LOCUS       CP119517                4301 bp    DNA     circular BCT 16-MAR-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Newport strain
            FSIS31903059 plasmid pFSIS31903059-3, complete sequence.
ACCESSION   CP119517
VERSION     CP119517.1
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 4301)
  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  JOURNAL   Unpublished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 4301)
  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 4301)
  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..4301
                     /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="pFSIS31903059-3"
                     /geo_loc_name="USA:UT"
                     /collection_date="2019"
                     /collected_by="USDA-FSIS"
     gene            complement(join(3823..4301,1..541))
                     /locus_tag="GT288_023855"
     CDS             complement(join(3823..4301,1..541))
                     /locus_tag="GT288_023855"
                     /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="replication initiation protein"
                     /protein_id="WEP10228.1"
                     /translation="MSAALQYFEENLPRRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASA
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTPETFAQYVANTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAEAVGVSRWTVRRWMDSSVEWLLSKQIIKI"
                     /name="replication initiation protein"
     gene            complement(2204..2944)
                     /locus_tag="GT288_023860"
                     /pseudo=""
     CDS             complement(2204..2944)
                     /locus_tag="GT288_023860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016230929.1"
                     /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="MobA/MobL family protein"
                     /name="MobA/MobL family protein"
     gene            3116..3562
                     /locus_tag="GT288_023865"
     CDS             3116..3562
                     /locus_tag="GT288_023865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000184721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WEP10227.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPRNHPKWQEWERRGKELLTKDSA"
                     /name="conjugal transfer protein TraD"
     Typing          complement(2..541)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.815"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(4083..4299)
                     /name="rep_cluster_2344"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.248"
                     /coverage="84.0"
                     /evalue="5.13e-100"
     Typing          complement(1089..2944)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgaacaggtg gcagtttcgc cccatcccgt aatgtttatc gatgctacga cgcgctgagg
       61 cgctcaaatc gagataatca gccagttcat cgagggtata ggcttcctcg cgccactcca
      121 tcacctgcca ttccaggtgg aacggatttt tgcaaatcag tccgctgtag ttcacatcag
      181 cacaaagttt ctcacacagc gaacgttcaa ccgctgcggc atatttcagc gccttaaccg
      241 acgcatcagg cgcggttctc acggcgatat tgagtgcata gagcaggtga gcgtgtccgt
      301 tcacaggatt tttaacggtg atgttcggcg cgggggcgtt ccggtcgctc cagtcaatcg
      361 ctgccccctc gcggtcaacg tcaaaaacca gccagaactg cgcatgaggc tggttctgct
      421 ggatgtaccg cgcaagcagc gcacgccctt tgccggagat gcgaagacca aaagcgagat
      481 catccgtgtg atagggacgg cggggtaaat tttcttcgaa gtattgaagc gcggcgctca
      541 tgtgttacga ttccttccag gttatcgacc gacatcgccc ctgtattttc gtgacagtct
      601 tggcggatag acacgaattt caggggcgtt tgtttttcag tcgcttacac tacccccaac
      661 gacaaaacct gtcgagtctt cccgcaaacc cgatccattt accataactc ctgttgtacg
      721 taccccttaa aacgccctca gtcgctttct gacgcaaaaa acgcaaaaag acaaggaaac
      781 accagggtaa accagaaaaa tgcgtcagaa ttgttttcag gggcctgcat aactatgcac
      841 aaaagcgatt cgcgaacagt ttcgaccgtt cagaagggcg aacggggcaa aatgacaaac
      901 ttgccgttct gaaaaaagca cattagaaca tttttgagaa tgcttccgtt tttgtttttc
      961 taccgtgcaa acaagtagtt aggttgcggt tgcattctca ctatacatca cagccaaacg
     1021 gtgaacggga cgcgaaatcc tttcgcggtc tgtgaggcgt tggacaagcg aagcgcgtca
     1081 gtaactacat ctccagctca tcatcttgtg accgctgctg tactcgttca aaaaggctct
     1141 ctttttcgat gtgtgtttgc tgattccatc cttcaagttc atcagtaaga tcaatgcgtt
     1201 cggcattttt catcactgta tcatcacctt ttcctatcaa ttcagcatca actcgataaa
     1261 caatgagatc acgcttaaaa cgatcatgaa gttcacactc aaccaacccc cactcgatag
     1321 catcatcgca cgactcaaac ggcctgattt ctgtcttaac gcccctgcac gcagagaaaa
     1381 aaacataagt ttttgggatg acgacttgcg gagattcttc ccgttcccac tcgatgtgcg
     1441 catctttctc gggacgtttc tgctggagag tttctgtctg ctgcccttcg caggcgtccc
     1501 cgtttagaac atcctgaatc tctcgcctga tttgccgccg ctcatcttca ctaaggcaaa
     1561 gttcggcagc tatagcagct tcttttcgtt gttctacgtc cagtacattc ttgttgaagg
     1621 cgatagtgct ctcactgggc aacagagcga attgcagttt taaaatcgaa cgaggtattc
     1681 cgctcaaaac cgcttccgaa tactgatatt ccggtgagtg tgagaaattc ttctgttcat
     1741 tatcagcctg catctgaagc tgctgataat tctcgtccaa ctgcttcacc tcgtgctcgg
     1801 tcttttccag ttggctgacc tgtgtcttga tttgttcctc aagctcacgt ttcatcccgc
     1861 ctttaaacag gccaataaaa cttctctcga gcgatttttt ctgttcaact aacgctgtaa
     1921 tattctgttt tttctcatca atcttgttct tataaacaga acgctgctcg tccatttttt
     1981 ttagttgttc tttcagtttc gccagttctt gctctttcgc ttctgccttc ataaacaagt
     2041 gatgttttag cgccagttcc tgactctcat tctgtcttgt ctccagtgtg atcactttcc
     2101 gggcaacatc ccgatactca tccattaatc gggcagaacg aacaggctca actgccttga
     2161 ttttttgctt ttgctcctgt tccggctgaa tggcatttgc ggcatctctg gcggtcttga
     2221 gttcccgctc ggcattcctc cgttcctgga ttgcaacaat ctgctcacca ttcagactgg
     2281 cggcctgaac ggggccaaga tgaacttccg gcgtgcgatt gataccctgt tctttcagcg
     2341 aacgatgatc tacgcgcgac tcgtgaccgt gacgcgcaag gtgctcattc tgcacatccg
     2401 cccagcggga acgtaattca acaagggcag attttcgctc ttgttgtgtt tcaccaaagc
     2461 gtgccttttt tgcgcctcct ctctccggta atttgctgtt agcacgttta aaaaactgct
     2521 gcggatcgcg ttcaatacca tcattaatcc gctcgcaaaa catgatatgc gcgtgtggtt
     2581 gttcctttcc gtcaattgca cctggcggat tgtggatcgc gtactggtag gcatggcgat
     2641 cgccaagttc cttttgcaca aaatcttcaa caagttctat ccgttgttcg cgtgtcagtt
     2701 cacgcggtaa cgcgatctca atttcacggt atgccgtccc gttttttcgt tcaaattcat
     2761 ctgcggcttt ccatagctcg gagggatttt tcttcgccca tgatggcatg ttaccggatg
     2821 acgaaaactc cagatcctcc cgcgatttat agttctcgta ttcgccggtt ctggaaatgt
     2881 aatcagcatg ttttaaggca ctgccttttg caccagtttt aacggtgcaa tggtaactag
     2941 ccatctgcct tttagccctc cgcaggagcg cacagtttct cgacgaagga gagaaacgtc
     3001 taagtgcgca tccctgaatt aatcagggat gattttacgg tctcacacgc aggcagacaa
     3061 ggtgatatta tgcacaataa caactcacat taacggcaaa agtgcagagg taagaatgac
     3121 aaatcgtgaa gagtggttaa gtgcaaaaat tgcctacatc aacggactga aatcaccgtc
     3181 agagcagcag agattacttg tgttactggc agagaaaaaa aaccgaacaa cgacggatga
     3241 aaaaacgttg tccgcactga tacgggcaga aaaaaccgca gagaaagcag ccgcagcaaa
     3301 agccagggta acggcaatca tagcggcaga acggaaggca gccgcaaggg cagaacgaaa
     3361 ggcgcgggat catgaactct acaaggccgc aggcctcatg attgtggcag gactggtgga
     3421 cagcaaaacc ggaaaaccaa agtttagtgc tgccgaactg gtaggcgcac tcgcaggaat
     3481 cgcagagcta ccgcgcaacc atccaaaatg gcaggaatgg gaaagacgcg ggaaggagct
     3541 actaaccaaa gacagtgcgt aagagcctcc gttcacgttc cggttccctg gtgcttcctc
     3601 gctcattcgc tcgctacgct cggtcatgag actgcggcga gcacaaccac ctcaatcatg
     3661 cggtaagccg caccattgct gggctgaaag gagaaaaccg ccggaaagcc cgctgctcaa
     3721 aaagacgccg aaaggcgctg ttatctgata taggcttgtt catgcaccca aaattaacag
     3781 aattttaaca aaacaggggg gggtatgtgc cattcttgtt aattaaattt taattatttg
     3841 tttactcagt agccattcta cagagctatc catccagcgt cgaactgtcc aacggctaac
     3901 accaaccgcc tctgcaatat cttctgttga ggctcccaag atgtacatat caagcgccct
     3961 acgacgtttg tcatcgttag cagtccaccg aacagcggcg ctttttttcc ctttgtccga
     4021 ctgattttct gacgaattgg ccttcccgcc cttgcgaccg cgtgctgcct gaatttctgg
     4081 cgtgtgcgta ttagccacat actgtgcgaa agtttccggc gtgaagttcc tgtgcgtgta
     4141 tttcgcaatg ctcttgccaa tagcccgaca ttcaggcgga gaaagcggaa cgggaagcga
     4201 tgcgttgtac atttcgacac gctgaatcac ggcatcaagc cactgtgaga atgctggcca
     4261 gccctgacga atcgccctgt aagcccattt gcgcgtcatt t
//
