LOCUS       NZ_CP085702             4081 bp    DNA     circular CON 13-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain S29
            plasmid unnamed2, complete sequence.
ACCESSION   NZ_CP085702
VERSION     NZ_CP085702.1
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 4081)
  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  JOURNAL   Unpublished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 4081)
  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
            CP085702.1.
            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..4081
                     /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="unnamed2"
                     /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(2142..4081,1..220)
                     /gene="mobQ"
                     /locus_tag="LJN59_RS25075"
                     /old_locus_tag="LJN59_25080"
     CDS             join(2142..4081,1..220)
                     /gene="mobQ"
                     /locus_tag="LJN59_RS25075"
                     /old_locus_tag="LJN59_25080"
                     /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_227697615.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAECRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGKMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(476..1168)
                     /locus_tag="LJN59_RS25080"
                     /old_locus_tag="LJN59_25085"
     CDS             complement(476..1168)
                     /locus_tag="LJN59_RS25080"
                     /old_locus_tag="LJN59_25085"
                     /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_001281403.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1700..1954)
                     /gene="mobC"
                     /locus_tag="LJN59_RS25085"
                     /old_locus_tag="LJN59_25090"
     CDS             complement(1700..1954)
                     /gene="mobC"
                     /locus_tag="LJN59_RS25085"
                     /old_locus_tag="LJN59_25090"
                     /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_000091747.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     Typing          complement(1962..2141)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.238"
                     /coverage="100.0"
                     /evalue="2.68e-81"
     Typing          2142..2500
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.056"
                     /coverage="100.0"
                     /evalue="3.94e-177"
     Typing          complement(477..1168)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2056..4079
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.259"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cgatgcagac agccacatat cacctgcgcc ggaacttatg gagtttcatc tgaaaacccg
       61 tgaggcaccg ctttttgctg ccgtcaacac accagaaaaa cagccggatc atctgttccg
      121 ctctctgggt ttcaatcgta cctgggatga atggcggcgc gaggaagatg caagaacaca
      181 caccaccgag aggagacatg atcgcggttg gtcacagtga atgtgaacaa tattttgttt
      241 tgtttaacat cgtgttatgt tcgtcgatgt tcttctatgt tcatcgacag ggatgaatgc
      301 aagaagcaca cacataatgc aagcatagtt ttgtttttcc gcccccaaaa attgggggtt
      361 cttttttcgc tgcattagag cgcttttgac gcaatttttc acttcaatag taccttcgca
      421 ctactaacac aaaaaaaacg cagcagggag cgttttaggt gccttaaaat cgattttaga
      481 tcgtcatctt gatctgtttg tcttccttga agcgaaaatg cagggctaca accgtgcgcc
      541 cctttttgat cgtctcaacc gttacagcca ggtcgctttt tttgttcagt tcgtcaacac
      601 agggttttat tagtatttta tttaagtctc tgaattgttt gtatttattt tcaatcccta
      661 acattgaacg aaagtcatta agagcaataa ttctctctcc cgtactgcgg aattgctgga
      721 ggaactcgta tattcttata ctgtaactac ttgataaacc tgatatgttt tttataacaa
      781 cgcgcgtgaa ttgccccttc agttgcgtca gataaggcat taccgcgtca gaaaaggtta
      841 ttcgagcctt ggcctcacct ttagcgtact gtgcccgata ctggatccag cggaactcct
      901 cacgcttctc gtcattcttg agaatgatcg acctgtccca taaacgatcg atcgcttcct
      961 gtaactgaac ctcggcattt ttccgcccca tgtcagggaa tgaatcaaaa tattccgcag
     1021 cggtaatggt cattgtcttt tgcaattcag catcagcacc agatttcaat cgactgatac
     1081 acagcaacag aaaacgttgt tcctgtaggg tcaacttgta gctggcctca accaaagcat
     1141 tcgacttgta ggcaatcaag tccgacatac aaagatcccg ttcaaatgtg gtgatgcttt
     1201 aatgtgcccc acaaataaga aatgtggaat attttttttt atatcctcac atttctgtga
     1261 ataacacctt aaattcctcc acctttacct taaattcctc cacctaaaca ccttaaattc
     1321 ctccaccttt accttaaatt cctccacata tacctctata acatattgat tttattaatg
     1381 aattttgacc ctaaaacaag tattaaaaac aagatcttaa aaacaagatc taaaaactta
     1441 acggcgagcc tgtggataac ttggggcgct gaaaacaaaa aaccaataaa aacaatgtgt
     1501 tgcaagaaag cagaattgca agttccgaat actccccttc caaccctgtg gaaatccagt
     1561 attcatgcgg gttcagcgca tatcacctac cgaaaaaccg tgcgtatgtg ctcaacctgg
     1621 cgacggattc acttccgctt cctcgcccac tcgctcgcta acgctcggtc gctggggctg
     1681 cggcgagcgg acgatacaat cactgtcctg gcagcgcctc cagctcgtta atcagcggca
     1741 gtatgcgcgt cacatcagcc tgtcgtgtca cctctgcctt caggaactgg agtaaccagg
     1801 cacgcaactg cacctcctcc ggctttctga cctttgccag caatgctgca cccacaacaa
     1861 ccttctgcgc tgtgtccagg ctccggctct tcgccttcag gcgctgtaat ctcgcctcag
     1921 catcagcaat cttctgttcg agcgttctgc tcatgatgta actccgtgcg cgatgaaaaa
     1981 tcgcatttta gcgcgtcact ggtagtttaa aaactgagct ggcataatgc acgacaaatc
     2041 acaaagtgca caaagtgcgc acttatacaa tctccactcc gtttcgattg tgtgcgccct
     2101 gcggggctga aagaaaacta caaaaaggca ttacggcaga aatggcgatt tatcatctca
     2161 gcatgaaaat tatctccaga agcagcggct acagcgccgt agcttccgct gcctatcgtt
     2221 ccggttcact gatgcttgat gagcgtaccg gactgactca cgactacacc cgcaaaagcg
     2281 gtgtggctga agctgtgatt ctgacccccg cgacagcccc tgcctggtgt acgaaccgtg
     2341 ccgaactctg gaatgccgtt gagaaggccg aatgccggaa gaactcacaa cttgcgcggg
     2401 aaattgaact cgctatcccc cgtgaactgc cgcaggatgc cgcacgggaa accgttctcg
     2461 cctttgtcag agaaaacttt gtcagtcagg gcatgattgc tgatgtggcg ttccatcaca
     2521 tggataaaac aaatccccat gcgcacatca tgctgaccac gagggctgtc ggacctgctg
     2581 ggttcggcgg aaaggtcagg gactggaacg accggacaca tgccgagacg tggcgtgcat
     2641 catgggctga ccatgcaaac agagcactgg cgaacgccgg ttatcaggaa gagatagacc
     2701 atcgttcata cgagcgacag gggcttgaga aaacgcctgg tattcacctc ggaaagtctg
     2761 cctgtgcgat ggaaacacgc ggtatcgaaa cagaacgcgg cgaacagaat cgtctgatta
     2821 acaggcttaa cctggaaata cagatttccc gcactgaact caggaacagc gggctgacag
     2881 agcctgcccg ccgtgtggct gaccttctga atatcgtgct tcctgacaac gcaacttcgt
     2941 acacactacg tgacatcatc gaagcgttgc cgaaggacag taatgcggca tggaaactca
     3001 ccagtaatgc catgtcgatg atggcagata tgcaggcgac gcgcagacgc tgggaagagc
     3061 tgaacaccga acgaaaggaa gcgatgagcc atgctgccag cctgaaaaaa tcatcgccgt
     3121 tttcgtccgg tttttcccgt attcccctga tgcaatgggc ggcaccggaa taccgtagcg
     3181 aacagggaaa aatccagtcg ctgagccagc aaatggaaaa attgcgacag cattaccgga
     3241 aggtggagaa acaggacatt cccgcgagtc agacggcatt tgaaaaacag tggcagcagt
     3301 ggggggcatc cggccttgca gctctcagag tccagttgct taaacgtgaa gaggaattgc
     3361 gccggaagga gcaggaggat acagaacgta gtcgcgcgga gcgacgagcg gaacagctca
     3421 ggaaaaatga caatgccgtt atggattcag gggtactgag cgcagtcgtt acggggtatg
     3481 gcgaggcccc catgcctggt aacgggaaaa tgacctgtta ccttctgctt cacaaccgga
     3541 acggagaata cacgctctgg gggaacgagc tggagaaata ccgcaccaga atctttgagc
     3601 gtgttgattt aatgcgtgac aggagtggtt atatctgtga ccgaagcgaa atcggtcaac
     3661 atccaccact gcaacgtgtt tattcctctg cgacctttga gcaacttctg acgcaggttt
     3721 gccagacatg gccgcaatat acccgcaatc tccgccagcc gaagacatgg ccggagtctt
     3781 tctgtcttgg agaagaccgc cagccagcca tgccatcact ggcagcaagg aaggtggatt
     3841 ttacgcaggg acgtctgcta ccgacgctga tgccggtaat gagttctgtc gaccgggaaa
     3901 cccgccagct tcagcttttg ctggtcatgg gcgtggatga ctctctgggc ggtgttgtcc
     3961 ggcttaatgg tacgctgtat cccgcgtttg ccgttccctc agccgataac agccagctgg
     4021 tcatcagtgc actgaccgat aaggggttac ggtatgcagg gtatggtgtt gccgtaaatc
     4081 a
//
