LOCUS       NZ_CP091612             5661 bp    DNA     circular CON 28-JAN-2024
DEFINITION  Salmonella enterica strain 1795 plasmid p1795-1, complete sequence.
ACCESSION   NZ_CP091612
VERSION     NZ_CP091612.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25270679
            Assembly: GCF_026873345.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 5661)
  AUTHORS   Ruan,Z.
  TITLE     Genome sequence of Salmonella Goldcoast recovered from children
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5661)
  AUTHORS   Ruan,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-JAN-2022) Department of Clinical laboratory, Sir Run
            Run Shaw Hospital, School of Medicine, Zhejiang University, 3
            Qingchun East Road, Hangzhou, Zhejiang 310016, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Oxford Nanopore; Illumina NovaSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/28/2024 13:25:48
            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)                     :: 4,508
            CDSs (total)                      :: 4,393
            Genes (coding)                    :: 4,288
            CDSs (with protein)               :: 4,288
            Genes (RNA)                       :: 115
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 105
            CDSs (without protein)            :: 105
            Pseudo Genes (ambiguous residues) :: 0 of 105
            Pseudo Genes (frameshifted)       :: 42 of 105
            Pseudo Genes (incomplete)         :: 74 of 105
            Pseudo Genes (internal stop)      :: 26 of 105
            Pseudo Genes (multiple problems)  :: 35 of 105
            Pseudo Genes (short protein)      :: 1 of 105
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091612.1.
            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..5661
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="1795"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="p1795-1"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2021-08"
                     /collected_by="Meina Yue"
     gene            join(5483..5661,1..166)
                     /locus_tag="L5512_RS22460"
                     /old_locus_tag="L5512_22475"
     CDS             join(5483..5661,1..166)
                     /locus_tag="L5512_RS22460"
                     /old_locus_tag="L5512_22475"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_039025506.1"
                     /translation="MSEKRNKMLTMWVTEGEHRRLLERCDGRPLAAWMRQTCLDEKPAR
                     TGKLPSLSPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHA
                     VLEKGTDDDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            375..>809
                     /locus_tag="L5512_RS22465"
                     /old_locus_tag="L5512_22480"
                     /pseudo=""
     CDS             375..>809
                     /locus_tag="L5512_RS22465"
                     /old_locus_tag="L5512_22480"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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            844..1335
                     /locus_tag="L5512_RS22470"
                     /old_locus_tag="L5512_22485"
     CDS             844..1335
                     /locus_tag="L5512_RS22470"
                     /old_locus_tag="L5512_22485"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /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_015060400.1"
                     /translation="MSSLLTLAKDLEQQSKAQKQSTGEMLKAAFSEHEQSVRAELSASA
                     RRISDAILAHEQSMSEAMEKNRRSVLRTAGRTWLTILMVSALLIGTSGSILWWQGQQIT
                     DNYTHLRQQEDTLAKMTARTWGVRYQESSDGRRFLILPPGMQTEAIPYDGTTWIRLKQE
                     "
                     /name="MbeB family mobilization protein"
     gene            1342..1557
                     /locus_tag="L5512_RS22475"
                     /old_locus_tag="L5512_22490"
     CDS             1342..1557
                     /locus_tag="L5512_RS22475"
                     /old_locus_tag="L5512_22490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /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_000137422.1"
                     /translation="MTELEKQLLSALEQLQQDYSQRLDEWESAFAEWRSMCGLMQRENA
                     VLNERVSDLSTQVLSLSEQLRRLSGN"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2106..2390
                     /locus_tag="L5512_RS22480"
                     /old_locus_tag="L5512_22495"
     CDS             2106..2390
                     /locus_tag="L5512_RS22480"
                     /old_locus_tag="L5512_22495"
                     /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_105645556.1"
                     /translation="MDLEKALKEAETGYSLKLTSTDEAEMLAYISTVLELHAKGDLLHE
                     SAIDRVMALCVLINTGNRQELSRTLRGFNNGGNWPSTTGNPSGGGRGNL"
                     /name="hypothetical protein"
     gene            complement(2829..3587)
                     /locus_tag="L5512_RS22485"
                     /old_locus_tag="L5512_22500"
     CDS             complement(2829..3587)
                     /locus_tag="L5512_RS22485"
                     /old_locus_tag="L5512_22500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013558434.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="PmeII family type II restriction endonuclease"
                     /protein_id="WP_052938555.1"
                     /translation="MIESRIISDFIESCIDEEFHQKKQEKIRAIKLSDITKRKNPYLFK
                     AKGLTSASDLIKSIMDATVSSGEETVFGNFMEKIAIFTCSQAFGGRKSSAVGIDLEFET
                     ESTKYLISIKSGPNWGNSSQKKKMQDNFIKAKKVLGTSGGINSKSITCIEGCCYGYDAR
                     PEKGTHIKLCGQDFWTFISNGNNELYSDIIEPIGKLADEKNKELIELTNAKLNLFTAEF
                     ISEYCNSDGSINWALFVARNSGSKSSYHSN"
                     /name="PmeII family type II restriction endonuclease"
     gene            complement(3580..4374)
                     /locus_tag="L5512_RS22490"
                     /old_locus_tag="L5512_22505"
     CDS             complement(3580..4374)
                     /locus_tag="L5512_RS22490"
                     /old_locus_tag="L5512_22505"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015164793.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="WP_227818858.1"
                     /translation="MLQSDSIDLIVTSPPYADQRKKTYGGVSADKYVEWFTPIAKELLR
                     VTKSSGSFVLNIKERAINGERHTYVIELILMMRKLGWLWTEEYIWHKKNSYPGKWPNRF
                     RDSWERCIHFTKSKKFNMYQEEVMVPMGDWKNSRLKNMSDTDKKRDESKVGSGFGKKIE
                     NWVTRDLAYPTNVLHMATECGNRSHSAAFPESLPEWFIKLFTTEGDTVLDPFSGSGTTL
                     KVAKAMKRNAVGIEILDEYCEITANRVGLKKSSQKKYRYTND"
                     /name="site-specific DNA-methyltransferase"
     Typing          5216..5389
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.0"
                     /coverage="100.0"
                     /evalue="1.21e-74"
     Typing          complement(4686..5292)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.82"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3..160
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="98.0"
                     /evalue="1.05e-23"
     Typing          157..1649
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          5505..5659
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.308"
                     /coverage="98.0"
                     /evalue="1.35e-24"
ORIGIN
        1 tgccggtatg ggcaataacc tgaaccagat agcccgccgt gttaacgccg gcggcggcac
       61 cggccatgac agggtacaga ttgtggcggc gctgatggcc atcgatgccg ggcttgagcg
      121 gctgcggcac gccgttcttg agaaaggaac ggacgatgat cgttaaattt catccacgcg
      181 gtcgcggcgg tggcgccggg ccggtggact atctgctggg taaagaccgg cagcgtgaag
      241 gcgccagcgt cctgcagggg aagccggaag aagtccggga gctgattgac gcgtcgcctt
      301 acgtgaagaa atacacctcc ggcgtactgt cgtttgcgga ggccgatctg cctcccggcc
      361 agcgggaaaa actgatggcc agcttcgagc gggttctgat gcccggactc gataaagatc
      421 agtacagcat tctgtgggtg gagcacgcgg acaaggggcg tctggagctg aactttctga
      481 tccccaatac cgaactgctg accggcaggc ggctccagcc gtactacgac cgcgccgacc
      541 ggccgcgcat cgatgcctgg cagaccatcg tgaacggcag actggggctg catgacccga
      601 acgcgccgga aaaccgccgg gcgctggtca cgccgtccgg actgccgaaa acgaagcagg
      661 aggccactga agccatcacg cgcggactgc tgacccttgc ttcgtccggg gagctgaaaa
      721 accgtcagga cgtcactgag gcgctggaac ggtcaggttt tgaggtggtg cgcaccacga
      781 aaagcagtat cagcattgcc gacccggacg gggggcgaaa catccgactg aagggagcca
      841 tctatgagca gtcttttaac gctggcgaag gacttagagc agcaatcgaa agcgcagaag
      901 cagagtaccg gcgagatgct gaaagccgca ttcagcgagc acgagcagtc tgtcagagcg
      961 gaactgagcg caagcgcgag gagaatcagc gacgccatcc tcgcccacga gcagagtatg
     1021 agcgaggcga tggagaaaaa ccggcggagc gtactgcgga ctgccgggcg gacatggctc
     1081 accatcctga tggtgtcagc gctgctgatc ggcacgagcg ggagcattct gtggtggcag
     1141 gggcagcaga taaccgacaa ttacacgcat cttcgtcagc aggaagatac cctggcgaaa
     1201 atgaccgccc ggacgtgggg agtgcgctat caggagagca gcgacggccg gaggtttctt
     1261 atcctgccgc cggggatgca aaccgaagcc atcccctacg acgggacgac atggatccgc
     1321 ctgaaacagg agtagcggaa aatgacagag ctggaaaagc agttgctgag cgcattagag
     1381 cagctacagc aggactactc gcaaaggctg gacgaatggg agagcgcctt cgcggaatgg
     1441 cggagcatgt gtgggcttat gcaacgggag aacgcggtgc tgaacgagcg cgtgtcggac
     1501 ttgagcacgc aggtgctgag tttaagcgag cagctgcgcc gcttgtccgg gaactgaatg
     1561 ccatcgagct ccggcagagg gagaatgagt atcagaaaac actggagctg gagcgccagc
     1621 cgcagaaaac ctaccgcggg ccgacacttt aaaccatcca ggcagctgac aacccgcacg
     1681 aagaggggct cttatttctc ccgctaaata ggttcgtgat caaaaaggtc acgacttatt
     1741 caggagcggg aaatgaagct gttaaatctt attgaatcat tgcttaactg cctgtatctg
     1801 gcggcggagc tgtgggactg gctggagaag catttgtcgg tttttaaggc attggcgcgg
     1861 attttagtgt gactttaaca tccatgcatc tggctgcatg actatgcacc agtgtaatat
     1921 tcagcggctg cgtttctggt gttttttcgt tatgtctgtc gccactttct cgcgtctggc
     1981 accggaaacg cagccaaccc cgtttcagcg gtgcgcccaa cagatgttat ggtaaatgcc
     2041 ggtgcgttgt gactcgtttt gatatgctat tttgttgcag tattgaatga accagagggt
     2101 tgaaaatgga tctagaaaaa gcactgaagg aagcagaaac cggatatagc ctcaagttaa
     2161 ccagtacaga tgaggctgaa atgctggctt atatctcaac cgtacttgaa ctccacgcta
     2221 aaggtgactt actacatgag tctgccatag acagggttat ggcattatgt gtgcttatta
     2281 acacaggaaa ccgacaggag ttaagccgga cgcttcgcgg gtttaataat ggtggtaact
     2341 ggcctagcac tacgggaaat ccatcaggtg gtggacgggg caatctctaa cacttggttt
     2401 cgtcataccc tgctttttac gtaaagcctg cgctcagcag gctttactgc atgttgcgta
     2461 caacggatgt tatggtaaat atgagtgttt aatctgatgc aaaaaagccg cctaaaaggc
     2521 ggctttttac taaggtgtgt tggttattgg tgtcagtctt tgtgcgacag tcccaccatt
     2581 agcactcaca tgtgtgacta tgttgttgtc ggttcgagtg tgtagctgta cgacgatatc
     2641 aaagcctgaa cttgcatgaa catcacagat gtaggcttca gtattgggtg cccagatcgc
     2701 actggtatcc tctctacgga gtcttacacc aaagttgtta gatgcatgat tctggcaacc
     2761 atttactatg catgctggca tggagtgtcc ttgtttttat tgaggtatca cccctttata
     2821 cccttctgtt agttgctatg gtagcttgat tttgaacctg agtttcttgc tacaaataaa
     2881 gcccaattta ttgagccatc actattacaa tattctgaaa tgaactcagc cgtaaaaaga
     2941 tttagtttgg catttgttag ttctatcagt tccttgtttt tttcgtcagc aagcttacca
     3001 ataggctcaa ttatatcact atataattcg ttgtttccgt tagatataaa tgtccagaag
     3061 tcttggccgc atagttttat gtgggttccc ttttcaggtc tggcgtcata accataacaa
     3121 caaccctcaa tgcaagttat tgatttagaa ttgatcccac cggatgtgcc taggactttt
     3181 ttggccttaa tgaagttgtc ttgcattttc tttttttgtg atgagttacc ccagtttggg
     3241 ccagatttga tgcttattag atattttgtg ctttcagttt cgaactcgag atctattcct
     3301 accgcactgg attttcttcc accaaatgct tgggaacatg tgaagattgc aatcttttcc
     3361 atgaaattgc caaaaacggt ctcctctcca gaggagaccg ttgcatccat gattgacttt
     3421 attaagtcac ttgctgatgt tagccccttc gccttaaata aatatgggtt ttttcttttt
     3481 gttatatctg ataattttat cgctcttatt ttttcttgtt ttttttgatg gaactcttca
     3541 tcaatgcaag attctataaa atctgaaata atccgtgatt caatcatttg tataccggta
     3601 ttttttttga gacgattttt tcaaacctac tctatttgcc gtaatctcgc aatattcatc
     3661 taatatttca atgcctacag cgttcctttt cattgctttc gccactttta atgtggttcc
     3721 agaaccggaa aatggatcca gaacggtgtc gccttctgtg gtgaaaagtt tgatgaacca
     3781 ttcaggtagg ctttcaggaa aagctgcgct gtgactgcgg tttccacact ctgtagccat
     3841 gtgtagcacg ttggttgggt atgccaaatc cctggtgacc cagttttcta tttttttacc
     3901 gaaaccactc cccactttcg attcatctct tttcttatca gtatcactca tgtttttaag
     3961 tcgtgagttt ttccaatccc ccataggcac cattacttcc tcttggtaca tattgaattt
     4021 tttacttttc gtaaagtgga tgcatctttc ccaagagtct ctaaaacgat ttggccattt
     4081 ccctgggtaa ctattttttt tatgccatat gtattcctct gtccataacc agcctaattt
     4141 tcgcatcatt agaattagct ctattacata cgtatggcgc tcgccattaa tcgccctttc
     4201 ctttatgttt agaacaaatg agcctgatga ttttgtcact ctcagtagtt ctttggctat
     4261 cggggtgaac cactcaacat atttgtctgc acttactccg ccataggttt ttttcctttg
     4321 gtctgcgtaa ggtggtgatg taacgatcag atctattgaa tcgctttgaa gcatctttaa
     4381 agcgattaaa caatcatcat tgattagttc tatcgtctgt tttttttctt taacttcttg
     4441 tttcattagc atttcttttg tcgcattcag tgttcgttat caggatatta cctccttttg
     4501 ttttggaggt ccagtcttgc tgatggttgt tgacctaagt gtaagatgcg acgtaatatc
     4561 ctcgtctgaa acgaaaaaac cgcctgggga ggcggttttt tcgagggttc agtaagttgg
     4621 ggaacttctg aaccgtggta acagggtgta caagaccgct gaaaccaaat tctgtccttt
     4681 cagtttagcc gtagttgggc tgagacttca agaactctgc atcagttatc tcttgtacac
     4741 cctcttactg ttggctgctg ccagtggcgt tttgtcgtgt ctttccgggt tggactcaag
     4801 tcgatagtta ccggataaga cgcagcagtc ggactgaacg gggggttcgt gcatacagtc
     4861 cagcttggag cgaactgcct tcccggaacc gagtgtcagg cgtggaatga gataaacgcg
     4921 gccataacag cggaatgaca ccggtaaacc gaaaggcagg aacaggagag cgcacgaggg
     4981 agccaccagg gggaaacgcc tggtatcttt aagtcctgtc gggtttcgcc accactgatt
     5041 tgagcgtcag atttcgtgat gcttgtcagg ggggcggagc ctatggaaaa acggcttcgc
     5101 cgcggcctca tcgtttcccc gttaagtttc ttcctggtat ccaccaggaa atttccgccc
     5161 cattcgtaag cccgcaccgc tcgccgcagc cgaacgaccg agcgcagcga gtcagtgagc
     5221 gaggaagcgg aatatatcct gtatcacata ttctgctgac gcaccggtgc cgcctttttc
     5281 ctcctgccac atgaagcact tcactgacac cctcgtccgt gtcaacatag taagccagta
     5341 tacactccgc tagcgttgcg tgactggttc agggctgcgc cccgaaaccc gccaaaagcc
     5401 actgacgcgc ctgcggcttg tccaaccccg cgccgaccgg gaaaggcttt cccgcccgtc
     5461 ccggcgttat caggaggccg gtttgtcaga gaaacggaac aagatgctca ccatgtgggt
     5521 gacggagggc gagcaccggc ggctgcttga gcgctgcgac ggcaggccgc tggcggcgtg
     5581 gatgcggcag acctgcctgg acgaaaagcc tgcgcgcacc ggaaagctcc cctcactctc
     5641 gccggcgctg ctgcgccagc t
//
