LOCUS       NZ_CP130105             2569 bp    DNA     circular CON 30-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Schwarzengrund strain
            SECVM-15 plasmid unnamed1, complete sequence.
ACCESSION   NZ_CP130105
VERSION     NZ_CP130105.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35361198
            Assembly: GCF_030505875.1
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 2569)
  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  JOURNAL   Unpublished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 2569)
  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                   :: 24.0x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/30/2023 12:00:53
            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)                     :: 4,952
            CDSs (total)                      :: 4,830
            Genes (coding)                    :: 4,671
            CDSs (with protein)               :: 4,671
            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)              :: 159
            CDSs (without protein)            :: 159
            Pseudo Genes (ambiguous residues) :: 0 of 159
            Pseudo Genes (frameshifted)       :: 78 of 159
            Pseudo Genes (incomplete)         :: 106 of 159
            Pseudo Genes (internal stop)      :: 30 of 159
            Pseudo Genes (multiple problems)  :: 49 of 159
            Pseudo Genes (short protein)      :: 1 of 159
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP130105.1.
            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..2569
                     /organism="Salmonella enterica subsp. enterica serovar
                     Schwarzengrund"
                     /mol_type="genomic DNA"
                     /strain="SECVM-15"
                     /serovar="Schwarzengrund"
                     /isolation_source="chicken breast"
                     /sub_species="enterica"
                     /db_xref="taxon:340190"
                     /plasmid="unnamed1"
                     /geo_loc_name="USA"
                     /lat_lon="37.0902 N 95.7129 W"
                     /collection_date="2013"
                     /collected_by="FDA"
     gene            complement(join(1932..2569,1..4))
                     /locus_tag="QPJ62_RS24755"
                     /old_locus_tag="QPJ62_24755"
     CDS             complement(join(1932..2569,1..4))
                     /locus_tag="QPJ62_RS24755"
                     /old_locus_tag="QPJ62_24755"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_052928735.1"
                     /translation="MNKQNIHISPEAQARVRQQELAEQDEAAKRAKKNYNFVQIEKRAL
                     RLVRELYEANPAAGKLLFILAEKMNRQNALVCSYDTMSKITGLGRTTLYKAVKYLKEHN
                     WVEVIKVGTANAYVINSRVFWQSHGDKKLTVFHATIVASSDEQDTPVEDWDKVKLNHFP
                     FLSHDDDVTVTNEQLPPPDQEELDFHKTPEPCFLDGDEPVEPPTHITLPK"
                     /name="replication/maintenance protein RepL"
     gene            965..1930
                     /gene="mobV"
                     /locus_tag="QPJ62_RS24760"
                     /old_locus_tag="QPJ62_24760"
     CDS             965..1930
                     /gene="mobV"
                     /locus_tag="QPJ62_RS24760"
                     /old_locus_tag="QPJ62_24760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010657476.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobV family relaxase"
                     /protein_id="WP_052928736.1"
                     /translation="MAFAIMRAKKLNGMGAVAASLQHCYRDRDTPNADQTRTAENEHRA
                     ATSTDEAMGRLRELLPEKRRKDAVLAVEYVMTASPEWWTKATSEQQADFFDQAHKWLAE
                     KYGADRIITATIHRDETSPHLSAFVVPLTADGRLSAKDFIGNRAKMTADQTSFAKAVQH
                     LGLERGIERSRATHTSIKQHYAAIEKGTKGEVTITPEAVQPRVLKKGLFSRQEETPEAV
                     AARLTDAINKGHAGTVANAAVSAQNARRAREMQKTMVDQQKKLKTLQEPFKGLSREQVA
                     EVIKMATTMQRENEAAKAAKLQRQKEQRQQRRSQDRGFSR"
                     /name="mobV"
     Typing          966..1540
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.75"
                     /coverage="98.0"
                     /evalue="1.01e-127"
ORIGIN
        1 tcatagcata cgttccattt gctgaatcaa ttgttcacct ataggcacac aatacgttca
       61 cttttaatga acgtcaagtg ccaccaaagt gatatatgtt cactctaggg gtgaacatat
      121 atgttcgccc taggggtgaa cataaggaaa caggctcaaa gccaataacg acaagggttt
      181 aagactgttt ttagtagttg tcccctctct atctcatagg gggcgttgcc ccctgccgca
      241 cttcgtttgg ctaacccccc tgtcgcttcg ctcctgaaaa tgcctgccct gcgggcagaa
      301 ggcttttgtt acttgcagcg gcctacggcc tcgctctaag ggggcgttgc cccctagcgc
      361 gcttcgcttg cctcccccac gttcgccacg tggcaggggg gcaggacggg cggcctacgg
      421 cctacttacc tgccccccat gcctaagcgt gtggtcgttc cagcagcgtc aagggtacgg
      481 cttcgcccac gtactcaccc gttcggtgct cgccttcggc tgcgctccgc gtgcggcttc
      541 cgtgcgtgcc cttgacaccg cttccactca aatggaaccg aacggaaagg gggtcaaggg
      601 aaccgtggaa taccgcagcc ccaacggggc gaggatatgc cgcgaaagtc ccttgatgcc
      661 cttggagtga cccacgctcc cgtctggggt ttgggttgtg caggccgaag gccggaactg
      721 cccacacccc tgacgacaga gggcgactcg ttccccccag cggggggcgg aggggggaga
      781 atgcaacgag tgaaacgagg cgcagggcga tagcccgaag agcaagccgc aggcgctgca
      841 acccgcttgc gggtcacgat tttacgaagt aaagtctagt gagtactctt tgactccaaa
      901 gaggcccgcc ggaggcactg cgttttccgt cgggatggca ccagcacaga ccgaggggga
      961 acgcatggct tttgcgatca tgagagcgaa aaagctcaac ggcatggggg ctgtcgcggc
     1021 ctcgttgcag cactgctacc gagaccgaga cacgcccaat gccgaccaga cgcgaacggc
     1081 agaaaacgaa cacagagccg ccacatcaac cgatgaggca atggggcgct tgcgtgagtt
     1141 gctgccagag aagcggcgca aagatgcggt gctggcggtt gagtacgtca tgacggcatc
     1201 gcccgaatgg tggacgaaag ccaccagcga acagcaggcg gatttcttcg accaggcaca
     1261 caagtggctg gccgaaaaat acggcgctga ccgcatcatc acggccacca ttcaccgcga
     1321 cgagaccagc ccacacctaa gcgcgtttgt ggtgccgttg accgctgacg gacgtttgag
     1381 cgccaaggat ttcattggca acagggcgaa aatgacggct gaccagacca gctttgccaa
     1441 agctgtgcag cacctagggc ttgaaagggg catcgagcgc agcagggcaa cgcataccag
     1501 catcaagcag cattacgccg ccatcgaaaa gggcaccaaa ggggaagtga ccatcacccc
     1561 cgaagccgtc cagccaaggg tgttgaagaa ggggcttttc agtcgtcagg aagaaacccc
     1621 agaagctgta gcagctcgtt taaccgatgc aatcaacaaa ggtcatgcgg gaacggttgc
     1681 aaatgccgct gtaagcgccc agaacgctcg tagagcgcga gaaatgcaaa agacaatggt
     1741 tgaccagcag aagaagctaa aaacgcttca ggagccgttt aaggggcttt cacgcgaaca
     1801 ggtagcggag gtcatcaaga tggccacaac catgcaacgg gaaaacgaag cggccaaggc
     1861 cgcgaagttg caacgccaaa aggaacagcg acagcagcga cgcagccaag acagggggtt
     1921 tagcagataa atcacttggg cagcgtgatg tgagttggcg gctcgacggg ctcgtcaccg
     1981 tctaagaaac acggctctgg tgtcttgtga aagtccaatt cctcttggtc tggcggcggt
     2041 agctgctcgt ttgtcacggt gacgtcatcg tcgtgactga ggaacgggaa atggttcaat
     2101 ttcaccttgt cccagtcctc tacgggggtg tcttgttcgt cgcttgatgc cacgatagta
     2161 gcgtggaaga ccgttagttt tttatcgccg tgagactgcc agaacacgcg ggaattgatg
     2221 acataagcgt tagctgtacc caccttaatg acttcaaccc aattgtgttc tttgaggtat
     2281 ttcacggcct tgtagagcgt tgttctgcct agtcctgtga tctttgacat ggtgtcatag
     2341 ctgcaaacca aagcgttttg tctgttcatt ttttcggcca gtatgaacag caatttgcca
     2401 gctgctgggt tggcttcgta cagctcacga acaagccgca aggctcgttt ttcaatctgc
     2461 acgaagttgt aattcttctt cgctcgctta gctgcttcgt cttgttctgc aagctcttgt
     2521 tgccttacac gggcttgcgc ctcggggctt atgtgtatgt tctgtttat
//
