LOCUS       CP050742                6062 bp    DNA     circular BCT 06-APR-2020
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain ST56
            plasmid pST56-3, complete sequence.
ACCESSION   CP050742
VERSION     CP050742.1
DBLINK      BioProject: PRJNA615288
            BioSample: SAMN14450164
KEYWORDS    .
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  JOURNAL   Unpublished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                     :: ST56
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 113x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 03/31/2020 17:33:49
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.11
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 5,169
            CDSs (total)                      :: 5,043
            Genes (coding)                    :: 4,884
            CDSs (with protein)               :: 4,884
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 159
            CDSs (without protein)            :: 159
            Pseudo Genes (ambiguous residues) :: 0 of 159
            Pseudo Genes (frameshifted)       :: 69 of 159
            Pseudo Genes (incomplete)         :: 92 of 159
            Pseudo Genes (internal stop)      :: 25 of 159
            Pseudo Genes (multiple problems)  :: 25 of 159
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..6062
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="ST56"
                     /serovar="Typhimurium"
                     /isolation_source="Diarrheal patient"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pST56-3"
                     /geo_loc_name="China:Shanghai"
                     /lat_lon="31.23 N 121.47 E"
                     /collection_date="2011-07-21"
                     /collected_by="Shanghai Municipal Center for Disease
                     Control and Prevention"
     gene            complement(233..670)
                     /locus_tag="HEC89_25775"
     CDS             complement(233..670)
                     /locus_tag="HEC89_25775"
                     /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="QIU23327.1"
                     /translation="MPKRGKSIRSSSRNEETKPSKSTAKTTDRFISISFKHFHNVDDVG
                     QSINTWKDDGSLPDLIEKLVYLTANGITKVISDGVFTNYTRFPESAVNDFRCPDEISSD
                     EDWGVIKNIGGQKRRVAGFLRDNVFYIVFFDRDHRFWKSQK"
                     /name="hypothetical protein"
     gene            complement(675..1973)
                     /locus_tag="HEC89_25780"
     CDS             complement(675..1973)
                     /locus_tag="HEC89_25780"
                     /inference="COORDINATES: protein motif:HMM:NF024700.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ATP-binding protein"
                     /protein_id="QIU23328.1"
                     /translation="MMVNFSLSNAFSFMEAQNMSMLAVSSSKDDINLANVVSVRDERIL
                     KSALIFGANASGKSNLMKTISLMKDIVLHSVQAIESSITKNVVPFLLDEAGPTKPSEME
                     MTFIADGIKYRYGLSLFQGKIKEEWLYYTPKTRETILFERDGQLIEINKAAFSESNLFI
                     KDGVIQKTREDVPFVSVVAGFNGEHSKRVVNWFSNVVFLSGSNEGMFTGITMKLINESE
                     DFKAWLKKILPAFQINDIYLDEVAPEFPFGNIKTDDDNLKNLFSSIQNFAKNQKVFSLR
                     VVKKTANGEISVPIDFESEGTKKIVYLLGPIYNAMINNNLLLVDEFDSKFHTLLSKFLF
                     RIFHAQSEGFSQVIAAVQDVNLMNTDCFRRDQIWFVDKDVKSGSSHLYSLVEYKEKQRS
                     LKPSYGNDYLSGAFDAIPLFDNLNEFEKLMPEG"
                     /name="ATP-binding protein"
     gene            complement(3280..3513)
                     /gene="mbeD"
                     /locus_tag="HEC89_25785"
     CDS             complement(3280..3513)
                     /gene="mbeD"
                     /locus_tag="HEC89_25785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137445.1"
                     /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="QIU23329.1"
                     /translation="MTELEIHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="mbeD"
     gene            complement(3520..4038)
                     /locus_tag="HEC89_25790"
     CDS             complement(3520..4038)
                     /locus_tag="HEC89_25790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001525988.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /protein_id="QIU23330.1"
                     /translation="MSNLLRTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDMLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEDIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPCGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="mobilization protein"
     gene            complement(4016..4774)
                     /locus_tag="HEC89_25795"
                     /pseudo=""
     CDS             complement(4016..4774)
                     /locus_tag="HEC89_25795"
                     /inference="COORDINATES: protein motif:HMM:NF015397.1"
                     /note="incomplete; partial on complete genome; 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            complement(4716..5039)
                     /locus_tag="HEC89_25800"
     CDS             complement(4716..5039)
                     /locus_tag="HEC89_25800"
                     /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="QIU23333.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            5104..5295
                     /locus_tag="HEC89_25805"
     CDS             5104..5295
                     /locus_tag="HEC89_25805"
                     /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="QIU23331.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            5947..6060
                     /locus_tag="HEC89_25810"
     CDS             5947..6060
                     /locus_tag="HEC89_25810"
                     /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="QIU23332.1"
                     /translation="MHEPPVQSDRCAFSGNYQLESNPERHDKTPMAAATGN"
                     /name="replication initiation protein"
     Typing          complement(5381..5468)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.753"
                     /coverage="100.0"
                     /evalue="1.48e-35"
     Typing          5479..6016
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.634"
                     /coverage="99.0"
                     /evalue="1.75e-177"
     Typing          complement(3177..4726)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.802"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tagaggagtt agtcttgaag ttatgcgcct gttaaggcta aactgaaaga acagatttgg
       61 ttactgcgct cctcataagc cagttacctt ggttcacaga gcgccaactc ttagaaccgt
      121 cgaaaaaccg cccgccaagg cggttttttc gtttacagag caagagatta cgacgagagc
      181 atcacaatct caagaagatc ttttcttaac atacaataca actgtatctc atctattttt
      241 gactcttcca gaagcgatga tctctatcaa aaaacacgat atagaacaca ttatctctca
      301 gaaatccggc gactcttctt ttctgcccgc caatgttttt tataaccccc caatcctcat
      361 cagaggatat ctcatctggg catctaaaat cgtttacagc tgactcagga aatcgagtgt
      421 agttagtaaa cacaccgtca gaaatcactt tagtgattcc attcgccgtt agataaacca
      481 atttttcaat gagatcaggt aggctaccat catctttcca tgtatttatg gactgcccaa
      541 catcatcgac gttatgaaaa tgcttaaaac taatagatat aaatctatca gtcgttttcg
      601 ctgtgctctt tgaaggtttt gtttcctcat tcctcgaaga gcttcgaatg cttttgcctc
      661 tctttggcat ataatcatcc ctcaggcatt agcttttcaa attcattaag attatcaaat
      721 aacgggattg catcaaaagc acctgataaa taatcattcc catatgatgg cttcaatgat
      781 ctttgtttct ctttgtactc aaccaaagaa taaagatggc tactccctga ctttacatcc
      841 ttgtcaacaa accaaatttg gtctcgtcta aagcaatcag tattcattaa attaacatcc
      901 tgaactgcag cgattacttg gctaaaccct tcactttgcg catgaaatat cctaaataaa
      961 aacttagata aaagggtatg gaactttgaa tcgaactcat caaccaataa taagttattg
     1021 ttaatcatgg cgttataaat aggcccaagg agatagacta tctttttggt cccctctgat
     1081 tcaaaatcaa tgggaaccga aatctcccca ttagcagttt ttttcacgac tctaagagaa
     1141 aatacttttt gattttttgc aaaattctga atcgagctga ataaattttt taaattatca
     1201 tcatctgttt ttatgttgcc aaacggaaat tcaggcgcaa cttcatcaag ataaatatca
     1261 ttaatctgaa aggctggtaa tatttttttt agccaagctt taaaatcttc agattcattt
     1321 ataagcttca tggtaattcc agtaaacatt ccttcgttag aaccagaaag aaataccaca
     1381 ttactaaacc aattcacaac acgctttgag tgctccccat taaatccagc aacaacagaa
     1441 acaaagggaa catcttctct tgtcttctga atgaccccat cctttataaa aagatttgac
     1501 tcgctaaatg ctgctttatt tatttcaata agttgaccat ctcgctcaaa gagaatagtc
     1561 tcccttgttt ttggcgtgta gtacaaccac tcttctttta tcttcccttg aaataaagat
     1621 aatccgtatc tgtatttaat cccatccgca ataaaagtca tttccatttc agatggttta
     1681 gtaggccccg cctcatcaag taaaaaaggg actacattct tcgtaatgct actttcgata
     1741 gcttgcacag aatgcaggac aatatctttc attaaagata ttgtcttcat gagattagat
     1801 tttccgctag cgttagctcc gaaaatcaaa gcagacttca gtatccgctc atcccttact
     1861 gacactacat tagccaagtt tatatcgtct ttcgatgacg acaccgccaa catgctcata
     1921 ttttgagctt ccatgaagga aaatgcgttt gaaagactaa agttaaccat cataagaaca
     1981 cccctaacaa cacccttaaa ctcaaaaatt gcacaatatt gacaaaattc tagattaaga
     2041 atagcataac cccgtactaa aacaacaaaa gggtccaata gacagcacat tatgagtaga
     2101 taagttaacg accagcttaa aaagaggtgt atatgaagtt ttttctatac caaatggtcc
     2161 catttgcctc agtgattagc tcagcagtgc tggcttttca ctcggtatct gggtggggat
     2221 ggttcctttt tgtcgcgttt atgctcagtg gcgctgacac tgtaaaaaaa tacgtaggga
     2281 gtgaaacatg aatgaggaga agcaaaaatt gttgaagtaa gtgggttagc ctgtaccacc
     2341 agaactaacc cgtaacaaac catacgcaaa tgcggcgctt gagtaccacc tcaagtgctt
     2401 tgataaagcc agccacaaga tctgttggtt gctacagtac aattttgata gcaaaaatca
     2461 acattcatgt ggcgaaaata ggaaatgcaa catgcagacg gacgagcctc aggcatacat
     2521 ttttcgccct tacataacgg taaagggcaa acggataacc cgtcctaacg ggggaatgtt
     2581 taagatccca attaatcggg aaaagaaaaa acaataacca ccgaagcatg caagcttcgg
     2641 tccctaactt agtttatgta aggaaagcaa catggccttt tatgtagata gcacagcgaa
     2701 atttttaaca aaaacaaccg agcctgaagg gagtgtatgg cggtattact ataagccggg
     2761 aaatacttgt ccggcttccg gcatttaccg ctgcacgaac tgtggtgatg aagtgacgtg
     2821 caataaagat gatcctttgc caccgcaaaa tcacaggcag cataatgtcc caggtgacat
     2881 ccgatgggaa ttggtagtga tgacaaagac gaagtaactt actaggccgt ctacggacgg
     2941 cttttttata cctgccaatc agctggattt accataacat ccgaattgta cgcaccgcta
     3001 aaacgcgttc agcgcgatca cggcagcaga caggtaaaaa tggcaacaaa ccacccgaaa
     3061 aaatgccgcg atcgcgcctg ataaatttta accgtatgaa tacctatgca accagatggt
     3121 acaggccaca ttccccccac ttaatccact gaagctgcca tttttcatgg tttcaccatc
     3181 ccagcgaagg gccatccagc gtgcgttcct gtatttccgg ctgacgctcc cgttccaggg
     3241 ataacacatg ttcgcgctcc tgtatcaacc gttcctctct tatctccagt tctcgctgta
     3301 taactggctc aagcgttctg tctgctcgct caagtgctgc acctgctgac tcaactgcat
     3361 gacccgctcg ttcagcatcg cgttgtcccg ttgcgtaagc gaaaacatct tctgcaattc
     3421 cacgaaggcg ctctcccatt cgctcagccg ctgcatatag tcctgttgca gctgctctaa
     3481 ggcgttcagc aaatgtattt ccagctctgt cactctgtgt cactccttca gatgtaccca
     3541 ctctttcccc tgaaagggaa tcacctccgc tgatttcccg cacggaagga caaggaattt
     3601 cctgttcccg tcctgcacaa actccacgcc ccatgtcttc gcgttcagtt tctgcaatgt
     3661 ctcttcctgc ttcctgatat cttccaggtt cgcctgtatc ctcccgccaa gataccagag
     3721 cgtcccgcca ctcgcggtaa acaggagaaa gactatcccc agtaacatca tgcccgtatt
     3781 ccctgccagc tttaacatgt ccttcctgtg ctgcatcatc gcctctttca ccccttcccg
     3841 gtgttttttc agcgactcct ctgtcgaggc ggtgaacagg gctatagcgt ctttgatttt
     3901 cgtctcgttt gatgtcacag cctcgcttac agattcgccg agcctcctga actcgttgtt
     3961 cagcattttc tctgtagatt cggctctctc tttcagcttt ttctcgaact ccgcgcccgt
     4021 ccgtaaaaga ttgctcataa aacgctcctt tcagtctgat attcctcccg ccgttcgggt
     4081 ctgcaatgct gatactgctt cgcgtcaccc tgaccacttc aagtcccacc tctgtgagcg
     4141 cctgaatcac atcctgacgg ccttttatct ctccggcacg gtaaagcaca tcaagccccc
     4201 gtgtaacgct ctcagcaagc gcctgtttct tttccggcag gttatcaggg agagtcagcg
     4261 tccggcggtt ctccggggcg ttggggtcat gcagcccgta atggtgattc accagcgtct
     4321 gccaggcatc aattctcggc ctgtctgcac ggtcgtagta cggctggagg cgttttccgg
     4381 tctgtagctc catgttcgga atgacaaaat tcagctcaag ccgtcccttg tcctggtgct
     4441 ccacccacag gatgctgtac tgattctttt cgagaccggg catcagtaca cgctcaaaac
     4501 tcgccatcac tttttcacgc cctcccggcg gcagctcctt ctccgcgaac gacagaacac
     4561 ctgacgtgta tttcttcgca aatggcgtgg catcgatgag ttcccggact tcttccggat
     4621 caccctgaag caccgttgcc ccttcccggt tacgctccct tcccagcagg taatcaaccg
     4681 gaccactgcc accacctttt cccctggcat gaaacttaac tatcatcccg cactccctgt
     4741 tccctgacgg ccagacgcag ccggcgcagc tcatccccga tggccatcag tgcggccacc
     4801 acctgaaccc ggtcaccgga agaccactgc ccgctgttca ccttacgggc tgtctgattc
     4861 aggttatttc cgatggcggc cagctgacgc agtaacggcg gtgccagtgt cggcagcttc
     4921 ccggaacggg caaccggctc acccaggcag acccgccgca tccataccgc cagttgttta
     4981 ccctcacagc gttccagtaa ccgggcatgt tcatcatcag taacccgtat cgtgagcatc
     5041 ctctcgcgtt tcatcggtat cattactccc gtgaacagaa atccccctta cacggaggca
     5101 tcagtgacta aacaggaaaa aaccgccctt aacatggccc gctttatcag aagccagaca
     5161 ttaacgctgc tggagaagct caacgaactg gacgcagatg aacaggcaga tatctgtgaa
     5221 tcgcttcacg accacgccga tgagctttac cgcagctgcc tcgcacgttt cggggatgac
     5281 ggtgaaaacc tctgacacat gcagctcccg gagacggtca cagcttgtct gtgagcggat
     5341 gccgggagca gacaagcccg tcagggcgcg tcagcaggtt ttagcgggtg ttggggcgca
     5401 gctctgaccc agtcacgtag cgatagcgga gtgtatactg gcttaaccat gcggcatcag
     5461 tgcggattgt atgaaaagta cgccatgccg ggtgtgaaat gccgcacaga tgcgtaagga
     5521 gaaaatgcat gtcccggcgc ttttccgctt cctccctcac tgactcgcta cgctcggtcg
     5581 ttcgactgcg gcgagcggta ctgactcaca caaaaacggt aacacagtta tccacagaat
     5641 caggggataa ggccggaaag aacatgtgag caaaagacca ggaacaggag gaaggccgcg
     5701 ccgctggcgt ttttccatag gctccgcccc cctgacgagc atcacaaaaa ccgacgctca
     5761 agtcagaggt ggcgaaaccc gacaggactt aaagatacca ggcgtttccc cctggtgact
     5821 ccctcgtgcg ctctcctgtt cctgccattc ggtttaccgg tgtcactccg ctgttatggc
     5881 cgcgtttgtc tcattccacg cctgacactc agttccgggt aggcagttcg ctccaagctg
     5941 gactgtatgc acgaaccccc cgttcagtcc gaccgctgcg ccttttccgg taactatcaa
     6001 cttgagtcca acccggaaag acacgacaaa acgccaatgg cagcagccac tggtaactga
     6061 tt
//
