LOCUS       NZ_CP084220             3428 bp    DNA     circular CON 14-NOV-2023
DEFINITION  Salmonella sp. JXY0409-18 plasmid unnamed4, complete sequence.
ACCESSION   NZ_CP084220
VERSION     NZ_CP084220.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21843235
            Assembly: GCF_020268625.1
KEYWORDS    RefSeq.
SOURCE      Salmonella sp. JXY0409-18
  ORGANISM  Salmonella sp. JXY0409-18
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3428)
  AUTHORS   Lu,X. and Li,R.
  TITLE     Salmonella JXY0409-18Chromosome sequence
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3428)
  AUTHORS   Lu,X. and Li,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-SEP-2021) College of Biological and Pharmaceutical
            Engineering, Wuhan Polytechnic University, No. 68 Xuefu South Road,
            Evergreen Garden, Dongxihu District, Wuhan, Hubei 430000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SPAdes v. August-2021
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 239.6x
            Sequencing Technology             :: PacBio; Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/14/2023 14:05:05
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,762
            CDSs (total)                      :: 4,642
            Genes (coding)                    :: 4,511
            CDSs (with protein)               :: 4,511
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 131
            CDSs (without protein)            :: 131
            Pseudo Genes (ambiguous residues) :: 0 of 131
            Pseudo Genes (frameshifted)       :: 54 of 131
            Pseudo Genes (incomplete)         :: 96 of 131
            Pseudo Genes (internal stop)      :: 18 of 131
            Pseudo Genes (multiple problems)  :: 35 of 131
            Pseudo Genes (short protein)      :: 1 of 131
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP084220.1.
            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..3428
                     /organism="Salmonella sp. JXY0409-18"
                     /mol_type="genomic DNA"
                     /strain="JXY0409-18"
                     /isolation_source="chicken"
                     /db_xref="taxon:2879113"
                     /plasmid="unnamed4"
                     /geo_loc_name="China: Jiangxi"
                     /collection_date="2021-04-08"
     gene            720..1417
                     /locus_tag="LDB27_RS23795"
                     /old_locus_tag="LDB27_23795"
     CDS             join(720..969,969..1417)
                     /locus_tag="LDB27_RS23795"
                     /old_locus_tag="LDB27_23795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558153.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
                     /protein_id="WP_094106546.1"
                     /translation="MASISIRCPSCSATEGVVRNGKSTAGHQRYLCSHCRKTWQLQFTY
                     TASQPGTHQKIIDMAMNGVGCRASARIMGVGLNTVLRHFKKLRPQSVTSRIQPGSDVIV
                     CAEMDEQWGYVGAKSRQRWLFYAYDRIRRTVVAHVFGERTLATLERLLSLLSAFEVVVW
                     MTDGWPLYESRLKGKLHVISKRYTQRIERHNLNLRQHLARLGRKSLSFSKSVELHDKVI
                     GHYLNIKHYQ"
                     /name="IS1 family transposase"
     gene            1956..2219
                     /locus_tag="LDB27_RS23800"
                     /old_locus_tag="LDB27_23800"
     CDS             1956..2219
                     /locus_tag="LDB27_RS23800"
                     /old_locus_tag="LDB27_23800"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_138627904.1"
                     /translation="MPLEQAAFLFSGVGGMLLTEMEISNTRNITLIARRLAWINAKRTH
                     IDIPSFAELLFSGQKALFFEQYNYFHSRRYTTAGTSKPPDLP"
                     /name="hypothetical protein"
     gene            2411..2599
                     /locus_tag="LDB27_RS23805"
                     /old_locus_tag="LDB27_23805"
     CDS             2411..2599
                     /locus_tag="LDB27_RS23805"
                     /old_locus_tag="LDB27_23805"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /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_024157493.1"
                     /translation="MNRQESAVLNIAKFIRAQTLLLLERIDLLDFDDEATDCEQLHEQA
                     EALYRKLSARLESDITA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(<3164..3259)
                     /locus_tag="LDB27_RS23810"
                     /old_locus_tag="LDB27_23810"
                     /pseudo=""
     CDS             complement(<3164..3259)
                     /locus_tag="LDB27_RS23810"
                     /old_locus_tag="LDB27_23810"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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="plasmid mobilization relaxosome protein MobC"
                     /name="plasmid mobilization relaxosome protein MobC"
ORIGIN
        1 tatctatttt aacactgtgc ggaaattgac agaaatcggg ctatgtggca gaggaaaatg
       61 cggcttcgaa gcataagcag aatgatgggc ggacggtgaa aatgacgcct cctcgctcat
      121 tcgctcacta cgttcggtca tgaagctgtg gcgggcgttg cggtgatctg actgagtgat
      181 aatgattttt ctggctctag atgtacaaaa gccccgtgac agaatcacag ggcttgagta
      241 ctctaattcg tgcagatacc tgctcggatc agaccgcaat caaatcctag cagggctggc
      301 taggaatgtc actaccagct taataccatt caacgacatt aaacccatat ctgcaccttg
      361 actctcaggt ctacgccccg gactccggca ggataaacag gcaagcggtg ggaacctgac
      421 cagctcggga aagaagctgg ctctacccgg tctcacgtta accaataacg tacctgataa
      481 agtgagagtg aaggcagcgg ttgcggtgaa gcgtgattgc caaggtctgg cgcaacaccc
      541 acaaaatcga agcagcatac gaacggcctg atgctggtcg cttcgctccc cgttttctgg
      601 tgtacccacc acgggggcat taggctttct ttgccctaat atgggtttgc gactctcaaa
      661 tccgggtaat gctgccaact tactgattta gtgtatgatg gtgattttaa ggtgcttgcg
      721 tggcttccat ttccatcaga tgtccttcct gctccgctac tgaaggcgtg gtgcgtaacg
      781 gcaaaagcac tgccggacat cagcgctatc tctgctctca ttgccgtaaa acatggcaac
      841 tacagttcac ttacaccgcc tctcagcccg gtacgcacca gaaaatcatt gatatggcca
      901 tgaatggcgt cggatgtcgc gccagtgcac gcattatggg cgttggcctc aacacggttt
      961 tacgtcactt aaaaaactca ggccgcagtc ggtaacctcg cgcatacaac cgggcagtga
     1021 tgtgattgtc tgcgctgaaa tggacgaaca gtggggctac gtcggtgcta aatcacgtca
     1081 gcgctggctg ttttacgcgt atgacaggat acggaggacg gttgtggcgc acgtcttcgg
     1141 tgaacgcact ctggccacac tggagcgtct tctgagcctg ctgtcggcct ttgaggtcgt
     1201 ggtatggatg acggatggct ggccgctgta tgaatcacgc ctgaagggaa agctgcacgt
     1261 tatcagcaag cgatatacgc agcgcattga gcgacataac ctgaatctga gacaacatct
     1321 ggcaaggctg ggacggaagt cactgtcgtt ctcaaaatcg gtggagctgc atgacaaggt
     1381 catcgggcat tatctgaaca taaaacacta tcagtaagtt ggagtcatta cccatcacga
     1441 tgactaaaaa acaagcaatt tgagtaaaca aatatacgcc tgacatattt gtttactcat
     1501 gaaataatat agccacaata ataactggtg tatttttttt ggctcccggt gatgtcaggg
     1561 ggccaacttt ttgaaaatta tcataaacat cagataaaac gaattgcaaa ggttaaaaaa
     1621 ataccgccag ttataataat tgtgatatga attacagtgt tatgaaaccc atctctggct
     1681 aaatcgccgc tctattcccg ttcccgttca cctgtaaagg gcatgcaggt ctctcaatac
     1741 gtggtgtaac acatatcgcc ttcaccgaaa tgatgtgaag acttcatcat tttagcaatc
     1801 acaggttgcc ctaatcactt aacgttatta ttgttctatt gaagccttaa cctaaaccca
     1861 ctcacaaaac gtggattatc tggttagtga ttcgcagcaa caaagcgtcc cggttcaaaa
     1921 cgaatcgtaa gacgtagttt cccttgatgt agggcttgcc gctggaacag gcggcttttt
     1981 tattctccgg cgtggggggg atgctgttga cagaaatgga aataagtaac acccggaata
     2041 ttacgcttat tgcccggcgt cttgcctgga ttaatgccaa aagaactcat atcgatatac
     2101 catcgtttgc agaactgctt ttctccggcc aaaaagcgct gttcttcgaa caatataatt
     2161 attttcactc acgacggtac acaacggcag gcacgtcaaa gccaccggat ttaccataac
     2221 atccgttgcc cgcaccgcct caggcgccct cagggcgttt ctgacggcgg tacggtaaaa
     2281 caggtaacaa accacccgaa aagccgccag aaacgtgcca ggtaaatttt aacgccatgc
     2341 atgactatgc accagaatga cggcatcctg ttttcacatc aaaatcatca caagacacag
     2401 gaaaacacac atgaaccgcc aggaatccgc cgttctcaac atagctaaat ttatccgcgc
     2461 ccagacactc ctcctgctgg aaagaattga cctgctcgac ttcgatgacg aagcgacaga
     2521 ctgcgaacag ctgcatgagc aggccgaagc gctttaccgg aagctcagcg cccgactgga
     2581 atcagacata acggcttagc ctttccgtcg cctgcatcat ggcatccaca tcatcttttg
     2641 agagatcttc atcctccagt cgtcgctcaa ggatgaacgg acacggaatt tattacgggt
     2701 cgtgaggcac tcagtatgaa agaaaaatgc agacaataca gactggaact gtaagcaagc
     2761 agtgacgaga ttaaaaatca ggataaccag agacggtatt tccgagactc agagaggtaa
     2821 tcaatacggt taaatgcccc gggatataat gcactaacga cacgccagaa atgtatctgg
     2881 gtcagctcat ctgccccacc ttccctgatg tcagaaagta cctcgtcgta agtctttcct
     2941 tcctcgcggg ctacaatcct catcgtgtcc cttgcaaggc gatcagtaca ccctccgaaa
     3001 atcagaacat caataaacac gaagtccctt ccggtaagaa aaaaaaccgg cacgggagcc
     3061 ggtaatactg tgaaaaacag cccgctttag catcgcggtt aatagtgaca tgttatgcca
     3121 ttgagcagag atataagcac ccaccaaaac taggaggaac agacatagca gacgggcgca
     3181 cccatgcaga aagctgtgta cccccgcagc gttccagcag tagccggtac tcatcctccg
     3241 tcacccacat ggtgagtatc ttgttccgtt tctcggacaa accagtctcc tgataacgcc
     3301 gtgacgggcg ggaaaccctt tcccggtcgg cgcggggttg gacaagccgc aggcgcgtca
     3361 ggcttttggc gggtttcggg gcgcagccct gaaccagtca catagcgcta gcggagtgta
     3421 tactggct
//
