LOCUS       NZ_CP098837             3554 bp    DNA     circular CON 26-JUN-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            GD19PS1 plasmid pYUGDPS1-3, complete sequence.
ACCESSION   NZ_CP098837
VERSION     NZ_CP098837.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28951059
            Assembly: GCF_023848645.1
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 3554)
  AUTHORS   Wang,J.
  TITLE     Whole genome of mcr-1 positive Salmonella Typhimurium GD19PS1
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3554)
  AUTHORS   Wang,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-JUN-2022) Key Laboratory of Prevention and Control of
            Biological Hazard Factors (Animal Origin) for Agrifood Safety and
            Quality, Ministry of Agriculture of China, Yangzhou University,
            No.48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/26/2023 02:41:40
            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)                     :: 5,176
            CDSs (total)                      :: 5,053
            Genes (coding)                    :: 4,929
            CDSs (with protein)               :: 4,929
            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)              :: 124
            CDSs (without protein)            :: 124
            Pseudo Genes (ambiguous residues) :: 0 of 124
            Pseudo Genes (frameshifted)       :: 37 of 124
            Pseudo Genes (incomplete)         :: 96 of 124
            Pseudo Genes (internal stop)      :: 18 of 124
            Pseudo Genes (multiple problems)  :: 26 of 124
            Pseudo Genes (short protein)      :: 1 of 124
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP098837.1.
            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..3554
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="GD19PS1"
                     /serovar="Typhimurium"
                     /isolation_source="pig"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pYUGDPS1-3"
                     /geo_loc_name="China: Guangdong"
                     /lat_lon="23.08 N 113.14 E"
                     /collection_date="2019"
                     /collected_by="Wang Yan"
     gene            143..466
                     /gene="mobA"
                     /locus_tag="NFH28_RS25815"
                     /old_locus_tag="NFH28_25815"
     CDS             143..466
                     /gene="mobA"
                     /locus_tag="NFH28_RS25815"
                     /old_locus_tag="NFH28_25815"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            complement(754..1368)
                     /locus_tag="NFH28_RS25820"
                     /old_locus_tag="NFH28_25820"
     CDS             complement(754..1368)
                     /locus_tag="NFH28_RS25820"
                     /old_locus_tag="NFH28_25820"
                     /inference="COORDINATES: protein motif:HMM:NF025107.2"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_052895292.1"
                     /translation="MSTKNAQKEQKKESLITTHWGDDATIHGWTAIPNSLLMLQGDLGI
                     GSTEMCILLNILMHQWPESGESISFPSIGTIASRIGVSKRTIQRGVSNLEALGILTRYQ
                     STRNDPLTNGANIFDSTPLKEYLNKKAKGITISNSNKKKERKKTGITPNIKLPRICPKC
                     LKTKATSHEEIVKFFGVRKTMAGEIINSYCKECRASEKDLF"
                     /name="helix-turn-helix domain-containing protein"
     gene            1688..2413
                     /locus_tag="NFH28_RS25825"
                     /old_locus_tag="NFH28_25825"
     CDS             1688..2413
                     /locus_tag="NFH28_RS25825"
                     /old_locus_tag="NFH28_25825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001307201.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="WP_001427890.1"
                     /translation="MASMETEQQPQQTTEQIEVKTKRVQCFIDGYNLYHAIEETGNKAL
                     HWVDLKSLCKRYLPKNASIDNVFWFSAKPSHLSRAINENYQNYTNALTECGVDVIGGRF
                     KKKNVTCEADNGCGGVFHKHEEKESDVNLAISLVSGACNDEYDIAIIITADSDLCPPIK
                     YVRERFPNKELWLVAPPGRIRRATDLCSLSSRSMEIKNDALRACCMRDEFYKDGVLVAR
                     RPQEWRAVANTRQRRARSR"
                     /name="NYN domain-containing protein"
     gene            complement(3219..3413)
                     /locus_tag="NFH28_RS25830"
                     /old_locus_tag="NFH28_25830"
     CDS             complement(3219..3413)
                     /locus_tag="NFH28_RS25830"
                     /old_locus_tag="NFH28_25830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_052895291.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLRLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2..134
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.3e-63"
     Typing          3449..3554
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.35e-48"
     Typing          complement(2660..3184)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.274"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          144..463
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.86e-62"
ORIGIN
        1 actgccgtgc ttttgtcggt aattcgagct tgctgacagg acaggatgtg caattgttat
       61 accgcgcata catgcacgct attacaatta ccctggtcag ggctttgccc cgacacccat
      121 gtcagatacg gagccatgtt ttatgacaaa acgaagtgga agtaatacgc gcaggcgggc
      181 tatcagtcgc cctgttcgtc tgacggcaga agaagaccag gaaatcagaa aaagggctgc
      241 tgaatgcggc aagaccgttt ccggtttttt acgggcggca gctctcggta agaaagttaa
      301 ctcactgact gatgatcggg tactgaaaga agttatgagg ctgggggcgt tacagaaaaa
      361 actctttatc gacggcaagc gtgtcgggga cagagagtat gcggaggtgc tgatagctat
      421 tacggagtat caccgggccc tgttatccag gcttatggca gattagcttc ccggagggaa
      481 actgtcgaaa acagacggta tgaacgccgt aagcccccaa accgatcgcc attcactttc
      541 atacatagct atgcagtgag ctgaaagcga tcctgccgca tttttccggt ttaccccggg
      601 gaaaacatct atttttgcgg tgtttgcggc agaatcgcgt tcagcgcgtt tctgcggtgc
      661 gcgtaatgag acgttatggt aaatgggagc gttagaaaca gtcccattta cttgagtggg
      721 gggcagttgg ccatataaaa aatggtcaac tgtttaaaat agatcttttt cagaagctcg
      781 gcattctttg caatatgaat ttattatttc cccagccatt gtttttcgca cgccaaaaaa
      841 tttaacaatt tcttcgtggc tggttgcttt agttttcaaa cattttgggc aaatgcgtgg
      901 taattttatg ttgggtgtaa ttccggtttt ctttctttct ttctttttgt tgctgttgct
      961 aattgttatg cctttagctt ttttgtttaa atattctttt agaggagttg agtcgaatat
     1021 attagcgcca ttggttagag ggtcattcct tgttgattgg tatctagtta atatccccaa
     1081 tgcctctagg ttactaaccc cgcgttgaat tgttctttta gatacaccta ttcttgatgc
     1141 aatggtacca attgacggaa aagatattga ctcccctgac tcaggccatt gatgcatcaa
     1201 tatattcagc agaatacaca tctcagtact cccaatacca agatcacctt gcagcataag
     1261 gaggctattt ggtatagccg tccacccatg tatggttgca tcatctcccc agtgagtagt
     1321 gattaatgac tctttttttt gttctttctg tgcgtttttt gtgctcatag atgcttttct
     1381 cgcgaaaaaa aatcaaaatg tgaacagtta ctacctaact actcttaata taagagtagt
     1441 taggtagtaa catgtatctt ttaggatgac ataaatgtca tccatttgct ctttttttat
     1501 atagaactta agttgagtcc actacctaag agttatgctc ttagtggcta tccaagtcga
     1561 ggcttggaag cgcattgtac aaaattcttc ctgtattgga tgcgtccata cagtggtctg
     1621 ttaactgcgg ttaagagacg caaaaaggcc tgcatatgca ggcctttttg ctatctagag
     1681 gtcaaaaatg gcaagtatgg aaacagagca gcaaccacaa caaactactg agcaaatcga
     1741 agtaaaaaca aagcgagtgc agtgctttat tgatgggtat aatttatatc atgcaattga
     1801 agagactggt aataaagctc ttcattgggt tgatcttaaa tctttatgca agagatacct
     1861 tcctaaaaat gcatctattg ataatgtttt ttggttttcc gctaagccat cacatttatc
     1921 aagagccata aatgaaaatt atcaaaatta caccaacgct ttaaccgaat gtggtgttga
     1981 tgttatcggt ggacgtttta aaaaaaagaa tgtaacgtgc gaagctgata atggatgtgg
     2041 tggagttttc cataagcatg aagaaaaaga gtccgatgtt aatttggcta taagtctagt
     2101 gtctggtgcg tgtaatgatg agtatgatat agccattatt atcactgcgg attctgactt
     2161 atgcccccct attaaatacg taagagagcg attccctaat aaagagcttt ggcttgtagc
     2221 tcctccgggg agaatcaggc gagcgacaga tctctgctct ctgtcatcga gaagtatgga
     2281 gatcaagaat gatgctttga gagcctgctg tatgcgtgat gagttctaca aagatggagt
     2341 acttgtagcc agaaggcctc aggaatggcg agctgttgcc aataccaggc aaagaagggc
     2401 tagaagtcgt taggctttgt tgacgcagct agcgcaagga gattaatcta actaggttga
     2461 aaacgaaaaa accgccttgg cgggcggttt ttcgaaggtt catagagttg gcgctctttg
     2521 aaccgaggta actggctttg aggagcacag tcgccaaaac ttgttctttc agtttagcct
     2581 tatcaggtgc ataacttcaa gactcaactc ctctaaatca gttaccaatg gctgctgcca
     2641 gtggcgttaa gtcgtgtctt tccgggttgg actcaagacg atagttaccg gataaggcgc
     2701 agcggtcggg ctgaacgggg ggttcgtgca cacagcccag cttggagcga acgacctaca
     2761 ccgaactgag ataccaacag cgtgagctat gagaaagcgc cacgcttccc gaagggagaa
     2821 aggcggacag gtatccggta agcggcaggg tcggaacagg agagcgcacg agggagcttc
     2881 cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt tcgccacctc tgacttgagc
     2941 gtcgattttt gtgatgctcg tcaggggggc ggagcctatg gaaaaacggc atcggcgctg
     3001 gcttgttccg gtgctttgct ttttgctcac atgttctttc cggcgttatc ccctgattct
     3061 gtggataacc gtattaccgc ctttgagtga gctgacaccg ctcgccgcag tcgaacgacc
     3121 gagcgtagcg agtcagtgag cgaggaagcg gaagagcgtc tgacgtggca ttttctcctt
     3181 acgctccgct atgccgttct gcatcctgtc cgggtgcgtt atatcccggt gcgattttcc
     3241 gcttcaaagc gtgtctgtat gctgttctga agttcttccg cgagttcgtg cagcttctca
     3301 cacatggcgg cctgttcgtc agcatcaagt gcgtccagtt tttcgagcag cctcaggctc
     3361 tggcttttta tgaatcccgc catgttgagt acggtttgct gctgcttgtt catctttctg
     3421 ttttctccgt tctttctgtc atctgcgttg tgtgattata tcgagtacca cttttcgact
     3481 gttttaccgc cggtattctg ctgtctgact ctttgacggg catttctgtc agacaacact
     3541 gtcactgcca aaaa
//
