LOCUS       NZ_CP130098             2569 bp    DNA     circular CON 30-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Schwarzengrund strain
            SECVM-17 plasmid unnamed1, complete sequence.
ACCESSION   NZ_CP130098
VERSION     NZ_CP130098.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35361200
            Assembly: GCF_030505835.1
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  JOURNAL   Unpublished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                   :: 517.9x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/30/2023 12:04:57
            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)                     :: 4,970
            CDSs (total)                      :: 4,848
            Genes (coding)                    :: 4,680
            CDSs (with protein)               :: 4,680
            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)              :: 168
            CDSs (without protein)            :: 168
            Pseudo Genes (ambiguous residues) :: 0 of 168
            Pseudo Genes (frameshifted)       :: 77 of 168
            Pseudo Genes (incomplete)         :: 116 of 168
            Pseudo Genes (internal stop)      :: 30 of 168
            Pseudo Genes (multiple problems)  :: 49 of 168
            Pseudo Genes (short protein)      :: 1 of 168
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP130098.1.
            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-17"
                     /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            join(2252..2569,1..324)
                     /locus_tag="QPE07_RS24845"
                     /old_locus_tag="QPE07_24845"
     CDS             join(2252..2569,1..324)
                     /locus_tag="QPE07_RS24845"
                     /old_locus_tag="QPE07_24845"
                     /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            complement(326..1291)
                     /gene="mobV"
                     /locus_tag="QPE07_RS24850"
                     /old_locus_tag="QPE07_24850"
     CDS             complement(326..1291)
                     /gene="mobV"
                     /locus_tag="QPE07_RS24850"
                     /old_locus_tag="QPE07_24850"
                     /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          complement(717..1291)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.75"
                     /coverage="98.0"
                     /evalue="1.01e-127"
ORIGIN
        1 gaagtcatta aggtgggtac agctaacgct tatgtcatca attcccgcgt gttctggcag
       61 tctcacggcg ataaaaaact aacggtcttc cacgctacta tcgtggcatc aagcgacgaa
      121 caagacaccc ccgtagagga ctgggacaag gtgaaattga accatttccc gttcctcagt
      181 cacgacgatg acgtcaccgt gacaaacgag cagctaccgc cgccagacca agaggaattg
      241 gactttcaca agacaccaga gccgtgtttc ttagacggtg acgagcccgt cgagccgcca
      301 actcacatca cgctgcccaa gtgatttatc tgctaaaccc cctgtcttgg ctgcgtcgct
      361 gctgtcgctg ttccttttgg cgttgcaact tcgcggcctt ggccgcttcg ttttcccgtt
      421 gcatggttgt ggccatcttg atgacctccg ctacctgttc gcgtgaaagc cccttaaacg
      481 gctcctgaag cgtttttagc ttcttctgct ggtcaaccat tgtcttttgc atttctcgcg
      541 ctctacgagc gttctgggcg cttacagcgg catttgcaac cgttcccgca tgacctttgt
      601 tgattgcatc ggttaaacga gctgctacag cttctggggt ttcttcctga cgactgaaaa
      661 gccccttctt caacaccctt ggctggacgg cttcgggggt gatggtcact tcccctttgg
      721 tgcccttttc gatggcggcg taatgctgct tgatgctggt atgcgttgcc ctgctgcgct
      781 cgatgcccct ttcaagccct aggtgctgca cagctttggc aaagctggtc tggtcagccg
      841 tcattttcgc cctgttgcca atgaaatcct tggcgctcaa acgtccgtca gcggtcaacg
      901 gcaccacaaa cgcgcttagg tgtgggctgg tctcgtcgcg gtgaatggtg gccgtgatga
      961 tgcggtcagc gccgtatttt tcggccagcc acttgtgtgc ctggtcgaag aaatccgcct
     1021 gctgttcgct ggtggctttc gtccaccatt cgggcgatgc cgtcatgacg tactcaaccg
     1081 ccagcaccgc atctttgcgc cgcttctctg gcagcaactc acgcaagcgc cccattgcct
     1141 catcggttga tgtggcggct ctgtgttcgt tttctgccgt tcgcgtctgg tcggcattgg
     1201 gcgtgtctcg gtctcggtag cagtgctgca acgaggccgc gacagccccc atgccgttga
     1261 gctttttcgc tctcatgatc gcaaaagcca tgcgttcccc ctcggtctgt gctggtgcca
     1321 tcccgacgga aaacgcagtg cctccggcgg gcctctttgg agtcaaagag tactcactag
     1381 actttacttc gtaaaatcgt gacccgcaag cgggttgcag cgcctgcggc ttgctcttcg
     1441 ggctatcgcc ctgcgcctcg tttcactcgt tgcattctcc cccctccgcc ccccgctggg
     1501 gggaacgagt cgccctctgt cgtcaggggt gtgggcagtt ccggccttcg gcctgcacaa
     1561 cccaaacccc agacgggagc gtgggtcact ccaagggcat caagggactt tcgcggcata
     1621 tcctcgcccc gttggggctg cggtattcca cggttccctt gacccccttt ccgttcggtt
     1681 ccatttgagt ggaagcggtg tcaagggcac gcacggaagc cgcacgcgga gcgcagccga
     1741 aggcgagcac cgaacgggtg agtacgtggg cgaagccgta cccttgacgc tgctggaacg
     1801 accacacgct taggcatggg gggcaggtaa gtaggccgta ggccgcccgt cctgcccccc
     1861 tgccacgtgg cgaacgtggg ggaggcaagc gaagcgcgct agggggcaac gcccccttag
     1921 agcgaggccg taggccgctg caagtaacaa aagccttctg cccgcagggc aggcattttc
     1981 aggagcgaag cgacaggggg gttagccaaa cgaagtgcgg cagggggcaa cgccccctat
     2041 gagatagaga ggggacaact actaaaaaca gtcttaaacc cttgtcgtta ttggctttga
     2101 gcctgtttcc ttatgttcac ccctagggcg aacatatatg ttcaccccta gagtgaacat
     2161 atatcacttt ggtggcactt gacgttcatt aaaagtgaac gtattgtgtg cctataggtg
     2221 aacaattgat tcagcaaatg gaacgtatgc tatgaataaa cagaacatac acataagccc
     2281 cgaggcgcaa gcccgtgtaa ggcaacaaga gcttgcagaa caagacgaag cagctaagcg
     2341 agcgaagaag aattacaact tcgtgcagat tgaaaaacga gccttgcggc ttgttcgtga
     2401 gctgtacgaa gccaacccag cagctggcaa attgctgttc atactggccg aaaaaatgaa
     2461 cagacaaaac gctttggttt gcagctatga caccatgtca aagatcacag gactaggcag
     2521 aacaacgctc tacaaggccg tgaaatacct caaagaacac aattgggtt
//
