LOCUS       CP082460                4087 bp    DNA     circular BCT 11-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Agona strain FSIS1607563
            plasmid pF18S017-4087, complete sequence.
ACCESSION   CP082460
VERSION     CP082460.1
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 4087)
  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 4087)
  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 4087)
  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..4087
                     /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="pF18S017-4087"
                     /geo_loc_name="USA:MN"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            104..2263
                     /locus_tag="BHM61_025260"
     CDS             104..2263
                     /locus_tag="BHM61_025260"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /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="UAE55367.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="MobA/MobL family protein"
     gene            complement(2519..3226)
                     /locus_tag="BHM61_025265"
     CDS             complement(2519..3226)
                     /locus_tag="BHM61_025265"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="UAE55368.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(3758..4012)
                     /locus_tag="BHM61_025270"
     CDS             complement(3758..4012)
                     /locus_tag="BHM61_025270"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091744.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /protein_id="UAE55366.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobilization protein"
     Typing          complement(2..103)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.76e-46"
     Typing          104..462
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2520..3226)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          18..2260
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.866"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cacggaaaat cacgaagtgc gcacttatac aatctccact ccgtttcgat tgtgtgcgcc
       61 ctgcggggct gaaagaaaac cacaaaaagg cattacggca gaaatggcga tttatcatct
      121 cagcatgaaa atcatctcca gaaacagcgg ctacagcgcc gttgcttctg ctgcctatcg
      181 ttccggttca ctgatgcttg atgagcgtac cggactgact cacgactaca cccgcaaaag
      241 cggtgtggct gaagctgtga ttctgactcc cgcgacagcc cctgcctggt gtacgaaccg
      301 tgccgaactc tggaatgccg ttgagaaggc cgaacgccgg aagaactcac aacttgcgcg
      361 ggaaattgaa ctcgccatcc cccgcgaact accgcaggat gccgcacggg aaaccgttct
      421 cgcctttgtc agagaaaact ttgtcagtca gggcatgatt gctgatgtgg cgttccatca
      481 catggataaa acaaatcccc atgcgcacat catgctgacc acgagagctg tcggacctgc
      541 tggattcggt ggaaaggtca gggactggaa cgaccggaca catgccgaga cgtggcgtgc
      601 atcatgggct gaccatgcga acagggcact ggcgaacgcc ggttatcagg aagagataga
      661 ccatcgttca tacgagcgac aggggcttga gaaaacgcct ggtattcacc tcggaaagtc
      721 tgcctgtgcg atggaaacac gcggtatcga aacagaacgc ggcgaacaga atcgtctgat
      781 taacagactt aacctggaaa tacagatttc ccgtaccgaa ctcagaaaca gcgggctgac
      841 agagcctgcc cgccgtgtgg ctgaccttct gaatatcgtg cttcctgaca acgcaacttc
      901 gtacacacta cgtgacatca tcgaagcgtt gccgaaggac agtaatgcgg catggaaact
      961 caccagtaat gccatgtcga tgatggcaga tatgcaggcg acgcgcagac gctgggaaga
     1021 gctgaacacc gaacgaaagg aagcgatgag ccatgctgcc agcctgaaaa aatcatcgcc
     1081 gttttcgtcc ggtttttccc gtattcccct gatgcaatgg gcggcaccgg aataccgtag
     1141 cgaacaggga aaaatccagt cgctgagcca gcaaatggaa aaattgcgac agcattaccg
     1201 gaaggtggag aaacaggaca ttcccgcgag tcagacggca tttgaaaaac agtggcagca
     1261 gtggggggca tccggccttg cagctctcag agtccagttg cttaaacgtg aagaggaatt
     1321 gcgccggaag gagcaggagg atacagaacg tagtcgcgcg gagcgacgag cggaacagct
     1381 caggaaaaat gacaatgccg ttatggattc aggggtactg agcgcagtcg ttacggggta
     1441 tggcgaggcc cccatgcctg gtaacgggga aatgacctgt taccttctgc ttcacaaccg
     1501 gaacggagaa tacacgctct gggggaacga gctggagaaa taccgcacca gaatctttga
     1561 gcgtgttgat ttaatgcgtg acaggagtgg ttatatctgt gaccgaagcg aaatcggtca
     1621 acatccacca ctgcaacgtg tttattcctc tgcgaccttt gagcaacttc tgacgcaggt
     1681 ttgccagaca tggccgcaat atacccgcaa tctccgccag ccgaagacat ggccggagtc
     1741 tttctgtctt ggagaagacc gccagccagc catgccatca ctggcagcaa ggaaggtgga
     1801 ttttacgcag ggacgtctgc taccgacgct gatgccggta atgagttctg tcgaccggga
     1861 aacccgccag cttcagcttt tgctggtcat gggcgtggat gactctctgg gcggtgttgt
     1921 ccggcttaat ggtacgctgt atcccgcgtt tgccgttccc tcagccgata acagccagct
     1981 ggtcatcagt gcactgaccg ataaggggtt acggtatgca gggtatggtg ttgccgtaaa
     2041 tcacgatgca gacagccaca tatcacctgc gccggaactt atggagtttc atctgaaaac
     2101 ccgtgaggca ccgctttttg ctgccgtcaa cacaccagaa aaacagccgg atcatctgtt
     2161 ccgctcgctg ggttttaatc gtacctggga cgaatggcgg cgcgaggaag atgcacgaac
     2221 acacgccacc gagaggagac atgatcgcgg ttggtcacag tgaatgtgaa caatattttg
     2281 ttttgtttaa catcgtgtta tgttcgtcga tgttcttcga tgttcatcga cagggatgaa
     2341 tgcaagaagc acacacataa tgcaagcata gttttgtttt tccgcccccg aaaaatgggg
     2401 gttctttttt cgctgcatta gagcgctttt gacgcaattt ttcacttcaa tagtaccttc
     2461 gcactactaa cacaaaaaaa acgcagcagg gagcgtttta ggtgccttaa aatcgattct
     2521 agatcgtcat cttgatctgt ttgtcttcct tgaagcgaaa atgcagggct acaaccgtgc
     2581 gccccttttt gatcgtctca accgttacag ccaggtcgct ttttttgttc agttcgtcaa
     2641 cacagggttt tattagatcc ctgtttaacg ttttgaaatc tttatattta ccatcaagca
     2701 tcagtgatga tttaaaatca tcgagggcga taatacgttc cccagtactg cggaattgct
     2761 ggagaatttc gtatattctt atgctgtaac ttcttgataa attagaaata tttttaatga
     2821 cgactctggt gaattgcccc ttcaactgtg tcagataagg cattaccgcg tcagaaaaag
     2881 tgatttgtgc tttcccctct cccctcgcgt actgtgcccg atactgaatc cagcggaact
     2941 cctcgcgctt ctcgtcgtcc ttgagaatga tcgacctgtc ccacaaacga tcgatcgctt
     3001 cctgtagctg aacctcggca tttttccgcc ccatatcagg gaatgaatca aaatattccg
     3061 cagctgtaat ggtcattgtc ttttgcaatt caggtgaagc tacgtcagta ccggagttaa
     3121 gtcggcttat gcagagcaat aagaaacgct gttcttgtaa agttagcttg taactggcct
     3181 caaccagcgc attggactta taggctatca gagggtttga tgtcatttta accaccaggc
     3241 caaaaatgag gtgaaataaa aacctatcac ctttagcatt ggtgagcaat tatattttca
     3301 ccccccattt tcctgtgaat attaccttaa atctcctcac ctttacctta aattacctca
     3361 cccaagcacc ttaaattata tcacctttac cttaaatcat atcacctata gcgttgtaac
     3421 attttgtttt ctataaggaa ttttggcgct aaaacaagta ttaaaaacaa gatcttaaaa
     3481 acaagatcta aaaacttaac gacgagcctg tggataactt ggagtgctga aaacaaaaaa
     3541 ccaataaaaa caatgcgttg caaaaaagca gaattgcaag ttccgaatac accccctcca
     3601 accctgtgga aatccagtat tcatgcgggt tcagcgcata tcacctcccg aaaaaccgtg
     3661 cgtatgtgct caatcaggcg acggattcac ttccgcttcc tcgcccactc gctcgctaac
     3721 gctcggtcgc tgggactgcg gcgagcggac gatacaatca ctgtcctggc agcgcttcca
     3781 gctcgttaat cagcggcagt atgcgcgtca catcagcctg tcgtgtcacc tctgccttca
     3841 ggaactggag taaccaggca cgcaactgca cctcctccgg ctttctgacc tttgccagca
     3901 atgctgcacc cacaatgacc ttctgcgctg tgtccagact cctgctcttc gccttcaggc
     3961 gctgtaatct ggcctcagca tcagcaatct tctgttcgag tgttctgctc atgatgtaac
     4021 tccgtgcgcg atgaaaaatc gcattttagc gcgtcactgg tagtttaaaa actgagctgg
     4081 cataatg
//
