LOCUS       NZ_CP061117             6079 bp    DNA     circular CON 20-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain S585
            plasmid pS585_2, complete sequence.
ACCESSION   NZ_CP061117
VERSION     NZ_CP061117.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15962528
            Assembly: GCF_015697745.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella
            typhimurium)
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 6079)
  AUTHORS   Hua,X. and Yu,Y.
  TITLE     Plasmid dynamics of mcr-1-positive Salmonella spp. in a general
            hospital in China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6079)
  AUTHORS   Hua,X. and Yu,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-SEP-2020) Sir Run Run Shaw Hospital, Zhejiang
            University, Qingchundong 3 RD, Hangzhou, Zhejiang 310016, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-JUN-2020
            Assembly Method                   :: other: Unicycler v. 0.4.8
            Assembly Name                     :: S585
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 300x
            Sequencing Technology             :: Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/20/2023 03:58:32
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,269
            CDSs (total)                      :: 5,146
            Genes (coding)                    :: 5,001
            CDSs (with protein)               :: 5,001
            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)              :: 145
            CDSs (without protein)            :: 145
            Pseudo Genes (ambiguous residues) :: 0 of 145
            Pseudo Genes (frameshifted)       :: 39 of 145
            Pseudo Genes (incomplete)         :: 118 of 145
            Pseudo Genes (internal stop)      :: 16 of 145
            Pseudo Genes (multiple problems)  :: 27 of 145
            Pseudo Genes (short protein)      :: 1 of 145
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP061117.1.
            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..6079
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="S585"
                     /serovar="Typhimurium"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pS585_2"
                     /geo_loc_name="China:Hangzhou"
                     /lat_lon="30.2 N 120.2 E"
                     /collection_date="2018-12"
                     /collected_by="Xiaoting Hua"
     gene            651..1169
                     /locus_tag="IBZ03_RS26120"
                     /old_locus_tag="IBZ03_26115"
     CDS             651..1169
                     /locus_tag="IBZ03_RS26120"
                     /old_locus_tag="IBZ03_26115"
                     /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="MbeB family mobilization protein"
                     /protein_id="WP_165808188.1"
                     /translation="MSNLLRTGAEFEKKLKERAESTEKMLNDEFSRLGESVSEAVTSNE
                     TKIKGAIARFTASTEESLEKHREGVKEAMMQHRRDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEDIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVTHYQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            1176..1409
                     /locus_tag="IBZ03_RS26125"
                     /old_locus_tag="IBZ03_26120"
     CDS             1176..1409
                     /locus_tag="IBZ03_RS26125"
                     /old_locus_tag="IBZ03_26120"
                     /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_029401705.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSERTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1722..2003)
                     /locus_tag="IBZ03_RS26130"
                     /old_locus_tag="IBZ03_26125"
     CDS             complement(1722..2003)
                     /locus_tag="IBZ03_RS26130"
                     /old_locus_tag="IBZ03_26125"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000786945.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024177387.1"
                     /translation="MKNEDDYKTGWTTQTTNPATGKKCSGGAARNLRIYQAGGANSVRV
                     KAAIEGVQSIQPIIDMQQSQIEQQQTQIAMLTQSLSQAINELTKSRNQ"
                     /name="hypothetical protein"
     gene            complement(2013..2270)
                     /locus_tag="IBZ03_RS26135"
                     /old_locus_tag="IBZ03_26130"
     CDS             complement(2013..2270)
                     /locus_tag="IBZ03_RS26135"
                     /old_locus_tag="IBZ03_26130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001508827.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001508827.1"
                     /translation="MPKKTSKPNDLSNTINNIKKEINSGFTELLNRVEALEASDAQHSM
                     AIRDLQIQARAARGDKRMDIARDFGLSEGRISQIVNAGRN"
                     /name="hypothetical protein"
     gene            2815..3525
                     /locus_tag="IBZ03_RS26140"
                     /old_locus_tag="IBZ03_26135"
     CDS             2815..3525
                     /locus_tag="IBZ03_RS26140"
                     /old_locus_tag="IBZ03_26135"
                     /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_024177388.1"
                     /translation="MLYWKRMPSLWIGIKISEFNDLDTAKAIAALKIYLTFCLFCKESD
                     SGQRTVELTFSNLCEIASLSRSLVNEGLKILYAKELIKNLSTTVRKKIYTIDVLEKHDD
                     GWCKLPFKGIVGEDGKISAFQSMHNRYPFELLALQTYMYLLYARDNRNEYTLARKKTIC
                     KKLKCKLPELNKAITYLIHIGLLDRIVKKSIENKPLEMFHDSCYFYFRAGSNSALTYKR
                     KSEVLNLSEEDLPF"
                     /name="hypothetical protein"
     gene            complement(3637..4152)
                     /locus_tag="IBZ03_RS26145"
                     /old_locus_tag="IBZ03_26140"
     CDS             complement(3637..4152)
                     /locus_tag="IBZ03_RS26145"
                     /old_locus_tag="IBZ03_26140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000675352.1"
                     /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_000675353.1"
                     /translation="MKFYTISSSYIKYLKDFDDKVPNSEDPTYNNPKAFIGIVLEIEGH
                     KYLAPLTSPKAWHANVKESSPAFFKLHENGVPDNQLGLINLKFMIPIIEAEVSLLDLDS
                     MPDTPYKRMLYKQLQFIRVNEDKISEKSKLLRNLALQGRMQGTCDFAVLEEKYQHFGKK
                     PEDMEIDD"
                     /name="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
     gene            complement(4207..4398)
                     /locus_tag="IBZ03_RS26150"
                     /old_locus_tag="IBZ03_26145"
     CDS             complement(4207..4398)
                     /locus_tag="IBZ03_RS26150"
                     /old_locus_tag="IBZ03_26145"
                     /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_196315241.1"
                     /translation="MLPLSAARNLGDLLPLSAARNSGDLLPLSAARNSGDLLPLSAARN
                     SGDLLPLSAARNLGHLLP"
                     /name="hypothetical protein"
     gene            complement(5473..5664)
                     /locus_tag="IBZ03_RS26155"
                     /old_locus_tag="IBZ03_26150"
     CDS             complement(5473..5664)
                     /locus_tag="IBZ03_RS26155"
                     /old_locus_tag="IBZ03_26150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165987.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGETL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            5729..6052
                     /locus_tag="IBZ03_RS26160"
                     /old_locus_tag="IBZ03_26155"
     CDS             5729..6052
                     /locus_tag="IBZ03_RS26160"
                     /old_locus_tag="IBZ03_26155"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001508824.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVVALMAIERELRSLRQVVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          5311..5392
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(4494..5011)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.792"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3..1486
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.731"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          5697..6049
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.373"
                     /coverage="100.0"
                     /evalue="1.82e-64"
ORIGIN
        1 cagtggtccg gttgattacc ttctggggag ggagcgtaac cgggaaggtg caacggtact
       61 tcagggtaac ccggaagaag tccgggagct tattgatgcc acgccatttg cgaagaaata
      121 cacgtccggt gttctgtcgt tcgcagagaa ggaactgccg ccgggaggac gtgaaaaagt
      181 gatggagagc tttgagcgcg tactgatgcc cggtctcgaa aaaaatcagt acagcattct
      241 gtgggtggag caccaggaca aggggcgtct tgagctgaat tttgtcattc cgaacatgga
      301 gctacagagc ggaaaacgcc tccagccgta ctacgaccgg gcagacaggc cgagaattga
      361 tgcctggcag acgctggtga atcaccatta cgggctgcat gaccccaacg ccccggagaa
      421 ccgcaggacg ctgacactcc ctgataacct gccggaaacg aaacaagcgc ttgctgaggg
      481 cgttactcgc gggatagacg cactttacca tgccggagag ataaaaggcc gtcaggatgt
      541 gattcaggcg ctcacagagg cggggcttga agtggtcagg gtgacgcgaa gcagtatcag
      601 cattgcagac ccgaacggcg ggaggaatat cagactgaaa ggagcgtttt atgagcaatc
      661 ttttacggac gggcgcggag ttcgagaaaa agctgaaaga gagagccgaa tctacagaga
      721 aaatgctgaa cgacgaattc agcaggctcg gcgaatctgt aagcgaggct gtgacctcaa
      781 acgagacgaa aatcaaaggc gctatagccc ggtttacggc ctcgacggag gaatcgctgg
      841 aaaaacaccg ggaaggggtg aaagaggcga tgatgcagca caggagggac gtgttaaagc
      901 tggcagggaa tacgggcatg atgttactgg ggatagtctt tctcctgttt accgcgagtg
      961 gcgggacgct ctggtatctt ggcgggagga tacaggcgaa cctggaagat atcaggaagc
     1021 aggaagagac attacagaaa ctgaacgcga agacatgggg cgtggagttt gtgcaggacg
     1081 ggaacaggaa atttctggtc cttccttacg ggaagtcagc agaggtgacg cactatcagg
     1141 ggaaggaatg ggtacatctg aaggagtgat acagagtgac agagctggaa acacatttgc
     1201 tgaacgcctt agagcagctg caacaggact atatgcagcg gctgagcgaa tgggagagcg
     1261 ccttcgtgga attgcagaag atgttttcgc ttacgcaacg ggacaacgcg atgctgaacg
     1321 agcgggtcat gcagttgagt cagcaggtgc agcacttgag cgagcggaca gaacgcttga
     1381 gccagttata cagcgagaac tggagataag agaggaacgg ttgatacatg agcgcgaaca
     1441 tgcgttatcc ctggaacggg aacgcacgct ggatggtcct tcgttgtcgc tgtgatggcg
     1501 aaactataaa aaatggcaga ttcagtggat tttgacgggc taatgtagtc tgcaccatct
     1561 ggttgcatag atattcatac ggttaaaatt tatcaggcgc gatcgcggta gcttttcggg
     1621 tgatttgttg ttggttttgg ctgactgccg ccccgttcgc ggcgaagctg tccggggcgg
     1681 tgcgggcaac ggatgttatg gtaaataaca tcctttatag cctattgatt cctgcttttt
     1741 gttagctcat tgattgcctg agacaaagat tgagtcagca ttgctatttg agtttgttgt
     1801 tgctcgattt gtgactgttg catatcgatg attggctgta ttgactggac accctcgatt
     1861 gcagctttta cccgcacgga gtttgctcca ccggcttgat atatccttaa gtttctggct
     1921 gcgcctccag aacatttttt ccctgttgcc gggtttgttg tctgagtcgt ccatcctgtt
     1981 ttgtagtcgt cttcattttt cataagtctg tcttagttac gacccgcatt aacgatctgg
     2041 ctaattcgtc cctcgctgag gccaaagtct cttgctatat ccatgcgctt gtctccgcga
     2101 gcggctctag cctgaatttg taaatcacgt atcgccatgc tgtgttgtgc gtcactagcc
     2161 tctaaggctt ctacgcgatt aagtaactca gtaaaacctg agttaatttc tttctttatg
     2221 ttgttgatag tgttgcttaa atcgtttggt tttgatgttt ttttaggcat ggcatatttc
     2281 tctatactcg gcggctaagt ccgctaaaga tttttagttt tgttaaagtt gtaaggtagg
     2341 gattattgct ccttttggca aggtgaattt aatgagataa agaaatttag tgctttatgc
     2401 agggtggctt gcaaggcaca acgctttgtt tgttctgatc taaagtccta atgtgaaaac
     2461 atttaacgta accagaaaag catcagcact gcatttacgg ttcaccatga accataatat
     2521 gatttctaag aataccaaaa gcaagataaa atatcttata taacatatag atatctttct
     2581 tttgccttat cttatctttc tagatagatt tttgtgaagg cgttacaacg ccttcacagc
     2641 ctgagataat caaaaaaaca aagctatcag gagggataaa aaatgtttga gaaaggtgtg
     2701 tttttggctg aaaggcttgc gaaggtcgca gtggtgctaa ctaatctggt gctatctatg
     2761 tctgtattgg ggttggtcta tttcattttt caaattctgg gaatgaggtg atttatgctg
     2821 tactggaaaa gaatgccttc actatggata ggtatcaaaa tatctgaatt caacgatctt
     2881 gatacagcaa aagccatcgc cgcgttaaag atttatttaa cattttgcct tttctgcaaa
     2941 gagtcagatt caggacagag aactgttgag ctaactttta gtaacctatg tgagatagca
     3001 tcattaagcc gatcgttagt taacgaaggg cttaaaattc tttatgcaaa agagttgata
     3061 aaaaatttat caacgacagt acgtaaaaaa atttatacca tagatgtatt agagaagcat
     3121 gatgatggtt ggtgtaagct tccctttaaa ggaattgtag gtgaagatgg aaaaataagt
     3181 gcatttcaat ccatgcacaa cagatatcca tttgagttgc tagctttaca aacctacatg
     3241 taccttcttt atgctcgaga taatagaaat gagtatactc ttgccaggaa aaaaacaata
     3301 tgtaaaaaac tgaaatgcaa actacctgaa ctaaataaag ctattaccta tcttattcat
     3361 atcggtttac ttgataggat tgttaaaaaa tcaatagaaa acaagccgtt ggaaatgttt
     3421 catgattcat gttacttcta ctttagagcg ggaagtaaca gcgctctcac ttacaaaagg
     3481 aaatcagagg tgcttaatct ttcagaggag gacttgcctt tttgattgct tctcgaaatc
     3541 aaaattagaa tatctcattc ttatattgga tgagagcaaa aaaaataggt ccaaaaccgc
     3601 ttgattttgg accttcaatt ccataaaaaa gaatggttaa tcgtctattt ccatgtcttc
     3661 aggtttttta ccgaaatgtt gatatttttc ttctaacacg gcaaagtcgc atgttccttg
     3721 cattctgcct tgcaaggcaa ggtttcttaa tagttttgat ttttcagata ttttatcttc
     3781 atttacacga ataaattgta actgtttata tagcattctt ttgtaaggcg tatcaggcat
     3841 gctatccaga tcaagtaaag acacttcagc ttcgattatt ggaatcataa atttcagatt
     3901 aatcaatcca agctgattat cagggacacc gttttcatga agtttgaaga aggcgggtga
     3961 tgactctttt acattagcat gccatgcttt tggcgatgtt aaaggtgcta aatatttatg
     4021 tccttcaatc tctagtacta tgccaatgaa agccttagga ttgttgtatg taggatcttc
     4081 gctattggga actttgtcat caaagtcctt caggtatttt atgtaactgc ttgatattgt
     4141 gtaaaatttc atttttttct cgtaaaaaag gcgactgtgt atagtcgcct tttttacttt
     4201 attactttaa ggtagtaaat gacctaaatt tctagctgca cttaaaggta gcaaatcacc
     4261 tgaatttcta gctgcactta aaggtagcaa atcacctgaa tttctagctg cacttaaagg
     4321 tagcaaatca cctgaatttc tagctgcact taaaggtagc aaatcaccta aatttctagc
     4381 tgcacttaaa ggtagcaaat caccttgaac taagtataca tgatcttcgc ttgggcttac
     4441 aactaggtgc ttagcatggg atgttcagtc aaatgacggc actaatcaaa aggatcttct
     4501 tgagatcatc tttttctgcg cgtaatctct tggtctgaaa acggaaaaac cacccggcaa
     4561 ggtggttttt tcgaaggttc agtaaaccgg caagtttctg gaccgtggta actggctttc
     4621 gcagagcaca gcaaccaaat ctgtccttcc agtgtagccg tactgaggcg cacacttcaa
     4681 gagcaacctc gtgtttagct aacaaatcat ctgcgaacca agttaccaat ggctgctgcc
     4741 agtggcgctt tgtcgtgtct ttccggtttg gactcaagtg gatagttacc ggataaggcg
     4801 cagcagtcgg actgaacggg gggttcgtgc atacagtcca gcttggagcg aactgcctac
     4861 ccggaaccga gtgtcaggcg tggaatgaga taaacgcggc cataacagcg gagtgacacc
     4921 ggtaaaccga atggcaggaa caggagagcg cacgagggag ccaccagggg gaaacgcctg
     4981 gtatctttaa gtcctgtcgg gtttcgccac ctctgacttg agcgtcggtt tttgtgatgc
     5041 tcgtcagggg ggcggagcct atggaaaaac gccagcggcg tggccttttc cgggttcttg
     5101 ttttttgctc acatgtttct tttggtgtta tcccctgatt ctgtggataa ccgcattacc
     5161 gtttttgagt gagctgatac cgctcgccgc agccgaacga ccgagcgtag cgagtcagtg
     5221 agcgaggaag cggaagagcg tctgatgctg cattttctcc ttacgcatct gtgcggcatt
     5281 tcacacccgg catggcgcac ttttcataca atctgcactg atgccgcatg gttaagccag
     5341 tatacactcc gctatcgcta cgtgactggt tcagggcttc gccccgaaac cccctgacgc
     5401 gccctgacgg gcttgtctgc tcccggcatc cgctcacaga caagctgtga ccgtctccgg
     5461 gagctgcttg tgtcagaggg tttcaccgtc atccccgaag cgtgcgaggc agctgcggta
     5521 aagctcatcg gcgtggtcgt gaagagattc acagatgtct gcctgttcat ccgcgtccag
     5581 ttcgttgagt ttctccagca gcgttaatgt ctggcttctg ataaagcggg ccatgttaag
     5641 ggcggttttt tcctgtttag tcactgatgc ctccgtgtaa gggggatttc tgttcatggg
     5701 ggtaatgata ccgatgaaac gagagaggat gctcacgata cgggttactg atgatgaaca
     5761 tgcccggtta ctggaacgct gtgagggtaa acaactggcg gtatggatgc ggcgggtctg
     5821 cctgggtgag ccggttgccc gttccgggaa gctgccgaca ctggcaccgc cgttactgcg
     5881 tcagctggct gccatcggga ataaccttaa tcagacggcg aggaaggtga acagcgggca
     5941 gtggtcttcc ggcgaccggg ttcaggtggt ggtcgcactg atggccatcg agagagagtt
     6001 gcgcagctta cgacaggtcg tcagggaaca gggagcgcgg gatgatagtt aagtttcatg
     6061 cccggggaaa aggtggtgg
//
