LOCUS       CP082510                4593 bp    DNA     circular BCT 12-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Muenchen strain
            FSIS1606504 plasmid pF18S006-4, complete sequence.
ACCESSION   CP082510
VERSION     CP082510.1
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 4593)
  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 4593)
  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 4593)
  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..4593
                     /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="pF18S006-4"
                     /geo_loc_name="USA:TN"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            join(4251..4593,1..371)
                     /locus_tag="A7Q27_024325"
                     /pseudo=""
     CDS             join(4251..4593,1..371)
                     /locus_tag="A7Q27_024325"
                     /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            346..906
                     /locus_tag="A7Q27_024330"
     CDS             346..906
                     /locus_tag="A7Q27_024330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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="UAE12667.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            913..1146
                     /locus_tag="A7Q27_024335"
     CDS             913..1146
                     /locus_tag="A7Q27_024335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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="UAE12668.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1834..2673)
                     /locus_tag="A7Q27_024340"
     CDS             complement(1834..2673)
                     /locus_tag="A7Q27_024340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAE12669.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     gene            complement(3684..3875)
                     /locus_tag="A7Q27_024345"
     CDS             complement(3684..3875)
                     /locus_tag="A7Q27_024345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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="UAE12666.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3938..4261
                     /locus_tag="A7Q27_024350"
     CDS             3938..4261
                     /locus_tag="A7Q27_024350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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="UAE12670.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          3512..3596
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(2943..3501)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.761"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4..1244
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          4240..4592
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="80.508"
                     /coverage="93.0"
                     /evalue="7.65e-59"
ORIGIN
        1 agagcggtaa gcgcctccag ccgtactacg accgtgcgga caggccgagg ataaatgcct
       61 ggcagacgct ggttaatcat cattacgggc tgcgtgaccc gaacgcaccg gagaacagac
      121 ggacgcttgt cacaccgaat aatctgccaa aagcgaaaca ggaggccgca gaagcgatta
      181 cacggggtct tgaggcgctt taccgtgccg gagcaataaa aacgcgtcag gatgtcactg
      241 aggcgctcac agcggcaggt tttgaggtgg tgaggacaac cagaagcagt atcagtattg
      301 ccgacccgga gggggggcgg aatctcaggc taaagggggc gctgtatgag caatctttta
      361 caaatgggaa cggacttcga gaagaaactg aaagagcgag ccgcttctac cgagaacatg
      421 ctgaacagcg agttcaggaa gctagaagag tctgtagaca aggcactgag cttaaacagg
      481 cagaaaatca gagacgctat cagcgaacat acaacatccg tgaaacagca actggatacg
      541 ctgagcacca ccgtgagcac gcagctcagc accacagagg ccgaactgtc ccggcagcag
      601 aaaaacctgc tctggcaggt gatcaaaggg cgggtactgt ttccggcgct gaccgcgctc
      661 agcgtcacgg gcggcatttt cctggggtgc tgggggctga ttcagtggca ggaaagcagg
      721 attgcgaaaa atatcttgac catcagagag caggaaaaca cgctggcgaa actcgaggca
      781 aaaacctggg gggtgacgtt cgtcaatggc gagaacggga aatttctggt gctgccggac
      841 ggggtgaaag gggaaaacac ctggacggtg ggcgacaaga acgccgtgag gctggtcagg
      901 gagtaaacga gtatgacgga actggaaggg catttgctga acgccttaga gcatttgcaa
      961 caggactata tgcggcggct gaacgagtgg gagagcgcct tcgcagaatt gcagaagatg
     1021 cacgcggtta cgcaacagaa caacgcgata ctgaacgagc gtgtcgtgaa cttgagtcag
     1081 caggtgcagc tattagccgg acaagtcgac cgcttgagtc ggttatttat cacgaacaac
     1141 agataaggga tgaacaggag cgtcaggcgc aggagcttgc ccggcgctgg catgaagagc
     1201 aggaacccga agcgcggatc tggcgtggcc cgtcaatggg gatgtgaccg gggtaccccc
     1261 tgaaatcgag ccagtttgtg gcacgcccta cccggatggc gccaatgtta atgtacgtac
     1321 attagcatta acaatatcca aacctcccca tttttccccg ttcgacggct ggaacgtgcg
     1381 aaactgatcg tcattcagtt tcgcgcataa ctatgcatga ggttaaaatt taccaggcgc
     1441 gatcgcggca gtttttcggg tggtttgttg ctgtttttac ctgtctgctg ccgtgatcgc
     1501 gctgaacgcg tttaagcggt acgcgcaatg cgacgttatg gtaaatacgg agtattttaa
     1561 ttgcgggcct ttgttgtata tctctgtcgt ttgtccccgg ggggaagcat tactgctaac
     1621 aagtcccgtg agaaaactgc gcaatcgtat tgcgcaccat gaacctattc tcaaccgcaa
     1681 tctggaggat gattttgcta cgataaagag aattatcgcg tatcggtgtc agcattcatt
     1741 ggagtggatg ctgaaaaacc aggtgttact ccctctactt acacttaaac ctctctaaaa
     1801 atataagtaa gtactatcga gggctatcat gaactatggt gccctctgag catagctacc
     1861 cattacttct tctatgtcat tgaataattc atttcttaac tctaagtatt ctagtaactc
     1921 catttctaat gactctgtcg tgaacttaaa tctagaagga tctttgattg agtttactag
     1981 tcttgataac gctctatatg ttttgagtga aggttgcatt atagatggaa agtatttgaa
     2041 aacctcttca tctctgttga aattaactaa aaacttgtag tcatcattta taaatctcaa
     2101 gcatacagcg tcaagcttat cgccttttct tattattatt tctttatagg aaagatattt
     2161 ttcagaagat aagtcccaca tcaagcgaaa atctctcttt gcgaacgagt tcgcgtcatc
     2221 attgaaaaga gatgatgtga tggctttgga tagaccttct gtgtttatct ctttgttgga
     2281 tgggtagtaa attttattaa ttgctttcat tctctcaaat gatgaatata ggtcattatg
     2341 ccaccttgtt gaaatcactc ctttagttat attctccttg ctaaaattaa gccctgtatc
     2401 aaaaataaat gcagccatca gtgaatatga tatgtttttt attaactcag acttaaatgg
     2461 ttccgctatg gagtagtaca gtgataaaat aactaaaaat aaaaggtatt gtcttacctt
     2521 tcccgatgag tatatgtaaa ggcgatattt atttattgat agttttattt tgtatggaat
     2581 gatctcattt ctgtcatatc ctcttcgtgg tggagcaaaa caaaagaaac atgcagctat
     2641 taataaaaca aaaaagatga acagtgtaag caagttcggc tcctgtgtat gctcactatg
     2701 catgattgtc ttgagatcta acgatcctga aggtagtctt gtccgtaaac gaaaaaaccg
     2761 cccagcaagg cggcttttcg aaggttctca gagcagcaac tctttgaacc aaggtaactg
     2821 gcttggagga gcacagccac caaatctgtc ctttcagttt agccttaacc ggcgcataac
     2881 ttcaagacta actcctctaa acggttacca atggctgctg ccagtggcgt ttttacgtgt
     2941 ctttccgggt tggactcaag acgatagtta ccggataagg cgcagcggtc gggctgaacg
     3001 gggggttcgt gcacacagcc cagcttggag cgaacgacct acaccgggcc gagataccaa
     3061 cagcgtgagc tatgagaaag cgccacgctt cccgaaggga gaaaggcgga caggtatccg
     3121 gtaagcggca gggtcggaac aggagagcgc acgagggagc ttccaggggg aaacgcctgg
     3181 tatctttata gtcctgtcgg gtttcgccac ctctgacttg agcatctgtt tttgtgatgc
     3241 tcgtcagggg ggcggagcct atggaaaaac gccagcggcg cggccttctt cctgttcctg
     3301 gccttttgct cacatgtttc ttttggcgtt atcccctgat tctgtggata accgcatcac
     3361 cgtctttgag tgagctgata ccgctcgccg cagccgaacg accgagcgta gcgagtcagt
     3421 gagcgaggaa gcggaagagc gcctgatgcg gcattttctc cttacgcatc tgtgcggtat
     3481 ttcacaccgc atatggtgca cttttcttat aatccgcact gatgccacat agttaagcca
     3541 gtatacactc cgctatcgct acgtgactgg gtcagggctg cgccccgaca cccgctaaaa
     3601 cccgctgacg cgccctgacg ggcttgtctg ctcccggcat ccgctcacag gcaagctgtg
     3661 aacgtctccg ggagctgcat gtttcagttg ctttcaccgt catcgccgaa gcgtgcgagg
     3721 caactacggt agagttcgtc ggcgtggtcg tgaagtgatt cgcagatgtc tgcctgttcg
     3781 tccgcgtcca gctcgttgag tttttccagc agggtcagcg tctggcttct gataaagcgg
     3841 gccatgttaa gggctgtttt ttcctgtttg gtcatggtct taaggctcct taatagggga
     3901 ttttttaggg ggaatgatac cgatgaaacg cgagaagatg ctcacgatac gggttagcga
     3961 tgaggagcac gcccggttac tggaacgctg cgagggtaaa cgactggcag aatggatgcg
     4021 gcgggtctgt ctgggggagc cggttgcgcg cacaggaaaa ctgccgacac tatcgccgcc
     4081 attgctgcgg catctggctg ccatcgggaa caatctgaac cagacagccc ggaaggtgaa
     4141 cagcggccac tggtcttcga ttgaccgggt tcatgtggtg gccgctttga tggccatcga
     4201 gggtgaattg cgccagttgc ggcaggctgt cagggaacag gggggacggg atgatagtta
     4261 aatttcatgc cagggggaaa ggcggtggaa gtggcccggt cgattacctg ctggggcggg
     4321 agcgtaaccg cgaaggcgca acggtgctcc ggggtaaccc ggaagaaatc cgggaactca
     4381 ttgatgccac gccattttcg aagaaataca cgtcaggcgt tctgtcgttc gcggagaagg
     4441 agttaccgcc gggtgaacgc gaaagagtga tgacgagctt tgagcgtgtt cttatgcccg
     4501 gtctcgaaaa agaccagtac agcattctct gggtggaaca ccaggataag gggcggctcg
     4561 aactgaattt tgtcattccg aacatggaac tac
//
