LOCUS       NZ_CP090544             3042 bp    DNA     circular CON 08-DEC-2023
DEFINITION  Salmonella enterica strain 2010112-SE plasmid p3, complete sequence.
ACCESSION   NZ_CP090544
VERSION     NZ_CP090544.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN24619907
            Assembly: GCF_021474345.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3042)
  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  JOURNAL   Unpublished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 3042)
  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 Date                   :: 12/08/2023 11:18:12
            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)                     :: 5,014
            CDSs (total)                      :: 4,888
            Genes (coding)                    :: 4,773
            CDSs (with protein)               :: 4,773
            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)              :: 115
            CDSs (without protein)            :: 115
            Pseudo Genes (ambiguous residues) :: 0 of 115
            Pseudo Genes (frameshifted)       :: 32 of 115
            Pseudo Genes (incomplete)         :: 93 of 115
            Pseudo Genes (internal stop)      :: 19 of 115
            Pseudo Genes (multiple problems)  :: 27 of 115
            Pseudo Genes (short protein)      :: 1 of 115
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP090544.1.
            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..3042
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="2010112-SE"
                     /isolation_source="patient"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="p3"
                     /geo_loc_name="China: Henan"
                     /collection_date="2010"
                     /collected_by="Pei Zhang"
     gene            complement(681..881)
                     /locus_tag="L0F62_RS24995"
                     /old_locus_tag="L0F62_25000"
     CDS             complement(681..881)
                     /locus_tag="L0F62_RS24995"
                     /old_locus_tag="L0F62_25000"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001558245.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="antitoxin VbhA family protein"
                     /protein_id="WP_064138465.1"
                     /translation="MTDDRTLQLRVTGFRKAEASLRLEGMDPSGTPLYESVKAHILSGE
                     ITYDEGRAEILAYHQKRANDN"
                     /name="antitoxin VbhA family protein"
     gene            complement(1769..2053)
                     /locus_tag="L0F62_RS25005"
                     /old_locus_tag="L0F62_25010"
     CDS             complement(1769..2053)
                     /locus_tag="L0F62_RS25005"
                     /old_locus_tag="L0F62_25010"
                     /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="type II toxin-antitoxin system RelB/DinJ family
                     antitoxin"
                     /protein_id="WP_154955540.1"
                     /translation="MDTKFHFRLDENVKMRAQKAAEARGKTLSEACRDFAEQLAREVEP
                     LSQHEKWLKKQVELAVAKANSGDARFTSNEEVKRVMASRKDEIRAKYKR"
                     /name="type II toxin-antitoxin system RelB/DinJ family
                     antitoxin"
     gene            2243..2647
                     /locus_tag="L0F62_RS25010"
                     /old_locus_tag="L0F62_25015"
     CDS             2243..2647
                     /locus_tag="L0F62_RS25010"
                     /old_locus_tag="L0F62_25015"
                     /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_154955541.1"
                     /translation="MGFISQLSKTKISTRRGSASQITVTQSFKPSTSAEELSIRISTEC
                     LKNVSLKIGDNVDVLYDADSDTWMIKKEAEGYKISGKPDAPTGLIRYTLKEGHKKFTST
                     RESLPVRKDSNDDTIVFMGDKMTFKLKESE"
                     /name="hypothetical protein"
     gene            2644..2940
                     /locus_tag="L0F62_RS25015"
                     /old_locus_tag="L0F62_25020"
     CDS             2644..2940
                     /locus_tag="L0F62_RS25015"
                     /old_locus_tag="L0F62_25020"
                     /inference="COORDINATES: protein motif:HMM:NF016876.3"
                     /GO_function="GO:0008657 - DNA topoisomerase type II
                     (double strand cut, ATP-hydrolyzing) inhibitor activity
                     [Evidence IEA]; GO:0042803 - protein homodimerization
                     activity [Evidence IEA]"
                     /GO_process="GO:0030541 - plasmid partitioning [Evidence
                     IEA]; GO:0051290 - protein heterotetramerization [Evidence
                     IEA]; GO:0009432 - SOS response [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_154955542.1"
                     /translation="MMASNLIWEEEAIDDRADYFEWLYKQNPKAAEDADQHIEDTVDLL
                     IENPFLGKDSEIVSGVRVLIIKGLSLNVYYQEGHGTVKVLRVLHQSRNIAKLI"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     Typing          925..1577
                     /name="rep_cluster_2324"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.578"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 agatcaaatc ctaaggaaag agttcattaa aacagagacc tttttcctta ggatacagac
       61 aataaacatg aatttaccat aacatccctt gggcgcaccg cctgagagcc tctcagcgcg
      121 tttctgcggc cccctgccga ttttcggcac ctttccccgc ccatacccct gaaaaacgcc
      181 cctgatgatt tctgaccggc tgcatggcta tgcacagaag tgaatggctg gcagtttcac
      241 gcgtatgttg tcactaaggc cgctttttcg caggaaacgg tcatttccta taacggtgaa
      301 cgggcgcgca gtttactgtg cgatcgtgag gcgttgagca acgagctttg cgaggcggta
      361 ggggttcaga gagccagctg caggctcagg agaaaacatt ctgttttcgg ggcaaacgcc
      421 gcaaatgacg tcattttgcg gcgtttgccc tatcctgcat cgcaacgtct aaaggatgtg
      481 agtgcaaacg ccagcacttt gcgaatcctg ccctcgatct gaacaaaagc aaaatttcgt
      541 acgtacgaaa ttcagggtat cgggctgcgc ctgatgaaat gtttttggtg ccggcggtac
      601 tccaaaaaca catcttgtcc gacagttttg tggtgccggc ggagcggcgg tggccacaaa
      661 acatttcctg tccgcccgcg tcagttatcg ttcgcccgct tctggtgata agccagtatc
      721 tcagcacggc cttcgtcgta ggtgatctct ccggaaagaa tgtgcgcctt tacggactca
      781 taaagcgggg ttccggacgg gtccatacct tcaagcctga gagaggcctc agctttacgg
      841 aacccggtta cgcggagttg cagtgtccga tcatcagtca tgggttttcc tttgagcagt
      901 tatgcgaata aggcaggcgt aaagtgggac cactttacat gtcctgcccg gacgttgccg
      961 tggtatagct atgcaggcaa aagtggaaaa cggcaggaaa ccgttgcagc agagcgtgta
     1021 accagggtgg aaaatggtgt accgagcgat acgagccctg ttcagcatta cagacattac
     1081 gcttcctcgg tcatttactc acttcgttcg gtcatgactc tgcggcgagc gttacttgct
     1141 aagacagaaa gccatgtaaa aagtctgggg gattgccggt tttccatagg cttcgccctc
     1201 ctgacgagcc tcacagaaat caggtgattt ccggcgctca aatcagaagt ggcgaaaccc
     1261 gacaggactt aaagatcccc accgtttccg atgggtcgct ccctcgtgcg ctctcctgtt
     1321 cccaccatga ggtttacccg ttgcagaccg ccgtaaggtg gcgttttctc attcctgccc
     1381 ttgcaactgg gttccttgta ggtggttcgc tccaagctgg gctgtatgca cgaactcccc
     1441 gttcaacccg actaccgcgt cttttcaggt aactgtactc ttgaatccaa tcctgaaaga
     1501 cacgaaaaag cgccactggc ggtagccatt ggtgacaggt ttacggagcg gagcagagca
     1561 gtgtatataa gtacacacag agttcttgaa gagtcagcct aactacagct acactggaag
     1621 gacagatttg gtcgctgcgc tccgtttaag ccagtcacca cggttcagaa gttccccaac
     1681 ttactgaacc ttgaaaaaac cgcctcccca ggcggttttt tcttttcaac gagattacgc
     1741 atattcagta ttagcgtcaa tatacaggct agcgcttgta cttagctctt atctcgtctt
     1801 ttcttgaagc cataactcgc ttcacttcct cattggaagt gaatctagcg tctccagaat
     1861 tagcttttgc aacagccagc tctacctgct tcttcagcca cttttcatgc tgactaagag
     1921 gctcaacttc tcttgccaat tgctcagcaa agtctctgca agcttcactt agagttttgc
     1981 cacgggcttc tgccgctttc tgggctctca tcttgacgtt ctcatcaagc ctgaaatgaa
     2041 atttagtatc cataagatcc tccgacaccc gtaatgttag tacatttgtg cgcacaagca
     2101 acacacatat ttttttatag aaaaactata aaaaacaatg aaataaaatt aaatttcgtg
     2161 tcagttagaa aaaaaacaag aaggatgctg atcgatcgat gaagatcagt taaaatacaa
     2221 acaagagata aaaggaggga acatgggatt cataagccag ctttcaaaaa cgaaaatatc
     2281 aacacgtcgg ggatctgcta gccagataac agtgacgcaa tcattcaagc catcaacgtc
     2341 agcagaagag ctttccatca ggatctcgac tgaatgccta aagaacgtaa gcttgaaaat
     2401 cggagataat gttgacgtac tttatgacgc agacagtgat acatggatga taaaaaaaga
     2461 ggcggaaggt tataaaatat ccgggaaacc tgatgctccg acaggactga ttcgttacac
     2521 gctaaaggaa ggccacaaga aatttaccag taccagggaa tcacttccgg ttagaaaaga
     2581 tagtaatgac gacaccatcg tattcatggg tgacaagatg acgtttaagc tgaaggaaag
     2641 cgaatgatgg caagcaatct catttgggaa gaagaagcta ttgatgatcg ggctgactac
     2701 ttcgaatggc tttataagca gaatccaaaa gctgctgagg atgcagatca gcacatcgaa
     2761 gacacagttg atttactaat agagaatcca tttctcggaa aagatagtga aatagtgtct
     2821 ggtgtgagag ttctcatcat caaaggccta tcgttgaatg tgtactatca agaaggccat
     2881 ggcacagtaa aagttctacg cgttcttcat caatcaagaa acatagcaaa gctaatttaa
     2941 agtaacgcaa cctgcatcag cgagggggaa agaaacaact taaaaatttt gttttctaga
     3001 cagaagacag agccagtcta cgcccttgta aattaggcaa ac
//
