LOCUS       NZ_CP100735             5423 bp    DNA     circular CON 23-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            R18.1932 plasmid pR18.1932_5.4k, complete sequence.
ACCESSION   NZ_CP100735
VERSION     NZ_CP100735.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21365156
            Assembly: GCF_024266565.1
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 5423)
  AUTHORS   Chiou,C.S., Chen,B.H., Wang,Y.W. and Teng,R.H.
  TITLE     28 Salmonella enterica strains that have azithromycin resistance
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5423)
  AUTHORS   Chiou,C.S., Chen,B.H., Wang,Y.W. and Teng,R.H.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-JUL-2022) Center for Diagnostics and Vaccine
            Development, Centers for Disease Control, Taiwan, No.20, Wenxin S.
            3rd Rd., Nantun Dist., Taichung City 408, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: flye v. 2.9; trycycler v. 0.5.3; medaka v. 1.6.0;
            homopolish v. 0.3.3; polca v. 4.0.5; polypolish v. 0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 311x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/23/2023 02:07:43
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,946
            CDSs (total)                      :: 4,822
            Genes (coding)                    :: 4,706
            CDSs (with protein)               :: 4,706
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 116
            CDSs (without protein)            :: 116
            Pseudo Genes (ambiguous residues) :: 0 of 116
            Pseudo Genes (frameshifted)       :: 37 of 116
            Pseudo Genes (incomplete)         :: 85 of 116
            Pseudo Genes (internal stop)      :: 20 of 116
            Pseudo Genes (multiple problems)  :: 25 of 116
            Pseudo Genes (short protein)      :: 1 of 116
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP100735.1.
            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..5423
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="R18.1932"
                     /serovar="Typhimurium"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pR18.1932_5.4k"
                     /geo_loc_name="Taiwan"
                     /collection_date="2018"
                     /collected_by="Centers for Disease Control, Taiwan"
     gene            complement(join(5258..5423,1..638))
                     /locus_tag="NL737_RS24675"
                     /old_locus_tag="NL737_24675"
     CDS             complement(join(5258..5423,1..638))
                     /locus_tag="NL737_RS24675"
                     /old_locus_tag="NL737_24675"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000510993.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000510993.1"
                     /translation="MGIFSQIGSALLNCISKPVDALCEWAKEPLKDREYRREEASKESE
                     HKRNMDVLTAKKRVEHELRMSELNAEYELREKEKTLEVDLEVRRVREIEKAVAEIQEWR
                     KSQELERMERTTAAIARYKEQLTKLNIEVINSIGNMQLDLKERAQKFVYEKAVQYKRLQ
                     DEATEEAMNDLIRIEEKFGDNERAKDILIRAVDTKMGNVIDTSTRFLEELNRDIVSLNQ
                     SIDRLTNQGQKFIESHLERFHIVDATSSLYITGDEKERLLLKNIN"
                     /name="hypothetical protein"
     gene            complement(625..1164)
                     /locus_tag="NL737_RS24680"
                     /old_locus_tag="NL737_24680"
     CDS             complement(625..1164)
                     /locus_tag="NL737_RS24680"
                     /old_locus_tag="NL737_24680"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000897048.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000897049.1"
                     /translation="MAGGRHINSLLYVLVAILERKVNDFKLSSSELPEILAALREAREC
                     LVSRSINEDPQLYSALFLYEKNEGLLSLSFEREYSIFINSNLECILRKVSDIKDKKQGK
                     LQKIMNEFVRFKYSSSDSCADLLFLSGKLEQIRKIYEVFDRDRNRLEFLNYMMKKERVI
                     FEREFERLLGEKNGDF"
                     /name="hypothetical protein"
     gene            complement(1167..1778)
                     /locus_tag="NL737_RS24685"
                     /old_locus_tag="NL737_24685"
     CDS             complement(1167..1778)
                     /locus_tag="NL737_RS24685"
                     /old_locus_tag="NL737_24685"
                     /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_000130481.1"
                     /translation="MTDKTTDIKMALENMIRFRDTIERLGGSMAKEFDVETKGKRTYSM
                     NNDMSDLYNVISRAVEASGADHSINEKLTNVLKRELVDYVSIAHLKTKLSVLYEFEKNY
                     LQLIAEYKEEIKFASSLQEDLRKERAKFFSETLKEVHQTLNESQVDNEVASKWIKELVG
                     SYTKSLDLSGGLVEEHTLDTIACIRAEAKLNKPSIEPGNN"
                     /name="hypothetical protein"
     gene            complement(2111..2344)
                     /locus_tag="NL737_RS24690"
                     /old_locus_tag="NL737_24690"
     CDS             complement(2111..2344)
                     /locus_tag="NL737_RS24690"
                     /old_locus_tag="NL737_24690"
                     /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_000137438.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2351..2869)
                     /locus_tag="NL737_RS24695"
                     /old_locus_tag="NL737_24695"
     CDS             complement(2351..2869)
                     /locus_tag="NL737_RS24695"
                     /old_locus_tag="NL737_24695"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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_087451033.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTTSTEESLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVIPQGKSATVIPYQ
                     GKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(<2907..3338)
                     /locus_tag="NL737_RS24700"
                     /old_locus_tag="NL737_24700"
                     /pseudo=""
     CDS             complement(<2907..3338)
                     /locus_tag="NL737_RS24700"
                     /old_locus_tag="NL737_24700"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /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            complement(3547..3870)
                     /locus_tag="NL737_RS24705"
                     /old_locus_tag="NL737_24705"
     CDS             complement(3547..3870)
                     /locus_tag="NL737_RS24705"
                     /old_locus_tag="NL737_24705"
                     /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_000955989.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRICLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3935..4126
                     /locus_tag="NL737_RS24710"
                     /old_locus_tag="NL737_24710"
     CDS             3935..4126
                     /locus_tag="NL737_RS24710"
                     /old_locus_tag="NL737_24710"
                     /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_000165990.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGGDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(4205..4289)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.674"
                     /coverage="100.0"
                     /evalue="6.569999999999999e-34"
     Typing          4313..4858
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.255"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2008..3557)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.076"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aattcttcca aaaaccgagt tgacgtatca ataacattcc ccatcttagt atcaactgca
       61 cgaattaaaa tatctttagc tctttcatta tcaccaaact tttcctcaat ccttataaga
      121 tcattcatag cctcttcagt tgcttcatct tgcaggcgct tatattgtac agctttctca
      181 tagacaaatt tctgtgcgcg ctcctttaaa tcaagctgca tgttcccaat agagttaatc
      241 acttctatat ttaatttcgt taattgctcc ttgtaacgtg caatagctgc tgttgttcgc
      301 tccatcctct caagttcctg tgactttctc cattcctgga tctcagctac tgctttttct
      361 atttcgcgaa cgcgacgaac ctctagatca acttcaagag ttttctcttt ttctctcagc
      421 tcatattcag cattcaattc actcattctg agttcatgtt caacacgttt cttggccgtc
      481 aagacatcca tgttgcgctt atgttcagac tcctttgaag cctcctctct tctatattcc
      541 ctatctttca atggttcttt agcccattca cagagtgcat caacaggctt actaatacaa
      601 ttaagcaaag cgctaccaat ctgactaaaa atccccattt ttttcaccta aaagccgttc
      661 aaactctctt tcaaaaataa cacgttcttt cttcatcata tagttaagaa attcaagtct
      721 atttctatcc ctatcaaaga cttcatatat tttacgtatc tgttcaagtt taccactcaa
      781 aaacaaaaga tccgcacaag aatcgctgct tgaatattta aacctcacaa attcattcat
      841 tattttttgc agtttaccct gctttttatc ttttatatca gaaactttcc tcaatatgca
      901 ctctaaattg gagttaataa aaatagagta ttctctctca aatgaaagac ttagcaaccc
      961 ttcatttttt tcatataaaa ataatgccga atataactga ggatcttcat tgatgctgcg
     1021 cgatacaagg cattcccttg cctctcgtaa agcagccaat atctcaggaa gttccgacga
     1081 agacaattta aagtcattca ctttacgttc taatatagcc acaagaacat aaagcaaact
     1141 atttatatgt ctacccccgg ccataattag ttattgcccg gctcaataga tggtttattt
     1201 aatttagcct cagcgcgaat acaagcaatt gtatctaatg tatgctcttc aacaaggcct
     1261 ccgcttagat ccaagctttt ggtataacta ccaacaagtt ctttaatcca ttttgatgcc
     1321 acttcattat caacttgaga ttcatttaga gtttgatgaa cctcttttaa tgtctcagaa
     1381 aagaatttag cacgttcttt acgtaaatcc tcttgcaaag aggaagcaaa ttttatttct
     1441 tccttatatt ctgcgataag ctgcaaataa ttcttttcaa actcatataa tacagacaat
     1501 ttggttttta gatgcgcaat gctgacataa tcaactaatt ctcttttcaa gacatttgtc
     1561 aatttttcat taattgaatg atcggcacca gacgcttcaa cagcccgtga tattacatta
     1621 tataaatcac tcatatcgtt attcatagaa taagtacgtt ttcctttggt ctcaacatca
     1681 aactctttcg ccatagaacc tcccaatctc tctatagtgt cacgaaatct gatcatgttt
     1741 tctaaagcca ttttaatatc ggtcgtttta tctgtcatga cttaggccta actcatctat
     1801 ttaccataac gtcgcattac gcgcaccgct aaaacgcgtt cagcgcgatc acggcagcag
     1861 acaggtaaaa atggcaacaa accacccgaa aaactgccgc gatcgcgcct gataaatttt
     1921 aaccgcatga atacctatgc aaccagatgg tacagaccac attagcccgt cttaatccac
     1981 ttaacctgcc atttttcata gtttcaccat cccagtgaag gaccatccag tgtgcgttcc
     2041 tgtatttcca gctggcgttc ccgctccagg gataactcat gttcgcgttc ctgtatcagc
     2101 cgttcgtccc ttatctcctg ttctcgctgt ataactggct caagcgttct gtccgctcgc
     2161 tcaagtgctg cacctgctga ctcaactgca tgacctgctc gttcagcatc gcgttgtccc
     2221 gttgcgtaag cgaaaacatt ttctgcaatt ccacgaaggc gctctcccat tcgttcagcc
     2281 gctgcatata gtcctgttgc agttgctcta atgcgttcag caaatgtctt tccagctccg
     2341 tcactctgtg tcactccgtc agttgtaccc agtccttccc ctgataggga atcaccgttg
     2401 ccgatttccc ctgcgggatg accagaaatt tccttctccc gtcctgcaca aactccacgc
     2461 cccatgtctt cgcgttcagt ttctgcaatg tttcttcctg tatcctgatt tcttccaggt
     2521 tcgcctgtat ccgcccgcca agataccaga gcgtcccgcc actcacggta aacaggaaaa
     2581 tgaccatccc cagtaacatc atgcccgtat tccctgccag ctttaacacg tccttcctgt
     2641 gctgcatcat cgcctctttc accccttccc ggtgtttttc cagcgattcc tctgtcgacg
     2701 ttgtgaacag ggctatagcg tctttgattt tcgtctcgtt tgaggtcaca gccttgctta
     2761 cagatttttc gagcttgctg aactcgtcgt tcagcattgt ctctgtagat tcggctctct
     2821 ctttcagctt tttctcgaac tccgcgcccg tctgtaaaag attgctcata aaatgctcct
     2881 ttcagcctga tattcttccc accgttcggg tctgcaatgc tgatactgct tcgcgtcacc
     2941 ctgaccactt caagccccgc ctctgtgagc gcctgaatca catcctgacg gccttttatc
     3001 tccccgacat gataaagagc gtctatcccg cgtgtgacgc tctcagcaag cgcctgtttc
     3061 gtttccggca ggttatcaga gagagtcagt atccggcggt tctccggggc gttggggtca
     3121 tgcagcccgt aatggtgatt caccagtgtc tgccaggcat caattctcgg cctgtctgcc
     3181 cggtcgtagt acggctggag gcgttttccg gtctgtagct ccatattcgg aatgacaaaa
     3241 ttcagctcaa gccgtccctt gtcctggtgc tccacccaca ggatgctgta ctgatttttt
     3301 tcgagaccgg gcatcagtac acgctcaaag ctcgccatca ctttttcacg ccctcccggc
     3361 ggcagctcct tctccgcgaa cgacagaaca cctgacgtgt atttcttcgc aaatggcgtg
     3421 gcatcgatga gttcccggac ttcttccgga tcaccctgaa gcaccgttgc cccttcccgg
     3481 ttacgctccc ttcccagcag gtaatcaacc ggactactgc caccgccttt tcccctggca
     3541 tgaaacttaa ctatcatccc gcgctccatg ttccctgacg acctgccgta agctgcgcaa
     3601 ctctctctcg atggccatca gtgcggccac cacctgaacc cggtcaccgg aagaccactg
     3661 cccgctgttc accttcctcg ccgtctgatt caggttattc ccgatggcag ccagctggcg
     3721 cagtaacggc ggtgccagtg tcggcagctt cccggaacgg gcaaccggct cacccaggca
     3781 gatccgccgc atccataccg ccagctgttt accctcacag cgttccagta accgtgcatg
     3841 ttcatcatca gtaacccgta tcgtgagcat cctctcgcgt ttcatcggta tcattacccc
     3901 atgaacagaa atcccccctt acacggaggc atcagtgact aaacaggaaa aaaccgccct
     3961 taacatggcc cgctttataa gaagccagac attaacgctg ctggagaagc tcaacgaact
     4021 ggacgcagat gaacaggccg atatttgtga atcacttcac gaccacgccg acgagcttta
     4081 ccgcagctgc ctcgcacgct tcgggggtga cggtgaaaac ctctgacaca tacagctccc
     4141 ggagacggtc acagcttgtc tgtgagcgga tgccgggagc agacaagccc gtcagggcgc
     4201 gtcagggggt ttcggggcga agccctgaac cagtcacgta gcgatagcgg agtgtatact
     4261 ggcttaacca tgcggcatta gtgcagattg tatgaaaagt gcgccatgcc gggtgtgaaa
     4321 tgccgcacag atgcgtaagg agaaaatgca gcttccgacg ctcttccgct tcctcgctca
     4381 ctgactcgct acgctcggtc gttcggctgc ggcgagcggt atcagctcac tcaaaggcgg
     4441 taatacggtt atccacagaa tcaggggata acgccggaaa gaacatgtgc gcaaaaggca
     4501 aaggccggga gaaaggccac gccgatggcg tttttccata ggctccgccc ccctgacgag
     4561 catcacaaaa atcgacgctc aagtcagagg tggcgaaacc cgacaggact ataaagatac
     4621 caggcgtttc cccctggaag ctccctcgtg cgctctcctg ttccgaccct gccgcttacc
     4681 ggatacctgt ccgcctttct cccttcggga agcgtggcgc tttctcatag ctcacgctgt
     4741 tggtatctca gttcggtgta ggtcgttcgc tccaagctgg gctgtgtgca cgaacccccc
     4801 gttcagcccg accgctgcgc cttatccggt aactatcgtc ttgagtccaa cccggtaaga
     4861 cacgacaaag cgccactggc agcagccact ggtaactgga caaggtggat tgagatatta
     4921 agagttcttg aagtggtggc ctaactgcgg ctacactaga aggacagtat ttggtatctg
     4981 tgctccacca agccagttac cttcggaaga aagagttggt agctctagat tccggcaaac
     5041 aaaccaccgt tggtagcggt ggtttttttg tttacaggca gcagattacg cgcagaaaaa
     5101 aaggatcaca agaggatcct tgaatctttt cactcccact cccaggtcat agccatagcg
     5161 ctcagttttc aaccacaaga caaaaactaa tgattagcaa ccgcaagaac aaacaatgcg
     5221 accattaaaa ataatgatcg ctattactca caaaatacta attaatattt ttcagcaaca
     5281 atcgttcttt ctcatcacct gtaatatata aagaagatgt cgcatcaaca atatgaaaac
     5341 gctccaaatg actttcaatg aatttttgtc cttgattagt cagcctatca atactttggt
     5401 ttaaactaac aatatctcta ttt
//
