LOCUS       CP123697                2699 bp    DNA     circular BCT 14-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain
            FSIS11809860 plasmid pFSIS11809860-5, complete sequence.
ACCESSION   CP123697
VERSION     CP123697.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN09372566
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 2699)
  AUTHORS   Ge,B., Mukherjee,S., Li,C., Harrison,L.B., Hsu,C.H., Tran,T.T.,
            Whichard,J.M., Dessai,U., Singh,R., Gilbert,J.M., Strain,E.A.,
            McDermott,P.F. and Zhao,S.
  TITLE     Genomic analysis of azithromycin-resistant Salmonella from food
            animals at slaughter and processing, and retail meats, 2011-2021,
            United States
  JOURNAL   Microbiol Spectr 12 (1), e0348523 (2024)
   PUBMED   37991374
REFERENCE   2  (bases 1 to 2699)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (06-JUN-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 2699)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-MAR-2023) CVM/OAS, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
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                   :: 294x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/20/2023 11:07:37
            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)                     :: 5,220
            CDSs (total)                      :: 5,094
            Genes (coding)                    :: 4,973
            CDSs (with protein)               :: 4,973
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 121
            CDSs (without protein)            :: 121
            Pseudo Genes (ambiguous residues) :: 0 of 121
            Pseudo Genes (frameshifted)       :: 35 of 121
            Pseudo Genes (incomplete)         :: 95 of 121
            Pseudo Genes (internal stop)      :: 18 of 121
            Pseudo Genes (multiple problems)  :: 26 of 121
            Pseudo Genes (short protein)      :: 1 of 121
            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..2699
                     /organism="Salmonella enterica subsp. enterica serovar
                     4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="FSIS11809860"
                     /serovar="4,[5],12:i:-"
                     /isolation_source="animal-swine-market swine"
                     /sub_species="enterica"
                     /db_xref="taxon:440524"
                     /plasmid="pFSIS11809860-5"
                     /geo_loc_name="USA:VA"
                     /collection_date="2018"
                     /collected_by="USDA-FSIS"
     gene            169..405
                     /locus_tag="DNB19_26090"
     CDS             169..405
                     /locus_tag="DNB19_26090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676031.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WGN69976.1"
                     /translation="MARLTNLTPAEKKFLDDAVAAAERASGKKLNQPNRHIVLNRARAQ
                     IELQRYADRQRALREDERQQSDFAWSRPRAPRR"
                     /name="hypothetical protein"
     gene            complement(907..1551)
                     /locus_tag="DNB19_26095"
     CDS             complement(907..1551)
                     /locus_tag="DNB19_26095"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017900990.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quinolone resistance pentapeptide repeat protein
                     QnrB19"
                     /protein_id="WGN69977.1"
                     /translation="MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQF
                     YDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNM
                     ITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFST
                     FDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAVIG"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrB19"
     gene            complement(1645..1800)
                     /locus_tag="DNB19_26100"
                     /pseudo=""
     CDS             complement(1645..1800)
                     /locus_tag="DNB19_26100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309907.2"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology.
                     GO_function: GO:0043565 - sequence-specific DNA binding
                     [Evidence IEA]"
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /name="helix-turn-helix domain-containing protein"
     ARG             complement(911..1551)
                     /name="qnrB19"
                     /gene="qnrB19"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrB19"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          2530..2699
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="98.0"
                     /evalue="4.2799999999999995e-84"
     Typing          complement(2060..2551)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 aaccggctaa aagctaatga cgcgcctgcg gcttgtccaa cgcctcacgg caccggatta
       61 aaatccgctc ccgttcaccg tttctgactg cctttcaccg tcgctggcgc ttcatcgttt
      121 ctactgtgtc tggcagactg tgctgattta ttctgactgg agaacgttat ggccagactg
      181 acaaacttga cgcctgcaga gaaaaaattt cttgatgatg ctgttgccgc agctgaaaga
      241 gcgtcaggta aaaagctaaa tcagcctaac cggcacatcg tcctgaacag agcgcgtgcg
      301 caaattgagt tgcagcgtta cgccgaccgc cagcgtgcat tacgtgagga tgagcggcag
      361 cagtccgatt ttgcctggtc acgtccgcgc gcgccgcgcc gctgattttg gcttttggcg
      421 gtttagtggt gctgacgctg cgaaatcacc tgccattcac ctgcgtgcat agccatgcag
      481 tcgcgcagaa atcatcaggg gcgtttttcc gggatactgg tgaggaaagg tgctggaaac
      541 ggccctgatg cagcaggatt gcgctgaggg cgcctgcggg ggtgcgggca agggatgtta
      601 tgtttaatcg gtctgaccgt caggtacaaa aaaaagccct tagggggctt tttttttgct
      661 atgagttagc catattttcg ttaagacatg gcttcatgat tcgggagtgg ttattcgttg
      721 ttctcgcgaa aatgaattgg ttagatattc atcaaattcc tgtccagaat gcagcattag
      781 atggcatgtc gttgatgcgg taggtcagga tattcgtcca ctggagaaaa cgtttcacaa
      841 tgcttgccag gagtcgtact ggttaaaagt aaatcgtcaa acgcatctcc cggtgtaaac
      901 gctgaactaa ccaatcacag cgatgccaag ccgctccatg agcaacgatg cctggtagct
      961 gtctaactta acgccttgta aatcaacacc ccgaatatct aagtcaccta actccgaatt
     1021 ggtcagatcg caatgtgtga agtttgctgc tcgccagtcg aaagtcgaaa actcgccgcc
     1081 ggagagatct gaaccactga acgtcgcacc cagtacctga gtccccatcc agcggttttc
     1141 ccacagctca cacttttcca acacgacttt cgaaaaattg gcgtagctta gattagtatt
     1201 agtgatatat gcgctgcaaa accaggtgcg cgtggtgatc atattcataa agcttgcacc
     1261 gcggaaatct gcgccttgtg cgcggcagtg gcgaatttca atgcccaagg cactgacgtt
     1321 gcggaaatct gccattgata aatcacagct tttgaaaatg gcatctttca gcattgcgcg
     1381 actaaaattg caccctttct gactttcgcg atcatagaac tggcagccga taaattcagt
     1441 gccgctcagg tcggcacctg aaaaatcgca gttaaaaaat gtactatttt caactttctc
     1501 accggtgaag cgatttctgt caattttttc gccaactaat gccagagtca tatctatgcc
     1561 tgtgttttta tacagtaatg acgccatggt aaaccttatg acgttatgcg tcaaacccgc
     1621 cagtatgaca cctgcaaatg cgtattagat ctggtgtttc ttcagcaagg cacgtagctg
     1681 atgataagtc agacccagta attcagcggc ttttttctgg ttaaatttag cctgctgtaa
     1741 gctggtttgt agaaagtctt tctcttgctg ctgctggaat tcacgcagat ccagcgttat
     1801 aacgatgtgt atcctatgtg ctcggattgg atagatttcc attacggtga aggatcttct
     1861 tgagatcctt tctgtggcgt cgtaatctct tgctctgtaa acgaaaaaac cgccctgcaa
     1921 ggcggttttt cgaaggttct cagagcagca actctttgaa ccgtggtaac tggcttacga
     1981 ggagcgcagt aaccaaatct gttctttcag tttagcctta acaggcgcat aacttcaaga
     2041 ctaactcctc taaatcagtt accagtggct gctgccagtg gcgataagtc gtgtctttcc
     2101 gggttggact caagatgata gttaccggat aaggcgcagc agtcggactg aacggggggt
     2161 tcgtgcatac agtccatcca ggagcgaact gccttcgcgg aactgagtgt caggcgtgga
     2221 atgagataaa cgcggccata acagcggaat gacaccggta aaccgaaagg caggaatgcg
     2281 ggggagcacg agggagccac cagggggaaa cgcctggtat ctttaagccg catcgggttt
     2341 cgccaccact gatttgagcg tcagatttca tgatgtttgt caggggggcg gagcctatgg
     2401 aaaaacggct tcgccgcggc cttatctctt ccctgttaag ctccttcctg gtatctccca
     2461 ggaaatttcc gccccgcctg taagccggca ccgctcgccg cagccgaacg accgagcgca
     2521 gcgagtcagt gagcgaggaa gcggaatata tcctgtacta catatcctgc tgacgcgctg
     2581 gtgccgcctt ttttctcctg ctacatgaag cacttcactg atttccacat ccgtgccaac
     2641 atagtcagcc agtatacact ccgctagcgc tacgtgactg gttcagggct gcgccccga
//
