LOCUS       CP082708                5559 bp    DNA     circular BCT 09-SEP-2021
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain CVM
            N17S380 plasmid pN17S380-2, complete sequence.
ACCESSION   CP082708
VERSION     CP082708.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN10132843
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 5559)
  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  JOURNAL   Unpublished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 5559)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (28-SEP-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 5559)
  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-MAR-2019
            Assembly Method :: SMRTLink Microbial Assembly v. SMRTLink9.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 798x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/01/2021 10:39:38
            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)                     :: 4,929
            CDSs (total)                      :: 4,806
            Genes (coding)                    :: 4,703
            CDSs (with protein)               :: 4,703
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 103
            CDSs (without protein)            :: 103
            Pseudo Genes (ambiguous residues) :: 0 of 103
            Pseudo Genes (frameshifted)       :: 35 of 103
            Pseudo Genes (incomplete)         :: 69 of 103
            Pseudo Genes (internal stop)      :: 19 of 103
            Pseudo Genes (multiple problems)  :: 18 of 103
            CRISPR Arrays                     :: 3
            ##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..5559
                     /organism="Salmonella enterica subsp. enterica serovar
                     4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="CVM N17S380"
                     /serovar="4,[5],12:i:-"
                     /isolation_source="ground turkey"
                     /sub_species="enterica"
                     /db_xref="taxon:440524"
                     /plasmid="pN17S380-2"
                     /geo_loc_name="USA:TN"
                     /collection_date="2017"
                     /collected_by="FDA"
     gene            1..399
                     /locus_tag="D7E94_024620"
     CDS             1..399
                     /locus_tag="D7E94_024620"
                     /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="UAH04176.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKEIKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            complement(660..1679)
                     /locus_tag="D7E94_024625"
     CDS             complement(660..1679)
                     /locus_tag="D7E94_024625"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221104.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="UAH04177.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREDAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDNSGEWLTKKQIIKC"
                     /name="replication initiation protein"
     gene            complement(2480..2710)
                     /locus_tag="D7E94_024630"
     CDS             complement(2480..2710)
                     /locus_tag="D7E94_024630"
                     /inference="COORDINATES: protein motif:HMM:NF013211.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAH04179.1"
                     /translation="MSGLVKGFRTGDWNEAFISGEKIAVGKVASVMVTVAFSAMAVNPI
                     GILGFAVIMAVTSALITDERLKQLNSFINGI"
                     /name="hypothetical protein"
     gene            complement(2694..3701)
                     /locus_tag="D7E94_024635"
     CDS             complement(2694..3701)
                     /locus_tag="D7E94_024635"
                     /inference="COORDINATES: protein motif:HMM:NF013211.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAH04178.1"
                     /translation="MSGGDGRGPGNTGLGHNGGKPSGNVNGSSGHGGPSSGGGYHYNPG
                     KGPASTVGPDGEVHINITGGMEKDPPGKHHGNGGSGNGHGAGNHNSNSGGNGKTTSIPG
                     WSPDSGKPGRYLPTNKDKLIKGLIQSIDDHSGTYTIHYTGGAVATVTVPNGDVNKMNVH
                     YNIGSGPSSGNKLTRDTIKSFLEFKAENEANAVNDAISKVNDFYKELASKYGDKLEKEA
                     KALADEAKGKKIRNANEAIKAFDRYKDVLNKKFSVSDREAIAKALESLNKDQMAKQLKI
                     FGKAFGVVGEAIQWGGFISGLVKGFRTGDWNEAFISGEKIAVGKVAGGIYQWLS"
                     /name="hypothetical protein"
     gene            complement(3921..4454)
                     /locus_tag="D7E94_024640"
     CDS             complement(3921..4454)
                     /locus_tag="D7E94_024640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAH04174.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQNLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTMLDRNYNATAAVYQKVVILED
                     KLPEKPVTGKNRKN"
                     /name="hypothetical protein"
     gene            complement(4457..5383)
                     /locus_tag="D7E94_024645"
     CDS             complement(4457..5383)
                     /locus_tag="D7E94_024645"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="UAH04175.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIEGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     PTQQKEQLRELRKRWEVKHNEHMRKNGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIMEWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQDRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     Typing          complement(905..1679)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.907"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(4461..5383)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgcgcatca gcaacatcga atggctgaag aaacggatcg gattcatcag gaagctcgga
       61 gaacagaccg cacgacagag acagattatt gacctgctcg acaacgaagc aggactcaca
      121 gaacaggaac gcaaactcct ccacgtactg gcaacagcgg aaaaaaacga cttacaggca
      181 caggagagcg aacgaaaaca ggcggtccaa aaacgaatcg agggaaaaaa acaacgacga
      241 gaacgcaatc accgactctt tctcgcggct gggctactga tcgaagcagg actggtagac
      301 acaaaaacag gcgagctatg ctataaaaaa gacaggatat tacaggcact taaggaaatt
      361 aagtacgatc tggagacatc cccaaaccca gacgcgtaag tgcctccatc cgtgttccgg
      421 ttccctggtg cttcctcgct cattcgctcg ctacgctcgg tcatgagact gcggcgagca
      481 cgaccacctc aatcatgcgg taagccgcac cattgctggg ctgagaggag aaaaccgccg
      541 gaaagcccgc tgctcaaaaa gacgccgaaa ggcgctgtta tctgatatag gcttgttcat
      601 gtccgcgaat ttaacatccc attaacaaaa aacggggggt agtgttgctt ctttgttaac
      661 taacatttaa ttatttgttt cttggttagc cattctccag aattatccat ccagcgtcga
      721 atagtccggc tgctaacacc aaccgccact gcaatatctt ccgttgacgc tcccaagata
      781 tacatatcaa gcgccctacg acgtttgtcg tcgttagcag tccaccgaac agcggcgctt
      841 tttttccctt tgtccgactg attttctgac gaattggcct tcccgccctt gcgaccgcgt
      901 gctgcctgaa tttctggcgt gtgcgtatca gccacatact gtgcgaaagt ttccggcgtg
      961 aagttcctgt gcgtgtattt cgcaatgctc ttgccaatag cccgacattc agccagtgaa
     1021 agcggaacgg gaagcgatgc attgtacatt tcgacacgct ggatcaccgc ttcaagccac
     1081 tgtgagaacg ctggccagcc ctgacgaatc gccctgtaag cccatttgcg cgtcatttcg
     1141 aacaggtggc agtttcgccc catcccgtaa tgtttatcga tgctacgacg ctctgaggcg
     1201 ctcaaatcga gataatctgc cagttcatcg agggtatagg cgtcctcgcg ccactccatc
     1261 acctgccatt ccaggtggaa cggatttttg caaatcaggc cgctgtagtt cacatcagca
     1321 caaagtttct cacacagcga acgttcaacc gctgcggcat atttcagcgc cttaaccgag
     1381 gcatcaggcg cggttctcac ggcgatgttg agtgcgtaga gcaggtgagc gtgtccgttc
     1441 acaggatttt taacggtgat gttcggcgcg ggggcgttcc ggtcgctcca gtcaatcgca
     1501 gccccctcgc ggtcaacgtc aaaaaccagc cagaactgcg catgaggctg gttctgctgg
     1561 atgtaccgcg caagaagcgc acgccctttg ccggagatgc gaaggccgaa agcgagatca
     1621 tccgtgtgat aggggcggtg gggtaaattt tcttcgaagt attgaagcgc ggcgctcatg
     1681 tgttacgatt ccttccaggt tatcgaccga cctcgcccct gtattctcgt gacaatcttg
     1741 gcggagagac acgaatttca ggggcgtttg tttttcagtc gcttacacta cccccaacaa
     1801 caaaacctgt cgagccttcc cgcaaaaccg atccatttac cataactccc gttgtacgta
     1861 ccccttaaaa cgccctcagt cgctttctgg cgcaaaaaac gcaaaaagac aaggaaacac
     1921 caggccaaac cagaaaaatg cgtcagaatc actttcaggg cgttgcataa ctatgcacga
     1981 aagcgattcg caaacagttt cgaccgttca aaagggcgaa cgagtcaaaa aagtaacttt
     2041 tgtgataact acttctagat ttatggataa agtaaggcaa tattataaac atttaactaa
     2101 cgaggatttt ataaatgaaa aaaatagata tggaattcta tttaaggaat tttatccttg
     2161 ccttatcctt ttacatttta tcttttatca tcgcaagttt gaatctaagc ccaacaagta
     2221 tagaattatt tatatttata cttatatctc tttttggatc gtccacatac cctttttgtc
     2281 tattactaat aaataagcaa gcacccttac taacaaaaac aacttttaac ttcgttaact
     2341 ggggttttat aatatgcatt atattatcac tacctccatt tggattgatt tttacagtct
     2401 attactttat aaccaacaaa aagcgataga aaaacaaaat aaaggtcata ccatatcaaa
     2461 cggtacgacc ttttgtttat taaatgccgt taataaagct gtttagttgt ttcagccttt
     2521 catctgtaat taaggcacta gtcactgcca taattactgc aaaccctaaa ataccaatag
     2581 gatttactgc catagcacta aatgccactg taaccataac agatgctacc ttgccgactg
     2641 cgattttttc cccgcttata aaagcctcat tccagtcacc agttctgaat cctttaacta
     2701 agccactgat aaatcccccc tgctaccttg ccgactgcga ttttttcccc gcttataaaa
     2761 gcctcattcc agtcaccagt tctgaatcct ttaactaagc cactgataaa tcccccccac
     2821 tgaatagcct cacctacgac accaaaggcc ttaccaaaaa tttttaactg tttagccatt
     2881 tgatctttat taagagactc cagtgctttt gcaatcgctt ctcggtcgga tacgctgaat
     2941 ttcttattaa gcacatcctt gtacctatca aaggctttaa tcgcctcatt agcattgcga
     3001 atttttttcc ctttagcttc atcggctagt gccttggctt ctttctccaa cttatcgccg
     3061 tattttgatg ctaactcttt ataaaagtca ttaactttgc ttattgcatc atttacagca
     3121 ttagcttcat tttctgcctt gaattctaaa aagcttttta tagtatcacg agtcagttta
     3181 ttacctgatg acggcccact accgatatta tagtgaacat tcattttatt cacatcaccg
     3241 tttggtacag ttactgtagc tactgcacca ccagtataat ggatagtgta cgttccagaa
     3301 tggtcatcta ttgactgaat aagtccctta attaacttat ctttatttgt cggtaaatat
     3361 ctgccaggtt tcccagagtc agggctccat ccaggaatag acgttgtttt tccattgccg
     3421 cctgaattgc tgttatgatt tccagcaccg tgaccattac ctgagccacc attaccgtga
     3481 tgttttcctg gaggatcttt ttccatacca ccggtaatgt tgatatgcac ctccccgtca
     3541 ggacctacag tgcttgcagg accttttccc ggattgtaat gatacccacc gccagatgat
     3601 ggtcctccat gtccagatga gccattcacg tttccactgg gtttaccacc gttatgtcca
     3661 agccctgtat taccagggcc acgaccatct ccaccactca taaaaattcc ctcttttaat
     3721 cgttaaaaca attaattaca tagttaatac tgtacataaa accactggtt ttatgtacag
     3781 atcaaaaagt actcgccatt attttttctg tcaagtcagg ggggatattt tttggcagtt
     3841 cggaggaatc actcatgaaa acggtgaacg gaacgcgaaa tcctttcgct gtccgtgagg
     3901 cgttggacaa gcgaagcgcg tcagtttttc cggttcttac ccgtgacagg tttttccggc
     3961 agtttatctt ccagtatcac aactttctga tacaccgccg ctgtggcgtt gtagttcctg
     4021 tcgagcattg ttttcattcc ccatccgagc acacagaaca taactagaaa agccactgac
     4081 accccaccca gccatttcca gctataccct ttaagggtgt tgtattcctg cacgatattg
     4141 ctgtgaattg tcgcaatatc cctgttcagg gcatccgcgt ttgccttcat gtttgcgact
     4201 gactcttcca gccgctgaaa atcctggctg atgcgctcac ctatcagccc tgctacgtcc
     4261 agattctgca cctcatttct gacttcatcc ctgacctgtt ttgccacacc gtcagaaata
     4321 tcccgatatc cgcgaagtgt ttcccttgcc acagccagag aatcagcaac agctttctgt
     4381 tgctccattg cggtatgttg caaatgctcc accgataaca ggagcgtgag taatttttct
     4441 tctgtgctgg ccatgttcag aatcccatag aaaatccacg tgacggtgat ttaacccgtt
     4501 caggttcagt tcggtcctgt ctgctcactc tgtctctcat gtcaaagcca tgctcccgcg
     4561 caacatcatg ttgcagcctt ctgaccagtt catgttgctt aaccggagtg tccagccatt
     4621 ccatgatgtc atgcccgacc gttcgcgcct gttcaagatg gcgggaatag tccggttcag
     4681 accgtttttg catgatgtca tgacgctggg catcatcaag ccgtccggca gcttcaaaac
     4741 ccagatgcac ttcgggacgt cgttcaatgc cctgttcttt cagcgtccga cagtcaatga
     4801 agcccctttc aaagccattt tttctcatat gttcgttgtg cttcacctcc cagcgttttc
     4861 gcaattcccg caactgctct ttttgctgag tgggagtcag gcttcctgaa tcctttttcg
     4921 cacctccccg ctcgggatac ctggcgttat agcgccggaa atactgttcc ggtgtacgtt
     4981 caatgccatc attcacacgc tgactcatca tgatatgcgc atgaggctgt tcgcctccct
     5041 caatgctcgc tttcggattg tgaatggcaa aactccatgc atgccgttcg ccagcttcct
     5101 gacgtacaaa atcctgcacc agttcaaggc gctgttccgg tgtcagttca cggggcagcg
     5161 ctatctccag ttcccgataa gtcgaaccgt ttgcacgttc aaactggtca gccgcctgcc
     5221 agaaatggga gggattatct cgcgcccatt ccggcatgtt tccgtgtgcg gaatattcca
     5281 aatcttgacg gtcgcggtat ttctctttgc gctcgatgta atcggcatgg tttgcagcct
     5341 gtcccttgcc accaaactta acgctgaggt gataggtcgc cacggtttca gccctccgca
     5401 ggagcgcact gtttctcgac gaaggagaga aacatataag tgcgcttcct tctaatttta
     5461 cgaattagca cggaagatac ccccagcacc cgccgaccgc aagcgatata ctgcacgacc
     5521 acaacacacc gcaaaaaaac accagggagc accacgaac
//
