LOCUS       CP123656                5907 bp    DNA     circular BCT 14-JUN-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Reading strain CVM
            N58646 plasmid pN58646-1, complete sequence.
ACCESSION   CP123656
VERSION     CP123656.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN05416439
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Reading
  ORGANISM  Salmonella enterica subsp. enterica serovar Reading
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5907)
  AUTHORS   Ge,B.
  TITLE     Genomic Analysis of Azithromycin-Resistant Salmonella from Food
            Animals and Retail Meats, 2015-2021, United States
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5907)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (22-JUL-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 5907)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-MAR-2023) CVM/OAS, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 24-SEP-2021
            Assembly Method                   :: HGAP v. 4
            Assembly Name                     :: Microbial assembly
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 632x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/20/2023 10:10:26
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,686
            CDSs (total)                      :: 4,567
            Genes (coding)                    :: 4,457
            CDSs (with protein)               :: 4,457
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 110
            CDSs (without protein)            :: 110
            Pseudo Genes (ambiguous residues) :: 0 of 110
            Pseudo Genes (frameshifted)       :: 52 of 110
            Pseudo Genes (incomplete)         :: 74 of 110
            Pseudo Genes (internal stop)      :: 17 of 110
            Pseudo Genes (multiple problems)  :: 30 of 110
            Pseudo Genes (short protein)      :: 1 of 110
            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..5907
                     /organism="Salmonella enterica subsp. enterica serovar
                     Reading"
                     /mol_type="genomic DNA"
                     /strain="CVM N58646"
                     /serovar="Reading"
                     /isolation_source="ground turkey"
                     /sub_species="enterica"
                     /db_xref="taxon:165302"
                     /plasmid="pN58646-1"
                     /geo_loc_name="USA:MN"
                     /collection_date="2015"
                     /collected_by="FDA"
     gene            602..1087
                     /locus_tag="BCP20_23340"
     CDS             602..1087
                     /locus_tag="BCP20_23340"
                     /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="MbeB family mobilization protein"
                     /protein_id="WGN09258.1"
                     /translation="MSEILNLAKGFEEKSKQQAQDTEQSVKREFVRLETSISAELQSSS
                     QSISNAIREQNGRLTGMLRKSVSTAMAWIFFCFALLIGIMGGIIWFQGTIITSRLSEMD
                     SYSQQLANLKAKSGAGVTIYSDDTRRNTYLVVLPKQAHGVETYTSTTDNTVVKYTAK"
                     /name="MbeB family mobilization protein"
     gene            1157..1381
                     /locus_tag="BCP20_23345"
     CDS             1157..1381
                     /locus_tag="BCP20_23345"
                     /inference="COORDINATES: protein motif:HMM:NF016769.2"
                     /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="WGN09262.1"
                     /translation="MEKQLLSALESLQTSYEQQQQAWQDSYSSLQHMFEATSQALTHSD
                     RVCQHLSSQVDSLRAQVESLSRNVSRLMR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            1543..1875
                     /locus_tag="BCP20_23350"
     CDS             1543..1875
                     /locus_tag="BCP20_23350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015873600.1"
                     /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="WGN09259.1"
                     /translation="MSHAIEFIETPMFTRQIKQIATDEELRELQKTLIESPDKGDIIQK
                     TGGLRKVRMATGNQGKSGSARVIYFLATAEVIYLVMAYPKSTKDSLTDAEKAALKTLTQ
                     QLKDEV"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            1877..2161
                     /gene="nadS"
                     /locus_tag="BCP20_23355"
     CDS             1877..2161
                     /gene="nadS"
                     /locus_tag="BCP20_23355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000007431.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NadS family protein"
                     /protein_id="WGN09260.1"
                     /translation="MSFFDELKASLEEAVEIKNGVREPARVTRYELADVKAIRAQLNVS
                     QSEMAKVLGTSLDTIKSWETGRRNPTGLAAKVLATIQANPKFFQELAAH"
                     /name="nadS"
     gene            2355..3278
                     /locus_tag="BCP20_23360"
     CDS             2355..3278
                     /locus_tag="BCP20_23360"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006674370.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WGN09261.1"
                     /translation="MHNAALELFNERLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRAGAAIDWSDRNAPAPTLTITNPDNGHAHLLYALKTSIRTAPDGKMK
                     PLRYAAAVENALRKKLEADAGYSGLICKNPNHGHWKIAVWQPELYTLDWLADFLDLNAA
                     NDKEIVADYGLGRNCTLFDRTRKWAYRAIRQGWPEYDQWLQACYERACVYNLQFAAPLD
                     ENEVSAIAKSIAKWTGKNFSKETFSSYVKKTHSSSIQSLRGRIGGSKSRGGGRYIDDFS
                     ERTLEPWLDMGISRATYYRRKKKSGI"
                     /name="replication initiation protein"
     gene            3268..5046
                     /locus_tag="BCP20_23365"
     CDS             3268..5046
                     /locus_tag="BCP20_23365"
                     /inference="COORDINATES: protein motif:HMM:NF016724.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0003677 - DNA binding [Evidence IEA]; GO_function:
                     GO:0005524 - ATP binding [Evidence IEA]; GO_function:
                     GO:0016787 - hydrolase activity [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="DEAD/DEAH box helicase family protein"
                     /protein_id="WGN09255.1"
                     /translation="MAFEKKDITAKHKLRRPQTEAFGKIREHYEKKELKEVGLILPVGC
                     GKSGLISITPYATESSRVLIIAPGKKIRDQLAKDMKFNEPDNFYNKCEFFDLVDDYPEV
                     CIIEAGGKTNIHDIRSSDIVVSNIQQIAGDENKWLEQLDADFFDLIIVDEAHHNKASTW
                     VKVKEKFPNAKVINYSATPMRSDGQLMSGEIIYSFPVVEAIREGYIKRLHAKMISPSKL
                     VYVDSDGNEITLTNPEDIKRLGEEEASFRRGVLMSDETLSTLVDLSIKELNRLREESGE
                     KRLKIIASALNYGHCIQIKEAFLARNLRADYVHSNEDGAVNDRVFSKLENHELDVIVQS
                     KMLGEGFDHKFLSVAMVGSVFSNLSPFVQFVGRVMRVVKQNSPGDLVNRGVVVFHVGAN
                     IANRWSDFRNFSQADQDFFADLLPEVEDVDFGSDGTSDRDPDETGGSNQLIPVEVTSTD
                     GVTASELDPIGDFQELKKELASLGMTTNEAIEILRRSRLSKQDQRRAGRQAINDLVNHH
                     AGLLINQLGFKPKGRNFNKSQDNYSWVVRELHNRVNEHIGCNSGDRENLSLEQVDEAKS
                     AVPNLAEDIRQEWSNG"
                     /name="DEAD/DEAH box helicase family protein"
     gene            5039..5272
                     /locus_tag="BCP20_23370"
     CDS             5039..5272
                     /locus_tag="BCP20_23370"
                     /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="WGN09256.1"
                     /translation="MAKFKSLIVGAKFEVASRKTTCKHDKKHVITKGEFRLSVKNSTQG
                     ESYYCLSCAKTMVTESQAKLEGLKSELDSLSL"
                     /name="hypothetical protein"
     gene            5505..5831
                     /locus_tag="BCP20_23375"
     CDS             5505..5831
                     /locus_tag="BCP20_23375"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006674374.1"
                     /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="WGN09257.1"
                     /translation="MEKRTKEIKIRLTETEHQRLLDRCDRTHLAEWLRQLGLGEHTSRK
                     RRVPDVAPELLRQVSGIGNNLNQIARRLNQTDSLTPSERASLLVVLTSLDRQLGDLLEQ
                     NRDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          2..1479
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.726"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gccagcgtac tgcgcggcaa ccccgaacat gtgcgcgagc tgatagacgg ctgcgacttt
       61 gcccgcgcct atacctccgg cgtgctgtcg tttcaggagc cggacattgc agatgccgag
      121 aaatcacgcc tgatggacga atgggagcac acgctgctgc ctggcctcga ccgtgaccag
      181 tacgcctgcc tgtgggtgga gcaccgcgac aagggacggc ttgagctgaa ttttgttatc
      241 ccgaacatcg aattacagag cggcaagcgc ctgcaaccct actttgaccg cgccgaccgc
      301 ccccgcgtca acgcatggca gaccctgacc aacgaccggc tggggctgcg cgacccgaac
      361 gacccgactt accgccgccc gctgacgcag gccagcgatc tgccccgcga caaacagcag
      421 gcggcagaga aaatcaccgc cggcctgatg aacctgatgc agcagggtgt gatccgcagc
      481 cggcaggacg tagtgacgca gctggaaagc tacggcctga ccgtggcgcg ggaaacgaaa
      541 agcagcatca gcattgccga tccggacggc ggccgaaata tccggctgaa aggaatgatt
      601 tatgagcgag attttaaatt tggcgaaggg cttcgaggag aaatcgaagc agcaggcgca
      661 ggataccgag cagagcgtga agcgcgagtt cgtgaggctg gagacgtcta tcagcgcgga
      721 actgcaatca agctcgcaga gcatcagcaa cgctatccgc gagcagaacg gcaggctgac
      781 gggcatgctc aggaagtcag tctcaacagc gatggcgtgg atattcttct gcttcgcact
      841 gctgatcggc atcatgggcg ggataatctg gtttcagggc acgatcatca cctcgcgcct
      901 gagcgagatg gacagctaca gccagcagct ggcgaacctg aaagcgaaaa gcggcgcggg
      961 cgtgacgatt tacagcgacg acacgcgccg gaacacctac ctggtggtgc tgccgaagca
     1021 ggcgcacggc gtggaaacct acacgtcgac gaccgacaac accgtggtga aatacacagc
     1081 gaaataaccc ctccagagcg ccctgaaacg ccacagcgcg tttttaacac tgaggacgac
     1141 caaaaccatg accgagatgg aaaaacagct tctgagcgcc ttagagagct tacagacaag
     1201 ctacgagcaa cagcagcagg cgtggcagga cagctacagc agtttgcagc acatgttcga
     1261 ggctacctca caggcgctca cgcacagcga ccgggtgtgt cagcacttga gcagtcaggt
     1321 ggacagcttg cgcgcgcagg tcgagagctt gagcaggaac gtcagccgct tgatgcgctg
     1381 atcaggcagc acgaccgcgc ctacgccgag aagctgcgtg agcagcagcc agagccggag
     1441 ccgcagaaaa aaccgacccg ctactatggc ccctcgatgt gaccgctttt ccggaatcag
     1501 aattaggtgt actatgtact ccattaaaaa caggagacag ccgtgagtca cgcgattgag
     1561 tttatcgaga ccccgatgtt tacccgtcag ataaaacaga tcgccacgga tgaagagctc
     1621 agggagctgc aaaagacgct gattgagtcg ccggacaaag gcgatatcat ccagaaaacc
     1681 ggcgggctgc gaaaagtcag gatggcgacg ggcaatcagg gaaaaagcgg cagtgcgagg
     1741 gtaatttatt ttctggccac agccgaggtg atttatctgg tgatggccta cccgaaaagc
     1801 accaaagaca gcctgacgga cgcggagaaa gccgcgctga agacgctgac ccaacaactg
     1861 aaagacgagg tgtgacatga gtttttttga cgagctgaaa gcatcgctgg aagaagccgt
     1921 tgaaatcaaa aacggcgtca gagagcctgc ccgcgtcacc cgttacgagc tggcagacgt
     1981 gaaggccatc agggcacagc tgaacgtttc acagagcgag atggcgaaag tgctgggaac
     2041 cagcctcgac actatcaaga gctgggaaac cggacgccgt aatccgaccg gactggcggc
     2101 gaaggtgctg gcaaccatcc aggcgaatcc gaaattcttc caggaactgg cggcgcacta
     2161 agccgttgtg acagaaggat tcgacatgcg aggccgttcg cgtgtaattt aacggcaaca
     2221 gaaaaaacaa agccccggaa atcatgctca ttcttggcgg agcgacatga taaccagggc
     2281 caggtacgaa accttgaaag gatattagca catgaaccgt gccagacaac agaccgccat
     2341 aagcgcaggg cgcattgcat aacgctgcac tcgaactctt caacgagcgc ttaccgcaca
     2401 agccgtactt ttcggacgat ctgcattttg gtgtacggat tgccggtaag gaacgcgcca
     2461 ttctggcgaa atatatccag ttcaatcagc ctcatgccat gttctggctg ggattcgacg
     2521 ttgatcgcgc cggtgccgcc atcgactgga gcgaccgcaa cgcgcccgcg cccacgctga
     2581 ccattaccaa ccccgacaac ggacatgcgc acctgctgta tgcgctgaaa acctcgatac
     2641 gcaccgcgcc ggacggaaaa atgaagcctc tgcgctacgc tgccgccgtg gagaacgcgc
     2701 tacgcaaaaa attagaggct gacgcggggt attcaggtct aatctgcaaa aatccgaacc
     2761 acggccactg gaaaattgcc gtgtggcagc cggaactcta cacgctggac tggctggccg
     2821 actttctcga cttaaacgca gcgaatgaca aagaaatcgt cgccgactac ggcttaggcc
     2881 gtaactgcac cctgttcgac agaacccgga agtgggcata tcgcgccatc cgtcagggct
     2941 ggcctgagta cgaccagtgg ctacaagcct gctatgaacg tgcctgcgtt tataacctgc
     3001 aatttgcagc gcctctggat gaaaatgagg ttagtgcgat agctaaaagt attgcgaagt
     3061 ggactggtaa aaacttttca aaagaaacct tttcttctta tgttaagaaa actcactcat
     3121 cttccattca atcattgagg gggcgaattg gaggaagtaa gagtagaggc ggaggaagat
     3181 atatagatga tttcagtgaa agaactctgg aaccatggtt agacatgggg atcagccgag
     3241 ctacctacta cagaaggaag aaaaaaagtg gcatttgaaa aaaaagacat cacagctaaa
     3301 cacaagttaa gaagaccaca gaccgaggca ttcggtaaga taagagaaca ctacgaaaaa
     3361 aaagaattga aagaagttgg gctcatactg ccggttggtt gcgggaagtc tggtcttata
     3421 tcaataactc catatgcaac agaatctagc cgtgttctta taattgcgcc tggtaaaaaa
     3481 ataagagacc agttagctaa agacatgaag tttaatgagc ctgataattt ttacaacaag
     3541 tgcgaatttt ttgatttggt agatgactat ccagaagttt gcataattga ggcaggtggt
     3601 aagactaata tacacgacat taggtcaagt gatattgtcg tttccaatat ccaacaaata
     3661 gctggagatg agaataaatg gcttgagcag ttggatgctg acttctttga tttgattatt
     3721 gttgatgaag cccaccacaa caaggcaagc acatgggtta aggttaaaga aaagttccca
     3781 aatgcgaagg tgataaacta tagcgccact ccaatgagga gtgatggcca gttgatgagc
     3841 ggtgaaatta tatatagttt ccctgtggtt gaagcaatta gggaagggta tattaaaagg
     3901 cttcacgcca agatgattag tccatcaaag ttggtatatg ttgatagtga tggtaatgaa
     3961 ataaccttaa caaaccctga ggatattaaa agattaggtg aggaagaagc atcatttagg
     4021 cgcggcgttc tcatgtctga tgaaacactt agtacattgg tagatctttc tattaaggaa
     4081 ctaaatagac ttcgagaaga gtctggggaa aaaaggttaa aaatcattgc atctgcactg
     4141 aattacggtc attgcattca gataaaagaa gcatttctgg ctagaaacct acgagctgat
     4201 tatgttcact ctaacgaaga tggggctgtt aatgataggg ttttctctaa actagagaat
     4261 catgagctag acgttattgt tcaatcgaaa atgcttggtg aagggtttga ccacaaattt
     4321 ttatctgtag ctatggttgg tagcgttttt tctaatttga gcccatttgt tcagtttgtt
     4381 ggccgagtaa tgcgagtagt aaaacaaaat tcccccggcg atttagttaa cagaggagtt
     4441 gttgttttcc atgttggtgc aaacattgcc aatcggtgga gtgactttag gaatttcagt
     4501 caggccgatc aggacttctt cgctgacttg ttaccagaag ttgaagatgt tgattttggc
     4561 tccgatggca caagtgacag ggatcctgat gagacagggg gtagtaacca gcttatacct
     4621 gtcgaggtta ctagcactga tggtgtaacg gcttccgagt tagatccaat cggagatttc
     4681 caagagctta aaaaagaact ggcatcttta ggtatgacaa ctaatgaggc gatagagatt
     4741 ttgcgtaggt ctaggttgag caaacaagat cagagaagag ctggaagaca ggctattaac
     4801 gatcttgtta atcatcatgc gggcttgctc attaatcaac ttgggttcaa accgaaaggc
     4861 cgaaatttca acaagtctca agataactac tcatgggttg taagagagtt gcataatcga
     4921 gttaacgaac atattgggtg taacagcggt gatagagaaa atcttagttt agagcaggtt
     4981 gatgaagcta aatcagctgt gcctaacctt gcagaagaca tccgacagga atggtctaat
     5041 ggctaaattc aagtctctta ttgttggcgc caagtttgag gttgcctcta ggaaaaccac
     5101 ctgtaaacat gacaaaaagc atgtgattac aaaaggtgag ttcaggctaa gcgtaaagaa
     5161 ttcgacgcaa ggtgaatctt actattgcct ctcctgtgcc aaaacgatgg ttactgaaag
     5221 ccaggccaaa ctagaaggtc tcaaaagcga gctcgattcc ctctcacttt aggtgagacc
     5281 ataacaagcc tatatcagat aacagccctc tctagcagag ggcttttttt ttgcagccag
     5341 tatataatct gacatactgc atcatactct aagccagtac acacagcgtc ccctctatcg
     5401 aggtgcctcc gtgactggtt cagggggctc gccgcccccc gaaacccctg gcatccactg
     5461 cgaaaaattc tcacggtggt gcgaattttc tctcagcgga gcctatggaa aagcgaacga
     5521 aagagatcaa aatccggctc accgaaaccg agcatcagcg actgcttgat cgctgcgacc
     5581 ggactcacct tgcggagtgg ctgcgtcagc taggtctggg tgaacacacc tcacgcaagc
     5641 gccgtgtgcc tgatgtggcg cccgaactgc ttcgacaggt cagcgggatt ggcaacaacc
     5701 tgaaccagat tgcccgccgc ctgaaccaga ctgattccct gacgccttct gaacgtgctt
     5761 cgctgctcgt cgtactgacc agccttgacc gtcagcttgg cgacctgctg gagcagaacc
     5821 gtgatcgtta aaattcactc acgcggtgca ggttccggca gtggtcctgt ggattacctg
     5881 cttggaaaag accgtcagcg cgaacag
//
