LOCUS       CP082485                3609 bp    DNA     circular BCT 13-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Agona strain FSIS1607113
            plasmid pF18S008-3, complete sequence.
ACCESSION   CP082485
VERSION     CP082485.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN05440588
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 3609)
  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 3609)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (22-JUL-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 3609)
  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                     :: F18S008
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 344x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/02/2021 13:43:29
            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)                     :: 5,068
            CDSs (total)                      :: 4,950
            Genes (coding)                    :: 4,840
            CDSs (with protein)               :: 4,840
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 110
            CDSs (without protein)            :: 110
            Pseudo Genes (ambiguous residues) :: 0 of 110
            Pseudo Genes (frameshifted)       :: 45 of 110
            Pseudo Genes (incomplete)         :: 65 of 110
            Pseudo Genes (internal stop)      :: 20 of 110
            Pseudo Genes (multiple problems)  :: 18 of 110
            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..3609
                     /organism="Salmonella enterica subsp. enterica serovar
                     Agona"
                     /mol_type="genomic DNA"
                     /strain="FSIS1607113"
                     /serovar="Agona"
                     /isolation_source="animal-swine-market swine"
                     /sub_species="enterica"
                     /db_xref="taxon:58095"
                     /plasmid="pF18S008-3"
                     /geo_loc_name="USA:IN"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            complement(join(3259..3609,1..1167))
                     /locus_tag="BEE22_025330"
     CDS             complement(join(3259..3609,1..1167))
                     /locus_tag="BEE22_025330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017899153.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NERD domain-containing protein"
                     /protein_id="UAE22236.1"
                     /translation="MKKNIVRQVLESYGPCISSELAERIKRQNPSMSSDAIRKMISRST
                     DIGKLPFLRFSHNRRFIYLKDDFGSFKFWRALKKCMREANSAYSHAILSVINNGGYLKV
                     KDFGIVSGSPIKQAKHLSYESVLKNLLSAKILRSVYIDGIGDCVLINNNIANDISIFNM
                     ANCESFFDKPIFELIKAWLRNLGIVAFNQIKTKYDGENNPVVGSFEWDITAPSYVSPLA
                     EYSSDGLIPGFVVCDFALGFNRNEITTDAADTFIRKVQMTKSSRTNQRIMFVLFARRFE
                     KNAFNKLRSEGVLAITIANAFGNKVDESLARLSKVIQGTLSIERHPDELLQMVKDLESI
                     SGENGNLRGYIFELFVSSQICNFYGYGNVRINKEYKINGKHAEADVVLETNDDIYIVEC
                     KNVKTLPSMEVSLWMKTRVPIINSYYKSNNPDNKNIHHRLWVTGNIYPKDINRLDEFKC
                     NNKKIDVDYLFGQSLDDFFYQKKQVFNLYRKVISPDYKKGQIPDFDL"
                     /name="NERD domain-containing protein"
     gene            complement(1599..1922)
                     /locus_tag="BEE22_025335"
     CDS             complement(1599..1922)
                     /locus_tag="BEE22_025335"
                     /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="UAE22237.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRIGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     gene            2206..2400
                     /locus_tag="BEE22_025340"
     CDS             2206..2400
                     /locus_tag="BEE22_025340"
                     /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="UAE22235.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAESGTGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(1932..2171)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          2444..2964
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.905"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          complement(1603..1922)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.131"
                     /coverage="100.0"
                     /evalue="4.38e-62"
ORIGIN
        1 ttccaataca acatcagctt cggcatgttt accgtttatt ttatattctt tattaatacg
       61 aacatttcca taaccataga aattacaaat ttgagaggaa acaaaaagct caaaaatata
      121 cccccttaaa tttccattct ctccagagat agactccaga tcttttacca tttgaagtaa
      181 ctcatcagga tgtctttcaa tagataaagt tccctgaatc accttcgata gtctggccaa
      241 gctctcatcg accttattac caaacgcatt agctatagtt atagccagaa ccccttcact
      301 ccttagcttg ttgaaggcat tcttctcaaa acgtctagca aaaagaacaa acataatcct
      361 ctggtttgtc ctagaggact tggtcatctg aacttttctt atgaaggtat cagcagcatc
      421 ggtggtaatt tcatttcgat taaaccctag agcaaaatca cagacaacaa aacctgggat
      481 gagtccatcg ctggaatatt cagcaagagg ggacacataa cttggcgctg ttatatccca
      541 ctcgaaagaa ccaaccacag gattgttctc tccatcatat tttgttttta tttgattaaa
      601 agccacaata cctaaatttc gcaaccatgc cttaatcagt tcaaatattg gcttatcaaa
      661 aaaagactcg caatttgcca tattaaagat gctgatatca ttagctatat tattatttat
      721 caaaacacaa tcaccaatac catcaatata cacagatcta agtattttag ctgaaagcag
      781 attttttaga acagattcat aacttaaatg cttggcctgc tttatcggag agccagacac
      841 aatcccgaaa tcctttacct tcaagtatcc gccattatta attacggaaa gtatagcgtg
      901 agaatacgcc gaatttgcct cacgcataca ttttttgagc gcccgccaaa atttgaagct
      961 accaaagtca tcttttagat aaatgaatct cctgttatga ctaaatctta aaaatggcaa
     1021 cttaccaata tcagtgcttc gagagatcat tttacgtatt gcatcagatg acatagaagg
     1081 attctgacgc ttaatcctct cagcaagttc agaagatatg cacggaccat aactctcaag
     1141 cacttgtcta acaatgtttt ttttcataaa ttcatcttat ttttgtcaca ctacgctatt
     1201 tataaaatta cactacgtgt aatatctata gatcccaaaa aaaaacacaa agaaaaaaat
     1261 cataaaaatc aaacatttaa caaaagcaac atatcacaaa aaacacacct gcgagattta
     1321 tccttaaaaa tcaagatgtt acgtttgtga catttcatca tcatatatca accgccctat
     1381 ttaccataat cccttaattg tacgcaccac tgaaacgcgc tgaacgcgat tctgacgcag
     1441 acaccgcaaa aagagatgtt ttaccccgga aaaataggaa ggatgcgtca ggatcgtttt
     1501 cagctcgctg catagttatg catgaaagcg aatggtgatc actttgggag cttacggtgt
     1561 tcataccgtc tgttttcaac agttttctcc ccgggaagct aatctgccat aagcctggat
     1621 aacagggcac ggtgatactc cgtaatagcg atcagcacct ccgcatactc cctgtccccg
     1681 atacgcttgc cgtcgataaa gagttttttc tgtaacgccc ccagtctcat aacttctttc
     1741 agtacccgat catcagtcag tgagttaact ttcttaccga gagctgccgc ccgtaaaaaa
     1801 ccggaaacgg tcttgccgca ttcagcagcc ctttttctga tttcctggtc ttcttctgcc
     1861 gtcagacgaa cagggcgact gatagcccgc ctgcgcgtat tacttccact tcgttttgtc
     1921 ataaaacatg gctccgtatc tgacatgggt gtcggggcaa agccctgacc agggtaattg
     1981 taatagcgtg catgtatgcg cggtataaca attgcacatc ctgtcctgtc agcaagctcg
     2041 aattaccgac aaaggcacgg cagttttttg gcagtgacag tgttgtctga cagaaatgcc
     2101 cgtcaaaaag ccaggcggca gaatagcggc agcaaaacag tcgaaaagtg gtacgcgata
     2161 taatcacata acgcagatga cagacagaac ggagaaaacg aaaagatgaa caagcagcag
     2221 caaaccgtac tcaacatggc gggattcata aaaagccaga gcctgacgct gctcgaaaag
     2281 ctggacgcac tcgatgccga cgaacaggcc gccatgtgtg agaagctgca cgaactcgcg
     2341 gaagaactcc agaacagcat acagacacgc tttgaagcgg aaagtggcac cggggtataa
     2401 cagtgtatcc tgctccagac aggatgcaga acggtatacc ggtgcgtaag gagaaaatgc
     2461 cacataaggc gctcttccgc ttcctcgctc actgactcgc tacgctcggt cgttcggctg
     2521 cggcgagcgg tatcagctca ctcaaagacg gtaatgcggt tatccacaga atcaggggat
     2581 aaagccaaaa gaaacatgtg agcaaaaaac aagaacccga aaaaggccgc gccggtggcg
     2641 tttttccata ggctccgccc ccctgacgag catcacaaaa atcgacgctc aagccagagg
     2701 tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctggaag ctccctcgtg
     2761 cgctctcctg ttccgaccct gccgtttacc ggatacctgt ccgcctttct cccttcggga
     2821 agcgtggcgc tttctcatag ctcacgctgt tggtatctcg gcccggtgta ggtcgttcgc
     2881 tccaagctgg gctgtgtgca cgaacccccc gttcagcccg accgctgcgc cttatccggt
     2941 aactatcgtc ttgagtccaa cccgaaaaga cacgacttat cgccactggc agcagccact
     3001 ggtaactgga atagcagagc gatgataatg cggtccgtac tacagagttc ttgaagtgat
     3061 gccccaacta cggctacact taaaggacag gatttggtat ctgcgctctg ctgaagccag
     3121 ttacctaggt taggtaatct gccaggatta actaaccttc gaaaaaccac cttgccgggt
     3181 ggttttttcg tttcatggag gaagatacgc ttttcaagcc gtcatcgtca agaaatgcag
     3241 agactagaaa acgtcattct ataagtcaaa atcgggtatt tgcccttttt tataatctgg
     3301 cgaaatgact ttcctatata aattaaacac ttgttttttt tggtagaaaa aatcatccaa
     3361 agactgacca aataaataat caacatcaat cttcttatta ttacatttaa actcgtccaa
     3421 tcggtttata tctttaggat atatattccc cgtaacccac aaacgatgat gtatattttt
     3481 gttatcaggg ttatttgatt tgtagtagga atttataatt ggcactcttg ttttcatcca
     3541 aagactaacc tccatcgaag gtaaagtctt aacatttttg cactcaacga tataaatatc
     3601 atcgttagt
//
