LOCUS       CP065862                3223 bp    DNA     circular BCT 21-DEC-2020
DEFINITION  Salmonella enterica subsp. enterica serovar Westhampton strain
            CFSAN103867 plasmid pUWI-H17.3, complete sequence.
ACCESSION   CP065862
VERSION     CP065862.1
DBLINK      BioProject: PRJNA186035
            BioSample: SAMN14677225
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Westhampton
  ORGANISM  Salmonella enterica subsp. enterica serovar Westhampton
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3223)
  AUTHORS   Maguire,M., Khan,A., Adesiyun,A., Georges,K. and
            Gonzalez-Escalona,N.
  TITLE     Closed genome of a Salmonella enterica serotype Senftenberg carrying
            the mcr-9 gene isolated from chicken in Trinidad and Tobago
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3223)
  CONSRTM   GenomeTrakr network: Whole genome sequencing for foodborne pathogen
            traceback
  TITLE     Direct Submission
  JOURNAL   Submitted (01-MAY-2020) Center for Food Safety and Applied
            Nutrition, US Food and Drug Administration, 5100 Paint Branch Pkwy,
            College Park, MD, USA
REFERENCE   3  (bases 1 to 3223)
  AUTHORS   Gonzalez-Escalona,N.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-DEC-2020) ORS/DM/MMSB, Food and Drug
            Administration-College Park, 5001 Campus Drive, College Park, MD
            20740-3835, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 65.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 12/10/2020 12:18:44
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 5.0
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 5,088
            CDSs (total)                      :: 4,968
            Genes (coding)                    :: 4,823
            CDSs (with protein)               :: 4,823
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 145
            CDSs (without protein)            :: 145
            Pseudo Genes (ambiguous residues) :: 0 of 145
            Pseudo Genes (frameshifted)       :: 75 of 145
            Pseudo Genes (incomplete)         :: 81 of 145
            Pseudo Genes (internal stop)      :: 24 of 145
            Pseudo Genes (multiple problems)  :: 27 of 145
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            Bacteria and source DNA available from Professor Emeritus Abiodun
            A. Adesiyun DVM (ABU), MPH, Ph.D. (Minnesota) School of Veterinary
            Medicine Faculty of Medical Sciences University of the West Indies
            St. Augustine, Trinidad and Tobago.
            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
                     Westhampton"
                     /mol_type="genomic DNA"
                     /strain="CFSAN103867"
                     /serovar="Westhampton"
                     /isolation_source="broken egg shells- hatchery"
                     /sub_species="enterica"
                     /db_xref="taxon:356621"
                     /plasmid="pUWI-H17.3"
                     /geo_loc_name="Trinidad and Tobago"
                     /collection_date="2019"
                     /collected_by="University of the West Indies, St. Augustine
                     Campus- Faculty of Medical Sciences- Veterinary Public
                     Health Laboratory, School of Veterinary Medicine"
     gene            complement(113..283)
                     /locus_tag="HIX68_0025380"
     CDS             complement(113..283)
                     /locus_tag="HIX68_0025380"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QQD62750.1"
                     /translation="MHEPPVQSDYHARSGNYQLESNPERHDKSPVAVAIGNWVHGAEIV
                     ENAYRVLEVKA"
                     /name="replication initiation protein"
     gene            922..1245
                     /locus_tag="HIX68_0025385"
     CDS             922..1245
                     /locus_tag="HIX68_0025385"
                     /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="QQD62751.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQIVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1184..1948
                     /locus_tag="HIX68_0025390"
                     /pseudo=""
     CDS             1184..1948
                     /locus_tag="HIX68_0025390"
                     /inference="COORDINATES: protein motif:HMM:NF015397.1"
                     /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            1923..2408
                     /locus_tag="HIX68_0025395"
     CDS             1923..2408
                     /locus_tag="HIX68_0025395"
                     /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="QQD62747.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGQFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            2412..2627
                     /locus_tag="HIX68_0025400"
     CDS             2412..2627
                     /locus_tag="HIX68_0025400"
                     /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="QQD62748.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLIQRENA
                     ALNERVTVLSRQVQSLSEQLRRLSKG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2795..3127
                     /locus_tag="HIX68_0025405"
     CDS             2795..3127
                     /locus_tag="HIX68_0025405"
                     /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="QQD62749.1"
                     /translation="MNTYIFLGGAIVAEVIGTTFMKYSEGFTRLWPSVGTAISYCAAFY
                     LLSQTLENIPTGIAYAIWSGAGIVLISLAGWLVSGQKLDWPAIAGMFLICVGVLVINIF
                     SKSSAH"
                     /name="EmrE family multidrug efflux SMR transporter"
     ARG             2796..3127
                     /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          635..826
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.308"
                     /coverage="89.0"
                     /evalue="3.38e-71"
     Typing          complement(172..652)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.867"
                     /coverage="93.0"
                     /evalue="1.73e-132"
     Typing          1236..2725
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.784"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctaccaacgg tggttcgttt gccggaattc agagctacca actctttgtt ccgatggtaa
       61 ctggctttca cggagcgcag atacctaaac tgtcctttca gtgtagccgc actcaggctt
      121 tcacttcaag aactctgtag gcattctcta caatctctgc tccgtgaacc cagttaccaa
      181 tggctaccgc cactggcgat ttgtcgtgtc tttccgggtt ggactcaagt tgatagttac
      241 cggaacgggc gtggtagtcg gactgaacgg ggggttcgtg catacagtcc atcctggagc
      301 gaactgccta cccggaaccg agtttcaggc gtggaatgag aaaccgcggc cataacagcg
      361 gaatgacacc ggtaaaccga aaggcaggaa tgcgggggag cacgagggag ccaccagggg
      421 gaaacgcctg gtatctttaa gccgcatcgg gtttcgccac cgctgatttg agcgtcattt
      481 tcgtgatact cgtcaggggg gcggagccta tggaaaaacg gcaactccgc atccttttct
      541 tggcctttcc tgcttcgagc ggcatttgct tatcccgtaa tctgtgagct ggtaacgccc
      601 gccgcagtct cacggcagga gcgtagcgac cgagtgagcg aggaggcgtc atttcatcac
      661 cacctgcatt ttgcacttac gcccggcagc cgcatttttc ccctgtcaca tgaagcactt
      721 tcataaattg ccactccgtc ataacatgtt tagccagtat acactccgct agcgctacgt
      781 gactggttca gggctgcgcc ccgaaacccg ctaaaaccac tgccgcgcct gcggcttgtc
      841 caacaccgtg ccgaccggga aaagatttcc cgtccgtccc ggcgttatca ggaggccgga
      901 ttggcagaca aacgcagcaa aatgctcacc atgtgggtga ctgaggacga gcaccggcgt
      961 ctgctggagc gctgcgaggg taagcaactc gcggcctgga tgcggcagac gtgcctggac
     1021 gagaagcccg cacgcgccgg caaacttccg tcgatctcgc cggcgctgct tcgtcagctt
     1081 gccggcatgg ggaacaacct taaccagatt gcccgccagg ttaacgccgg gggtggaagc
     1141 ggacacgacc gcgtgcagat tgtcgccgcg ctgatggcca tcgatgccgg actcgagcgg
     1201 ttgcggcatg ccgtactgga aaagggtgct gatgatgatc gttaagtttc atcctcgggg
     1261 gcgcggcggc ggcggcgggc cggtcgatta tctgctgggt aaagatcgcc agcgcgacgg
     1321 cgccagcgtt ctgcagggga agccggatga agtccgggag cttatcgacg cctcgcccta
     1381 cgccaaaaag tacacttccg gcgttctgtc ttttgccgaa caggatttac cgcccggcca
     1441 gcgcgaaaag ctgatggcga gtttcgagcg ggttctgatg cccggactcg ataaagacca
     1501 gtacagcgtg ctgtgggttg agcaccggga caaggggcgg ctggagctga acttcctgat
     1561 cccgaacacg gagcttctga ccggcaagcg gctacagccg tattacgacc gcgccgaccg
     1621 tccgcgcatc gatgcctggc agaccatagt gaacggcagg ctggggctgc atgacccgaa
     1681 cgcgccggag aaccggcggg tgctggtctc gccttccgcg ctgccggaag cgaagcagga
     1741 agccgcccag gcgattacga gcggcctgct tgcccttgcc tcatccgggg agctgaaaac
     1801 gcgtcaggac gtcactgagg cgctggaaag cgcaggtttt gaggtggtgc gcaccacaaa
     1861 aagcagcatc agcattgccg acccggacgg ggggcgaaac atccgactga agggagccat
     1921 ctatgaacag tcttttaacg ctggcgaagg acttagagca gaaatcgaaa gcgcagcagc
     1981 agactaccgg cgagatgctg aaagccgcat tcagcgagca cgagaagtct gtcagagcgg
     2041 aactgagcga aagcgagaag agaatcagcg ccgccatcct cgaccacgac cggaagctgt
     2101 cctcagccat gagccagcgc acgaaaggga tgctgcgcat ggtcagccag acgtggctga
     2161 ccatcgttct ggtctccgcg ctgctgatag cgtcgagcgc gggcattctg tggtggcagg
     2221 ggcagcagat actcgagaac tatacgacca tccgggagca gaagagcacg caggccatgc
     2281 tgtcagagag gaacagcggc gtacagctct cgacctgcgg cgagcagaga cgccgctgcg
     2341 tgagggtgaa cccggaagcg ggacagttcg gagaggactc gagctggatg atactggcgg
     2401 ggaaatagca catgacggag ctggaaaaac agttgctgag cgcattagag cagctacagc
     2461 aggactactc gaaaaggctg gacgagtggg agaacgcctt cgcggaatgg cggacgatgt
     2521 ctggtcttat tcaacgggag aacgcggcgc tgaacgagcg cgtcacggtc ttgagcaggc
     2581 aggtgcagag tttgagcgag cagctgcgcc ggttgtcgaa aggctgaacg cgatagaaac
     2641 tcaccggcag caggagcggg cggtgcagca ccagaaagcg ctggagctgg aacgatcgca
     2701 gtggcagcat catggtcctt cgctatgata agccgggttc tattaattag ttgttatgta
     2761 aagatattta aatttttcaa catgaggtat ttttatgaat acatatattt tcctgggagg
     2821 ggctattgtg gctgaagtca taggcaccac ctttatgaaa tattcagaag gatttacacg
     2881 cctgtggccg tctgtaggaa ctgcaataag ttattgcgct gccttttatc tgctttccca
     2941 aacattggaa aatataccta ccggtattgc ttacgcaatt tggtctggtg cgggaattgt
     3001 actaataagc ctagctggtt ggttggttag cggtcaaaaa cttgattggc ccgcaattgc
     3061 aggaatgttc cttatttgcg ttggagtttt ggttattaat attttttcaa aatcttctgc
     3121 gcattaactt tttaccgaag catattggcc aaagcaaaag gatttccttg agatcctttc
     3181 tttctgcgcg taatcttttt ccctgtaaac aaaaaaacca ccg
//
