LOCUS       NZ_CP090531             3373 bp    DNA     circular CON 31-MAY-2024
DEFINITION  Salmonella enterica strain 2008079-SE plasmid p2, complete sequence.
ACCESSION   NZ_CP090531
VERSION     NZ_CP090531.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN24619911
            Assembly: GCF_021474265.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3373)
  AUTHORS   Bai,L., Li,R., Du,P. and Zhang,P.
  TITLE     Emergence and genomic epidemiology insights on Salmonella
            4,[5],12:i:- from clinical patients in China, 2008 to 2017
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3373)
  AUTHORS   Bai,L., Li,R., Du,P. and Zhang,P.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-JAN-2022) College of Veterinary Medicine (Institute of
            Comparative Medicine), Yangzhou University, Wenhui Road, Yangzhou,
            Jiangsu 225009, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_021474265.1-RS_2024_05_31
            Annotation Date                   :: 05/31/2024 04:04:29
            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)                     :: 5,238
            CDSs (total)                      :: 5,116
            Genes (coding)                    :: 4,982
            CDSs (with protein)               :: 4,982
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 134
            CDSs (without protein)            :: 134
            Pseudo Genes (ambiguous residues) :: 0 of 134
            Pseudo Genes (frameshifted)       :: 32 of 134
            Pseudo Genes (incomplete)         :: 109 of 134
            Pseudo Genes (internal stop)      :: 22 of 134
            Pseudo Genes (multiple problems)  :: 26 of 134
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP090531.1.
            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..3373
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="2008079-SE"
                     /isolation_source="patient"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="p2"
                     /geo_loc_name="China: Henan"
                     /collection_date="2008"
                     /collected_by="Pei Zhang"
     gene            complement(1042..1275)
                     /locus_tag="L0F60_RS25580"
                     /old_locus_tag="L0F60_25580"
     CDS             complement(1042..1275)
                     /locus_tag="L0F60_RS25580"
                     /old_locus_tag="L0F60_25580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /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_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1282..1842)
                     /locus_tag="L0F60_RS25585"
                     /old_locus_tag="L0F60_25585"
     CDS             complement(1282..1842)
                     /locus_tag="L0F60_RS25585"
                     /old_locus_tag="L0F60_25585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<1874..2530)
                     /locus_tag="L0F60_RS25590"
                     /old_locus_tag="L0F60_25590"
                     /pseudo=""
     CDS             complement(<1874..2530)
                     /locus_tag="L0F60_RS25590"
                     /old_locus_tag="L0F60_25590"
                     /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(2520..2843)
                     /locus_tag="L0F60_RS25595"
                     /old_locus_tag="L0F60_25595"
     CDS             complement(2520..2843)
                     /locus_tag="L0F60_RS25595"
                     /old_locus_tag="L0F60_25595"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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_001696562.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     APPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2907..3098
                     /locus_tag="L0F60_RS25600"
                     /old_locus_tag="L0F60_25600"
     CDS             2907..3098
                     /locus_tag="L0F60_RS25600"
                     /old_locus_tag="L0F60_25600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_062914769.1"
                     /translation="MTKQEKTALNMARFIRNQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(3180..3260)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.585"
                     /coverage="93.0"
                     /evalue="4.04e-16"
     Typing          complement(960..2530)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.628"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aatgcttgcc tctgtgactc ttccgcttcc tcgcccactc gctcactacg ttcggtcgct
       61 ggggctgcgg cgagcggtgg gatcactctc gttgtgatgc agatccgttt ttttttttgc
      121 actggagtta tcaggagtag cggtgcacat gggatcgtgc gatatgctgg atggtggaag
      181 gtcggaggga acggcaacaa ctcacccctc ccagtgaagg gacgggtagt ttgccgctct
      241 cgatatgccg gacggagcca aggccatcga tcacggggcg cgtcagtgga agaacccgcg
      301 cctgcgtgac gtatgcgtct tcgccgcacc atctcacccg tcacgccacc acataccggg
      361 aactgccgcc aaggtctaac tcaaccaatc tagccgcgct acatacggtt tttgtggcaa
      421 ctcatcaggt gtccgctgtc gatgaaactc tctgcgccgg tagcggaact ctcacgcgtg
      481 cggtcgccgt cgtcacagct cccccaaccg caaacgattc tcgcaaatac gcaagtatct
      541 gcaaaaacag gtttttttcg gggttcctgg gagactgtgc tgttgaaaaa ctcttgaaga
      601 atacagaagg ctcatgcaaa ctgaatgaac tggtttctgt tgtggatctc aacagtttcc
      661 acaggaacat tgaggaggtc agagacctca atgaacccga aacagctcgc cttcctggcg
      721 agctgttttc gttctacgcc caccgacgaa agatcgcaag tgcaataacg agatttttca
      781 cgtctttacg ctcaaaaagt aaaaaaacca tgttttcccc tggctgaatc cccaaaaacg
      841 cgtgaaatgc gttttcagga tgttgcatag ctatgcacaa atacggcaca cgatttgttt
      901 cgctcgcccc agccgtcgaa cgggtcaaaa tggcaagatt tcgtcacttc tccggtcaca
      961 tctccattga tggcccactc cgaacccgtg ccgcgcgttc ctgtacctca tgtctgtacc
     1021 gggcacgctc ctgttcatcc cttagctgtt gttcgcgata aataaccgac tcaagcgatc
     1081 cacttgcccg gctaatctct gcacctgctg actcaatatc acgacgcgct cgttcagtat
     1141 cgcgttgttc cgttgcgtaa cctcgtgcat cttctgcaat tccgcgaagg cgctctccca
     1201 ctcgttcagc cgccgcatat agtcctgttg caaatgctct aaggcgttca gcaaatgccc
     1261 ttccagttcc gtcatactcg tttactccct gaccagcctc acggcgttct tgtcgcccac
     1321 cgtccaggtg ttttcccctt tcaccccgtc cggcaacacc agaaatttcc cgttctcgcc
     1381 attgacgaac gtcacccccc aggtttttgc ctcgagtttc gccagcgtgt tttcctgctc
     1441 tctgatagtc aggatatttt tcgcaatctt gctttcctgc cactccatca gcccccagca
     1501 ccccaggaaa atcccgcccg tgacgctgag cgcggtcagc gccggaaaca gtatccgccc
     1561 tttgatcacc cgccagagca gttttttctg ctgccgggac agttcggcct ctgtggtgct
     1621 gaactgcatg ctcacggtgg tgctcagcgt atccagttgc tttttcacgg atgttgtatg
     1681 ttcgctgata gcgtctctga ttttctgcct gtttaagctc aatgccttgt ctacagactc
     1741 ttcgagcttc ctgaactcgc tgttcagcat gttctcggta gaagcggctc gctctttcag
     1801 tttcttctcg aagtctgttc ccatttgtaa aagattgctc atacagcgcc ccctttagcc
     1861 tgagattccg ccccccctcc gggtcggcaa tactgatgct gcttttggtt gtcctcacca
     1921 cctcaaaacc tgccgctgta agcgcctctg tgacatcctg acgcgttttt attgctccgg
     1981 catggtaaag agcctcaaga ccccgtgtaa tcgcttctgc ggcctcctgt ttcgcttttg
     2041 gcagattatt tggcgtgaca agcgtccgtc tgttctccgg tgcgttcggg tcacgcagcc
     2101 cgtaatgatg attaaccagc gtctgccagg catttatcct cggcctgtcc gcacggtcgt
     2161 agtacggctg gaggcgctta ccgctctgta gctccatgtt cgggatgaca aaattcagtt
     2221 cgagccgccc cttatcctgg tgttccaccc agagaatgct gtactggtct ttttcgagac
     2281 cgggcataag aacacgctca aagctcgtca tcactctttc gcgttcaccc ggtggtagct
     2341 ccttctccgc gaacgacaga acgcctgacg tgtatttctt cgaaaatggc gtggaatcaa
     2401 tgagttcccg cacttcttcc gggttacccc ggagcaccgt tgcgccttcg cggttacgct
     2461 cccgccccag caggtaatcg accgggccac ttccaccgcc tttccccctg gcatgaaatt
     2521 taactatcat cccgtacccc ctgttccctg acagcctgcc gcaactggcg caattcaccc
     2581 tcgatggcca tcagtgcggc caccacatga acccggtcaa tcgaagacca ctggccgctg
     2641 ttcaccttcc gggctgtctg gttcaggttg ttcccgatgg cagccagatg ccgcagcaat
     2701 ggcggtgcca gtgtcggcag ttttcctgtg cgtgcaaccg gctcccccag acagacccgc
     2761 cgcatccatt ccgccagtcg tttaccctcg cagcgttcca gtaaccgggc gtgctcctca
     2821 tcggtaaccc gtatcgtgag catcttctcg cgtttcatcg gtatcattcc ccctaacaaa
     2881 tcccccatac aaggagcctt aagaccatga ccaaacagga aaaaacagcc cttaacatgg
     2941 ctcgctttat cagaaaccag acgctaaccc tgctggaaaa actcaacgat ctggacgcgg
     3001 acgaacaggc agacatctgc gaatcacttc acgaccacgc cgacgaactc taccgcagtt
     3061 gcctcgcacg cttcggcgat gacggtgaaa gcaactgaaa catgcagctc ccggagacgt
     3121 tcacagcttg cctgtgagcg gatgccggga gcagacaagc ccgccagggc gcgtcagtgc
     3181 gggtgtcggg gcgcagccct gacccagttc acagagcgat agcgatgtgt atactggctt
     3241 tcctcatttt gcatcggtgc agagtggatg ggaagtgcac catgtcagga gtaaaaagcc
     3301 gcacagatgc gtaaaaacag cgcgcccgat aaacaacaca cacgcggaca ctggcacagg
     3361 cgcgtaagtg cac
//
