LOCUS       NZ_CP091617             6431 bp    DNA     circular CON 28-JAN-2024
DEFINITION  Salmonella enterica strain 1653 plasmid p1653-2, complete sequence.
ACCESSION   NZ_CP091617
VERSION     NZ_CP091617.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25270678
            Assembly: GCF_026873365.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 6431)
  AUTHORS   Ruan,Z.
  TITLE     Genome sequence of Salmonella Goldcoast recovered from children
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6431)
  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 13:38:11
            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)                     :: 4,773
            CDSs (total)                      :: 4,658
            Genes (coding)                    :: 4,529
            CDSs (with protein)               :: 4,529
            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)              :: 129
            CDSs (without protein)            :: 129
            Pseudo Genes (ambiguous residues) :: 0 of 129
            Pseudo Genes (frameshifted)       :: 48 of 129
            Pseudo Genes (incomplete)         :: 92 of 129
            Pseudo Genes (internal stop)      :: 30 of 129
            Pseudo Genes (multiple problems)  :: 38 of 129
            Pseudo Genes (short protein)      :: 1 of 129
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091617.1.
            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..6431
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="1653"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="p1653-2"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2021-07"
                     /collected_by="Meina Yue"
     gene            join(<6107..6431,1..260)
                     /locus_tag="L5511_RS23810"
                     /old_locus_tag="L5511_23820"
                     /pseudo=""
     CDS             join(<6107..6431,1..260)
                     /locus_tag="L5511_RS23810"
                     /old_locus_tag="L5511_23820"
                     /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            257..1936
                     /locus_tag="L5511_RS23815"
                     /old_locus_tag="L5511_23825"
     CDS             257..1936
                     /locus_tag="L5511_RS23815"
                     /old_locus_tag="L5511_23825"
                     /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(2173..2367)
                     /locus_tag="L5511_RS23820"
                     /old_locus_tag="L5511_23830"
     CDS             complement(2173..2367)
                     /locus_tag="L5511_RS23820"
                     /old_locus_tag="L5511_23830"
                     /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(3161..3871)
                     /locus_tag="L5511_RS23825"
                     /old_locus_tag="L5511_23835"
     CDS             complement(3161..3871)
                     /locus_tag="L5511_RS23825"
                     /old_locus_tag="L5511_23835"
                     /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            complement(4285..4800)
                     /locus_tag="L5511_RS23830"
                     /old_locus_tag="L5511_23840"
     CDS             complement(4285..4800)
                     /locus_tag="L5511_RS23830"
                     /old_locus_tag="L5511_23840"
                     /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            complement(5406..5537)
                     /locus_tag="L5511_RS23895"
     CDS             complement(5406..5537)
                     /locus_tag="L5511_RS23895"
                     /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          2404..2503
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.02"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          2628..2883
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.574"
                     /coverage="89.0"
                     /evalue="2.65e-108"
     Typing          complement(5210..5718)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.553"
                     /coverage="99.0"
                     /evalue="1.7000000000000002e-157"
ORIGIN
        1 acaacctgca gttctccgca cctttagacg agaacgaagt catgggtatt gccaaaagtg
       61 tagctaagtg gactaataaa aattttacag agtcatcatt tgatgatttt ataaaaaaga
      121 cccattcggc agacatccaa tctctatgtg ggaaaaaaag taaaggagga ggtaggcctt
      181 cattaaactc tccatggatt aatttaggaa ttagtcgttc aacgtatttt agattaaaag
      241 ctaaagagaa aggaaaatga taaaagttca gttacctact agagaacatc gtcttcatga
      301 gcttaatctt aattatggcg atgtcgtttt ttttattggt cagaatggta gtggtaaatc
      361 cagcctatta aataatcttt ttcaaaaaat aggatctcaa tcatcagtat atgttttagc
      421 gcatagaaaa aatacattca gcagcgacat tattgatttc agtaatagtg agtataaaaa
      481 tgcgcaggga tggattttta atgaaattaa aggcagtcaa tgtagataca gagttaatta
      541 tgactcacag atggttgcca tacctatagt aaaattaaaa aacaaagtga tagccagggc
      601 tttaagtttc gtagattcat ttaaatcaaa taacaatcag ccggcagggt taataaagtc
      661 agaggttgat gttctaaaca tggtttttgc tgatgccaaa ttatctattg agttctttct
      721 agatgatgaa gccaacgtta tggcaaggaa tattaaaggt gaaaatcctg atatttatcc
      781 tatatcaatg ctttctgacg gtgaaaaaag tgcactaatt attgccagtg agattatttg
      841 cgctgatgaa aacacaacta ttttcttaga tgagcctgag cgacatatgc acagaagcat
      901 tgtgtctccg ctgctttcat ctttaatgaa atatcgtaga gattgtgttt tttttgttgc
      961 cacccacgag ttaagcttgc ctgcgttttt tgataacgtg aaagtggtta acgttaaaaa
     1021 ctgctatttt tccgaacaaa gagaaccgat atactgggat ttcaatgttg ttgaggatta
     1081 tgacgaatta ttcaatggtg ttgatgagca aactaaaata gatatacttg gcgctaggga
     1141 taaggttcta tttgttgaag gtgttacgtc tagccttgac cgtgatttat attcggccat
     1201 atttcctatg gtttcagttg tatctaaaca aaaatgtgat ttggttgaat tggcggtaaa
     1261 aggcttgaga ctaaatgacg aaattcatcg agtatcggcg tttggtatca ttgataatga
     1321 taacaaggtg caggcgaagg tcgataactt aaagaaagac ttcattttta gtctcgacgt
     1381 tcattctatt gagtcgattt attatcatcc tagaatgatt aagtttgtca ttgactttgt
     1441 aaaagaggct aatgggatag ataatgttga tgccttattt atggaaattc atgacttcgc
     1501 tattgatgcc ataaatgaaa agcgcgatca cttatgctgc cgtgcagttg aaaaaacaat
     1561 aagggccgac ttaatgtcgg ccataccaaa acagcaagat attaagaacc gcattaagtt
     1621 taataaagaa attgatattg aatgttatgt taataaagaa attgctgcat ttgatgcaat
     1681 gatcgcggaa cgaaatttgg atgcgttagt ctcacgctac cctatccgag aaacaaattt
     1741 gttggcacat gtagctaaaa aatgtggttt tgccgatcgc tctagatatg agttaaacgt
     1801 gattcgtacg atcaagagta atgctgacgc tagagcattt gttttatccc tcctcggagg
     1861 gttagatgaa gctattttgg gatgttcaga tacggaaaat agcccagctg atacccatac
     1921 agtttttgct atgtgagact aaacaaccta tatcagataa cagccctgct tttgcggggc
     1981 tttttgtttg tgcgtgactt gaccgcgatg tacgatagtt gctgtattaa gtcagtatac
     2041 actccgctat cgctacgtga ctgggtcagg gctgcgcccc gacacccgtt aaaacccgct
     2101 gacgcgccct gacgggcttg tctgctgacg aaaatgctca cgggcaagcc gtgaccgcct
     2161 tcgtcagctt cgttatgttc ctgtttcatt ttcggcctca aagtgaacct ggatgctgtt
     2221 ctggagttct tctgcgagtt cgtgcagtcg ttcacacatg gccgcctgta cgtcggcatc
     2281 cagagcatcc agtttttcaa gcagtgtcag gctctggctt ttgataaatc gcgccatatt
     2341 cagcgcagtt tgttgctgtt tgttcacctt ccgttgttct ccgtcagtac cgggtgtcgg
     2401 gtggaccctg actaggtggt aattgtaaga cgttgcgggc gacggtatta caattgcaca
     2461 tcctgtcctg ttttttttag gacgtatcat ggcacagcat atcaactgat aaataatccc
     2521 tgtgcagtgc agccgctgtt gcataaaatt tcgctctgcg tcgagtgttt cttaatcaat
     2581 aattccgctg atactccgga aaaacgcgag tctgttctca tgcctgaaat gcccacaccc
     2641 cacgcaaaaa caattttttg ctgatttttc tttataaata gagagttatg acaaattagt
     2701 ttctcttgct ctctttgtga tatttaaaaa agcggtgtcg gcgcggctac aacaccgcgc
     2761 cgacaccgct ttgtaggggt ggtactgact attttcataa aaaacatcat tttatattag
     2821 gggtgctgct agcggcgcgg tgtgtttttt tacaggatgc ccctgggggc gctgctaggg
     2881 gtgtctgttc agatatgtag caatgagtca gggattcacg aactgaaaat gtccgaaaat
     2941 gtgtctcatg ggcaccgtat gcgcccaaac cgttcgccat tcactttcat gcatagctat
     3001 gcagcgagct gaaaacgatc ctgacgcatt ttttcggttt accttgggga aaacatctct
     3061 ttttgcggta tttgcgtcag aatcgcgttc agcgcgtttc tgaggtgcgg gcaacggatg
     3121 ttatgttcaa tccgtgtgat aattggtgtg gaataaacaa tcaaaatggt aagtcggctt
     3181 ctggaataac tggcggttct gatttccttc tgtaggttag agcgctctta ctgcctgttt
     3241 ttatatagaa atagtacgag tcatgaaaca tctctagagg tatgttttct atggattttt
     3301 tcacaactct atcaagcaaa cctatatgga taaggtaggt gattgctttg tttagttcag
     3361 gtaatttgca tttcaatttt ttgcatatgg tctttttcct agccagtgtg tagtcgctgt
     3421 tattatcacg agcgtaaaga agatacatgt aagtttgtaa ggctagtaac tcaaagggat
     3481 atctgttgtg catggattga aatgcactta tttttttgtc ctcgtcgaca actcctttaa
     3541 atggaagctt gcaccatcca tcattatgat tttctagcac atccacggta taaatctttt
     3601 ttcgtgcagt cggcgatatg ttttttatca gctcttttgc ataaagaatt ttaaggcctt
     3661 cgttcaccaa ggaacggctt aatgacgcta tctcgcaaag gttgctaaag gttaactcaa
     3721 ccgttctgtg gccagagtct gactctttgc aaaacaggca gaatgttaaa taaattttta
     3781 atgccgctat agcttttgct gtatcaagat cgctgaattc agcgatccta tttcctatcc
     3841 atagtgaagg catttttttc cagtacagca tgaatcacct caaggccaag ttttgaaaga
     3901 tgaaatagac caatcccaat atagaaagtg agagcacaag gttagttatt accgctgcga
     3961 ctttcgcaag cctctcaacc agacacacgc ctttctcaaa catttttcac ccctcgtaat
     4021 cgcttcttgt tgtttttatt atctcagggt gtgaaggcgt tgtaacgcct tcacaaaaat
     4081 ctatctagaa agataaaagt gatgttaatt ttttatcttg ttgtttttaa cggtttttta
     4141 tttgagtttt ggtatttgta ttaatcataa tatggttcac cgtgaactat gtatgtgagt
     4201 cgaaccgttg agttttgaat attagacctg aatagtgtcc aagatcactc ggtttcggac
     4261 actattcagg atggcaatga agcgttactc gccttcttcc gtgtcattag cttctttgcc
     4321 gaaatctcgg tatttttctt ctaacaggga aaaattacat gttccttgca tttttccttg
     4381 caggacgagc ttccttaaaa gctctgattt ctcagctatt ttgtctgaat ttacacgaat
     4441 aaactggagc tgcttataga gcattctctt gtaggcggta ttcggcatac cgttcaagtc
     4501 aagtaaggat acttcggctt cgatgattgg aatcatgaac ttcagattaa tcaatccgag
     4561 ctgattttcg gggacaccat tttcatggag cttaaagaag ctaggcgatg attctttaat
     4621 agtgctatgc catggctttg gggatgttaa aggggctaga tacttatgcc cttgaatctc
     4681 taacacaatg ccaatgaaag ctttcggatt ctgatagtta ggatcttcgc tattgggaac
     4741 tttgtcttcg aatcccttta ggtattcaat gtatctgctt gatatagtgt aaaatttcat
     4801 ttttttctcg taaaaaaggc gactgtgtag tcgcctcttt tactgtatta ctttaaggta
     4861 gtaaatgacc taaatttcta gctgcactta aggtagcaaa tcacctgaat ttctagctgc
     4921 acttaaaggt agcaaatcac ctgaatttct agctgcactt aaggtagcaa atcacctgaa
     4981 tttctagctg cacttaaagg tagcaaatca ccttgattcg agtatacctg atcttcgcct
     5041 aggcttacaa ctaggtaact tgcagctgtg tagttgtagc ccttgccgct gtatcccctc
     5101 aaaatgtcat ttgaggtttt tttaaagtac tgattccaga gttgactgtt tttttcatca
     5161 gttcagtgtg gggggggggt aagttgggtt atgacatgaa tcaaaaagga tctgcttgag
     5221 atcctttttt tctacgcgta atctcttgct ctgaaaacga aaaaaccacc tggggaggtg
     5281 gtttttcgat ggttcagtaa gttggggaac ttctgaaccg tggtaacagg gtgtacaaga
     5341 ccgctgccac caaattcgtc cttccagttt agccgtagtt tggttctaac ttcaagaact
     5401 ctgcatcagt aatctcttgt acacccctta ccaatggccg cagccagtgg cgataagtcg
     5461 tgtctttccg ggttggactc aagatgatag ttaccggaca aggcgcagcg gtcggactga
     5521 acgggggggt cgtgcataca gtccagcttg gagcgaactg cctacccgga accgagtgtc
     5581 aggcgtggaa tgagataaac gcggccataa cagcggaatg acaccggtaa accgaaaggc
     5641 aggaacagga gagcgcacga gggagccacc agggggaaac gcctggtatc tttaagtcct
     5701 gtcgggtttc gccaccactg atttgagcgt cagattctgt gatgcttgtc aggggggcgg
     5761 agcctatgga aaaacgccag cggcgcggcc ttttgccctg gctttgcctt tttgctcaca
     5821 tgttctttcc ggccttatcc cctgattctg tggataaccg tattaccgtc tctgagtgag
     5881 ctgataccgc tcgccacagc cgaacgaccg agcgcagcga gttagtgagc gaggaagcgg
     5941 aagagcgtag gcatttgcat tttctcctta cgcatctgtg cggcatttca caccgtcaat
     6001 agcgcacttt tcatacaatc cgcactgata ccgcatagtt aagtcagtac tcacagcgtc
     6061 ccctctgcga ggtgccttct gtgactggtt cagggggctc gccgcccccc tcaaatatgc
     6121 agccgtcatt gagaatgcgc tgcgtaaaaa attgggcgcc gatgcggggt attcagggct
     6181 aatttgcgag aatccgaacc acctgcactg gcagatcacc gtttggcagc ctgagctcta
     6241 caccctcgac tgattagccg actacctcga ccttggcgca gctaatgacc gcgaaatcct
     6301 accggactac ggtttaggcc gtaactgcac cctcttcgat aaaacccgca agtgggctta
     6361 ccgcgctatc caccaaggct ggccgcagta tgaccaatgg ctacaagctt gctttgaacg
     6421 cgctaaagcc t
//
