LOCUS       NZ_CP050755             4074 bp    DNA     circular CON 13-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain ST45
            plasmid pST45-2, complete sequence.
ACCESSION   NZ_CP050755
VERSION     NZ_CP050755.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14450161
            Assembly: GCF_012052225.1
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 4074)
  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  JOURNAL   Unpublished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 4074)
  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                     :: ST45
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 40x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/13/2023 03:30:19
            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)                     :: 5,192
            CDSs (total)                      :: 5,067
            Genes (coding)                    :: 4,924
            CDSs (with protein)               :: 4,924
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 143
            CDSs (without protein)            :: 143
            Pseudo Genes (ambiguous residues) :: 0 of 143
            Pseudo Genes (frameshifted)       :: 40 of 143
            Pseudo Genes (incomplete)         :: 112 of 143
            Pseudo Genes (internal stop)      :: 21 of 143
            Pseudo Genes (multiple problems)  :: 28 of 143
            Pseudo Genes (short protein)      :: 1 of 143
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP050755.1.
            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..4074
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="ST45"
                     /serovar="Typhimurium"
                     /isolation_source="Diarrheal patient"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pST45-2"
                     /geo_loc_name="China:Shanghai"
                     /lat_lon="31.23 N 121.47 E"
                     /collection_date="2011-05-25"
                     /collected_by="Shanghai Municipal Center for Disease
                     Control and Prevention"
     gene            complement(join(2467..4074,1..552))
                     /gene="mobQ"
                     /locus_tag="HEC86_RS25780"
                     /old_locus_tag="HEC86_25780"
     CDS             complement(join(2467..4074,1..552))
                     /gene="mobQ"
                     /locus_tag="HEC86_RS25780"
                     /old_locus_tag="HEC86_25780"
                     /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="MobQ family relaxase"
                     /protein_id="WP_084568118.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRTERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREVPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            731..985
                     /gene="mobC"
                     /locus_tag="HEC86_RS25785"
                     /old_locus_tag="HEC86_25785"
     CDS             731..985
                     /gene="mobC"
                     /locus_tag="HEC86_RS25785"
                     /old_locus_tag="HEC86_25785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091747.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            1517..2209
                     /locus_tag="HEC86_RS25790"
                     /old_locus_tag="HEC86_25790"
     CDS             1517..2209
                     /locus_tag="HEC86_RS25790"
                     /old_locus_tag="HEC86_25790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_001281403.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(195..553)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.333"
                     /coverage="100.0"
                     /evalue="8.460000000000002e-179"
     Typing          554..730
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          1518..2209
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2..639)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.592"
                     /coverage="100.0"
                     /evalue="2.67e-135"
ORIGIN
        1 ctcttcctga taaccggcgt tcgccagtgc tctgtttgca tggtcagccc atgatgcacg
       61 ccacgtctcg gcatgtgtcc ggtcgttcca gtccctgacc tttccgccga acccagcagg
      121 tccgacagcc ctcgtggtca gcatgatgtg cgcatgggga tttgttttat ccatgtgatg
      181 gaacgccaca tcagcaatca tgccctgact gacaaagttt tctctgacaa aggcgagaac
      241 ggtttcccgt gcggcatcct gcggcagttc acgggggata gcgagttcaa tttcccgcgc
      301 aagttgtgag ttcttccggc gttcggcctt ctcaacggca ttccagagtt cggcacggtt
      361 cgtacaccag gcaggggctg tcgcgggggt cagaatcaca gcttcagcca caccgctttt
      421 gcgggtgtag tcgtgagtca gtccggtacg ctcatcaagc atcagtgaac cggaacgata
      481 ggcagcggaa gctacggcgc tgtagccgct gcttctggag ataattttca tgctgagatg
      541 ataaatcgcc atttctgccg taatgccttt ttgtagtttt ctttcagccc cgcagggcgc
      601 acacaatcga aacggagtgg agattgtata agtgcgcact tcgtgatttg ccgtgcatta
      661 tgccagctca gtttttaaac taccagtgac gcgctaaaat gcgatttttc atcgcgcacg
      721 gagttacatc atgagcagaa cgctcgaaca gaagattgct gatgctgagg cgagattaca
      781 gcgcctgaag gcgaagagcc ggagcttgga cacagcgcag aaggttgttg tgggtgcagc
      841 attgctggca aaggtcagaa agccggagga ggtgcagttg cgtgcctggt tactccagtt
      901 cctgaaggca gaggtgacac gacaggctga tgtgacgcgc atactgccgc tgattaacga
      961 gctggaggcg ctgccaggac agtgattgta tcgtccgctc gccgcagccc cagcgaccga
     1021 gcgttagcga gcgagtgggc gaggaagcgg aagtgaatcc gtcgccaggt tgagcacata
     1081 cgcacggttt ttcggcaggt gatatgcgct gaacccgcat gaatactgga tttccacagg
     1141 gttggaaggg gagtattcgg aacttgcaat tctactttct tgcaacacat tgtttttatt
     1201 tgttttttgt tttcagcacc ccaagttatc cacaggctcg ccgttaagtt tttagatctt
     1261 gtttttaaga tcttgttttt aatacttgtt ttaggggcga aattcattaa taaaatcaat
     1321 atgttgcagt ggtatatgtg gaggaattta aggtatatgt ggaggaattt aaggtgttta
     1381 ggtggaggaa tttaaggtaa aggtggagga atttaaggtg ttattcacag aaatgtgagg
     1441 atataaaaaa aaatattcca catttcttat ttgtggggca cattaaagca tcaccacatt
     1501 tgaacgggat ctttgtatgt cggacttgat tgcctacaag tcgaatgctt tggttgaggc
     1561 cagctacaag ttgaccctac aggaacaacg ttttctgttg ctgtgtatca gtcgattgaa
     1621 atctggtgct gatgctgaat tgcaaaagac aatgaccatt accgctgcgg aatattttga
     1681 ttcattccct gacatggggc ggaaaaatgc cgaggttcag ttacaggaag cgatcgatcg
     1741 tttatgggac aggtcgatca ttctcaagaa tgacgagaag cgtgaggagt tccgctggat
     1801 ccagtatcgg gcacagtacg ctaaaggtga ggccaaggct cgaataacct tttctgacgc
     1861 ggtaatgcct tatctgacgc aactgaaggg gcaattcacg cgcgttgtta taaaaaacat
     1921 atcaggttta tcaagtagtt acagtataag aatatacgag ttcctccagc aattccgcag
     1981 tacgggagag agaattattg ctcttaatga ctttcgttca atgttaggga ttgaaaataa
     2041 atacaaacaa ttcagagact taaataaaat actaataaaa ccctgtgttg acgaactgaa
     2101 caaaaaaagc gacctggctg taacggttga gacgatcaaa aaggggcgca cggttgtagc
     2161 cctgcatttt cgcttcaagg aagacaaaca gatcaagatg acgatctaaa atcgatttta
     2221 aggcacctaa aacgctccct gctgcgtttt ttttgtgtta gtagtgcgaa ggtactattg
     2281 aagtgaaaaa ttgcgccaaa aacgctctga tgcagcgaaa aaagaacccc caatttttgg
     2341 gggcggaaaa acaaaactat gcttgcgtta tgtgagtgtg cttcttgcat tcatccctgt
     2401 cgatgaacat cgaagaacat caacgaacat aacacgatgt taaacaaaac aaaatattgt
     2461 tcacattcac tgtgaccaac cgcgatcatg tctcctctcg gtggtgtgtg ttcttgcatc
     2521 ttcctcgcgc cgccattcgt cccaggtacg attgaaaccc agcgagcgga acagatgatc
     2581 cggctgtttt tctggtgtgt tgacggcagc aaaaagcggt acctcacggg ttttcagatg
     2641 aaactccata agttccggcg caggtgatat gtggctgtct gcatcgtgat ttacggcaac
     2701 accataccct gcataccgta accccttatc ggtcagtgca ctgatgacca gctggctgtt
     2761 atcggctgag ggaacggcaa acgcgggata cagcgtacca ttaagccgga caacaccgcc
     2821 cagagagtca tccacgccca tgaccagcaa aagctgaagc tggcgggttt cccggtcgac
     2881 agaactcatt accggcatca gcgtcggtgg cagacgtccc tgcgtaaaat ccaccttcct
     2941 tgctgccagt gatggcatgg ctggctggcg gtcttctcca agacagaaag actccggcca
     3001 tgtcttcggc tggcggagat tgcgggtata ttgcggccat gtctggcaaa cctgcgtcag
     3061 aagttgctca aaggtcgcag aggaataaac acgttgcagt ggtggatgtt gaccgatttc
     3121 gcttcggtca cagatataac cactcctgtc acgcattaaa tcaacacgct caaagattct
     3181 ggtgcggtat ttctccagct cgttccccca gagcgtgtat tctccgttcc ggttgtgaag
     3241 cagaaggtaa caggtcattt ccccgttacc aggcatgggg gcctcgccat accccgtaac
     3301 gactgcgctc agtacccctg aatccataac ggcattgtca tttttcctga gctgttccgc
     3361 tcgtcgctcc gtgcgactac gttctgtatc ctcctgctcc ttccggcgca attcctcttc
     3421 acgtttaagc aactggactc tgagagctgc aaggccggat gccccccact gctgccactg
     3481 tttttcaaat gccgtctgac tcgcgggaat gtcctgtttc tccaccttcc ggtaatgctg
     3541 tcgcaatttt tccatttgct ggctcagcga ctgaattttt ccctgttcgc tacggtattc
     3601 cggtgccgcc cattgcatca ggggaatacg ggaaaaaccg gacgaaaacg gtgatgattt
     3661 tttcaggctg gcagcatggc tcatcgcttc ctttcgttcg gtgttcagct cttcccagcg
     3721 tctgcgcgtc gcctgcatat ctgccatcat cgacatggca ttactggtga gtttccatgc
     3781 cgcattactg tccttcggca acgcttcgat gatgtcacgt agtgtgtacg aagttgcgtt
     3841 gtcaggaagc acgatattca gaaggtcagc cacacggcgg gcaggctctg tcagcccgct
     3901 gttcctgagt tcagtgcggg aaatctgtat ttccaggtta agcctgttaa tcagacgatt
     3961 ctgttcgccg cgttctgttt cgataccgcg tgtttccatc gcacaggcag actttccgag
     4021 gtgaatacca ggcgttttct caagcccctg tcgctcgtat gaacgatggt ctat
//
