LOCUS       CP065863                3001 bp    DNA     circular BCT 21-DEC-2020
DEFINITION  Salmonella enterica subsp. enterica serovar Westhampton strain
            CFSAN103867 plasmid pUWI-H17.4, complete sequence.
ACCESSION   CP065863
VERSION     CP065863.1
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 3001)
  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  JOURNAL   Unpublished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 3001)
  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 3001)
  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..3001
                     /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-H17.4"
                     /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            831..944
                     /locus_tag="HIX68_0025410"
     CDS             831..944
                     /locus_tag="HIX68_0025410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QQD62753.1"
                     /translation="MHEPPVQSDCCALSGNYQLESNPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     gene            1467..2402
                     /locus_tag="HIX68_0025415"
     CDS             1467..2402
                     /locus_tag="HIX68_0025415"
                     /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="hypothetical protein"
                     /protein_id="QQD62754.1"
                     /translation="MTAQDVINVLTILKANDSTSFSKIQRALKMSISQLEGIIDGLTAM
                     GILYKSSFTSYSLTELTSKPVVSDGVRKAFEDIITNRGIYLSEELLQKVSTPFIPLMTH
                     EYKNAPVKVMIVGQETLGMEDAFSTIVSVDDYINESIESFNKFNFGEDLRNSHFWYAFD
                     EVVKYFNLPSRRHAYWTNLHKFQLIENDGDSVSISKLPSKDIMTMIHMQRELFLAEIKD
                     TKPDIIIYFTGGQTWVLDHYLNNGKKLAVKAIDERSHLGIIQTEFLHCPIAICTDHPGR
                     RGYTQAIVDHRANLLKYAADKFYASESARV"
                     /name="hypothetical protein"
     gene            2432..2535
                     /locus_tag="HIX68_0025420"
                     /pseudo=""
     CDS             2432..2535
                     /locus_tag="HIX68_0025420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558297.1"
                     /note="frameshifted; incomplete; partial on complete
                     genome; missing N-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS3 family transposase"
                     /name="IS3 family transposase"
     gene            complement(2757..2993)
                     /locus_tag="HIX68_0025425"
     CDS             complement(2757..2993)
                     /locus_tag="HIX68_0025425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016230891.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QQD62752.1"
                     /translation="MTRLTNLTPAEKKFIDDAIAAAERAAGKKLNQPNRHIVLNRARAQ
                     IESQRYADRQRALREDERQQSDFAWSRPRAPRR"
                     /name="hypothetical protein"
     Typing          451..986
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.333"
                     /coverage="89.0"
                     /evalue="0.0"
ORIGIN
        1 ccgtatgaga atagtccctg cagtctgcca gacacagtag gaacgatgaa gcgtaagcga
       61 cggtgaaagg cagtcagaaa cggtgaacgg gagcggattt taatccggtg ccgtgaggcg
      121 ttgggcaagc cgcaggcgcg tcagtgcttt tagcgggttt cggggcgcag ccctgaacca
      181 gtcacgtagc gctagcggag tgtatactgg ctaaacttca gagatgccaa ggaagggaca
      241 ggatatgttt tgtagcaccg ccaccactgt ggcgatactc caaaacgcct ggtcagggca
      301 cagccccgac accccagagc cgactgtagg tcactgggcg aacgcggcgg aatgatgtcg
      361 gatgacgtca ttttgcggcg tttgccctat cctgcatcgt attaaaaaat gcagctatgg
      421 cgcgtacggt gccaaagata agcccggaga tattccgctt cctcgctcac tgactcgctc
      481 cgctcggtcg ttcggctgcg gcgagcggta ccggcttact ggcggggcgg aaatttccta
      541 gcatcttcca ggaagaaact taacagggaa acgataaggc cgcggcgaag ccgtttttcc
      601 ataggctccg cccccctgac aagcatcacg aaatctgacg ctcaaatcag tggtggcgaa
      661 acccgacagg acttaaagat accaggcgtt tccccctggt ggctccctcg tgcgctctcc
      721 tgttcctgcc tttcggttta ccggtgtcat tccgctgtta tggccgcgtt tatctcattc
      781 cacgcctgac actcagttcc gggtaggcag ttcgctccaa gctggactgt atgcacgaac
      841 cccccgttca gtccgactgc tgcgccttat ccggtaacta tcaacttgag tccaacccgg
      901 aaagacacga caaagcacca ctggcagcag ccactggtaa ctgagatgtg cgagagattt
      961 atctgaagtt cttgaagtgg gagcctggga acagctacac tggaaggaca gttttggtga
     1021 ctcgtctcgc acaagacagt tacctggtta agcagttccc caactgacct aaccttcgat
     1081 caaaccacct ccccaggtgg ttttttcgtt tcttggagaa gagactacga cgacaaacga
     1141 cggatctcaa gaagatcctt ttaacgtaca aaaatttccg ttctccaaac tacccaccat
     1201 gataacttac caatcataaa aatcatgata ggccactacg gtcgatgtct tgaagcaatg
     1261 ctcggttata gtcgtttatc tctgaggatt tttagcttgt aacccatcag gcaaagtcgt
     1321 tattgatgcc ggttcattag agaaatatag gggccaatcc agggattacc ggggcatgtg
     1381 atttttgact aatttttgta ctgcgaccgt cagaatgagt taaacgcgta tctacattga
     1441 ggcagttcaa tatgcggaaa acaggaatga cagcacaaga tgtaatcaac gttctcacta
     1501 ttcttaaggc caacgactca accagtttta gcaagattca acgcgcgtta aagatgagta
     1561 tttcgcagtt ggagggcatc attgatgggt taactgcaat gggaattttg tataaatcat
     1621 cattcacttc atacagtctt actgagttaa cctctaaacc tgttgttagt gacggtgtaa
     1681 gaaaggcatt cgaagatatc attaccaatc gcggtattta cctgtcagaa gaactactac
     1741 aaaaggtaag tacaccattc atcccactga tgacgcacga atacaaaaat gccccagtta
     1801 aagtgatgat cgtggggcaa gaaactctgg gaatggaaga tgctttcagt accatcgttt
     1861 cggtcgatga ctacattaat gagagcattg aatccttcaa taaattcaat tttggtgaag
     1921 atttaaggaa tagccacttt tggtatgcat ttgatgaagt agtaaagtat tttaacctac
     1981 catccagaag gcatgcttat tggactaatc ttcataagtt tcaattaatt gaaaatgatg
     2041 gagatagtgt cagcatttcc aaactacctt caaaagatat catgacaatg attcatatgc
     2101 agcgtgaatt attcttggct gaaattaaag ataccaagcc agatatcatc atctacttca
     2161 cgggtgggca aacctgggtg ttagatcatt atctaaacaa tggtaaaaaa ttagcagtta
     2221 aggcaataga tgaacgctcg catctgggga ttatccagac agaatttttg cattgcccaa
     2281 tcgctatatg taccgaccac cctggtagaa ggggatatac tcaagccatc gtagatcata
     2341 gagctaatct gcttaaatat gctgctgaca aattttatgc aagtgaatcg gcacgggttt
     2401 aacagaccac ccagagtcat ttaagatcgc ttacatcgaa atgttttata acagtaacgt
     2461 cggcatggtt ctagcgaaca catgtcaccg acagaatatg aaaaccagta ttatcaacgg
     2521 ctcggaagtg tctagattat ccgtggcgat tcaatttacc ataacatccg ttatcagcac
     2581 cccctgacag gccctcagcg caattctggc gcatcagagc cgtttccggc acatttcctc
     2641 acccgcatcc cggaaaaacg cccctgatga tttctgcgcg actgcatggc tatgcacgcg
     2701 ggtgaatcgc aggtgatttc gcagcgtcag caccactaaa ccgccaaaat ccgcaatcag
     2761 cggcgcggcg cgcgcggacg tgaccaggca aaatcggact gctgccgctc atcctcacgt
     2821 aatgcacgct ggcggtcggc gtaacgctgc gactcaatct gcgcacgcgc tctgttcagg
     2881 acgatatgcc ggttaggctg attgagcttc ttcccggccg cacgttcggc agcggctata
     2941 gcgtcgtcga taaacttttt ctcagcgggg gtcaggtttg tcagtctcgt catgtttatc
     3001 t
//
