LOCUS       NZ_CP103773             5269 bp    DNA     circular CON 20-SEP-2023
DEFINITION  Salmonella enterica strain S1905 plasmid pS1905_2, complete
            sequence.
ACCESSION   NZ_CP103773
VERSION     NZ_CP103773.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30507085
            Assembly: GCF_024917195.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5269)
  AUTHORS   Yue,M.
  TITLE     Genome sequence of Salmonella
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5269)
  AUTHORS   Yue,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-AUG-2022) Clinical laboratory, Hangzhou Children's
            Hospital, 195 Wenhui Road, Hangzhou, Zhejiang 310014, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: Illumina HiSeq; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/20/2023 05:35:37
            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)                     :: 4,942
            CDSs (total)                      :: 4,824
            Genes (coding)                    :: 4,681
            CDSs (with protein)               :: 4,681
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 143
            CDSs (without protein)            :: 143
            Pseudo Genes (ambiguous residues) :: 0 of 143
            Pseudo Genes (frameshifted)       :: 53 of 143
            Pseudo Genes (incomplete)         :: 108 of 143
            Pseudo Genes (internal stop)      :: 28 of 143
            Pseudo Genes (multiple problems)  :: 40 of 143
            Pseudo Genes (short protein)      :: 1 of 143
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103773.1.
            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..5269
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="S1905"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="pS1905_2"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2021"
                     /collected_by="Meina Yue"
     gene            10..201
                     /locus_tag="NYS49_RS24570"
                     /old_locus_tag="NYS49_24570"
     CDS             10..201
                     /locus_tag="NYS49_RS24570"
                     /old_locus_tag="NYS49_24570"
                     /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            870..1028
                     /locus_tag="NYS49_RS24755"
     CDS             870..1028
                     /locus_tag="NYS49_RS24755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_071791734.1"
                     /translation="MHEPPVQPDCCALPGNYRLESNPVRHALTPLAAAIGNWTRWIEIL
                     RVLEVVA"
                     /name="replication initiation protein"
     gene            complement(1264..2412)
                     /locus_tag="NYS49_RS24575"
                     /old_locus_tag="NYS49_24575"
     CDS             complement(1264..2412)
                     /locus_tag="NYS49_RS24575"
                     /old_locus_tag="NYS49_24575"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001529706.1"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [Evidence IEA];
                     GO:0008168 - methyltransferase activity [Evidence IEA];
                     GO:1904047 - S-adenosyl-L-methionine binding [Evidence
                     IEA]"
                     /GO_process="GO:0006304 - DNA modification [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WP_040088069.1"
                     /translation="MRSLEIFSGAGGLAKGLELAGFQHVGFVELNKHACDSLRLNFDEE
                     KVFQGDIKNYDLSSIDKIDIVAGGPPCQPFSLGGKHKAHDDSRDMFPFAIKAIEVLQPK
                     AFIFENVKGLLRKSFADYFEYIILRLTYPCLSLSNVGDWRIHLDALRKARKDKHCGCTY
                     DVSFKLINAADYGVPQIRERVIIVGVRSDLNKKWSFPSVTHTQEKLLWEQHVTGDYWRK
                     HNIDAVIDKGISERLMKRFGIFPPSGKSWVTVRDALKNVPQPYESHGIGDHIFKDGARV
                     YPGHTGSYIDLPSKTLKAGAHGVPGGENMIRYEDGTVRYFTVYEGKLLQTFPREFLIAG
                     AWGEAMRQIGNAVPVLLAQKIGQQLYNLLNEEVEPLLCSNFN"
                     /name="DNA cytosine methyltransferase"
     gene            complement(2412..3056)
                     /locus_tag="NYS49_RS24580"
                     /old_locus_tag="NYS49_24580"
     CDS             complement(2412..3056)
                     /locus_tag="NYS49_RS24580"
                     /old_locus_tag="NYS49_24580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001529705.1"
                     /GO_function="GO:0004518 - nuclease activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Eco29kI family restriction endonuclease"
                     /protein_id="WP_011017202.1"
                     /translation="MHNKKFDRSEHVYRNDSFLELIKDAVRFFSGTPVHSLPPPERFQG
                     AGVYALYYTGHYSLYDEYSRINRLAYNLPIYVGKAVPAGWRQSRISDHETRAGSELSNR
                     IREHSRNIAKTSNLNLCDFSCRFVIFEATGSDMISTVEAALIKIYKPLWNTVVDGFGNH
                     TPGAGRFAQAKSDWDVIHPGREWAEKCTGVHSEPYFIEERIKQYFSKSNFT"
                     /name="Eco29kI family restriction endonuclease"
     gene            complement(3456..3689)
                     /locus_tag="NYS49_RS24585"
                     /old_locus_tag="NYS49_24585"
     CDS             complement(3456..3689)
                     /locus_tag="NYS49_RS24585"
                     /old_locus_tag="NYS49_24585"
                     /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"
     gene            complement(3696..4214)
                     /locus_tag="NYS49_RS24590"
                     /old_locus_tag="NYS49_24590"
     CDS             complement(3696..4214)
                     /locus_tag="NYS49_RS24590"
                     /old_locus_tag="NYS49_24590"
                     /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_001749510.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQTNLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            complement(<4252..4950)
                     /locus_tag="NYS49_RS24760"
                     /pseudo=""
     CDS             complement(<4252..4950)
                     /locus_tag="NYS49_RS24760"
                     /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            complement(4892..5215)
                     /locus_tag="NYS49_RS24600"
                     /old_locus_tag="NYS49_24600"
     CDS             complement(4892..5215)
                     /locus_tag="NYS49_RS24600"
                     /old_locus_tag="NYS49_24600"
                     /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_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(287..372)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          394..942
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.043"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3353..4902)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.183"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gaggcatcag tgactaaaca ggaaaaaaca gcccttaaca tggcgcgctt tatcagaagc
       61 cagacattaa cgctgctgga aaagctcaac gaactggacg cggatgaaca ggcagacatc
      121 tgtgaatcgc ttcacgacca cgccgatgag ctttaccgca gctgcctcgc acgtttcggg
      181 gatgacggtg aaaacctctg acacatgcag ctcccggaga cggtcacagc ttgtctgtga
      241 gcggatgccg ggagcagaca agcccgtcag ggcgcgtcag caggttttag cgggtgtcgg
      301 ggcgcagccc tgacccagtc acgtagcgat agcggagtgt atactggctt aaccatgcgg
      361 catcagtgca gataataaga aaagagcacc atatacggtg tgaaataccg cacagatgcg
      421 taaggagaaa atgccgcatc aggcgctctt ccgcttcctc gctcactgac tcgctacgct
      481 cggtcgttcg gctgcggcga gcggtatcag ctcactcaaa gacggtaatg cggttatcca
      541 cagaatcagg ggataacgcc aaaagaaaca tgtgagcaaa aaacaagaac ccggaaaagg
      601 ccacgccgct ggcgtttttc cataggctcc gcccccctga cgagcatcac aaaaacagac
      661 gctcaagtca gaggtggcga aacccgacag gactataaag ataccaggcg tttccccctg
      721 gaagctccct cgtgcgctct cctgttccga ccctgccgct taccggatac ctgtccgcct
      781 ttctcccttc gggaagcgtg gcgctttctc atagctcacg ctgttggtat ctcagttcgg
      841 tgtaggtcgt tcgctccaag ctgggctgtg tgcacgaacc ccccgttcag cccgactgct
      901 gcgccttgcc cggtaactat cgtcttgagt ccaacccggt aagacacgcc ttaacgccac
      961 tggcagcagc cattggtaac tggacaaggt ggattgagat attaagagtt cttgaagtgg
     1021 tggcctaact gaggctacac tagaaggaca gtatttggta tctgcgctcc accaagccag
     1081 ttaccttcgg gaaaaagagt tggtagctct tgattccggc aaacgaacca ccgttggtag
     1141 cggtggtttt tttgtttaca ggcagcagat tacgcgcaga aaaaaaggat ctcaagaaga
     1201 tcctttgatc tttttttgca aattgcctct atggctgtat caccaccata gagacacaaa
     1261 cttttaattg aagttagagc acaataaagg ctcaacctct tcattcaata agttatacaa
     1321 ttgctgtcct atcttctgag ctagcaacac aggaactgca ttaccaatct gcctcatagc
     1381 ctccccccaa gctcctgcaa tcagaaactc tcgaggaaaa gtctgaagaa gcttcccttc
     1441 ataaaccgta aaataacgaa cagtcccatc ctcataccta atcatatttt cacctccagg
     1501 tacgccatga gcgccagcct taagtgtttt tgaaggcaaa tcgatataac ttccagtatg
     1561 accaggataa actcgagcgc catctttaaa gatatgatct ccaataccat gtgactcata
     1621 tggttgagga acattcttta atgcgtccct aacagtaacc cagcttttcc ccgatggggg
     1681 gaaaatacca aaacgtttca ttaaacgctc agaaatacct ttatctataa ccgcatcaat
     1741 attatgcttt cgccaatagt caccagtaac atgctgttcc cacagtaatt tttcttgagt
     1801 atgcgttacg cttggaaaag accatttttt attcaaatca cttcgaacac caacaattat
     1861 gacccgttcc ctaatttgtg gaactccata atcagctgca ttgatcaatt taaaactgac
     1921 atcatatgta cacccacagt gtttatcctt gcgagctttt cttaatgcat ctagatgtat
     1981 tctccaatca cctacattac ttaacgataa acaaggataa gtcaaacgaa gaattatgta
     2041 ttcaaaataa tccgcaaatg attttctaag caacccttta acattttcaa aaataaaagc
     2101 ttttggttgc aatacttcaa ttgcttttat tgcaaatggg aacatatccc tagagtcatc
     2161 atgagcttta tgttttccgc ccaatgaaaa tggttggcag ggaggcccgc cagcaacaat
     2221 atctatttta tctatagatg aaaggtcata atttttaata tctccctgaa ataccttctc
     2281 ctcatcaaaa ttaagtcgca aagaatcaca tgcatgcttg tttaactcaa caaatcctac
     2341 atgctgaaat cctgccaact ctagaccttt agccaaaccg ccggctcctg aaaaaatctc
     2401 taatgatctc attatgtaaa attactctta gaaaaatact gtttaattct ctcctcaata
     2461 aagtatggct cagaatgaac acctgtacat ttctcagccc actccctgcc aggatgtatt
     2521 acatcccaat cagatttagc ttgcgcaaat cgcccggcac caggggtatg atttccaaag
     2581 ccatcaacaa ctgtattcca caaaggctta taaattttaa taagagcggc ctcaactgta
     2641 ctaatcatat cagaccccgt agcctcaaat ataacaaagc gacatgaaaa atcacacaaa
     2701 tttagattcg atgtttttgc tatatttcgg ctatgttctc taattctatt agatagttca
     2761 gaaccagccc tagtttcatg atcactaatt ctagactgac gccaaccagc aggaacagcc
     2821 ttgccaacat aaataggaag gttatatgcc aacctattta tacgagagta ttcatcatat
     2881 aatgaataat gccctgtata gtaaagagca tacaccccag caccttgaaa ccgttccggt
     2941 ggtggtaatg aatgaacagg cgtaccacta aaaaaacgaa cggcatcttt tattaactct
     3001 aggaaagagt catttctata aacatgctca gatctatcaa atttcttatt gtgcattatg
     3061 ttttccgaaa ggtttttata ttaacactcc tactcaacat cacctatgat acgatcataa
     3121 agctgatacc caaaaccata cgcatttacc ataacgtcac attacgcgca ccgctaaaac
     3181 gcgttcagcg cgatcacggc agcagacagg taaaaatggc aacaaaccac ccgaaaaact
     3241 gccgcgatcg cgcctgataa attttaaccg catgaatacc tatgcaacca gatggtacag
     3301 gccacattaa cccctcttaa tccactgaag ctgccatttt tcatggtttc accatcccag
     3361 cgaaggacca tccagcgtgc gttcctgtat ttccggctga cgctcccgtt ccagggataa
     3421 cgcatgttcg cgctcctgta tcagccgttc ctctcttatc tccagttctc gctgtataac
     3481 tggctcaagc gttctgtctg ctcgctcaag tgctgcacct gctgactcaa ctgcatgacc
     3541 cgctcgttca gcatcgcgtt gtcccgttgc gtaagcgaaa acatcttctg caattccacg
     3601 aaggcgctct cccattcgct cagccgctgc atatagtcct gttgcagctg ctctaaggcg
     3661 ttcagcaaat gtatttccag ctctgtcact ctgtgtcact ccttcagatg tacccactct
     3721 ttcccctgaa agggaatcac ctccgctgat ttcccgtacg gaaggacaag gaatttcctg
     3781 ttcccgtcct gcacaaactc cacgccccat gtcttcgcgt tcagtttctg caatgtctct
     3841 tcctgcttcc tgatttcttc caggttcgtc tgtatccgtc cgccaagata ccagagcgtc
     3901 ccgccactcg cggtaaacag gagaaagact atccccagta acatcatgcc cgtattccct
     3961 gccagcttta acacgtcctt cctgtgctgc atcatcgcct ctttcacccc ttctcggtgt
     4021 ttttccagcg atttctctgt cgaggctgtg aacagggcta tagcgtctct gattttcgtc
     4081 tcgtttgagg tcacagcctc gctgacagac tcgccgagct tcctgaactc gtcgttcagc
     4141 attttctctg tagattcggc tctctctttc agctttttct cgaactccgc gcccgtctgt
     4201 aaaagattgc tcataaaatg ctcctttcag cctgatattc ttcccgccgt tcgggtctga
     4261 aatgctgata ctgcttcgcg tcaccctgac cacttcaagc cccgcctctg tgagcgcctg
     4321 aatcacatcc tgacggcctt ttatctctcc ggcatggtaa agtgcgtcta taccgcgtgt
     4381 aacgctctca gcaagtgcct gtttcgtttc cggcaggtta tcaggaaggg tcagcgtccg
     4441 gcggttctcc ggggcgttgg ggtcatgcag tccgtaatgg tgattcacca gcgtctgcca
     4501 ggcatcaatt ctcggcctgt ctgcgcggtc gtagtacggc tggagacgtt ttccggtctg
     4561 tagctccatg ttcggaatga caaaattcag ctcaagccgt cccttgtcct ggtgctccac
     4621 ccacaggatg ctgtactgat ttttttcgag accgggcatc agtacacgct caaagctcgc
     4681 catcactttt tcacgtcctc ccggcggcag ctccttctcc gcgaacgaca gaacaccgga
     4741 cgtgtatttc ttcgcaaatg gcgtggcatc gatgagttcc cggacttctt ccggattacc
     4801 ctgaagcacc gttgcgcctt cgcggttacg ctccctcccc agcaggtaat caaccggacc
     4861 actgccacca ccttttcccc tggcatgaaa tttaactatc atcccgcgcc ccctgttccc
     4921 tgacggccag acgcagccgg cgcagctcat ccccgatggc catcagtgcg gccactacct
     4981 gaacccggtc accggaagac cactgcccgc tgttcacctt acgggctgtc tgattcaggt
     5041 tatttccgat ggcggccagc tgacgcagta acggcggtgc cagtgtcggc agtttcccgg
     5101 aacgggcaac cggctcaccc aggcagaccc gccgcatcca taccgccagt tgtttaccct
     5161 cacagcgttc aagtaacctg gcatgttcat catcagtaac ccgtatcgtg agcatcctct
     5221 cgcgtttcat cggtatcatt accccatgaa cagaaatccc ccttacacg
//
