LOCUS       NZ_CP130080             4085 bp    DNA     linear   CON 30-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Schwarzengrund strain
            SEWLSH-25 plasmid unnamed3.
ACCESSION   NZ_CP130080
VERSION     NZ_CP130080.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35361205
            Assembly: GCF_030505755.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Schwarzengrund
  ORGANISM  Salmonella enterica subsp. enterica serovar Schwarzengrund
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4085)
  AUTHORS   Sopovski,D., Commichaux,S., Zhao,S., Grim,C.J., Foley,S.L. and
            Khajanchi,B.K.
  TITLE     Complete genome sequences of 17 Salmonella enterica serovar
            Schwarzengrund strains carrying IncFIB-IncFIC (IncFII) fusion
            plasmid
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4085)
  AUTHORS   Sopovski,D., Commichaux,S., Zhao,S., Grim,C.J., Foley,S.L. and
            Khajanchi,B.K.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-JUN-2023) Office of Applied Research and Safety
            Assessment, CFSAN, U.S. Food and Drug Administration, 8301 Muirkirk
            Rd MOD1, Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Hybrid assembly using Unicyler v. not specified
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 455.0x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/30/2023 12:12:39
            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)                     :: 4,982
            CDSs (total)                      :: 4,860
            Genes (coding)                    :: 4,685
            CDSs (with protein)               :: 4,685
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 175
            CDSs (without protein)            :: 175
            Pseudo Genes (ambiguous residues) :: 0 of 175
            Pseudo Genes (frameshifted)       :: 93 of 175
            Pseudo Genes (incomplete)         :: 108 of 175
            Pseudo Genes (internal stop)      :: 32 of 175
            Pseudo Genes (multiple problems)  :: 51 of 175
            Pseudo Genes (short protein)      :: 1 of 175
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP130080.1.
            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..4085
                     /organism="Salmonella enterica subsp. enterica serovar
                     Schwarzengrund"
                     /mol_type="genomic DNA"
                     /strain="SEWLSH-25"
                     /serovar="Schwarzengrund"
                     /isolation_source="stool"
                     /sub_species="enterica"
                     /db_xref="taxon:340190"
                     /plasmid="unnamed3"
                     /geo_loc_name="USA"
                     /lat_lon="37.0902 N 95.7129 W"
                     /collection_date="2013"
                     /collected_by="Wisconsin State Laboratory of Hygiene"
     gene            247..1056
                     /gene="cdtB"
                     /locus_tag="QPJ64_RS24855"
                     /old_locus_tag="QPJ64_24855"
     ARG             248..1053
                     /name="cdtB"
                     /gene="cdtB"
                     /gene_name="cytolethal distending toxin S-CDT"
                     /tool="amrfinderplus"
                     /drug_class="nan"
                     /identity="100.0"
                     /coverage="100.0"
     gene            1129..1506
                     /locus_tag="QPJ64_RS24860"
                     /old_locus_tag="QPJ64_24860"
     CDS             1129..1506
                     /locus_tag="QPJ64_RS24860"
                     /old_locus_tag="QPJ64_24860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001277616.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF1353 domain-containing protein"
                     /protein_id="WP_001277616.1"
                     /translation="MSCFTSPAIMEMLGHYKWRVYEPFRFYLSEDKNDVIEVPVGFVTD
                     LATVPRIFWSLLPPDGEYAKAAIIHDYLYHYPLRNRKESDLIFLDGMKVLGVPKWKRII
                     MYLAVRIFGWKYYHSHTIQHN"
                     /name="DUF1353 domain-containing protein"
     gene            complement(1654..2196)
                     /locus_tag="QPJ64_RS24865"
                     /old_locus_tag="QPJ64_24865"
     CDS             complement(1654..2196)
                     /locus_tag="QPJ64_RS24865"
                     /old_locus_tag="QPJ64_24865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012016429.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="glycosyl hydrolase 108 family protein"
                     /protein_id="WP_000158843.1"
                     /translation="MTKDEIFAAILSREGGYVDHPDDRGGPTHWGITLTTARANGYMGD
                     MRNLTRNQALKILEADYWYGPRLDQVAIISHSIAAELCDTGVNMGPSIPIKYFQRWLNV
                     FNDQQKIYPDLIADGQIGPRTLSALTFFLSHRRDEGEMILIRALNCSQGQRYLELAEKR
                     QANESFVYGWIKERVRL"
                     /name="glycosyl hydrolase 108 family protein"
     gene            complement(2389..3117)
                     /gene="pltA"
                     /locus_tag="QPJ64_RS24870"
                     /old_locus_tag="QPJ64_24870"
     CDS             complement(2389..3117)
                     /gene="pltA"
                     /locus_tag="QPJ64_RS24870"
                     /old_locus_tag="QPJ64_24870"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001766395.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="typhoid-like toxin S-CDT ADP-ribosylating subunit
                     PltA"
                     /protein_id="WP_000733630.1"
                     /translation="MKKLILLTLSIVSFNNYAVDFVYRVDSTPPDVIFRDGFSLLGYNR
                     NFQQFISGRSCSGGSSDSRYIATTSSVNQTYAIARAYYSRSTFKGNLYRYQIRADNNFY
                     SLLPSITYLETQGGHFNAYEKTMMRLQREYVSTLSILPENIQKAVALVYDSATGLVKDG
                     VSTMNSSYLGLSTTSNPGVIPFLPEPQTYTQQRIDAFGPLISSCFSIGSVCQSHRGQRA
                     DVYNMSFYDARPVIELILSK"
                     /name="pltA"
     gene            complement(3134..3547)
                     /gene="pltB"
                     /locus_tag="QPJ64_RS24875"
                     /old_locus_tag="QPJ64_24875"
     CDS             complement(3134..3547)
                     /gene="pltB"
                     /locus_tag="QPJ64_RS24875"
                     /old_locus_tag="QPJ64_24875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000281950.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="typhoid-like toxin S-CDT binding subunit PltB"
                     /protein_id="WP_000275700.1"
                     /translation="MYINKFVPVYTLLILLYSFNASAEWTGDKTNAYYSDEVISEIHVG
                     QIDTSPYFCIKTVKANGSGTPVVACAVSKQSIWAPSFKELLDQARYFYSTGQSVRIHVQ
                     KNIWTYPLFVNTFSANALVGLSSCSATQCFGPK"
                     /name="pltB"
ORIGIN
        1 tctatagttg tctctttggt attaacaata attaattgat tgtactgaat aaactatcat
       61 tttacctctg taatagacat ctattttagt tttattgacg ttagactatg tatcttacta
      121 tctgcacaag acatagaacc agaaacaagt caggcattgc cagaataaaa tcaacgtcat
      181 gaaacaatgg gttatgaaca catatatcat tcagataaag aagtaataat cgggagagta
      241 gatatcatga aaaaacctgt ttttttcctt ctgaccatga tcatctgcag ctatatttct
      301 tttgcctgcg ctaatatcag tgactacaaa gttatgacct ggaatcttca gggctcttca
      361 gcatctacag aaagtaaatg gaatgtcaat gtcagacagc ttttaagtgg tactgccggt
      421 gtggatattc ttatggtaca ggaggccggt gctgttccca cctcagcggt tcctaccgga
      481 cgacatattc agccttttgg agtgggtatt cccattgatg aatacacctg gaatctcgga
      541 accaccagcc gtcaggatat aagatatatc taccactcgg ctattgatgt tggagcgcgc
      601 cgtgttaatc tggcaatagt ttccagacaa agagcggata atgtttatgt cttgcgtccg
      661 acaactgtcg catctcgccc cgtcattggc atcggactgg gtaatgatgt ttttctgaca
      721 gcgcacgcac tggctagtgg aggtccggat gctgcagcta ttgtcagggt taccattaat
      781 ttttttagac aacctcagat gcggcattta tcctggtttc ttgccgggga ttttaatcgc
      841 agcccagaca gacttgaaaa tgacctgatg actgagcatc tggaacgagt tgtagccgta
      901 ctcgcaccta cagaacccac gcaaattggc ggtggtattt tagattatgg ggtcattgtc
      961 gatcgagcac cttattcaca aagggttgaa gcattacgta atccacaact cgcttctgat
     1021 cattatcccg tagccttttt ggcacgaagc tgttaatgag taaatagcgt tgacgacatg
     1081 tactttgagc gtaaggtgca gaatatatat ttattgtaag gtaaaattat gagttgtttt
     1141 accagtccag caattatgga aatgttaggt cattataaat ggcgtgttta tgagccattc
     1201 aggttttatc tcagtgaaga taaaaatgat gtcattgaag taccggtagg attcgttacc
     1261 gaccttgcca ctgttccgcg tattttctgg tcattattgc caccggatgg tgaatatgcc
     1321 aaagcggcaa tcattcatga ctacctgtat cattatccat tacgtaacag aaaagagtcc
     1381 gatctcatat tcctggatgg aatgaaagtt ctgggcgtgc caaaatggaa aaggataata
     1441 atgtatttag ccgtaagaat atttggctgg aaatactatc attctcatac catacaacat
     1501 aattaatttc tcgtttttaa cacacaaaga actatagaaa aacctgacgc cttaatatag
     1561 taataatgag acttagtggc tttcaccagt tctctgtgtg aatatatcat tatatgctat
     1621 catcacaaac cgccatagtg gtaagtaagg gaattacaac cttacccgtt cctttatcca
     1681 tccataaaca aatgactcat tcgcctggcg cttttcagct aactccagat agcgttgtcc
     1741 ctgactacaa ttcaatgcac ggataagtat catttcgccc tcatctctcc ggtgagagag
     1801 aaaaaatgtt agtgccgaaa gcgtccgtgg cccaatctga ccatctgcta tcaaatccgg
     1861 ataaattttt tgctgatcat taaaaacatt aagccaacgc tggaagtact taatcgggat
     1921 tgagggtccc atgttcacac cagtatcaca aagctcagct gcgatagagt gagagataat
     1981 ggcaacctga tcaagtcgtg gaccatacca ataatctgcc tcaaggattt ttaatgcttg
     2041 attacgggta agattccgca tatcccccat atagccatta gcccgggccg tcgtcagggt
     2101 tataccccaa tgcgttggtc cccccctgtc gtcagggtga tcaacgtaac caccttctct
     2161 actaaggata gctgcaaaga tttcatcttt agtcataatg actccttcta atattaataa
     2221 aatacgtacc tgaatgctat gattgataat gcaatgaatc tgataaaaaa cttattgaag
     2281 tatataaaca atttatattt aagtggatag ccaacttaat aaacaatatt aaccagacca
     2341 ctaataaacg gtctgtttaa tttaataggc aacataggta agtttcattt atttagaaag
     2401 tataagttct attacaggtc ttgcatcata aaaagacatg ttgtatacgt cagctctttg
     2461 ccctcgatgt gattgacata cgctacctat tgaaaagcat gaacttatta atgggccgaa
     2521 tgcatcaatt cgttgttggg tatacgtctg cggttccgga agaaaaggta tcacgccagg
     2581 attagacgta gtgcttaaac ctaaataact ggaattcatt gtgcttacac catcctttac
     2641 cagacctgtt gcgctatcat aaacaagcgc cacggccttt tgaatattct cgggtaaaat
     2701 agataatgtg gaaacatact ctctttgcaa tcgcatcatc gttttttcat aagcattaaa
     2761 gtgaccacct tgcgtttcca gataggtgat ggatgggagc aagctgtaga aattattatc
     2821 tgcacgaatc tgatatctgt ataaattacc tttgaatgtt gagcgagaat agtacgccct
     2881 ggctatagca tatgtttgat taacacttga ggttgttgca atatagcgac tgtcactact
     2941 tccaccacta catgaccttc cactgataaa ttgctgaaag ttacggttat acccaagtag
     3001 tgaaaaccca tcgcgaaaaa taacgtccgg cggggttgag tccacacgat acacaaaatc
     3061 tactgcatag ttattaaagc taactataga taaggttaag agtattaact ttttcattat
     3121 ttcttccccc ctcttacttg ggtccaaagc attgtgtcgc actgcacgat gatagtccca
     3181 caagagcatt tgctgaaaag gtatttacaa aaagcggata ggtccagata tttttttgaa
     3241 catgaatcct tacggattgc cctgtactat aaaaatatct tgcctggtca agaagttctt
     3301 taaaggaggg tgcccatatg ctctgctttg ataccgcaca tgcaacaact ggtgtaccac
     3361 taccgttagc tttaaccgtt tttatgcaaa aataaggact agtatctatc tgaccaacat
     3421 gtatttcact gataacttcg tctgagtaat aggcgttcgt tttatctcct gtccactcag
     3481 cgctggcatt aaaagaataa aggagaatta ataatgtata aacaggcaca aacttattta
     3541 tatacatgct actctcctgt acatttaaaa taattaacaa agcacaaatt tattatatct
     3601 catcacatct aaatccagtc tatcatgatt tacttcaaca caatgttacc aaccacaaca
     3661 aacactcaaa ttacttgtga atagcaatta atacatatat aaaaaatttc atcactgata
     3721 ataagcacac ctgttttatc agttacagaa ttcctgccac ggtaataaca caggtacttc
     3781 cggctcgtat tgatcgccgt cgtctgtcta ctggttttca ttttcagcaa agcaggacat
     3841 aactcattaa gaaattgacg ataatttaac aagcccgttc tttgcaagaa cgttctggat
     3901 aactatcaga tcactattgt aggatcaaag agtggggaat aaatcattat catccaactg
     3961 aatcatggac gacatcttat taactggcaa tctttttccg gtgtagtgat cctacccgcg
     4021 taatctgtct gtaccctcca ggtaaagtgt ctggcaattt agtcagccta ttgttgataa
     4081 ccgcc
//
