LOCUS       CP082498                5698 bp    DNA     circular BCT 12-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain
            FSIS1607481 plasmid pF18S014-2, complete sequence.
ACCESSION   CP082498
VERSION     CP082498.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN05720502
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 5698)
  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 5698)
  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 5698)
  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                     :: F18S014
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 158x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 08/31/2021 18:54:30
            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)                     :: 5,052
            CDSs (total)                      :: 4,929
            Genes (coding)                    :: 4,813
            CDSs (with protein)               :: 4,813
            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)              :: 116
            CDSs (without protein)            :: 116
            Pseudo Genes (ambiguous residues) :: 0 of 116
            Pseudo Genes (frameshifted)       :: 43 of 116
            Pseudo Genes (incomplete)         :: 74 of 116
            Pseudo Genes (internal stop)      :: 20 of 116
            Pseudo Genes (multiple problems)  :: 19 of 116
            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..5698
                     /organism="Salmonella enterica subsp. enterica serovar
                     4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="FSIS1607481"
                     /serovar="4,[5],12:i:-"
                     /isolation_source="animal-cattle-steer"
                     /sub_species="enterica"
                     /db_xref="taxon:440524"
                     /plasmid="pF18S014-2"
                     /geo_loc_name="USA:WI"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     ARG             complement(5113..5696)
                     /name="APH(3')-Ia"
                     /gene="APH(3')-Ia"
                     /gene_name="APH(3')"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="99.48"
                     /coverage="71.59"
     ARG             complement(3..229)
                     /name="APH(3')-Ia"
                     /gene="APH(3')-Ia"
                     /gene_name="APH(3')"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="96.05"
                     /coverage="28.04"
     Typing          complement(3450..3534)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(3922..4463)
                     /name="ColRNAI_rep_cluster_1857"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1209..2794)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccgtcagcca gtttagtctg accatctcat ctgtaacatc attggcaacg ctacctttgc
       61 catgtttcag aaacaactct ggcgcatcgg gcttcccata caatcgatag attgtcgcac
      121 ctgattgccc gacattatcg cgagcccatt tatacccata taaatcagca tccaggttgg
      181 aatttaatcg ctgcctcgag caagacgttt cccgttgaat atggctcata acaccccttg
      241 tattactgtt tatgtaagca gacagtttta ttgttcatga tgatatattt ttatcttgtg
      301 caatgtaaca tcagagattt tgagacacaa cgtggttccc gccatatgaa aatccggcca
      361 gaccaacatc attctggcgc tccgaaagaa gggatattcg ccgccgtgac cagcctggag
      421 cgggtcgcat aatctttggc cgcttcgtag tcgaggaaca tggcatcaag actagtaaac
      481 tcaatcaaag atccttctag atttaagttc acgacagagt cattagaaat ggagttacta
      541 gaatacttag agttaagaaa tgaattattc aatgacatag aagaagtaat gggtagctat
      601 gctcagaggg caccatagtt catgatagcc ctcgatagta cttacttata tttttagaga
      661 ggtttaagtg taagtagagg gagtaacacc tggtttttca gcatccactc caatgaatgc
      721 tgacaccgat acgcgataat tctctttatc gtagcaaaat catcctccag attgcggttg
      781 agaataggtt catggtgcgc aatacgattg cgcagttttc tcacgggact tgttagcagt
      841 aatgcttccc cccggggaca aacgacagag atatacaaca aaggcccgca attaaaatac
      901 tccgtattta ccataacgtc gcattgcgcg taccgcttaa acgcgttcag cgcgatcacg
      961 gcagcagaca ggtaaaaaca gcaacaaacc acccgaaaaa ctgccgcgat cgcgcctggt
     1021 aaattttaac ctcatgcata gttatgcgcg aaactgaatg acgatcagtt tcgcacgttc
     1081 cagccgtcga acggggcaaa atggggaggt ttggatattg ttaatgctaa tgtacgtaca
     1141 ttaacattgg cgccatccgg gtagggcgtg ccacaaactg gctcgatttc agggggtacc
     1201 ccggtcacat ccccattgac gggccacgcc agatccgcgc ttcgggttcc tgctcttcat
     1261 gccagcgccg ggcaagctcc tgcgcctgac gctcctgttc atcccttatc tgttgttcgt
     1321 gataaataac cgactcaagc ggtcgacttg tccggctaat agctgcacct gctgactcaa
     1381 gttcacgaca cgctcgttca gtatcgcgtt gttctgttgc gtaaccgcgt gcatcttctg
     1441 caattctgcg aaggcgctct cccactcgtt cagccgccgc atatagtcct gttgcaaatg
     1501 ctctaaggcg ttcagcaaat gcccttccag ttccgtcata ctcgtttact ccctgaccag
     1561 cctcacggcg ttcttgtcgc ccaccgtcca ggtgttttcc cctttcaccc cgtccggcag
     1621 caccagaaat ttcccgttct cgccattgac gaacgtcacc ccccaggttt ttgcctcgag
     1681 tttcgccagc gtgttttcct gctctctgat ggtcaagata tttttcgcaa tcctgctttc
     1741 ctgccactga atcagccccc agcaccccag gaaaatgccg cccgtgacgc tgagcgcggt
     1801 cagcgccgga aacagtaccc gccctttgat cacctgccag agcaggtttt tctgctgccg
     1861 ggacagttcg gcctctgtgg tgctgagctg cgtgctcacg gtggtgctca gcgtatccag
     1921 ttgctgtttc acggatgttg tatgttcgct gatagcgtct ctgattttct gcctgtttaa
     1981 gctcagtgcc ttgtctacag actcttctag cttcctgaac tcgctgttca gcatgttctc
     2041 ggtagaagcg gctcgctctt tcagtttctt ctcgaagtcc gttcccattt gtaaaagatt
     2101 gctcatacag cgcccccttt agcctgagat tccgcccccc ctccgggtcg gcaatactga
     2161 tactgcttct ggttgtcctc accacctcaa aacctgccgc tgtgagcgcc tcagtgacat
     2221 cctgacgcgt ttttattgct ccggcacggt aaagcgcctc aagaccccgt gtaatcgctt
     2281 ctgcggcctc ctgtttcgct tttggcagat tattcggtgt gacaagcgtc cgtctgttct
     2341 ccggtgcgtt cgggtcacgc agcccgtaat gatgattaac cagcgtctgc caggcattta
     2401 tcctcggcct gtccgcacgg tcgtagtacg gctggaggcg cttaccgctc tgtagttcca
     2461 tgttcggaat gacaaaattc agttcgagcc gccccttatc ctggtgttcc acccagagaa
     2521 tgctgtactg gtctttttcg agaccgggca taagaacacg ctcaaagctc gtcatcactc
     2581 tttcgcgttc acccggcggt aactccttct ccgcgaacga cagaacgcct gacgtgtatt
     2641 tcttcgaaaa tggcgtggca tcaatgagtt cccggatttc ttccgggtta ccccggagca
     2701 ccgttgcgcc ttcgcggtta cgctcccgcc ccagcaggta atcgaccggg ccacttccac
     2761 cgcctttccc cctggcatga aatttaacta tcatcccgtc ccccctgttc cctgacagcc
     2821 tgccgcaact ggcgcaattc accctcgatg gccatcagag cggccaccac atgaacccgg
     2881 tcaatcgaag accagtggcc gctgttcacc ttccgggctg tctggttcag attgttcccg
     2941 atggcagcca gatgccgcag caatggcggc gatagtgtcg gcagttttcc tgtgcgcgca
     3001 accggctccc ccagacagac ccgccgcatc cattctgcca gtcgtttacc ctcgcagcgt
     3061 tccagtaacc gggcgtgctc ctcatcgcta acccgtatcg tgagcatctt ctcgcgtttc
     3121 atcggtatca ttccccctaa aaaatcccct attaaggagc cttaagacca tgaccaaaca
     3181 ggaaaaaaca gcccttaaca tggcccgctt tatcagaagc cagacgctga ccctgctgga
     3241 aaaactcaac gagctggacg cggacgaaca ggcagacatc tgcgaatcac ttcacgacca
     3301 cgccgacgaa ctctaccgta gttgcctcgc acgcttcggc gatgacggtg aaagcaactg
     3361 aaacatgcag ctcccggaga cgttcacagc ttgcctgtga gcggatgccg ggagcagaca
     3421 agcccgtcag ggcgcgtcag cgggttttag cgggtgtcgg ggcgcagccc tgacccagtc
     3481 acgtagcgat agcggagtgt atactggctt aactatgtgg catcagtgcg gattataaga
     3541 aaagtgcacc atatgcggtg tgaaataccg cacagatgcg taaggagaaa atgccgcatc
     3601 aggcgctctt ccgcttcctc gctcactgac tcgctacgct cggtcgttcg gctgcggcga
     3661 gcggtatcag ctcactcaaa gacggtgatg cggttatcca cagaatcagg ggataacgcc
     3721 aaaagaaaca tgtgagcaaa aggccaggaa caggaagaag gccgcgccgc tggcgttttt
     3781 ccataggctc cgcccccctg acgagcatca caaaaacaga tgctcaagtc agaggtggcg
     3841 aaacccgaca ggactataaa gataccaggc gtttccccct ggaagctccc tcgtgcgctc
     3901 tcctgttccg accctgccgc ttaccggata cctgtccgcc tttctccctt cgggaagcgt
     3961 ggcgctttct catagctcac gctgttggta tctcggcccg gtgtaggtcg ttcgctccaa
     4021 gctgggctgt gtgcacgaac cccccgttca gcccgaccgc tgcgccttat ccggtaacta
     4081 tcgtcttgag tccaacccgg aaagacacgt aaaaacgcca ctggcagcag ccattggtaa
     4141 ccgtttagag gagttagtct tgaagttatg cgccggttaa ggctaaactg aaaggacaga
     4201 tttggtggct gtgctcctcc aagccagtta ccttggttca aagagttgct gctctgagaa
     4261 ccttcgaaaa gccgccttgc tgggcggttt tttcgtttac ggacaagact accttcagga
     4321 tcgttagatc tcaagacaat catgcatagt gagcatacac aggagccgaa cttctcaagc
     4381 gcaaggacgg cagtaaagtg acgtggctgg catggctgcg ccagtcgcct gccaaaccga
     4441 actctcgcca catgctcgaa catattgagc gcctgaaatc ctggcaagca cttgatctgc
     4501 ccgcaggcat cgagcggcag gttcaccaga accgcctgct caaaatcgct cgtgaaggtg
     4561 gccagatgac gcctgctgat ctggcaaagt tcgaggtgca acgacgctat gccacgctgg
     4621 tagcgctggc catcgaaggc atggccaccg tcaccgatga aatcatcgac cttcacgatc
     4681 gcatcatcgg caagctgttc aacgcggcca agaacaagca tcagcagcag ttccaggctt
     4741 ccggcaaggc gatcaacgac aaggtgcgga tgtatgggcg catcggtcaa gcgttgattg
     4801 aggccaagca aagcggcagc gatccgttcg ccgccatcga ggccgttatg ccctgggaca
     4861 ccttcgccgc cagcgtcacc gaagcgcaaa cattggcgcg gcctgccgac tttgatttcc
     4921 tgcaccacat cggtgaaagc tatgccacgc tacgccgcta cgcgccgcag ttcctgggcg
     4981 tgctcaaatt gcgggctgcg cccgccgcca agggtgtgct cgatgccatc gacatgctgc
     5041 gcggcatgaa cagcgacagc gcgcgcaagg tgcccgccga tgcgccaacc gcattcatta
     5101 aagactaact atcagaaaaa ctcatcgagc atcaaatgaa actgcaattt attcatatca
     5161 ggattatcaa taccatattt ttgaaaaagc cgtttctgta atgaaggaga aaattcaccg
     5221 aggcagttcc atagaatggc aagatcctgg tatcggtctg cgattccgac tcgtccaaca
     5281 tcaatacaac ctattaattt cccctcgtca aaaataagat tatcaagtga gaaatcacca
     5341 tgagtgacga ctgaatccgg tgagaatggc aaaagcttat gcatttcttt ccagacttgt
     5401 tcaacaggcc agccattacg ctcatcatca aaatcactcg catcaaccaa accgttattc
     5461 attcgtgatt gcgcctgagc gagacgaaat acgcgatcgc tgttaaaagg acaattacaa
     5521 acaggaatcg aatgcaaccg gcgcaggaac gctgccagcg catcaacaat attttcacct
     5581 gaatcaggat attcttctaa tacctggaat gctgttttcc cggggatcgc agtggtgagt
     5641 aaccatgcat catcaggagt acggataaaa tgcttgatgg tcggaagagg cataaatt
//
