LOCUS       CP066323                4050 bp    DNA     circular BCT 07-JAN-2021
DEFINITION  Salmonella enterica strain UWI_PP98 isolate CFSAN103862 plasmid
            pUWI-PP98.2, complete sequence.
ACCESSION   CP066323
VERSION     CP066323.1
DBLINK      BioProject: PRJNA186035
            BioSample: SAMN16678597
KEYWORDS    .
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4050)
  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  JOURNAL   Unpublished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 4050)
  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 4050)
  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                   :: 125x
            Sequencing Technology :: Illumina MiSeq, Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 12/17/2020 15:06:25
            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)                     :: 4,908
            CDSs (total)                      :: 4,786
            Genes (coding)                    :: 4,639
            CDSs (with protein)               :: 4,639
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 147
            CDSs (without protein)            :: 147
            Pseudo Genes (ambiguous residues) :: 0 of 147
            Pseudo Genes (frameshifted)       :: 66 of 147
            Pseudo Genes (incomplete)         :: 92 of 147
            Pseudo Genes (internal stop)      :: 24 of 147
            Pseudo Genes (multiple problems)  :: 31 of 147
            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..4050
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="UWI_PP98"
                     /isolate="CFSAN103862"
                     /isolation_source="environmental"
                     /db_xref="taxon:28901"
                     /plasmid="pUWI-PP98.2"
                     /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(3911..4050,1..55))
                     /locus_tag="ITK55_24525"
     CDS             complement(join(3911..4050,1..55))
                     /locus_tag="ITK55_24525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="QQL83536.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            340..663
                     /locus_tag="ITK55_24530"
     CDS             340..663
                     /locus_tag="ITK55_24530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nikA protein"
                     /protein_id="QQL83537.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     gene            1727..2866
                     /locus_tag="ITK55_24535"
     CDS             1727..2866
                     /locus_tag="ITK55_24535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761319.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="RNA-directed DNA polymerase"
                     /protein_id="QQL83538.1"
                     /translation="MNKPRFNGTPVASLDSLSAMLGIERKRLDWIVKSVSMSYKQFKVE
                     TGKNKKERQIFEPKRSLKGIQKKINKEIFEKIDYPHYLHGALSGRDYISNAAVHTRKRT
                     VICLDITNFYPSISKKDVCSIFKNLMRFSPEVSLCLTELVTLNNKVPQGGCCSSYIANL
                     LFFNSEYNLYNRLKSMGLSYSRLLDDITISSDKDLSSEEKTKVIKLVHGMVNQYRLSIN
                     ESKTTIEHSKDSSSKLSVTGLWVKHGVPKLTKENRRYIRYLVYICKKQGAYERHTKEYH
                     DLWNRCSGKVAQMSRLGHVQAVELRAILSEIMPVYDDYKISKLKLMAKHYLNKFTPPLT
                     DEQIRKIDRMLYDFDIVGRTNKNLAKLYRRKLVALLPDR"
                     /name="RNA-directed DNA polymerase"
     gene            2871..3074
                     /locus_tag="ITK55_24540"
     CDS             2871..3074
                     /locus_tag="ITK55_24540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000427298.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="retron Se72 family effector protein"
                     /protein_id="QQL83535.1"
                     /translation="MENGFVNFYDHVKGYGFIRRERGRDVFFRYDDFLFLGHDVDICKG
                     ILVRFKLEKTDKGFKAVAIQKV"
                     /name="retron Se72 family effector protein"
     Typing          91..331
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.174"
                     /coverage="100.0"
                     /evalue="1.65e-119"
     Typing          complement(3274..3722)
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          341..660
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="3.32e-62"
ORIGIN
        1 tctggctttt tatgaatcct gccatgttga gtacggtttg ctgctgcttg ttcatctttc
       61 tgttttctcc gttctttctg tcatctgctt tgtgtgatta tatcgcgtac cacttttcga
      121 ctgttttacc gtcggtattc tgctgtctga ctctttgacg ggcatttctg tcagacaaca
      181 ctgtcactgc caaaaaactg ccgtgccttt gtcggtaatt cgagcttgct gacaggacag
      241 gatgtgtaat tgttataccg cgcatacatg cacgctatta caattaccct ggtcagggct
      301 ttgccccgac accccatgtc agatacggag ccatgtttta tgacaaaacg aagtggaagt
      361 aatacgcgca ggcgggctat cagtcgccct gttcgtctga cggcagaaga agaccaggaa
      421 atcagaaaaa gggctgctga atgcggcaag accgtttccg gttttttacg ggcggcagct
      481 ctcggtaaga aagttaactc actgactgat gatcgggtac tgaaagaagt tatgagactg
      541 ggggcgttac agaaaaaact ctttatcgac ggcaagcgtg tcggggacag ggagtatgcg
      601 gaggtactga tcgctattac ggagtatcac cgtgccctgt tatccaggct tatggcagat
      661 tagcttcccg gggagaaaac tgtcgaaaac agacggtatg aacaccgtaa gctcccaaag
      721 tgatcaccat tcgctttcat gcatagctat gcagtgagct gaaaacgatc ctgacgcatc
      781 cttcctgttt tttcggggct aaacctctct ttttgcggta tttgcgtcag aattgcgttc
      841 agcgcgtttc agcggtgcgt acaattaagg gattatggta aatacaattg gttaaattac
      901 tattggtgat aaatgaatat ttcaataaaa acaatgactt aaaactattg ctcggtttga
      961 cggtaaaacc ttaagagatg ccttttcgag aaaaatagcg acttttgatg gcaaggtttt
     1021 aagggatgcc tctttaaaaa aagtagcaac ctttgacggt cagaatttaa gagatgctag
     1081 ttcaaaaatt atcctgagtg ccgatgctga ggttgggatt gttgttatgg cctttgtagc
     1141 tgagttgatt tgaatctcat gctgcatacc ttttagccta tcgctggcag gataaggcgc
     1201 tttcttgttg gtgacagaaa gataaaaaac tttataataa tcagcgaagc gggcgaacca
     1261 cgcctggctc tcgctcttta acaaatggtt acgtgtatgt tgcgcaagga aaccgatgcc
     1321 ttgtttttaa ggcgatctcg catgagatca tgaccggcct ggccgctaat taatggtgag
     1381 aacgcccctg agcgtgtatc agcactaaaa gaatagcgac gattgtctgg caatgtgagt
     1441 taaaagtccc aaagagccaa tagagttttt ccttgctttc ctactggtct ggcaaaattt
     1501 cataaccaat aggagttgca tcatgtttat tatcaacatc aacattaacg taaccaagag
     1561 ctcttcatct tgttctggag acggtcagat gaagaaaaaa agagaggttg gctctctgga
     1621 ggcactgaaa aaaacacagt ttttgttttc tatgtgcttg attatgttta aagtaataga
     1681 ttacgtatcg aaacttttta actaatcgac ttttaactca aacatcatga ataaacccag
     1741 gtttaatgga actcctgttg catctttgga ttctttatct gcgatgttag gcatagaaag
     1801 aaaaagattg gactggatag tcaagtctgt atcgatgtcg tacaagcagt ttaaggttga
     1861 aacagggaag aataaaaaag aaaggcaaat ttttgaaccc aagagatctt tgaaaggaat
     1921 tcaaaaaaaa ataaataaag aaatttttga gaaaattgat taccctcatt atttgcatgg
     1981 ggcgttaagt ggtcgcgatt atatatctaa tgccgctgtt catactagga aaagaacagt
     2041 tatatgtctt gatatcacca atttttatcc cagcattagt aaaaaagatg tttgttctat
     2101 ttttaaaaat ttaatgcgtt tttctcctga ggtttctttg tgcttaacgg aacttgtgac
     2161 gttgaataat aaggttcctc agggtgggtg ctgttctagt tatattgcaa atcttttatt
     2221 ttttaatagt gagtataatc tctataatag attgaagtct atggggcttt catattcaag
     2281 gcttttagat gatattacta tatcctctga taaggatctt tcatcagagg aaaaaacaaa
     2341 agtaataaaa ctcgttcacg gaatggtgaa tcagtacaga ctttcaataa atgaaagtaa
     2401 gacaacgata gagcactcaa aagattcgtc ttctaaactt agtgtcactg ggttgtgggt
     2461 aaagcatggc gttcctaagt taacaaaaga aaatagacgt tatatcaggt acttagttta
     2521 tatatgtaaa aaacaaggtg cttatgaacg tcatacgaaa gagtaccatg atttatggaa
     2581 tagatgctct ggcaaggttg ctcaaatgtc gaggcttggg catgtccagg cggttgaatt
     2641 gagggcgatt ctttctgaga taatgccagt ttatgatgat tacaagatat ctaaattaaa
     2701 gttgatggct aagcattatc taaataaatt tacgccgcct ttaactgatg agcagataag
     2761 gaaaatagat aggatgctct atgattttga tatagtaggg cggactaata agaatcttgc
     2821 aaaactatat agacgtaagc ttgtggcatt acttccagat aggtgattat atggaaaatg
     2881 gatttgttaa tttttatgac catgttaaag ggtatggctt tataaggcgt gagcgtggac
     2941 gtgatgtttt ctttcggtat gatgattttt tgtttttagg gcatgatgtc gatatatgta
     3001 aaggtatttt agttaggttt aaattagaaa aaacagataa agggtttaaa gctgtagcga
     3061 ttcaaaaggt ataacatcgt ggatgtgtca gcttgttttt atgatatgag aacttgagat
     3121 cctttctatc tcgtcgtaat ctcttgctgt gtaaacgaaa aaaccgcctt gcagggcggt
     3181 ttttcgaagg ttctcagagc taccaactct ttgagccgag gtaactggct tggaggagcg
     3241 cagtcaccaa aacttgttct ttcagtttag ccttaacggg cgcatgactt caaggctaac
     3301 tcctctaatt cggttaccag tggctgctgc cagtggcgat aagtcgtgtc ttctcggttt
     3361 ggattcaagt cgatagttac cggataaggc gcagcggtcg gactgaacgg ggggttcgtg
     3421 catacagtcc agcttggagc gaacgaccta caccgggccg agataccaac agcgtgagct
     3481 atgagaaagc gccacgtttc ccgaagggag aaaggcggac aggtatccgg taagcggcag
     3541 ggtcggaaca ggagagcgca cgagggagct tccaggggga aacgcctggt atctttatag
     3601 tcctgtcggg tttcgccacc tctgacttga gcgtcggttt ttgtgatgct cgtcaggggg
     3661 gcggagccta tggaaaaacg cctcctgctc gcccttcttc tgggcctttg tcttttgctc
     3721 acatgttctt tccggcttta tcccctgatt ctgtggataa ccgtattacc gcctttgagt
     3781 gagctgacac cgctcgccgc agtcgaacga ccgagcgtag cgagtcagtg agcgaggaag
     3841 cggaagagcg ccttatgtga cattttctcc ttacgctcct ctatgccgtt ctgcatcctg
     3901 tcctgatgcg ttatatcccg gtgcgatttt ccgcttcaaa gcgtgtctgt atgctgttct
     3961 gaagttcttc cgcgagttcg tgcagcttct cacacatggc tgcctgttcg tcagcatcaa
     4021 gtgcgtccag tttttcgagc agcgtcaggc
//
