LOCUS       CP082550                4681 bp    DNA     circular BCT 13-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain CVM
            N18S1634 plasmid pN18S1634-4, complete sequence.
ACCESSION   CP082550
VERSION     CP082550.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN12360211
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 4681)
  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 4681)
  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 4681)
  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                   :: 507x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 08/30/2021 17:28:48
            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)                     :: 4,935
            CDSs (total)                      :: 4,813
            Genes (coding)                    :: 4,698
            CDSs (with protein)               :: 4,698
            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)              :: 115
            CDSs (without protein)            :: 115
            Pseudo Genes (ambiguous residues) :: 0 of 115
            Pseudo Genes (frameshifted)       :: 37 of 115
            Pseudo Genes (incomplete)         :: 78 of 115
            Pseudo Genes (internal stop)      :: 20 of 115
            Pseudo Genes (multiple problems)  :: 18 of 115
            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..4681
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="CVM N18S1634"
                     /serovar="Typhimurium"
                     /isolation_source="Chicken Mixed Parts"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pN18S1634-4"
                     /geo_loc_name="USA:SC"
                     /collection_date="2018"
                     /collected_by="FDA"
     gene            join(4430..4681,1..336)
                     /locus_tag="FQD83_000235"
     CDS             join(4430..4681,1..336)
                     /locus_tag="FQD83_000235"
                     /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="UAI38565.1"
                     /translation="MIRKIFFASAIVIAISGCTAMDKLAGMGVVSQQTSTFDNSTVIEV
                     SPNSLYDPNSTWGTQLQLGAIWSSAYPEEVGLILSYNSNVSSGNAAYLGLTGIDINIDG
                     KISSYKAQQQTNLSSSAYNSVSKTIYTSSKNTVVIPYKLLESMVSAKNCRIRIHTSQGN
                     QDIDFSAQSIPGGKATAIVSIKEFMVKVESFK"
                     /name="hypothetical protein"
     gene            complement(437..742)
                     /locus_tag="FQD83_000240"
     CDS             complement(437..742)
                     /locus_tag="FQD83_000240"
                     /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="UAI38569.1"
                     /translation="MAYQCLADIESYKSGYIGSLKAGDLVDNLLQESVACIIQDPERYH
                     YNFHLQDRGMLLRERLDVESEYRVLYDFDGTNIEILLFVSMKQDFEKQLYRYNLLN"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(790..1059)
                     /locus_tag="FQD83_000245"
     CDS             complement(790..1059)
                     /locus_tag="FQD83_000245"
                     /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="UAI38570.1"
                     /translation="MNQTMSQKLARDSLGNAQTFEGGVYVTKNGVAELFIQTAAERDAE
                     VREMREERNINALFKLATLAKKEITEGKGMTPEEVLGRLRAARK"
                     /name="hypothetical protein"
     gene            complement(1369..1551)
                     /locus_tag="FQD83_000250"
     CDS             complement(1369..1551)
                     /locus_tag="FQD83_000250"
                     /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="UAI38566.1"
                     /translation="MDRRCNKPDKTGLSANICGESRCHSPVCMAMHSGEIYQAQAARFT
                     GELTVFFSGLTAHSR"
                     /name="hypothetical protein"
     gene            complement(1648..1857)
                     /locus_tag="FQD83_000255"
     CDS             complement(1648..1857)
                     /locus_tag="FQD83_000255"
                     /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="UAI38567.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1861..2346)
                     /locus_tag="FQD83_000260"
     CDS             complement(1861..2346)
                     /locus_tag="FQD83_000260"
                     /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="UAI38568.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKNTQAMLSERNSGVQLTTCGEQRRRCVRVNPEAGGFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(2321..3034)
                     /locus_tag="FQD83_000265"
                     /pseudo=""
     CDS             complement(2321..3034)
                     /locus_tag="FQD83_000265"
                     /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(3024..3347)
                     /locus_tag="FQD83_000270"
     CDS             complement(3024..3347)
                     /locus_tag="FQD83_000270"
                     /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="UAI38571.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(3457..3636)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.813"
                     /coverage="83.0"
                     /evalue="1.62e-49"
     Typing          3616..4098
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.164"
                     /coverage="93.0"
                     /evalue="2.1e-176"
     Typing          complement(1539..3034)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.385"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtatctagcg gaaatgccgc atacttaggt ttgacgggga ttgatataaa tattgatggc
       61 aaaatatcca gctataaagc acagcagcaa actaatctaa gcagtagcgc atataactcc
      121 gtatctaaaa cgatctatac ctctagcaag aacactgttg ttatccccta taaattgctg
      181 gagagcatgg tatcagctaa aaactgccgc attcgcatac acacaagcca aggaaatcaa
      241 gacatcgact tctcggcgca aagcatccct ggaggtaaag cgacagcgat cgtttccatt
      301 aaagagttca tggtcaaagt cgaaagtttt aaataaggac acgtaagccc acctatatct
      361 actaacttag tgttaatagg cataggtgga aatttttgtc tgcacgaaaa aacccgacga
      421 tgccgggtgt ttagtgttaa ttcagcaaat tatagcgata cagctgcttt tcaaaatcct
      481 gcttcatgct cacaaacaac agtatttcga tgttcgttcc gtcaaaatcg taaagcaccc
      541 tgtattcact ctcaacatcg agccgctcac gtaaaagcat acctcgatcc tgtaagtgga
      601 aattgtagtg ataacgttca gggtcttgga taatgcaggc aactgattcc tgaagtaagt
      661 tatcaaccag atcaccggcc ttgagtgacc caatgtatcc actcttgtaa gactcgatat
      721 cagctaaaca ttgatatgcc atcggcgcga ttgaaaccgt gtattgctgg gacactaaac
      781 acctctctgt tattttctag cggcacgcaa cctccctaag acctcttctg gggtcatgcc
      841 tttgccttct gtgatttcct ttttagccaa cgttgccagc ttaaaaaggg cgttgatatt
      901 gcgttcttct ctcatctcac gaacttcagc atcacgttct gctgcggttt ggatgaataa
      961 ctcagctact ccgtttttag tgacgtaaac acctccttca aaggtttgtg catttccgag
     1021 actgtctctt gcgagtttct gggacatggt ctggttcata ggcatttttt tctcatcata
     1081 taggggcgct tccggcgaga acggcgctgc acgattcaag ggtcatagtt tccggtttgt
     1141 ggtttcaggt ttcaggtttc aggtttcagg tttcagtgtt gatttattag gccagtacaa
     1201 attctcgcta tggcacatgg tggccagtgt ccgtgctttg aatagagttt atcagttggt
     1261 gtataaattg agtacatatt tttacacaga aaggtgaaag aagggaaaat tagtttaatt
     1321 cagaatcatt taccataaca tctcttaccg gcaccgctcc ggacgggttc agcgcgaatg
     1381 cgccgtcagc ccggaaaaaa atacagttaa ctccccggta aaacgcgccg cctgcgcctg
     1441 ataaatttca cccgaatgca tagccatgca gacaggtgaa tggcaccggc tttcgccgca
     1501 gatattcgcc gaaagccccg ttttatccgg tttgttacag cgacggtcca ttgtacgtcc
     1561 gctgccgctg cgatcgttca agctccagcg ttttctggtg ctgcaccgcc cgctcatgct
     1621 cccggtgtgc ttcaatgccg tctagtctca cgacaaccgg cgaagctgct cgctcaaact
     1681 ctgcacctgc ctgctcaagc ccgtgacgcg ctcgctcagc gccgcgttct cccgttgcat
     1741 aagaccagac atcgtccgcc attccgcgaa ggcgttctcc cactcgtcca gccttttcga
     1801 gtagtcctgc tgtagctgct ctaatgcgct cagcagctgt ttttccagct ccgtcatgtg
     1861 ctatttcccc gccagtatca tccagctcga atcctctccg aacccgcccg cttccgggtt
     1921 caccctcacg cagcggcgtc tctgctctcc gcaggtcgtg agctgcacac cgctgttcct
     1981 ctctgacagc atggcctgcg tgttcttctg ctcccggatg gtcgtgtagt tctcgagtat
     2041 ctgctgcccc tgccaccaca gaatgcccgc gctcgaggcg atcagcagcg cggagaccag
     2101 cacgatggtc agccacgtct ggctgaccat gcgcagcatc cctttcgtgc gctggctcat
     2161 ggctgaggac agcttccggt cgtggtcgag gatggcggcg ctgattctct tctcgctttc
     2221 gctcagttcc gctctgacag acttctcgtg ctcgctgaat gcggctttca gcatctcgcc
     2281 ggtagtctgc tgctgcgctt tcgatttctg ctctaagtcc ttcgccagcg ttaaaagact
     2341 gttcatagat ggctcccttc agtcggatgt ttcgcccccc gtccgggtcg gcaatgctga
     2401 tgctgctttt tgtggtgcgc accacctcaa aacctgcgtt ttccagcgcc tcagtgacgt
     2461 cctgtcgcgt tttcagctcc ccggacgagg ctaaggccag taaaccccgc gtaatagtct
     2521 gggcagcttc ctgcttcgtt tccggcagcg cggacggcgt ggccagcgcc cgccggttct
     2581 ccggcgcgtt cgggtcgtgc agccccagcc gaccgttcac gatggtctgc caggcatcga
     2641 tgcgcggacg gtcggcgcgg tcgtaatacg gctggagacg cctgccggtc agcagctccg
     2701 tgtttggtat caggaaattc agctcaagcc gccctttgtc gttgtgctca acccacagca
     2761 cgctgtactg atctttatcg agtccgggca tcagaacccg ctcgaagctc gccatcagct
     2821 tttcacgctg tccgggcggt aagtcctgtt cggcaaatga caggacgccg gaggtgtact
     2881 ttttggcgta aggcgaggca tcgataagct cccggacttc ctccggcttc ccctgcagaa
     2941 cgctggcgcc gtcgcggtgc cggtctttgc ccagcagata atccaccgga ccggcaccgc
     3001 cgccgcgccc tctcgggtga aacttaacga tcatcgtctg cccctttttc cagtacggcg
     3061 tgccgcagcc gctcgagtcc tgcgtcgatg gccatcagcg cagcgacaac ctgcacgcgg
     3121 tcgtgcccgc tgccgccacc ggcgttaacc tgccgggcaa tctggttgag gttgtttccc
     3181 atgccggcaa gctgacgaag cagcgccggc gagatcgagg gaagtttgcc ggcgcgggcg
     3241 ggcttctcgt ccaggcacgt ctggcgcatc caggccgcga gctgtttacc ctcgcagcgc
     3301 tccagcagac gcctgtgctc atcttccgtc acccacatcg tgagcatttt gctgcgttta
     3361 tctgccaatc cggcctcctg ataacgccgg gacgggcggg aaattctttc ccgggcggcg
     3421 cggtgttggg caagccgcag gcgcgtcagt ggcttttagc gggtttcggg gcgcagccct
     3481 gaaccagtca cgtagcgcta gcggagtgta tactggctta atatagtaaa tcgaagtggg
     3541 aattcaggga agtgcttcat gtgacagagg aaaaatgcgg ctgtggggcg taagtgcaga
     3601 atgtaggtaa aagtgaaatg acgcctcctc gctcactcgg tcgctgcgct cctgccgtga
     3661 gactgcggcg ggcgttacag gctcacggat aacgagataa agcggaaggc gacacatcag
     3721 aaaggaacag aaaaaggatg cggcgttgcc gtttttccat aggctccgcc cccctgacga
     3781 gcatcacgaa atctgacgct caaatcagtg gcggcgaaac ccgacaggac tataaagatc
     3841 ccaggcgttt ccccctggta gctccctcat gcgctctcct gttcctgcct ttcggtttac
     3901 cggtgtcatt ccgctgttat ggccgcggtt tctcattcca cgcctgacac tcagttccgg
     3961 gtaggcagtt cgctccaagc tggactgtat gcacgaaccc cccgttcagt ccgaccgctg
     4021 cgccttatcc ggtaactatc atcttgagtc caacccggaa agacacgact tatcgccact
     4081 ggcagcagcc attggtaaga ggatgtacaa gagattacta acgcagagtt cttgaagtat
     4141 cagcccaact acggctaaac tggaaggacg aatttggtgg cagcggtctt gtacaccctg
     4201 ttaccacggt tcagaagttc cccaacttac tgaaccatcg aaaaaccacc tccccaggtg
     4261 gttttttcgt ttctgggtca agagattacg actcccaccc gagaatctca agaagatcct
     4321 tcaactctgt gttcaaaaca ctgtttaaaa cagctataag ccttcaagat agtttcagaa
     4381 atacaatgct atttcactct ctggaaaaca aaccaaaaag gtcaaaaaaa tgataagaaa
     4441 gatttttttt gcttctgcaa tcgtaatagc catctctggc tgtacagcaa tggataaatt
     4501 ggcaggaatg ggtgttgttt ctcagcaaac atcaaccttt gataactcga ccgttataga
     4561 ggtatctcca aattcgctat acgatcctaa cagcacttgg ggaacacaac ttcagttggg
     4621 cgcgatatgg tctagtgcct atccagaaga ggttgggcta attctttcct acaactcgaa
     4681 t
//
