LOCUS       NZ_CP084219             4633 bp    DNA     circular CON 14-NOV-2023
DEFINITION  Salmonella sp. JXY0409-18 plasmid unnamed3, complete sequence.
ACCESSION   NZ_CP084219
VERSION     NZ_CP084219.1
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 4633)
  AUTHORS   Lu,X. and Li,R.
  TITLE     Salmonella JXY0409-18Chromosome sequence
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4633)
  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
            CP084219.1.
            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..4633
                     /organism="Salmonella sp. JXY0409-18"
                     /mol_type="genomic DNA"
                     /strain="JXY0409-18"
                     /isolation_source="chicken"
                     /db_xref="taxon:2879113"
                     /plasmid="unnamed3"
                     /geo_loc_name="China: Jiangxi"
                     /collection_date="2021-04-08"
     gene            complement(join(4487..4633,1..693))
                     /locus_tag="LDB27_RS23765"
                     /old_locus_tag="LDB27_23765"
     CDS             complement(join(4487..4633,1..693))
                     /locus_tag="LDB27_RS23765"
                     /old_locus_tag="LDB27_23765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001354646.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     gene            complement(885..1034)
                     /locus_tag="LDB27_RS23895"
     CDS             complement(885..1034)
                     /locus_tag="LDB27_RS23895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032194431.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPERHVKTPLAAAIGNRLEELVLK
                     LCAG"
                     /name="hypothetical protein"
     gene            complement(1704..1895)
                     /locus_tag="LDB27_RS23770"
                     /old_locus_tag="LDB27_23770"
     CDS             complement(1704..1895)
                     /locus_tag="LDB27_RS23770"
                     /old_locus_tag="LDB27_23770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_000165986.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1958..2281
                     /locus_tag="LDB27_RS23775"
                     /old_locus_tag="LDB27_23775"
     CDS             1958..2281
                     /locus_tag="LDB27_RS23775"
                     /old_locus_tag="LDB27_23775"
                     /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_001677263.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2490..>2930
                     /locus_tag="LDB27_RS23870"
                     /pseudo=""
     CDS             2490..>2930
                     /locus_tag="LDB27_RS23870"
                     /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            2959..3519
                     /locus_tag="LDB27_RS23785"
                     /old_locus_tag="LDB27_23785"
     CDS             2959..3519
                     /locus_tag="LDB27_RS23785"
                     /old_locus_tag="LDB27_23785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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_000067488.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            3526..3759
                     /locus_tag="LDB27_RS23790"
                     /old_locus_tag="LDB27_23790"
     CDS             3526..3759
                     /locus_tag="LDB27_RS23790"
                     /old_locus_tag="LDB27_23790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_000137388.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          1532..1616
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(963..1521)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.761"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2272..3857
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.811"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcttgataac gctctatatg ttttgagtga aggttgcatt atagatggaa agtatttgaa
       61 aacctcttca tctctgttga aattaactaa aaacttgtag tcatcattta taaatctcaa
      121 gcatacagcg tcaagcttat cgccttttct tattattatt tctttatagg aaagatattt
      181 ttcagaagat aagtcccaca tcaagcgaaa atctctcttt gcgaacgagt tcgcgtcatc
      241 attgaaaaga gatgatgtga tggctttgga tagaccttct gtgtttatct ctttgttgga
      301 tgggtagtaa attttattaa ttgctttcat tctctcaaat gatgaatata ggtcattatg
      361 ccaccttgtt gaaatcaccc ctttagttat attctccttg ctaaaattaa gccctgtatc
      421 aaaaataaat gcagccatca gtgaatatga tatgtttttt attaactcag acttaaatgg
      481 ttccgctatg gagtagtaca gtgataaaat aactaaaaat aaaaggtatt gtcttacctt
      541 tcccgatgag tatatgtaaa ggcgatattt atttattgat agttttattt tgtatggaat
      601 gatctcattt ctgtcatatc ctcttcgtgg tggagcaaaa caaaagaaac atgcagctat
      661 taataaaaca aaaaagatga acagtgtaag caagttcggc tcctgtgtat gctcactatg
      721 catgattgtc ttgagatcta acgatcctga aggtagtctt gtccgtaaac gaaaaaaccg
      781 cccagcaagg cggcttttcg aaggttctca gagcagcaac tctttgaacc aaggtaactg
      841 gcttggagga gcacagccac caaatctgtc ctttcagttt agccttaacc ggcgcataac
      901 ttcaagacta actcctctaa acggttacca atggctgctg ccagtggcgt ttttacgtgt
      961 ctttccgggt tggactcaag acgatagtta ccggataagg cgcagcggtc gggctgaacg
     1021 gggggttcgt gcacacagcc cagcttggag cgaacgacct acaccgggcc gagataccaa
     1081 cagcgtgagc tatgagaaag cgccacgctt cccgaaggga gaaaggcgga caggtatccg
     1141 gtaagcggca gggtcggaac aggagagcgc acgagggagc ttccaggggg aaacgcctgg
     1201 tatctttata gtcctgtcgg gtttcgccac ctctgacttg agcgtctgtt tttgtgatgc
     1261 tcgtcagggg ggcggagcct atggaaaaac gccagcggcg cggccttctt cctgttcttg
     1321 gccttttgct cacatgtttc ttttggcgtt atcccctgat tctgtggata accgcatcac
     1381 cgtctttgag tgagctgata ccgctcgccg cagccgaacg accgagcgta gcgagtcagt
     1441 gagcgaggaa gcggaagagc gcctgatgcg gcattttctc cttacgcatc tgtgcggtat
     1501 ttcacaccgc atatggtgca cttttcttat aatccgcact gatgccacat agttaagcca
     1561 gtatacactc cgctatcgct acgtgactgg gtcagggctg cgccccgaca cccgctaaaa
     1621 cccgctgacg cgccctgacg ggcttgtctg ctcccggcat ccgctcacag gcaagctgtg
     1681 aacgtctccg ggagctgcat gtttcagttg ctttcaccgt catcgccgaa gcgtgcgagg
     1741 caactacggt agagttcgtc ggcgtggtcg tgaagtgatt cgcagatgtc tgcctgttcg
     1801 tccgcgtcca gctcgttgag tttttccagc agggtcagcg tctggcttct gataaagcgg
     1861 gccatgttaa gggctgtttt ttcctgtttg gtcatggtct taaggctcct taatagggga
     1921 ttttttaggg ggaatgatac cgatgaaacg cgagaagatg ctcacgatac gggttagcga
     1981 tgaggagcac gcccggttac tggaacgctg cgagggtaaa cgactggcag aatggatgcg
     2041 gcgggtctgt ctgggggagc cggttgcgcg cacaggaaaa ctgccgacac tatcgccgcc
     2101 attgctgcgg catctggctg ccatcgggaa caatctgaac cagacagccc ggaaggtgaa
     2161 cagcggccac tggtcttcga ttgaccgggt tcatgtggtg gccgcactga tggccatcga
     2221 gggtgaattg cgccagttgc ggcaggctgt cagggaacag gggggacggg atgatagtta
     2281 aatttcatgc cagggggaaa ggcggtggaa gtggcccggt cgattacctg ctggggcggg
     2341 agcgtaaccg cgaaggcgca acggtgctcc ggggtaaccc ggaagaaatc cgggaactca
     2401 ttgatgccac gccattttcg aagaaataca cgtcaggcgt tctgtcgttc gcggagaagg
     2461 agttaccgcc gggtgaacgc gaaagagtga tgacgagctt tgagcgtgtt cttatgcccg
     2521 gtctcgaaaa agaccagtac agcattctct gggtggaaca ccaggataag gggcggctcg
     2581 aactgaattt tgtcattccg aacatggaac tacagagcgg taagcgcctc cagccgtact
     2641 acgaccgtgc ggacaggccg aggataaatg cctggcagac gctggttaat catcattacg
     2701 ggctgcgtga cccgaacgca ccggagaaca gacggacgct tgtcacaccg aataatctgc
     2761 caaaagcgaa acaggaggcc gcagaagcga ttacacgggg tcttgaggcg ctttaccgtg
     2821 ccggagcaat aaaaacgcgt caggatgtca ctgaggcgct cacagcggca ggttttgagg
     2881 tggtgaggac aaccagaagc agtatcagta ttgccgaccc ggaggggggg cggaatctca
     2941 ggctaaaggg ggcgctgtat gagcaatctt ttacaaatgg gaacagactt cgagaagaaa
     3001 ctgaaagagc gagccgcttc taccgagaac atgctgaaca gcgagttcag gaagctagaa
     3061 gagtctgtag acaaggcact gagcttaaac aggcagaaaa tcagagacgc tatcagcgaa
     3121 catacaacat ccgtgaaaca gcaactggat acgctgagca ccaccgtgag cacgcagctc
     3181 agcaccacag aggccgaact gtcccggcag cagaaaaacc tgctctggca ggtgatcaaa
     3241 gggcgggtac tgtttccggc gctgaccgcg ctcagcgtca cgggcggcat tttcctgggg
     3301 tgctgggggc tgattcagtg gcaggaaagc aggattgcga aaaatatctt gaccatcaga
     3361 gagcaggaaa acacgctggc gaaactcgag gcaaaaacct ggggggtgac gttcgtcaat
     3421 ggcgagaacg ggaaatttct ggtgctgccg gacggggtga aaggggaaaa cacctggacg
     3481 gtgggcgaca agaacgccgt gaggctggtc agggagtaaa cgagtatgac ggaactggaa
     3541 gggcatttgc tgaacgcctt agagcatttg caacaggact atatgcggcg gctgaacgag
     3601 tgggagagcg ccttcgcaga attgcagaag atgcacgcgg ttacgcaaca gaacaacgcg
     3661 atactgaacg agcgtgtcgt gaacttgagt cagcaggtgc agctattagc cggacaagtc
     3721 gaccgcttga gtcggttatt tatcacgaac aacagataag ggatgaacag gagcgtcagg
     3781 cgcaggagct tgcccggcgc tggcatgaag agcaggaacc cgaagcgcgg atctggcgtg
     3841 gcccgtcaat ggggatgtga ccggggtgcc ccctgaaatc gagccagttt gtggcacgcc
     3901 ctacccggat ggcgccaatg ttaatgtacg tacattagca ttaacaatat ccaaacctcc
     3961 ccattttgcc ccgttcgacg gctggaacgt gcgaaactga tcgtcattca gtttcgcgca
     4021 taactatgca tgaggttaaa atttaccagg cgcgatcgcg gcagtttttc gggtggtttg
     4081 ttgctgtttt tacctgtctg ctgccgtgat cgcgctgaac gcgtttaagc ggtacgcgca
     4141 atgcgacgtt atggtaaata cggagtattt taattgcggg aattaaaaca acaaaggccc
     4201 gctgtactct atacagcggg cctttgttgt atatctctgt cgtttgtccc cggggggaag
     4261 cattactgct aacaagtccc gtgagaaaac tgcgcaatcg tattgcgcac catgaaccta
     4321 ttctcaaccg caatctggag gatgattttg ctacgataaa gagaattatc gcgtatcggt
     4381 gtcagcattc attggagtgg atgctgaaaa accaggtgtt actccctcta cttacactta
     4441 aacctctcta aaaatataag taagtactat cgagggctat catgaactat ggtgccctct
     4501 gagcatagct acccattact tcttctatgt cattgaataa ttcatttctt aactctaagt
     4561 attccagtaa ctccatttct aatgactctg tcgtgaactt aaatctagaa ggatctttga
     4621 ttgagtttac tag
//
