LOCUS       NZ_CP050752             4074 bp    DNA     circular CON 09-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain ST46
            plasmid pST46-2, complete sequence.
ACCESSION   NZ_CP050752
VERSION     NZ_CP050752.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14450162
            Assembly: GCF_012050025.1
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  JOURNAL   Unpublished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                     :: ST46
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 33x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/09/2023 11:43:47
            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)                     :: 5,193
            CDSs (total)                      :: 5,068
            Genes (coding)                    :: 4,922
            CDSs (with protein)               :: 4,922
            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)              :: 146
            CDSs (without protein)            :: 146
            Pseudo Genes (ambiguous residues) :: 0 of 146
            Pseudo Genes (frameshifted)       :: 42 of 146
            Pseudo Genes (incomplete)         :: 113 of 146
            Pseudo Genes (internal stop)      :: 21 of 146
            Pseudo Genes (multiple problems)  :: 28 of 146
            Pseudo Genes (short protein)      :: 1 of 146
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP050752.1.
            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="ST46"
                     /serovar="Typhimurium"
                     /isolation_source="Diarrheal patient"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pST46-2"
                     /geo_loc_name="China:Shanghai"
                     /lat_lon="31.23 N 121.47 E"
                     /collection_date="2011-05-26"
                     /collected_by="Shanghai Municipal Center for Disease
                     Control and Prevention"
     gene            complement(join(3872..4074,1..52))
                     /gene="mobC"
                     /locus_tag="HEC87_RS25780"
                     /old_locus_tag="HEC87_25780"
     CDS             complement(join(3872..4074,1..52))
                     /gene="mobC"
                     /locus_tag="HEC87_RS25780"
                     /old_locus_tag="HEC87_25780"
                     /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            231..2390
                     /gene="mobQ"
                     /locus_tag="HEC87_RS25785"
                     /old_locus_tag="HEC87_25785"
     CDS             231..2390
                     /gene="mobQ"
                     /locus_tag="HEC87_RS25785"
                     /old_locus_tag="HEC87_25785"
                     /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            complement(2648..3340)
                     /locus_tag="HEC87_RS25790"
                     /old_locus_tag="HEC87_25790"
     CDS             complement(2648..3340)
                     /locus_tag="HEC87_RS25790"
                     /old_locus_tag="HEC87_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(54..230)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          231..589
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.333"
                     /coverage="100.0"
                     /evalue="8.460000000000002e-179"
     Typing          complement(2649..3340)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          145..2387
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.064"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gctgtaatct cgcctcagca tcagcaatct tctgttcgag cgttctgctc atgatgtaac
       61 tccgtgcgcg atgaaaaatc gcattttagc gcgtcactgg tagtttaaaa actgagctgg
      121 cataatgcac ggcaaatcac gaagtgcgca cttatacaat ctccactccg tttcgattgt
      181 gtgcgccctg cggggctgaa agaaaactac aaaaaggcat tacggcagaa atggcgattt
      241 atcatctcag catgaaaatt atctccagaa gcagcggcta cagcgccgta gcttccgctg
      301 cctatcgttc cggttcactg atgcttgatg agcgtaccgg actgactcac gactacaccc
      361 gcaaaagcgg tgtggctgaa gctgtgattc tgacccccgc gacagcccct gcctggtgta
      421 cgaaccgtgc cgaactctgg aatgccgttg agaaggccga acgccggaag aactcacaac
      481 ttgcgcggga aattgaactc gctatccccc gtgaactgcc gcaggatgcc gcacgggaaa
      541 ccgttctcgc ctttgtcaga gaaaactttg tcagtcaggg catgattgct gatgtggcgt
      601 tccatcacat ggataaaaca aatccccatg cgcacatcat gctgaccacg agggctgtcg
      661 gacctgctgg gttcggcgga aaggtcaggg actggaacga ccggacacat gccgagacgt
      721 ggcgtgcatc atgggctgac catgcaaaca gagcactggc gaacgccggt tatcaggaag
      781 agatagacca tcgttcatac gagcgacagg ggcttgagaa aacgcctggt attcacctcg
      841 gaaagtctgc ctgtgcgatg gaaacacgcg gtatcgaaac agaacgcggc gaacagaatc
      901 gtctgattaa caggcttaac ctggaaatac agatttcccg cactgaactc aggaacagcg
      961 ggctgacaga gcctgcccgc cgtgtggctg accttctgaa tatcgtgctt cctgacaacg
     1021 caacttcgta cacactacgt gacatcatcg aagcgttgcc gaaggacagt aatgcggcat
     1081 ggaaactcac cagtaatgcc atgtcgatga tggcagatat gcaggcgacg cgcagacgct
     1141 gggaagagct gaacaccgaa cgaaaggaag cgatgagcca tgctgccagc ctgaaaaaat
     1201 catcaccgtt ttcgtccggt ttttcccgta ttcccctgat gcaatgggcg gcaccggaat
     1261 accgtagcga acagggaaaa attcagtcgc tgagccagca aatggaaaaa ttgcgacagc
     1321 attaccggaa ggtggagaaa caggacattc ccgcgagtca gacggcattt gaaaaacagt
     1381 ggcagcagtg gggggcatcc ggccttgcag ctctcagagt ccagttgctt aaacgtgaag
     1441 aggaattgcg ccggaaggag caggaggata cagaacgtag tcgcacggag cgacgagcgg
     1501 aacagctcag gaaaaatgac aatgccgtta tggattcagg ggtactgagc gcagtcgtta
     1561 cggggtatgg cgaggccccc atgcctggta acggggaaat gacctgttac cttctgcttc
     1621 acaaccggaa cggagaatac acgctctggg ggaacgagct ggagaaatac cgcaccagaa
     1681 tctttgagcg tgttgattta atgcgtgaca ggagtggtta tatctgtgac cgaagcgaaa
     1741 tcggtcaaca tccaccactg caacgtgttt attcctctgc gacctttgag caacttctga
     1801 cgcaggtttg ccagacatgg ccgcaatata cccgcaatct ccgccagccg aagacatggc
     1861 cggagtcttt ctgtcttgga gaagaccgcc agccagccat gccatcactg gcagcaagga
     1921 aggtggattt tacgcaggga cgtctgccac cgacgctgat gccggtaatg agttctgtcg
     1981 accgggaaac ccgccagctt cagcttttgc tggtcatggg cgtggatgac tctctgggcg
     2041 gtgttgtccg gcttaatggt acgctgtatc ccgcgtttgc cgttccctca gccgataaca
     2101 gccagctggt catcagtgca ctgaccgata aggggttacg gtatgcaggg tatggtgttg
     2161 ccgtaaatca cgatgcagac agccacatat cacctgcgcc ggaacttatg gagtttcatc
     2221 tgaaaacccg tgaggtaccg ctttttgctg ccgtcaacac accagaaaaa cagccggatc
     2281 atctgttccg ctcgctgggt ttcaatcgta cctgggacga atggcggcgc gaggaagatg
     2341 caagaacaca caccaccgag aggagacatg atcgcggttg gtcacagtga atgtgaacaa
     2401 tattttgttt tgtttaacat cgtgttatgt tcgttgatgt tcttcgatgt tcatcgacag
     2461 ggatgaatgc aagaagcaca ctcacataac gcaagcatag ttttgttttt ccgcccccaa
     2521 aaattggggg ttcttttttc gctgcatcag agcgtttttg gcgcaatttt tcacttcaat
     2581 agtaccttcg cactactaac acaaaaaaaa cgcagcaggg agcgttttag gtgccttaaa
     2641 atcgatttta gatcgtcatc ttgatctgtt tgtcttcctt gaagcgaaaa tgcagggcta
     2701 caaccgtgcg cccctttttg atcgtctcaa ccgttacagc caggtcgctt tttttgttca
     2761 gttcgtcaac acagggtttt attagtattt tatttaagtc tctgaattgt ttgtatttat
     2821 tttcaatccc taacattgaa cgaaagtcat taagagcaat aattctctct cccgtactgc
     2881 ggaattgctg gaggaactcg tatattctta tactgtaact acttgataaa cctgatatgt
     2941 tttttataac aacgcgcgtg aattgcccct tcagttgcgt cagataaggc attaccgcgt
     3001 cagaaaaggt tattcgagcc ttggcctcac ctttagcgta ctgtgcccga tactggatcc
     3061 agcggaactc ctcacgcttc tcgtcattct tgagaatgat cgacctgtcc cataaacgat
     3121 cgatcgcttc ctgtaactga acctcggcat ttttccgccc catgtcaggg aatgaatcaa
     3181 aatattccgc agcggtaatg gtcattgtct tttgcaattc agcatcagca ccagatttca
     3241 atcgactgat acacagcaac agaaaacgtt gttcctgtag ggtcaacttg tagctggcct
     3301 caaccaaagc attcgacttg taggcaatca agtccgacat acaaagatcc cgttcaaatg
     3361 tggtgatgct ttaatgtgcc ccacaaataa gaaatgtgga atattttttt ttatatcctc
     3421 acatttctgt gaataacacc ttaaattcct ccacctttac cttaaattcc tccacctaaa
     3481 caccttaaat tcctccacat ataccttaaa ttcctccaca tataccactg caacatattg
     3541 attttattaa tgaatttcgc ccctaaaaca agtattaaaa acaagatctt aaaaacaaga
     3601 tctaaaaact taacggcgag cctgtggata acttggggtg ctgaaaacaa aaaacaaata
     3661 aaaacaatgt gttgcaagaa agtagaattg caagttccga atactcccct tccaaccctg
     3721 tggaaatcca gtattcatgc gggttcagcg catatcacct gccgaaaaac cgtgcgtatg
     3781 tgctcaacct ggcgacggat tcacttccgc ttcctcgccc actcgctcgc taacgctcgg
     3841 tcgctggggc tgcggcgagc ggacgataca atcactgtcc tggcagcgcc tccagctcgt
     3901 taatcagcgg cagtatgcgc gtcacatcag cctgtcgtgt cacctctgcc ttcaggaact
     3961 ggagtaacca ggcacgcaac tgcacctcct ccggctttct gacctttgcc agcaatgctg
     4021 cacccacaac aaccttctgc gctgtgtcca agctccggct cttcgccttc aggc
//
