LOCUS       CP082682                4674 bp    DNA     circular BCT 09-SEP-2021
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain CVM
            N18S0597 plasmid pN18S0597, complete sequence.
ACCESSION   CP082682
VERSION     CP082682.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN11968039
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., Hsu,C.-H., Harrison,L., Strain,E., Tran,T.-T.,
            Tillman,G., Dessai,U., McDermott,P. and Zhao,S.
  TITLE     Long-read sequencing reveals evolution and acquisition of
            antimicrobial resistance and virulence genes in Salmonella enterica
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4674)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (06-JUN-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                   :: 477x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 08/30/2021 17:17:52
            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)                     :: 4,863
            CDSs (total)                      :: 4,741
            Genes (coding)                    :: 4,632
            CDSs (with protein)               :: 4,632
            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)       :: 36 of 109
            Pseudo Genes (incomplete)         :: 72 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 N18S0597"
                     /serovar="Typhimurium"
                     /isolation_source="Chicken Legs"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pN18S0597"
                     /geo_loc_name="USA:NC"
                     /collection_date="2018"
                     /collected_by="FDA"
     gene            146..469
                     /locus_tag="FH362_024280"
     CDS             146..469
                     /locus_tag="FH362_024280"
                     /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="UAH74211.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            459..1172
                     /locus_tag="FH362_024285"
                     /pseudo=""
     CDS             459..1172
                     /locus_tag="FH362_024285"
                     /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            1147..1632
                     /locus_tag="FH362_024290"
     CDS             1147..1632
                     /locus_tag="FH362_024290"
                     /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="UAH74208.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKNTQAMLSERNSGVQLTTCGEQRRRCVRVNPEAGGFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            1636..1845
                     /locus_tag="FH362_024295"
     CDS             1636..1845
                     /locus_tag="FH362_024295"
                     /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="UAH74209.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            1942..2124
                     /locus_tag="FH362_024300"
     CDS             1942..2124
                     /locus_tag="FH362_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="UAH74210.1"
                     /translation="MDRRCNKPDKTGLSANICGESRCHSPVCMAMHSGEIYQAQAARFT
                     GELTVFFSGLTAHSR"
                     /name="hypothetical protein"
     gene            2427..2696
                     /locus_tag="FH362_024305"
     CDS             2427..2696
                     /locus_tag="FH362_024305"
                     /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="UAH74212.1"
                     /translation="MNQTMSQKLARDSLGNAQTFEGGVYVTKNGVAELFIQTAAERDAE
                     VREMREERNINALFKLATLAKKEITEGKGMTPEEVLGRLRAARK"
                     /name="hypothetical protein"
     gene            2744..3049
                     /locus_tag="FH362_024310"
     CDS             2744..3049
                     /locus_tag="FH362_024310"
                     /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="UAH74213.1"
                     /translation="MAYQCLADIESYKSGYIGSLKAGDLVDNLLQESVACIIQDPERYH
                     YNFHLQDRGMLLRERLDVESEYRVLYDFDGTNIEILLFVSMKQDFEKQLYRYNLLN"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(3150..3737)
                     /locus_tag="FH362_024315"
     CDS             complement(3150..3737)
                     /locus_tag="FH362_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="UAH74207.1"
                     /translation="MIRKIFFASAIVIAISGCTAMDKLAGMGVVSQQTSTFDNSTVIEV
                     SPNSLYDPNSTWGTQLQLGAIWSSAYPEEVGLILSYNSNVSSGNAAYLGLTGIDINIDG
                     KISSYKAQQQTNLSSSAYNSVSKTIYTSSKNTVVIPYKLLESMVSAKNCRIRIHTSQGN
                     QDIDFSAQSIPGGKATAIVSIKEFMVKVESFK"
                     /name="hypothetical protein"
     Typing          4566..4674
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="80.18"
                     /coverage="80.0"
                     /evalue="6.08e-13"
     Typing          complement(4070..4549)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.309"
                     /coverage="92.0"
                     /evalue="2.1e-176"
     Typing          460..1955
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.385"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgtgactggt tcagggctgc gccccgaaac ccgctaaaag ccactgacgc gcctgcggct
       61 tgcccaacac cgcgccgccc gggaaagaat ttcccgcccg tcccggcgtt atcaggaggc
      121 cggattggca gataaacgca gcaaaatgct cacgatgtgg gtgacggaag atgagcacag
      181 gcgtctgctg gagcgctgcg agggtaaaca gctcgcggcc tggatgcgcc agacgtgcct
      241 ggacgagaag cccgcccgcg ccggcaaact tccctcgatc tcgccggcgc tgcttcgtca
      301 gcttgccggc atgggaaaca acctcaacca gattgcccgg caggttaacg ccggtggcgg
      361 cagcgggcac gaccgcgtgc aggttgtcgc tgcgctgatg gccatcgacg caggactcga
      421 gcggctgcgg cacgccgtac tggaaaaagg ggcagacgat gatcgttaag tttcacccga
      481 gagggcgcgg cggcggtgcc ggtccggtgg attatctgct gggcaaagac cggcaccgcg
      541 acggcgccag cgttctgcag gggaagccgg aggaagtccg ggagcttatc gatgcctcgc
      601 cttacgccaa aaagtacacc tccggcgtcc tgtcatttgc cgaacaggac ttaccgcccg
      661 gacagcgtga aaagctgatg gcgagcttcg agcgggttct gatgcccgga ctcgataaag
      721 atcagtacag cgtgctgtgg gttgagcaca acgacaaagg gcggcttgag ctgaatttcc
      781 tgataccaaa cacggagctg ctgaccggca ggcgtctcca gccgtattac gaccgcgccg
      841 accgtccgcg catcgatgcc tggcagacca tcgtgaacgg tcggctgggg ctgcacgacc
      901 cgaacgcgcc ggagaaccgg cgggcgctgg ccacgccgtc cgcgctgccg gaaacgaagc
      961 aggaagctgc ccagactatt acgcggggtt tactggcctt agcctcgtcc ggggagctga
     1021 aaacgcgaca ggacgtcact gaggcgctgg aaaacgcagg ttttgaggtg gtgcgcacca
     1081 caaaaagcag catcagcatt gccgacccgg acggggggcg aaacatccga ctgaagggag
     1141 ccatctatga acagtctttt aacgctggcg aaggacttag agcagaaatc gaaagcgcag
     1201 cagcagacta ccggcgagat gctgaaagcc gcattcagcg agcacgagaa gtctgtcaga
     1261 gcggaactga gcgaaagcga gaagagaatc agcgccgcca tcctcgacca cgaccggaag
     1321 ctgtcctcag ccatgagcca gcgcacgaaa gggatgctgc gcatggtcag ccagacgtgg
     1381 ctgaccatcg tgctggtctc cgcgctgctg atcgcctcga gcgcgggcat tctgtggtgg
     1441 caggggcagc agatactcga gaactacacg accatccggg agcagaagaa cacgcaggcc
     1501 atgctgtcag agaggaacag cggtgtgcag ctcacgacct gcggagagca gagacgccgc
     1561 tgcgtgaggg tgaacccgga agcgggcggg ttcggagagg attcgagctg gatgatactg
     1621 gcggggaaat agcacatgac ggagctggaa aaacagctgc tgagcgcatt agagcagcta
     1681 cagcaggact actcgaaaag gctggacgag tgggagaacg ccttcgcgga atggcggacg
     1741 atgtctggtc ttatgcaacg ggagaacgcg gcgctgagcg agcgcgtcac gggcttgagc
     1801 aggcaggtgc agagtttgag cgagcagctt cgccggttgt cgtgagacta gacggcattg
     1861 aagcacaccg ggagcatgag cgggcggtgc agcaccagaa aacgctggag cttgaacgat
     1921 cgcagcggca gcggacgtac aatggaccgt cgctgtaaca aaccggataa aacggggctt
     1981 tcggcgaata tctgcggcga aagccggtgc cattcacctg tctgcatggc tatgcattcg
     2041 ggtgaaattt atcaggcgca ggcggcgcgt tttaccgggg agttaactgt atttttttcc
     2101 gggctgacgg cgcattcgcg ctgaacccgt ccggagcggt gccggtaaga gatgttatgg
     2161 taaatgattc tgaattaaac taattttccc ttctttcacc tttctgtgta aaaatatgta
     2221 ctcaatttat acaccaactg ataaactcta ttcaaagcac ggacactggc caccatgtgc
     2281 catagcgaga atttgtactg gcctaataaa tcaacactga aacctgaaac ctgaaacctg
     2341 aaaccacaaa ccggaaacta tgacccttga atcgtgcagc gccgttctcg ccggaagcgc
     2401 ccctatatga tgagaaaaaa atgcctatga accagaccat gtcccagaaa ctcgcaagag
     2461 acagtctcgg aaatgcacaa acctttgaag gaggtgttta cgtcactaaa aacggagtag
     2521 ctgagttatt catccaaacc gcagcagaac gtgatgctga agttcgtgag atgagagaag
     2581 aacgcaatat caacgccctt tttaagctgg caacgttggc taaaaaggaa atcacagaag
     2641 gcaaaggcat gaccccagaa gaggtcttag ggaggttgcg tgccgctaga aaataacaga
     2701 gaggtgttta gtgtcccagc aatacacggt ttcaatcgcg ccgatggcat atcaatgttt
     2761 agctgatatc gagtcttaca agagtggata cattgggtca ctcaaggccg gtgatctggt
     2821 tgataactta cttcaggaat cagttgcctg cattatccaa gaccctgaac gttatcacta
     2881 caatttccac ttacaggatc gaggtatgct tttacgtgag cggctcgatg ttgagagtga
     2941 atacagggtg ctttacgatt ttgacggaac gaacatcgaa atactgttgt ttgtgagcat
     3001 gaagcaggat tttgaaaagc agctgtatcg ctataatttg ctgaattaac actaaacacc
     3061 cggcatcgtc gggttttttc gtgcagacaa aaatttccac ctatgcctat taacactaag
     3121 ttagtagata taggtgggct tacgtgtcct tatttaaaac tttcgacttt gaccatgaac
     3181 tctttaatgg aaacgatcgc tgtcgcttta cctccaggga tgctttgcgc cgagaagtcg
     3241 atgtcttgat ttccttggct tgtgtgtatg cgaatgcggc agtttttagc tgataccatg
     3301 ctctccagca atttataggg gataacaaca gtgttcttgc tagaggtata gatcgtttta
     3361 gatacggagt tatatgcgct actgcttaga ttagtttgct gctgtgcttt atagctggat
     3421 attttgccat caatatttat atcaatcccc gtcaaaccta agtatgcggc atttccgcta
     3481 gatacattcg agttgtagga aagaattagc ccaacctctt ctggataggc actagaccat
     3541 atcgcgccca actgaagttg tgttccccaa gtgctgttag gatcgtatag cgaatttgga
     3601 gatacctcta taacggtcga gttatcaaag gttgatgttt gctgagaaac aacacccatt
     3661 cctgccaatt tatccattgc tgtacagcca gagatggcta ttacgattgc agaagcaaaa
     3721 aaaatctttc ttatcatttt tttgaccttt ttggtttgtt ttccagagag tgaaatagca
     3781 ttgtatttct gaaactatct tgaaggctta tagctgtttt aaacagtgtt ttgaacacag
     3841 agttgaagga tcttcttgag attctcgggt gggagtcgta atctcttgac ccagaaacga
     3901 aaaaaccacc tggggaggtg gtttttcgat ggttcagtaa gttggggaac ttctgaaccg
     3961 tggtaacagg gtgtacaaga ccgctgccac caaattcgtc cttccagttt agccgtagtt
     4021 gggctgatac ttcaagaact ctgcgttagt aatctcttgt acatcctctt accaatggct
     4081 gctgccagtg gcgataagtc gtgtctttcc gggttggact caagatgata gttaccggat
     4141 aaggcgcagc ggtcggactg aacggggggt tcgtgcatac agtccagctt ggagcgaact
     4201 gcctacccgg aactgagtgt caggcgtgga atgagaaacc gcggccataa cagcggaatg
     4261 acaccggtaa accgaaaggc aggaacagga gagcgcatga gggagctacc agggggaaac
     4321 gcctgggatc tttatagtcc tgtcgggttt cgccgccact gatttgagcg tcagatttcg
     4381 tgatgctcgt caggggggcg gagcctatgg aaaaacggca acgccgcatc ctttttctgt
     4441 tcctttctga tgtgtcgcct tccgctttat ctcgttatcc gtgagcctgt aacgcccgcc
     4501 gcagtctcac ggcaggagcg cagcgaccga gtgagcgagg aggcgtcatt tcacttttac
     4561 ctacattctg cacttacgcc ccacagccgc atttttcctc tgtcacatga agcacttccc
     4621 tgaattccca cttcgattta ctatattaag ccagtataca ctccgctagc gcta
//
