LOCUS       NZ_CP103775             4657 bp    DNA     circular CON 20-SEP-2023
DEFINITION  Salmonella enterica strain S1905 plasmid pS1905_4, complete
            sequence.
ACCESSION   NZ_CP103775
VERSION     NZ_CP103775.1
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 4657)
  AUTHORS   Yue,M.
  TITLE     Genome sequence of Salmonella
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4657)
  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
            CP103775.1.
            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..4657
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="S1905"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="pS1905_4"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2021"
                     /collected_by="Meina Yue"
     gene            complement(join(4499..4657,1..87))
                     /locus_tag="NYS49_RS24625"
                     /old_locus_tag="NYS49_24625"
     CDS             complement(join(4499..4657,1..87))
                     /locus_tag="NYS49_RS24625"
                     /old_locus_tag="NYS49_24625"
                     /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_058818351.1"
                     /translation="MQPQPAVHDGLPGINARTVGAVVIRLETLAGQQLRVRDQEVQLQP
                     PLILVLNPQHAVLVFIESGHQNPFKARHQLFALPGR"
                     /name="hypothetical protein"
     gene            338..823
                     /locus_tag="NYS49_RS24630"
                     /old_locus_tag="NYS49_24630"
     CDS             338..823
                     /locus_tag="NYS49_RS24630"
                     /old_locus_tag="NYS49_24630"
                     /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="MbeB family mobilization protein"
                     /protein_id="WP_001086854.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSAAMSQRTKGMLRMVSQTWLTIVLVSTLLTASGASILWWQGQQIL
                     DNYTTIREQKRTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            827..1042
                     /locus_tag="NYS49_RS24635"
                     /old_locus_tag="NYS49_24635"
     CDS             827..1042
                     /locus_tag="NYS49_RS24635"
                     /old_locus_tag="NYS49_24635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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_000137421.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1241..2008)
                     /locus_tag="NYS49_RS24640"
                     /old_locus_tag="NYS49_24640"
     CDS             complement(1241..2008)
                     /locus_tag="NYS49_RS24640"
                     /old_locus_tag="NYS49_24640"
                     /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_196042596.1"
                     /translation="MQPRELLMLSMYILVQAPVLTGLSKNQTESLTTNNKRGRRTAFYR
                     IKKHLQHDFYRIDSIKNEIHSPIKGFYMKDMKAVVVFTGKDLNIMRTEGGSGYWHARTD
                     RLNDADYLIAVRNRRETWAVKDLEHGTAFLIAKITGCFKSPDYDDRNVITFDEYAEIHT
                     PKAWKMLTDGQRYPVAYLSAQEAFLRIGVTPEQLEWKKFHPSSPSVPNTVIPGLAEEKT
                     EKLSLNEAIERAKKDISNATGIDSSAITISIKI"
                     /name="hypothetical protein"
     gene            2268..2747
                     /locus_tag="NYS49_RS24645"
                     /old_locus_tag="NYS49_24645"
     CDS             2268..2747
                     /locus_tag="NYS49_RS24645"
                     /old_locus_tag="NYS49_24645"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001050742.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023138585.1"
                     /translation="MNLLLPRDIVEAVLNDKKTKNARVAKCDGSEFFLELPSMNADFPA
                     GKIILKLGDSGFYNKRTKSLEGAYGLRHIWDKHRVEIGATSAEDIVIFLESILLAGAEV
                     LIDPKKGQNKAIVVESGTGMMILELKKPNGEDPYYSIITAYDRKSHPGTKLHTII"
                     /name="hypothetical protein"
     gene            3994..4317
                     /locus_tag="NYS49_RS24650"
                     /old_locus_tag="NYS49_24650"
     CDS             3994..4317
                     /locus_tag="NYS49_RS24650"
                     /old_locus_tag="NYS49_24650"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_001347450.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSL
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          3707..3890
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.561"
                     /coverage="86.0"
                     /evalue="2.7100000000000003e-47"
     Typing          complement(3248..3724)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.083"
                     /coverage="92.0"
                     /evalue="3.51e-174"
     Typing          2..1146
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.576"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4308..4657
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.581"
                     /coverage="86.0"
                     /evalue="6.439999999999999e-67"
ORIGIN
        1 aagcgtctcc agccgtatta cgaccgcgcc gaccgtccgc gcattgatgc ctggcagacc
       61 atcgtgaacg gcaggctggg gctgcatgac ccgaacgcgc ctgaaaaccg gcgggtgctg
      121 gtcacgccgt ccgcgctgcc ggaaacgaag caggaagccg ctcaggcaat tacacggggt
      181 ttactggcct tagcctcgtc cggggagctg aaaacccgcc aggacgtcac tgaggcgctg
      241 gaaagcgcag gttttgaggt ggtacgcacc acaaaaagca gcatcagcat tgccgacccg
      301 gacggggggc gaaacatccg actgaaggga gccatctatg aacagtcttt taacgctggc
      361 gaaggactta gagcagaaat cgaaagcgca gcagcagagt accggcgaga tgctgaaagc
      421 cgcattcagc gagcacgaga agtctgtcag agcggaactg agcgaaagcg agaagagaat
      481 cagcgccgcc atcctcgacc acgacaggaa gctgtccgct gccatgagcc agcgcacgaa
      541 aggtatgctg cggatggtca gccagacgtg gctgaccatc gtcttggtgt ctacactgct
      601 gacagcatcg ggcgcaagta ttctgtggtg gcaggggcag cagatactcg acaattacac
      661 gaccatccgg gagcagaagc gcacgcaggc catgctgtcc gagaggaaca gcggtgtgca
      721 gctctcgacc tgcggagagc agagacgccg ctgcgtgagg gtgaacccgg aagcgggacg
      781 gttcggagag gattcgagct ggatgatact ggcggggaaa tagcacatga cggagctgga
      841 aaaacagttg ctgagcgcat tagagcagct acagcaggac tactcgaaaa ggctggacga
      901 gtgggagaac gccttcgcgg aatggcggac gatgtctggt cttatgcaac gggagaacgc
      961 ggcgctgagc gagcgcgtca cgggcttgag caggcaggtg cagagtttga gcgagcagct
     1021 gcgccggttg tcacaaggct gaacgtgata gaggcacatc gtgagcagga acgggcggcg
     1081 cagcatcaga aagcgctgga gctggaacga tctcagcgac agcgaacgta caacggtccg
     1141 tcactttgaa tctgtgcgcc ggaaaagcat gggcttgctg tttctggcgt acaggttcag
     1201 ttctagaaca tgaggctgct atcttgttgt tcacgcttca tcagatcttg atgcttattg
     1261 ttatggctga gctatcaatc cctgttgcgt tgctaatatc ctttttggct ctttcaattg
     1321 cctcgttaag ggagagtttt tctgttttct cttcagccag accaggaatc actgtattag
     1381 gaaccgatgg ggatgaagga tggaatttct tccattccag ttgttccggt gttaccccaa
     1441 tacgtaaaaa agcttcctgt gcgctcaggt aagcaaccgg atagcgctga ccatcggtta
     1501 gcattttcca tgcttttggc gtgtgaattt ctgcgtattc atcaaaggtt atgacgttcc
     1561 tgtcgtcgta atcagggctt ttaaaacacc cggtaatttt ggcgatcagg aatgctgtgc
     1621 cgtgttccag gtcttttact gcccacgttt cccttctgtt tcttactgct atgaggtaat
     1681 cggcatcgtt gagcctgtct gttctggcat gccagtagcc tgaccccccc tcagttctca
     1741 ttatgttcaa atccttcccg gtaaaaacca caacagcttt catatctttc atatagaaac
     1801 ccttaatagg tgagtgaatt tcatttttta tggaatctat acgataaaaa tcgtgttgta
     1861 aatgtttttt tatgcgataa aatgcagtcc tcctacctct tttattgtta gtggtaaggc
     1921 tttctgtttg gttttttgat aaaccggtta aaacaggggc ttggacgagg atatacattg
     1981 aaagcatgag caattcacgt ggctgcatgg ctatgcagcc acgtgaaatt tatcaggcgc
     2041 agaatgcgcg gtttagcggg gagtttactg ccgattttac cgggctaacg ccgctttcac
     2101 gctgaacccg tccggagcgg tgcgggcaag gaatgttatg gtaaatacaa ctggtttttt
     2161 ctatcaagat ttactggaaa ttgctcatta cgtcagtgtt agaatcagcc cttcaaaaag
     2221 ggatttaacg cctaaacata atagtgaagg ctatagaggt gtagtttgtg aacttgttac
     2281 ttccacgcga tatagttgaa gctgttctta atgataagaa aacaaaaaat gcacgagtgg
     2341 ctaagtgtga tggaagtgaa ttttttctag aactgccaag catgaatgca gactttcccg
     2401 cagggaaaat catcctcaag ctaggagatt ccggttttta caacaaaagg acaaaaagtc
     2461 tcgagggagc ctatggcctt aggcatatat gggacaagca tcgtgtcgag ataggagcta
     2521 cttccgctga ggatattgtc atctttttgg agagcatatt attagctggg gcagaagtgc
     2581 tcatagatcc taaaaaaggc caaaacaaag cgattgttgt agagtcagga acggggatga
     2641 tgatactaga attgaaaaaa ccaaacggcg aagacccgta ctacagcatc attactgctt
     2701 atgataggaa gagccatcca ggtacaaaac ttcataccat aatatgaaaa aagccggcta
     2761 aatagccgac ttcttcgtaa tagtgttgtt cgtggcattc ccttagcatt tcggttcggg
     2821 acaggtcttt gaccttaaca acgcattgtc gaaatctggt ttccgacaag tagcctacaa
     2881 atatgtaacc aatccagagt tcaggttaca taccaagccc ttctacacat acagaataca
     2941 actctatcac tgctcatctt tttgcaaaaa gtgctatttt ggtgttcagt ggaaaccaaa
     3001 acgaagccaa atcactggta aacggtcaga tctccttgtg atcgttttac tctcgtcgta
     3061 atctctctcc ctgtaaacga aaaaaccacc cggcaaggtg gtttttcgaa ggttcagtaa
     3121 accggcaagt ttctgaaccg tggtaacagt cttgtgcgag acatgtcacc aaatactgtc
     3181 cttccagtgt agcctcacta aggcctccac ttcaagaact ctcgatacat ctctcgcaca
     3241 tcctgcttac cagtggccgc tgccagtggc gttaagtcgt gtcttttcgg gttggactca
     3301 agacgatagt taccggataa ggcgcagcgg tcggactgaa cggggggttc gtgcatacag
     3361 tccagcttgg agcgaactgc ctacccggaa ctgagtgtca ggcgtggaat gagataaacg
     3421 cggccataac agcggaatga caccggtaaa ccgaaaggca ggaacaggag agcgcacgag
     3481 ggagccacca gggggaaacg cctggtatct ttatagtcct gtcgggtttc gccaccactg
     3541 atttgagcgt cagatttcgt gatgcttgtc aggggggcgg agcctatgga aaaacggcaa
     3601 cgccggatcc ttttcccctt ccttcttgat ttgagcgcta tttatctcgt cattcttgag
     3661 caggtaacgc ccgccgcagt ctcacggcag gagcgtagcg accgagtgag cgaggaggcg
     3721 tcatttcatc gtctccagca tttcgcactt acgccccaca gctgaatttt ttacctgcca
     3781 catgaagcac ttccctgaat ttccacttcg atttaccata ctaagccagt atacactccg
     3841 ctagcgctac gtgactggtt cagggctgcg ccccgaaacc cgctaaaacc actgacgcgc
     3901 ctgcggcttg tccaacaccg cgccgaccgg gaaaagattt cccgcccgtc tcggcgttat
     3961 caggaggccg gattggcaga caaacgcagc aaaatgctca cgatgtgggt gaccgaagat
     4021 gagcaccgcc gtctgctgga gcgctgcgac ggtaaacagc ttgcagcctg gatgcgccag
     4081 acgtgcctgg acgagaaacc cgcccgcgcc ggcaagcttc cctcgctctc gccggcgctg
     4141 cttcgtcagc ttgccggcat ggggaacaac ctcaaccaga ttgcccggca ggttaacgcc
     4201 ggtggtggca gcgggcacga ccgcgtgcag gtcgtcgccg cgctgatggc catagatgcc
     4261 ggactcgagc ggctgcggca tgccgtgctg gaaaagggtg cagacgatga tcgttaagtt
     4321 tcacccgcga gggcgcggcg gtggcgccgg tccggtggat tatctgctgg ggaaagaccg
     4381 acagcgcgac ggcgccaccg ttctgcaggg gaagccggaa gaagtcaggg agcttatcga
     4441 cgcctcgccc tacgcaaaaa agtacacatc cggcgtcttg tcctttgccg aaaaggattt
     4501 accgcccggg cagcgcgaaa agctgatggc gagctttgaa cgggttctga tgcccggact
     4561 cgataaagac cagtacagcg tgctgtgggt tgagcaccag gataaggggc ggctggagct
     4621 gaacttcctg atcccgaaca cggagctgct gaccggc
//
