LOCUS       CP082462                4074 bp    DNA     circular BCT 11-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Agona strain FSIS1607563
            plasmid pF18S017-4074, complete sequence.
ACCESSION   CP082462
VERSION     CP082462.1
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 4074)
  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 4074)
  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 4074)
  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..4074
                     /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="pF18S017-4074"
                     /geo_loc_name="USA:MN"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            complement(join(2528..4074,1..613))
                     /locus_tag="BHM61_025285"
     CDS             complement(join(2528..4074,1..613))
                     /locus_tag="BHM61_025285"
                     /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="UAE55371.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="MobA/MobL family protein"
     gene            792..1046
                     /locus_tag="BHM61_025290"
     CDS             792..1046
                     /locus_tag="BHM61_025290"
                     /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="UAE55372.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKTEVTRQADVTRILPLINELEALPGQ"
                     /name="mobilization protein"
     gene            1578..2270
                     /locus_tag="BHM61_025295"
     CDS             1578..2270
                     /locus_tag="BHM61_025295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="UAE55373.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(256..614)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.778"
                     /coverage="100.0"
                     /evalue="1.83e-175"
     Typing          615..791
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          1579..2270
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.821"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3..700)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.712"
                     /coverage="99.0"
                     /evalue="2.44e-151"
     Typing          complement(2532..4072)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.611"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ttccgaggtg aataccaggc gttttctcaa gcccctgtcg ctcgtatgaa cgatggtcta
       61 tctcttcctg ataaccggcg ttcgccagtg ctctgtttgc atggtcagcc catgatgcac
      121 gccacgtctc ggcatgtgtc cggtcgttcc agtccctgac ctttccgccg aacccagcag
      181 gtccgacagc cctcgtggtc agcatgatgt gcgcatgggg atttgtttta tccatgtgat
      241 ggaacgccac atcagcaatc atgccctgac tgacaaaatt ttctctgaca aaggcgagaa
      301 cggtttcccg tgcggcatcc tgcggcagtt cacgggggat agcgagttca atttcccgcg
      361 caagttgtga gttcttccgg cgttcggcct tctcaacggc attccagagt tcggcacggt
      421 tcgtacacca agcaggggct gtcgcggggg tcagaatcac agcttcagcc acaccgcttt
      481 tgcgggtgta gtcgtgagtc agtccggtac gctcatcaag catcagtgaa ccggaacgat
      541 aggcagcgga agctacggcg ctgtagccgc tgcttctgga gataattttc atgctgagat
      601 gataaatcgc catttctgcc gtaatgcctt tttgtagttt tctttcagcc ccgcagggcg
      661 cacacaatcg aaacggagtg gagattgtat aagtgcgcac ttcgtgattt gtcgtgcatt
      721 atgccagctc agtttttaaa ctaccagtgg cgcgctaaaa tgcgattttt catcgcgcac
      781 ggagttacat catgagcaga acgctcgaac agaagattgc tgatgctgag gcgagattac
      841 agcgcctgaa ggcgaagagc cggagcctgg atacagcgca gaaggttgtt gtgggtgcag
      901 cattgctggc aaaggtcaga aagccggagg aggtgcagtt gcgtgcctgg ttactccagt
      961 tcctgaagac agaggtgaca cgacaggctg atgtgacgcg catactgccg ctgattaacg
     1021 agctggaggc gctgccagga cagtgattgt atcgtccgct cgccgcagcc ccagcgaccg
     1081 agcgttagcg agcgagtggg cgaggaagcg gaagtgaatc cgtcgccagg ttgagcacat
     1141 acgcacggtt tttcggcagg tgatatgcgc tgaacccgca tgaatactgg atttccacag
     1201 ggttggaggg ggagtattcg gaacttgcaa ttctgctttc ttgcaacaca ttgtttttat
     1261 tggttttttg tttttagcac cccaagttat ccacaggctc gccgttaagt ttttagatct
     1321 tgtttttaag atcttgtttt taatacttgt tttaggggtg aaattcatta ataaaatcaa
     1381 tatgttatag tggtatatgt ggaggaattt aaggtaaagg tggaggaatt taaggtgttt
     1441 aggtggagga atttaaggta aaggtggagg aatttaaggt gttattcaca gaaatgtgag
     1501 gatataaaaa aaaacattcc acatttctta tttgtggggc acattaaagc atcaccacat
     1561 ttgaacggga tctttgtatg tcggacttga ttgcctacaa gtcgaatgct ttggttgagg
     1621 ccagctacaa gttgacccta caggaacagc gttttctgtt gctgtgtatc agtcgattga
     1681 aatctggtgc tgatgctgaa ttgcaaaaga caatgaccat taccgctgcg gaatattttg
     1741 attcattccc tgacatgggg cggaaaaatg ccgaggttca gttacaggaa gcgatcgatc
     1801 gtttatggga caggtcgatc attctcaaga atgacgagaa gcgtgaggag ttccgctgga
     1861 tccagtatcg agcacagtac gctaaaggtg aggccaaggc tcgaataacc ttttctgacg
     1921 cggtaatgcc ttatctgacg caactgaagg ggcaattcac gcgcgttgtt ataaaaaaca
     1981 tatcaggttt atcaagtagt tacagtataa gaatatacga gttcctccag caattccgca
     2041 gtacgggaga gagaattatt gctcttaatg actttcgttc aatgttaggg attgaaaata
     2101 aatacaaaca attcagagac ttaaataaaa tactaataaa accctgtgtt gacgaactga
     2161 acaaaaaaag cgacctggct gtaacggttg agacgatcaa aaaggggcgc acggttgtag
     2221 ccctgcattt tcgcttcaag gaagacaaac agatcaagat gacgatctaa aatcgatttt
     2281 aaggcaccta aaacgctccc tgctgcgttt tttttgtgtt agtagtgcga aggtactatt
     2341 gaagtgaaaa attgcgtcaa aaacgctctg atgcagcgaa aaaagaaccc ccaatttttg
     2401 ggggcggaaa aacaaaacta tgcttgcgtt atgtgagtgt gcttcttgca ttcatccctg
     2461 tcgatgaaca ttgaagaaca tcgacgaaca taacacgatg ttaaacaaaa caaaatattg
     2521 ttcacattca ctgtgaccaa ccgcgatcat gtctcctctc ggtggtgtgt gttcttgcat
     2581 cttcctcgcg ccgccattcg tcccaggtac gattgaaacc cagcgagcgg aacagatgat
     2641 ccggctgttt ttctggtgtg ttgacggcag caaaaagcgg tgcctcacgg gttttcagat
     2701 gaaactccat tagttccggc gcaggtgata tgtggctgtc tgcatcgtga tttacggcaa
     2761 caccataccc tgcataccgt aaccccttat cggtcagtgc actgatgacc agctggctgt
     2821 tatcggctga gggaacggca aacgcgggat acagcgtacc attaagccgg acaacaccgc
     2881 ccagagagtc atccacgccc atgaccagca aaagctgaag ctggcgggtt tcccggtcga
     2941 cagaactcat taccggcatc agcgtcggtg gcagacgtcc ctgcgtaaaa tccaccttcc
     3001 ttgctgccag tgatggcatg gctggctggc ggtcttctcc aagacagaaa gactccggcc
     3061 atgtcttcgg ctggcggaga ttgcgggtat attgcggcca tgtctggcaa acctgcgtca
     3121 gaagttgctc aaaggtcgca gaggaataaa cacgttgcag tggtggatgt tgaccgattt
     3181 cgcttcggtc acagatataa ccactcctgt cacgcattaa atcaacacgc tcaaagattc
     3241 tggtgcggta tttctccagc tcgttccccc agagcgtata ttctccgttc cggttgtgaa
     3301 gcagaaggta acaggtcatt tccccgttac caggcatggg ggcctcgcca taccccgtaa
     3361 cgactgcgct cagtacccct gaatccataa cggcattgtc atttttcctg agctgttccg
     3421 ctcgtcgctc cgcgcgacta cgttctgtat cctcctgctc cttccggcgc aattcctctt
     3481 cacgtttaag caactggact ctgagagctg caaggccgga tgccccccac tgctgccact
     3541 gtttttcaaa tgccgtctga ctcgcgggaa tgtcctgttt ctccaccttc cggtaatgct
     3601 gtcgcaattt ttccatttgc tggctcagcg actggatttt tccctgttcg ctacggtatt
     3661 ccggtgccgc ccattgcatc aggggaatac gggaaaaacc ggacgaaaac ggcgatgatt
     3721 ttttcaggct ggcagcatgg ctcatcgctt cctttcgttc ggtgttcagc tcttcccagc
     3781 gtctgcgcgt cgcctgcata tctgccatca tcgacatggc attactggtg agtttccatg
     3841 ccgcattact gtccttcggc aacgcttcga tgatgtcacg tagtgtgtac gaagttgcgt
     3901 tgtcaggaag cacgatattc agaaggtcag ccacacggcg ggcaggctct gtcagcccgc
     3961 tgttcctgag ttcagtgcgg gaaatctgta tttccaggtt aagcctgtta atcagacgat
     4021 tctgttcgcc gcgttctgtt tcgataccgc gtgtttccat cgcacaggca gact
//
