LOCUS       NZ_CP091628             6432 bp    DNA     circular CON 28-JAN-2024
DEFINITION  Salmonella enterica strain 1165 plasmid p1165-3, complete sequence.
ACCESSION   NZ_CP091628
VERSION     NZ_CP091628.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25270674
            Assembly: GCF_026873445.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 6432)
  AUTHORS   Ruan,Z.
  TITLE     Genome sequence of Salmonella Goldcoast recovered from children
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6432)
  AUTHORS   Ruan,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-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; Illumina NovaSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/28/2024 13:46:28
            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)                     :: 4,720
            CDSs (total)                      :: 4,605
            Genes (coding)                    :: 4,480
            CDSs (with protein)               :: 4,480
            Genes (RNA)                       :: 115
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 125
            CDSs (without protein)            :: 125
            Pseudo Genes (ambiguous residues) :: 0 of 125
            Pseudo Genes (frameshifted)       :: 47 of 125
            Pseudo Genes (incomplete)         :: 89 of 125
            Pseudo Genes (internal stop)      :: 28 of 125
            Pseudo Genes (multiple problems)  :: 36 of 125
            Pseudo Genes (short protein)      :: 1 of 125
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091628.1.
            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..6432
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="1165"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="p1165-3"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2020-08"
                     /collected_by="Meina Yue"
     gene            join(6055..6432,1..138)
                     /locus_tag="L5507_RS23545"
                     /old_locus_tag="L5507_23555"
     CDS             join(6055..6432,1..138)
                     /locus_tag="L5507_RS23545"
                     /old_locus_tag="L5507_23555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000675351.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
                     /protein_id="WP_000675351.1"
                     /translation="MKFYTISSRYIEYLKGFEDKVPNSEDPNYQNPKAFIGIVLEIQGH
                     KYLAPLTSPKPWHSTIKESSPSFFKLHENGVPENQLGLINLKFMIPIIEAEVSLLDLNG
                     MPNTAYKRMLYKQLQFIRVNSDKIAEKSELLRKLVLQGKMQGTCNFSLLEEKYRDFGKE
                     ANDTEEGE"
                     /name="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
     gene            552..1262
                     /locus_tag="L5507_RS23550"
                     /old_locus_tag="L5507_23560"
     CDS             552..1262
                     /locus_tag="L5507_RS23550"
                     /old_locus_tag="L5507_23560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000967646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000967645.1"
                     /translation="MLYWKKMPSLWIGNRIAEFSDLDTAKAIAALKIYLTFCLFCKESD
                     SGHRTVELTFSNLCEIASLSRSLVNEGLKILYAKELIKNISPTARKKIYTVDVLENHND
                     GWCKLPFKGVVDEDKKISAFQSMHNRYPFELLALQTYMYLLYARDNNSDYTLARKKTIC
                     KKLKCKLPELNKAITYLIHIGLLDRVVKKSIENIPLEMFHDSYYFYIKTGSKSALTYRR
                     KSEPPVIPEADLPF"
                     /name="hypothetical protein"
     gene            2056..2250
                     /locus_tag="L5507_RS23555"
                     /old_locus_tag="L5507_23565"
     CDS             2056..2250
                     /locus_tag="L5507_RS23555"
                     /old_locus_tag="L5507_23565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041636.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADVQAAMCERLHELA
                     EELQNSIQVHFEAENETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2487..4166)
                     /locus_tag="L5507_RS23560"
                     /old_locus_tag="L5507_23570"
     CDS             complement(2487..4166)
                     /locus_tag="L5507_RS23560"
                     /old_locus_tag="L5507_23570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000598747.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0016887 - ATP hydrolysis activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="AAA family ATPase"
                     /protein_id="WP_241467032.1"
                     /translation="MIKVQLPTREHRLHELNLNYGDVVFFIGQNGSGKSSLLNNLFQKI
                     GSQSSVYVLAHRKNTFSSDIIDFSNSEYKNAQGWIFNEIKGSQCRYRVNYDSQMVAIPI
                     VKLKNKVIARALSFVDSFKSNNNQPAGLIKSEVDVLNMVFADAKLSIEFFLDDEANVMA
                     RNIKGENPDIYPISMLSDGEKSALIIASEIICADENTTIFLDEPERHMHRSIVSPLLSS
                     LMKYRRDCVFFVATHELSLPAFFDNVKVVNVKNCYFSEQREPIYWDFNVVEDYDELFNG
                     VDEQTKIDILGARDKVLFVEGVTSSLDRDLYSAIFPMVSVVSKQKCDLVELAVKGLRLN
                     DEIHRVSAFGIIDNDNKVQAKVDNLKKDFIFSLDVHSIESIYYHPRMIKFVIDFVKEAN
                     GIDNVDALFMEIHDFAIDAINEKRDHLCCRAVEKTIRADLMSAIPKQQDIKNRIKFNKE
                     IDIECYVNKEIAAFDAMIAERNLDALVSRYPIRETNLLAHVAKKCGFADRSRYELNVIR
                     TIKSNADARAFVLSLLGGLDEAILGCSDTENSPADTHTVFAM"
                     /name="AAA family ATPase"
     gene            complement(4163..>4747)
                     /locus_tag="L5507_RS23565"
                     /old_locus_tag="L5507_23575"
                     /pseudo=""
     CDS             complement(4163..>4747)
                     /locus_tag="L5507_RS23565"
                     /old_locus_tag="L5507_23575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001697689.1"
                     /note="internal stop; incomplete; partial in the middle of
                     a contig; missing N-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            5317..5448
                     /locus_tag="L5507_RS23630"
     CDS             5317..5448
                     /locus_tag="L5507_RS23630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /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_071525238.1"
                     /translation="MHDPPVQSDRCALSGNYHLESNPERHDLSPLAAAIGKGCTRDY"
                     /name="replication initiation protein"
     Typing          complement(1541..1796)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.574"
                     /coverage="89.0"
                     /evalue="2.65e-108"
     Typing          complement(1921..2020)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.02"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          5137..5645
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.553"
                     /coverage="99.0"
                     /evalue="1.7000000000000002e-157"
ORIGIN
        1 aaaatagctg agaaatcaga gcttttaagg aagctcgtcc tgcaaggaaa aatgcaagga
       61 acatgtaatt tttccctgtt agaagaaaaa taccgagatt tcggcaaaga agctaatgac
      121 acggaagaag gcgagtaacg cttcattgcc atcctgaata gtgtccgaaa ccgagtgatc
      181 ttggacacta ttcaggtcta atattcaaaa ctcaacggtt cgactcacat acatagttca
      241 cggtgaacca tattatgatt aatacaaata ccaaaactca aataaaaaac cgttaaaaac
      301 aacaagataa aaaattaaca tcacttttat ctttctagat agatttttgt gaaggcgtta
      361 caacgccttc acaccctgag ataataaaaa caacaagaag cgattacgag gggtgaaaaa
      421 tgtttgagaa aggcgtgtgt ctggttgaga ggcttgcgaa agtcgcagcg gtaataacta
      481 accttgtgct ctcactttct atattgggat tggtctattt catctttcaa aacttggcct
      541 tgaggtgatt catgctgtac tggaaaaaaa tgccttcact atggatagga aataggatcg
      601 ctgaattcag cgatcttgat acagcaaaag ctatagcggc attaaaaatt tatttaacat
      661 tctgcctgtt ttgcaaagag tcagactctg gccacagaac ggttgagtta acctttagca
      721 acctttgcga gatagcgtca ttaagccgtt ccttggtgaa cgaaggcctt aaaattcttt
      781 atgcaaaaga gctgataaaa aacatatcgc cgactgcacg aaaaaagatt tataccgtgg
      841 atgtgctaga aaatcataat gatggatggt gcaagcttcc atttaaagga gttgtcgacg
      901 aggacaaaaa aataagtgca tttcaatcca tgcacaacag atatcccttt gagttactag
      961 ccttacaaac ttacatgtat cttctttacg ctcgtgataa taacagcgac tacacactgg
     1021 ctaggaaaaa gaccatatgc aaaaaattga aatgcaaatt acctgaacta aacaaagcaa
     1081 tcacctacct tatccatata ggtttgcttg atagagttgt gaaaaaatcc atagaaaaca
     1141 tacctctaga gatgtttcat gactcgtact atttctatat aaaaacaggc agtaagagcg
     1201 ctctaaccta cagaaggaaa tcagaaccgc cagttattcc agaagccgac ttaccatttt
     1261 gattgtttat tccacaccaa ttatcacacg gattgaacat aacatccgtt gcccgcacct
     1321 cagaaacgcg ctgaacgcga ttctgacgca aataccgcaa aaagagatgt tttccccaag
     1381 gtaaaccgaa aaaatgcgtc aggatcgttt tcagctcgct gcatagctat gcatgaaagt
     1441 gaatggcgaa cggtttgggc gcatacggtg cccatgagac acattttcgg acattttcag
     1501 ttcgtgaatc cctgactcat tgctacatat ctgaacagac acccctagca gcgcccccag
     1561 gggcatcctg taaaaaaaca caccgcgccg ctagcagcac ccctaatata aaatgatgtt
     1621 ttttatgaaa atagtcagta ccacccctac aaagcggtgt cggcgcggtg ttgtagccgc
     1681 gccgacaccg cttttttaaa tatcacaaag agagcaagag aaactaattt gtcataactc
     1741 tctatttata aagaaaaatc agcaaaaaat tgtttttgcg tggggtgtgg gcatttcagg
     1801 catgagaaca gactcgcgtt tttccggagt atcagcggaa ttattgatta agaaacactc
     1861 gacgcagagc gaaattttat gcaacagcgg ctgcactgca cagggattat ttatcagttg
     1921 atatgctgtg ccatgatacg tcctaaaaaa aacaggacag gatgtgcaat tgtaataccg
     1981 tcgcccgcaa cgtcttacaa ttaccaccta gtcagggtcc acccgacacc cggtactgac
     2041 ggagaacaac ggaaggtgaa caaacagcaa caaactgcgc tgaatatggc gcgatttatc
     2101 aaaagccaga gcctgacact gcttgaaaaa ctggatgctc tggatgccga cgtacaggcg
     2161 gccatgtgtg aacgactgca cgaactcgca gaagaactcc agaacagcat ccaggttcac
     2221 tttgaggccg aaaatgaaac aggaacataa cgaagctgac gaaggcggtc acggcttgcc
     2281 cgtgagcatt ttcgtcagca gacaagcccg tcagggcgcg tcagcgggtt ttaacgggtg
     2341 tcggggcgca gccctgaccc agtcacgtag cgatagcgga gtgtatactg acttaataca
     2401 gcaactatcg tacatcgcgg tcaagtcacg cacaaacaaa aagccccgca aaagcagggc
     2461 tgttatctga tataggttgt ttagtctcac atagcaaaaa ctgtatgggt atcagctggg
     2521 ctattttccg tatctgaaca tcccaaaata gcttcatcta accctccgag gagggataaa
     2581 acaaatgctc tagcgtcagc attactcttg atcgtacgaa tcacgtttaa ctcatatcta
     2641 gagcgatcgg caaaaccaca ttttttagct acatgtgcca acaaatttgt ttctcggata
     2701 gggtagcgtg agactaacgc atccaaattt cgttccgcga tcattgcatc aaatgcagca
     2761 atttctttat taacataaca ttcaatatca atttctttat taaacttaat gcggttctta
     2821 atatcttgct gttttggtat ggccgacatt aagtcggccc ttattgtttt ttcaactgca
     2881 cggcagcata agtgatcgcg cttttcattt atggcatcaa tagcgaagtc atgaatttcc
     2941 ataaataagg catcaacatt atctatccca ttagcctctt ttacaaagtc aatgacaaac
     3001 ttaatcattc taggatgata ataaatcgac tcaatagaat gaacgtcgag actaaaaatg
     3061 aagtctttct ttaagttatc gaccttcgcc tgcaccttgt tatcattatc aatgatacca
     3121 aacgccgata ctcgatgaat ttcgtcattt agtctcaagc cttttaccgc caattcaacc
     3181 aaatcacatt tttgtttaga tacaactgaa accataggaa atatggccga atataaatca
     3241 cggtcaaggc tagacgtaac accttcaaca aatagaacct tatccctagc gccaagtata
     3301 tctattttag tttgctcatc aacaccattg aataattcgt cataatcctc aacaacattg
     3361 aaatcccagt atatcggttc tctttgttcg gaaaaatagc agtttttaac gttaaccact
     3421 ttcacgttat caaaaaacgc aggcaagctt aactcgtggg tggcaacaaa aaaaacacaa
     3481 tctctacgat atttcattaa agatgaaagc agcggagaca caatgcttct gtgcatatgt
     3541 cgctcaggct catctaagaa aatagttgtg ttttcatcag cgcaaataat ctcactggca
     3601 ataattagtg cacttttttc accgtcagaa agcattgata taggataaat atcaggattt
     3661 tcacctttaa tattccttgc cataacgttg gcttcatcat ctagaaagaa ctcaatagat
     3721 aatttggcat cagcaaaaac catgtttaga acatcaacct ctgactttat taaccctgcc
     3781 ggctgattgt tatttgattt aaatgaatct acgaaactta aagccctggc tatcactttg
     3841 ttttttaatt ttactatagg tatggcaacc atctgtgagt cataattaac tctgtatcta
     3901 cattgactgc ctttaatttc attaaaaatc catccctgcg catttttata ctcactatta
     3961 ctgaaatcaa taatgtcgct gctgaatgta ttttttctat gcgctaaaac atatactgat
     4021 gattgagatc ctattttttg aaaaagatta tttaataggc tggatttacc actaccattc
     4081 tgaccaataa aaaaaacgac atcgccataa ttaagattaa gctcatgaag acgatgttct
     4141 ctagtaggta actgaacttt tatcattttc ctttctcttt agcttttaat ctaaaatacg
     4201 ttgaacgact aattcctaaa ttaatccatg gagagtttaa tgaaggccta cctcctcctt
     4261 tacttttttt cccacataga gattggatgt ctgccgaatg ggtctttttt ataaaatcat
     4321 caaatgatga ctctgtaaaa tttttattag tccacttagc tacacttttg gcaataccca
     4381 tgacttcgtt ctcgtctaaa ggtgcggaga actgcaggtt gtaggcttta gcgcgttcaa
     4441 agcaagcttg tagccattgg tcatactgcg gccagccttg gtggatagcg cggtaagccc
     4501 acttgcgggt tttatcgaag agggtgcagt tacggcctaa accgtagtcc ggtaggattt
     4561 cgcggtcatt agctgcgcca aggtcgaggt agtcggctaa tcagtcgagg gtgtagagct
     4621 caggctgcca aacggtgatc tgccagtgca ggtggttcgg attctcgcaa attagccctg
     4681 aataccccgc atcggcgccc aattttttac gcagcgcatt ctcaatgacg gctgcatatt
     4741 tgaggggggc ggcgagcccc ctgaaccagt cacagaaggc acctcgcaga ggggacgctg
     4801 tgagtactga cttaactatg cggtatcagt gcggattgta tgaaaagtgc gctattgacg
     4861 gtgtgaaatg ccgcacagat gcgtaaggag aaaatgcaaa tgcctacgct cttccgcttc
     4921 ctcgctcact aactcgctgc gctcggtcgt tcggctgtgg cgagcggtat cagctcactc
     4981 agagacggta atacggttat ccacagaatc aggggataag gccggaaaga acatgtgagc
     5041 aaaaaggcaa agccagggca aaaggccgcg ccgctggcgt ttttccatag gctccgcccc
     5101 cctgacaagc atcacagaat ctgacgctca aatcagtggt ggcgaaaccc gacaggactt
     5161 aaagatacca ggcgtttccc cctggtggct ccctcgtgcg ctctcctgtt cctgcctttc
     5221 ggtttaccgg tgtcattccg ctgttatggc cgcgtttatc tcattccacg cctgacactc
     5281 ggttccgggt aggcagttcg ctccaagctg gactgtatgc acgacccccc cgttcagtcc
     5341 gaccgctgcg ccttgtccgg taactatcat cttgagtcca acccggaaag acacgactta
     5401 tcgccactgg ctgcggccat tggtaagggg tgtacaagag attactgatg cagagttctt
     5461 gaagttagaa ccaaactacg gctaaactgg aaggacgaat ttggtggcag cggtcttgta
     5521 caccctgtta ccacggttca gaagttcccc aacttactga accatcgaaa aaccacctcc
     5581 ccaggtggtt ttttcgtttt cagagcaaga gattacgcgt agaaaaaaag gatctcaagc
     5641 agatcctttt tgattcatgt cataacccaa cttacccccc cccccacact gaactgatga
     5701 aaaaaacagt caactctgga atcagtactt taaaaaaacc tcaaatgaca ttttgagggg
     5761 atacagcggc aagggctaca actacacagc tgcaagttac ctagttgtaa gcctaggcga
     5821 agatcaggta tactcgaatc aaggtgattt gctaccttta agtgcagcta gaaattcagg
     5881 tgatttgcta ccttaagtgc agctagaaat tcaggtgatt tgctaccttt aagtgcagct
     5941 agaaattcag gtgatttgct accttaagtg cagctagaaa tttaggtcat ttactacctt
     6001 aaagtaatac agtaaaagag gcgactacac agtcgccttt tttacgagaa aaaaatgaaa
     6061 ttttacacta tatcaagcag atacattgaa tacctaaagg gattcgaaga caaagttccc
     6121 aatagcgaag atcctaacta tcagaatccg aaagctttca ttggcattgt gttagagatt
     6181 caagggcata agtatctagc ccctttaaca tccccaaagc catggcatag cactattaaa
     6241 gaatcatcgc ctagcttctt taagctccat gaaaatggtg tccccgaaaa tcagctcgga
     6301 ttgattaatc tgaagttcat gattccaatc atcgaagccg aagtatcctt acttgacttg
     6361 aacggtatgc cgaataccgc ctacaagaga atgctctata agcagctcca gtttattcgt
     6421 gtaaattcag ac
//
