LOCUS       NZ_CP091562             5430 bp    DNA     circular CON 10-JUN-2024
DEFINITION  Salmonella enterica strain 179 plasmid p179-3, complete sequence.
ACCESSION   NZ_CP091562
VERSION     NZ_CP091562.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16419720
            Assembly: GCF_023330825.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5430)
  AUTHORS   Ruan,Z.
  TITLE     Genome sequence of Salmonella carrying the mcr gene in China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5430)
  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_023330825.1-RS_2024_06_10
            Annotation Date                   :: 06/10/2024 04:41:36
            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)                     :: 5,146
            CDSs (total)                      :: 5,023
            Genes (coding)                    :: 4,894
            CDSs (with protein)               :: 4,894
            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)              :: 129
            CDSs (without protein)            :: 129
            Pseudo Genes (ambiguous residues) :: 0 of 129
            Pseudo Genes (frameshifted)       :: 36 of 129
            Pseudo Genes (incomplete)         :: 105 of 129
            Pseudo Genes (internal stop)      :: 18 of 129
            Pseudo Genes (multiple problems)  :: 27 of 129
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091562.1.
            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..5430
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="179"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="p179-3"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2017-06-01"
                     /collected_by="Meina Yue"
     gene            complement(join(5215..5430,1..270))
                     /locus_tag="INN78_RS25805"
     CDS             complement(join(5215..5430,1..270))
                     /locus_tag="INN78_RS25805"
                     /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_001749519.1"
                     /translation="MSSLLALAKDLEKQSKAQQQNTCEMLKAAFSEHEKSVKAELSASA
                     KRISDAISAHEQGMTAAMQSNRLSVLRMVGRTWLTITLVSVLLIATSGSILWWQGQQIT
                     GNYQTIRAQERTQAMLSEKNHGVQLSLCGEQKLSCVKVNPKAGAYGEEGNWMVLERK"
                     /name="MbeB family mobilization protein"
     gene            complement(<305..985)
                     /locus_tag="INN78_RS25810"
                     /pseudo=""
     CDS             complement(<305..985)
                     /locus_tag="INN78_RS25810"
                     /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(948..1268)
                     /locus_tag="INN78_RS25660"
                     /old_locus_tag="INN78_25650"
     CDS             complement(948..1268)
                     /locus_tag="INN78_RS25660"
                     /old_locus_tag="INN78_25650"
                     /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_000957082.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGRLPSI
                     SPALLRQLAGMGNNLNQIARKVNTGGAGHDRVQIVAALMAIDAGLERLRHAVLEKGGND
                     DR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1906..1989
                     /locus_tag="INN78_RS25815"
     CDS             1906..1989
                     /locus_tag="INN78_RS25815"
                     /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_071532987.1"
                     /translation="MHEPPVQSDRCAFSGNYRLESNPERHD"
                     /name="replication initiation protein"
     gene            2291..2917
                     /locus_tag="INN78_RS25665"
                     /old_locus_tag="INN78_25655"
     CDS             2291..2917
                     /locus_tag="INN78_RS25665"
                     /old_locus_tag="INN78_25655"
                     /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_227697613.1"
                     /translation="MSPTLNKQASKERCAVEFATRKKSKTQRKKSKALSYRGLCFFCTL
                     VTGKCQWTSKMSKQDYIQLRTLTDQFYADNKGLQEALDGSNDGKVRGYGIVVIDLNGLV
                     FGIPLRSHLNHKFGFVSERSEGVKKGLDYTKALLIKKEEYVSRAYKIPTPEFTHVNDNK
                     EKIQEDFNKFVNRYIEANVKKDENILRNYRYSTLKNYHKELGLED"
                     /name="hypothetical protein"
     gene            complement(2946..3509)
                     /locus_tag="INN78_RS25670"
                     /old_locus_tag="INN78_25660"
     CDS             complement(2946..3509)
                     /locus_tag="INN78_RS25670"
                     /old_locus_tag="INN78_25660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015959180.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001749520.1"
                     /translation="MHALSILPSVARANLATKFSSHLKVIELFNTMQDSQVVVLSSLIE
                     GHHLTSSGNSVKADFEVTRLPAIIEMLEKKYFFPIRHLNVSVKSVTTGRMTGQTVYFIE
                     PEHIEQLLADPELVFANQERSLFFRSLEKEGKNLGKLIEKKGSVSQAVLSLLHHAYKDK
                     PLSDEMWKEIEDKFTHMLDELSAA"
                     /name="hypothetical protein"
     gene            complement(3767..4177)
                     /locus_tag="INN78_RS25675"
                     /old_locus_tag="INN78_25665"
     CDS             complement(3767..4177)
                     /locus_tag="INN78_RS25675"
                     /old_locus_tag="INN78_25665"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000874179.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000874179.1"
                     /translation="MAFISLSNLAAKTGRIIQSQCVTATQTKKSTGAVELGFRLSKSAM
                     DETGITIGDRVDILYDKEENQWMIKKISEGGFGVSGQKNKHGGYSSCAVRLTLRPGFPR
                     LSEDEEDNKKLLSDDSFTQLSEGVIVFRLDDE"
                     /name="hypothetical protein"
     gene            complement(4999..5211)
                     /locus_tag="INN78_RS25680"
                     /old_locus_tag="INN78_25670"
     CDS             complement(4999..5211)
                     /locus_tag="INN78_RS25680"
                     /old_locus_tag="INN78_25670"
                     /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(1377..1556)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.339"
                     /coverage="83.0"
                     /evalue="7.539999999999999e-48"
     Typing          1502..2015
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.217"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3..958)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.536"
                     /coverage="99.0"
                     /evalue="1.04e-179"
     Typing          complement(4884..5428)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.154"
                     /coverage="99.0"
                     /evalue="8.37e-100"
ORIGIN
        1 ggcgatcagc agtactgaga ccagggtgat ggtcagccac gtccggccaa ccatacgcag
       61 cacgctcagc cggttcgact gcatcgccgc ggtcataccc tgctcgtggg cgctgatggc
      121 gtcgctgatt ctcttcgcgc ttgcgctcag ttccgctttt acagacttct cgtgctcgct
      181 gaatgcggct ttcagcatct cgcaggtatt ctgctgctgc gctttcgatt gcttttccaa
      241 gtccttcgcc agcgctaaaa gactgctcat aaatggctcc cttcagtcgg atgtttcgcc
      301 ccccgtccgg gtcggcaatg ctgatactgt tctttgtggt gcggaccacc tcaaaacctg
      361 ccgcagtgag cgaccctgtg acgtcctcgc gcgttttgag cgccccggat gaggctaagg
      421 ccagcaaacc ccgtgtaatc gcctgagcgg cttccagctt cgtttccggc agtgcggacg
      481 gcgtgaccag taaccgccgg ttcttcgggg cgtttggatc atgcagcccc agtctgccgt
      541 tcaccacggt ctgccaggca tcgatgcgcg gccggtcggc gcgatcgtaa tacggctgca
      601 ggcgtttccc ggtcagcagc tctgtgttgg ggatcaggaa attcagctcc agccgcccct
      661 tgtcggtgtg ctccacccac agaatgctgt actggtcttt atcgagcccg ggcatcagaa
      721 cccgctcaaa gctggccatg atctgctccc gctgcccggg cggcagctca gcctccgcga
      781 acgacagtac gccggaggtg tactttttcg catacggcga ggcatcgata agctcccgga
      841 cttcctccgg ctttccctgc agcacggtcg ccccctcgcg ctgccggtct tttcccagca
      901 ggtaatccac cggaccggca ccaccaccgc gcccccgggg atggaattta acgatcatca
      961 ttcccccctt tttccagcac cgcatgccgc agccgctcca gtcccgcgtc gattgccatc
     1021 agggcggcca cgatctgcac ccggtcatga ccggcaccac cggtattcac tttccgggcg
     1081 atctggttca ggttattacc cataccggca agctggcgca gcagcgccgg cgatatcgac
     1141 ggcagtctgc cggcacgcgc cggcttctca tcgaggcagg tctgacgcat ccacgccgcc
     1201 agctgcttgc cgtcgcaccg ctcgagcagc cgccggtgtt cgtcttccgt cacccacatc
     1261 gtgagcatct tgttgcgttt gtctgccaga gtagcctcct gataacaccg ggacgggcgg
     1321 gaaatgtttc ccggtcggca cggtgttgga caagccgcag gcgcgtcagt ggcttttagc
     1381 gggtttcggg gcgcagccct gaaccagtca cgtagcgcta gcggagtgta tactggctta
     1441 atatgttacg gcggagtaac actttataaa agtgcttcat gtggcagggg aaaatgcagc
     1501 tgcagggcgt acgggagaac atggaggttg cggtgatatt acgcctcctc gctcactcgg
     1561 tcgcttccgc tcctgccgtt cggctgcggc gggcgttacc tgcacacgga taagagcaaa
     1621 ggcatacggc atgacaaaca gggcaagaaa aggatgcggc gctgccgttt ttccataggc
     1681 tccgcccccc tgacaagcat cacgaaatct gacgctcaaa tcagtggtgg cgaaacccga
     1741 caggactata aagataccag gcgtttcccc ctggtggctc cctcgtgcgc tctcctgttc
     1801 ctgcctttcg gtttaccggt gtcattccgc tgttatggcc gcgtttatct cattccacgc
     1861 ctgacactca gttccgggta ggcagttcgc tccaagctgg actgtatgca cgaacccccc
     1921 gttcagtccg accgctgcgc cttttccggt aactatcgac ttgagtccaa cccggaaaga
     1981 cacgactaat cgccattggc aacggccact ggtaaacatg atgtgcgaga gatgtattga
     2041 gagttcttga agtggtggcc ttactgaggc tacactggaa ggacggattt ggtgacacgt
     2101 ctcgcacaag actgttacca cggttagata atctgccagg attaaataac cttcgaaaaa
     2161 ccacctgcca gggtggtttt ttcgtttcag gagaagatta cgctggcaaa gtaagtccag
     2221 tcaagaacag ctacgaaatt gacttcacat ataatttttg atataagtaa atctagaagt
     2281 ggcggtagga atgagcccca cgttaaacaa acaagcttcc aaagaaagat gtgcggtaga
     2341 gttcgccaca cgtaaaaaat ccaagactca acgaaagaaa agcaaagccc tctcttacag
     2401 agggctttgc tttttttgta cattggttac aggaaaatgc caatggacat caaaaatgag
     2461 caaacaggat tacatacagt taagaaccct tacagaccag ttttatgctg ataacaaagg
     2521 cctacaagag gctctcgacg gcagtaatga tggaaaagta agaggctacg gaatcgtagt
     2581 tattgatctc aacggattgg tgttcgggat acccttacga agccatttaa accataaatt
     2641 tggattcgtt tcggagcgat cagaaggtgt taagaaagga ctggattaca ccaaagcgtt
     2701 gctaattaag aaagaagagt atgtatcgcg agcctataag ataccaactc ctgaatttac
     2761 ccatgtcaat gataacaaag aaaaaataca agaagatttc aacaaattcg taaacagata
     2821 catagaagcg aacgtcaaga aagatgaaaa catactcaga aactatcgtt actctacgct
     2881 gaaaaactat cacaaagaat taggtttaga agactaaaaa ggcggtctaa cgaccgccct
     2941 tgcctttacg ccgcgctcaa ttcatccagc atatgggtga acttatcttc tatctccttc
     3001 cacatctcgt cagaaagagg tttatctttg taggcgtgat gtagaaggct taagacggct
     3061 tgagaaacac tacctttttt ctcgataagc ttgccgagat ttttcccttc tttttcgaga
     3121 gaacgaaaga agaggctcct ttcctgatta gcaaacacaa gctcaggatc agcgagaagt
     3181 tgctcgatgt gttcaggctc tatgaaatag acagtttgtc cagtcatcct tcctgtagtt
     3241 acagatttaa cagatacatt tagatgacga atagggaaaa aatatttttt ctctaacatc
     3301 tcgataatcg ccggtaagcg agtgacctca aagtcggctt tgacactgtt accagaactg
     3361 gtgaggtgat ggccttcgat cagtgatgac aagacaacaa cttgggaatc ctgcatcgtg
     3421 ttgaagagct cgatcacctt caaatgagac gagaatttag ttgccaggtt agcgcgggca
     3481 actgaaggta gtattgataa agcgtgcata tgtatagcct catatgtttt taaaaacata
     3541 aacttaagag accaaagcca atagcatcgc acctatcaga atagaaaatg tcgtgttcac
     3601 atccctcaaa agaaacgatt ttttctttat tagaatgcaa gtttatgaac ataatgccgc
     3661 ccataacact ccacccttcc aaaggtagtg atgtgttgac cagaaggcgg agttagtcga
     3721 ttgtttggcg acgctcacta actctgcctt tcctttttgg tccttcctat tcatcatcca
     3781 gcctgaagac gattacacct tcacttagct gagtgaatga atcatcggaa agtagcttct
     3841 tgttgtcctc ttcatcctca gaaaggcgag gaaaacctgg tcgcaaggtc aatctaacag
     3901 cacacgatga gtaaccgccg tgcttgtttt tttgcccaga cacaccaaag ccaccttcac
     3961 taattttctt aatcatccac tggttttctt ctttgtcgta aagaatgtcg acacgatccc
     4021 caatggtaat accagtctcg tccatagcgc tcttgctcaa gcggaatccc agctcgacag
     4081 cgcccgtgct ttttttcgtt tgcgtggccg taacacactg cgactggatt atccttccag
     4141 tcttcgctgc caagttcgat agagagataa aagccataat acaatccgtt ttagacatcg
     4201 atcagttctt atacggaagt gtacccaggg agcgaggtgg ctttcaagat cttttgtatt
     4261 gatttttcta gagccgcaaa aaacggcgat aagaaacctt aaatacaaaa acaattgctc
     4321 gtattgaacc tcgtcaagat acacatccag atcgatcttt atgtaagtaa agggtatttt
     4381 tctatggtga tttaaagtcg agcaacgtca gcgcatccaa aaaaatcacc aagtaggtgc
     4441 aagaaagccg cttatagaaa ctgattttta tgcctgtata ggttgccgat gagatgaatt
     4501 taacataaga gttcttgccc gcaccgcttc gggctggttc ggcgcaaata cggtgcctgt
     4561 cgggtgaaac ccctagcaaa gcacccggta aaccgccccg tttacgccag ataaatttca
     4621 cctggctgca tggttatgca gccaggtgaa tgacagcagt tttcgcgtat aaatacggtg
     4681 taaagcacta aaaaggccac tttcccccga atcgctccca cagatccatt gccagtttga
     4741 cgcattgcag tatcagactg agcgctttta gtatcttcat aaatccccct ctcttgagcc
     4801 gtgatctttt catcacgacc gtatttagcg ggaaatttat gagcccttct tcttggggtt
     4861 tgtcactgga tgcgcgcagt cagcccagcg tcggaccgtt atagctccgc tgacggaaac
     4921 ggggttctgc cagctctttt tcatgctgtc gctgctcgta tgcccgttcg gcggccaccg
     4981 ccatttcatg ccgctgcact actgactcaa acgctgtaac tgcctgctca agttcgccac
     5041 ctgctgactc aagcgcgtga cgcgctcgtt cagcgccgcg ttctcccgtt gcataagacc
     5101 agacatcttc tgccattccg cgaaggcgct ctcccactcg tccagccttt gcgagtagtc
     5161 ctgatgtagc tgctctaatg cggtcagcaa ctgtttttcc agttccgtca tgggctattt
     5221 cctctccagt accatccagt tcccttcctc cccgtaagct cccgctttcg ggttcacttt
     5281 gacgcaggac agtttctgtt ccccacagag cgacagctgc acgccgtggt tcttctccga
     5341 cagcatggcc tgcgtccgct cctgcgcccg gatagtctgg taattcccgg tgatctgctg
     5401 cccctgccac cacagaatgc tcccgctcgt
//
