LOCUS       CP082419                4593 bp    DNA     circular BCT 11-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain
            FSIS11704067 plasmid pF18S032-2, complete sequence.
ACCESSION   CP082419
VERSION     CP082419.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN07608142
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
  ORGANISM  Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
            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 (02-JUL-2019) 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                     :: F18S032
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 956x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/02/2021 13:06:25
            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)                     :: 5,213
            CDSs (total)                      :: 5,092
            Genes (coding)                    :: 4,974
            CDSs (with protein)               :: 4,974
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 118
            CDSs (without protein)            :: 118
            Pseudo Genes (ambiguous residues) :: 0 of 118
            Pseudo Genes (frameshifted)       :: 39 of 118
            Pseudo Genes (incomplete)         :: 83 of 118
            Pseudo Genes (internal stop)      :: 17 of 118
            Pseudo Genes (multiple problems)  :: 19 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..4593
                     /organism="Salmonella enterica subsp. enterica serovar
                     4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="FSIS11704067"
                     /serovar="4,[5],12:i:-"
                     /isolation_source="animal-swine-market swine"
                     /sub_species="enterica"
                     /db_xref="taxon:440524"
                     /plasmid="pF18S032-2"
                     /geo_loc_name="USA:MN"
                     /collection_date="2017"
                     /collected_by="USDA-FSIS"
     gene            409..1248
                     /locus_tag="CLN51_026025"
     CDS             409..1248
                     /locus_tag="CLN51_026025"
                     /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="UAF06114.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     gene            complement(1936..2169)
                     /locus_tag="CLN51_026030"
     CDS             complement(1936..2169)
                     /locus_tag="CLN51_026030"
                     /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="UAF06115.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2176..2736)
                     /locus_tag="CLN51_026035"
     CDS             complement(2176..2736)
                     /locus_tag="CLN51_026035"
                     /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="UAF06116.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(2711..3424)
                     /locus_tag="CLN51_026040"
                     /pseudo=""
     CDS             complement(2711..3424)
                     /locus_tag="CLN51_026040"
                     /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            complement(3414..3737)
                     /locus_tag="CLN51_026045"
     CDS             complement(3414..3737)
                     /locus_tag="CLN51_026045"
                     /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="UAF06117.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3800..3991
                     /locus_tag="CLN51_026050"
     CDS             3800..3991
                     /locus_tag="CLN51_026050"
                     /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="UAF06113.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(4080..4164)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(2..410)
                     /name="ColRNAI_rep_cluster_1857"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.268"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          4175..4593
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.112"
                     /coverage="99.0"
                     /evalue="4.9000000000000006e-173"
     Typing          complement(1839..3424)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.811"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gctttctcat agctcacgct gttggtatct cggttcggtg taggtcgttc gctccaagct
       61 gggctgtatg cacgaacccc ccgttcagcc cgaccgctgc gccttatccg gtaactatcg
      121 tcttgagtcc aacccggaaa gacacgtaaa aacgccactg gcagcagcca ttggtaaccg
      181 tttagaggag ttagtcttga agttatgcgc cggttaaggc taaactgaaa ggacagattt
      241 ggtggctgtg ctcctccaag ccagttacct tggttcaaag agttgctgct ctgagaacct
      301 tcgaaaagcc gccttgctgg gcggtttttt cgtttacgga caagactacc ttcaggatcg
      361 ttagatctca agacaatcat gcatagtgag catacacagg agccgaactt gcttacactg
      421 ttcatctttt ttgttttatt aatagctgca tgtttctttt gttttgctcc accacgaaga
      481 ggatatgaca gaaatgagat cattccatac aaaataaaac tatcaataaa taaatatcgc
      541 ctttacatat actcatcggg aaaggtaaga caataccttt tatttttagt tattttatca
      601 ctgtactact ccatagcgga accatttaag tctgagttaa taaaaaacat atcatattca
      661 ctgatggctg catttatttt tgatacaggg cttaatttta gcaaggagaa tataactaaa
      721 ggagtgattt caacaaggtg gcataatgac ctatattcat catttgagag aatgaaagca
      781 attaataaaa tttactaccc atccaacaaa gagataaaca cagaaggtct atccaaagcc
      841 atcacatcat ctcttttcaa tgatgacgcg aactcgttcg caaagagaga ttttcgcttg
      901 atgtgggact tatcttctga aaaatatctt tcctataaag aaataataat aagaaaaggc
      961 gataagcttg acgctgtatg cttgagattt ataaatgatg actacaagtt tttagttaat
     1021 ttcaacagag atgaagaggt tttcaaatac tttccatcta taatgcaacc ttcactcaaa
     1081 acatatagag cgttatcaag actagtaaac tcaatcaaag atccttctag atttaagttc
     1141 acgacagagt cattagaaat ggagttacta gaatacttag agttaagaaa tgaattattc
     1201 aatgacatag aagaagtaat gggtagctat gctcagaggg caccatagtt catgatagcc
     1261 ctcgatagta cttacttata tttttagaga ggtttaagtg taagtagagg gagtaacacc
     1321 tggtttttca gcatccactc caatgaatgc tgacaccgat acgcgataat tctctttatc
     1381 gtagcaaaat catcctccag attgcggttg agaataggtt catggtgcgc aatacgattg
     1441 cgcagttttc tcacgggact tgttagcagt aatgcttccc cccggggaca aacgacagag
     1501 atatacaaca aaggcccgca attaaaatac tccgtattta ccataacgtc gcattgcgcg
     1561 taccgcttaa acgcgttcag cgcgatcacg gcagcagaca ggtaaaaaca gcaacaaacc
     1621 acccgaaaaa ctgccgcgat cgcgcctggt aaattttaac ctcatgcata gttatgcgcg
     1681 aaactgaatg acgatcagtt tcgcacgttc cagccgtcga acggggcaaa atggggaggt
     1741 ttggatattg ttaatgctaa tgtacgtaca ttaacattgg cgccatccgg gtagggcgtg
     1801 ccacaaactg gctcgatttc agggggtacc ccggtcacat ccccattgac gggccacgcc
     1861 agatccgcgc ttcgggttcc tgctcttcat gccagcgccg ggcaagctcc tgcgcctgac
     1921 gctcctgttc atcccttatc tgttgttcgt gataaataac cgactcaagc ggtcgacttg
     1981 cccggctaat agctgcacct gctgactcaa gttcacgaca cgctcgttca gtatcgcgtt
     2041 gttctgttgc gtaaccgcgt gcatcttctg caattctgcg aaggcgctct cccactcgtt
     2101 cagccgccgc atatagtcct gttgcaaatg ctctaaggcg ttcagcaaat gcccttccag
     2161 ttccgtcata ctcgtttact ccctgaccag cctcacggcg ttcttgtcgc ccaccgtcca
     2221 ggtgttttcc cctttcaccc cgtccggcag caccagaaat ttcccgttct cgccattgac
     2281 gaacgtcacc ccccaggttt ttgcctcgag tttcgccagc gtgttttcct gctctctgat
     2341 ggtcaagata tttttcgcaa tcctgctttc ctgccactga atcagccccc agcaccccag
     2401 gaaaatgccg cccgtgacgc tgagcgcggt cagcgccgga aacagtaccc gccctttgat
     2461 cacctgccag agcaggtttt tctgctgccg ggacagttcg gcctctgtgg tgctgagctg
     2521 cgtgctcacg gtggtgctca gcgtatccag ttgctgtttc acggatgttg tatgttcgct
     2581 gatagcgtct ctgattttct gcctgtttaa gctcagtgcc ttgtctacag actcttctag
     2641 cttcctgaac tcgctgttca gcatgttctc ggtagaagcg gctcgctctt tcagtttctt
     2701 ctcgaagtcc gttcccattt gtaaaagatt gctcatacag cgcccccttt agcctgagat
     2761 tccgcccccc ctccgggtcg gcaatactga tactgcttct ggttgtcctc accacctcaa
     2821 aacctgccgc tgtgagcgcc tcagtgacat cctgacgcgt ttttattgct ccggcacggt
     2881 aaagcgcctc aagaccccgt gtaatcgctt ctgcggcctc ctgtttcgct tttggcagat
     2941 tattcggtgt gacaagcgtc cgtctgttct ccggtgcgtt cgggtcacgc agcccgtaat
     3001 gatgattaac cagcgtctgc caggcattta tcctcggcct gtccgcacgg tcgtagtacg
     3061 gctggaggcg cttaccgctc tgtagttcca tgttcggaat gacaaaattc agttcgagcc
     3121 gccccttatc ctggtgttcc acccagagaa tgctgtactg gtctttttcg agaccgggca
     3181 taagaacacg ctcaaagctc gtcatcactc tttcgcgttc acccggcggt aactccttct
     3241 ccgcgaacga cagaacgcct gacgtgtatt tcttcgaaaa tggcgtggca tcaatgagtt
     3301 cccggatttc ttccgggtta ccccggagca ccgttgcgcc ttcgcggtta cgctcccgcc
     3361 ccagcaggta atcgaccggg ccacttccac cgcctttccc cctggcatga aatttaacta
     3421 tcatcccgtc ccccctgttc cctgacagcc tgccgcaact ggcgcaattc accctcgatg
     3481 gccatcagag cggccaccac atgaacccgg tcaatcgaag accagtggcc gctgttcacc
     3541 ttccgggctg tctggttcag attgttcccg atggcagcca gatgccgcag caatggcggc
     3601 gatagtgtcg gcagttttcc tgtgcgcgca accggctccc ccagacagac ccgccgcatc
     3661 cattctgcca gtcgtttacc ctcgcagcgt tccagtaacc gggcgtgctc ctcatcgcta
     3721 acccgtatcg tgagcatctt ctcgcgtttc atcggtatca ttccccctaa aaaatcccct
     3781 attaaggagc cttaagacca tgaccaaaca ggaaaaaaca gcccttaaca tggcccgctt
     3841 tatcagaagc cagacgctga ccctgctgga aaaactcaac gagctggacg cggacgaaca
     3901 ggcagacatc tgcgaatcac ttcacgacca cgccgacgaa ctctaccgta gttgcctcgc
     3961 acgcttcggc gatgacggtg aaagcaactg aaacatgcag ctcccggaga cgttcacagc
     4021 ttgcctgtga gcggatgccg ggagcagaca agcccgtcag ggcgcgtcag cgggttttag
     4081 cgggtgtcgg ggcgcagccc tgacccagtc acgtagcgat agcggagtgt atactggctt
     4141 aactatgtgg catcagtgcg gattataaga aaagtgcacc atatgcggtg tgaaataccg
     4201 cacagatgcg taaggagaaa atgccgcatc aggcgctctt ccgcttcctc gctcactgac
     4261 tcgctacgct cggtcgttcg gctgcggcga gcggtatcag ctcactcaaa gacggtgatg
     4321 cggttatcca cagaatcagg ggataacgcc aaaagaaaca tgtgagcaaa aggccaggaa
     4381 caggaagaag gctgcgccgc tggcgttttt ccataggctc cgcccccctg acgagcatca
     4441 caaaaatcga cgctctagtc agaggtggcg aaacccgaca ggactataaa gataccaggc
     4501 gtttccccct ggaagctccc tcgtgcgctc tcctgttccg accctgccgc ttaccggata
     4561 cctgtccgcc tttctccctt cgggaagcgt ggc
//
