LOCUS       CP119475                4301 bp    DNA     circular BCT 16-MAR-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Newport strain CVM 46267
            plasmid pFSIS12033266-2, complete sequence.
ACCESSION   CP119475
VERSION     CP119475.1
DBLINK      BioProject: PRJNA242847
            BioSample: SAMN33394022
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  JOURNAL   Unpublished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)
  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                   :: 352x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 03/08/2023 11:48:33
            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)                     :: 4,836
            CDSs (total)                      :: 4,716
            Genes (coding)                    :: 4,592
            CDSs (with protein)               :: 4,592
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 124
            CDSs (without protein)            :: 124
            Pseudo Genes (ambiguous residues) :: 0 of 124
            Pseudo Genes (frameshifted)       :: 51 of 124
            Pseudo Genes (incomplete)         :: 87 of 124
            Pseudo Genes (internal stop)      :: 21 of 124
            Pseudo Genes (multiple problems)  :: 31 of 124
            Pseudo Genes (short protein)      :: 1 of 124
            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="CVM 46267"
                     /serovar="Newport"
                     /isolation_source="comminuted beef"
                     /sub_species="enterica"
                     /db_xref="taxon:108619"
                     /plasmid="pFSIS12033266-2"
                     /geo_loc_name="USA:FL"
                     /collection_date="2020"
                     /collected_by="FSIS"
     gene            join(4128..4301,1..846)
                     /locus_tag="P1A08_24165"
     CDS             join(4128..4301,1..846)
                     /locus_tag="P1A08_24165"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001271372.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WEM84303.1"
                     /translation="MSAALQYFEENLPRRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASA
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTPETFAQYVANTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAEAVGVSRWTVRRWMDSSVEWLLSKQIIKI"
                     /name="replication initiation protein"
     gene            complement(1107..1553)
                     /locus_tag="P1A08_24170"
     CDS             complement(1107..1553)
                     /locus_tag="P1A08_24170"
                     /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="WEM84304.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPRNHPKWQEWERRGKELLTKDSA"
                     /name="conjugal transfer protein TraD"
     gene            1725..2465
                     /locus_tag="P1A08_24175"
                     /pseudo=""
     CDS             1725..2465
                     /locus_tag="P1A08_24175"
                     /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"
     Typing          2..602
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.668"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          1726..3581
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ggggcagcga ttgactggag cgaccggaac gcccccgcgc cgaacatcac cgttaaaaat
       61 cctgtgaacg gacacgctca cctgctctat gcactcaata tcgccgtgag aaccgcgcct
      121 gatgcgtcgg ttaaggcgct gaaatatgcc gcagcggttg aacgttcgct gtgtgagaaa
      181 ctttgtgctg atgtgaacta cagcggactg atttgcaaaa atccgttcca cctggaatgg
      241 caggtgatgg agtggcgcga ggaagcctat accctcgatg aactggctga ttatctcgat
      301 ttgagcgcct cagcgcgtcg tagcatcgat aaacattacg ggatggggcg aaactgccac
      361 ctgttcgaaa tgacgcgcaa atgggcttac agggcgattc gtcagggctg gccagcattc
      421 tcacagtggc ttgatgccgt gattcagcgt gtcgaaatgt acaacgcatc gcttcccgtt
      481 ccgctttctc cgcctgaatg tcgggctatt ggcaagagca ttgcgaaata cacgcacagg
      541 aacttcacgc cggaaacttt cgcacagtat gtggctaata cgcacacgcc agaaattcag
      601 gcagcacgcg gtcgcaaggg cgggaaggcc aattcgtcag aaaatcagtc ggacaaaggg
      661 aaaaaaagcg ccgctgttcg gtggactgct aacgatgaca aacgtcgtag ggcgcttgat
      721 atgtacatct tgggagcctc aacagaagat attgcagagg cggttggtgt tagccgttgg
      781 acagttcgac gctggatgga tagctctgta gaatggctac tgagtaaaca aataattaaa
      841 atttaattaa caagaatggc acataccccc ccctgttttg ttaaaattct gttaattttg
      901 ggtgcatgaa caagcctata tcagataaca gcgcctttcg gcgtcttttt gagcagcggg
      961 ctttccggcg gttttctcct ttcagcccag caatggtgcg gcttaccgca tgattgaggt
     1021 ggttgtgctc gccgcagtct catgaccgag cgtagcgagc gaatgagcga ggaagcacca
     1081 gggaaccgga acgtgaacgg aggctcttac gcactgtctt tggttagtag ctccttcccg
     1141 cgtctttccc attcctgcca ttttggatgg ttgcgcggta gctctgcgat tcctgcgagt
     1201 gcgcctacca gttcggcagc actaaacttt ggttttccgg ttttgctgtc caccagtcct
     1261 gccacaatca tgaggcctgc ggccttgtag agttcatgat cccgcgcctt tcgttctgcc
     1321 cttgcggctg ccttccgttc tgccgctatg attgccgtta ccctggcttt tgctgcggct
     1381 gctttctctg cggttttttc tgcccgtatc agtgcggaca acgttttttc atccgtcgtt
     1441 gttcggtttt ttttctctgc cagtaacaca agtaatctct gctgctctga cggtgatttc
     1501 agtccgttga tgtaggcaat ttttgcactt aaccactctt cacgatttgt cattcttacc
     1561 tctgcacttt tgccgttaat gtgagttgtt attgtgcata atatcacctt gtctgcctgc
     1621 gtgtgagacc gtaaaatcat ccctgattaa ttcagggatg cgcacttaga cgtttctctc
     1681 cttcgtcgag aaactgtgcg ctcctgcgga gggctaaaag gcagatggct agttaccatt
     1741 gcaccgttaa aactggtgca aaaggcagtg ccttaaaaca tgctgattac atttccagaa
     1801 ccggcgaata cgagaactat aaatcgcggg aggatctgga gttttcgtca tccggtaaca
     1861 tgccatcatg ggcgaagaaa aatccctccg agctatggaa agccgcagat gaatttgaac
     1921 gaaaaaacgg gacggcatac cgtgaaattg agatcgcgtt accgcgtgaa ctgacacgcg
     1981 aacaacggat agaacttgtt gaagattttg tgcaaaagga acttggcgat cgccatgcct
     2041 accagtacgc gatccacaat ccgccaggtg caattgacgg aaaggaacaa ccacacgcgc
     2101 atatcatgtt ttgcgagcgg attaatgatg gtattgaacg cgatccgcag cagtttttta
     2161 aacgtgctaa cagcaaatta ccggagagag gaggcgcaaa aaaggcacgc tttggtgaaa
     2221 cacaacaaga gcgaaaatct gcccttgttg aattacgttc ccgctgggcg gatgtgcaga
     2281 atgagcacct tgcgcgtcac ggtcacgagt cgcgcgtaga tcatcgttcg ctgaaagaac
     2341 agggtatcaa tcgcacgccg gaagttcatc ttggccccgt tcaggccgcc agtctgaatg
     2401 gtgagcagat tgttgcaatc caggaacgga ggaatgccga gcgggaactc aagaccgcca
     2461 gagatgccgc aaatgccatt cagccggaac aggagcaaaa gcaaaaaatc aaggcagttg
     2521 agcctgttcg ttctgcccga ttaatggatg agtatcggga tgttgcccgg aaagtgatca
     2581 cactggagac aagacagaat gagagtcagg aactggcgct aaaacatcac ttgtttatga
     2641 aggcagaagc gaaagagcaa gaactggcga aactgaaaga acaactaaaa aaaatggacg
     2701 agcagcgttc tgtttataag aacaagattg atgagaaaaa acagaatatt acagcgttag
     2761 ttgaacagaa aaaatcgctc gagagaagtt ttattggcct gtttaaaggc gggatgaaac
     2821 gtgagcttga ggaacaaatc aagacacagg tcagccaact ggaaaagacc gagcacgagg
     2881 tgaagcagtt ggacgagaat tatcagcagc ttcagatgca ggctgataat gaacagaaga
     2941 atttctcaca ctcaccggaa tatcagtatt cggaagcggt tttgagcgga atacctcgtt
     3001 cgattttaaa actgcaattc gctctgttgc ccagtgagag cactatcgcc ttcaacaaga
     3061 atgtactgga cgtagaacaa cgaaaagaag ctgctatagc tgccgaactt tgccttagtg
     3121 aagatgagcg gcggcaaatc aggcgagaga ttcaggatgt tctaaacggg gacgcctgcg
     3181 aagggcagca gacagaaact ctccagcaga aacgtcccga gaaagatgcg cacatcgagt
     3241 gggaacggga agaatctccg caagtcgtca tcccaaaaac ttatgttttt ttctctgcgt
     3301 gcaggggcgt taagacagaa atcaggccgt ttgagtcgtg cgatgatgct atcgagtggg
     3361 ggttggttga gtgtgaactt catgatcgtt ttaagcgtga tctcattgtt tatcgagttg
     3421 atgctgaatt gataggaaaa ggtgatgata cagtgatgaa aaatgccgaa cgcattgatc
     3481 ttactgatga acttgaagga tggaatcagc aaacacacat cgaaaaagag agcctttttg
     3541 aacgagtaca gcagcggtca caagatgatg agctggagat gtagttactg acgcgcttcg
     3601 cttgtccaac gcctcacaga ccgcgaaagg atttcgcgtc ccgttcaccg tttggctgtg
     3661 atgtatagtg agaatgcaac cgcaacctaa ctacttgttt gcacggtaga aaaacaaaaa
     3721 cggaagcatt ctcaaaaatg ttctaatgtg cttttttcag aacggcaagt ttgtcatttt
     3781 gccccgttcg cccttctgaa cggtcgaaac tgttcgcgaa tcgcttttgt gcatagttat
     3841 gcaggcccct gaaaacaatt ctgacgcatt tttctggttt accctggtgt ttccttgtct
     3901 ttttgcgttt tttgcgtcag aaagcgactg agggcgtttt aaggggtacg tacaacagga
     3961 gttatggtaa atggatcggg tttgcgggaa gactcgacag gttttgtcgt tgggggtagt
     4021 gtaagcgact gaaaaacaaa cgcccctgaa attcgtgtct atccgccaag actgtcacga
     4081 aaatacaggg gcgatgtcgg tcgataacct ggaaggaatc gtaacacatg agcgccgcgc
     4141 ttcaatactt cgaagaaaat ttaccccgcc gtccctatca cacggatgat ctcgcttttg
     4201 gtcttcgcat ctccggcaaa gggcgtgcgc tgcttgcgcg gtacatccag cagaaccagc
     4261 ctcatgcgca gttctggctg gtttttgacg ttgaccgcga g
//
