LOCUS       CP082459                3003 bp    DNA     circular BCT 11-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Agona strain FSIS1607563
            plasmid pF18S017-3003, complete sequence.
ACCESSION   CP082459
VERSION     CP082459.1
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 3003)
  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 3003)
  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 3003)
  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..3003
                     /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="pF18S017-3003"
                     /geo_loc_name="USA:MN"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            complement(825..1019)
                     /locus_tag="BHM61_025240"
     CDS             complement(825..1019)
                     /locus_tag="BHM61_025240"
                     /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="UAE55364.1"
                     /translation="MNKQQQTALNMAKFIKSQSLTLLEKLDALDADEQATMCEKLHELA
                     EELQNSIQTRFEVENSTEI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1291..1614
                     /locus_tag="BHM61_025245"
     CDS             1291..1614
                     /locus_tag="BHM61_025245"
                     /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="UAE55365.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     gene            complement(1922..2305)
                     /locus_tag="BHM61_025250"
     CDS             complement(1922..2305)
                     /locus_tag="BHM61_025250"
                     /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="UAE55362.1"
                     /translation="MKFFKPKTDAIEYIRVEPSFSKTSSNINNAKSGSDTNSQPGFILR
                     SQIEEMIKNHRPKTEKEIKAESEGLIRLCSMAFIFLIVLSIFMLIVYFGIKDRELPDFA
                     NNLMALMTTLVGAIGGFIYGTKK"
                     /name="hypothetical protein"
     gene            complement(2302..2979)
                     /locus_tag="BHM61_025255"
     CDS             complement(2302..2979)
                     /locus_tag="BHM61_025255"
                     /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="UAE55363.1"
                     /translation="MENKAVTISTQLAIFIDSTIARPDLLFNSLNSEIGEVIDAMPQTL
                     PLPADAPADIPRVIGTSSFGKFNLNISLNRIDFVENYTPTEEIEKSVTEFKLKCNTLIA
                     TIFQKYGVVRIGLVGNYYIPHKNPSQLIADLYLNENKRNLDEITIRINNRDTFKNIQIN
                     NVINLSQGQVTAQNYNGNAVIVQLDYNSTDNNTPLEEGLTLALFKEKSIAYNSKHVEDV
                     SGL"
                     /name="hypothetical protein"
     Typing          1057..1282
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="89.583"
                     /coverage="99.0"
                     /evalue="1.05e-76"
     Typing          complement(267..796)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.413"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          1292..1611
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="1.96e-62"
ORIGIN
        1 tattaattga agtattgcga aattaacgtg ttgtgagtat cttaaacgaa aaaaccaccc
       61 tggcaggtgg tttttcgaag gttagctaat cctggcagat tgtctaaccg ggtaactggc
      121 ttcagcagag cgcagatacc aaatactgtc cttctagtgt agccgtagtc aggccatcac
      181 ttcaagaact ctgtaagcat ctggacaaat ctcgctctgc taactcggtt accaatggct
      241 gctgccagtg gtgcttttgc atgtcttacc gggttggact caagacgata gttaccggat
      301 aaggcgcagt ggtcgggctg aacggggggt tcgtgcacac agcccagctt ggagcgaacg
      361 acctacaccg ggccgagata cctacagcgt gagctatgag aaagcgccac gcttcccgaa
      421 gggagaaagg cggacaggta tccggtaagc ggcagggtcg gaacaggaga gcgcacgagg
      481 gagcttccag ggggaaacgc ctggtatctt tatagtcctg tcgggtttcg ccacctctga
      541 cttgagcgtc gatttttgtg atgctcgtca ggggggcgga gcctatggaa aaacgcctgc
      601 ggtgctggct tcttccggtg ctttgctttt tgctcacatg ttctttccgg ctttatcccc
      661 tgattctgtg gataaccgta ttaccgcctt tgagtgagct gacaccgctc gccgcagtcg
      721 aacgaccgag cgtagcgagt cagtgagcga ggaagcggaa gagcgcctta tgtgacattt
      781 tctccttacg ctctgttgtg ccgttcggca tcctgccctg agcgttatat ctctgtgcta
      841 ttttctactt caaagcgtgt ctgtatgctg ttctggagtt cttctgcgag ttcgtgcagc
      901 ttctcacaca tggtggcctg ctcgtcagca tcgagtgcgt ccagtttttc gagcagcgtc
      961 aggctctggc tttttatgaa ttttgccatg ttgagtgcgg tttgctgctg cttgttcatc
     1021 tttctgcttt ctccgttctg tctgtcatct gcgtcgtgtg attatatcgc gcaccacttt
     1081 tcgaccgtct taccgccggt attctgccga cggacatttc agtcagacaa cactgtcact
     1141 gccaaaaaac agcagtgctt tgttggtaat tcgaacttgc agacaggaca ggatgtgtaa
     1201 ttgttatacc gcgcatacat gcacgctatt acaattaccc tggtcagggc ttcgccccga
     1261 caccccatgt cagatacgga gccatgtttt atgacaaaac gaagtggaag taatacgcgc
     1321 aggcgggcta tcagtcgccc tgttcgtctg acggcagaag aagaccagga aatcagaaaa
     1381 agggctgctg aatgcggcaa gaccgtttct ggttttttac gggcggcagc tctcggtaag
     1441 aaagttaact cactgactga tgaccgggtg ctgaaagaag ttatgcgact gggggcgttg
     1501 cagaaaaaac tctttatcga cggcaagcgt gtcggggaca gggagtatgc ggaggtgctg
     1561 atcgctatta cggagtatca ccgtgccctg ttatccaggc ttatggcaga ttagcttccc
     1621 ggagagaaac tgtcgaaaac agacggtatg aacgccgtaa gcccccaaac cgatcgccat
     1681 tcactttcat gcatagctat gcagtgagct gaaagcgatc ctgacgcatt tttccggttt
     1741 atcccgggga aaacatctct ttttgcggtg tctgcgtcag aatcgcgttc agcgcgtttt
     1801 ggcggtgcgc gtaatgagac gttatggtaa atggtgtcag gtaacggttg taaaagcccc
     1861 gaagtatggg gctggtgtgc ttgtgtgtta tttgtttttt ttatttgtgt ttttgtctgt
     1921 gttatttttt tgttccatat ataaaaccac ctatcgctcc aactaatgtt gtcattagtg
     1981 ccatcaggtt atttgcaaaa tctggtagtt ctctatcttt tattccgaaa taaacgatta
     2041 acataaaaat tgataaaact attaaaaata taaaggccat ggagcaaagc cttataagac
     2101 cttcgctttc agcctttatt tctttttctg ttttcggtct gtggtttttt atcatttcct
     2161 ctatttgaga tcttaaaatg aatccaggct gtgagtttgt gtcacttcct gatttcgcat
     2221 tatttatatt gctacttgtt tttgagaatg atggttctac acgaatgtat tcaatcgcat
     2281 ctgtttttgg tttgaaaaat ttcataatcc actcacatcc tcaacatgct tggagttata
     2341 agcaatggat ttttctttaa atagggctaa ggttaaccct tcttcaagtg gtgtgttatt
     2401 atcggttgag ttgtagtcaa gttgaactat caccgcattt ccattgtagt tctgtgcggt
     2461 tacttgtcct tggcttaaat tgatgacatt gtttatttgt atatttttga atgtatcgcg
     2521 gttatttatt cttattgtta tttcatctaa atttcttttg ttttcgttta aatacagatc
     2581 agctattagt tgagatggat ttttatgtgg gatgtaatag ttaccaacta ggccgattct
     2641 tacgactcca tatttttgga atattgttgc tattagcgta ttgcacttta atttgaattc
     2701 cgttactgat ttttcgatct cctcagtagg ggtgtagttt tctacaaaat ctattctgtt
     2761 tagtgatatg tttaagttga acttgccaaa ggacgatgtg ccaataacgc gagggatatc
     2821 tgcgggtgca tctgcaggca ggggaagcgt ctgtggcatt gcgtctataa cttcgccaat
     2881 ttctgagttt aggctattaa agagaagatc tggtctagct atggtgctgt caataaatat
     2941 tgctagctgt gttgatattg tgacggcctt gttttccatt ttttctttcc tattttgcat
     3001 tgg
//
