LOCUS       NZ_CP091549             3988 bp    DNA     circular CON 10-JUN-2024
DEFINITION  Salmonella enterica strain 1559 plasmid p1559-3, complete sequence.
ACCESSION   NZ_CP091549
VERSION     NZ_CP091549.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25249354
            Assembly: GCF_023330725.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3988)
  AUTHORS   Ruan,Z.
  TITLE     Genome sequence of Salmonella carrying the mcr gene in China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3988)
  AUTHORS   Ruan,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-JAN-2022) Department of Clinical laboratory, Sir Run
            Run Shaw Hospital, School of Medicine, Zhejiang University, 3
            Qingchun East Road, Hangzhou, Zhejiang 310016, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100X
            Sequencing Technology :: Oxford Nanopore GridION; Illumina NovaSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023330725.1-RS_2024_06_10
            Annotation Date                   :: 06/10/2024 04:42:23
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,258
            CDSs (total)                      :: 5,135
            Genes (coding)                    :: 4,989
            CDSs (with protein)               :: 4,989
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 146
            CDSs (without protein)            :: 146
            Pseudo Genes (ambiguous residues) :: 0 of 146
            Pseudo Genes (frameshifted)       :: 41 of 146
            Pseudo Genes (incomplete)         :: 119 of 146
            Pseudo Genes (internal stop)      :: 17 of 146
            Pseudo Genes (multiple problems)  :: 28 of 146
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091549.1.
            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..3988
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="1559"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="p1559-3"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2021-06-14"
                     /collected_by="Meina Yue"
     gene            complement(join(3638..3988,1..135))
                     /locus_tag="L4413_RS26355"
     CDS             complement(join(3638..3988,1..135))
                     /locus_tag="L4413_RS26355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001749519.1"
                     /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_013631087.1"
                     /translation="MSSLLALAKDLEQQSKAQQQSTGEMLKAAFSEHEQSVKAELSASA
                     KRISDAISAHEQGMTAAMQSNRLSVLRMVGRTWLTITLVSVLLIATSGSILWWQGQQIT
                     GNYQTIRAQERTQAMLSEKNHGVQLSLCGEKKLSCVKVNPKAGAYGEEGNWMVLERK"
                     /name="MbeB family mobilization protein"
     gene            complement(<176..850)
                     /locus_tag="L4413_RS26360"
                     /pseudo=""
     CDS             complement(<176..850)
                     /locus_tag="L4413_RS26360"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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            complement(813..1133)
                     /locus_tag="L4413_RS26215"
                     /old_locus_tag="L4413_26215"
     CDS             complement(813..1133)
                     /locus_tag="L4413_RS26215"
                     /old_locus_tag="L4413_26215"
                     /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_045265547.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGRLPSI
                     SPALLRQLAGMGNNLNQIARKVNAGGAGHDRVQIVAALMAIDAGLERLRHAVLETGGDD
                     DR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1770..1853
                     /locus_tag="L4413_RS26365"
     CDS             1770..1853
                     /locus_tag="L4413_RS26365"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_072050248.1"
                     /translation="MHEPPVQSDRCALSGNYLLESNPDRHD"
                     /name="replication initiation protein"
     gene            2197..2577
                     /locus_tag="L4413_RS26220"
                     /old_locus_tag="L4413_26220"
     CDS             2197..2577
                     /locus_tag="L4413_RS26220"
                     /old_locus_tag="L4413_26220"
                     /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_032201349.1"
                     /translation="MKKITSLLLLGVFGLTGCAQNVSPQVAAQAQAPIYCENKQQCDAY
                     WTKAKAWIAMNSGWKIQMADETVIATYSPIGNSAILGYQVVKTPIGGERHEIVVQTACA
                     NMFGCIPNAIEQTAKLKNYIKN"
                     /name="hypothetical protein"
     gene            complement(2633..2842)
                     /locus_tag="L4413_RS26225"
                     /old_locus_tag="L4413_26225"
     CDS             complement(2633..2842)
                     /locus_tag="L4413_RS26225"
                     /old_locus_tag="L4413_26225"
                     /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_058679818.1"
                     /translation="MTKFEAFKDQITNAAKASFPEWVTFEYENDFPGYNESFVYESVCA
                     IKKTGELEVRNNADRYFSVKFISV"
                     /name="hypothetical protein"
     gene            complement(3422..3634)
                     /locus_tag="L4413_RS26230"
                     /old_locus_tag="L4413_26230"
     CDS             complement(3422..3634)
                     /locus_tag="L4413_RS26230"
                     /old_locus_tag="L4413_26230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137423.1"
                     /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_000137423.1"
                     /translation="MTELEKQLLTALEQLHQDYSQRLDEWESAFAEWQKMSGLMQRENA
                     ALNERVTRLSQQVANLSRQLQRLSQ"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          complement(1248..1420)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="84.659"
                     /coverage="100.0"
                     /evalue="9.74e-41"
     Typing          1367..1879
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.829"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3..823)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.876"
                     /coverage="99.0"
                     /evalue="1e-158"
     Typing          complement(3307..3986)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.238"
                     /coverage="99.0"
                     /evalue="9.44e-138"
ORIGIN
        1 cgcgcttgcg ctcagttccg cttttacaga ctgctcgtgc tcgctgaatg cggctttcag
       61 catctcgccg gtactctgct gctgcgcttt cgattgctgc tccaagtcct tcgctagcgc
      121 taaaagactg ctcataaatg gctcccttca gtcggatgtt tcgccccccg tccgggtcgg
      181 caatgctgat actgtttttt gtggtgcgga ccacctcaaa acctgccgct atgagcgccc
      241 ctgtgacgtc ctcgcgcgtt ttgagctccc cggatgaggc taaggccagt aaaccccgtg
      301 taatcgcctg agcggcttcc agcttcgttt ccggcagtgc ggacggcgtg accagtaacc
      361 gccggttctc cggggcgttt ggatcatgca gccccagtct gccgttcacc acggtctgcc
      421 aggcatcgat gcgcggccgg tcggcgcgat cgtagtacgg ctgcaggcgt ttcccggtca
      481 gcagttcagt gttggggatc aggaaattca gctccagccg ccccttgtcg gtgtgctcca
      541 cccacagaat gctgtactgg tctttatcga gcccgggcat cagaacccgc tcaaagctgg
      601 ccatgatctg ctcccgctgc ccgggcggta gttcagcctc cgcgaacgac agcacaccgg
      661 aggtgtactt tttcgcatac ggcgaggcat cgataagctc ccggacttcc tccggctttc
      721 cctgcagcac ggtcgccccc tcgcgctgcc ggtcttttcc cagcaggtaa tccaccggac
      781 cggcaccacc accacgcccc cggggatgga atttaacgat catcatcccc ccctgtttcc
      841 agcaccgcat gccgcagccg ctccagtccc gcgtcgattg ccatcagggc ggccacgatc
      901 tgcacccgat catgaccggc accaccggca ttcactttcc gggcgatctg gttcaggttg
      961 ttacccatac cggcaagctg gcgcagcagc gccggcgata tcgacggcag tctgccggca
     1021 cgtgccggct tctcatcgag gcaggtctga cgcatccacg ccgccagctg cttgccgtcg
     1081 caccgctcga gcagccgccg gtgttcgtct tccgtcaccc acatcgtgag catcttgttg
     1141 cgtttatctg ccagagtagc ctcctgataa caccgggacg ggcgggaaat ttttcccggg
     1201 cggcacggtg ttggacaagc cgcaggcgcg tcagtcgctt ttagcgggtt tcggggcgca
     1261 gccctgaacc agtcacgtag cgctagcgga gtgtatactg gcttattatg ttggcatgag
     1321 tgcggtaatc aggaaagtgc ttcatgtgac agaggaaaat gcagctgcgg gcgtaaggca
     1381 gaaaatggaa gttcagagga tatgacgcct cctcgctcac tcagtcgcgg acgctcctgc
     1441 cgttcggctg cggcgggcgt tacctgcaca cggagaagag caaaagcata tggcatgaca
     1501 aacggggcag aaaaaggatg cggcgctgcc gtttttccat aggctccgcc cccctgacaa
     1561 acatcacgaa atctgacgct caaatcagtg gtggcgaaac ccgacaggac tataaagata
     1621 ccaggcgttt ccccctggtg gctccctcgt gcgctctcct gttcctgcct ttcggtttac
     1681 cggtgtcatt ccgctgttat ggccgcgttt atctcattcc acgcctgaca ctcagttccg
     1741 ggtaggcagt tcgctccaag ctggactgta tgcacgaacc ccccgttcag tccgaccgct
     1801 gcgccttgtc cggtaactat cttcttgagt ccaacccgga tagacacgac taatcgccat
     1861 tggcaacggc cactggtaaa caggatgtgc gagagatatt gtgagagttc ttgaagtggt
     1921 gcccttacta cggctacact ggaaggacag attgggtgac acgtctcgca caagactgtt
     1981 accacggttc agaagttccc caacttactg aaccttcgaa aaaccacctc cccaggtggt
     2041 tttttcgttt acagagcagg agattacgcg ctgctcaaaa ggatctcaag aagatcattt
     2101 ttcttttgca acctaaccac acctactttc ttctttccta cgtatagata atgttaaaat
     2161 cagcacataa aaaacaataa acaacagagg cttaaaatga aaaaaataac ttctctatta
     2221 ttactcggag tctttggctt gaccggctgc gctcaaaatg tcagcccaca agtagcagct
     2281 caagctcaag cgcctatata ttgcgaaaat aagcagcaat gtgatgctta ctggactaaa
     2341 gcaaaagctt ggatagcaat gaactcaggc tggaaaatac aaatggcgga tgaaacggtt
     2401 attgcaacgt actcacctat tggtaatagt gcaattttag gatatcaagt ggtaaaaact
     2461 ccaattggag gggaaaggca cgaaattgtc gttcaaacag cctgcgccaa tatgtttggc
     2521 tgcattccta atgccatcga acaaacagca aaattaaaaa actacataaa aaactgatga
     2581 ttatattcat gaaagcccac gtttagcggg ctttccgaaa caatcaaaca tgctagaccg
     2641 atataaactt cacactaaaa tatctgtccg cattatttct tacttctaac tcacccgttt
     2701 ttttaatagc acagacggat tcataaacaa aggattcatt atatccagga aaatcatttt
     2761 catattcaaa cgttacccac tcaggaaaag atgctttagc ggcattcgtt atctgatctt
     2821 tgaaagcttc aaacttggtc atggatatat cctatgtaag aaccgggtgg ctcagagaga
     2881 ttttaccaca gaaagaatta gcatgatgag atcaccaatt taccataaca tccgttgccc
     2941 gcaccgctcc ggacaggttc gccacaaacg gggcggcagt caggtaaaac cggcaacaaa
     3001 ccacccgata caccgccccg ttcgtgacag ataaatttta cccggctgca tggtcatgca
     3061 gccagatgca tacggtctga tttcaggcca gaatccggat gaacgcctta aaaacaggaa
     3121 aatgcttctc cagccagtcc cagatctcca gcgccatgta caggcagttc agcaccgtct
     3181 caatcacgtt aaacagtctc ataatccctc cgttgtatac gctgtgatgg aaacatcacg
     3241 accgtattta gcgggaaatt tatgagccct tcttcttggg gtttgtcact ggatgcgcgc
     3301 agtcagccca gcgtcggacc gttatagctc cgctgccggg aacgggtttc agccagctct
     3361 ttttcatgct gtttctgctc gtatgcccgt tcggcggcca ccgccatttc atgccgctgc
     3421 actactggct caaacgctgt aactgcctgc tcaagttcgc cacctgctga ctcaagcgcg
     3481 tgacgcgctc gttcagcgcc gcgttctccc gttgcataag accagacatc ttctgccatt
     3541 ccgcgaaggc gctctcccac tcgtccagcc tttgcgagta gtcctgatgt aactgctcta
     3601 atgcggtcag caactgtttt tccagttccg tcatgggcta tttcctctcc agtaccatcc
     3661 agttcccttc ctccccgtaa gctcccgctt tcgggttcac tttgacgcag gacagtttct
     3721 tctccccgca gagcgacagc tgcacgccgt ggttcttctc cgacagcatg gcctgcgtcc
     3781 gctcctgcgc ccggatagtc tggtaattcc cggtgatctg ctgcccctgc caccacagaa
     3841 tgctcccgct cgtggcgatc agcagtaccg agaccagggt gatggtcagc cacgtccggc
     3901 caaccatacg caacacgctc agccggttcg actgcatcgc cgcggtcata ccctgctcgt
     3961 gggcgctgat ggcgtcgctg attctctt
//
