LOCUS       CP082576                4674 bp    DNA     circular BCT 13-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain CVM
            N18S0981 plasmid pN18S0981-2, complete sequence.
ACCESSION   CP082576
VERSION     CP082576.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN12360091
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                   :: 325x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/01/2021 10:17:35
            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)                     :: 4,896
            CDSs (total)                      :: 4,774
            Genes (coding)                    :: 4,665
            CDSs (with protein)               :: 4,665
            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)              :: 109
            CDSs (without protein)            :: 109
            Pseudo Genes (ambiguous residues) :: 0 of 109
            Pseudo Genes (frameshifted)       :: 35 of 109
            Pseudo Genes (incomplete)         :: 73 of 109
            Pseudo Genes (internal stop)      :: 22 of 109
            Pseudo Genes (multiple problems)  :: 18 of 109
            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..4674
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="CVM N18S0981"
                     /serovar="Typhimurium"
                     /isolation_source="Chicken Breasts"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pN18S0981-2"
                     /geo_loc_name="USA:PA"
                     /collection_date="2018"
                     /collected_by="FDA"
     gene            370..957
                     /locus_tag="FQC63_000005"
     CDS             370..957
                     /locus_tag="FQC63_000005"
                     /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="UAI01525.1"
                     /translation="MIRKIFFASAIVIAISGCTAMDKLAGMGVVSQQTSTFDNSTVIEV
                     SPNSLYDPNSTWGTQLQLGAIWSSAYPEEVGLILSYNSNVSSGNAAYLGLTGIDINIDG
                     KISSYKAQQQTNLSSSAYNSVSKTIYTSSKNTVVIPYKLLESMVSAKNCRIRIHTSQGN
                     QDIDFSAQSIPGGKATAIVSIKEFMVKVESFK"
                     /name="hypothetical protein"
     gene            complement(1058..1363)
                     /locus_tag="FQC63_000010"
     CDS             complement(1058..1363)
                     /locus_tag="FQC63_000010"
                     /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="UAI01528.1"
                     /translation="MAYQCLADIESYKSGYIGSLKAGDLVDNLLQESVACIIQDPERYH
                     YNFHLQDRGMLLRERLDVESEYRVLYDFDGTNIEILLFVSMKQDFEKQLYRYNLLN"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(1411..1680)
                     /locus_tag="FQC63_000015"
     CDS             complement(1411..1680)
                     /locus_tag="FQC63_000015"
                     /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="UAI01529.1"
                     /translation="MNQTMSQKLARDSLGNAQTFEGGVYVTKNGVAELFIQTAAERDAE
                     VREMREERNINALFKLATLAKKEITEGKGMTPEEVLGRLRAARK"
                     /name="hypothetical protein"
     gene            complement(1983..2165)
                     /locus_tag="FQC63_000020"
     CDS             complement(1983..2165)
                     /locus_tag="FQC63_000020"
                     /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="UAI01526.1"
                     /translation="MDRRCNKPDKTGLSANICGESRCHSPVCMAMHSGEIYQAQAARFT
                     GELTVFFSGLTAHSR"
                     /name="hypothetical protein"
     gene            complement(2262..2471)
                     /locus_tag="FQC63_000025"
     CDS             complement(2262..2471)
                     /locus_tag="FQC63_000025"
                     /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="UAI01527.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2475..2960)
                     /locus_tag="FQC63_000030"
     CDS             complement(2475..2960)
                     /locus_tag="FQC63_000030"
                     /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="UAI01524.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKNTQAMLSERNSGVQLTTCGEQRRRCVRVNPEAGGFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(2935..3648)
                     /locus_tag="FQC63_000035"
                     /pseudo=""
     CDS             complement(2935..3648)
                     /locus_tag="FQC63_000035"
                     /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(3638..3961)
                     /locus_tag="FQC63_000040"
     CDS             complement(3638..3961)
                     /locus_tag="FQC63_000040"
                     /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="UAI01530.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(4071..4250)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.813"
                     /coverage="83.0"
                     /evalue="1.62e-49"
     Typing          4230..4674
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.646"
                     /coverage="85.0"
                     /evalue="2.75e-165"
     Typing          complement(2153..3648)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.385"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agacacgact tatcgccact ggcagcagcc attggtaaga ggatgtacaa gagattacta
       61 acgcagagtt cttgaagtat cagcccaact acggctaaac tggaaggacg aatttggtgg
      121 cagcggtctt gtacaccctg ttaccacggt tcagaagttc cccaacttac tgaaccatcg
      181 aaaaaccacc tccccaggtg gttttttcgt ttctgggtca agagattacg actcccaccc
      241 gagaatctca agaagatcct tcaactctgt gttcaaaaca ctgtttaaaa cagctataag
      301 ccttcaagat agtttcagaa atacaatgct atttcactct ctggaaaaca aaccaaaaag
      361 gtcaaaaaaa tgataagaaa gatttttttt gcttctgcaa tcgtaatagc catctctggc
      421 tgtacagcaa tggataaatt ggcaggaatg ggtgttgttt ctcagcaaac atcaaccttt
      481 gataactcga ccgttataga ggtatctcca aattcgctat acgatcctaa cagcacttgg
      541 ggaacacaac ttcagttggg cgcgatatgg tctagtgcct atccagaaga ggttgggcta
      601 attctttcct acaactcgaa tgtatctagc ggaaatgccg catacttagg tttgacgggg
      661 attgatataa atattgatgg caaaatatcc agctataaag cacagcagca aactaatcta
      721 agcagtagcg catataactc cgtatctaaa acgatctata cctctagcaa gaacactgtt
      781 gttatcccct ataaattgct ggagagcatg gtatcagcta aaaactgccg cattcgcata
      841 cacacaagcc aaggaaatca agacatcgac ttctcggcgc aaagcatccc tggaggtaaa
      901 gcgacagcga tcgtttccat taaagagttc atggtcaaag tcgaaagttt taaataagga
      961 cacgtaagcc cacctatatc tactaactta gtgttaatag gcataggtgg aaatttttgt
     1021 ctgcacgaaa aaacccgacg atgccgggtg tttagtgtta attcagcaaa ttatagcgat
     1081 acagctgctt ttcaaaatcc tgcttcatgc tcacaaacaa cagtatttcg atgttcgttc
     1141 cgtcaaaatc gtaaagcacc ctgtattcac tctcaacatc gagccgctca cgtaaaagca
     1201 tacctcgatc ctgtaagtgg aaattgtagt gataacgttc agggtcttgg ataatgcagg
     1261 caactgattc ctgaagtaag ttatcaacca gatcaccggc cttgagtgac ccaatgtatc
     1321 cactcttgta agactcgata tcagctaaac attgatatgc catcggcgcg attgaaaccg
     1381 tgtattgctg ggacactaaa cacctctctg ttattttcta gcggcacgca acctccctaa
     1441 gacctcttct ggggtcatgc ctttgccttc tgtgatttcc tttttagcca acgttgccag
     1501 cttaaaaagg gcgttgatat tgcgttcttc tctcatctca cgaacttcag catcacgttc
     1561 tgctgcggtt tggatgaata actcagctac tccgttttta gtgacgtaaa cacctccttc
     1621 aaaggtttgt gcatttccga gactgtctct tgcgagtttc tgggacatgg tctggttcat
     1681 aggcattttt ttctcatcat ataggggcgc ttccggcgag aacggcgctg cacgattcaa
     1741 gggtcatagt ttccggtttg tggtttcagg tttcaggttt caggtttcag tgttgattta
     1801 ttaggccagt acaaattctc gctatggcac atggtggcca gtgtccgtgc tttgaataga
     1861 gtttatcagt tggtgtataa attgagtaca tatttttaca cagaaaggtg aaagaaggga
     1921 aaattagttt aattcagaat catttaccat aacatctctt accggcaccg ctccggacgg
     1981 gttcagcgcg aatgcgccgt cagcccggaa aaaaatacag ttaactcccc ggtaaaacgc
     2041 gccgcctgcg cctgataaat ttcacccgaa tgcatagcca tgcagacagg tgaatggcac
     2101 cggctttcgc cgcagatatt cgccgaaagc cccgttttat ccggtttgtt acagcgacgg
     2161 tccattgtac gtccgctgcc gctgcgatcg ttcaagctcc agcgttttct ggtgctgcac
     2221 cgcccgctca tgctcccggt gtgcttcaat gccgtctagt ctcacgacaa ccggcgaagc
     2281 tgctcgctca aactctgcac ctgcctgctc aagcccgtga cgcgctcgct cagcgccgcg
     2341 ttctcccgtt gcataagacc agacatcgtc cgccattccg cgaaggcgtt ctcccactcg
     2401 tccagccttt tcgagtagtc ctgctgtagc tgctctaatg cgctcagcag ctgtttttcc
     2461 agctccgtca tgtgctattt ccccgccagt atcatccagc tcgaatcctc tccgaacccg
     2521 cccgcttccg ggttcaccct cacgcagcgg cgtctctgct ctccgcaggt cgtgagctgc
     2581 acaccgctgt tcctctctga cagcatggcc tgcgtgttct tctgctcccg gatggtcgtg
     2641 tagttctcga gtatctgctg cccctgccac cacagaatgc ccgcgctcga ggcgatcagc
     2701 agcgcggaga ccagcacgat ggtcagccac gtctggctga ccatgcgcag catccctttc
     2761 gtgcgctggc tcatggctga ggacagcttc cggtcgtggt cgaggatggc ggcgctgatt
     2821 ctcttctcgc tttcgctcag ttccgctctg acagacttct cgtgctcgct gaatgcggct
     2881 ttcagcatct cgccggtagt ctgctgctgc gctttcgatt tctgctctaa gtccttcgcc
     2941 agcgttaaaa gactgttcat agatggctcc cttcagtcgg atgtttcgcc ccccgtccgg
     3001 gtcggcaatg ctgatgctgc tttttgtggt gcgcaccacc tcaaaacctg cgttttccag
     3061 cgcctcagtg acgtcctgtc gcgttttcag ctccccggac gaggctaagg ccagtaaacc
     3121 ccgcgtaata gtctgggcag cttcctgctt cgtttccggc agcgcggacg gcgtggccag
     3181 cgcccgccgg ttctccggcg cgttcgggtc gtgcagcccc agccgaccgt tcacgatggt
     3241 ctgccaggca tcgatgcgcg gacggtcggc gcggtcgtaa tacggctgga gacgcctgcc
     3301 ggtcagcagc tccgtgtttg gtatcaggaa attcagctca agccgccctt tgtcgttgtg
     3361 ctcaacccac agcacgctgt actgatcttt atcgagtccg ggcatcagaa cccgctcgaa
     3421 gctcgccatc agcttttcac gctgtccggg cggtaagtcc tgttcggcaa atgacaggac
     3481 gccggaggtg tactttttgg cgtaaggcga ggcatcgata agctcccgga cttcctccgg
     3541 cttcccctgc agaacgctgg cgccgtcgcg gtgccggtct ttgcccagca gataatccac
     3601 cggaccggca ccgccgccgc gccctctcgg gtgaaactta acgatcatcg tctgcccctt
     3661 tttccagtac ggcgtgccgc agccgctcga gtcctgcgtc gatggccatc agcgcagcga
     3721 caacctgcac gcggtcgtgc ccgctgccgc caccggcgtt aacctgccgg gcaatctggt
     3781 tgaggttgtt tcccatgccg gcaagctgac gaagcagcgc cggcgagatc gagggaagtt
     3841 tgccggcgcg ggcgggcttc tcgtccaggc acgtctggcg catccaggcc gcgagctgtt
     3901 taccctcgca gcgctccagc agacgcctgt gctcatcttc cgtcacccac atcgtgagca
     3961 ttttgctgcg tttatctgcc aatccggcct cctgataacg ccgggacggg cgggaaattc
     4021 tttcccgggc ggcgcggtgt tgggcaagcc gcaggcgcgt cagtggcttt tagcgggttt
     4081 cggggcgcag ccctgaacca gtcacgtagc gctagcggag tgtatactgg cttaatatag
     4141 taaatcgaag tgggaattca gggaagtgct tcatgtgaca gaggaaaaat gcggctgtgg
     4201 ggcgtaagtg cagaatgtag gtaaaagtga aatgacgcct cctcgctcac tcggtcgctg
     4261 cgctcctgcc gtgagactgc ggcgggcgtt acaggctcac ggataacgag ataaagcgga
     4321 aggcgacaca tcagaaagga acagaaaaag gatgcggcgt tgccgttttt ccataggctc
     4381 cgcccccctg acgagcatca cgaaatctga cgctcaaatc agtggcggcg aaacccgaca
     4441 ggactataaa gatcccaggc gtttccccct ggtagctccc tcatgcgctc tcctgttcct
     4501 gcctttcggt ttaccggtgt cattccgctg ttatggccgc ggtttctcat tccacgcctg
     4561 acactcagtt ccgggtaggc agttcgctcc aagctggact gtatgcacga accccccgtt
     4621 cagtccgacc gctgcgcctt atccggtaac tatcatcttg agtccaaccc ggaa
//
