LOCUS       CP082593                3223 bp    DNA     circular BCT 13-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain CVM
            N18S0736 plasmid pN18S0736-5, complete sequence.
ACCESSION   CP082593
VERSION     CP082593.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN12930391
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
  ORGANISM  Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3223)
  AUTHORS   Li,C., Tyson,G.H., Hsu,C.H., Harrison,L., Strain,E., Tran,T.T.,
            Tillman,G.E., Dessai,U., McDermott,P.F. and Zhao,S.
  TITLE     Long-Read Sequencing Reveals Evolution and Acquisition of
            Antimicrobial Resistance and Virulence Genes in Salmonella enterica
  JOURNAL   Front Microbiol 12, 777817 (2021)
   PUBMED   34867920
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3223)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (07-OCT-2019) 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 (31-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                   :: 503x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/01/2021 16:59:44
            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)                     :: 4,862
            CDSs (total)                      :: 4,741
            Genes (coding)                    :: 4,642
            CDSs (with protein)               :: 4,642
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 99
            CDSs (without protein)            :: 99
            Pseudo Genes (ambiguous residues) :: 0 of 99
            Pseudo Genes (frameshifted)       :: 37 of 99
            Pseudo Genes (incomplete)         :: 63 of 99
            Pseudo Genes (internal stop)      :: 22 of 99
            Pseudo Genes (multiple problems)  :: 19 of 99
            CRISPR Arrays                     :: 2
            ##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
                     4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="CVM N18S0736"
                     /serovar="SI 4,5,12:i:-"
                     /isolation_source="ground turkey"
                     /sub_species="enterica"
                     /db_xref="taxon:440524"
                     /plasmid="pN18S0736-5"
                     /geo_loc_name="USA:NY"
                     /collection_date="2018"
                     /collected_by="FDA"
     gene            70..555
                     /locus_tag="F9183_024195"
     CDS             70..555
                     /locus_tag="F9183_024195"
                     /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="UAH92642.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGQFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            559..774
                     /locus_tag="F9183_024200"
     CDS             559..774
                     /locus_tag="F9183_024200"
                     /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="UAH92643.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLIQRENA
                     ALNERVTVLSRQVQSLSEQLRRLSKG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            942..1274
                     /locus_tag="F9183_024205"
     CDS             942..1274
                     /locus_tag="F9183_024205"
                     /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="UAH92644.1"
                     /translation="MNTYIFLGGAIVAEVIGTTFMKYSEGFTRLWPSVGTAISYCAAFY
                     LLSQTLENIPTGIAYAIWSGAGIVLISLAGWLVSGQKLDWPAIAGMFLICVGVLVINIF
                     SKSSAH"
                     /name="EmrE family multidrug efflux SMR transporter"
     gene            complement(1483..1653)
                     /locus_tag="F9183_024210"
     CDS             complement(1483..1653)
                     /locus_tag="F9183_024210"
                     /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="UAH92645.1"
                     /translation="MHEPPVQSDYHARSGNYQLESNPERHDKSPVAVAIGNWVHGAEIV
                     ENAYRVLEVKA"
                     /name="replication initiation protein"
     gene            2292..2615
                     /locus_tag="F9183_024215"
     CDS             2292..2615
                     /locus_tag="F9183_024215"
                     /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="UAH92646.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQIVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2554..3216
                     /locus_tag="F9183_024220"
                     /pseudo=""
     CDS             2554..3216
                     /locus_tag="F9183_024220"
                     /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"
     ARG             943..1274
                     /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          2005..2196
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.308"
                     /coverage="89.0"
                     /evalue="3.38e-71"
     Typing          complement(1542..2022)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.867"
                     /coverage="93.0"
                     /evalue="1.73e-132"
     Typing          4..872
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="89.384"
                     /coverage="99.0"
                     /evalue="1.01e-167"
     Typing          2606..3222
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.146"
                     /coverage="99.0"
                     /evalue="2.63e-129"
ORIGIN
        1 ccacaaaaag cagcatcagc attgccgacc cggacggggg gcgaaacatc cgactgaagg
       61 gagccatcta tgaacagtct tttaacgctg gcgaaggact tagagcagaa atcgaaagcg
      121 cagcagcaga ctaccggcga gatgctgaaa gccgcattca gcgagcacga gaagtctgtc
      181 agagcggaac tgagcgaaag cgagaagaga atcagcgccg ccatcctcga ccacgaccgg
      241 aagctgtcct cagccatgag ccagcgcacg aaagggatgc tgcgcatggt cagccagacg
      301 tggctgacca tcgttctggt ctccgcgctg ctgatagcgt cgagcgcggg cattctgtgg
      361 tggcaggggc agcagatact cgagaactat acgaccatcc gggagcagaa gagcacgcag
      421 gccatgctgt cagagaggaa cagcggcgta cagctctcga cctgcggcga gcagagacgc
      481 cgctgcgtga gggtgaaccc ggaagcggga cagttcggag aggactcgag ctggatgata
      541 ctggcgggga aatagcacat gacggagctg gaaaaacagt tgctgagcgc attagagcag
      601 ctacagcagg actactcgaa aaggctggac gagtgggaga acgccttcgc ggaatggcgg
      661 acgatgtctg gtcttattca acgggagaac gcggcgctga acgagcgcgt cacggtcttg
      721 agcaggcagg tgcagagttt gagcgagcag ctgcgccggt tgtcgaaagg ctgaacgcga
      781 tagaaactca ccggcagcag gagcgggcgg tgcagcacca gaaagcgctg gagctggaac
      841 gatcgcagtg gcagcatcat ggtccttcgc tatgataagc cgggttctat taattagttg
      901 ttatgtaaag atatttaaat ttttcaacat gaggtatttt tatgaataca tatattttcc
      961 tgggaggggc tattgtggct gaagtcatag gcaccacctt tatgaaatat tcagaaggat
     1021 ttacacgcct gtggccgtct gtaggaactg caataagtta ttgcgctgcc ttttatctgc
     1081 tttcccaaac attggaaaat atacctaccg gtattgctta cgcaatttgg tctggtgcgg
     1141 gaattgtact aataagccta gctggttggt tggttagcgg tcaaaaactt gattggcccg
     1201 caattgcagg aatgttcctt atttgcgttg gagttttggt tattaatatt ttttcaaaat
     1261 cttctgcgca ttaacttttt accgaagcat attggccaaa gcaaaaggat ttccttgaga
     1321 tcctttcttt ctgcgcgtaa tctttttccc tgtaaacaaa aaaaccaccg ctaccaacgg
     1381 tggttcgttt gccggaattc agagctacca actctttgtt ccgatggtaa ctggctttca
     1441 cggagcgcag atacctaaac tgtcctttca gtgtagccgc actcaggctt tcacttcaag
     1501 aactctgtag gcattctcta caatctctgc tccgtgaacc cagttaccaa tggctaccgc
     1561 cactggcgat ttgtcgtgtc tttccgggtt ggactcaagt tgatagttac cggaacgggc
     1621 gtggtagtcg gactgaacgg ggggttcgtg catacagtcc atcctggagc gaactgccta
     1681 cccggaaccg agtttcaggc gtggaatgag aaaccgcggc cataacagcg gaatgacacc
     1741 ggtaaaccga aaggcaggaa tgcgggggag cacgagggag ccaccagggg gaaacgcctg
     1801 gtatctttaa gccgcatcgg gtttcgccac cgctgatttg agcgtcattt tcgtgatact
     1861 cgtcaggggg gcggagccta tggaaaaacg gcaactccgc atccttttct tggcctttcc
     1921 tgcttcgagc ggcatttgct tatcccgtaa tctgtgagct ggtaacgccc gccgcagtct
     1981 cacggcagga gcgtagcgac cgagtgagcg aggaggcgtc atttcatcac cacctgcatt
     2041 ttgcacttac gcccggcagc cgcatttttc ccctgtcaca tgaagcactt tcataaattg
     2101 ccactccgtc ataacatgtt tagccagtat acactccgct agcgctacgt gactggttca
     2161 gggctgcgcc ccgaaacccg ctaaaaccac tgccgcgcct gcggcttgtc caacaccgtg
     2221 ccgaccggga aaagatttcc cgtccgtccc ggcgttatca ggaggccgga ttggcagaca
     2281 aacgcagcaa aatgctcacc atgtgggtga ctgaggacga gcaccggcgt ctgctggagc
     2341 gctgcgaggg taagcaactc gcggcctgga tgcggcagac gtgcctggac gagaagcccg
     2401 cacgcgccgg caaacttccg tcgatctcgc cggcgctgct tcgtcagctt gccggcatgg
     2461 ggaacaacct taaccagatt gcccgccagg ttaacgccgg tggtggaagc ggacacgacc
     2521 gcgtgcagat tgtcgccgcg ctgatggcca tcgatgccgg actcgagcgg ttgcggcatg
     2581 ccgtactgga aaagggtgct gatgatgatc gttaagtttc atcctcgggg gcgcggcggc
     2641 ggcggcgggc cggtcgatta tctgctgggt aaagatcgcc agcgcgacgg cgccagcgtt
     2701 ctgcagggga agccggatga agtccgggag cttatcgacg cctcgcccta cgccaaaaag
     2761 tacacttccg gcgttctgtc ttttgccgaa caggatttac cgcccggcca gcgcgaaaag
     2821 ctgatggcga gtttcgagcg ggttctgatg cccggactcg ataaagacca gtacagcgtg
     2881 ctgtgggttg agcaccggga caaggggcgg ctggagctga acttcctgat cccgaacacg
     2941 gagcttctga ccggcaagcg gctacagccg tattacgacc gcgccgaccg tccgcgcatc
     3001 gatgcctggc agaccatagt gaacggcagg ctggggctgc atgacccgaa cgcgccggag
     3061 aaccggcggg tgctggtctc gccttccgcg ctgccggaag cgaagcagga agccgcccag
     3121 gcgattacga gcggcctgct tgcccttgcc tcatccgggg agctgaaaac gcgtcaggac
     3181 gtcactgagg cgctggaaag cgcaggtttt gaggtggtgc gca
//
