LOCUS       CP082471                5463 bp    DNA     circular BCT 12-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            FSIS1607455 plasmid pF18S013-2, complete sequence.
ACCESSION   CP082471
VERSION     CP082471.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN05661217
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella
            typhimurium)
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5463)
  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 5463)
  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 5463)
  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                     :: F18S013
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 379x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/02/2021 13:43:58
            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)                     :: 5,291
            CDSs (total)                      :: 5,168
            Genes (coding)                    :: 5,039
            CDSs (with protein)               :: 5,039
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 129
            CDSs (without protein)            :: 129
            Pseudo Genes (ambiguous residues) :: 0 of 129
            Pseudo Genes (frameshifted)       :: 51 of 129
            Pseudo Genes (incomplete)         :: 78 of 129
            Pseudo Genes (internal stop)      :: 23 of 129
            Pseudo Genes (multiple problems)  :: 20 of 129
            CRISPR Arrays                     :: 3
            ##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..5463
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="FSIS1607455"
                     /serovar="Typhimurium"
                     /isolation_source="Animal-Turkey-Young Turkey"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pF18S013-2"
                     /geo_loc_name="USA:VA"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            151..549
                     /locus_tag="BGP52_026415"
     CDS             151..549
                     /locus_tag="BGP52_026415"
                     /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="UAE45986.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKEIKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            complement(810..1829)
                     /locus_tag="BGP52_026420"
     CDS             complement(810..1829)
                     /locus_tag="BGP52_026420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221104.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="UAE45987.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREDAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDNSGEWLTKKQIIKC"
                     /name="replication initiation protein"
     gene            complement(2630..3754)
                     /locus_tag="BGP52_026425"
     CDS             complement(2630..3754)
                     /locus_tag="BGP52_026425"
                     /inference="COORDINATES: protein motif:HMM:NF013211.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAE45988.1"
                     /translation="MSGGDGRGPGNTGLGHNGGKPSGNVNGSSGHGGPSSGGGYHYNPG
                     KGPASTVGPDGEVHINITGGMEKDPPGKHHGNGGSGNGHGAGNHNSNSGGNGKTTSIPG
                     WSPDSGKPGRYLPTNKDKLIKGLIQSIDDHSGTYTIHYTGGAVATVTVPNGDVNKMNVH
                     YNIGSGPSSGNKLTRDTIKSFLEFKAENEANAVNDAISKVNDFYKELASKYGDKLEKEA
                     KALADEAKGKKIRNANEAIKAFDRYKDVLNKKFSVSDREAIAKALESLNKDQMAKQLKI
                     FGKAFGVVGEAIQWGGFISGLVKGFRTGDWNEAFISGEKIAVGKVASVMVTVAFSAMAV
                     NPIGILGFAVIMAVTSALITDERLKQLNSFINGI"
                     /name="hypothetical protein"
     gene            complement(3975..4508)
                     /locus_tag="BGP52_026430"
     CDS             complement(3975..4508)
                     /locus_tag="BGP52_026430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAE45984.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQNLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTMLDRNYNATAAVYQKVVILED
                     KLAEKPVTGKNRKN"
                     /name="hypothetical protein"
     gene            complement(4511..5437)
                     /locus_tag="BGP52_026435"
     CDS             complement(4511..5437)
                     /locus_tag="BGP52_026435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /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="UAE45985.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIEGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     PTQQKEQLRELRKRWEVKHNEHMRKNGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIMEWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQDRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     Typing          complement(1055..1829)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.907"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(4515..5437)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgtttctcga cgaaggagag aaacatataa gtgcgcttcc ttctaatttt acgaattagc
       61 acggaagata ccccctgcac ccgccgaccg caagcgatat actgcacgac cacaacacac
      121 cgcaaaaaaa caccagggag caccacgaac atgcgcatca gcaacatcga atggctgaag
      181 aaacggatcg gattcatcag gaagctcgga gaacagaccg cacgacagag acagattatt
      241 gacctgctcg acaacgaagc aggactcaca gaacaggaac gcaaactcct ccacgtactg
      301 gcaacagcgg aaaaaaacga cttacaggca caggagagcg aacgaaaaca ggcggtccaa
      361 aaacgaatcg agggaaaaaa acaacgacga gaacgcaatc accgactctt tctcgcggct
      421 gggctactga tcgaagcagg actggtagac acaaaaacag gcgagctatg ctataaaaaa
      481 gacaggatat tacaggcact taaggaaatt aagtacgatc tggagacatc cccaaaccca
      541 gacgcgtaag tgcctccatc cgtgttccgg ttccctggtg cttcctcgct cattcgctcg
      601 ctacgctcgg tcatgagact gcggcgagca cgaccacctc aatcatgcgg taagccgcac
      661 cattgctggg ctgagaggag aaaaccgccg gaaagcccgc tgctcaaaaa gacgccgaaa
      721 ggcgctgtta tctgatatag gcttgttcat gtccgcgaat ttaacatccc attaacaaaa
      781 aacggggggt agtgttgctt ctttgttaac taacatttaa ttatttgttt cttggttagc
      841 cattctccag aattatccat ccagcgtcga atagtccggc tgctaacacc aaccgccact
      901 gcaatatctt ccgttgacgc tcccaagata tacatatcaa gcgccctacg acgtttgtcg
      961 tcgttagcag tccaccgaac agcggcgctt tttttccctt tgtccgactg attttctgac
     1021 gaattggcct tcccgccctt gcgaccgcgt gctgcctgaa tttctggcgt gtgcgtatca
     1081 gccacatact gtgcgaaagt ttccggcgtg aagttcctgt gcgtgtattt cgcaatgctc
     1141 ttgccaatag cccgacattc agccagtgaa agcggaacgg gaagcgatgc attgtacatt
     1201 tcgacacgct ggatcaccgc ttcaagccac tgtgagaacg ctggccagcc ctgacgaatc
     1261 gccctgtaag cccatttgcg cgtcatttcg aacaggtggc agtttcgccc catcccgtaa
     1321 tgtttatcga tgctacgacg ctctgaggcg ctcaaatcga gataatctgc cagttcatcg
     1381 agggtatagg cgtcctcgcg ccactccatc acctgccatt ccaggtggaa cggatttttg
     1441 caaatcaggc cgctgtagtt cacatcagca caaagtttct cacacagcga acgttcaacc
     1501 gctgcggcat atttcagcgc cttaaccgag gcatcaggcg cggttctcac ggcgatgttg
     1561 agtgcgtaga gcaggtgagc gtgtccgttc acaggatttt taacggtgat gttcggcgcg
     1621 ggggcgttcc ggtcgctcca gtcaatcgca gccccctcgc ggtcaacgtc aaaaaccagc
     1681 cagaactgcg catgaggctg gttctgctgg atgtaccgcg caagaagcgc acgccctttg
     1741 ccggagatgc gaaggccgaa agcgagatca tccgtgtgat aggggcggtg gggtaaattt
     1801 tcttcgaagt attgaagcgc ggcgctcatg tgttacgatt ccttccaggt tatcgaccga
     1861 cctcgcccct gtattctcgt gacaatcttg gcggagagac acgaatttca ggggcgtttg
     1921 tttttcagtc gcttacacta cccccaacaa caaaacctgt cgagccttcc cgcaaaaccg
     1981 atccatttac cataactccc gttgtacgta ccccttaaaa cgccctcagt cgctttctgg
     2041 cgcaaaaaac gcaaaaagac aaggaaacac caggccaaac cagaaaaatg cgtcagaatc
     2101 actttcaggg cgttgcataa ctatgcacga aagcgattcg caaacagttt cgaccgttca
     2161 aaagggcgaa cgagtcaaaa aagtaacttt tgtgataact acttctagat ttatggataa
     2221 agtaaggcaa tattataaac atttaactaa cgaggatttt ataaatgaaa aaaatagata
     2281 tggaattcta tttaaggaat tttatccttg ccttatcctt ttacatttta tcttttatca
     2341 tcgcaagttt gaatctaagc ccaacaagta tagaattatt tatatttata cttatatctc
     2401 tttttggatc gtccacatac cctttttgtc tattactaat aaataagcaa gcacccttac
     2461 taacaaaaac aacttttaac ttcgttaact ggggttttat aatatgcatt atattatcac
     2521 tacctccatt tggattgatt tttacagtct attactttat aaccaacaaa aagcgataga
     2581 aaaacaaaat aaaggtcata ccatatcaaa cggtacgacc ttttgtttat taaatgccgt
     2641 taataaagct gtttagttgt ttcagccttt catctgtaat taaggcacta gtcactgcca
     2701 taattactgc aaaccctaaa ataccaatag gatttactgc catagcacta aatgccactg
     2761 taaccataac agatgctacc ttgccgactg cgattttttc cccgcttata aaagcctcat
     2821 tccagtcacc agttctgaat cctttaacta agccactgat aaatcccccc cactgaatag
     2881 cctcacctac gacaccaaag gccttaccaa aaatttttaa ctgtttagcc atttgatctt
     2941 tattaagaga ctccagtgct tttgcaatcg cttctcggtc ggatacgctg aatttcttat
     3001 taagcacatc cttgtaccta tcaaaggctt taatcgcctc attagcattg cgaatttttt
     3061 tccctttagc ttcatcggct agtgccttgg cttctttctc caacttatcg ccgtattttg
     3121 atgctaactc tttataaaag tcattaactt tgcttattgc atcatttaca gcattagctt
     3181 cattttctgc cttgaattct aaaaagcttt ttatagtatc acgagtcagt ttattacctg
     3241 atgacggccc actaccgata ttatagtgaa cattcatttt attcacatca ccgtttggta
     3301 cagttactgt agctactgca ccaccagtat aatggatagt gtacgttcca gaatggtcat
     3361 ctattgactg aataagtccc ttaattaact tatctttatt tgtcggtaaa tatctgccag
     3421 gtttcccaga gtcagggctc catccaggaa tagacgttgt ttttccattg ccgcctgaat
     3481 tgctgttatg atttccagca ccgtgaccat tacctgagcc accattaccg tgatgttttc
     3541 ctggaggatc tttttccata ccaccggtaa tgttgatatg cacctccccg tcaggaccta
     3601 cagtgcttgc aggacctttt cccggattgt aatgataccc accgccagat gatggtcctc
     3661 catgtccaga tgagccattc acgtttccac tgggtttacc accgttatgt ccaagccctg
     3721 tattaccagg gccacgacca tctccaccac tcataaaaat tccctctttt aatcgttaaa
     3781 acaattaatt acatagttaa tactgtacat aaaaccactg gttttatgta cagatcaaaa
     3841 agtactcgcc attatttttt ctgtcaagtc agggagggat attttttggc agttcggagg
     3901 aatcactcat gaaaacggtg aacggaacgc gaaatccttt cgctgtccgt gaggcgttgg
     3961 acaagcgaag cgcgtcagtt tttccggttc ttacccgtga caggtttttc cgccagttta
     4021 tcttccagta tcacaacttt ctgatacacc gccgctgtgg cgttgtagtt cctgtcgagc
     4081 attgttttca ttccccatcc gagcacacag aacataacta gaaaagccac tgacacccca
     4141 cccagccatt tccagctata ccctttaagg gtgttgtatt cctgcacgat attgctgtga
     4201 attgtcgcaa tatccctgtt cagggcatcc gcgtttgcct tcatgtttgc gactgactct
     4261 tccagccgct gaaaatcctg gctgatgcgc tcacctatca gccctgctac gtccagattc
     4321 tgcacctcat ttctgacttc atccctgacc tgttttgcca caccgtcaga aatatcccga
     4381 tatccgcgaa gtgtttccct tgccacagcc agagaatcag caacagcttt ctgttgctcc
     4441 attgcggtat gttgcaaatg ctccaccgat aacaggagcg tgagtaattt ttcttctgtg
     4501 ctggccatgt tcagaatccc atagaaaatc cacgtgacgg tgatttaacc cgttcaggtt
     4561 cagttcggtc ctgtctgctc actctgtctc tcatgtcaaa gccatgctcc cgcgcaacat
     4621 catgttgcag ccttctgacc agttcatgtt gcttaaccgg agtgtccagc cattccatga
     4681 tgtcatgccc gaccgttcgc gcctgttcaa gatggcggga atagtccggt tcagaccgtt
     4741 tttgcatgat gtcatgacgc tgggcatcat caagccgtcc ggcagcttca aaacccagat
     4801 gcacttcggg acgtcgttca atgccctgtt ctttcagcgt ccgacagtca atgaagcccc
     4861 tttcaaagcc attttttctc atatgttcgt tgtgcttcac ctcccagcgt tttcgcaatt
     4921 cccgcaactg ctctttttgc tgagtgggag tcaggcttcc tgaatccttt ttcgcacctc
     4981 cccgctcggg atacctggcg ttatagcgcc ggaaatactg ttccggtgta cgttcaatgc
     5041 catcattcac acgctgactc atcatgatat gcgcatgagg ctgttcgcct ccctcaatgc
     5101 tcgctttcgg attgtgaatg gcaaaactcc atgcatgccg ttcgccagct tcctgacgta
     5161 caaaatcctg caccagttca aggcgctgtt ccggtgtcag ttcacggggc agcgctatct
     5221 ccagttcccg ataagtcgaa ccgtttgcac gttcaaactg gtcagccgcc tgccagaaat
     5281 gggagggatt atctcgcgcc cattccggca tgtttccgtg tgcggaatat tccaaatctt
     5341 gacggtcgcg gtatttctct ttgcgctcga tgtaatcggc atggtttgca gcctgtccct
     5401 tgccaccaaa cttaacgctg aggtgatagg tcgccacggt ttcagccctc cgcaggagcg
     5461 cac
//
