LOCUS       CP082458                4657 bp    DNA     circular BCT 11-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Agona strain FSIS1607563
            plasmid pF18S017-4657, complete sequence.
ACCESSION   CP082458
VERSION     CP082458.1
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 4657)
  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 4657)
  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 4657)
  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..4657
                     /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="pF18S017-4657"
                     /geo_loc_name="USA:MN"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            complement(join(4285..4657,1..179))
                     /locus_tag="BHM61_025210"
     CDS             complement(join(4285..4657,1..179))
                     /locus_tag="BHM61_025210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000654246.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAE55359.1"
                     /translation="MKDMKAVVVFTGKDLNIMRTEGGSGYWHARTDRLNDADYLIAVRN
                     RRETWAVKDLEHGTAFLIAKITGCFKSPDYDDRNVITFDEYAEIHTPKAWKMLTDGQRY
                     PVAYLSAQEAFLRIGVTPEQLEWKKFHPSSPSVPNTVIPGLAEEKTEKLSLNEAIERAK
                     KDISNATGIDSSAITISIKI"
                     /name="hypothetical protein"
     gene            655..1134
                     /locus_tag="BHM61_025215"
     CDS             655..1134
                     /locus_tag="BHM61_025215"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001050742.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAE55360.1"
                     /translation="MNLLLPRDIVEAVLNDKKTKNARVAKCDGSEFFLELPSMNADFPA
                     GKIILKLGDSGFYNKRTKSLEGAYGLRHIWDKHRVEIGATSAEDIVIFLESILLAGAEV
                     LIDPKKGQNKAIVVESGTGMMILELKKPNGEDPYYSIITAYDRKSHPGTKLHTLI"
                     /name="hypothetical protein"
     gene            2381..2704
                     /locus_tag="BHM61_025220"
     CDS             2381..2704
                     /locus_tag="BHM61_025220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="UAE55361.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSL
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2643..3407
                     /locus_tag="BHM61_025225"
                     /pseudo=""
     CDS             2643..3407
                     /locus_tag="BHM61_025225"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            3382..3867
                     /locus_tag="BHM61_025230"
     CDS             3382..3867
                     /locus_tag="BHM61_025230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012565228.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="UAE55357.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSAAMSQRTKGMLRMVSQTWLTIVLVSTLLTASGASILWWQGQQIL
                     DNYTTIREQKRTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            3871..4086
                     /locus_tag="BHM61_025235"
     CDS             3871..4086
                     /locus_tag="BHM61_025235"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="UAE55358.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          2094..2277
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.561"
                     /coverage="86.0"
                     /evalue="2.7100000000000003e-47"
     Typing          complement(1635..2111)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.083"
                     /coverage="92.0"
                     /evalue="3.51e-174"
     Typing          2695..4190
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.583"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gctgtgccgt gttccaggtc ttttactgcc cacgtttccc ttctgtttct tactgctatg
       61 aggtaatcgg catcgttgag cctgtctgtt ctggcatgcc agtagcctga ccccccctca
      121 gttctcatta tgttcaaatc cttcccggta aaaaccacaa cagctttcat atctttcata
      181 tagaaaccct taataggtga gtgaatttca ttttttatgg aatctatacg ataaaaatcg
      241 tgttgtaaat gtttttttat gcgataaaat gcagtcctcc tacctctttt attgttagtg
      301 gtaaggcttt ctgtttggtt ttttgataaa ccggttaaaa caggggcttg gacgaggata
      361 tacattgaaa gcatgagcaa ttcacgtggc tgcatggcta tgcagccacg tgaaatttat
      421 caggcgcaga atgcgcggtt tagcggggag tttactgccg attttaccgg gctaacgccg
      481 ctttcacgct gaacccgtcc ggagcggtgc gggcaaggaa tgttatggta aatacaactg
      541 gttttttcta tcaagattta ctggaaattg ctcattacgt cagtgttaga atcagccctt
      601 caaaaaggga tttaacgcct aaacataata gtgaaggcta tagaggtgta gtttgtgaac
      661 ttgttacttc cacgcgatat agttgaagct gttcttaatg ataagaaaac aaaaaatgca
      721 cgagtggcta agtgtgatgg aagtgaattt tttctagaac tgccaagcat gaatgcagac
      781 tttcccgcag ggaaaatcat cctcaagcta ggagattccg gtttttacaa caaaaggaca
      841 aaaagtctcg agggagccta tggccttagg catatatggg acaagcatcg tgtcgagata
      901 ggagctactt ccgctgagga tattgtcatc tttttggaga gcatattatt agctggggca
      961 gaagtgctca tagatcctaa aaaaggccaa aacaaagcga ttgttgtaga gtcaggaacg
     1021 gggatgatga tactagaatt gaaaaaacca aacggcgaag acccgtacta cagcatcatt
     1081 actgcttatg ataggaagag ccatccaggt acaaaacttc ataccctaat atgaaaaaag
     1141 ccggctaaat agccgacttc ttcgtaatag tgttgttcgt ggcattccct tagcatttcg
     1201 gttcgggaca ggtctttgac cttaacaacg cattgtcgaa atctggtttc cgacaagtag
     1261 cctacaaata tgtaaccaat ccagagttca ggttacatac caagcccttc tacacataca
     1321 gaatacaact ctatcactgc tcatattttt gcaaaaagtg ctattttggt gttcagtgga
     1381 aaccaaaacg aagccaaatc actggtaaac ggtcagatct ccttgtgatc gttttactct
     1441 cgtcgtaatc tctctccctg taaacgaaaa aaccacccgg caaggtggtt tttcgaaggt
     1501 tcagtaaacc ggcaagtttc tgaaccgtgg taacagtctt gtgcgagaca tgtcaccaaa
     1561 tactgtcctt ccagtgtagc ctcactaagg cctccacttc aagaactctc gatacatctc
     1621 tcgcacatcc tgcttaccag tggccgctgc cagtggcgtt aagtcgtgtc ttttcgggtt
     1681 ggactcaaga cgatagttac cggataaggc gcagcggtcg gactgaacgg ggggttcgtg
     1741 catacagtcc agcttggagc gaactgccta cccggaactg agtgtcaggc gtggaatgag
     1801 ataaacgcgg ccataacagc ggaatgacac cggtaaaccg aaaggcagga acaggagagc
     1861 gcacgaggga gccaccaggg ggaaacgcct ggtatcttta tagtcctgtc gggtttcgcc
     1921 accactgatt tgagcgtcag atttcgtgat gcttgtcagg ggggcggagc ctatggaaaa
     1981 acggcaacgc cggatccttt tccccttcct tcttgatttg agcgctattt atctcgtcat
     2041 tcttgagcag gtaacgcccg ccgcagtctc acggcaggag cgtagcgacc gagtgagcga
     2101 ggaggcgtca tttcatcgtc tccagcattt cgcacttacg ccccacagct gaatttttta
     2161 cctgccacat gaagcacttc cctgaatttc cacttcgatt taccatacta agccagtata
     2221 cactccgcta gcgctacgtg actggttcag ggctgcgccc cgaaacccgc taaaaccact
     2281 gacgcgcctg cggcttgtcc aacaccgcgc cgaccgggaa aagatttccc gcccgtctcg
     2341 gcgttatcag gaggccggat tggcagacaa acgcagcaaa atgctcacga tgtgggtgac
     2401 cgaagatgag caccgccgtc tgctggagcg ctgcgacggt aaacagcttg cagcctggat
     2461 gcgccagacg tgcctggacg agaaacccgc ccgcgccggc aagcttccct cgctctcgcc
     2521 ggcgctgctt cgtcagcttg ccggcatggg gaacaacctc aaccagattg cccggcaggt
     2581 taacgccggt ggtggcagcg ggcacgaccg cgtgcaggtc gtcgccgcgc tgatggccat
     2641 agatgccgga ctcgagcggc tgcggcatgc cgtgctggaa aagggtgcag acgatgatcg
     2701 ttaagtttca cccgcgaggg cgcggcggtg gcgccggtcc ggtggattat ctgctgggga
     2761 aagaccgaca gcgcgacggc gccaccgttc tgcaggggaa gccggaagaa gtcagggagc
     2821 ttatcgacgc ctcgccctac gcaaaaaagt acacatccgg cgtcttgtcc tttgccgaaa
     2881 aggatttacc gcccgggcag cgcgaaaagc tgatggcgag ctttgaacgg gttctgatgc
     2941 ccggactcga taaagaccag tacagcgtgc tgtgggttga gcaccaggat aaggggcggc
     3001 tggagctgaa cttcctgatc ccgaacacgg agctgctgac cggcaagcgt ctccagccgt
     3061 attacgaccg cgccgaccgt ccgcgcattg atgcctggca gaccatcgtg aacggcaggc
     3121 tggggctgca tgacccgaac gcgcctgaaa accggcgggt gctggtcacg ccgtccgcgc
     3181 tgccggaaac gaagcaggaa gccgctcagg caattacacg gggtttactg gccttagcct
     3241 cgtccgggga gctgaaaacc cgccaggacg tcactgaggc gctggaaagc gcaggttttg
     3301 aggtggtacg caccacaaaa agcagcatca gcattgccga cccggacggg gggcgaaaca
     3361 tccgactgaa gggagccatc tatgaacagt cttttaacgc tggcgaagga cttagagcag
     3421 aaatcgaaag cgcagcagca gagtaccggc gagatgctga aagccgcatt cagcgagcac
     3481 gagaagtctg tcagagcgga actgagcgaa agcgagaaga gaatcagcgc cgccatcctc
     3541 gaccacgaca ggaagctgtc cgctgccatg agccagcgca cgaaaggtat gctgcggatg
     3601 gtcagccaga cgtggctgac catcgtcttg gtgtctacac tgctgacagc atcgggcgca
     3661 agtattctgt ggtggcaggg gcagcagata ctcgacaatt acacgaccat ccgggagcag
     3721 aagcgcacgc aggccatgct gtccgagagg aacagcggtg tgcagctctc gacctgcgga
     3781 gagcagagac gccgctgcgt gagggtgaac ccggaagcgg gacggttcgg agaggattcg
     3841 agctggatga tactggcggg gaaatagcac atgacggagc tggaaaaaca gttgctgagc
     3901 gcattagagc agctacagca ggactactcg aaaaggctgg acgagtggga gaacgccttc
     3961 gcggaatggc ggacgatgtc tggtcttatg caacgggaga acgcggcgct gagcgagcgc
     4021 gtcacgggct tgagcaggca ggtgcagagt ttgagcgagc agctgcgccg gttgtcacaa
     4081 ggctgaacgt gatagaggca catcgtgagc aggaacgggc ggcgcagcat cagaaagcgc
     4141 tggagctgga acgatctcag cgacagcgaa cgtacaacgg tccgtcactt tgaatctgtg
     4201 cgccggaaaa gcatgggctt gctgtttctg gcgtacaggt tcagttctag aacatgaggc
     4261 tgctatcttg ttgttcacgc ttcatcagat cttgatgctt attgttatgg ctgagctatc
     4321 aatccctgtt gcgttgctaa tatccttttt ggctctttca attgcctcgt taagggagag
     4381 tttttctgtt ttctcttcag ccagaccagg aatcactgta ttaggaaccg atggggatga
     4441 aggatggaat ttcttccatt ccagttgttc cggtgttacc ccaatacgta aaaaagcttc
     4501 ctgtgcgctc aggtaagcaa ccggatagcg ctgaccatcg gttagcattt tccatgcttt
     4561 tggcgtgtga atttctgcgt attcatcaaa ggttatgacg ttcctgtcgt cgtaatcagg
     4621 gcttttaaaa cacccggtaa ttttggcgat caggaat
//
