LOCUS       NZ_CP085703             4062 bp    DNA     circular CON 13-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain S29
            plasmid unnamed3, complete sequence.
ACCESSION   NZ_CP085703
VERSION     NZ_CP085703.1
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 4062)
  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  JOURNAL   Unpublished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 4062)
  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
            CP085703.1.
            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..4062
                     /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="unnamed3"
                     /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(2135..4062,1..220)
                     /gene="mobQ"
                     /locus_tag="LJN59_RS25090"
                     /old_locus_tag="LJN59_25095"
     CDS             join(2135..4062,1..220)
                     /gene="mobQ"
                     /locus_tag="LJN59_RS25090"
                     /old_locus_tag="LJN59_25095"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_070749924.1"
                     /translation="MAIYHLSMKIISRSNGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQKEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NHLINRLNLEIQISHTELRNSGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKLEKQDIPASQTAFEKQWQQWGESGLAALRSQL
                     LKREEELRRKELEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQYPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWDEW
                     RREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(468..1169)
                     /locus_tag="LJN59_RS25095"
                     /old_locus_tag="LJN59_25100"
     CDS             complement(468..1169)
                     /locus_tag="LJN59_RS25095"
                     /old_locus_tag="LJN59_25100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001281396.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVEITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1702..1956)
                     /gene="mobC"
                     /locus_tag="LJN59_RS25100"
                     /old_locus_tag="LJN59_25105"
     CDS             complement(1702..1956)
                     /gene="mobC"
                     /locus_tag="LJN59_RS25100"
                     /old_locus_tag="LJN59_25105"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091744.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(1958..2134)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2135..2493
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.5"
                     /coverage="100.0"
                     /evalue="8.52e-174"
     Typing          complement(470..1169)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          2049..4060
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.741"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tgatgcagac agccacatat cacctgcgcc ggaacttatg gagtttcatc tgaaaacccg
       61 tgaggcaccg ctttttgctg ccgtcaacac accagaaaaa cagccggatc atctgttccg
      121 ctcgctgggt ttcaatcgta cctgggacga atggcggcgc gaggaagatg cacgaacaca
      181 cgccaccgag aggagacatg atcgcggttg gtcacagtga atgtgaacaa tattttgttt
      241 tgtttaacat cgtgttatgt tcgtcgatgt tcatcgacag ggatgaatgc aagaagcaca
      301 ctcacataac gcaagcatag ttttgttttt ccgcccccaa aaattggggg ttcttttttc
      361 gctgcatcag agcgtttttg acgcaatttt tcacttcaat agtaccttcg cactactaac
      421 acaaaaaaaa cgcaacaggg agtgttttag gtgccttaaa atcgattcta gatcgtcatc
      481 ttgatctgtt tgtcttcctt gaagcgaaaa tgcagggcta caaccgtgcg cccctttttg
      541 atcgtctcaa ccgttacaac cagatcgctt ttttcgttca gttcggcgat ggctggcttg
      601 attatcatct tattcaagtc tttgaattgt tgatatttat cttcaacggc aagcatggtt
      661 cggaaatcat cgatagctat cgttctgtca ccggtgctgc ggaactgctg gagcagctcg
      721 taaatgcgga tgctgtaggt gctggagagg ctggagacgt tcttcacgac tacccgcgta
      781 aactgcccct tgagctgtgt cagatacggc atgatggcat cggagaaggt gatctctact
      841 ttcgcctcac ctttgaaata ctgcgcccgg tactgcaccc agcggaactc ttctcgtttt
      901 tcctcgttct tgatgattac tgacctgtcc cagaggcgat ctatcgcttc cttgagccta
      961 gcttcagcgt gctgccgtcc catgtcagga aaggcatcat gaaactctgc agccgtgatg
     1021 gtcatggttt tttgttcatc cggcgaaggg gaatcttctc cggatttcag gcggctgata
     1081 cagaccagca ggaagcgctg ttcctgcaaa gtgagcttgt agcttgcctc gataagggcg
     1141 tttgatttgt aagctatcag atctgacatt tcgcttgctc gttgctattg gtggcgtttt
     1201 tttactgtac gccacccatc atattggtgg aagttttttt tttgcaaccc cttttttctg
     1261 tggattacac ccccaaaagc tccacctatc acccccaaaa gctccaccta tcacccccaa
     1321 aagctccacc tatcaccccc aaaagctcca cctatctcgc cagaacacct ttaaaatcat
     1381 gtggttacaa gacctaaaaa ggttttaaaa aaaaagatct aaaaataaga tcttaaaaac
     1441 ttaacggcga gcctgtggat aacttggggt gctgaaaata aaaatccaat aaaaacaatg
     1501 tgttgaaaaa aatcaggatt gaagattccg aatacacccc ctccaaccct gtggaaatcc
     1561 agtattcatg cgggttcagc gcatatcacc tgtcgaaaaa ccgtgcgtat gtgctcaaca
     1621 tggcgactga ttcacttccg cttcctcgcc cactcgctcg ctaacgctcg gtcgctgggc
     1681 tgcggcgagc ggacgataca atcactgctc tggcagcgcc tccagctcgt taatcagcgg
     1741 cagtattcgc gtcacatcag cctgccgtgt cacctctgcc ttcaggaact ggagtaacca
     1801 agctcgcaac tgcacttcct ccggctttct gacttttgcc agcaatgctg cacccacaat
     1861 gaccttctgc gctgtgtcca ggctccggct cttcgccttc aggcgctgta atctcgcctc
     1921 agcatcagca atcttctgtt cgagcgttct gctcatgatg taactccatg cgcgatgaaa
     1981 aatcgcattt tagcgcgtca ctggtagttt aaaaactgag ctggcataat gcacggcaaa
     2041 tcacgaagtg cgcacttata caatctccac tccgtttcga ttgtgtgcgc cctgcggggc
     2101 tgaaagaaaa ctgcaaaaag gcattacggc agaaatggcg atttatcatc tcagtatgaa
     2161 aatcatctcc agaagcaacg gctacagcgc cgttgcttct gctgcctatc gttctggttc
     2221 actaatgctt gatgagcgta ccggactgac tcacgactac acccgcaaaa gcggtgtggc
     2281 tgaggctgtg attctgaccc ccgcgacagc ccctgcctgg tgtacgaacc gtgccgaact
     2341 ctggaatgcc gttgagaagg ccgaacgccg gaagaactca caacttgcgc gggaaattga
     2401 actcgccatc ccccacgaac tgccgcagga tgccgcacgg gaaaccgttc tcgcctttgt
     2461 cagagaaaac tttgtcagtc agggcatgat tgctgatgtg gcgttccatc acatggataa
     2521 aacaaatccc catgcgcaca tcatgctgac cacgagggct gtcgggcctg ctgggttcgg
     2581 cggaaaggtc agggactgga acgaccggac acatgccgag acgtggcgtg catcatgggc
     2641 tgaccatgca aacagggcac tggcgaacgc cggttatcag aaagagatag accatcgttc
     2701 atacgagcga caggggcttg agaaaacgcc gggtattcac ctcggaaagt ctgcctgtgc
     2761 gatggaaaca cgcggtatcg aaacagaacg cggcgaacag aatcatctga ttaacaggct
     2821 taacctggaa atacagattt cccacaccga actcaggaac agcgggctga cagagcctgc
     2881 ccgccgtgtg gctgaccttc tgaatatcgg gcttcctgac aacgcaactt cgtacacact
     2941 acgtgacatc atcgaagcgt tgccgaagga cagtaacgcg gcatggaaac tcaccagtaa
     3001 cgccatgtcg atgatggcag atatgcaggc gacgcgcaga cgctgggaag agctgaacac
     3061 cgaacgaaag gaagcgatga gccatgctgc cagcctgaaa aaatcatcgc cgttttcgtc
     3121 cggtttttcc cgtattcccc tgatgcaatg ggctgcaccg gaataccgta gtgagcaggg
     3181 aaaaatccag tctctgagcc agcaaatgga aaaattgcga cagcattacc ggaagctgga
     3241 gaaacaggac attcccgcga gtcagacggc atttgaaaaa cagtggcagc agtgggggga
     3301 atccggcctt gcagctctca gatcccagtt gcttaaacgt gaagaggaat tgcgccggaa
     3361 ggagctggag gatacagaac gtagtcgcgc ggagcagctc aggaaaaatg acaatgccgt
     3421 tatggattca ggggtgctga gagcagtcgt tacggggtat ggcgaggctc ccatgcctgg
     3481 taacggggaa atgacctgtt accttctgct tcacaaccgg aacggagaat atacgctctg
     3541 ggggaacgag ctggagaaat accgcaccag gatctttgag agtgttgatt taatgcgtga
     3601 caggagtggt tatatctgtg accgaagcga aatcggtcaa tatccaccac tgcaacgtgt
     3661 ttattcctct gcgacctttg agcaacttct gacgcaggtt tgccagacat ggccgcaaca
     3721 tacccgcaat ctccgccaac cgaagacatg gccggagtct ttctgtcttg gagaagaccg
     3781 ccagccagcc atgccatcac tggcagcaag gaaggtggat tttacgcagg gacgtctgcc
     3841 accgacgctg atgccggtca tgagttctgt cgaccgggaa acccgccagc ttcagctttt
     3901 gctggtcatg ggcgtggatg actctctggg cggtgttgtc cggcttaatg gtacgctgta
     3961 tcccgcgttt gccgttccct cagccgataa cagccagctg gtcatcagtg cactgaccga
     4021 taaggggtta cggtatgcag ggtatggtgt tgccgtaaat ca
//
