LOCUS       NZ_CP130093             4694 bp    DNA     circular CON 30-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Schwarzengrund strain
            SEMDH-29 plasmid Col440I, complete sequence.
ACCESSION   NZ_CP130093
VERSION     NZ_CP130093.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35361201
            Assembly: GCF_030505815.1
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 4694)
  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  JOURNAL   Unpublished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 4694)
  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. unspecified
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 38.3x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/30/2023 12:04:17
            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)                     :: 4,973
            CDSs (total)                      :: 4,851
            Genes (coding)                    :: 4,682
            CDSs (with protein)               :: 4,682
            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)              :: 169
            CDSs (without protein)            :: 169
            Pseudo Genes (ambiguous residues) :: 0 of 169
            Pseudo Genes (frameshifted)       :: 79 of 169
            Pseudo Genes (incomplete)         :: 114 of 169
            Pseudo Genes (internal stop)      :: 32 of 169
            Pseudo Genes (multiple problems)  :: 50 of 169
            Pseudo Genes (short protein)      :: 1 of 169
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP130093.1.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..4694
                     /organism="Salmonella enterica subsp. enterica serovar
                     Schwarzengrund"
                     /mol_type="genomic DNA"
                     /strain="SEMDH-29"
                     /serovar="Schwarzengrund"
                     /isolation_source="urine"
                     /sub_species="enterica"
                     /db_xref="taxon:340190"
                     /plasmid="Col440I"
                     /geo_loc_name="USA"
                     /lat_lon="37.0902 N 95.7129 W"
                     /collection_date="2017"
                     /collected_by="Minnesota Department of Health"
     gene            283..522
                     /locus_tag="QPJ60_RS24820"
                     /old_locus_tag="QPJ60_24820"
     CDS             283..522
                     /locus_tag="QPJ60_RS24820"
                     /old_locus_tag="QPJ60_24820"
                     /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="WP_302102579.1"
                     /translation="MQRLNEWESAFVELQKMFSLTQRDNAMLNERVMQLSQQVQHLSEQ
                     TERLSEQTERLSEQTERLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1214..1495)
                     /locus_tag="QPJ60_RS24825"
                     /old_locus_tag="QPJ60_24825"
     CDS             complement(1214..1495)
                     /locus_tag="QPJ60_RS24825"
                     /old_locus_tag="QPJ60_24825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000586174.1"
                     /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="WP_000586174.1"
                     /translation="MIINIKHKGLRKFAETGNNAGIPQQFTQRLKLILTALSTATNLQD
                     MMDLKALRCHPLKGDRQGEYSLEVNGNWRVVFKLEEPNVFDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            1840..2136
                     /locus_tag="QPJ60_RS24830"
                     /old_locus_tag="QPJ60_24830"
     CDS             1840..2136
                     /locus_tag="QPJ60_RS24830"
                     /old_locus_tag="QPJ60_24830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609270.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antitoxin"
                     /protein_id="WP_000609270.1"
                     /translation="MINLVDPVHPGVFIREMFMEPFEISAADLSEKLHVSPSTLSRVLN
                     GKADLSVEMALRLSRVLGRSAESWINMQTQYSLNASRKSPNVIKELDELVPIF"
                     /name="HigA family addiction module antitoxin"
     gene            complement(3138..3329)
                     /locus_tag="QPJ60_RS24835"
                     /old_locus_tag="QPJ60_24835"
     CDS             complement(3138..3329)
                     /locus_tag="QPJ60_RS24835"
                     /old_locus_tag="QPJ60_24835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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="WP_130568415.1"
                     /translation="MTKQEKTALNMARFIKSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGGDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3394..3717
                     /locus_tag="QPJ60_RS24840"
                     /old_locus_tag="QPJ60_24840"
     CDS             3394..3717
                     /locus_tag="QPJ60_RS24840"
                     /old_locus_tag="QPJ60_24840"
                     /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="WP_000955989.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRICLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3926..>4357
                     /locus_tag="QPJ60_RS24845"
                     /old_locus_tag="QPJ60_24845"
                     /pseudo=""
     CDS             3926..>4357
                     /locus_tag="QPJ60_RS24845"
                     /old_locus_tag="QPJ60_24845"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial in the middle of a contig;
                     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"
     Typing          2976..3060
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.837"
                     /coverage="100.0"
                     /evalue="1.41e-35"
     Typing          complement(2408..2965)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.464"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4..626
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="83.654"
                     /coverage="99.0"
                     /evalue="7.77e-77"
     Typing          3708..4693
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.745"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 accgcgagtg gcgggacgct ctggtatctt ggcgggcgga tacaggcgaa cctggaagaa
       61 atcaggatac aggaagagac attgcagaaa ctgaacgcga agacatgggg cgtggagttt
      121 gtgcaggacg ggaacaggaa atttctggtc atcccgcagg ggaaatcggc aacggtgatt
      181 ccctatcagg ggaaggactg ggtacaactg acggagtgac acagagtgac ggagctggaa
      241 agacatttgc tgaacgcatt agagcaactg caacaggact atatgcagcg gctgaacgaa
      301 tgggagagcg ccttcgtgga attgcagaag atgttttcgc ttacgcaacg ggacaacgcg
      361 atgctgaacg agcgggtcat gcagttgagt cagcaggtgc agcacttgag cgagcagaca
      421 gaacgcttga gcgagcagac agaacgcttg agcgagcaga cagaacgctt gagcgagcag
      481 acagaacgct tgagccagtt atacagcgag aactggagat aagagaggaa cggctgatac
      541 aggagcgcga acatgcatta tccctggaac gggagcgtca gccggaaata caggaacgca
      601 cgctggatgg tccttcgctg ggatggtgaa accatgaaaa atggcagctt cagtggatta
      661 agaggggtta atgtggcctg taccatctgg ttgcataggt attcatgcgg ttaaaattta
      721 tcaggcgcga tcgcggcagt ttttcgggtg gtttgttgcc atttttacct gtctgctgcc
      781 gtgatcgtgc tgaacgcgtt ttagcggtgc gtgtaatgcg acgttatggt aaatgctgtg
      841 atttacggga tggttttatc tatgttgata tcaataccac ctcttatgga ggtggcttac
      901 accgattttt ccttgttgtc tgtttcagaa cagatagagg cttttttggc aattatccaa
      961 ccactattga tagtgtttat tactacttag ataactgagc ctttactgta tctgcccctg
     1021 caagcaggaa cccaacagtt aagaaccacc cccagccatt gatacctttt agcgctagaa
     1081 ttgctgcgca aatgatggct gctataggga ctatctggta cagaaaatac ttcatataac
     1141 ttaccccgag gttttgcttt tttatgagac cctaaagcat cgatactgtc actttgatgc
     1201 tttaaggacc ttcttagtga taatcctcga gatccacgtc aaagacgtta ggttcttcga
     1261 gcttaaacac tacgcgccag tttccattga cctctaacga atactctcct tgacggtctc
     1321 ccttcaatgg atggcagcgc aatgccttta aatccatcat atcctgcaag ttcgtcgctg
     1381 tgcttaaggc tgttaggatc agcttcagac gttgagtaaa ctgttgcgga attcctgcgt
     1441 tgttacctgt ttcggcaaac ttacgcaaac ctttatgctt gatatttatg atcattaatc
     1501 accatcccat atttgtttag atagaaacat cgcagtttat ttttccggtt catccgtatt
     1561 tccattgcaa accccttgct ctatttgaat aaatgacgta ggttttactt aaccaagtcg
     1621 cattttaatc tgttgacatt ggtttgatgc gctgtacaat gccggggcct tgaatttcac
     1681 atcaagtacc cacatcataa ggaatgatta gacgcaccaa tgtgcatcat aatgtcattc
     1741 ttttttttag tcaacaatga gttgcgttat gcgcaatgcg caatctgaaa acgcaatagg
     1801 cctatctttt taaaactaat ataggcttca gaggaaggta tgattaatct tgtcgatcca
     1861 gtacatccag gggtttttat ccgtgagatg tttatggaac cgtttgaaat atcagccgcg
     1921 gacctgtctg aaaaactgca tgtatcacct tccactctaa gtagagtgct gaatggaaaa
     1981 gctgatttaa gtgttgagat ggcattaagg ctttctcgag ttcttggtcg cagtgccgag
     2041 tcgtggataa acatgcagac tcaatacagt cttaacgcga gcaggaagtc acctaatgtc
     2101 attaaggaat tagatgaatt ggttcctata ttttgagaaa agaaaaggcc gctatatgcg
     2161 gcctttttct gtcttgactc tcaggcaact ggatcgtatc gtttctcgta aacgaaaaaa
     2221 ccacccggca aggtggtttt ttcgaaggtt cagtaaccgg caagtttctg aaccagggta
     2281 actggcttgg aggagcgcag tcaccaaaac ttgttctttc agtttagcct taactggcgc
     2341 ataacttcaa gactaactcc tctaaatcag ttaccagtgg ctgctgccaa tggtgttttg
     2401 catgtctttc cgggttggac tcaagatgat agttaccgga taaggcgcag cggtcgggct
     2461 gaacgggggg ttcgtgcaca cagcccagct tggagcgaac gacctacact gaaccgagat
     2521 acctacagcg tgagctatga gaaagcgcca cgcttcccga agggagaaag gcggacaggt
     2581 atccggtaag cggcagggtc ggaacaggag agcgcacgag ggagccacca gggggaaacg
     2641 tctggtatct ttaagtcctg tcgggtttcg ccacctctga cttgagcgtc gatttctgtg
     2701 atgctcgtca ggggggcgga gcctatggaa aaacgcctgc ggcgcggcct tcttcctgtt
     2761 cttggtcttt tgctcacatg ttctttccgg ccttatcccc tgattctgtg gataaccgtg
     2821 ctgccgtttt tgtgtaagtc agtaccgctc gccgcagccg aacgaccgag cgtagcgagt
     2881 cagtgagcga ggaagcggaa aagcgcctgg acgcgcattt tctccttacg catctgtgcg
     2941 gaatttcaca cccggcatgg ggcacttttc atacaatctg cactgatgtc gcatagttaa
     3001 gccagtatac actccgctat cgctacgtga ctggttcagg gcttcgcccc gaaaccccct
     3061 gacgcgccct gacgggcttg tcagctcccg gcatccgctc acagacaagc tgtgaccgtc
     3121 tccgggagct gtatgtgtca gaggttttca ccgtcacccc cgaagcgtgc gaggcagctg
     3181 cggtaaagct cgtcggcgtg gtcgtgaagt gattcacaaa tatcggcctg ttcatctgcg
     3241 tccagttcgt tgagcttctc cagcagcgtt aatgtctggc tttttataaa gcgggccatg
     3301 ttaagggcgg ttttttcctg tttagtcact gatgcctccg tgtaaggggg gatttctgtt
     3361 catggggtaa tgataccgat gaaacgcgag aggatgctca cgatacgggt tactgatgat
     3421 gaacatgcac ggttactgga acgctgtgag ggtaaacagc tggcggtatg gatgcggcgg
     3481 atctgcctgg gtgagccggt tgcccgttcc gggaagctgc cgacactggc accgccgtta
     3541 ctgcgccagc tggctgccat cgggaataac ctgaatcaga cggcgaggaa ggtgaacagc
     3601 gggcagtggt cttccggtga ccgggttcag gtggtggccg cactgatggc catcgagaga
     3661 gagttgcgca gcttacggca ggtcgtcagg gaacatggag cgcgggatga tagttaagtt
     3721 tcatgccagg ggaaaaggcg gtggcagtgg tccggttgat tacctgctgg gaagggagcg
     3781 taaccgggaa ggggcaacgg tgcttcaggg tgatccggaa gaagtccggg aactcatcga
     3841 tgccacgcca tttgcgaaga aatacacgtc aggtgttctg tcgttcgcgg agaaggagct
     3901 gccgccggga gggcgtgaaa aagtgatggc gagctttgag cgtgtactga tgcccggtct
     3961 cgaaaaaaat cagtacagca tcctgtgggt ggagcaccag gacaagggac ggcttgagct
     4021 gaattttgtc attccgaata tggagctaca gaccggaaaa cgcctccagc cgtactacga
     4081 ccgggcagac aggccgagaa ttgatgcctg gcagacactg gtgaatcacc attacgggct
     4141 gcatgacccc aacgccccgg agaaccgccg gatactgact ctctctgata acctgccgga
     4201 aacgaaacag gcgcttgctg agagcgtcac acgcgggata gacgctcttt atcatgtcgg
     4261 ggagataaaa ggccgtcagg atgtgattca ggcgctcacg gaggcaggga ttgaagtggt
     4321 cagggtgacg cgaagcagta tcagcattgc agacccgaac ggcgggagga atatcaggct
     4381 gaaaggagca ttttatgagc aatcttttac agacgggcgc ggagttcgag aaaaagctga
     4441 aagagagagc cgaatctaca gagaaaatgc tgaacaacga gttcaggagg ctcggcgaat
     4501 ctgtaagcga ggctgtgaca tcaaacgaga cgaaaatcag agacgctata gccctgttca
     4561 caacgtcgac agaggaatcg ctgaaaaaac accgggaagg ggtgaaagag gcgatgatgc
     4621 agcaccggaa ggacgtgtta aagctggcag ggaatacggg cgtgatgtta ctggggatag
     4681 tctttctcct gttt
//
