LOCUS       CP082528                5310 bp    DNA     circular BCT 13-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Hadar strain CVM
            N18S2154 plasmid pN18S2154-2, complete sequence.
ACCESSION   CP082528
VERSION     CP082528.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN12587116
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Hadar
  ORGANISM  Salmonella enterica subsp. enterica serovar Hadar
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5310)
  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 5310)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (16-AUG-2019) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 5310)
  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                   :: 446x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 08/30/2021 17:06:38
            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)                     :: 4,689
            CDSs (total)                      :: 4,564
            Genes (coding)                    :: 4,467
            CDSs (with protein)               :: 4,467
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 19
            Pseudo Genes (total)              :: 97
            CDSs (without protein)            :: 97
            Pseudo Genes (ambiguous residues) :: 0 of 97
            Pseudo Genes (frameshifted)       :: 44 of 97
            Pseudo Genes (incomplete)         :: 63 of 97
            Pseudo Genes (internal stop)      :: 18 of 97
            Pseudo Genes (multiple problems)  :: 26 of 97
            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..5310
                     /organism="Salmonella enterica subsp. enterica serovar
                     Hadar"
                     /mol_type="genomic DNA"
                     /strain="CVM N18S2154"
                     /serovar="Hadar"
                     /isolation_source="ground turkey"
                     /sub_species="enterica"
                     /db_xref="taxon:149385"
                     /plasmid="pN18S2154-2"
                     /geo_loc_name="USA:NM"
                     /collection_date="2018"
                     /collected_by="FDA"
     gene            227..508
                     /locus_tag="FWW82_000005"
                     /pseudo=""
     CDS             227..508
                     /locus_tag="FWW82_000005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /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="hypothetical protein"
                     /name="hypothetical protein"
     gene            506..601
                     /locus_tag="FWW82_000010"
                     /pseudo=""
     CDS             506..601
                     /locus_tag="FWW82_000010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014605854.1"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus and C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="amino acid ABC transporter substrate-binding
                     protein"
                     /name="amino acid ABC transporter substrate-binding
                     protein"
     gene            747..1562
                     /locus_tag="FWW82_000015"
     CDS             747..1562
                     /locus_tag="FWW82_000015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032492145.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(3')-Ia"
                     /protein_id="UAI66306.1"
                     /translation="MSHIQRETSCSRQRLNSNLDADLYGYKWARDNVGQSGATIYRLYG
                     KPDAPELFLKHGKGSVANDVTDEMVRLNWLTEFMPLPTIKHFIRTPDDAWLLTTAIPGK
                     TAFQVLEEYPDSGENIVDALAAFLRRLHSIPVCNCPFNSDRVFRLAQAQSRMNNGLVDA
                     SDFDDERNGWPVEQVWKEMHKLLPFSPDSVVTHGDFSLDNLIFDEGKLIGCIDVGRVGI
                     ADRYQDLAILWNCLGEFSPSLQKRLFQKYGIDNPDMNKLQFHLMLDEFF"
                     /name="aminoglycoside O-phosphotransferase APH(3')-Ia"
     gene            complement(1572..1844)
                     /locus_tag="FWW82_000020"
                     /pseudo=""
     CDS             complement(1572..1844)
                     /locus_tag="FWW82_000020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_021138877.1"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus and C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            2761..3006
                     /locus_tag="FWW82_000025"
     CDS             2761..3006
                     /locus_tag="FWW82_000025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001751880.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAI66308.1"
                     /translation="MSEEAEERLNWHFLLTHLCGISHRTWRTFHTIRTDAEWLSQYTLR
                     YRYVTGSGLRPDTPKVNGLTRPGGLVCSRHPLTDKL"
                     /name="hypothetical protein"
     gene            complement(3029..3220)
                     /locus_tag="FWW82_000030"
     CDS             complement(3029..3220)
                     /locus_tag="FWW82_000030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="UAI66303.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3285..3608
                     /locus_tag="FWW82_000035"
     CDS             3285..3608
                     /locus_tag="FWW82_000035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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="UAI66307.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3550..4308
                     /locus_tag="FWW82_000040"
                     /pseudo=""
     CDS             3550..4308
                     /locus_tag="FWW82_000040"
                     /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            4286..4816
                     /locus_tag="FWW82_000045"
     CDS             4286..4816
                     /locus_tag="FWW82_000045"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /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="UAI66304.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            4823..5056
                     /locus_tag="FWW82_000050"
     CDS             4823..5056
                     /locus_tag="FWW82_000050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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="UAI66305.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     ARG             748..1559
                     /name="aph(3')-Ia"
                     /gene="aph(3')-Ia"
                     /gene_name="aminoglycoside O-phosphotransferase APH(3')-Ia"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          2854..2935
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          2210..2397
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          3599..5160
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgccgtgatc gcaccgaacg cgttttggcg gtgcgtacaa tgcgacgtta tggtaaatgg
       61 agcggatttt caggaaggag tgatactaac aactcgaaca ctgtgcaaat aatgattttt
      121 ttaaaatatc ggtaacgata ataaattatt tcgttttacg ccggtaataa atataatgta
      181 gtttcagtat ataaaaaaat atatgaggtg tcttgtggga gctttcatga atcttcaaca
      241 acgtataaat aaactaccac aattatcatc cagtttttca tttggaaaag atattgataa
      301 tattcattca tttatcttta acgaaacttc taaagataaa attgaagatt tactaagaaa
      361 atgggtgtca ggcaatcagc cctgtgtatt tggtaaattg gcaagcaaga aaattaaagg
      421 gcttgatttc catttatcta ttgtaaatag cccccaacta tataatgatg atggtcattt
      481 gtttgatttt ttgcgtaatg aaagagttca tgccatgttc ctcgactacg aagcggccaa
      541 agattatgcg acccgctcca ggctggtcac ggcggcgaat atcccttctt tcggagcgcc
      601 agaatgatgt tggtctggcc ggattttcat atggcgggaa ccacgttgtg tctcaaaatc
      661 tctgatgtta cattgcacaa gataaaaata tatcatcatg aacaataaaa ctgtctgctt
      721 acataaacag taatacaagg ggtgttatga gccatattca acgggaaacg tcttgctcga
      781 ggcagcgatt aaattccaac ctggatgctg atttatatgg gtataaatgg gctcgcgata
      841 atgtcgggca atcaggtgcg acaatctatc gattgtatgg gaagcccgat gcgccagagt
      901 tgtttctgaa acatggcaaa ggtagcgttg ccaatgatgt tacagatgag atggtcagac
      961 taaactggct gacggaattt atgcctcttc cgaccatcaa gcattttatc cgtactcctg
     1021 atgatgcatg gttactcacc actgcgatcc ccgggaaaac agcattccag gtattagaag
     1081 aatatcctga ttcaggtgaa aatattgttg atgcgctggc agcgttcctg cgccggttgc
     1141 attcgattcc tgtttgtaat tgtcctttta acagcgatcg cgtatttcgt ctcgctcagg
     1201 cgcaatcacg aatgaataac ggtttggttg atgcgagtga ttttgatgat gagcgtaatg
     1261 gctggcctgt tgaacaagtc tggaaagaaa tgcataagct tttgccattc tcaccggatt
     1321 cagtcgtcac tcatggtgat ttctcacttg ataatcttat ttttgacgag gggaaattaa
     1381 taggttgtat tgatgttgga cgagtcggaa tcgcagaccg ataccaggat cttgccattc
     1441 tatggaactg cctcggtgaa ttttctcctt cattacagaa acggcttttt caaaaatatg
     1501 gtattgataa tcctgatatg aataaattgc agtttcattt gatgctcgat gagtttttct
     1561 gatagttagt ctttaatgaa tgcggttggc gcatcggcgg gcaccttgcg cgcgctgtcg
     1621 ctgttcatgc cgcgcagcat gtcgatggca tcgagcacac ccttggcggc gggcgcagcc
     1681 cgcaatttga gcacgcccag gaactgcggc gcgtagcggc gtagcgtggc atagctttca
     1741 ccgatgtggt gcaggaaatc aaagtcggca ggccgcgcca atgtttgcgc ttcggtgacg
     1801 ctggcggcga aggtgtccca gggcataacg gcctcgagga ttgcccccca gcctccatcg
     1861 ataccgtgcc aaatgcacgt aaaaaacggg agcgtttctg gtgtcggaat gtaaccaagg
     1921 gggtcagagg cgcgctaaaa cgctctcagg ggagtcaaat agagacgttt gtaacaaaaa
     1981 gatcaaagga tcctcttgag atcctttttt tctgcgcgta atctgctgcc tgtaaacgaa
     2041 aaaaccgcct tgcagggcgg tttgatcgaa ggttaagtca gcttgcagac tgcttaacca
     2101 ggtaactgtc ttatgcgaga cgagtcacca aaattgttct tctagtgtag ccgcactccg
     2161 gcagccactt caagtactct ctaaatatct cgcacatgac ttttaccaat ggctgctgcc
     2221 agtggcgctt tgtggtgtct tttccgggtt ggacccaaga gaacagttac cggagaaggc
     2281 gcagcagtcg ggctgaacgg ggggttcctg catacagccc agcccggagc gaactgccta
     2341 agtcgccccg agataccaga agacgtgagc tatgagaaag cgccacgtgt cccgtaaggg
     2401 agaaaggcgg aaaaggtatc cggtaatcga tatggcggga acgtgggggc gcaggaggga
     2461 gcgattcacc ggaaacggtg atgatcttta agccacgtcg ggtttcgcca ccgctggcgg
     2521 atttcatggt tgagccgcaa ggctcccaca gatgcaccga aaaagtgtct gttttgtgaa
     2581 gtccgtcagg ggggcggagc ctatggaaaa agcgcctccg gcgcggcctt tcccggggtt
     2641 tcgttttttg cgcacatgtt ctttcctggt ttatccccgg gttctgtgga taacagggtt
     2701 agcgtttttg agaaaggaga gtccgctcgc cgcagccgaa cgaccgagcg tagcgagtca
     2761 gtgagcgagg aagcggaaga gcgcctgaac tggcattttc tccttacgca tctgtgcggc
     2821 atttcacacc ggacatggcg cacttttcat acaatccgca ctgatgccga atggttaagc
     2881 cagtatacac tccgctatcg ctacgtgact gggtcagggc ttcgccccga caccccaaag
     2941 gtcaacggcc tgacgcgccc tggcgggctt gtctgctccc ggcatccgct cacagacaag
     3001 ctgtgaccgt ctccgggagc tgcatgtgtc agcggttttc accgtcatcc ccgaagcgtg
     3061 cgaggcaact gcggtaaagc tcatcggcgt ggtcgtgaag cgattcacag atgtctgcct
     3121 gttcatccgc gtccagttcg ttgagcttct ccagcagcgt taatgtctgg cctctgatga
     3181 agcgggccat gttaagggcg gttttttcct gtttggtcac tgatgcctcc gtgtaagggg
     3241 gggttctgtt catgggggta atgataccga tgaaacgcga gaggatgctc acgatacggg
     3301 ttactgatga tgaacatgcc cggttactgg aacgctgtga gggtaaacaa ctggcggtat
     3361 ggatgcggcg ggtctgcctg ggtgagccgg ttgcccgttc cgggaagctg ccgacactgg
     3421 caccgccgtt actgcgtcag ctggccgcca tcgggaataa ccttaaccag acagcgagga
     3481 aggtgaacag cgggcagtgg tcttccggtg accgggttca ggtggtggcc gcactgatgg
     3541 ccatcgggga tgagctgcgc cggctgcgtc tggcggtcag ggaacagggg gcgcgggatg
     3601 atagttaagt ttcatgccag gggaaaaggt ggtggcagtg gtccggttga ttacctgctg
     3661 ggaagggagc gtaaccggga aggggcaacg gtgcttcagg ggaatccgga agaggtccgg
     3721 gaactcatcg atgccacgcc atttgcgaag aaatacacgt caggtgttct gtcgttcgcg
     3781 gagaaggagc tgccgcctgg agggcgtgaa aaagtgatgg cgagctttga gcgtgtactg
     3841 atgcccggtc tcgagaaaaa tcagtacagc atcctgtggg tggagcacca ggacaaggga
     3901 cggcttgagc tgaattttgt cattccgaac atggagctac agaccggaaa acgcctccag
     3961 ccgtactacg accgggcaga caggccgaga attgatgcct ggcagacgct ggtgaatcac
     4021 cattacggtc tgcatgaccc caacgccccg gagaaccgcc ggacgctgac ccttcctgat
     4081 aacctgccgg aaacgaaaca ggcgcttgct gagggcgtca cacgcgggat agacgcgctt
     4141 taccatgccg gagagataaa aggccgtcag gatgtgattc aggcgctcac agaggcgggg
     4201 cttgaagtgg tcagggtgac gcgaagcagt atcagcattg cagacccgaa cggcgggagg
     4261 aatatcagac tgaaaggagc gttttatgag caatctttta cagacgggcg cggagttcga
     4321 gaaaaagctg aaagagagag ccgaatctac agagaaaatg ctgaacgacg agttcaggaa
     4381 gctcgaagaa tctgtaaaca gggaactgac ctcaaacgaa tctttaatca ggaacgctat
     4441 caacgaccat acaacagccc tgaaagaact gctggagagg tatcagaaaa cgaccgtcga
     4501 tacgatggac gcgcactgga aaaccgtact gaaaatgagc gtgaaacgct ggctgtggct
     4561 gattatcgtc tcagtactga tgtttgccac gaccgggagt ctgctgtggt accagggcat
     4621 gaagataaac gcgaatatga atattctccg cgagcagaaa gagagtctgg agaagctgaa
     4681 cgcgaagaca tggggcgtgc gttatcacga ggacagcaac ggacgttttc tggtgttgcc
     4741 gaaggggatg aaagccgaaa cgaactggac gaaggacaac ggcaaactga acgcagtgag
     4801 actggtgcag gagtgacaga gcatgacgga gctggaaaga catttgctga acgcattaga
     4861 gcaactgcaa caggactata tgcagcggct gaacgaatgg gagaacgcct tcgtggaatt
     4921 gcagaaaatg ttttcgctta cgcaacggga caacgcgatg ctgaacgggc gagtcatgca
     4981 gttgagtcag caggtgcagc acttgagcga gcggacagaa cgcttgagcc agttatacag
     5041 cgagaacagg agataaggga tgaacggctg atgcaggaac gcgaacatga gttatctctg
     5101 gagcgggagc gtcagccgga aatccaggag cggacactgg atggcccttc gctgggatgg
     5161 tgaaaccatg aaaaatgacg tgttcagtgg attaaggcgg gctaatgtgg cctgtagcat
     5221 ctggttgcat aggtattcat gcggttaaaa tttatcaggt gcgatcgcgg cagtttttcg
     5281 ggtggtttgt tgccattttt acctgtctgc
//
