LOCUS       CP082589                4773 bp    DNA     circular BCT 13-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain CVM
            N18S0736 plasmid pN18S0736-3, complete sequence.
ACCESSION   CP082589
VERSION     CP082589.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN12930391
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 4773)
  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 4773)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (07-OCT-2019) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 4773)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-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                   :: 503x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/01/2021 16:59:44
            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)                     :: 4,862
            CDSs (total)                      :: 4,741
            Genes (coding)                    :: 4,642
            CDSs (with protein)               :: 4,642
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 99
            CDSs (without protein)            :: 99
            Pseudo Genes (ambiguous residues) :: 0 of 99
            Pseudo Genes (frameshifted)       :: 37 of 99
            Pseudo Genes (incomplete)         :: 63 of 99
            Pseudo Genes (internal stop)      :: 22 of 99
            Pseudo Genes (multiple problems)  :: 19 of 99
            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..4773
                     /organism="Salmonella enterica subsp. enterica serovar
                     4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="CVM N18S0736"
                     /serovar="SI 4,5,12:i:-"
                     /isolation_source="ground turkey"
                     /sub_species="enterica"
                     /db_xref="taxon:440524"
                     /plasmid="pN18S0736-3"
                     /geo_loc_name="USA:NY"
                     /collection_date="2018"
                     /collected_by="FDA"
     gene            complement(join(4091..4773,1..82))
                     /locus_tag="F9183_023725"
                     /pseudo=""
     CDS             complement(join(4091..4773,1..82))
                     /locus_tag="F9183_023725"
                     /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(21..344)
                     /locus_tag="F9183_023730"
     CDS             complement(21..344)
                     /locus_tag="F9183_023730"
                     /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="UAH92555.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLAEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            complement(1659..2126)
                     /locus_tag="F9183_023735"
     CDS             complement(1659..2126)
                     /locus_tag="F9183_023735"
                     /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="UAH92554.1"
                     /translation="MPAPNNYGVAGSPNSAIAHPDGLDCYGRVPEINSKGDVIPAGDIF
                     LRVGRHTGPNRGFGVRHIWAEHEQELVKLGYATVNDVARFVRDIIRRGVPIYCEFNSTS
                     GKHRPAVLKSSVGIVILEPREAPETESGWIYVVVTAYTRRTAHGTLVGHIE"
                     /name="hypothetical protein"
     gene            2662..3213
                     /locus_tag="F9183_023740"
     CDS             2662..3213
                     /locus_tag="F9183_023740"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000654246.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAH92551.1"
                     /translation="MKDMKAVVVFTGKDLNIMRTEGGSGYWHARTDRLNDADYLIAVRN
                     RRETWAVKDLEHGTAFLIAKITGCFKSPDYDDRNVITFDEYAEIHTPKAWKMLTDGQRY
                     PVAYLSAQEAFLRIGVTPEQLEWKKFHPSSPSVPNTVIPGLAEEKTEKLSLNEAIERAK
                     KDISNATGIDSSAITISIKI"
                     /name="hypothetical protein"
     gene            complement(3412..3627)
                     /locus_tag="F9183_023745"
     CDS             complement(3412..3627)
                     /locus_tag="F9183_023745"
                     /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="UAH92552.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMFGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3631..4116)
                     /locus_tag="F9183_023750"
     CDS             complement(3631..4116)
                     /locus_tag="F9183_023750"
                     /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="UAH92553.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKVAFSEHEKFVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSTLLTASGASILWWQGQQIL
                     DNYTIIREQKSTQAMLSERNSGVQISTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     Typing          complement(446..633)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.34"
                     /coverage="87.0"
                     /evalue="2.7100000000000003e-47"
     Typing          579..1091
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.636"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(25..344)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.131"
                     /coverage="100.0"
                     /evalue="1.63e-63"
     Typing          complement(3309..4771)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.803"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 cgcgccctcg cgggtgaaac ttaacgatca tcgtctgcac ccttttccag cacggcatgc
       61 cgcagccgct cgagtccggc atctatggcc atcagcgcgg cgacgacctg cacgcggtcg
      121 tgcccgctgc cgccaccggc gttaacctgc cgggcaatct ggttgaggtt attccccatg
      181 ccggcaagct gacgaagcag cgccggcgag attgagggaa gcttgccggc gcgggcgggt
      241 ttctcggcca ggcacgtctg gcgcatccag gctgcaagct gtttaccgtc gcagcgttcc
      301 agcagacggc ggtgctcatc ttcggtcacc cacatggtga gcatcttgtt ccgtttctct
      361 gacaaaccga tctcctgata acgccgggac gggcgggaaa tcttttcccg gtcggcgcgg
      421 tgttggacaa gccgcaggcg cgtcagtggt tttagcaggt ttcggggcgc agccctgaac
      481 cagtcacgta gcgctagcgg agtgtatact ggctcaatat gttacggcgg agtaacacgt
      541 aatgaaagtg cttcatgtgg caggagaaaa atgcagctgc agggcgtaca ggagaaaatg
      601 gaggttacgg tgatatgacg cctcctcgct cactcggtcg cttccgctcc tgacgttcgg
      661 ctgcggcggg cgttacctgc aaacggataa gagcaaaggc atacggcatg gcaagcagga
      721 caggaaaagg atgcggcgct gccgtttttc cataggctcc gcccccctga caagcatcac
      781 gaaatctgac gctcaaatca gtggtggcga aacccgacag gacttaaaga taccaggcgt
      841 ttccccctgg tggctccctc gtgcgctctc ctgttcctgc ctttcggttt accggtgtca
      901 ttccgctgtt atggccgcgt ttatctcatt ccacgcctga cactcagttc cgggtaggca
      961 gttcgctcca agctggactg tatgcacgac ccccccgttc agtccgaccg ctgcgccttg
     1021 tccggtaact atcgtcttga gtccaacccg gatagacacg actaatcgcc attggcaacg
     1081 gccactggta agcaggatgt gcgagagatg taacgagagt tcttgaagtg gcggcctaac
     1141 tgaggctaca ctgaaaggac agtatttggt gacatgtctc gcacaagact gttaccacgg
     1201 ttagagaatc tgccaggatt aactaacctt cgaaaaaacc acctgccagg gtggtttttt
     1261 cgtttctgag caagagacta cgacgagcca ctgatgatct caagtgttca tttctgatat
     1321 tcacagcaga ataactgtta ggatataggg tatctatagc caggagcttc aagaaatcca
     1381 gacacagcaa tggattccag ggttatcgaa aaaaattagt atataggttg caaccaaaat
     1441 gttggttgca aatctacatc acgatgttta tgattattgt actgcaagag cattcgcagg
     1501 gggcatcaac cagtaatagg ccttctgtgc cgggcagtca gatggctggt catctgccgg
     1561 gtagttacga caagcgtcgg tttctgaacc ctatgtgcta aggaaatgct gcgactacca
     1621 acgaattcat aaagggcgct ttttagcgcc ctattttttt attcaatatg accaaccaaa
     1681 gtaccgtgcg ccgtccttcg tgtgtacgca gtcacaacga catagatcca acctgactca
     1741 gtttcaggcg cttctctggg ctcaagaatt acgatgccta ccgacgactt tagcactgca
     1801 ggccgatgtt taccgcttgt actgttgaac tcgcaatata ttggtacgcc acgacgaata
     1861 atatcccgga caaaacgagc cacatcatta acggtcgcat atcccagctt aaccagttcc
     1921 tgctcgtgct cagcccagat atggcgaaca ccaaagcccc ggttagggcc agtatgccta
     1981 ccaacacgca agaagatgtc gccagcagga ataacatcac ctttagaatt aatttcaggg
     2041 acacggccat agcaatcaag cccatcaggg tgagctatag cgctgttagg tgaaccagct
     2101 acaccgtaat tgtttggagc aggcacaaaa cgatccttat tgagtagagt ccgcatatgg
     2161 taccagagag gaaacaagcg gaaggagccc aagaaaaaag cagagacgat aaaaagaatc
     2221 cttatggatt atttttttgt cctttcatcc ttggcgcata aggatatcac acctgaaaat
     2281 gtgacgtgcg aatcgcccta gcagctagat ttaccataac atcccttgcc cgcaccgctc
     2341 cggacgggtt cagcgtgaaa gcggcgttag cccggtaaaa ccggcagtaa actccccgct
     2401 aaaccgcgca ttctgcgcct gataaatttc acgcggctgc atagccatgc agccacgtga
     2461 atggctcatg ctttcaatgt atatcctcgt ccaagcccct gttttaaccg gtttatcaaa
     2521 aaaacaaaca ggaagcctta tcactaacaa taaaagaggt agggggctgc attttatcgc
     2581 ataaaaaaca tttacaacac gaattctatc gtatagattt cataaaaaaa tgaaattgac
     2641 tcacctatta agggtttcta tatgaaagat atgaaagctg ttgtggtttt taccgggaag
     2701 gatttgaaca taatgagaac cgaggggggg tcaggctact ggcatgccag aacagacagg
     2761 ctcaacgatg ccgattacct catagcagta agaaacagaa gggaaacgtg ggcagtaaaa
     2821 gacctggaac acggcacagc attcctgatc gccaaaatta ccgggtgttt taaaagccct
     2881 gattacgacg acaggaacgt cataaccttt gatgaatacg cagaaattca cactccaaaa
     2941 gcatggaaaa tgctaaccga tggtcagcgc tatccggttg cttacctgag cgcacaggaa
     3001 gcttttttac gtattggggt aacaccggaa caactggaat ggaagaaatt ccatccttca
     3061 tccccatcgg ttcctaatac agtgattcct ggtctggctg aagagaaaac agaaaaactc
     3121 tcccttaacg aggcaattga aagagccaaa aaggatatta gcaacgcaac agggattgat
     3181 agctcagcca taacaataag catcaagatc tgatgaagcg tgaacaacaa gatagcagcc
     3241 tcatgttcta gaactgaacc tgtgcgccag aaacagcaag cccatgcttt tccggcgcac
     3301 agattcaaag tgacggaccg ttgtacgttc gctgtcgctg agatcgttcc agctccagcg
     3361 ctttctgatg ctgcgccgcc cgttcctgct cacgatgtgc ctctatcacg ttcagccttg
     3421 tgacaaccgg cgcagctgct cgctcaaact ctgcacctgc ctgctcaagc ccgtgacgcg
     3481 ctcgctcagc gccgcgttct cccgttgcat aagaccaaac atcgtccgcc attccgcgaa
     3541 ggcgttctcc cactcgtcca gccttttcga gtagtcctgc tgtagctgct ctaatgcgct
     3601 cagcaactgt ttttccagct ccgtcatgtg ctatttcccc gccagtatca tccagctcga
     3661 atcctctccg aaccgtcccg cttccgggtt caccctcacg cagcggcgtc tctgctctcc
     3721 gcaggtcgag atctgcacgc cgctgttcct ctcggacagc atggcctgcg tgctcttctg
     3781 ctcccggatg atcgtgtaat tgtcgagtat ctgctgtccc tgccaccata gaatgcttgc
     3841 gcccgatgct gtcagcagtg tagacaccag gacgatggtc agccacgtct ggctgaccat
     3901 acgcaccatg cctttcgtgc gctggctcat ggctgaggac agcttccggt cgtggtcgag
     3961 gatggcggcg ctgattctct tctcgctttc gctcagttcc gctctgacaa acttctcgtg
     4021 ctcgctgaat gcgactttca gcatctcgcc ggtactctgc tgctgcgctt tcgatttctg
     4081 ctctaagtcc ttcgccagcg ttaaaagact gttcatagat ggctcccttc agtcggatgt
     4141 ttcgcccccc gtccgggtcg gcaatgctga tgctgctttt tgtggtgcgc accacctcaa
     4201 aacctgcgct ttctagcgcc tcagtgacgt cctggcgggt tttcagcccc ccggacgagg
     4261 ctaaggccag taaaccccgt gtaattgcct gagcggcttc ctgcttcgtt ttcggcagcg
     4321 cggacggcgt gaccagcgcc cgccggtttt caggcgcgtt cgggtcatgc agccccagcc
     4381 tgccgttcac gatggtctgc caggcatcaa tgcgcggacg gtcggcgcgg tcgtaatacg
     4441 gctggagacg cctgcctgtc agcagctcca tgttcgggat caggaagttc agctccagcc
     4501 gccccttatc ctggtgctca acccatagca cgctgtactg gtctttatcg agtccgggca
     4561 tcagaacccg ttcaaagctc gccatcagct tttcgcgctg cccgggcggt aaatcctttt
     4621 cggcaaagga caggacgccg gatgtgtact tttttgcgta gggcgaggcg tcgataagct
     4681 ccctgacttc ttccggcttc ccctgcagaa cggtggcgcc gtcgcgctgt cggtctttcc
     4741 ccagcagata atccaccgga ccggcgccac cgc
//
