LOCUS       CP119516                5209 bp    DNA     circular BCT 16-MAR-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Newport strain
            FSIS31903059 plasmid pFSIS31903059-2, complete sequence.
ACCESSION   CP119516
VERSION     CP119516.1
DBLINK      BioProject: PRJNA242847
            BioSample: SAMN13763817
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Newport
  ORGANISM  Salmonella enterica subsp. enterica serovar Newport
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5209)
  AUTHORS   Ge,B.
  TITLE     Genomic Analysis of Azithromycin-Resistant Salmonella from Food
            Animals and Retail Meats, 2015-2021, United States
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5209)
  CONSRTM   GenomeTrakr network: Whole genome sequencing for foodborne pathogen
            traceback
  TITLE     Direct Submission
  JOURNAL   Submitted (08-JAN-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 5209)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-MAR-2023) CVM/OAS, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 24-SEP-2021
            Assembly Method                   :: HGAP v. 4
            Assembly Name                     :: Microbial assembly
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 132x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 03/09/2023 08:23:47
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.4
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,773
            CDSs (total)                      :: 4,654
            Genes (coding)                    :: 4,523
            CDSs (with protein)               :: 4,523
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 131
            CDSs (without protein)            :: 131
            Pseudo Genes (ambiguous residues) :: 0 of 131
            Pseudo Genes (frameshifted)       :: 57 of 131
            Pseudo Genes (incomplete)         :: 90 of 131
            Pseudo Genes (internal stop)      :: 20 of 131
            Pseudo Genes (multiple problems)  :: 32 of 131
            Pseudo Genes (short protein)      :: 1 of 131
            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..5209
                     /organism="Salmonella enterica subsp. enterica serovar
                     Newport"
                     /mol_type="genomic DNA"
                     /strain="FSIS31903059"
                     /serovar="Newport"
                     /isolation_source="product-raw-intact-beef"
                     /sub_species="enterica"
                     /db_xref="taxon:108619"
                     /plasmid="pFSIS31903059-2"
                     /geo_loc_name="USA:UT"
                     /collection_date="2019"
                     /collected_by="USDA-FSIS"
     gene            complement(join(4866..5209,1..625))
                     /locus_tag="GT288_023835"
     CDS             complement(join(4866..5209,1..625))
                     /locus_tag="GT288_023835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076611102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0004803 - transposase activity [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="IS5 family transposase"
                     /protein_id="WEP10225.1"
                     /translation="MKDQITYLPDNADRSVAKQKFKITNWPTYNKALINRGSITFWLDD
                     EAIQAWYESATPSSRGRPQRYSDLAITTVLVIKRVFRLTLRAAQGFIDSIFTLMNVPLR
                     CPDYTSVSKRAKSVNVSFKTFTRGEIAHLVIDSTGLKVFGEGEWKVKKHGQERRRIWRK
                     LHLAVDSKTHEIICADLSLNNVTDSEAFPGLIRQTHRKIRAASADGAYDTRLCHDELRR
                     KKISALIPPRKGAGYWPGEYADRNRAVANQRMTGSNARWKWTTDYNRRSIAETAMYRVK
                     QLFGGSLTLRDYDGQVAEAMALVRALNKMTKAGMPESVRIT"
                     /name="IS5 family transposase"
     gene            complement(1738..1932)
                     /locus_tag="GT288_023840"
     CDS             complement(1738..1932)
                     /locus_tag="GT288_023840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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="WEP10226.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2860..3828)
                     /locus_tag="GT288_023845"
     CDS             complement(2860..3828)
                     /locus_tag="GT288_023845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076611102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0004803 - transposase activity [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="IS5-like element IS903B family transposase"
                     /protein_id="WEP10224.1"
                     /translation="MKDQITYLPDNADRSVAKQKFKITNWPTYNKALINRGSITFWLDD
                     EAIQAWYESATPSSRGRPQRYSDLAITTVLVIKRVFRLTLRAAQGFIDSIFSLMNVPLR
                     CPDYSCVSRRAKSVNVSFKTPTRGEIAHLVIDSTGLKVFGEGEWKVKKHGQERRRIWRK
                     LHLAVDSKTHEIICADLSLNNVTDSEAFPGLIRQTHRKIRAASADGAYDTRLCHDELRR
                     KKISALIPPRKGAGYWPGEYADRNRAVANQRMTGSNARWKWTTDYNRRSIAETAMYRVK
                     QLFGGSLTLRDYDGQVAEAMALVRALNKMTKAGMPESVRIA"
                     /name="IS5-like element IS903B family transposase"
     gene            complement(3879..4693)
                     /locus_tag="GT288_023850"
                     /pseudo=""
     CDS             complement(3879..4693)
                     /locus_tag="GT288_023850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032492145.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology.
                     GO_process: GO:0046677 - response to antibiotic [Evidence
                     IEA]"
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="APH(3')-I family aminoglycoside
                     O-phosphotransferase"
                     /name="APH(3')-I family aminoglycoside
                     O-phosphotransferase"
     ARG             complement(3880..4412)
                     /name="APH(3')-Ia"
                     /gene="APH(3')-Ia"
                     /gene_name="APH(3')"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="98.3"
                     /coverage="65.31"
     Typing          1573..1658
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          1969..2067
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.0"
                     /coverage="100.0"
                     /evalue="6.26e-40"
     Typing          2192..2447
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.899"
                     /coverage="89.0"
                     /evalue="2.61e-118"
     Typing          complement(1002..1547)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.255"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cgtctgccga tgctgccctg atttttctgt gagtctgccg gataagaccc gggaaggctt
       61 ctgagtccgt cacattgttc agcgacaggt cagcgcagat gatttcatgt gttttactgt
      121 caacggcgag atgcagctta cgccagatac ggcggcgttc ctggccatgc tttttgactt
      181 tccactcgcc ttcaccgaag accttcagcc cggtggaatc aatcaccaga tgcgcgattt
      241 caccccgggt gaacgttttg aaactgacat taaccgactt tgcgcgcttg ctgacactgg
      301 tgtaatccgg gcagcgcaac ggaacattca tcagtgtaaa aatggaatca ataaaaccct
      361 gtgcagcccg cagggtcaac ctgaacacgc gtttaatgac cagcacagtc gtgatggcaa
      421 ggtcagaata gcgctgaggt ctgcctcgtg aagaaggtgt tgctgactca taccaggcct
      481 gaatagcttc atcatccagc cagaaagtta tggagccacg gttgatgagg gctttattgt
      541 aggtgggcca gttggtgatt ttgaactttt gctttgccac ggaacggtct gcgttgtcgg
      601 gaagatacgt gatctgatcc ttcaactcag caaaagttcg atttattcaa caaagccgtt
      661 gctaatcatt agtttttgtc ttgtggttga aaactgagcg ctatggctat gacctaggag
      721 tgggagtgaa aagattcaag gatcctcttg tgatcctttt tttctgcgcg taatctgctg
      781 cctgtaaaca aaaaaaccac cgctaccaac ggtggtttgt ttgccggaat ctagagctac
      841 caactctttc ttccgaaggt aactggcttg gtggagcaca gataccaaat actgtccttc
      901 tagtgtagcc gcagttaggc caccacttca agaactctta atatctcaat ccaccttgtc
      961 cagttaccag tggctgctgc cagtggcgct ttgtcgtgtc ttaccgggtt ggactcaaga
     1021 cgatagttac cggataaggc gcagcggtcg ggctgaacgg ggggttcgtg cacacagccc
     1081 agcttggagc gaacgaccta caccgaactg agataccaac agcgtgagct atgagaaagc
     1141 gccacgcttc ccgaagggag aaaggcggac aggtatccgg taagcggcag ggtcggaaca
     1201 ggagagcgca cgagggagct tccaggggga aacgcctggt atctttatag tcctgtcggg
     1261 tttcgccacc tctgacttga gcgtcgattt ttgtgatgct cgtcaggggg gcggagccta
     1321 tggaaaaacg ccatcggcgt ggcctttctc ccggcctttg ccttttgcgc acatgttctt
     1381 tccggcgtta tcccctgatt ctgtggataa ccgtattacc gcctttgagt gagctgatac
     1441 cgctcgccgc agccgaacga ccgagcgtag cgagtcagtg agcgaggaag cggaagagcg
     1501 tcggaagctg cattttctcc ttacgcatct gtgcggcatt tcacacccgg catggcgcac
     1561 ttttcataca atctgcactg atgccgcatg gttaagccag tatacactcc gctatcgcta
     1621 cgtgactggg tcatggctgc gccccgacac ccgctaaaac cccctgacgc gccctgacgg
     1681 gcttgtctgc tgacgaaaac gcccacggga aagccgtgac cgcctccgtc agcttcgtta
     1741 tgttcctgtt tcactttcgg cctcaaagcg aatctggatg ctgttctgga gttcttctgc
     1801 gagttcgtgc agtcgttcgc acatggccgc ctgttcgtcg gcatccagag catccagttt
     1861 ttcaagcagt gtcaggctct ggcttttgat aaatcgcgcc atattcagcg cagtttgttg
     1921 ttgtttgttc accttccgtt gttctccgtc agttccgggt gtcgggggga ccctgagcag
     1981 gtggtaattg taagacattg cgggcgacgg tattacaatt gcacatcctg tcctgtttct
     2041 ttaggacgta tcatggcaca gcatatcaac tgataaataa tccctgtgca gtgcagccgc
     2101 tgttgcataa aatttcgctc tgcgtcgagt gtttcttaat caataattcc gctgatactc
     2161 cggaaaaacg cgagtctgtt ctcatgcctg aaatgcccac accccacgca aaaacaagtt
     2221 tttgctgatt tttctttata aatagagagt tatgacaaat tagttcttct tgctctcttt
     2281 gtgatattta aaaaagcggt gtcggcgcgg tgttgtagct gcgccaacac cgctttttag
     2341 gggtggtact gactattttc ataaaaaaca tcatcttata ttaggggtgc tgctagcggc
     2401 gcggtgtgtt tttttacagg acacccctgg gggcgctgct aggggtgtct gttcagatat
     2461 gtagcaatga gtcagggatt cacgaactga aaatgtccga aaatgtgtct catgggcact
     2521 gtatgcgccc aaaccgatcg tcattcactt tcatgcatag ctatgcagtg agctgaaagc
     2581 gatcctgacg catttttccg gtttaccccg gggagaacat ctctttttgc ggtgttcgcg
     2641 gcagaatcgc tttcagcgcg ttttagcggt gcgcgcaatg cgacgttatg gtaaatagat
     2701 gagttaggcc taagtcatga cagataaaac gaccgatatt aaaatggctt tagaaaacat
     2761 gatcagattt cgtgacacta tagagagatt gggaggttct atgggctttg ttgaataaat
     2821 cagatttcgg gtaagtctcc cccgtagcgg gttgtgtttt caggcaatac gcacgctttc
     2881 aggcatacct gctttcgtca ttttgttcag cgctcgtacc agggccatag cctccgcaac
     2941 ctgaccatcg tagtcacgca gcgtcagtga acccccgaac agctgtttta cccggtacat
     3001 cgccgtttcc gctatcgagc gacggttgta atctgttgtc catttccacc gcgcattact
     3061 cccggtcatt cgctgattag ccactgcacg gttacggtct gcatattcac cgggccagta
     3121 acccgcacct tttcggggtg ggataagcgc gctgattttc ttacgccgca gttcatcgtg
     3181 acagagccgg gtgtcgtaag cgccgtctgc cgatgctgcc ctgatttttc tgtgagtctg
     3241 ccggataaga cccgggaagg cttctgagtc cgtcacattg ttcagcgaca ggtcagcgca
     3301 gatgatttca tgtgttttac tgtcaacggc gagatgcagc ttacgccaga tacggcggcg
     3361 ttcctggcca tgctttttga ctttccactc gccttcaccg aagaccttca gcccggtgga
     3421 atcaattacc aggtgtgcga tttcaccccg ggtgggcgtt ttgaaactga cattaaccga
     3481 ctttgcccgc ctgctgacac agctgtaatc cgggcagcgt agcggaacgt tcatcagaga
     3541 aaaaatggaa tcaataaagc cctgcgcagc gcgcagggtc agcctgaata cgcgtttaat
     3601 gaccagcaca gtcgtgatgg caaggtcaga atagcgctga ggtctgcctc gtgaagaagg
     3661 tgttgctgac tcataccagg cctgaatagc ttcatcatcc agccagaaag ttatggagcc
     3721 acggttgatg agggctttat tgtaggtggg ccagttggtg attttgaact tttgctttgc
     3781 cacggaacgg tctgcgttgt cgggaagata cgtgatctga tccttcaact cagcaaaagt
     3841 tcgatttatt caacaaagcc ccaattaacc aattctgatt agaaaaactc atcgagcatc
     3901 aaatgaaact gcaatttatt catatcagga ttatcaatgc catatttatg aaaaagccgt
     3961 ttctgtaatg aaggtgaaaa ctcaccgagg cagttccata ggatggcaag atcctggtat
     4021 cggtctgcga ttccgactcg tccaacatca atacaaccta ttaatttccc ctcgtcaaaa
     4081 ataaggttat caagtgagaa atcaccatga gtgacgactg aatccggtga gaatggcaaa
     4141 agcttatgca tttctttcca gacttgttca acaggccagc cattacgctc gtcatcaaaa
     4201 tcactcgcat caaccaaacc gttattcatt cgtgattgcg cctgagcgag acgaaatacg
     4261 tgatcgctgt taaaaggaca attacaaaca ggaatcgaat gcaaccggcg caggaacgct
     4321 gccagcgcat caacaatatt ttcacctgaa tcaggatatt cttctaatac ctggaatgct
     4381 gttttcccgg ggatcgcagt ggtgagtaac atgcatcatc aggagtacgg ataaaatgct
     4441 tgatggtcgg aagaggcata aattccgtca gccagtttag tctgaccatc tcatctgtaa
     4501 catcattggc aacgctacct ttgccatgtt tcagaaacaa ctctggcgca tcgggcttcc
     4561 catacaatcg atagattgtc gcacctgatt gcccgacatt atcgcgagcc catctatacc
     4621 catataaatc agcatccagg ttggaattta atcgcggtct cgagcaagac gtttcccgtt
     4681 gaatatggct cataacaccc cttgtattac tgtttatgta agcagacagt tttattgttc
     4741 atgatgatat atttttatct tgtgcaatgt aacatcagag attttgagac acaatgtggt
     4801 tcccgccatg gctttgttga ataaatcaga tttcgggtaa gtctcccccg tagcgggttg
     4861 tgttttcagg taatacgcac gctttcaggc atacctgctt tcgtcatttt gttcagcgct
     4921 cgtaccaggg ccatagcctc cgcaacctga ccatcgtagt cacgcagcgt cagtgaaccc
     4981 ccgaacagct gttttacccg gtacatcgcc gtttccgcta tcgagcgacg gttgtaatct
     5041 gttgtccatt tccaccgcgc attactcccg gtcattcgct gattagccac tgcacggtta
     5101 cggtctgcat attcaccggg ccagtaaccc gcaccttttc ggggtgggat aagcgcgctg
     5161 attttcttac gccgcagttc atcgtgacag agccgggtgt cgtaagcgc
//
