LOCUS       NZ_CP085701             5430 bp    DNA     circular CON 13-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain S29
            plasmid unnamed1, complete sequence.
ACCESSION   NZ_CP085701
VERSION     NZ_CP085701.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22488165
            Assembly: GCF_020691725.1
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 5430)
  AUTHORS   Shihan,Z., Xiaoyan,L., Zhenxu,Z. and Chao,Z.
  TITLE     The Molecular Transmission Mechanisms of blaCTX-M-55 gene in
            Nontyphoidal Salmonella from Guangzhou, China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5430)
  AUTHORS   Shihan,Z., Xiaoyan,L., Zhenxu,Z. and Chao,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-OCT-2021) KingMed School of Laboratory Medicine,
            Guangzhou Medical University, 195 Dongfeng West Road, Guangzhou,
            Guangdong 510000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: SPAdes v. 3.13.1; unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 110.0x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore
            PromethION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/13/2023 04:00:19
            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)                     :: 5,031
            CDSs (total)                      :: 4,909
            Genes (coding)                    :: 4,788
            CDSs (with protein)               :: 4,788
            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)              :: 121
            CDSs (without protein)            :: 121
            Pseudo Genes (ambiguous residues) :: 0 of 121
            Pseudo Genes (frameshifted)       :: 34 of 121
            Pseudo Genes (incomplete)         :: 99 of 121
            Pseudo Genes (internal stop)      :: 18 of 121
            Pseudo Genes (multiple problems)  :: 28 of 121
            Pseudo Genes (short protein)      :: 1 of 121
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP085701.1.
            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..5430
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="S29"
                     /serovar="Typhimurium"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="unnamed1"
                     /geo_loc_name="China: Guangzhou, Guangdong"
                     /lat_lon="22.26 N 112.57 E"
                     /collection_date="2014-07-02"
                     /collected_by="a patient in a tertiary hospital"
     gene            join(5243..5430,1..223)
                     /locus_tag="LJN59_RS25040"
                     /old_locus_tag="LJN59_25045"
     CDS             join(5243..5430,1..223)
                     /locus_tag="LJN59_RS25040"
                     /old_locus_tag="LJN59_25045"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000874179.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000874179.1"
                     /translation="MAFISLSNLAAKTGRIIQSQCVTATQTKKSTGAVELGFRLSKSAM
                     DETGITIGDRVDILYDKEENQWMIKKISEGGFGVSGQKNKHGGYSSCAVRLTLRPGFPR
                     LSEDEEDNKKLLSDDSFTQLSEGVIVFRLDDE"
                     /name="hypothetical protein"
     gene            481..1044
                     /locus_tag="LJN59_RS25045"
                     /old_locus_tag="LJN59_25050"
     CDS             481..1044
                     /locus_tag="LJN59_RS25045"
                     /old_locus_tag="LJN59_25050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015959180.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001749520.1"
                     /translation="MHALSILPSVARANLATKFSSHLKVIELFNTMQDSQVVVLSSLIE
                     GHHLTSSGNSVKADFEVTRLPAIIEMLEKKYFFPIRHLNVSVKSVTTGRMTGQTVYFIE
                     PEHIEQLLADPELVFANQERSLFFRSLEKEGKNLGKLIEKKGSVSQAVLSLLHHAYKDK
                     PLSDEMWKEIEDKFTHMLDELSAA"
                     /name="hypothetical protein"
     gene            complement(1073..1699)
                     /locus_tag="LJN59_RS25050"
                     /old_locus_tag="LJN59_25055"
     CDS             complement(1073..1699)
                     /locus_tag="LJN59_RS25050"
                     /old_locus_tag="LJN59_25055"
                     /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_227697613.1"
                     /translation="MSPTLNKQASKERCAVEFATRKKSKTQRKKSKALSYRGLCFFCTL
                     VTGKCQWTSKMSKQDYIQLRTLTDQFYADNKGLQEALDGSNDGKVRGYGIVVIDLNGLV
                     FGIPLRSHLNHKFGFVSERSEGVKKGLDYTKALLIKKEEYVSRAYKIPTPEFTHVNDNK
                     EKIQEDFNKFVNRYIEANVKKDENILRNYRYSTLKNYHKELGLED"
                     /name="hypothetical protein"
     gene            complement(2001..2084)
                     /locus_tag="LJN59_RS25235"
     CDS             complement(2001..2084)
                     /locus_tag="LJN59_RS25235"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_071532987.1"
                     /translation="MHEPPVQSDRCAFSGNYRLESNPERHD"
                     /name="replication initiation protein"
     gene            2722..3042
                     /locus_tag="LJN59_RS25055"
                     /old_locus_tag="LJN59_25060"
     CDS             2722..3042
                     /locus_tag="LJN59_RS25055"
                     /old_locus_tag="LJN59_25060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_000957082.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGRLPSI
                     SPALLRQLAGMGNNLNQIARKVNTGGAGHDRVQIVAALMAIDAGLERLRHAVLEKGGND
                     DR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3251..>3685
                     /locus_tag="LJN59_RS25140"
                     /pseudo=""
     CDS             3251..>3685
                     /locus_tag="LJN59_RS25140"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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            3720..4205
                     /locus_tag="LJN59_RS25065"
                     /old_locus_tag="LJN59_25070"
     CDS             3720..4205
                     /locus_tag="LJN59_RS25065"
                     /old_locus_tag="LJN59_25070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001749519.1"
                     /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_001749519.1"
                     /translation="MSSLLALAKDLEKQSKAQQQNTCEMLKAAFSEHEKSVKAELSASA
                     KRISDAISAHEQGMTAAMQSNRLSVLRMVGRTWLTITLVSVLLIATSGSILWWQGQQIT
                     GNYQTIRAQERTQAMLSEKNHGVQLSLCGEQKLSCVKVNPKAGAYGEEGNWMVLERK"
                     /name="MbeB family mobilization protein"
     gene            4209..4421
                     /locus_tag="LJN59_RS25070"
                     /old_locus_tag="LJN59_25075"
     CDS             4209..4421
                     /locus_tag="LJN59_RS25070"
                     /old_locus_tag="LJN59_25075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137423.1"
                     /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_000137423.1"
                     /translation="MTELEKQLLTALEQLHQDYSQRLDEWESAFAEWQKMSGLMQRENA
                     ALNERVTRLSQQVANLSRQLQRLSQ"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          2435..2614
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.339"
                     /coverage="83.0"
                     /evalue="7.539999999999999e-48"
     Typing          complement(1976..2489)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.217"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3033..4537
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.227"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agaaaaccag tggatgatta agaaaattag tgaaggtggc tttggtgtgt ctgggcaaaa
       61 aaacaagcac ggcggttact catcgtgtgc tgttagattg accttgcgac caggttttcc
      121 tcgcctttct gaggatgaag aggacaacaa gaagctactt tccgatgatt cattcactca
      181 gctaagtgaa ggtgtaatcg tcttcaggct ggatgatgaa taggaaggac caaaaaggaa
      241 aggcagagtt agtgagcgtc gccaaacaat cgactaactc cgccttctgg tcaacacatc
      301 actacctttg gaagggtgga gtgttatggg cggcattatg ttcataaact tgcattctaa
      361 taaagaaaaa atcgtttctt ttgagggatg tgaacacgac attttctatt ctgataggtg
      421 cgatgctatt ggctttggtc tcttaagttt atgtttttaa aaacatatga ggctatacat
      481 atgcacgctt tatcaatact accttcagtt gcccgcgcta acctggcaac taaattctcg
      541 tctcatttga aggtgatcga gctcttcaac acgatgcagg attcccaagt tgttgtcttg
      601 tcatcactga tcgaaggcca tcacctcacc agttctggta acagtgtcaa agccgacttt
      661 gaggtcactc gcttaccggc gattatcgag atgttagaga aaaaatattt tttccctatt
      721 cgtcatctaa atgtatctgt taaatctgta actacaggaa ggatgactgg acaaactgtc
      781 tatttcatag agcctgaaca catcgagcaa cttctcgctg atcctgagct tgtgtttgct
      841 aatcaggaaa ggagcctctt ctttcgttct ctcgaaaaag aagggaaaaa tctcggcaag
      901 cttatcgaga aaaaaggtag tgtttctcaa gccgtcttaa gccttctaca tcacgcctac
      961 aaagataaac ctctttctga cgagatgtgg aaggagatag aagataagtt cacccatatg
     1021 ctggatgaat tgagcgcggc gtaaaggcaa gggcggtcgt tagaccgcct ttttagtctt
     1081 ctaaacctaa ttctttgtga tagtttttca gcgtagagta acgatagttt ctgagtatgt
     1141 tttcatcttt cttgacgttc gcttctatgt atctgtttac gaatttgttg aaatcttctt
     1201 gtattttttc tttgttatca ttgacatggg taaattcagg agttggtatc ttataggctc
     1261 gcgatacata ctcttctttc ttaattagca acgctttggt gtaatccagt cctttcttaa
     1321 caccttctga tcgctccgaa acgaatccaa atttatggtt taaatggctt cgtaagggta
     1381 tcccgaacac caatccgttg agatcaataa ctacgattcc gtagcctctt acttttccat
     1441 cattactgcc gtcgagagcc tcttgtaggc ctttgttatc agcataaaac tggtctgtaa
     1501 gggttcttaa ctgtatgtaa tcctgtttgc tcatttttga tgtccattgg cattttcctg
     1561 taaccaatgt acaaaaaaag caaagccctc tgtaagagag ggctttgctt ttctttcgtt
     1621 gagtcttgga ttttttacgt gtggcgaact ctaccgcaca tctttctttg gaagcttgtt
     1681 tgtttaacgt ggggctcatt cctaccgcca cttctagatt tacttatatc aaaaattata
     1741 tgtgaagtca atttcgtagc tgttcttgac tggacttact ttgccagcgt aatcttctcc
     1801 tgaaacgaaa aaaccaccct ggcaggtggt ttttcgaagg ttatttaatc ctggcagatt
     1861 atctaaccgt ggtaacagtc ttgtgcgaga cgtgtcacca aatccgtcct tccagtgtag
     1921 cctcagtaag gccaccactt caagaactct caatacatct ctcgcacatc atgtttacca
     1981 gtggccgttg ccaatggcga ttagtcgtgt ctttccgggt tggactcaag tcgatagtta
     2041 ccggaaaagg cgcagcggtc ggactgaacg gggggttcgt gcatacagtc cagcttggag
     2101 cgaactgcct acccggaact gagtgtcagg cgtggaatga gataaacgcg gccataacag
     2161 cggaatgaca ccggtaaacc gaaaggcagg aacaggagag cgcacgaggg agccaccagg
     2221 gggaaacgcc tggtatcttt atagtcctgt cgggtttcgc caccactgat ttgagcgtca
     2281 gatttcgtga tgcttgtcag gggggcggag cctatggaaa aacggcagcg ccgcatcctt
     2341 ttcttgccct gtttgtcatg ccgtatgcct ttgctcttat ccgtgtgcag gtaacgcccg
     2401 ccgcagccga acggcaggag cggaagcgac cgagtgagcg aggaggcgta atatcaccgc
     2461 aacctccatg ttctcccgta cgccctgcag ctgcattttc ccctgccaca tgaagcactt
     2521 ttataaagtg ttactccgcc gtaacatatt aagccagtat acactccgct agcgctacgt
     2581 gactggttca gggctgcgcc ccgaaacccg ctaaaagcca ctgacgcgcc tgcggcttgt
     2641 ccaacaccgt gccgaccggg aaacatttcc cgcccgtccc ggtgttatca ggaggctact
     2701 ctggcagaca aacgcaacaa gatgctcacg atgtgggtga cggaagacga acaccggcgg
     2761 ctgctcgagc ggtgcgacgg caagcagctg gcggcgtgga tgcgtcagac ctgcctcgat
     2821 gagaagccgg cgcgtgccgg cagactgccg tcgatatcgc cggcgctgct gcgccagctt
     2881 gccggtatgg gtaataacct gaaccagatc gcccggaaag tgaataccgg tggtgccggt
     2941 catgaccggg tgcagatcgt ggccgccctg atggcaatcg acgcgggact ggagcggctg
     3001 cggcatgcgg tgctggaaaa aggggggaat gatgatcgtt aaattccatc cccgggggcg
     3061 cggtggtggt gccggtccgg tggattacct gctgggaaaa gaccggcagc gcgagggggc
     3121 gaccgtgctg cagggaaagc cggaggaagt ccgggagctt atcgatgcct cgccgtatgc
     3181 gaaaaagtac acctccggcg tactgtcgtt cgcggaggct gagctgccgc ccgggcagcg
     3241 ggagcagatc atggccagct ttgagcgggt tctgatgccc gggctcgata aagaccagta
     3301 cagcattctg tgggtggagc acaccgacaa ggggcggctg gagctgaatt tcctgatccc
     3361 caacacagag ctgctgaccg ggaaacgcct gcagccgtat tacgatcgcg ccgaccggcc
     3421 gcgcatcgat gcctggcaga ccgtggtgaa cggcagactg gggctgcatg atccaaacgc
     3481 cccgaagaac cggcggttac tggtcacgcc gtccgcactg ccggaaacga agctggaagc
     3541 cgctcaggcg attacacggg gtttgctggc cttagcctca tccggggcgc tcaaaacgcg
     3601 cgaggacgtc acagggtcgc tcactgcggc aggttttgag gtggtccgca ccacaaagaa
     3661 cagtatcagc attgccgacc cggacggggg gcgaaacatc cgactgaagg gagccattta
     3721 tgagcagtct tttagcgctg gcgaaggact tggaaaagca atcgaaagcg cagcagcaga
     3781 atacctgcga gatgctgaaa gccgcattca gcgagcacga gaagtctgta aaagcggaac
     3841 tgagcgcaag cgcgaagaga atcagcgacg ccatcagcgc ccacgagcag ggtatgaccg
     3901 cggcgatgca gtcgaaccgg ctgagcgtgc tgcgtatggt tggccggacg tggctgacca
     3961 tcaccctggt ctcagtactg ctgatcgcca cgagcgggag cattctgtgg tggcaggggc
     4021 agcagatcac cgggaattac cagactatcc gggcgcagga gcggacgcag gccatgctgt
     4081 cggagaagaa ccacggcgtg cagctgtcgc tctgtgggga acagaaactg tcctgcgtca
     4141 aagtgaaccc gaaagcggga gcttacgggg aggaagggaa ctggatggta ctggagagga
     4201 aatagcccat gacggaactg gaaaaacagt tgctgaccgc attagagcag ctacatcagg
     4261 actactcgca aaggctggac gagtgggaga gcgccttcgc ggaatggcag aagatgtctg
     4321 gtcttatgca acgggagaac gcggcgctga acgagcgcgt cacgcgcttg agtcagcagg
     4381 tggcgaactt gagcaggcag ttacagcgtt tgagtcagta gtgcagcggc atgaaatggc
     4441 ggtggccgcc gaacgggcat acgagcagcg acagcatgaa aaagagctgg cagaaccccg
     4501 tttccgtcag cggagctata acggtccgac gctgggctga ctgcgcgcat ccagtgacaa
     4561 accccaagaa gaagggctca taaatttccc gctaaatacg gtcgtgatga aaagatcacg
     4621 gctcaagaga gggggattta tgaagatact aaaagcgctc agtctgatac tgcaatgcgt
     4681 caaactggca atggatctgt gggagcgatt cgggggaaag tggccttttt agtgctttac
     4741 accgtattta tacgcgaaaa ctgctgtcat tcacctggct gcataaccat gcagccaggt
     4801 gaaatttatc tggcgtaaac ggggcggttt accgggtgct ttgctagggg tttcacccga
     4861 caggcaccgt atttgcgccg aaccagcccg aagcggtgcg ggcaagaact cttatgttaa
     4921 attcatctca tcggcaacct atacaggcat aaaaatcagt ttctataagc ggctttcttg
     4981 cacctacttg gtgatttttt tggatgcgct gacgttgctc gactttaaat caccatagaa
     5041 aaataccctt tacttacata aagatcgatc tggatgtgta tcttgacgag gttcaatacg
     5101 agcaattgtt tttgtattta aggtttctta tcgccgtttt ttgcggctct agaaaaatca
     5161 atacaaaaga tcttgaaagc cacctcgctc cctgggtaca cttccgtata agaactgatc
     5221 gatgtctaaa acggattgta ttatggcttt tatctctcta tcgaacttgg cagcgaagac
     5281 tggaaggata atccagtcgc agtgtgttac ggccacgcaa acgaaaaaaa gcacgggcgc
     5341 tgtcgagctg ggattccgct tgagcaagag cgctatggac gagactggta ttaccattgg
     5401 ggatcgtgtc gacattcttt acgacaaaga
//
