtga
     1021 ggatataaaa aaaaatattc cacatttctt atttgtgggg cacattaaag catcaccaca
     1081 tttgaacggg atctttgtat gtcggacttg attgcctaca agtcgaatgc tttggttgag
     1141 gccagctaca agttgaccct acaggaacaa cgttttctgt tgctgtgtat cagtcgattg
     1201 aaatctggtg ctgatgctga attgcaaaag acaatgacca ttaccgctgc ggaatatttt
     1261 gattcattcc ctgacatggg gcggaaaaat gccgaggttc agttacagga agcgatcgat
     1321 cgtttatggg acaggtcgat cattctcaag aatgacgaga agcgtgagga gttccgctgg
     1381 atccagtatc gggcacagta cgctaaaggt gaggccaagg ctcgaataac cttttctgac
     1441 gcggtaatgc cttatctgac gcaactgaag gggcaattca cgcgcgttgt tataaaaaac
     1501 atatcaggtt tatcaagtag ttacagtata agaatatacg agttcctcca gcaattccgc
     1561 agtacgggag agagaattat tgctcttaat gactttcgtt caatgttagg gattgaaaat
     1621 aaatacaaac aattcagaga cttaaataaa atactaataa aaccctgtgt tgacgaactg
     1681 aacaaaaaaa gcgacctggc tgtaacggtt gagacgatca aaaaggggcg cacggttgta
     1741 gccctgcatt ttcgcttcaa ggaagacaaa cagatcaaga tgacgatcta aaatcgattt
     1801 taaggcacct aaaacgctcc ctgctgcgtt ttttttgtgt tagtagtgcg aaggtactat
     1861 tgaagtgaaa aattgcgtca aaagcgctct aatgcagcga aaaaagaacc cccaattttt
     1921 gggggcggaa aaacaaaact atgctgtgtg tgcttcttgc attcatccct gtcgatgaac
     1981 atcgaagaac atcgacgaac ataacacgat gttaaacaaa acaaaatatt gttcacattc
     2041 actgtgacca accgcgatca tgtctcctct cggtggtgtg tgttcttgca tcttcctcgc
     2101 gccgccattc atcccaggta cgattgaaac ccagagagcg gaacagatga tccggctgtt
     2161 tttctggtgt gttgacggca gcaaaaagcg gtgcctcacg ggttttcaga tgaaactcca
     2221 taagttccgg cgcaggtgat atgtggctgt ctgcatcgtg atttacggca acaccatacc
     2281 ctgcataccg taacccctta tcggtcagtg cactgatgac cagctggctg ttatcggctg
     2341 agggaacggc aaacgcggga tacagcgtac cattaagccg gacaacaccg cccagagagt
     2401 catccacgcc catgaccagc aaaagctgaa gctggcgggt ttcccggtcg acagaactca
     2461 ttaccggcat cagcgtcggt agcagacgtc cctgcgtaaa atccaccttc cttgctgcca
     2521 gtgatggcat ggctggctgg cggtcttctc caagacagaa agactccggc catgtcttcg
     2581 gctggcggag attgcgggta tattgcggcc atgtctggca aacctgcgtc agaagttgct
     2641 caaaggtcgc agaggaataa acacgttgca gtggtggatg ttgaccgatt tcgcttcggt
     2701 cacagatata accactcctg tcacgcatta aatcaacacg ctcaaagatt ctggtgcggt
     2761 atttctccag ctcgttcccc cagagcgtgt attctccgtt ccggttgtga agcagaaggt
     2821 aacaggtcat ttccccgtta ccaggcatgg gggcctcgcc ataccccgta acgactgcgc
     2881 tcagtacccc tgaatccata acggcattgt catttttcct gagctgttcc gctcgtcgct
     2941 ccgcgcgact acgttctgta tcctcctgct ccttccggcg caattcctct tcacgtttaa
     3001 gcaactggac tctgagagct gcaaggccgg atgcccccca ctgctgccac tgtttttcaa
     3061 atgccgtctg actcgcggga atgtcctgtt tctccacctt ccggtaatgc tgtcgcaatt
     3121 tttccatttg ctggctcagc gactggattt ttccctgttc gctacggtat tccggtgccg
     3181 cccattgcat caggggaata cgggaaaaac cggacgaaaa cggcgatgat tttttcaggc
     3241 tggcagcatg gctcatcgct tcctttcgtt cggtgttcag ctcttcccag cgtctgcgcg
     3301 tcgcctgcat atctgccatc atcgacatgg cattactggt gagtttccat gccgcattac
     3361 tgtccttcgg caacgcttcg atgatgtcac gtagtgtgta cgaagttgcg ttgtcaggaa
     3421 gcacgatatt cagaaggtca gccacacggc gggcaggctc tgtcagcccg ctgttcctga
     3481 gttcagtgcg ggaaatctgt atttccaggt taagcctgtt aatcagacga ttctgttcgc
     3541 cgcgttctgt ttcgataccg cgtgtttcca tcgcacaggc agactttccg aggtgaatac
     3601 caggcgtttt ctcaagcccc tgtcgctcgt atgaacgatg gtctatctct tcctgataac
     3661 cggcgttcgc cagtgctctg tttgcatggt cagcccatga tgcacgccac gtctcggcat
     3721 gtgtccggtc gttccagtcc ctgacctttc cgccgaaccc agcaggtccg acagccctcg
     3781 tggtcagcat gatgtgcgca tggggatttg ttttatccat gtgatggaac gccacatcag
     3841 caatcatgcc ctgactgaca aagttttctc tgacaaaggc gagaacggtt tcccgtgcgg
     3901 catcctgcgg cagttcacgg gggatagcga gttcaatttc ccgcgcaagt tgtgagttct
     3961 tccggcattc ggccttctca acggcattcc agagttcggc acggttcgta caccaggcag
     4021 gggctgtcgc gggggtcaga atcacagctt cagccacacc gcttttgcgg gtg
//
