LOCUS       CP082559                4674 bp    DNA     circular BCT 13-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain CVM
            N18S1595 plasmid pN18S1595-2, complete sequence.
ACCESSION   CP082559
VERSION     CP082559.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN12360196
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 4674)
  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 4674)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (29-JUL-2019) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 4674)
  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
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 414x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 08/30/2021 17:19:57
            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)                     :: 4,990
            CDSs (total)                      :: 4,868
            Genes (coding)                    :: 4,741
            CDSs (with protein)               :: 4,741
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 127
            CDSs (without protein)            :: 127
            Pseudo Genes (ambiguous residues) :: 0 of 127
            Pseudo Genes (frameshifted)       :: 41 of 127
            Pseudo Genes (incomplete)         :: 82 of 127
            Pseudo Genes (internal stop)      :: 25 of 127
            Pseudo Genes (multiple problems)  :: 18 of 127
            CRISPR Arrays                     :: 3
            ##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..4674
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="CVM N18S1595"
                     /serovar="Typhimurium"
                     /isolation_source="Chicken Wings"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pN18S1595-2"
                     /geo_loc_name="USA:TN"
                     /collection_date="2018"
                     /collected_by="FDA"
     gene            193..780
                     /locus_tag="FQD68_024300"
     CDS             193..780
                     /locus_tag="FQD68_024300"
                     /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="UAI33984.1"
                     /translation="MIRKIFFASAIVIAISGCTAMDKLAGMGVVSQQTSTFDNSTVIEV
                     SPNSLYDPNSTWGTQLQLGAIWSSAYPEEVGLILSYNSNVSSGNAAYLGLTGIDINIDG
                     KISSYKAQQQTNLSSSAYNSVSKTIYTSSKNTVVIPYKLLESMVSAKNCRIRIHTSQGN
                     QDIDFSAQSIPGGKATAIVSIKEFMVKVESFK"
                     /name="hypothetical protein"
     gene            complement(881..1186)
                     /locus_tag="FQD68_024305"
     CDS             complement(881..1186)
                     /locus_tag="FQD68_024305"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015379333.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="UAI33988.1"
                     /translation="MAYQCLADIESYKSGYIGSLKAGDLVDNLLQESVACIIQDPERYH
                     YNFHLQDRGMLLRERLDVESEYRVLYDFDGTNIEILLFVSMKQDFEKQLYRYNLLN"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(1234..1503)
                     /locus_tag="FQD68_024310"
     CDS             complement(1234..1503)
                     /locus_tag="FQD68_024310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019080654.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAI33989.1"
                     /translation="MNQTMSQKLARDSLGNAQTFEGGVYVTKNGVAELFIQTAAERDAE
                     VREMREERNINALFKLATLAKKEITEGKGMTPEEVLGRLRAARK"
                     /name="hypothetical protein"
     gene            complement(1806..1988)
                     /locus_tag="FQD68_024315"
     CDS             complement(1806..1988)
                     /locus_tag="FQD68_024315"
                     /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="UAI33985.1"
                     /translation="MDRRCNKPDKTGLSANICGESRCHSPVCMAMHSGEIYQAQAARFT
                     GELTVFFSGLTAHSR"
                     /name="hypothetical protein"
     gene            complement(2085..2294)
                     /locus_tag="FQD68_024320"
     CDS             complement(2085..2294)
                     /locus_tag="FQD68_024320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /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="UAI33986.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2298..2783)
                     /locus_tag="FQD68_024325"
     CDS             complement(2298..2783)
                     /locus_tag="FQD68_024325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012565228.1"
                     /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="UAI33987.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKNTQAMLSERNSGVQLTTCGEQRRRCVRVNPEAGGFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(2758..3471)
                     /locus_tag="FQD68_024330"
                     /pseudo=""
     CDS             complement(2758..3471)
                     /locus_tag="FQD68_024330"
                     /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(3461..3784)
                     /locus_tag="FQD68_024335"
     CDS             complement(3461..3784)
                     /locus_tag="FQD68_024335"
                     /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="UAI33990.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(3894..4073)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.813"
                     /coverage="83.0"
                     /evalue="1.62e-49"
     Typing          4053..4535
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.164"
                     /coverage="93.0"
                     /evalue="2.1e-176"
     Typing          complement(1976..3471)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.385"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcgaaaaacc acctccccag gtggtttttt cgtttctggg tcaagagatt acgactccca
       61 cccgagaatc tcaagaagat ccttcaactc tgtgttcaaa acactgttta aaacagctat
      121 aagccttcaa gatagtttca gaaatacaat gctatttcac tctctggaaa acaaaccaaa
      181 aaggtcaaaa aaatgataag aaagattttt tttgcttctg caatcgtaat agccatctct
      241 ggctgtacag caatggataa attggcagga atgggtgttg tttctcagca aacatcaacc
      301 tttgataact cgaccgttat agaggtatct ccaaattcgc tatacgatcc taacagcact
      361 tggggaacac aacttcagtt gggcgcgata tggtctagtg cctatccaga agaggttggg
      421 ctaattcttt cctacaactc gaatgtatct agcggaaatg ccgcatactt aggtttgacg
      481 gggattgata taaatattga tggcaaaata tccagctata aagcacagca gcaaactaat
      541 ctaagcagta gcgcatataa ctccgtatct aaaacgatct atacctctag caagaacact
      601 gttgttatcc cctataaatt gctggagagc atggtatcag ctaaaaactg ccgcattcgc
      661 atacacacaa gccaaggaaa tcaagacatc gacttctcgg cgcaaagcat ccctggaggt
      721 aaagcgacag cgatcgtttc cattaaagag ttcatggtca aagtcgaaag ttttaaataa
      781 ggacacgtaa gcccacctat atctactaac ttagtgttaa taggcatagg tggaaatttt
      841 tgtctgcacg aaaaaacccg acgatgccgg gtgtttagtg ttaattcagc aaattatagc
      901 gatacagctg cttttcaaaa tcctgcttca tgctcacaaa caacagtatt tcgatgttcg
      961 ttccgtcaaa atcgtaaagc accctgtatt cactctcaac atcgagccgc tcacgtaaaa
     1021 gcatacctcg atcctgtaag tggaaattgt agtgataacg ttcagggtct tggataatgc
     1081 aggcaactga ttcctgaagt aagttatcaa ccagatcacc ggccttgagt gacccaatgt
     1141 atccactctt gtaagactcg atatcagcta aacattgata tgccatcggc gcgattgaaa
     1201 ccgtgtattg ctgggacact aaacacctct ctgttatttt ctagcggcac gcaacctccc
     1261 taagacctct tctggggtca tgcctttgcc ttctgtgatt tcctttttag ccaacgttgc
     1321 cagcttaaaa agggcgttga tattgcgttc ttctctcatc tcacgaactt cagcatcacg
     1381 ttctgctgcg gtttggatga ataactcagc tactccgttt ttagtgacgt aaacacctcc
     1441 ttcaaaggtt tgtgcatttc cgagactgtc tcttgcgagt ttctgggaca tggtctggtt
     1501 cataggcatt tttttctcat catatagggg cgcttccggc gagaacggcg ctgcacgatt
     1561 caagggtcat agtttccggt ttgtggtttc aggtttcagg tttcaggttt cagtgttgat
     1621 ttattaggcc agtacaaatt ctcgctatgg cacatggtgg ccagtgtccg tgctttgaat
     1681 agagtttatc agttggtgta taaattgagt acatattttt acacagaaag gtgaaagaag
     1741 ggaaaattag tttaattcag aatcatttac cataacatct cttaccggca ccgctccgga
     1801 cgggttcagc gcgaatgcgc cgtcagcccg gaaaaaaata cagttaactc cccggtaaaa
     1861 cgcgccgcct gcgcctgata aatttcaccc gaatgcatag ccatgcagac aggtgaatgg
     1921 caccggcttt cgccgcagat attcgccgaa agccccgttt tatccggttt gttacagcga
     1981 cggtccattg tacgtccgct gccgctgcga tcgttcaagc tccagcgttt tctggtgctg
     2041 caccgcccgc tcatgctccc ggtgtgcttc aatgccgtct agtctcacga caaccggcga
     2101 agctgctcgc tcaaactctg cacctgcctg ctcaagcccg tgacgcgctc gctcagcgcc
     2161 gcgttctccc gttgcataag accagacatc gtccgccatt ccgcgaaggc gttctcccac
     2221 tcgtccagcc ttttcgagta gtcctgctgt agctgctcta atgcgctcag cagctgtttt
     2281 tccagctccg tcatgtgcta tttccccgcc agtatcatcc agctcgaatc ctctccgaac
     2341 ccgcccgctt ccgggttcac cctcacgcag cggcgtctct gctctccgca ggtcgtgagc
     2401 tgcacaccgc tgttcctctc tgacagcatg gcctgcgtgt tcttctgctc ccggatggtc
     2461 gtgtagttct cgagtatctg ctgcccctgc caccacagaa tgcccgcgct cgaggcgatc
     2521 agcagcgcgg agaccagcac gatggtcagc cacgtctggc tgaccatgcg cagcatccct
     2581 ttcgtgcgct ggctcatggc tgaggacagc ttccggtcgt ggtcgaggat ggcggcgctg
     2641 attctcttct cgctttcgct cagttccgct ctgacagact tctcgtgctc gctgaatgcg
     2701 gctttcagca tctcgccggt agtctgctgc tgcgctttcg atttctgctc taagtccttc
     2761 gccagcgtta aaagactgtt catagatggc tcccttcagt cggatgtttc gccccccgtc
     2821 cgggtcggca atgctgatgc tgctttttgt ggtgcgcacc acctcaaaac ctgcgttttc
     2881 cagcgcctca gtgacgtcct gtcgcgtttt cagctccccg gacgaggcta aggccagtaa
     2941 accccgcgta atagtctggg cagcttcctg cttcgtttcc ggcagcgcgg acggcgtggc
     3001 cagcgcccgc cggttctccg gcgcgttcgg gtcgtgcagc cccagccgac cgttcacgat
     3061 ggtctgccag gcatcgatgc gcggacggtc ggcgcggtcg taatacggct ggagacgcct
     3121 gccggtcagc agctccgtgt ttggtatcag gaaattcagc tcaagccgcc ctttgtcgtt
     3181 gtgctcaacc cacagcacgc tgtactgatc tttatcgagt ccgggcatca gaacccgctc
     3241 gaagctcgcc atcagctttt cacgctgtcc gggcggtaag tcctgttcgg caaatgacag
     3301 gacgccggag gtgtactttt tggcgtaagg cgaggcatcg ataagctccc ggacttcctc
     3361 cggcttcccc tgcagaacgc tggcgccgtc gcggtgccgg tctttgccca gcagataatc
     3421 caccggaccg gcaccgccgc cgcgccctct cgggtgaaac ttaacgatca tcgtctgccc
     3481 ctttttccag tacggcgtgc cgcagccgct cgagtcctgc gtcgatggcc atcagcgcag
     3541 cgacaacctg cacgcggtcg tgcccgctgc cgccaccggc gttaacctgc cgggcaatct
     3601 ggttgaggtt gtttcccatg ccggcaagct gacgaagcag cgccggcgag atcgagggaa
     3661 gtttgccggc gcgggcgggc ttctcgtcca ggcacgtctg gcgcatccag gccgcgagct
     3721 gtttaccctc gcagcgctcc agcagacgcc tgtgctcatc ttccgtcacc cacatcgtga
     3781 gcattttgct gcgtttatct gccaatccgg cctcctgata acgccgggac gggcgggaaa
     3841 ttctttcccg ggcggcgcgg tgttgggcaa gccgcaggcg cgtcagtggc ttttagcggg
     3901 tttcggggcg cagccctgaa ccagtcacgt agcgctagcg gagtgtatac tggcttaata
     3961 tagtaaatcg aagtgggaat tcagggaagt gcttcatgtg acagaggaaa aatgcggctg
     4021 tggggcgtaa gtgcagaatg taggtaaaag tgaaatgacg cctcctcgct cactcggtcg
     4081 ctgcgctcct gccgtgagac tgcggcgggc gttacaggct cacggataac gagataaagc
     4141 ggaaggcgac acatcagaaa ggaacagaaa aaggatgcgg cgttgccgtt tttccatagg
     4201 ctccgccccc ctgacgagca tcacgaaatc tgacgctcaa atcagtggcg gcgaaacccg
     4261 acaggactat aaagatccca ggcgtttccc cctggtagct ccctcatgcg ctctcctgtt
     4321 cctgcctttc ggtttaccgg tgtcattccg ctgttatggc cgcggtttct cattccacgc
     4381 ctgacactca gttccgggta ggcagttcgc tccaagctgg actgtatgca cgaacccccc
     4441 gttcagtccg accgctgcgc cttatccggt aactatcatc ttgagtccaa cccggaaaga
     4501 cacgacttat cgccactggc agcagccatt ggtaagagga tgtacaagag attactaacg
     4561 cagagttctt gaagtatcag cccaactacg gctaaactgg aaggacgaat ttggtggcag
     4621 cggtcttgta caccctgtta ccacggttca gaagttcccc aacttactga acca
//
