LOCUS       CP082745                3223 bp    DNA     circular BCT 09-SEP-2021
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium var. 5-
            strain CVM N16S070 plasmid pN16S070-7, complete sequence.
ACCESSION   CP082745
VERSION     CP082745.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN08113949
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium var. 5-
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium var. 5-
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3223)
  AUTHORS   Li,C., Tyson,G., Hsu,C.-H., Harrison,L., Strain,E., Tran,T.-T.,
            Tillman,G., Dessai,U., McDermott,P. and Zhao,S.
  TITLE     Long-read sequencing reveals evolution and acquisition of
            antimicrobial resistance and virulence genes in Salmonella enterica
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3223)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (27-JUL-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 3223)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-AUG-2021) CVM/OR, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-JUN-2020
            Assembly Method :: SMRTLink Microbial Assembly v. SMRTLink9.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 671x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 08/31/2021 18:30:13
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 5.2
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 4,994
            CDSs (total)                      :: 4,872
            Genes (coding)                    :: 4,744
            CDSs (with protein)               :: 4,744
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 128
            CDSs (without protein)            :: 128
            Pseudo Genes (ambiguous residues) :: 0 of 128
            Pseudo Genes (frameshifted)       :: 42 of 128
            Pseudo Genes (incomplete)         :: 85 of 128
            Pseudo Genes (internal stop)      :: 24 of 128
            Pseudo Genes (multiple problems)  :: 20 of 128
            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..3223
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium var. 5-"
                     /mol_type="genomic DNA"
                     /strain="CVM N16S070"
                     /serovar="Typhimurium var. 5-"
                     /isolation_source="chicken breast"
                     /sub_species="enterica"
                     /db_xref="taxon:1620419"
                     /plasmid="pN16S070-7"
                     /geo_loc_name="USA:NM"
                     /collection_date="2016"
                     /collected_by="FDA"
     gene            complement(join(2573..3223,1..114))
                     /locus_tag="CWX32_024940"
                     /pseudo=""
     CDS             complement(join(2573..3223,1..114))
                     /locus_tag="CWX32_024940"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial on complete genome; 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            complement(53..376)
                     /locus_tag="CWX32_024945"
     CDS             complement(53..376)
                     /locus_tag="CWX32_024945"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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="UAG07361.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQIVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1015..1185
                     /locus_tag="CWX32_024950"
     CDS             1015..1185
                     /locus_tag="CWX32_024950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="UAG07359.1"
                     /translation="MHEPPVQSDYHARSGNYQLESNPERHDKSPVAVAIGNWVHGAEIV
                     ENAYRVLEVKA"
                     /name="replication initiation protein"
     gene            complement(1394..1726)
                     /locus_tag="CWX32_024955"
     CDS             complement(1394..1726)
                     /locus_tag="CWX32_024955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001070439.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EmrE family multidrug efflux SMR transporter"
                     /protein_id="UAG07360.1"
                     /translation="MNTYIFLGGAIVAEVIGTTFMKYSEGFTRLWPSVGTAISYCAAFY
                     LLSQTLENIPTGIAYAIWSGAGIVLISLAGWLVSGQKLDWPAIAGMFLICVGVLVINIF
                     SKSSAH"
                     /name="EmrE family multidrug efflux SMR transporter"
     gene            complement(1894..2109)
                     /locus_tag="CWX32_024960"
     CDS             complement(1894..2109)
                     /locus_tag="CWX32_024960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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="UAG07357.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLIQRENA
                     ALNERVTVLSRQVQSLSEQLRRLSKG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2113..2598)
                     /locus_tag="CWX32_024965"
     CDS             complement(2113..2598)
                     /locus_tag="CWX32_024965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012565228.1"
                     /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="UAG07358.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGQFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     ARG             complement(1395..1726)
                     /name="qacG"
                     /gene="qacG"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="41.35"
                     /coverage="102.8"
     Typing          complement(473..664)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.308"
                     /coverage="89.0"
                     /evalue="3.38e-71"
     Typing          644..1127
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.756"
                     /coverage="93.0"
                     /evalue="1.73e-132"
     Typing          complement(57..376)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="8.510000000000001e-64"
     Typing          complement(1797..3223)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.632"
                     /coverage="96.0"
                     /evalue="0.0"
ORIGIN
        1 cagcagataa tcgaccggcc cgccgccgcc gccgcgcccc cgaggatgaa acttaacgat
       61 catcatcagc acccttttcc agtacggcat gccgcaaccg ctcgagtccg gcatcgatgg
      121 ccatcagcgc ggcgacaatc tgcacgcggt cgtgtccgct tccaccaccg gcgttaacct
      181 ggcgggcaat ctggttaagg ttgttcccca tgccggcaag ctgacgaagc agcgccggcg
      241 agatcgacgg aagtttgccg gcgcgtgcgg gcttctcgtc caggcacgtc tgccgcatcc
      301 aggccgcgag ttgcttaccc tcgcagcgct ccagcagacg ccggtgctcg tcctcagtca
      361 cccacatggt gagcattttg ctgcgtttgt ctgccaatcc ggcctcctga taacgccggg
      421 acggacggga aatcttttcc cggtcggcac ggtgttggac aagccgcagg cgcggcagtg
      481 gttttagcgg gtttcggggc gcagccctga accagtcacg tagcgctagc ggagtgtata
      541 ctggctaaac atgttatgac ggagtggcaa tttatgaaag tgcttcatgt gacaggggaa
      601 aaatgcggct gccgggcgta agtgcaaaat gcaggtggtg atgaaatgac gcctcctcgc
      661 tcactcggtc gctacgctcc tgccgtgaga ctgcggcggg cgttaccagc tcacagatta
      721 cgggataagc aaatgccgct cgaagcagga aaggccaaga aaaggatgcg gagttgccgt
      781 ttttccatag gctccgcccc cctgacgagt atcacgaaaa tgacgctcaa atcagcggtg
      841 gcgaaacccg atgcggctta aagataccag gcgtttcccc ctggtggctc cctcgtgctc
      901 ccccgcattc ctgcctttcg gtttaccggt gtcattccgc tgttatggcc gcggtttctc
      961 attccacgcc tgaaactcgg ttccgggtag gcagttcgct ccaggatgga ctgtatgcac
     1021 gaaccccccg ttcagtccga ctaccacgcc cgttccggta actatcaact tgagtccaac
     1081 ccggaaagac acgacaaatc gccagtggcg gtagccattg gtaactgggt tcacggagca
     1141 gagattgtag agaatgccta cagagttctt gaagtgaaag cctgagtgcg gctacactga
     1201 aaggacagtt taggtatctg cgctccgtga aagccagtta ccatcggaac aaagagttgg
     1261 tagctctgaa ttccggcaaa cgaaccaccg ttggtagcgg tggttttttt gtttacaggg
     1321 aaaaagatta cgcgcagaaa gaaaggatct caaggaaatc cttttgcttt ggccaatatg
     1381 cttcggtaaa aagttaatgc gcagaagatt ttgaaaaaat attaataacc aaaactccaa
     1441 cgcaaataag gaacattcct gcaattgcgg gccaatcaag tttttgaccg ctaaccaacc
     1501 aaccagctag gcttattagt acaattcccg caccagacca aattgcgtaa gcaataccgg
     1561 taggtatatt ttccaatgtt tgggaaagca gataaaaggc agcgcaataa cttattgcag
     1621 ttcctacaga cggccacagg cgtgtaaatc cttctgaata tttcataaag gtggtgccta
     1681 tgacttcagc cacaatagcc cctcccagga aaatatatgt attcataaaa atacctcatg
     1741 ttgaaaaatt taaatatctt tacataacaa ctaattaata gaacccggct tatcatagcg
     1801 aaggaccatg atgctgccac tgcgatcgtt ccagctccag cgctttctgg tgctgcaccg
     1861 cccgctcctg ctgccggtga gtttctatcg cgttcagcct ttcgacaacc ggcgcagctg
     1921 ctcgctcaaa ctctgcacct gcctgctcaa gaccgtgacg cgctcgttca gcgccgcgtt
     1981 ctcccgttga ataagaccag acatcgtccg ccattccgcg aaggcgttct cccactcgtc
     2041 cagccttttc gagtagtcct gctgtagctg ctctaatgcg ctcagcaact gtttttccag
     2101 ctccgtcatg tgctatttcc ccgccagtat catccagctc gagtcctctc cgaactgtcc
     2161 cgcttccggg ttcaccctca cgcagcggcg tctctgctcg ccgcaggtcg agagctgtac
     2221 gccgctgttc ctctctgaca gcatggcctg cgtgctcttc tgctcccgga tggtcgtata
     2281 gttctcgagt atctgctgcc cctgccacca cagaatgccc gcgctcgacg ctatcagcag
     2341 cgcggagacc agaacgatgg tcagccacgt ctggctgacc atgcgcagca tccctttcgt
     2401 gcgctggctc atggctgagg acagcttccg gtcgtggtcg aggatggcgg cgctgattct
     2461 cttctcgctt tcgctcagtt ccgctctgac agacttctcg tgctcgctga atgcggcttt
     2521 cagcatctcg ccggtagtct gctgctgcgc tttcgatttc tgctctaagt ccttcgccag
     2581 cgttaaaaga ctgttcatag atggctccct tcagtcggat gtttcgcccc ccgtccgggt
     2641 cggcaatgct gatgctgctt tttgtggtgc gcaccacctc aaaacctgcg ctttccagcg
     2701 cctcagtgac gtcctgacgc gttttcagct ccccggatga ggcaagggca agcaggccgc
     2761 tcgtaatcgc ctgggcggct tcctgcttcg cttccggcag cgcggaaggc gagaccagca
     2821 cccgccggtt ctccggcgcg ttcgggtcat gcagccccag cctgccgttc actatggtct
     2881 gccaggcatc gatgcgcgga cggtcggcgc ggtcgtaata cggctgtagc cgcttgccgg
     2941 tcagaagctc cgtgttcggg atcaggaagt tcagctccag ccgccccttg tcccggtgct
     3001 caacccacag cacgctgtac tggtctttat cgagtccggg catcagaacc cgctcgaaac
     3061 tcgccatcag cttttcgcgc tggccgggcg gtaaatcctg ttcggcaaaa gacagaacgc
     3121 cggaagtgta ctttttggcg tagggcgagg cgtcgataag ctcccggact tcatccggct
     3181 tcccctgcag aacgctggcg ccgtcgcgct ggcgatcttt acc
//
