LOCUS       CP123696                3223 bp    DNA     circular BCT 14-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain
            FSIS11809860 plasmid pFSIS11809860-4, complete sequence.
ACCESSION   CP123696
VERSION     CP123696.1
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 3223)
  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 3223)
  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 3223)
  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..3223
                     /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="pFSIS11809860-4"
                     /geo_loc_name="USA:VA"
                     /collection_date="2018"
                     /collected_by="USDA-FSIS"
     gene            complement(379..813)
                     /locus_tag="DNB19_26065"
                     /pseudo=""
     CDS             complement(379..813)
                     /locus_tag="DNB19_26065"
                     /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(1022..1345)
                     /locus_tag="DNB19_26070"
     CDS             complement(1022..1345)
                     /locus_tag="DNB19_26070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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="WGN69975.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQIVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1984..2154
                     /locus_tag="DNB19_26075"
     CDS             1984..2154
                     /locus_tag="DNB19_26075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WGN69972.1"
                     /translation="MHEPPVQSDYHARSGNYQLESNPERHDKSPVAVAIGNWVHGAEIV
                     ENAYRVLEVKA"
                     /name="replication initiation protein"
     gene            complement(2363..2695)
                     /locus_tag="DNB19_26080"
     CDS             complement(2363..2695)
                     /locus_tag="DNB19_26080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008784643.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EmrE family multidrug efflux SMR transporter"
                     /protein_id="WGN69973.1"
                     /translation="MNTYIFLGGAIVAEVIGTTFMKYSEGFTRLWPSVGTAISYCAAFY
                     LLSQTLENIPTGIAYAIWSGAGIVLISLAGWLVSGQKLDWPAIAGMFLICVGVLVINIF
                     SKSSAH"
                     /name="EmrE family multidrug efflux SMR transporter"
     gene            complement(2863..3078)
                     /locus_tag="DNB19_26085"
     CDS             complement(2863..3078)
                     /locus_tag="DNB19_26085"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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="WGN69974.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLIQRENA
                     ALNERVTVLSRQVQSLSEQLRRLSKG"
                     /name="MbeD family mobilization/exclusion protein"
     ARG             complement(2364..2695)
                     /name="qacG"
                     /gene="qacG"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="41.35"
                     /coverage="102.8"
     Typing          complement(1442..1633)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.308"
                     /coverage="89.0"
                     /evalue="3.38e-71"
     Typing          1613..2096
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.756"
                     /coverage="93.0"
                     /evalue="1.73e-132"
     Typing          complement(5..1032)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.461"
                     /coverage="89.0"
                     /evalue="0.0"
     Typing          complement(2766..3223)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="86.452"
                     /coverage="100.0"
                     /evalue="2.6900000000000004e-72"
ORIGIN
        1 ctcttctgct cccggatggt cgtatagttc tcgagtatct gctgcccctg ccaccacaga
       61 atgcccgcgc tcgacgctat cagcagcgcg gagaccagaa cgatggtcag ccacgtctgg
      121 ctgaccatgc gcagcatccc tttcgtgcgc tggctcatgg ctgaggacag cttccggtcg
      181 tggtcgagga tggcggcgct gattctcttc tcgctttcgc tcagttccgc tctgacagac
      241 ttctcgtgct cgctgaatgc ggctttcagc atctcgccgg tagtctgctg ctgcgctttc
      301 gatttctgct ctaagtcctt cgccagcgtt aaaagactgt tcatagatgg ctcccttcag
      361 tcggatgttt cgccccccgt ccgggtcggc aatgctgatg ctgctttttg tggtgcgcac
      421 cacctcaaaa cctgcgcttt ccagcgcctc agtgacgtcc tgacgcgttt tcagctcccc
      481 ggatgaggca agggcaagca ggccgctcgt aatcgcctgg gcggcttcct gcttcgcttc
      541 cggcagcgcg gaaggcgaga ccagcacccg ccggttctcc ggcgcgttcg ggtcatgcag
      601 ccccagcctg ccgttcacta tggtctgcca ggcatcgatg cgcggacggt cggcgcggtc
      661 gtaatacggc tgtagccgct tgccggtcag aagctccgtg ttcgggatca ggaagttcag
      721 ctccagccgc cccttgtccc ggtgctcaac ccacagcacg ctgtactggt ctttatcgag
      781 tccgggcatc agaacccgct cgaaactcgc catcagcttt tcgcgctggc cgggcggtaa
      841 atcctgttcg gcaaaagaca gaacgccgga agtgtacttt ttggcgtagg gcgaggcgtc
      901 gataagctcc cggacttcat ccggcttccc ctgcagaacg ctggcgccgt cgcgctggcg
      961 atctttaccc agcagataat cgaccggccc gccgccgccg ccgcgccccc gaggatgaaa
     1021 cttaacgatc atcatcagca cccttttcca gtacggcatg ccgcaaccgc tcgagtccgg
     1081 catcgatggc catcagcgcg gcgacaatct gcacgcggtc gtgtccgctt ccaccaccgg
     1141 cgttaacctg gcgggcaatc tggttaaggt tgttccccat gccggcaagc tgacgaagca
     1201 gcgccggcga gatcgacgga agtttgccgg cgcgtgcggg cttctcgtcc aggcacgtct
     1261 gccgcatcca ggccgcgagt tgcttaccct cgcagcgctc cagcagacgc cggtgctcgt
     1321 cctcagtcac ccacatggtg agcattttgc tgcgtttgtc tgccaatccg gcctcctgat
     1381 aacgccggga cggacgggaa atcttttccc ggtcggcacg gtgttggaca agccgcaggc
     1441 gcggcagtgg ttttagcggg tttcggggcg cagccctgaa ccagtcacgt agcgctagcg
     1501 gagtgtatac tggctaaaca tgttatgacg gagtggcaat ttatgaaagt gcttcatgtg
     1561 acaggggaaa aatgcggctg ccgggcgtaa gtgcaaaatg caggtggtga tgaaatgacg
     1621 cctcctcgct cactcggtcg ctacgctcct gccgtgagac tgcggcgggc gttaccagct
     1681 cacagattac gggataagca aatgccgctc gaagcaggaa aggccaagaa aaggatgcgg
     1741 agttgccgtt tttccatagg ctccgccccc ctgacgagta tcacgaaaat gacgctcaaa
     1801 tcagcggtgg cgaaacccga tgcggcttaa agataccagg cgtttccccc tggtggctcc
     1861 ctcgtgctcc cccgcattcc tgcctttcgg tttaccggtg tcattccgct gttatggccg
     1921 cggtttctca ttccacgcct gaaactcggt tccgggtagg cagttcgctc caggatggac
     1981 tgtatgcacg aaccccccgt tcagtccgac taccacgccc gttccggtaa ctatcaactt
     2041 gagtccaacc cggaaagaca cgacaaatcg ccagtggcgg tagccattgg taactgggtt
     2101 cacggagcag agattgtaga gaatgcctac agagttcttg aagtgaaagc ctgagtgcgg
     2161 ctacactgaa aggacagttt aggtatctgc gctccgtgaa agccagttac catcggaaca
     2221 aagagttggt agctctgaat tccggcaaac gaaccaccgt tggtagcggt ggtttttttg
     2281 tttacaggga aaaagattac gcgcagaaag aaaggatctc aaggaaatcc ttttgctttg
     2341 gccaatatgc ttcggtaaaa agttaatgcg cagaagattt tgaaaaaata ttaataacca
     2401 aaactccaac gcaaataagg aacattcctg caattgcggg ccaatcaagt ttttgaccgc
     2461 taaccaacca accagctagg cttattagta caattcccgc accagaccaa attgcgtaag
     2521 caataccggt aggtatattt tccaatgttt gggaaagcag ataaaaggca gcgcaataac
     2581 ttattgcagt tcctacagac ggccacaggc gtgtaaatcc ttctgaatat ttcataaagg
     2641 tggtgcctat gacttcagcc acaatagccc ctcccaggaa aatatatgta ttcataaaaa
     2701 tacctcatgt tgaaaaattt aaatatcttt acataacaac taattaatag aacccggctt
     2761 atcatagcga aggaccatga tgctgccact gcgatcgttc cagctccagc gctttctggt
     2821 gctgcaccgc ccgctcctgc tgccggtgag tttctatcgc gttcagcctt tcgacaaccg
     2881 gcgcagctgc tcgctcaaac tctgcacctg cctgctcaag accgtgacgc gctcgttcag
     2941 cgccgcgttc tcccgttgaa taagaccaga catcgtccgc cattccgcga aggcgttctc
     3001 ccactcgtcc agccttttcg agtagtcctg ctgtagctgc tctaatgcgc tcagcaactg
     3061 tttttccagc tccgtcatgt gctatttccc cgccagtatc atccagctcg agtcctctcc
     3121 gaactgtccc gcttccgggt tcaccctcac gcagcggcgt ctctgctcgc cgcaggtcga
     3181 gagctgtacg ccgctgttcc tctctgacag catggcctgc gtg
//
