LOCUS       NZ_CP033225             6758 bp    DNA     circular CON 25-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica strain CFSA122 plasmid
            pCFSA122-2, complete sequence.
ACCESSION   NZ_CP033225
VERSION     NZ_CP033225.2
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10279393
            Assembly: GCF_004124035.2
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica
  ORGANISM  Salmonella enterica subsp. enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 6758)
  AUTHORS   Hu,Y., Fanning,S., Gan,X., Liu,C., Nguyen,S., Wang,M., Wang,W.,
            Jiang,T., Xu,J. and Li,F.
  TITLE     Foodborne Salmonella harbouring mcr-1 gene isolated from food
            samples in China, 2012-2016
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6758)
  AUTHORS   Hu,Y., Li,F. and Fanning,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-MAY-2019) Microbiology Laboratory, China National
            Centre for Food Safety Risk Assessment, No.7,Panjiayuan Nanli,
            Chaoyang District, Beijing, Beijing 100031, China
  REMARK    Sequence update by submitter
REFERENCE   3  (bases 1 to 6758)
  AUTHORS   Hu,Y., Li,F. and Fanning,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-OCT-2018) Microbiology Laboratory, China National
            Centre for Food Safety Risk Assessment, No.7,Panjiayuan Nanli,
            Chaoyang District, Beijing, Beijing 100031, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 3
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 127.12x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/25/2023 04:37:46
            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)                     :: 5,083
            CDSs (total)                      :: 4,957
            Genes (coding)                    :: 4,834
            CDSs (with protein)               :: 4,834
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 123
            CDSs (without protein)            :: 123
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 36 of 123
            Pseudo Genes (incomplete)         :: 93 of 123
            Pseudo Genes (internal stop)      :: 21 of 123
            Pseudo Genes (multiple problems)  :: 26 of 123
            Pseudo Genes (short protein)      :: 1 of 123
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP033225.2.
            On May 20, 2019 this sequence version replaced NZ_CP033225.1.
            Bacteria and source DNA available from CFSA.
            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..6758
                     /organism="Salmonella enterica subsp. enterica"
                     /mol_type="genomic DNA"
                     /strain="CFSA122"
                     /isolation_source="pork dumplings"
                     /sub_species="enterica"
                     /db_xref="taxon:59201"
                     /plasmid="pCFSA122-2"
                     /geo_loc_name="China"
                     /collection_date="2013-05-01"
     gene            102..1913
                     /locus_tag="EBF18_RS02095"
                     /old_locus_tag="EBF18_26715"
     CDS             102..1913
                     /locus_tag="EBF18_RS02095"
                     /old_locus_tag="EBF18_26715"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000379077.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008168 - methyltransferase activity [Evidence IEA];
                     GO:1904047 - S-adenosyl-L-methionine binding [Evidence
                     IEA]"
                     /GO_process="GO:0006306 - DNA methylation [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="WP_254698940.1"
                     /translation="MQTELIKELNKVLKAFPQFWNGEELQRSMVSDAISQKQPDLIKAL
                     VDNEKVRSVYGVDIDGIFIFDFDKLCGLLKYKEYWANSFTKYRNKVGLTSEGKYLDYSS
                     DVVLDFPFKDCILEGGMTKENQGKDEIYYNEIIAMDEVDSLLSPKAFTNAKRYTKEGVK
                     ENITKFNDDENLIIKGNNLIALHSIKKLYAGKVKLIYIDPPYNTGSDSFKYNDRFNRST
                     WLTFMKNRLEVAKEMLSDDGFIFIQCDDNESAYLKVLCDSIFGEENYRNSIYWHRTYAG
                     KTVKSKLPWNTDTILFYSKKESSLLEPYTAELSAADIKSYNKDDFDGRGKYNTVSLQKT
                     SSPGPQTTYDYIDNTGKKWSCPEKGWRMTKEKLKALENDNRLYITDKTIREKYYLKERK
                     EIGKQIDNFWHDIGNLNRVSDVAFIDGQKTEKLMQRIISLASKENDIVLDFHLGSGTSA
                     AAAHKMGRRYIGIEQMDYINEITVPRLQKVIEGEQGGISKDVNWQGSGSFVYVELVELN
                     AYFIHEIQKAQSTEELEKLFAVMKTEAYLNYQVALENVLSAEYEVDGILHKVAFSELEL
                     HEQKQLLIEILDKNQLYVNVSEWRTAT"
                     /name="site-specific DNA-methyltransferase"
     gene            1971..4607
                     /locus_tag="EBF18_RS02100"
                     /old_locus_tag="EBF18_01055"
     CDS             1971..4607
                     /locus_tag="EBF18_RS02100"
                     /old_locus_tag="EBF18_01055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012443154.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 -
                     hydrolase activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DEAD/DEAH box helicase family protein"
                     /protein_id="WP_052512605.1"
                     /translation="MAKKPKSAGREKLLFNKLKQFDEPGLFHDNYQTPDYIQANLKDIL
                     RPYQHSALRYLHYTQRKRDDALLHYRHLLFHMATGAGKTMVMAGTILYLFKEFGYQNFI
                     FFVHTDAIIQKTRENLLNPQSPKYLFSHELEIDGEKITIAPVDIFPSVPERNTIYLKLS
                     TIHKMHDELNSYRENSITYEDLKEIPLVLLGDEAHHFNAGTKARGKSKTSPENEEQTWE
                     RTIENILDLRPDNRLFEFTATIDLANKDIGQKYRDKVVYQYDLKQFMSDGYSKKVMLLE
                     ANQNDSDKMLDAVLLSQYRKLTAADHGITGFKPVILFKSNKIAISKAKQEEFSQLIAAM
                     TPESIRRHLANKKLQLSSDTSIWHKVIQRYADSDLVTVTGQIQEDFNDFNLLNVNKSDL
                     LEENPVLLNTLEEVDNPVRAVFAVAKVNEGWDVLNLYDIVRISEQASSSKTSTDSEAQL
                     IGRGARYYPFIYDGQRSFTRRFDNSTKDLSVLEQLHYHTINEPAYIKTLHASLEQADID
                     VHQDGGGTVEHARLKEDFKKSAVYQAGKLYFNEVEEIERSSRNWETYSLETRFEIQYQI
                     ACEESLDNLTGTKGGIIKPEPLVLDERFYRKAMQRISFYALDNLKRFFPKLTGIREFIR
                     SDAYLGKLKITVSVPQSLDFTTVPAKDKLHLLENVLLRISENVRRNDQKVKGTYRFISQ
                     PVKEVIKDYSLHIDPSVAINQKITAAPTIGKKWYVYDNAILNQLEHRLIKMLEAFMPKL
                     KARYDDIYVLRNDEQSTRFKLTEFGGVRGFMPDFIMILTRHSDNTYWQVFLEPKGDDRL
                     LDDAWKERMLETLNDRERIVIDENEHVRLVGIKFFANSQMDVFVSDMQNKLNDGESLET
                     SSLSLPL"
                     /name="DEAD/DEAH box helicase family protein"
     gene            complement(5008..5121)
                     /locus_tag="EBF18_RS26975"
     CDS             complement(5008..5121)
                     /locus_tag="EBF18_RS26975"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_071588254.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLSPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(5786..5980)
                     /locus_tag="EBF18_RS02120"
                     /old_locus_tag="EBF18_01075"
     CDS             complement(5786..5980)
                     /locus_tag="EBF18_RS02120"
                     /old_locus_tag="EBF18_01075"
                     /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_001041631.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          5621..5706
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          6017..6115
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          6240..6495
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.248"
                     /coverage="89.0"
                     /evalue="2.69e-98"
     Typing          complement(5050..5603)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.075"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gcattttccc gcaactgaat ccaactcatc gctgttgggt tccagcgccg aacgctatac
       61 cttacaatca ttccaatatt taacagtcat aaggccatga catgcagacc gaattaataa
      121 aagaacttaa caaggtttta aaagcgttcc cgcaattctg gaatggagag gaattacaac
      181 gttcaatggt gagtgacgct atcagtcaaa agcagccaga tcttatcaag gcattagtcg
      241 ataatgaaaa agtccgctct gtttatggtg tggatattga tggcattttt atctttgatt
      301 ttgacaaatt atgtggtctt ctaaaataca aagaatattg ggctaatagc tttactaaat
      361 accggaacaa agtgggatta actagcgaag gtaaatacct tgattacagt tctgatgtgg
      421 tgctggattt tcctttcaag gattgtattc ttgaaggtgg aatgaccaaa gaaaatcagg
      481 gaaaagatga gatttattat aatgaaatca tagcaatgga tgaagttgac tctttgcttt
      541 ctcccaaggc gttcactaat gctaagcgat ataccaaaga gggggtaaaa gaaaatatca
      601 ctaaatttaa cgatgatgaa aatttaataa ttaagggaaa caatctcatt gcactacatt
      661 caataaaaaa actttacgca ggaaaagtaa agttaattta tatagacccg ccttacaata
      721 cagggagtga tagctttaag tataatgatc gattcaatcg ctcaacatgg ttgacattca
      781 tgaaaaatag gcttgaggtg gctaaagaaa tgctttccga tgatggcttt atttttattc
      841 aatgcgatga taatgaatca gcatatctta aagttttatg tgattcaatt tttggagaag
      901 agaattatag aaactcaatc tattggcata gaacctacgc agggaaaact gtaaaaagta
      961 agttgccatg gaatacagat acaatattgt tttattctaa aaaagaaagt tcattattag
     1021 agccatatac agcagaactt agtgctgctg acattaaatc ctataacaag gatgattttg
     1081 atggaagggg taaatacaac actgttagct tgcaaaaaac aagctctcca gggccgcaaa
     1141 caacttatga ttatatagat aatacaggta agaaatggag ttgccctgaa aaagggtgga
     1201 gaatgacaaa ggaaaagtta aaggctttgg aaaacgacaa taggctatat atcactgaca
     1261 aaacaatacg agaaaaatat tatcttaaag aaagaaaaga gatcgggaaa caaatagata
     1321 atttttggca tgacattggg aatttaaata gggtttccga tgttgctttt attgatggac
     1381 aaaaaactga aaaattaatg caacggataa ttagccttgc ttccaaagaa aatgatatcg
     1441 tcttggactt tcatctcggc agcggaacta gcgcagcagc agcccataaa atgggacgtc
     1501 gctatatcgg tattgagcag atggattaca tcaatgagat caccgtgcca cgtttgcaaa
     1561 aagtcattga gggtgagcag ggaggtatct caaaagacgt caactggcag gggagcggca
     1621 gctttgtcta cgttgaacta gtggaactga acgcttactt catacatgaa atccagaaag
     1681 cgcagtccac ggaagaactc gaaaaactct ttgccgtgat gaagacagag gcatatctca
     1741 actatcaggt ggctctggaa aatgtgctgt ccgctgagta cgaagtggat gggatcctcc
     1801 ataaggtagc attcagtgaa ctggaactgc atgagcagaa gcagcttttg attgaaatcc
     1861 tagataagaa ccagctctac gtgaatgtct ctgaatggag gacagcgacc tgaacatttc
     1921 agagagtgat aaagccttta cccgcagctt ctacggaatg gagtgacggc atggcgaaga
     1981 aaccgaagtc agcaggtaga gagaagctgc tgtttaacaa gctgaagcag ttcgatgaac
     2041 caggactgtt ccacgataac tatcagacgc cggactatat tcaggcaaac ctgaaagata
     2101 tcctgcgtcc ctatcagcac agcgcactgc gttacctgca ttacacgcaa cgtaaacgtg
     2161 atgacgcgct tctgcattac cgtcacctgc tgtttcacat ggcaaccggt gcagggaaaa
     2221 cgatggttat ggcaggaacg atactctatc tatttaaaga gttcgggtat cagaacttca
     2281 tctttttcgt acataccgac gcgattatcc agaaaacgcg agagaaccta cttaacccgc
     2341 aatcgccgaa gtacctgttc agtcatgagc tggaaatcga cggggaaaaa atcaccatcg
     2401 caccggtaga tatattcccg tccgtaccgg aacgcaacac gatttacctc aagctctcga
     2461 ctatccataa gatgcacgat gagctgaaca gctatcgaga gaacagcatt acctacgagg
     2521 atttaaaaga aatcccgctt gtgctactcg gtgacgaggc gcatcacttc aacgccggca
     2581 ccaaagctag aggcaagtcg aaaacctcac cggagaacga ggagcagact tgggagcgta
     2641 cgattgagaa catcctcgac ctgcgaccgg ataaccgcct gttcgagttc accgctacca
     2701 ttgaccttgc aaacaaagat atcggacaga aataccgtga caaggtggta tatcagtatg
     2761 atctgaagca gttcatgtca gacggttact cgaaaaaggt catgctgttg gaagcaaacc
     2821 agaacgacag cgacaagatg ctcgatgcag tactgttaag ccagtaccgt aaactgacgg
     2881 cagcagatca cggcatcacc ggctttaaac cggtcattct gttcaagtcg aataagattg
     2941 cgatatcaaa ggcgaagcag gaggagtttt cgcaactgat tgccgccatg acacctgaga
     3001 gcatcagacg tcatctggct aacaaaaaac tccagctcag ctctgacacc agtatctggc
     3061 ataaagtgat tcagcgttac gctgacagtg atttagtgac ggtgactgga caaattcagg
     3121 aggactttaa cgactttaac ctgctgaacg tcaacaagtc agacctgctg gaggaaaacc
     3181 ccgtcctgct gaatacactg gaagaagtcg ataatccagt gagagccgtc tttgctgtcg
     3241 cgaaggtgaa tgaaggctgg gacgtactta acctctacga tattgttcgc ataagcgagc
     3301 aggcgagcag cagcaaaacc agcacggaca gcgaagcgca gcttattggg cgaggtgcgc
     3361 gttactaccc gttcatttat gacggtcaac gtagcttcac ccgccgtttt gataacagta
     3421 cgaaggattt gagcgtactg gagcaactgc actatcacac catcaatgaa ccggcgtaca
     3481 tcaaaacact gcacgcctct ctggagcagg cggacattga cgtgcatcag gatggcggag
     3541 gtacggttga acacgccaga ttgaaagaag actttaaaaa gtccgccgtg tatcaggcgg
     3601 gtaagctgta ctttaacgaa gtggaagaga ttgagagaag cagccgaaac tgggaaacct
     3661 actcgctgga aacacgcttt gaaatacagt atcagatcgc ttgcgaggag tcgctggaca
     3721 acctgacagg cacaaagggg gggatcataa aaccggaacc actggtactg gacgagcgtt
     3781 tttaccgcaa ggcgatgcaa agaatcagct tttacgcgct agataacctg aaacgcttct
     3841 tcccgaaact gacaggtatt cgggagttca tacgcagtga cgcctatctt ggtaagctga
     3901 aaatcaccgt cagcgtaccg cagtcactgg atttcaccac cgtaccggca aaagataagc
     3961 tgcacctact ggaaaacgtt ttgctgcgta tctcagagaa tgtgcgtcgc aatgaccaga
     4021 aggtaaaagg cacgtaccga tttatcagcc agccggtgaa agaggtgatt aaagattaca
     4081 gtttgcatat tgacccgtcg gtagccatta accagaaaat caccgccgct cccaccattg
     4141 gtaaaaaatg gtacgtgtac gataatgcga tactaaatca gcttgagcat cgtctgataa
     4201 aaatgctgga agcattcatg ccgaagctaa aagcgcgtta tgacgatatt tacgtactgc
     4261 gtaacgacga gcagtcaacg cgctttaagc tcacggagtt cggcggcgtg cgtgggttta
     4321 tgccagattt catcatgata ctgacgcgcc attcagacaa cacttactgg caggtgttcc
     4381 ttgaaccgaa gggggatgac cgtctgctgg atgacgcatg gaaagaacgg atgctcgaaa
     4441 cactgaatga cagggagcgc attgtaattg atgaaaatga gcacgtcaga ctggttggga
     4501 ttaaattctt tgccaatagc cagatggacg tttttgtcag cgacatgcag aacaagctga
     4561 atgatggaga atcgctcgaa acctcctcgc tctccctacc actgtaagtc acgacaataa
     4621 aataacggag cattacgctc cgttatttta ttgttatctc gaactacctc ccagggaggt
     4681 gatgattgct cctgtaatgg ttgcattgtt tgttcttgct gttgcgaatc attagttttg
     4741 aatggtggtt aaaaaccgtt cgctatgttt atgcctgggg ggggatgagg gggaaaagat
     4801 tcaaggatcc tcttgtgatc ctttttttct gcgcgtaatc tgcagcctgt aaacgaaaaa
     4861 accaccctgg caggtggttt ttcgaaggtt agctaatcct ggcagattat ctaaccgggt
     4921 aactggcttg gaggagcgca gtcaccaaaa tctgttcttt cagtttagcc ttaacaggtg
     4981 cataacttca agacaaactc ctctaaatca gttaccagtg gctgctgcca gtggcgataa
     5041 gtcgtgtctt accgggttgg actcaagacg atagttaccg gataaggcgc agcggtcggg
     5101 ctgaacgggg ggttcgtgca cacagcccag cttggagcga acgacctaca ccgaaccgag
     5161 ataccaacag cgtgagctat gagaaagcgc cacgcttccc gaagggagaa aggcggacag
     5221 gtatccggta agcggcaggg tcggaacagg agagcgcacg agggagcttc cagggggaaa
     5281 cgcctggtat ctttatagtc ctgtcgggtt tcgccgactc tgacttgagc gtcgattttt
     5341 gtgatgctcg tcaggggggc ggagcctatg gaaaaacgcc agcggcgcgg cctttttccg
     5401 gttcctgctc ttttgctcac atgttctttc cggccttatc ccctgattcg gtggataatc
     5461 taattactgt ctttgcgtga gttgataccg ctcgccgcag ccgaacgacc gagcgtagcg
     5521 agtcagtgag cgaggaagcg gaagagcgtc ggaagttgca ttttctcctt acgcatctgt
     5581 gcggcatttc acatcggtta tggtgtactt ttcatacaat ctgcactgat gccgcatagt
     5641 taagccagta tacactccgc tatcgctacg tgactgggtc atggctgcgc cccgacaccc
     5701 gctaaaaccc tctgacgcgc cctgacgggc ttgtctgctg acgaaaacgc ccacgggaaa
     5761 gccgtgaccg cctccgtcag cttcgttatg ttcctgtttc actttcggcc tcaaagcgaa
     5821 tctggatgct gttctggagt tcttctgcga gttcgtgcag tcgttcgcac atggccgcct
     5881 gttcgtcggc atccagagca tccagttttt caagcagtgt caggctctgg cttttgataa
     5941 atcgcgccat attcagcgca gtttgttgtt gtttgttcac cttccgttgt tctccgtcag
     6001 ttccgggtgt cggggggacc ctgagcaggt ggtaattgta agacgttgcg ggcgacggta
     6061 ttacaattgc acatcctgtc ctgtttcttt aggacgtatc atggcacagc atatcaactg
     6121 ataaataatc cctgtgcagt gcagccgctg ttgcataaaa tttcgctctg cgtcgagtgt
     6181 ttcttaatca ataattccgc tgatactccg gaaaaacgcg agtctgttct catgcctgaa
     6241 atgcccacac cccacgcaaa aacaagtttt tgctgatttt tctttataaa tagagagtta
     6301 tgacaaatta gttcttcttg ctctctttgt gatatttaaa aaagcggtgt tggcgcagct
     6361 acaacaccgc gccgacaccg ctttttaggg gtggtactga ctattttcat aaaaaacatc
     6421 atcttatatt aggggtgctg ctagcggcgc ggtgtgtttt tttacaggac gcccctgggg
     6481 gcgctgctag gggtgtctgt tcagatatgt agcaatgagt cagggattca cgaactgaaa
     6541 atgtccgaaa atgtgtctca tgggtactgt atgcgcccaa accgatcgtc attcactttc
     6601 atgcatagct atgcagtgag ctgaaagtga tcctgacgca tttttccggt ttaccccggg
     6661 gaaaacatct ctttttgcgg tgtttgcggc agaatcgcgt tcagcgcgtt ttagcggtgc
     6721 gcgcaagagc gtttatgtta aatactactc gttctggt
//
