LOCUS       CP065861                4096 bp    DNA     circular BCT 21-DEC-2020
DEFINITION  Salmonella enterica subsp. enterica serovar Westhampton strain
            CFSAN103867 plasmid pUWI-H17.2, complete sequence.
ACCESSION   CP065861
VERSION     CP065861.1
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 4096)
  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  JOURNAL   Unpublished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 4096)
  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 4096)
  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..4096
                     /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-H17.2"
                     /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(join(4096,1..233))
                     /locus_tag="HIX68_0025345"
     CDS             complement(join(4096,1..233))
                     /locus_tag="HIX68_0025345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001036746.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YgdI/YgdR family lipoprotein"
                     /protein_id="QQD62744.1"
                     /translation="MNKKTLLAAMMVALVTFAAAGCSSNQEIKTTDDRTIVTDGKPKVD
                     SDTGLVSYKDAHTGRTEQINRDKITNMSELDN"
                     /name="YgdI/YgdR family lipoprotein"
     gene            315..584
                     /locus_tag="HIX68_0025350"
     CDS             315..584
                     /locus_tag="HIX68_0025350"
                     /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="QQD62745.1"
                     /translation="MNGQEFRLLLTEHGEKEAVLLFGKKSFVAVPDTQNLYGGCYYLYL
                     EDAHKNELLIELNESDLYPGGAIELQHNGGRKIHCEILKVRWSR"
                     /name="hypothetical protein"
     gene            1618..1941
                     /locus_tag="HIX68_0025355"
     CDS             1618..1941
                     /locus_tag="HIX68_0025355"
                     /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="QQD62746.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGSSGLDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1880..2644
                     /locus_tag="HIX68_0025360"
                     /pseudo=""
     CDS             1880..2644
                     /locus_tag="HIX68_0025360"
                     /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            2619..3104
                     /locus_tag="HIX68_0025365"
     CDS             2619..3104
                     /locus_tag="HIX68_0025365"
                     /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="QQD62741.1"
                     /translation="MNSLLTLAKDLEQKSKVQQQTTGEMLKAAFSEHEKSVRAELNESE
                     KRISAAIHDHDRMLSSAMSQRTKGMLRMVSQTWLTIVLVSVLLIASSAGILWWQGQQIL
                     DNYTTIREQKSTQAMLSERNSGVQLTTCGEERRRCVRVNPDAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            3108..3317
                     /locus_tag="HIX68_0025370"
     CDS             3108..3317
                     /locus_tag="HIX68_0025370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /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="QQD62742.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWESAFAEWRTMCGLMQRENA
                     ALSERVTDLSTQVLSLSEQLRRLS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3847..4074)
                     /locus_tag="HIX68_0025375"
     CDS             complement(3847..4074)
                     /locus_tag="HIX68_0025375"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010615788.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YgdI/YgdR family lipoprotein"
                     /protein_id="QQD62743.1"
                     /translation="MKKIFVSVFAAAVALSALTGCTRTSYAIHTNDGRTIVSDGKPTES
                     DSGLLGYKDANGVKQQINKADVKEVSEIPH"
                     /name="YgdI/YgdR family lipoprotein"
     Typing          1432..1510
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.8899999999999995e-34"
     Typing          complement(868..1356)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.747"
                     /coverage="94.0"
                     /evalue="7.82e-151"
     Typing          1932..3427
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.998"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cagttgtcta gttcactcat gttggtaatt ttgtcacggt tgatctgttc ggttcggcct
       61 gtatgggcat ctttgtagga tactaatccc gtatcactgt caactttggg tttgccgtct
      121 gtaacgatag tgcgatcatc tgtggttttt atttcttggt ttgaagaaca tccagcagcg
      181 gcaaaggtca ccaacgcgac catcatggcc gccaacagcg tttttttatt cataataggt
      241 tccctgctta aaggtaaagt ggatatggtc actaaccatc taagtatagg tcgttttttc
      301 atgcgaaaag aggattgaat ggacaagaat ttcgattatt gctgacagag catggagaaa
      361 aagaggctgt tttactgttc ggaaagaaat cttttgttgc cgtgccagat acgcagaacc
      421 tttatggtgg gtgttattac ctttatttag aggatgctca caagaacgag cttttaattg
      481 agttaaacga aagtgattta taccccggtg gcgcaataga acttcaacac aacggcggtc
      541 ggaagattca ttgcgagata ctaaaagtaa ggtggagtcg ttaactcaag taatgtttcc
      601 taagtatgtt gataggcaaa catagtggta gttagtctct ctgagtaaat gatcttcttg
      661 tgatcctgtc gttacagtcg taatctcttg ctctgaaaac gaaaaaacca cctggggagg
      721 tggtttgatc gaaggttaag tcagttgggg aactgcttaa ccaggtaact gggtatacga
      781 gaccgcagaa accaaaactg ttctttcagt gtagcctctc tcaggcccat acttcaagac
      841 ctcttaattt gtctctcgta tacctccagt tactaatggc tgctgccagt agcgattttt
      901 cgtgtctttc cgggttggac tcaagacgat agttaccgga taaggcgcag cagtcggact
      961 gaacgggggg ttcgtgcata cagtcaatcc tggagcgaac tgccttcgcg gaactgagtg
     1021 tcaggcgtgg aatgagaaac cgcggccata acagcggaat gacaccggta aaccgaaagg
     1081 caggaatgcg ggggagcacg agggagccat cagggggaaa cgcctggtat ctttaagccg
     1141 catcgggttt cgccaccact gatttgagcg tcagattctg tgatgcttgt caggggggcg
     1201 gagcctatgg aaaaccggca gcggcgcatc ctttcttccc ctcctgcatt cacgtatttc
     1261 cccgccacgt ctttatccgt gagtccgtac cgctcgccgc agccgaacga ccgagcgtag
     1321 cgagtcagtg agcgaggaag cggaatatcc accgggacag gcatcagcct cttacgcacc
     1381 tgagcctcat ctcacagttt tcatgactga ctatttcatc ccgattcccg tcgtgccacc
     1441 atagtaagcc agtatacact ccgctagcgc tacgtgactg gttcagggct gcgccccgaa
     1501 acccgctaaa tgccactgac gcgcctgcgg cttgcccaac accgcgccga ccgggaaaag
     1561 atttcccgcc cgtcccggcg ttatcaggag gccggattgg cagacaaacg cagcaaaatg
     1621 ctcacgatgt gggtaacaga agatgagcac cgccgtctgc tggaacgctg cgacggtaaa
     1681 cagctcgcgg cctggatgcg gcagacgtgc ctggacgaga agcccgcccg ggccggcaaa
     1741 cttccctcga tctcgccggc gctgcttcgt cagcttgccg gcatggggaa caacctcaac
     1801 cagattgccc gccaggttaa cgccggtggc agtagcggtc tcgaccgcgt gcaggtcgtc
     1861 gccgcgctga tggccatcga tgccggactc gagcggctgc ggcatgccgt actggaaaag
     1921 ggggctgacg atgatcgtta agtttcatcc ccggggacgc ggaggcggtg ccggcccggt
     1981 tgattatctg ctggggaaag accgccagcg cgacggtgcc agcgttcttc aggggaagcc
     2041 ggaggaagtc cgggagctta tcgacgcctc gccctacgcc aaaaagtaca cctccggggt
     2101 gctgtccttt gccgaacagg acttaccgcc cgggcagcgt gaaacgctga tggcgagctt
     2161 cgagcgggtt ctgatgcccg gactcgataa agaccagtac agcgtgctgt gggttgagca
     2221 ccgggacaag gggcggctgg agctgaactt cctgatcccg aacacggagc tgctgaccgg
     2281 caaacggctc cagccatact atgaccgcgc cgaccgtcct cgcattgatg cctggcagac
     2341 catcgtgaac ggcagtctgg ggctgcacga cccgaacgcg ccggaaaacc ggcgggcact
     2401 ggtcacgccg tccgcgctgc cggaaacgaa gcaggaagcc gctcaggcga ttacgcgggg
     2461 tttactggcc ttagcctcgt ccggggagct gaaaacgcgt caggacgtca ctgaggcgct
     2521 ggaaagcgca ggttttgagg tggttcgcac cacaaaaagc agcatcagca ttgccgaccc
     2581 ggacgggggg cgaaacatcc gactgaaggg agccatctat gaacagtctt ttaacgctgg
     2641 cgaaggactt agagcagaaa tcgaaagtgc agcagcagac taccggcgag atgctgaaag
     2701 ccgcattcag cgagcacgag aagtctgtca gagcggaact gaacgaaagc gagaagagaa
     2761 tcagcgccgc catccacgac cacgaccgga tgctgtcctc agccatgagc cagcgtacga
     2821 aagggatgct gcgcatggtc agccagacgt ggctgaccat cgtcctggtc tccgtgctgc
     2881 tgatagcctc aagtgcgggc attctatggt ggcaggggca gcagatactc gacaattaca
     2941 cgaccatccg ggagcagaag agcacgcagg ccatgctgtc cgagaggaac agcggcgtgc
     3001 agctcacgac ctgcggagag gaacgacgcc gctgcgtgag ggtgaacccg gacgcgggac
     3061 ggttcggaga ggattcgagc tggatgatac tggcggggaa atagcacatg acggaactgg
     3121 aaaaacagtt gctgagcgca ttagagcagc tacagcagga ctactcgaaa aggctggacg
     3181 agtgggagag cgccttcgcg gaatggcgga cgatgtgtgg tcttatgcaa cgggagaacg
     3241 cagcgctgag cgagcgcgtc acggacttga gcacgcaggt gctgagttta agcgagcagc
     3301 tgcgccggtt gtcgtaaggc tgaacgacat cgaggcacac cgggagcagg agcgcgcagc
     3361 gcagcaccag aaagcgctgg agctggaacg atcgcagcgt cagcaggagt atgacggtcc
     3421 gtcgctgtga taaccggata aaacggggct ttcattgagg atctgcgccg aaacccggtg
     3481 ccattcaccc ggctgcatgg ctatgcagtc gggtgagatt tatcaggcgc agaatgcacg
     3541 gtttgcgggg tggtttactg tcggttttgc aggactgacg ccgcattcgc gctgaacccg
     3601 tccggagagg tgcgggcaag ggatgttatg gtaaaagcat gatgcctggc gggtacggaa
     3661 aaattgtggc gaccgagcct gcagacgcaa aaatccggcc catacttatt cgtctccttc
     3721 atcaggaatg cagtactatc cagccactgc aggtatttgg cccccagcgg gggctttttt
     3781 tgcctgttgt tggggcagat aaagaaaagg gccgcattag cggccctttt cggagagagc
     3841 gatgcctcaa tgcggaattt cagagacttc tttaacgtcg gctttattga tctgctgttt
     3901 gacaccattt gcgtctttat agcccagcag gcctgagtct gattctgtag gcttgccgtc
     3961 gctgacaatt gtacgcccgt cgttggtgtg gatggcatag cttgtgcgcg tgcagccggt
     4021 tagggctgaa agcgcaactg ccgctgcgaa cactgaaaca aaaatctttt tcaaagccag
     4081 ctccttttat ccgtat
//
