LOCUS       CP066326                2579 bp    DNA     circular BCT 07-JAN-2021
DEFINITION  Salmonella enterica strain UWI_PP122 isolate CFSAN103840 plasmid
            pUWI-PP122.1, complete sequence.
ACCESSION   CP066326
VERSION     CP066326.1
DBLINK      BioProject: PRJNA186035
            BioSample: SAMN16678602
KEYWORDS    .
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 2579)
  AUTHORS   Maguire,M., Khan,A., Adesiyun,A., Georges,K. and
            Gonzalez-Escalona,N.
  TITLE     Closed genomes of eight multidrug resistance Salmonella enterica
            strains isolated from chicken in Trinidad and Tobago by using a
            combination of long and short reads
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2579)
  CONSRTM   GenomeTrakr network: Whole genome sequencing for foodborne pathogen
            traceback
  TITLE     Direct Submission
  JOURNAL   Submitted (06-NOV-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 2579)
  AUTHORS   Maguire,M. and Gonzalez-Escalona,N.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-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                   :: 100x
            Sequencing Technology :: Illumina MiSeq, Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 12/17/2020 14:38:22
            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)                     :: 4,385
            CDSs (total)                      :: 4,268
            Genes (coding)                    :: 4,166
            CDSs (with protein)               :: 4,166
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 102
            CDSs (without protein)            :: 102
            Pseudo Genes (ambiguous residues) :: 0 of 102
            Pseudo Genes (frameshifted)       :: 46 of 102
            Pseudo Genes (incomplete)         :: 51 of 102
            Pseudo Genes (internal stop)      :: 29 of 102
            Pseudo Genes (multiple problems)  :: 21 of 102
            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..2579
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="UWI_PP122"
                     /isolate="CFSAN103840"
                     /isolation_source="environmental"
                     /db_xref="taxon:28901"
                     /plasmid="pUWI-PP122.1"
                     /geo_loc_name="Trinidad and Tobago"
                     /collection_date="2018"
                     /collected_by="Professor Emeritus Abiodun A. Adesiyun DVM
                     (ABU), MPH, Ph.D., University of the West Indies, St.
                     Augustine Campus- Faculty of Medical Sciences- Veterinary
                     Public Health Laboratory, School of Veterinary Medicine"
     gene            complement(join(2343..2579,1..408))
                     /locus_tag="ITK14_21915"
     CDS             complement(join(2343..2579,1..408))
                     /locus_tag="ITK14_21915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017900990.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quinolone resistance pentapeptide repeat protein
                     QnrB19"
                     /protein_id="QQL74568.1"
                     /translation="MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQF
                     YDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNM
                     ITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFST
                     FDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAVIG"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrB19"
     gene            complement(502..657)
                     /gene="pspF"
                     /locus_tag="ITK14_21920"
                     /pseudo=""
     CDS             complement(502..657)
                     /gene="pspF"
                     /locus_tag="ITK14_21920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309907.2"
                     /note="transcriptional activator for pspABCE which are
                     induced in response to phage proteins, membrane altering
                     stresses, and impaired proton expor; 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="phage shock protein operon transcriptional
                     activator"
                     /name="pspF"
     gene            1725..1961
                     /locus_tag="ITK14_21925"
     CDS             1725..1961
                     /locus_tag="ITK14_21925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676031.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QQL74567.1"
                     /translation="MARLTNLTPAEKKFLDDAVAAAERASGKKLNQPNRHIVLNRARAQ
                     IELQRYADRQRALREDERQQSDFAWSRPRAPRR"
                     /name="hypothetical protein"
     ARG             complement(2..444)
                     /name="QnrB10"
                     /gene="QnrB10"
                     /gene_name="quinolone resistance protein (qnr)"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="99.32"
                     /coverage="65.49"
     ARG             complement(2344..2579)
                     /name="QnrB19"
                     /gene="QnrB19"
                     /gene_name="quinolone resistance protein (qnr)"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="100.0"
                     /coverage="36.45"
     Typing          1387..1560
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          complement(917..1408)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 cagctcacac ttttccaaca cgactttcga aaaattggcg tagcttagat tagtattagt
       61 gatatatgcg ctgcaaaacc aggtgcgcgt ggtgatcata ttcataaagc ttgcaccgcg
      121 gaaatctgcg ccttgtgcgc ggcagtggcg aatttcaatg cccaaggcac tgacgttgcg
      181 gaaatctgcc attgataaat cacagctttt gaaaatggca tctttcagca ttgcgcgact
      241 aaaattgcac cctttctgac tttcgcgatc atagaactgg cagccgataa attcagtgcc
      301 gctcaggtcg gcacctgaaa aatcgcagtt aaaaaatgta ctattttcaa ctttctcacc
      361 ggtgaagcga tttctgtcaa ttttttcgcc aactaatgcc agagtcatat ctatgcctgt
      421 gtttttatac agtaatgacg ccatggtaaa ccttatgacg ttatgcgtca aacccgccag
      481 tatgacacct gcaaatgcgt attagatctg gtgtttcttc agcaaggcac gtagctgatg
      541 ataagtcaga cccagtaatt cagcggcttt tttctggtta aatttagcct gctgtaagct
      601 ggtttgtaga aagtctttct cttgctgctg ctggaattca cgcagatcca gcgttataac
      661 gatgtgtatc ctatgtgctc ggattggata gatttccatt acggtgaagg atcttcttga
      721 gatcctttct gtggcgtcgt aatctcttgc tctgtaaacg aaaaaaccgc cctgcaaggc
      781 ggtttttcga aggttctcag agcagcaact ctttgaaccg tggtaactgg cttacgagga
      841 gcgcagtaac caaatctgtt ctttcagttt agccttaaca ggcgcataac ttcaagacta
      901 actcctctaa atcagttacc agtggctgct gccagtggcg ataagtcgtg tctttccggg
      961 ttggactcaa gatgatagtt accggataag gcgcagcagt cggactgaac ggggggttcg
     1021 tgcatacagt ccatccagga gcgaactgcc ttcgcggaac tgagtgtcag gcgtggaatg
     1081 agataaacgc ggccataaca gcggaatgac accggtaaac cgaaaggcag gaatgcgggg
     1141 gagcacgagg gagccaccag ggggaaacgc ctggtatctt taagccgcat cgggtttcgc
     1201 caccactgat ttgagcgtca gatttcatga tgtttgtcag gggggcggag cctatggaaa
     1261 aacggcttcg ccgcggcctt atctcttccc tgttaagctc cttcctggta tctcccagga
     1321 aatttccgcc ccgcctgtaa gccggcaccg ctcgccgcag ccgaacgacc gagcgcagcg
     1381 agtcagtgag cgaggaagcg gaatatatcc tgtactacat atcctgctga cgcgctggtg
     1441 ccgccttttt tctcctgcta catgaagcac ttcactgatt tccacatccg tgccaacata
     1501 gtcagccagt atacactccg ctagcgctac gtgactggtt cagggctgcg ccccgaaacc
     1561 ggctaaaagc taatgacgcg cctgcggctt gtccaacgcc tcacggcacc ggattaaaat
     1621 ccgctcccgt tcaccgtttc tgactgcctt tcaccgtcgc tggcgcttca tcgtttctac
     1681 tgtgtctggc agactgtgct gatttattct gactggagaa cgttatggcc agactgacaa
     1741 acttgacgcc tgcagagaaa aaatttcttg atgatgctgt tgccgcagct gaaagagcgt
     1801 caggtaaaaa gctaaatcag cctaaccggc acatcgtcct gaacagagcg cgtgcgcaaa
     1861 ttgagttgca gcgttacgcc gaccgccagc gtgcattacg tgaggatgag cggcagcagt
     1921 ccgattttgc ctggtcacgt ccgcgcgcgc cgcgccgctg attttggctt ttggcggttt
     1981 agtggtgctg acgctgcgaa atcacctgcc attcacctgc gtgcatagcc atgcagtcgc
     2041 gcagaaatca tcaggggcgt ttttccggga tactggtgag gaaaggtgct ggaaacggcc
     2101 ctgatgcagc aggattgcgc tgagggcgcc tgcgggggtg cgggcaaggg atgttatgtt
     2161 taatcggtct gaccgtcagg tacaaaaaaa agcccttagg gggctttttt tttgctatga
     2221 gttagccata ttttcgtgcg aatttttcat cggaatcgca tagataaata ataaactcaa
     2281 taaacgcgat gatcgcgggt aaaagtaaat cgtcaaacgc atctcccggt gtaaacgctg
     2341 aactaaccaa tcacagcgat gccaagccgc tccatgagca acgatgcctg gtagctgtct
     2401 aacttaacgc cttgtaaatc aacaccccga atatctaagt cacctaactc cgaattggtc
     2461 agatcgcaat gtgtgaagtt tgctgctcgc cagtcgaaag tcgaaaactc gccgccggag
     2521 agatctgaac cactgaacgt cgcacccagt acctgagttc ccatccagcg gttttccca
//
