LOCUS       CP082509                4715 bp    DNA     circular BCT 12-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Muenchen strain
            FSIS1606504 plasmid pF18S006-3, complete sequence.
ACCESSION   CP082509
VERSION     CP082509.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN04964189
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Muenchen
  ORGANISM  Salmonella enterica subsp. enterica serovar Muenchen
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4715)
  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 4715)
  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 4715)
  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                     :: F18S006
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 343x
            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)                     :: 4,870
            CDSs (total)                      :: 4,747
            Genes (coding)                    :: 4,638
            CDSs (with protein)               :: 4,638
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 109
            CDSs (without protein)            :: 109
            Pseudo Genes (ambiguous residues) :: 0 of 109
            Pseudo Genes (frameshifted)       :: 54 of 109
            Pseudo Genes (incomplete)         :: 63 of 109
            Pseudo Genes (internal stop)      :: 15 of 109
            Pseudo Genes (multiple problems)  :: 22 of 109
            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..4715
                     /organism="Salmonella enterica subsp. enterica serovar
                     Muenchen"
                     /mol_type="genomic DNA"
                     /strain="FSIS1606504"
                     /serovar="Muenchen"
                     /isolation_source="animal-cattle-dairy cow"
                     /sub_species="enterica"
                     /db_xref="taxon:596"
                     /plasmid="pF18S006-3"
                     /geo_loc_name="USA:TN"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            949..1143
                     /locus_tag="A7Q27_024305"
     CDS             949..1143
                     /locus_tag="A7Q27_024305"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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="UAE12664.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2132..2785)
                     /locus_tag="A7Q27_024310"
     CDS             complement(2132..2785)
                     /locus_tag="A7Q27_024310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016249761.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein phosphatase 2C family protein"
                     /protein_id="UAE12665.1"
                     /translation="MIAFSFSDIGNRCENLDLLSTINCQNDVFGMVIMDGYSCSEWNMK
                     ILSGRLDKCVFSGDLNKDIIEPCKSVPVKAAVCFLFKNNTHLHIYNAGDCRVYNKSGVL
                     LTEDNSVAWKRLKENGIDNKKIPHLVCYCPDRNYLTSFVDFCSDEIIFNHSVFDLNDEN
                     KEVILCTDGFWEHFNDGTVIDLMKDNPESNLAKFTKNIPGNAENHTVCYVRFPS"
                     /name="protein phosphatase 2C family protein"
     gene            complement(2782..3648)
                     /locus_tag="A7Q27_024315"
     CDS             complement(2782..3648)
                     /locus_tag="A7Q27_024315"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000409995.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nucleotidyl transferase AbiEii/AbiGii toxin
                     family protein"
                     /protein_id="UAE12662.1"
                     /translation="MEKEINNWIEESGGKYRLMRQAVHIILKSISIEESLNEMMVMKGG
                     TLLGVKHGSDRYTKDIDFSTEKKLSEIDLGDFFNRFNDSMDVAEAELGYGIKCKVQSHK
                     IQPNAQGTFPTVQINIAFCDRSNASAMKRLESNQSPSVINIDFSFNEKTYDFDFLSLDG
                     DDDNDSVKTYSLTDLMAEKYRSVLQQKVRERNREQDIYDINYLLGKYEFSRQDKYKILE
                     SLLKKSEGKQLDNLLNVKGIRDVEIIERSSQRYQDLSSTVKSLPLFEDAYEKVACFYES
                     LPWDIFK"
                     /name="nucleotidyl transferase AbiEii/AbiGii toxin family
                     protein"
     gene            complement(3632..4588)
                     /locus_tag="A7Q27_024320"
     CDS             complement(3632..4588)
                     /locus_tag="A7Q27_024320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000280763.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAE12663.1"
                     /translation="MYLIEEALTSWLLNEYKKPVITKEEISLQIYLFYLKKEYNGERIY
                     QIRKNKAGPNEFEKNILKLLKSGVLSRVESNDKHHAYPHLIGGFYEVFFVKGNDGSPEN
                     DIVCSTYPYGYLSYLSAMDWHNITDKIPKIIHFTTCRSEQWKNKFYHDFQKDNPDIDEA
                     KQFMPRFPRNSEVNGIKIIVTQETNYVEPMKARNSPVRVSSIGKTFMDMTRRPDYCGGE
                     EHVLESFIEHGKKYAPLIIKEVDKLGRHIDKVRVGFILDRIIGVNNKKISEWKQEAGKY
                     RGSSKVLSPKSPFSPYFDEEWFISINVDMVKSYGKRN"
                     /name="hypothetical protein"
     Typing          complement(435..690)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(815..913)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          complement(1217..1299)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.81"
                     /coverage="100.0"
                     /evalue="1.76e-34"
     Typing          1312..1869
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.831"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tataaaataa atccttagga tttattttat aggataataa gtgggaagtc aagaaaaagt
       61 ttacttatat caccgttttc ataacacctc atgcgatcaa ttcagcggcg gttatagttc
      121 aaatccatga ttaggacatc tgttgctcat aaacgatgag cgtaaaagat catttttcag
      181 cgtcatttac cataacgtcg cattacgcgc accgctaaaa cgcgctgaac gcgattctgc
      241 cgcgaacacc gcaaaaagag atgttttacc aagcgaaaac cggaaaaatg cgtcaggatc
      301 gctttcagct cactgcatag ctatgcatga aagtgaatgg cgatcggttt gggcgcatac
      361 ggtgcccatg agacacattt tcggacattt tcagttcgtg aatccctgac tcattgctac
      421 atatctgaac agacacccct agcagcgccc ccaggggcgt cctgtaaaaa aacacaccgc
      481 gccgctagca gcacccctaa tataaaatga tgttttttat gaaaatagtc agtaccaccc
      541 ctaaaaagcg gtgttggcgc agctacaaca ccgcgccgac accgcttttt taaatatcac
      601 aaagagagca agaagaacta atttgtcata actctctatt tataaagaaa aatcagcaaa
      661 aaattgtttt tgcgtggggt gtgggcattt caggcatgag aacagactcg cgtttttccg
      721 gagtatcagc ggaattattg attaagaaac actcgacgca gagcgaaatt ttatgcaaca
      781 gcggctgcac tgcacaggga ttatttatca gttgatatgc tgtgccatga tacgtcctaa
      841 aaaaacagga caggatgtgc aattgtaata ccgtcgcccg caacgtctta caattaccac
      901 ctggtcaggg tccacccgac acccggtact gacggagaac aacggaaggt gaacaaacag
      961 caacaaactg cgctgaatat ggcgcgattt atcaaaagcc agagcctgac actgcttgaa
     1021 aaactggatg ctctggatgc cgacgaacag gcggccatgt gcgaacgact gcacgaactc
     1081 gcggaagaac tccagaacag catccaggtt cgctttgaga ccgaaagtga aacaggaaca
     1141 taacgaagct gacggaggcg ctcacggctt gtccgcgagc gttttcggca gcagacaagc
     1201 ccgccagggc gcgtcagcgg gtgtcggggc gaagccctga cccagtcacg tagcgatagc
     1261 ggagtgtata ctggcttaac tatgcggcat caatgcagat tgtatgaaaa gtgccccatg
     1321 ccgggtgtga aattccgcac agatgcgtaa ggagaaaatg cgcgtccagg cgcttttccg
     1381 cttcctcgct cactgactcg ctacgctcgg tcgttcggct gcggcgagcg gtactgactt
     1441 acacaaaaac ggcagcacgg ttatccacag aatcagggga taaggccgga aagaacatgt
     1501 gagcaaaaga ccaagaacag gaagaaggcc gcgccgcagg cgtttttcca taggctccgc
     1561 ccccctgacg agcatcacag aaatcgacgc tcaagtcaga ggtggcgaaa cccgacagga
     1621 cttaaagata ccagacgttt ccccctggtg gctccctcgt gcgctctcct gttccgaccc
     1681 tgccgcttac cggatacctg tccgcctttc tcccttcggg aagcgtggcg ctttctcata
     1741 gctcacgctg ttggtatctc agttcggtgt aggtcgttcg ctccaagctg ggctgtgtgc
     1801 acgaaccccc cgttcagccc gactgctgcg ccttatccgg taactatcgt cttgagtcca
     1861 acccggtaag acacgcctta acgccactgg cagcagccac tggtaactga tttagaggag
     1921 ttagtcttga agtcatgcgc cagttaaggc taaactgaaa gaacaggttt tggtgactgc
     1981 gctcctccaa gccagttacc ttggttcttc gagccgcaaa ctctttgaac ctaagagaaa
     2041 accgccccgc aaaggcggtt tttttctttt acagaaaaga gattatctat atgacacgaa
     2101 gatctcaata gcttcttcaa aaaacacgaa atcaagaagg gaatctaacg tagcaaaccg
     2161 tatgattctc tgcgttaccc gggatatttt tagtaaattt agccaagtta gattctgggt
     2221 tatctttcat gaggtcaata acagtaccat cattaaaatg ctcccaaaac ccatcagtac
     2281 ataaaataac ctctttgttt tcatcattta aatcaaaaac tgaatgattg aaaattatct
     2341 catcagagca gaaatcaaca aatgatgtta gataatttct gtctgggcaa taacaaacga
     2401 ggtgaggtat ttttttatta tcgattccat tttcctttaa tcttttccag gcaaccgagt
     2461 tatcctctgt tagaaggact ccacttttgt tatatacacg gcaatctcct gcgttatata
     2521 tatggaggtg cgtattattt ttaaaaagga aacatactgc agccttaaca ggaactgact
     2581 tgcatggttc aataatatct ttattcagat caccagaaaa cacgcactta tctaacctac
     2641 cagagagaat tttcatattc cactcagagc aggaataccc atccataata accattccaa
     2701 acacatcatt ttgacaattt atcgtagata ataagtctaa gttttcacat ctgttaccaa
     2761 tatcactaaa actgaacgct atcatttgaa tatatcccac ggaagacttt catagaaaca
     2821 ggcaactttt tcataagcat cttcaaaaag aggtaatgat ttaacggtgg atgataaatc
     2881 ctgatatcgc tgactggaac gctcgataat ttctacatcc cttatacctt taacgtttaa
     2941 gagattatcc aattgtttac cttcactctt ttttaaaaga gactccagta ttttatactt
     3001 atcttgccga gaaaactcat atttacctaa aagataattg atatcatata tatcttgctc
     3061 tcgatttctc tctctaactt tttgttgcaa aacggatcga tatttttcag ccatcaaatc
     3121 agttaagctg taggtcttta cgctatcatt gtcatcatca ccatctaatg ataaaaagtc
     3181 aaaatcatac gttttttcgt taaagctaaa atcgatattt atcactgaag gtgattgatt
     3241 agattcaagc cttttcattg cagacgcatt agaacgatcg caaaaggcta tatttatctg
     3301 tacagttgga aatgttcctt gtgcattagg ttgaatttta tgagattgaa ctttacattt
     3361 aataccatat cccaattcag cctcagcaac atccattgag tcattaaacc tattgaaaaa
     3421 atcccccaag tcaatttcag aaagtttttt ttcggtagaa aaatcaatat cctttgtgta
     3481 tctatcacta ccatgcttaa caccaagaag agtccctccc ttcataacca tcatttcatt
     3541 caaactctcc tctatagaaa tagatttaag tattatatgt acagcctgcc gcatcaacct
     3601 gtacttccca ccagactctt cgatccaatt attaatttct ttttccataa gacttaacca
     3661 tatcaacatt aatagaaata aaccattctt catcaaagta aggtgagaat ggactctttg
     3721 gagatagcac tttcgaacta cctctgtatt tacccgcctc ttgtttccat tcgcttattt
     3781 ttttattatt aaccccaata attctatcca aaatgaatcc aacccttacc ttgtcaatat
     3841 gacggccaag cttatcgact tcctttataa tcagaggtgc atatttttta ccgtgctcaa
     3901 taaatgattc caatacatgc tcctcaccac cacagtaatc aggccgcctg gtcatatcca
     3961 taaaggtctt accgatagat gataccctga caggggaatt acgagccttc attggctcaa
     4021 cataatttgt ttcttgtgta acgataattt ttattccatt gacctcagaa tttcttggaa
     4081 atctaggcat gaattgtttg gcttcgtcta tatcaggatt atccttttga aaatcatgat
     4141 agaacttatt cttccactgt tcggaacgac atgtcgtaaa gtggattatc ttgggtattt
     4201 tatctgtgat gttatgccaa tccatagcgg ataaatagga taagtatcca tatggatacg
     4261 tagagcacac tatatcattt tccggagaac catcgttacc tttaacaaaa aagacctcat
     4321 agaaaccgcc aattaaatgg gggtaagcat gatgcttatc gttactttca actcttgata
     4381 aaacccctga ctttaataat tttaatatat ttttttcaaa ttcattaggt cctgctttgt
     4441 tctttctaat ttgatatatc ctctcaccat tatattcttt ttttaaataa aaaaggtaaa
     4501 tctgcaaaga gatttcttct ttggttatga ctggtttttt atattcattc aacaaccaag
     4561 acgttagcgc ttcttcgata agatacatat tcaacctttt cggtttagtc tctaatagaa
     4621 tatacgtcct taggacgtat attctattag agattgattg tcaagaaaaa aataataaca
     4681 aacaagcgtt tgccattttt atatttttga tatcc
//
