LOCUS       CP082463                3749 bp    DNA     circular BCT 11-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Agona strain FSIS1607563
            plasmid pF18S017-3749, complete sequence.
ACCESSION   CP082463
VERSION     CP082463.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN05750475
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Agona
  ORGANISM  Salmonella enterica subsp. enterica serovar Agona
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3749)
  AUTHORS   Li,C., Tyson,G.H., Hsu,C.H., Harrison,L., Strain,E., Tran,T.T.,
            Tillman,G.E., Dessai,U., McDermott,P.F. and Zhao,S.
  TITLE     Long-Read Sequencing Reveals Evolution and Acquisition of
            Antimicrobial Resistance and Virulence Genes in Salmonella enterica
  JOURNAL   Front Microbiol 12, 777817 (2021)
   PUBMED   34867920
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3749)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (23-JUL-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 3749)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-AUG-2021) CVM/OR, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-JUN-2020
            Assembly Method :: SMRTLink Microbial Assembly v. SMRTLink9.0
            Assembly Name                     :: F18S017
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 267x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/02/2021 13:15:02
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 5.2
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 5,063
            CDSs (total)                      :: 4,942
            Genes (coding)                    :: 4,824
            CDSs (with protein)               :: 4,824
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 118
            CDSs (without protein)            :: 118
            Pseudo Genes (ambiguous residues) :: 0 of 118
            Pseudo Genes (frameshifted)       :: 53 of 118
            Pseudo Genes (incomplete)         :: 67 of 118
            Pseudo Genes (internal stop)      :: 18 of 118
            Pseudo Genes (multiple problems)  :: 18 of 118
            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..3749
                     /organism="Salmonella enterica subsp. enterica serovar
                     Agona"
                     /mol_type="genomic DNA"
                     /strain="FSIS1607563"
                     /serovar="Agona"
                     /isolation_source="Animal-Turkey-Young Turkey"
                     /sub_species="enterica"
                     /db_xref="taxon:58095"
                     /plasmid="pF18S017-3749"
                     /geo_loc_name="USA:MN"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            join(3713..3749,1..983)
                     /locus_tag="BHM61_025300"
     CDS             join(3713..3749,1..983)
                     /locus_tag="BHM61_025300"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221104.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="UAE55375.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREDAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDNSGEWLTKKQIIKC"
                     /name="replication initiation protein"
     gene            complement(1243..1641)
                     /locus_tag="BHM61_025305"
     CDS             complement(1243..1641)
                     /locus_tag="BHM61_025305"
                     /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="hypothetical protein"
                     /protein_id="UAE55376.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKEIKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            1818..2744
                     /locus_tag="BHM61_025310"
     CDS             1818..2744
                     /locus_tag="BHM61_025310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="UAE55377.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTAEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGYDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            2747..3280
                     /locus_tag="BHM61_025315"
     CDS             2747..3280
                     /locus_tag="BHM61_025315"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAE55374.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTMLDRNYNATAAVYQKVVTLED
                     KLAEKPVTGKSRKN"
                     /name="hypothetical protein"
     Typing          2..739
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.752"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          1819..2741
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.727"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cccaccgccc ctatcacacg gatgatctcg ctttcggcct tcgcatctcc ggcaaagggc
       61 gtgcgcttct tgcgcggtac atccagcaga accagcctca tgcgcagttc tggctggttt
      121 ttgacgttga ccgcgagggg gctgcgattg actggagcga ccggaacgcc cccgcgccga
      181 acatcaccgt taaaaatcct gtgaacggac acgctcacct gctctacgca ctcaacatcg
      241 ccgtgagaac cgcgcctgat gcctcggtta aggcgctgaa atatgccgca gcggttgaac
      301 gttcgctgtg tgagaaactt tgtgctgatg tgaactacag cggcctgatt tgcaaaaatc
      361 cgttccacct ggaatggcag gtgatggagt ggcgcgagga cgcctatacc ctcgatgaac
      421 tggcagatta tctcgatttg agcgcctcag agcgtcgtag catcgataaa cattacggga
      481 tggggcgaaa ctgccacctg ttcgaaatga cgcgcaaatg ggcttacagg gcgattcgtc
      541 agggctggcc agcgttctca cagtggcttg aagcggtgat ccagcgtgtc gaaatgtaca
      601 atgcatcgct tcccgttccg ctttcactgg ctgaatgtcg ggctattggc aagagcattg
      661 cgaaatacac gcacaggaac ttcacgccgg aaactttcgc acagtatgtg gctgatacgc
      721 acacgccaga aattcaggca gcacgcggtc gcaagggcgg gaaggccaat tcgtcagaaa
      781 atcagtcgga caaagggaaa aaaagcgccg ctgttcggtg gactgctaac gacgacaaac
      841 gtcgtagggc gcttgatatg tatatcttgg gagcgtcaac ggaagatatt gcagtggcgg
      901 ttggtgttag cagccggact attcgacgct ggatggataa ttctggagaa tggctaacca
      961 agaaacaaat aattaaatgt tagttaacaa agaagtaaca ctacccccgt tttttgttaa
     1021 tggggggtta aattcgcgga catgaacaag cctatatcag ataacagcgc ctttcggcgt
     1081 ctttttgagc agcgggcttt ccggcggttt tctcctctca gcccagcaat ggtgcggctt
     1141 accgcatgat tgaggtggtc gtgctcgccg cagtctcatg accgagcgta gcgagcgaat
     1201 gagcgaggaa gcaccaggga accggaacac ggatggaggc acttacgcgt ctgggtttgg
     1261 ggatgtctcc agatcgtact taatttcctt aagtgcctgt aatatcctgt cttttttata
     1321 gcatagctcg cctgtttttg tgtctaccag tcctgcttcg atcagtagcc cagccgcgag
     1381 aaagagtcgg tgattgcgtt ctcgtcgttg tttttttccc tcgattcgtt tttggaccgc
     1441 ctgttttcgt tcgctctcct gtgcctgtaa gtcgtttttt tccgctgttg ccagtacgtg
     1501 gaggagtttg cgttcctgtt ctgtgagtcc tgcttcgttg tcgagcaggt caataatctg
     1561 tctctgtcgt gcggtctgtt ctccgagctt cctgatgaat ccgatccgtt tcttcagcca
     1621 ttcgatgttg ctgatgcgca tgttcgtggt gctccctggt gtttttttgc ggtgtgttgt
     1681 ggtcgtgcag tatatcgctt gcggtcggcg ggtgcagggg gtatcttccg tgctaattcg
     1741 taaaattaga aggaagcgca cttatatgtt tctctccttc gtcgagaaac agtgcgctcc
     1801 tgcggagggc tgaaaccgtg gcaacctatc acctcagcgt taaatttggt ggcaaggggc
     1861 aggctgcaaa ccacgccgat tacatcgagc gcaaagagaa ataccgcgac cgtcaggatt
     1921 tggaatattc cgcacacgga aacatgccgg aatgggcgcg agataatccc tcacatttct
     1981 ggcaggctgc tgaccagttt gaacgtgcga acggttcgac ctatcgggaa cttgaaattg
     2041 cattaccccg tgaactgaca gcggaacagc gccttgaact ggtgcaggat tttgtacgtc
     2101 aggaagctgg cgaacggcac gcctggagtt ttgcaattca caatccgaaa gcgagcattg
     2161 acggcggcga acagcctcat gcgcatatca tgatgagcca gcgtgtgaat gatggcattg
     2221 aacgtacacc ggaacagtat ttccggcgct ataacgccag gtatcccgag cggggaggtg
     2281 cgaaaaagga ttccggaagc ctgactctca ctcagcaaaa agagcagttg cgggaattgc
     2341 gaaaacgctg ggaggtgaag cacaacgaac atatgagaaa gcatggcttt gaaaggggct
     2401 tcattgactg ccggacgctg aaagaacagg gcattgaacg acgtcccgaa gtgcatctgg
     2461 gttttgaagc tgccggacgg cttgatgatg cccagcgtca tgacatcatg caaaaacggt
     2521 ctgaaccgga ctattcccgc catcttgaac aggcgcgaac ggtcgggtat gacatcaggg
     2581 aatggctgga cactccggtt aagcaacatg aactggtcag aaggctgcaa catgatgttg
     2641 cgcgggagca tggctttgac atgagagaca gagtgagcag acagaaccga actgaacctg
     2701 aacgggttaa atcaccgtca cgtggatttt ctatgggatt ctgaacatgg ccagcacaga
     2761 agaaaaatta ctcacgctcc tgttatcggt ggagcatctg caacataccg caatggagca
     2821 acagaaagct gttgctgatt ctctggctgt ggcaagggaa acacttcgcg gatatcggga
     2881 tatttctgac ggtgtggcaa aacaggtcag ggatgaagtc agaaacgagg tgcagaagct
     2941 ggatgttgca gggctgatag gtgagcgcat cagccaggat tttcagcggc tggaagagtc
     3001 agtcgcaaac atgaaggcaa acgcggatgc cctgaacagg gatattgcga caattcacag
     3061 caatatcgtg caggaataca acacccttaa agggtatagc tggaaatggc tgggtggggt
     3121 gtcagtggct tttctggtta tgttctgtgt gcttggatgg ggaatgaaaa caatgctcga
     3181 caggaactac aacgccacag cggcggtgta tcagaaagtt gtgacactgg aagataaact
     3241 ggcggagaaa cctgtcacgg gcaagagccg gaaaaactga cgcgcttcgc ttgtccaacg
     3301 cctcacgacc cgcgaaaaaa ttccgcgtcc cgttcaccgt tttctgatga gaaagtttgc
     3361 tgttttgacc cgttcgccct tctgaacgct cgaaacagat cgcgcatcgc tttcgtgcat
     3421 agttatgcaa cgcgctaaaa acgattctga cgcatttttc tggtttagcc tggtgtttcc
     3481 ttgtcttttt gcgttttttg cgccagagag cgactgaggg cgttttaagg gggcgtacaa
     3541 cgggagttat ggtaaatgga tcggttttgc gggaaggctc gacaggtttt gttgttgggg
     3601 gtagtgtaag cgactgaaaa acaaacgccc ctgaaattcg tgtctctccg ccaagattgt
     3661 cacgagaata caggggcgag gtcggtcgat aacctggaag gaatcgtaac acatgagcgc
     3721 cgcgcttcaa tacttcgaag aaaatttac
//
