LOCUS       CP082425                3188 bp    DNA     circular BCT 05-MAY-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            FSIS11704063 plasmid pF18S031-4, complete sequence.
ACCESSION   CP082425
VERSION     CP082425.2
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN07605937
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 3188)
  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 3188)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (26-JUL-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 3188)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-AUG-2021) CVM/OR, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
REFERENCE   4  (bases 1 to 3188)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-MAR-2023) CVM/OAS, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
  REMARK    Nucleotide sequence updated by submitter
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 24-SEP-2021
            Assembly Method                   :: HGAP v. 4
            Assembly Name                     :: Microbial assembly
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 260x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/28/2023 11:44:12
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,254
            CDSs (total)                      :: 5,133
            Genes (coding)                    :: 4,996
            CDSs (with protein)               :: 4,996
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 137
            CDSs (without protein)            :: 137
            Pseudo Genes (ambiguous residues) :: 0 of 137
            Pseudo Genes (frameshifted)       :: 53 of 137
            Pseudo Genes (incomplete)         :: 90 of 137
            Pseudo Genes (internal stop)      :: 26 of 137
            Pseudo Genes (multiple problems)  :: 30 of 137
            Pseudo Genes (short protein)      :: 1 of 137
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            On May 5, 2023 this sequence version replaced CP082425.1.
            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..3188
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="FSIS11704063"
                     /serovar="Typhimurium"
                     /isolation_source="animal-swine-market swine"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pF18S031-4"
                     /geo_loc_name="USA:MN"
                     /collection_date="2017"
                     /collected_by="USDA-FSIS"
     gene            488..682
                     /locus_tag="CLJ14_026140"
     CDS             488..682
                     /locus_tag="CLJ14_026140"
                     /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="UAF11098.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1763..2350
                     /locus_tag="CLJ14_026135"
     CDS             1763..2350
                     /locus_tag="CLJ14_026135"
                     /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="UAF11097.1"
                     /translation="MIRKIFFASAIVVAISGCTAMDKLAGMGVVSQQTSTFDNSTVIEV
                     SPNSLYDPNSTWGTPLQLGAIWSSAYPEEAGLILSYNSNVSSGNAAYLGLTGIDINVDG
                     KISSYKAQQQTNLSSSSYNSVSKTIYTSSKNTIVIPYKLLESMVSAKNCRIRIHTSQGN
                     QDIDFSAQSIPGGKATAIVSIKEFLAKVERFK"
                     /name="hypothetical protein"
     gene            2360..2857
                     /locus_tag="CLJ14_026145"
     CDS             2360..2857
                     /locus_tag="CLJ14_026145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004793705.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAF11096.1"
                     /translation="MKKQILALALLSLPLIGMAKDSGYGNTEWGMTPNQVVAAQKGKAH
                     LIPPQKYKDQWGKVSIEDVNIGSGIYTVTFIFDASDKLVQTNVASKEKKNEGIANNQFN
                     TLNQLLTQKYGKPQFVSDEKATWKTDTTTIELNKMIISGIMAQTLVRYIPNKTVISDTS
                     NL"
                     /name="hypothetical protein"
     Typing          complement(354..452)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          complement(756..838)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          851..1405
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.434"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tgtaaaaaaa acacaccgcg ccgctagcag cacccctaat ataaaatgat gttttttatg
       61 aaaatagtca gtaccacccc taaaaagcgg tgttggcgca gctacaacac cgcgccgaca
      121 ccgctttttt aaatatcaca aagagagcaa gaagaactaa tttgtcataa ctctctattt
      181 ataaagaaaa atcagcaaaa aattgttttt gcgtggggtg tgggcatttc aggcatgaga
      241 acagactcgc gtttttccgg agtatcagcg gaattattga ttaagaaaca ctcgacgcag
      301 agcgaaattt tatgcaacag cggctgcact gcacagggat tatttatcag ttgatatgct
      361 gtgccatgat acgtcctaaa aaaacaggac aggatgtgca attgtaatac cgtcgcccgc
      421 aacgtcttac aattaccacc tggtcagggt ccacccgaca cccggtactg acggagaaca
      481 acggaaggtg aacaaacagc aacaaactgc gctgaatatg gcgcgattta tcaaaagcca
      541 gagcctgaca ctgcttgaaa aactggatgc tctggatgcc gacgaacagg cggccatgtg
      601 cgaacgactg cacgaactcg cggaagaact ccagaacagc atccaggttc gctttgagac
      661 cgaaagtgaa acaggaacat aacgaagctg acggaggcgc tcacggcttg tccgcgagcg
      721 ttttcggcag cagacaagcc cgccagggcg cgtcagcggg tgtcggggcg aagccctgac
      781 ccagtcacgt agcgatagcg gagtgtatac tggcttaact atgcggcatc agtgcagatt
      841 gtatgaaaag tgccccatgg cgggtgtgaa attccgcaca gatgcgtaag gagaaaatgc
      901 gcgtccaggc gcttttccgc ttcctcgctc actgactcgc tacgctcggt cgttcggctg
      961 cggcgagcgg tactgactta cacaaaaacg gcagcacggt tatccacaga atcaggggat
     1021 aaggccggaa agaacatgtg agcaaaagac caagaacagg aagaaggccg cgccgcaggc
     1081 gtttttccat aggctccgcc cccctgacga gcatcacaga aatcgacgct caagtcagag
     1141 gtggcgaaac ccgacaggac ttaaagatac cagacgtttc cccctggtgg ctccctcgtg
     1201 cgctctcctg ttccgaccct gccgcttacc ggatacctgt ccgcctttct cccttcggga
     1261 agcgtggcgc tttctcatag ctcacgctgt aggtatctcg gttcagtgta ggtcgttcgc
     1321 tccaagctgg gctgtgtgca cgaacccccc gttcagcccg accgctgcgc cttatccggt
     1381 aactatcatc ttgagtccaa cccggaaaga cacgacaaag cgccactggc agcagccact
     1441 ggtaactgat ttagaggagt tagtcttgaa gttatgcgcc ggttcaggct aaactgaaag
     1501 gacaagtttt ggtgactgcg ctcctccaag ccagttacct cggttcaaag agttggtagc
     1561 tctgagaacc ttcgaaaaac cgccctccaa ggcggttttt tcgtttcgtg gttaagagat
     1621 tacgactctc gcttaaggat ctcaagaaga tctgcccgca tcctttcaaa atccttttaa
     1681 aaaagaatat cgtgtgcaaa atggtttcgg gaatacgatg ttttttcagt ctctgttaaa
     1741 aagaaaaaaa taggataacg atatgataag gaagattttt tttgcttctg cgatcgtagt
     1801 agcgatctct ggctgtacag caatggataa attggcggga atgggtgttg tttctcagca
     1861 aacatcaacc tttgataact cgactgtcat agaggtatct ccaaattcgc tatacgatcc
     1921 taacagcact tggggaacac cacttcagtt gggcgcgata tggtctagtg cctatccaga
     1981 agaggctgga ctaatccttt cctacaactc gaatgtatct agcggaaatg ccgcatactt
     2041 aggtttgacg gggattgata taaatgttga tggtaaaata tccagctata aagcacagca
     2101 acaaactaat ctaagcagca gctcatataa ctccgtatcc aagacgatct atacctctag
     2161 caagaatact atcgttatcc cgtataaatt gctggagagc atggtatcag ctaaaaactg
     2221 ccgcattcgc atacacacaa gccaaggaaa tcaagacatc gacttctcag cacaaagtat
     2281 ccccggaggt aaagcgacag cgatcgtttc cattaaagag ttcttggcca aagtcgaacg
     2341 ttttaaataa ggaggcgtca tgaagaagca gattcttgca ctcgctttgc tatcattgcc
     2401 actgattggc atggcaaagg actctggtta tggcaatacc gaatggggta tgaccccaaa
     2461 tcaggtcgtt gcagcccaga aaggaaaagc tcatttaatc ccccctcaaa agtataaaga
     2521 ccaatgggga aaagtgagca ttgaagacgt gaatataggt agtggaatat atacagttac
     2581 gtttattttt gacgcatcag ataaattagt ccaaaccaac gttgccagca aagaaaagaa
     2641 aaacgaggga atagcaaaca accaatttaa cacattaaat caattactta cacaaaagta
     2701 tggcaaacca cagtttgtaa gtgatgaaaa agcaacatgg aaaactgata ctacaacaat
     2761 tgagctaaat aagatgatca tctccggaat tatggctcaa acactagttc gctacattcc
     2821 taataagacc gtgatttctg acacgtctaa cctgtaataa ttgtcgcctc actgagtgtc
     2881 tctctcctgt ttctatacct gaggtgggag attgaacata acgtcgcatt acgcgcaccg
     2941 ctaaaacgcg ctgaacgcga ttctgccgcg aacaccgcaa aaagagatgt tttaccaagc
     3001 gaaaaccgga aaaatgcgtc aggatcgctt tcagctcact gcatagctat gcatgaaagt
     3061 gaatggcgat cggtttgggc gcatacggtg cccatgagac acattttcgg acattttcag
     3121 ttcgtgaatc cctgactcat tgctacatat ctgaacagac acccctagca gcgcccccag
     3181 gggcgtcc
//
