LOCUS       NZ_CP130079             4267 bp    DNA     linear   CON 30-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Schwarzengrund strain
            SEWLSH-25 plasmid unnamed2.
ACCESSION   NZ_CP130079
VERSION     NZ_CP130079.1
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 4267)
  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  JOURNAL   Unpublished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 4267)
  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
            CP130079.1.
            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..4267
                     /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="unnamed2"
                     /geo_loc_name="USA"
                     /lat_lon="37.0902 N 95.7129 W"
                     /collection_date="2013"
                     /collected_by="Wisconsin State Laboratory of Hygiene"
     gene            349..981
                     /gene="siiA"
                     /locus_tag="QPJ64_RS24835"
                     /old_locus_tag="QPJ64_24835"
     CDS             349..981
                     /gene="siiA"
                     /locus_tag="QPJ64_RS24835"
                     /old_locus_tag="QPJ64_24835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_463122.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="SPI-4 type I secretion system auxiliary protein
                     SiiA"
                     /protein_id="WP_000389240.1"
                     /translation="MEDESNPWPSFVDTFSTVLCIFIFLMLVFALNNMIIMYDNSIKVY
                     KANIENKTKSTAQNSGANDNSNPNEIVNKEVNTQDVSDGMTTMSGKEVGVYDIADGQKI
                     DITSTKNELVITYHGRLRSFSEEDTHKIKAWLEDKINSNLLIEMVIPQADISFSDSLRL
                     GYERGIILMKEIKKIYPDVVIDMSVNSAASSTTSKAIITTINKKVSE"
                     /name="siiA"
     gene            978..2366
                     /locus_tag="QPJ64_RS24840"
                     /old_locus_tag="QPJ64_24840"
     CDS             978..2366
                     /locus_tag="QPJ64_RS24840"
                     /old_locus_tag="QPJ64_24840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_463123.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MotA/TolQ/ExbB proton channel family protein"
                     /protein_id="WP_000875200.1"
                     /translation="MKYINHYRYLFVCFFLAILPFSALSFPGIREYVFDNFMVSAIYNG
                     VIIAIYITGSLCALFTIFKNISAKDILIAQDASRKNSILSNLNQILFSGEPKQCDFNLL
                     MELDDNVSTARNQRLSFIMSCSNVSTLVGLLGTFAGLSITIGSIGNLLSSPSDVGGDNA
                     SNTLNMIVTMVASLSEPLKGMNTAFVSSIYGVVCAILLTSQSVFVRSSYSLVSTEIKKL
                     KIISNRSNNKQRSLRVESETLVEFKELFKAFFDNYLTVENLRTQDEEKKRVMLSDSFVT
                     LQNRLSDNSAKLEQLSTLIDGYLVSSNENLKKLSDGVITITSRLSEGNILLADNNARLE
                     AMSTIQNIIDKKNDSIMASVDKCYQESLSHGKTINDIAAGSADISHTLDGLRKEMDEDM
                     NNVHLALSDLSATDKKIIANTKEISAEMVSYRDTYMPLMEKITSMHQEIVKQRLLNKEE
                     KNED"
                     /name="MotA/TolQ/ExbB proton channel family protein"
     gene            2356..3675
                     /gene="siiC"
                     /locus_tag="QPJ64_RS24845"
                     /old_locus_tag="QPJ64_24845"
     CDS             2356..3675
                     /gene="siiC"
                     /locus_tag="QPJ64_RS24845"
                     /old_locus_tag="QPJ64_24845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_463124.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="SPI-4 type I secretion system protein SiiC"
                     /protein_id="WP_001541306.1"
                     /translation="MKIKMFFLTTAFITQSTYASELPVIPLRDLVNAALTHQPSVAVSY
                     YETEKKNSDLDLSRAALYPTLDLTSGLNNNRKESSGTERNVENKVSLSYRITDFGVRGA
                     NIRKSEYERDNSKTDYEKTKNIVSQEVVTTYYNISKYREMIDGVNLEKEFYKKMLETFS
                     LLVSSGVAMQSDMRKVQVSIDALNTRSIMYQSMLDDEMYKMQNMTGLNLSPVQIQSDEK
                     FNLFKKYIFVESPEKLMDMVMKYNDDYKMLVNTRKAATEDINAAKSSYFPTVDLVSSYV
                     QNNPSGSAKKSDYEDEFKTGINVSFNIFNGFRNSAQERKMVASYSQAKLQIDDFLIKTR
                     YNIDSQLSRYAAAKETYSVAERSHTNALQLTELYEQEFQLGQKSLLDLISSRNEAFQAY
                     VSMIDSKYSLYILKLQQLSLIFHLMDYLKGNTESELNVMK"
                     /name="siiC"
     gene            3672..>4267
                     /gene="siiD"
                     /locus_tag="QPJ64_RS24850"
                     /old_locus_tag="QPJ64_24850"
                     /pseudo=""
     CDS             3672..>4267
                     /gene="siiD"
                     /locus_tag="QPJ64_RS24850"
                     /old_locus_tag="QPJ64_24850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_463125.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="SPI-4 type I secretion system protein SiiD"
                     /name="siiD"
ORIGIN
        1 tcggcgagtg gttttaattt gctgatgact attttttatt tatgagctga gagcttatgc
       61 gatacctatt attggggaag atatagttag tgcaataatt gatgtctacc taattaaaaa
      121 ataaagagtg tttttaatta aagcactcat ctttgttgtg ggcgcataaa aatggcgtca
      181 ttgtttttat ttttctgatt acgagatgta ggaaaactga aatctataaa gcgtattggt
      241 agcaggaagc caagggcggt agcgttcact ttctgaataa gttgagcatc ctttatcctt
      301 tctaatccac aaaaacattt tattcacaat gtaatatcag gagacaacat ggaagacgaa
      361 agtaatccgt ggcctagttt tgttgataca ttctctacgg tattgtgcat ttttatattt
      421 cttatgttgg tgtttgcact taataatatg attattatgt atgacaactc aattaaagtt
      481 tataaagcaa atatagagaa taagactaaa tctactgctc aaaatagcgg agccaatgac
      541 aattcaaatc ctaatgaaat agttaataag gaagtgaata ctcaagatgt gtcggacgga
      601 atgactacaa tgtcaggtaa ggaggttgga gtatacgata tcgccgatgg tcagaaaatt
      661 gatataacat ctacaaaaaa tgagcttgtt attacgtatc atggcaggct gagaagcttt
      721 tcagaagagg acacccataa aataaaggct tggttagaag acaaaatcaa tagtaattta
      781 ttgatagaaa tggttattcc tcaggcagac atctctttct ctgactcttt acgactggga
      841 tatgaacggg gaattatttt aatgaaagag attaagaaga tatatcctga tgtagttatt
      901 gacatgagtg ttaactccgc agcatcaagt acaacgagta aagctattat cacgactatt
      961 aataaaaagg tgtcagagtg aaatatataa atcattaccg ctatttgttt gtctgttttt
     1021 tccttgccat actccctttt tccgctttat cttttcccgg tataagagag tatgtttttg
     1081 ataactttat ggtttctgca atttacaatg gagtcattat tgccatttat attacaggct
     1141 ctttgtgtgc attattcact atttttaaaa atatttcagc aaaagacata ttaatagctc
     1201 aggacgccag cagaaaaaat agtattcttt ctaacctcaa tcagattttg ttttccggag
     1261 aacccaaaca gtgtgatttc aatttgctga tggaattaga tgacaatgtg tctaccgccc
     1321 gtaaccaacg attgtcattt attatgagtt gtagcaatgt gtcgacgctt gttggcctgt
     1381 tggggacgtt tgcgggtctg tctattacga ttggttcaat cgggaattta ttgagctcgc
     1441 catcagatgt tggcggtgat aatgcaagta atacactcaa tatgatcgtg acaatggtag
     1501 cgtcgctttc tgaaccattg aaagggatga ataccgcatt tgtatcttct atctatggtg
     1561 ttgtttgcgc catactcctg acctcacaaa gtgtttttgt tcgcagctcc tattcccttg
     1621 tttctacgga aatcaaaaaa ttaaaaatca taagcaacag atccaataat aaacaacgaa
     1681 gcctgcgggt tgaatcagag acgcttgtag aatttaaaga gttgtttaaa gcgttttttg
     1741 ataactacct gacagttgaa aacttacgga cgcaggatga agaaaagaaa cgagtgatgc
     1801 tatcagatag ctttgtcact ttgcaaaacc gactatcgga taactcagca aaactggaac
     1861 aactttctac gctgattgat ggttatctgg taagcagtaa cgaaaatctc aaaaaattat
     1921 ctgacggtgt aataacaatt acctctcgtt tatctgaagg taatatcctg cttgctgata
     1981 ataatgcacg gctggaggca atgagtacaa tacaaaatat tatagacaaa aagaatgatt
     2041 caataatggc atcagttgat aaatgttatc aggaatctct ttcacatggt aagaccataa
     2101 acgatattgc cgctggcagt gccgatattt ctcatactct cgatgggctg agaaaagaaa
     2161 tggatgagga tatgaacaat gttcatttag cgctatccga tctatcggct actgataaaa
     2221 agattattgc caatactaaa gagattagtg ctgaaatggt tagctaccgt gatacctata
     2281 tgccattaat ggaaaaaata acatctatgc accaggaaat agtaaagcaa cgtttgttaa
     2341 acaaggagga aaaaaatgaa gattaagatg ttttttctga cgactgcttt tattacacaa
     2401 agcacatacg ccagcgagct tccggtcatt cctctaagag acttagttaa tgccgcatta
     2461 acgcatcagc cctctgttgc tgtttcatat tatgagactg aaaagaaaaa cagtgactta
     2521 gatctttcac gggcagcact ttatcctacc ctggatctaa catctggcct taataataac
     2581 aggaaagagt catcaggtac cgagagaaac gttgaaaata aggtgtcttt atcataccga
     2641 ataacggact ttggagtgag gggggctaat atcaggaaat ctgaatacga aagagataat
     2701 agtaaaactg actatgaaaa aacaaagaat atagtgtctc aggaggttgt gacaacctat
     2761 tataacatca gtaaatatcg tgaaatgatt gatggcgtaa atctggagaa agagttttat
     2821 aaaaagatgc tggaaacttt ttcgctgttg gtatcttccg gtgtagcgat gcaatctgat
     2881 atgcgtaaag tacaagtatc tatcgatgca ttaaataccc gaagcattat gtatcagtcg
     2941 atgttggatg atgaaatgta taaaatgcag aatatgactg gtctgaattt atcaccagtt
     3001 cagattcaaa gcgatgaaaa attcaacctc ttcaaaaaat atatctttgt cgaaagtcct
     3061 gaaaaactta tggacatggt gatgaaatac aatgatgact ataagatgct tgtcaatacc
     3121 cgaaaagccg cgaccgaaga tattaatgcc gcaaaatcat cctattttcc gactgtagat
     3181 ctcgtttcca gctatgtaca gaataacccg agcggtagtg ccaaaaaaag tgattatgaa
     3241 gatgaattca aaacgggtat caatgtcagt ttcaacattt ttaatgggtt cagaaattca
     3301 gcccaggaaa gaaaaatggt ggcaagttac tcgcaggcta agctgcaaat tgacgatttt
     3361 ttgattaaaa cgcgttataa cattgattca caactttcaa gatacgccgc tgcaaaagag
     3421 acttactcag tggcggaacg ttcacataca aacgcgttac agcttactga attatatgag
     3481 caggagtttc agttagggca aaaaagtttg cttgatttaa tttcaagccg taatgaagca
     3541 tttcaggcat atgtaagcat gatcgacagc aaatatagcc tgtatatttt aaagttacag
     3601 caactctcat tgatttttca tttaatggat tatttaaaag gaaatactga aagtgagtta
     3661 aatgtaatga aatgaataga agacaaagcg atcatctcat gatgataatt atttctttga
     3721 cgatcttaat tattatcctt acctacttta tagaaattaa ttcagtggtt catggtcagg
     3781 gcgttatcac cactaaagat aatgctcagt taatatctct ttctaaagga gggacgatac
     3841 aagatattta tgtagccgag ggtgatactg taaaaaaagg agaactcctt gcaaaggtcg
     3901 ttaaccttga tctgcaaaaa gaatatcaaa ggtatagaac tcaaaaaggg tatctggata
     3961 aagatgttaa cgaaatatct ttcattcttg ataaagaaaa tgagagtgga ttgattaccc
     4021 tggatggcac ccgttcttta agtaataaag aggtaaaagc gaatattgaa ttagtgcata
     4081 gtcagataag agctaaagag ttaaaaaaaa cctctcttga ttctgagatt agcggattac
     4141 aagagaagct gagttcgaaa gaaaaagaac tcgcattgct tgccgaagaa ataaatattc
     4201 tttccccact ggtaaaaaaa ggaattagcc catataccaa ttttcttaac gagaaacagg
     4261 cgtatat
//
