LOCUS       NZ_CP084218             4781 bp    DNA     circular CON 14-NOV-2023
DEFINITION  Salmonella sp. JXY0409-18 plasmid unnamed2, complete sequence.
ACCESSION   NZ_CP084218
VERSION     NZ_CP084218.1
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 4781)
  AUTHORS   Lu,X. and Li,R.
  TITLE     Salmonella JXY0409-18Chromosome sequence
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4781)
  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
            CP084218.1.
            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..4781
                     /organism="Salmonella sp. JXY0409-18"
                     /mol_type="genomic DNA"
                     /strain="JXY0409-18"
                     /isolation_source="chicken"
                     /db_xref="taxon:2879113"
                     /plasmid="unnamed2"
                     /geo_loc_name="China: Jiangxi"
                     /collection_date="2021-04-08"
     gene            join(4599..4781,1..174)
                     /locus_tag="LDB27_RS23730"
                     /old_locus_tag="LDB27_23730"
     CDS             join(4599..4781,1..174)
                     /locus_tag="LDB27_RS23730"
                     /old_locus_tag="LDB27_23730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000075993.1"
                     /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_023316024.1"
                     /translation="MSQATRKPSTVGDIILYEYLEPSGLKINDLAEMLNVHRNSASALV
                     NNNRKLSTDMAFRLAKAFDTTAKFWLNIQQSVDLWEVTSSPRLQEEIDRVIPAHEIIER
                     KHIVDSSEKKHAIA"
                     /name="HigA family addiction module antitoxin"
     gene            complement(<494..616)
                     /locus_tag="LDB27_RS23890"
                     /pseudo=""
     CDS             complement(<494..616)
                     /locus_tag="LDB27_RS23890"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001487656.1"
                     /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="replication initiation protein"
                     /name="replication initiation protein"
     gene            1265..1588
                     /locus_tag="LDB27_RS23735"
                     /old_locus_tag="LDB27_23735"
     CDS             1265..1588
                     /locus_tag="LDB27_RS23735"
                     /old_locus_tag="LDB27_23735"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_163063187.1"
                     /translation="MLTMWVTEGEHRRLLERCDGRPLAAWMRQTCLDEKPARTGKLPSL
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1797..>2231
                     /locus_tag="LDB27_RS23865"
                     /pseudo=""
     CDS             1797..>2231
                     /locus_tag="LDB27_RS23865"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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"
     gene            2266..2757
                     /locus_tag="LDB27_RS23745"
                     /old_locus_tag="LDB27_23745"
     CDS             2266..2757
                     /locus_tag="LDB27_RS23745"
                     /old_locus_tag="LDB27_23745"
                     /inference="COORDINATES: protein motif:HMM:NF016710.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_032629998.1"
                     /translation="MSSLLTLAKDLEQQSKAQQQSTGEMLKAAFSEHEQSVRAELSASA
                     RRISDAILAHEQSMSEAMEKNRRSVLRTAGRTWFTILMVSALLIGTSGSILWWQGQQIT
                     DNYTHLRQQEDTLAKMTARTWGVRYQESSDGRRFLILPPGMQTEAIPYDGTTWIRLKQE
                     "
                     /name="MbeB family mobilization protein"
     gene            2764..2979
                     /locus_tag="LDB27_RS23750"
                     /old_locus_tag="LDB27_23750"
     CDS             2764..2979
                     /locus_tag="LDB27_RS23750"
                     /old_locus_tag="LDB27_23750"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /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_000137422.1"
                     /translation="MTELEKQLLSALEQLQQDYSQRLDEWESAFAEWRSMCGLMQRENA
                     VLNERVSDLSTQVLSLSEQLRRLSGN"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3650..3892)
                     /locus_tag="LDB27_RS23755"
                     /old_locus_tag="LDB27_23755"
     CDS             complement(3650..3892)
                     /locus_tag="LDB27_RS23755"
                     /old_locus_tag="LDB27_23755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001713065.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023316026.1"
                     /translation="MALVRSGNKSKIFEADTKFNSVFDTEYKPGETCEYEGIYKCTGCG
                     KEVTIAGGKTIPPQNHHQHTPAQGNIRWQLFVYAQ"
                     /name="hypothetical protein"
     gene            4079..4396
                     /locus_tag="LDB27_RS23760"
                     /old_locus_tag="LDB27_23760"
     CDS             4079..4396
                     /locus_tag="LDB27_RS23760"
                     /old_locus_tag="LDB27_23760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001183575.1"
                     /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_023316025.1"
                     /translation="MQQDHEHDDCRIQFRDDWLYQFYKYGKANRKIPTAISASLGRKLD
                     MLNAADKVGDLRSPPGNRFENLNPPLTGYSSIRVNEKYRLIFKWGENGVEDLYLDPHDY
                     R"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     Typing          979..1152
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.0"
                     /coverage="100.0"
                     /evalue="1.21e-74"
     Typing          complement(504..1012)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.51"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          1266..1582
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="99.0"
                     /evalue="1.5100000000000001e-59"
     Typing          1579..3071
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.2"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gccttcgata ccactgcaaa gttctggcta aatatacagc agtctgttga tttatgggag
       61 gttactagta gccctcgatt gcaagaagaa atagacagag tgattcccgc tcatgaaatc
      121 atagaaagga aacacattgt tgatagttct gagaagaaac atgctattgc atgatttttt
      181 ttaaaaaaat ataagttatc cctcaaaaag aaggcttcta gttatagaag ccttcttttt
      241 gagggataaa aacgctcatg ttaactttct tcttacgatc ttcttgagat ccgtgctctg
      301 tacgcgtaat ctcttgctct gtaaacgaaa aaaccgcctg gggaggcggt ttttcgaagg
      361 ttaagtcagt tggggaactg cttaacctgg taactggctt cagcagagcg cagataccaa
      421 atactgtcct tccagtgtag ccgtagttag gccaccactt caagaactct gtagcaccgc
      481 ctacatacct cgctctgcta atcctgttac cagtggctgc tgccagtggc gttttgtcgt
      541 gtctttccgg gttggactca agtcgatagt taccggaaca ggcgcagcgg tcggactgaa
      601 cggggggttc gtgcatacag tccagcttgg agcgaactgc ctacccggaa ccgagtgtca
      661 ggcgtggaat gagacaaacg cggccataac agcggaatga caccggtaaa ccgaaaggca
      721 ggaacaggag agcgcacgag ggagccatca gggggaaacg cctggtatct ttatagtcct
      781 gtcgggtttc gccaccactg atttgagcgt cagattctgt gatgctcgtc aggggggcgg
      841 agcctatgga aaaccggctc tgccgtggcc ttatcgcttc cctgttaagt ttcttcctgg
      901 catcttccag gaaatttccg ccccgttcgt aagcccgcac cgctcgccgc agccgaacga
      961 ccgagcgcag cgagtcagtg agcgaggaag cggaatatat cctgtatcgc atattctgct
     1021 gacgcgccgt tgccgccttt tttctcctgc cacatgaagc acttcactga tttccgtatc
     1081 cgtgccaaca tattaagcca gtatacactc cgctagcgct acgtgactgg ttcagggctg
     1141 cgccccgaaa cccgccaaaa gcctgacgcg cctgcggctt gtccaacccc gcgccgaccg
     1201 ggaaaggctt tcccgcccgt cccggcgtta tcaggaggcc ggtttgtcag agaaacggaa
     1261 caagatgctc accatgtggg tgacggaggg cgagcaccgg cggctgcttg agcgctgcga
     1321 cggcaggccg ctggcggcgt ggatgcggca gacctgcctg gacgaaaagc ctgcgcgcac
     1381 cggaaagctc ccctcactct cgccggcgct gctgcgccag cttgccggta tgggcaataa
     1441 cctgaaccag atagcccgcc gtgttaacgc cggcggcggc accggccatg acagggtaca
     1501 gattgtggcg gcgctgatgg ccatcgatgc cgggcttgag cggctgcggc acgccgttct
     1561 tgagaaagga acggacgatg atcgttaaat ttcatccacg cggtcgcggc ggtggcgccg
     1621 ggccggtgga ctatctgctg ggtaaagacc ggcagcgtga aggcgccagc gtcctgcagg
     1681 ggaagccgga agaagtccgg gagctgattg acgcgtcgcc ttacgtgaag aaatacacct
     1741 ccggcgtact gtcgtttgcg gaggccgatc tgcctcccgg ccagcgggaa aaactgatgg
     1801 ccagcttcga gcgggttctg atgcccggac tcgataaaga tcagtacagc attctgtggg
     1861 tggagcacgc ggacaagggg cgtctggagc tgaactttct gatccccaat accgaactgc
     1921 tgaccggcag gcggctccag ccgtactacg accgcgccga ccggccgcgc atcgatgcct
     1981 ggcagaccat cgtgaacggc agactggggc tgcatgaccc gaacgcgccg gaaaaccgcc
     2041 gggcgctggt cacgccgtcc ggactgccga aaacgaagca ggaggccact gaagccatca
     2101 cgcgcggact gctgaccctt gcttcgtccg gggagctgaa aaaccgtcag gacgtcactg
     2161 aggcgctgga acggtcaggt tttgaggtgg tgcgcaccac gaaaagcagt atcagcattg
     2221 ccgacccgga cggggggcga aacatccgac tgaagggagc catctatgag cagtctttta
     2281 acgctggcga aggacttaga gcagcaatcg aaagcgcagc agcagagtac cggcgagatg
     2341 ctgaaagccg cattcagcga gcacgagcag tctgtcagag cggaactgag cgcaagcgcg
     2401 aggagaatca gcgacgccat cctcgcacac gagcagagta tgagcgaggc gatggagaaa
     2461 aaccggcgga gcgtactgcg gactgccggg cggacatggt tcaccatcct gatggtgtca
     2521 gcgctgctga tcggcacgag cgggagcata ctgtggtggc aggggcagca gataaccgac
     2581 aattacacgc atcttcgtca gcaggaagat accctggcga aaatgactgc ccggacgtgg
     2641 ggagtgcgct atcaggagag cagcgacggc cggaggtttc ttatcctgcc gcccgggatg
     2701 caaaccgaag ccatccccta cgacgggacg acatggatcc gcctgaaaca ggagtagcgg
     2761 aaaatgacag agctggaaaa gcagttgctg agcgcattag agcagctaca gcaggactac
     2821 tcgcaaaggc tggacgaatg ggagagcgcc ttcgcggaat ggcggagcat gtgtgggctt
     2881 atgcaacggg agaacgcggt gctgaacgag cgcgtgtcgg acttgagcac gcaggtgctg
     2941 agtttaagcg agcagctgcg ccgcttgtcc gggaactgaa tgccatcgag ctccggcaga
     3001 gggagaatga gtatcagaaa acactggagc tggagcgcca gccgcagaaa acctaccgcg
     3061 ggccgacact ttaaaccatc caggcagctg acaacccgca cgaagagggg ctcttatttc
     3121 tcccgctaaa taggttcgtg atcaaaaagg tcacgactta ttcaggagcg ggaaatgaag
     3181 ctgttaaatc ttattgaatc attgcttaac tgcctgtatc tggcggcgga gctgtgggac
     3241 tggctggaga agtatttgtc ggtttttaag gcattggcgc ggattttagt gtgactttaa
     3301 catccatgca tctggctgca tgactatgca ccagtgtaat attcagcggc tgcgtttctg
     3361 gtgttttttc gttatgtctg tcgccacttt ctcgcgtctg gcaccggaaa cgcagccaac
     3421 cccgtttcag cggtgcgccc aacggatgtt atggtaaatc agtatcagct gcagatataa
     3481 aaaagccgcc aggctggcgg cttgctgtta ttttcgtggc tttcctgcat ctgagcgttt
     3541 tcctctgacc cttccgtcat tgttacggtc acgaggttga gttccgccgc ctggtttagg
     3601 aacgacaacg tgtgggttga gtggtcgacg atctgccatt ttctatacct cactgagcat
     3661 aaacaaacaa ttgccaacga atgttccctt gcgcgggggt atgttggtgg tggttttgtg
     3721 gtgggattgt tttcccgcct gcgatagtta cttctttacc gcaaccggta catttataaa
     3781 tcccttcata ttcacatgtt tctcccggct tatattcagt gtcaaaaacc gagttaaact
     3841 tcgtatctgc ttcaaaaatc ttgcttttgt ttcctgagcg aacaagagcc atgcaacctc
     3901 caaattatca tttattttgc acacctgcac tgtgcatgag tgcattctac agcatagcca
     3961 ttgattgcac aagtgcactg tgctgttgtg catttgagat gtttgctgta ctatatcgga
     4021 ggtaagaagg tgatcgaaaa aattgccaag ttgcggcaaa aattgaggta aaagaaaaat
     4081 gcagcaagat catgaacatg atgattgccg cattcagttt cgagacgatt ggctatacca
     4141 gttttacaaa tatggtaaag ccaatcgaaa gattccaact gcgattagtg cttcattagg
     4201 tcgcaagctg gatatgctga atgctgctga taaagttgga gatttgcggt ctcccccggg
     4261 aaaccgattt gagaatctca accctccatt gacagggtat tcatccatac gggtgaatga
     4321 gaagtaccgc ttgatattta agtggggtga aaacggagtc gaggatttgt atctcgatcc
     4381 acatgattac cgatagataa caggtcgtgg ctgttatctt ataaaacaag taggtgaggc
     4441 gttccctcac ctacattaaa atgtcattac aaataatgat taataaaaaa aatgacgtga
     4501 ctatatttaa gataattact catcgctaca gctggtaata gacgaaatac ttatcttcct
     4561 catctaacag agagaagtaa aaaatttagg agtaaagcat gtcccaagca actagaaaac
     4621 catcaactgt aggggatatt attctttatg aatatctcga accaagtggt ttaaaaatca
     4681 atgacttggc tgaaatgttg aatgtgcata gaaactctgc cagtgcttta gttaacaata
     4741 atagaaagct gtctaccgat atggctttta ggttggctaa a
//
