LOCUS       NZ_CP050737             6062 bp    DNA     circular CON 09-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain ST90
            plasmid pST90-3, complete sequence.
ACCESSION   NZ_CP050737
VERSION     NZ_CP050737.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14450165
            Assembly: GCF_012051625.1
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 6062)
  AUTHORS   Chen,Z.
  TITLE     Genomic analyses of multidrug-resistant Salmonella Indiana,
            Typhimurium, and Enteritidis isolates using MinION and MiSeq
            sequencing technologies
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6062)
  AUTHORS   Chen,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-MAR-2020) Joint Institute for Food Safety and Applied
            Nutrition, University of Maryland, 5145 Campus Drive, Patapsco
            Building, Suite 2134, College Park, MD 20742, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Assembly Name                     :: ST90
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 94x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/09/2023 12:00:55
            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)                     :: 5,136
            CDSs (total)                      :: 5,013
            Genes (coding)                    :: 4,845
            CDSs (with protein)               :: 4,845
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 168
            CDSs (without protein)            :: 168
            Pseudo Genes (ambiguous residues) :: 0 of 168
            Pseudo Genes (frameshifted)       :: 59 of 168
            Pseudo Genes (incomplete)         :: 123 of 168
            Pseudo Genes (internal stop)      :: 25 of 168
            Pseudo Genes (multiple problems)  :: 36 of 168
            Pseudo Genes (short protein)      :: 1 of 168
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP050737.1.
            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..6062
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="ST90"
                     /serovar="Typhimurium"
                     /isolation_source="feces"
                     /host="duck"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pST90-3"
                     /geo_loc_name="China:Shanghai"
                     /lat_lon="31.23 N 121.47 E"
                     /collection_date="2012-10-08"
                     /collected_by="Shanghai Municipal Center for Disease
                     Control and Prevention"
     gene            1026..2324
                     /locus_tag="HEC90_RS25460"
                     /old_locus_tag="HEC90_25460"
     CDS             1026..2324
                     /locus_tag="HEC90_RS25460"
                     /old_locus_tag="HEC90_25460"
                     /inference="COORDINATES: protein motif:HMM:NF024700.3"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ATP-binding protein"
                     /protein_id="WP_052918197.1"
                     /translation="MMVNFSLSNAFSFMEAQNMSMLAVSSSKDDINLANVVSVRDERIL
                     KSALIFGANASGKSNLMKTISLMKDIVLHSVQAIESSITKNVVPFLLDEAGPTKPSEME
                     MTFIADGIKYRYGLSLFQGKIKEEWLYYTPKTRETILFERDGQLIEINKAAFSESNLFI
                     KDGVIQKTREDVPFVSVVAGFNGEHSKRVVNWFSNVVFLSGSNEGMFTGITMKLINESE
                     DFKAWLKKILPAFQINDIYLDEVAPEFPFGNIKTDDDNLKNLFSSIQNFAKNQKVFSLR
                     VVKKTANGEISVPIDFESEGTKKIVYLLGPIYNAMINNNLLLVDEFDSKFHTLLSKFLF
                     RIFHAQSEGFSQVIAAVQDVNLMNTDCFRRDQIWFVDKDVKSGSSHLYSLVEYKEKQRS
                     LKPSYGNDYLSGAFDAIPLFDNLNEFEKLMPEG"
                     /name="ATP-binding protein"
     gene            2329..2766
                     /locus_tag="HEC90_RS25465"
                     /old_locus_tag="HEC90_25465"
     CDS             2329..2766
                     /locus_tag="HEC90_RS25465"
                     /old_locus_tag="HEC90_25465"
                     /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_052918195.1"
                     /translation="MPKRGKSIRSSSRNEETKPSKSTAKTTDRFISISFKHFHNVDDVG
                     QSINTWKDDGSLPDLIEKLVYLTANGITKVISDGVFTNYTRFPESAVNDFRCPDEISSD
                     EDWGVIKNIGGQKRRVAGFLRDNVFYIVFFDRDHRFWKSQK"
                     /name="hypothetical protein"
     gene            complement(3001..3114)
                     /locus_tag="HEC90_RS25470"
                     /old_locus_tag="HEC90_25470"
     CDS             complement(3001..3114)
                     /locus_tag="HEC90_RS25470"
                     /old_locus_tag="HEC90_25470"
                     /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_072101919.1"
                     /translation="MHEPPVQSDRCAFSGNYQLESNPERHDKTPMAAATGN"
                     /name="replication initiation protein"
     gene            complement(3766..3957)
                     /locus_tag="HEC90_RS25475"
                     /old_locus_tag="HEC90_25475"
     CDS             complement(3766..3957)
                     /locus_tag="HEC90_RS25475"
                     /old_locus_tag="HEC90_25475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4022..4345
                     /locus_tag="HEC90_RS25480"
                     /old_locus_tag="HEC90_25480"
     CDS             4022..4345
                     /locus_tag="HEC90_RS25480"
                     /old_locus_tag="HEC90_25480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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_000956001.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4554..>4985
                     /locus_tag="HEC90_RS25820"
                     /pseudo=""
     CDS             4554..>4985
                     /locus_tag="HEC90_RS25820"
                     /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            5023..5541
                     /locus_tag="HEC90_RS25490"
                     /old_locus_tag="HEC90_25490"
     CDS             5023..5541
                     /locus_tag="HEC90_RS25490"
                     /old_locus_tag="HEC90_25490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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_052918199.1"
                     /translation="MSNLLRTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDMLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEDIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPCGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            5548..5781
                     /locus_tag="HEC90_RS25495"
                     /old_locus_tag="HEC90_25495"
     CDS             5548..5781
                     /locus_tag="HEC90_RS25495"
                     /old_locus_tag="HEC90_25495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_004026237.1"
                     /translation="MTELEIHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          3594..3681
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.876"
                     /coverage="100.0"
                     /evalue="3.19e-37"
     Typing          complement(3043..3580)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.634"
                     /coverage="99.0"
                     /evalue="1.75e-177"
     Typing          4336..5885
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.802"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcggtgcgta caattcggat gttatggtaa atccagctga ttggcaggta taaaaaagcc
       61 gtccgtagac ggcctagtaa gttacttcgt ctttgtcatc actaccaatt cccatcggat
      121 gtcacctggg acattatgct gcctgtgatt ttgcggtggc aaaggatcat ctttattgca
      181 cgtcacttca tcaccacagt tcgtgcagcg gtaaatgccg gaagccggac aagtatttcc
      241 cggcttatag taataccgcc atacactccc ttcaggctcg gttgtttttg ttaaaaattt
      301 cgctgtgcta tctacataaa aggccatgtt gctttcctta cataaactaa gttagggacc
      361 gaagcttgca tgcttcggtg gttattgttt tttcttttcc cgattaattg ggatcttaaa
      421 cattcccccg ttaggacggg ttatccgttt gccctttacc gttatgtaag ggcgaaaaat
      481 gtatgcctga ggctcgtccg tctgcatgtt gcatttccta ttttcgccac atgaatgttg
      541 atttttgcta tcaaaattgt actgtagcaa ccaacagatc ttgtggctgg ctttatcaaa
      601 gcacttgagg tggtactcaa gcgccgcatt tgcgtatggt ttgttacggg ttagttctgg
      661 tggtacaggc taacccactt acttcaacaa tttttgcttc tcctcattca tgtttcactc
      721 cctacgtatt tttttacagt gtcagcgcca ctgagcataa acgcgacaaa aaggaaccat
      781 ccccacccag ataccgagtg aaaagccagc actgctgagc taatcactga ggcaaatggg
      841 accatttggt atagaaaaaa cttcatatac acctcttttt aagctggtcg ttaacttatc
      901 tactcataat gtgctgtcta ttggaccctt ttgttgtttt agtacggggt tatgctattc
      961 ttaatctaga attttgtcaa tattgtgcaa tttttgagtt taagggtgtt gttaggggtg
     1021 ttcttatgat ggttaacttt agtctttcaa acgcattttc cttcatggaa gctcaaaata
     1081 tgagcatgtt ggcggtgtcg tcatcgaaag acgatataaa cttggctaat gtagtgtcag
     1141 taagggatga gcggatactg aagtctgctt tgattttcgg agctaacgct agcggaaaat
     1201 ctaatctcat gaagacaata tctttaatga aagatattgt cctgcattct gtgcaagcta
     1261 tcgaaagtag cattacgaag aatgtagtcc cttttttact tgatgaggcg gggcctacta
     1321 aaccatctga aatggaaatg acttttattg cggatgggat taaatacaga tacggattat
     1381 ctttatttca agggaagata aaagaagagt ggttgtacta cacgccaaaa acaagggaga
     1441 ctattctctt tgagcgagat ggtcaactta ttgaaataaa taaagcagca tttagcgagt
     1501 caaatctttt tataaaggat ggggtcattc agaagacaag agaagatgtt ccctttgttt
     1561 ctgttgttgc tggatttaat ggggagcact caaagcgtgt tgtgaattgg tttagtaatg
     1621 tggtatttct ttctggttct aacgaaggaa tgtttactgg aattaccatg aagcttataa
     1681 atgaatctga agattttaaa gcttggctaa aaaaaatatt accagccttt cagattaatg
     1741 atatttatct tgatgaagtt gcgcctgaat ttccgtttgg caacataaaa acagatgatg
     1801 ataatttaaa aaatttattc agctcgattc agaattttgc aaaaaatcaa aaagtatttt
     1861 ctcttagagt cgtgaaaaaa actgctaatg gggagatttc ggttcccatt gattttgaat
     1921 cagaggggac caaaaagata gtctatctcc ttgggcctat ttataacgcc atgattaaca
     1981 ataacttatt attggttgat gagttcgatt caaagttcca taccctttta tctaagtttt
     2041 tatttaggat atttcatgcg caaagtgaag ggtttagcca agtaatcgct gcagttcagg
     2101 atgttaattt aatgaatact gattgcttta gacgagacca aatttggttt gttgacaagg
     2161 atgtaaagtc agggagtagc catctttatt ctttggttga gtacaaagag aaacaaagat
     2221 cattgaagcc atcatatggg aatgattatt tatcaggtgc ttttgatgca atcccgttat
     2281 ttgataatct taatgaattt gaaaagctaa tgcctgaggg atgattatat gccaaagaga
     2341 ggcaaaagca ttcgaagctc ttcgaggaat gaggaaacaa aaccttcaaa gagcacagcg
     2401 aaaacgactg atagatttat atctattagt tttaagcatt ttcataacgt cgatgatgtt
     2461 gggcagtcca taaatacatg gaaagatgat ggtagcctac ctgatctcat tgaaaaattg
     2521 gtttatctaa cggcgaatgg aatcactaaa gtgatttctg acggtgtgtt tactaactac
     2581 actcgatttc ctgagtcagc tgtaaacgat tttagatgcc cagatgagat atcctctgat
     2641 gaggattggg gggttataaa aaacattggc gggcagaaaa gaagagtcgc cggatttctg
     2701 agagataatg tgttctatat cgtgtttttt gatagagatc atcgcttctg gaagagtcaa
     2761 aaatagatga gatacagttg tattgtatgt taagaaaaga tcttcttgag attgtgatgc
     2821 tctcgtcgta atctcttgct ctgtaaacga aaaaaccgcc ttggcgggcg gtttttcgac
     2881 ggttctaaga gttggcgctc tgtgaaccaa ggtaactggc ttatgaggag cgcagtaacc
     2941 aaatctgttc tttcagttta gccttaacag gcgcataact tcaagactaa ctcctctaaa
     3001 tcagttacca gtggctgctg ccattggcgt tttgtcgtgt ctttccgggt tggactcaag
     3061 ttgatagtta ccggaaaagg cgcagcggtc ggactgaacg gggggttcgt gcatacagtc
     3121 cagcttggag cgaactgcct acccggaact gagtgtcagg cgtggaatga gacaaacgcg
     3181 gccataacag cggagtgaca ccggtaaacc gaatggcagg aacaggagag cgcacgaggg
     3241 agtcaccagg gggaaacgcc tggtatcttt aagtcctgtc gggtttcgcc acctctgact
     3301 tgagcgtcgg tttttgtgat gctcgtcagg ggggcggagc ctatggaaaa acgccagcgg
     3361 cgcggccttc ctcctgttcc tggtcttttg ctcacatgtt ctttccggcc ttatcccctg
     3421 attctgtgga taactgtgtt accgtttttg tgtgagtcag taccgctcgc cgcagtcgaa
     3481 cgaccgagcg tagcgagtca gtgagggagg aagcggaaaa gcgccgggac atgcattttc
     3541 tccttacgca tctgtgcggc atttcacacc cggcatggcg tacttttcat acaatccgca
     3601 ctgatgccgc atggttaagc cagtatacac tccgctatcg ctacgtgact gggtcagagc
     3661 tgcgccccga cacccgctaa aacctgctga cgcgccctga cgggcttgtc tgctcccggc
     3721 atccgctcac agacaagctg tgaccgtctc cgggagctgc atgtgtcaga ggttttcacc
     3781 gtcatccccg aaacgtgcga ggcagctgcg gtaaagctca tcggcgtggt cgtgaagcga
     3841 ttcacagata tctgcctgtt catctgcgtc cagttcgttg agcttctcca gcagcgttaa
     3901 tgtctggctt ctgataaagc gggccatgtt aagggcggtt ttttcctgtt tagtcactga
     3961 tgcctccgtg taagggggat ttctgttcac gggagtaatg ataccgatga aacgcgagag
     4021 gatgctcacg atacgggtta ctgatgatga acatgcccgg ttactggaac gctgtgaggg
     4081 taaacaactg gcggtatgga tgcggcgggt ctgcctgggt gagccggttg cccgttccgg
     4141 gaagctgccg acactggcac cgccgttact gcgtcagctg gccgccatcg gaaataacct
     4201 gaatcagaca gcccgtaagg tgaacagcgg gcagtggtct tccggtgacc gggttcaggt
     4261 ggtggccgca ctgatggcca tcggggatga gctgcgccgg ctgcgtctgg ccgtcaggga
     4321 acagggagtg cgggatgata gttaagtttc atgccagggg aaaaggtggt ggcagtggtc
     4381 cggttgatta cctgctggga agggagcgta accgggaagg ggcaacggtg cttcagggtg
     4441 atccggaaga agtccgggaa ctcatcgatg ccacgccatt tgcgaagaaa tacacgtcag
     4501 gtgttctgtc gttcgcggag aaggagctgc cgccgggagg gcgtgaaaaa gtgatggcga
     4561 gttttgagcg tgtactgatg cccggtctcg aaaagaatca gtacagcatc ctgtgggtgg
     4621 agcaccagga caagggacgg cttgagctga attttgtcat tccgaacatg gagctacaga
     4681 ccggaaaacg cctccagccg tactacgacc gtgcagacag gccgagaatt gatgcctggc
     4741 agacgctggt gaatcaccat tacgggctgc atgaccccaa cgccccggag aaccgccgga
     4801 cgctgactct ccctgataac ctgccggaaa agaaacaggc gcttgctgag agcgttacac
     4861 gggggcttga tgtgctttac cgtgccggag agataaaagg ccgtcaggat gtgattcagg
     4921 cgctcacaga ggtgggactt gaagtggtca gggtgacgcg aagcagtatc agcattgcag
     4981 acccgaacgg cgggaggaat atcagactga aaggagcgtt ttatgagcaa tcttttacgg
     5041 acgggcgcgg agttcgagaa aaagctgaaa gagagagccg aatctacaga gaaaatgctg
     5101 aacaacgagt tcaggaggct cggcgaatct gtaagcgagg ctgtgacatc aaacgagacg
     5161 aaaatcaaag acgctatagc cctgttcacc gcctcgacag aggagtcgct gaaaaaacac
     5221 cgggaagggg tgaaagaggc gatgatgcag cacaggaagg acatgttaaa gctggcaggg
     5281 aatacgggca tgatgttact ggggatagtc tttctcctgt ttaccgcgag tggcgggacg
     5341 ctctggtatc ttggcgggag gatacaggcg aacctggaag atatcaggaa gcaggaagag
     5401 acattgcaga aactgaacgc gaagacatgg ggcgtggagt ttgtgcagga cgggaacagg
     5461 aaattccttg tccttccgtg cgggaaatca gcggaggtga ttccctttca ggggaaagag
     5521 tgggtacatc tgaaggagtg acacagagtg acagagctgg aaatacattt gctgaacgcc
     5581 ttagagcagc tgcaacagga ctatatgcag cggctgagcg aatgggagag cgccttcgtg
     5641 gaattgcaga agatgttttc gcttacgcaa cgggacaacg cgatgctgaa cgagcgggtc
     5701 atgcagttga gtcagcaggt gcagcacttg agcgagcaga cagaacgctt gagccagtta
     5761 tacagcgaga actggagata agagaggaac ggttgataca ggagcgcgaa catgtgttat
     5821 ccctggaacg ggagcgtcag ccggaaatac aggaacgcac gctggatggc ccttcgctgg
     5881 gatggtgaaa ccatgaaaaa tggcagcttc agtggattaa gtggggggaa tgtggcctgt
     5941 accatctggt tgcataggta ttcatacggt taaaatttat caggcgcgat cgcggcattt
     6001 tttcgggtgg tttgttgcca tttttacctg tctgctgccg tgatcgcgct gaacgcgttt
     6061 ta
//
