LOCUS       NZ_CP090537             4074 bp    DNA     circular CON 08-DEC-2023
DEFINITION  Salmonella enterica strain 2016089-SE plasmid p2, complete sequence.
ACCESSION   NZ_CP090537
VERSION     NZ_CP090537.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN24619909
            Assembly: GCF_021474305.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4074)
  AUTHORS   Bai,L., Li,R., Du,P. and Zhang,P.
  TITLE     Emergence and genomic epidemiology insights on Salmonella
            4,[5],12:i:- from clinical patients in China, 2008 to 2017
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4074)
  AUTHORS   Bai,L., Li,R., Du,P. and Zhang,P.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-JAN-2022) College of Veterinary Medicine (Institute of
            Comparative Medicine), Yangzhou University, Wenhui Road, Yangzhou,
            Jiangsu 225009, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/08/2023 10:59:33
            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)                     :: 5,114
            CDSs (total)                      :: 4,993
            Genes (coding)                    :: 4,870
            CDSs (with protein)               :: 4,870
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 123
            CDSs (without protein)            :: 123
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 33 of 123
            Pseudo Genes (incomplete)         :: 99 of 123
            Pseudo Genes (internal stop)      :: 20 of 123
            Pseudo Genes (multiple problems)  :: 27 of 123
            Pseudo Genes (short protein)      :: 1 of 123
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP090537.1.
            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..4074
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="2016089-SE"
                     /isolation_source="patient"
                     /host="Homo sapiens"
                     /db_xref="taxon:28901"
                     /plasmid="p2"
                     /geo_loc_name="China: Henan"
                     /collection_date="2016"
                     /collected_by="Pei Zhang"
     gene            96..2255
                     /gene="mobQ"
                     /locus_tag="L0F58_RS25010"
                     /old_locus_tag="L0F58_25010"
     CDS             96..2255
                     /gene="mobQ"
                     /locus_tag="L0F58_RS25010"
                     /old_locus_tag="L0F58_25010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_084568118.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRTERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREVPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(2513..3205)
                     /locus_tag="L0F58_RS25015"
                     /old_locus_tag="L0F58_25015"
     CDS             complement(2513..3205)
                     /locus_tag="L0F58_RS25015"
                     /old_locus_tag="L0F58_25015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001281403.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(3737..3991)
                     /gene="mobC"
                     /locus_tag="L0F58_RS25020"
                     /old_locus_tag="L0F58_25020"
     CDS             complement(3737..3991)
                     /gene="mobC"
                     /locus_tag="L0F58_RS25020"
                     /old_locus_tag="L0F58_25020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091747.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     Typing          complement(2..95)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.739999999999999e-42"
     Typing          96..454
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.333"
                     /coverage="100.0"
                     /evalue="8.460000000000002e-179"
     Typing          complement(3993..4074)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.63e-35"
     Typing          complement(2514..3205)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          10..2252
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.064"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atcacgaagt gcgcacttat acaatctcca ctccgtttcg attgtgtgcg ccctgcgggg
       61 ctgaaagaaa actacaaaaa ggcattacgg cagaaatggc gatttatcat ctcagcatga
      121 aaattatctc cagaagcagc ggctacagcg ccgtagcttc cgctgcctat cgttccggtt
      181 cactgatgct tgatgagcgt accggactga ctcacgacta cacccgcaaa agcggtgtgg
      241 ctgaagctgt gattctgacc cccgcgacag cccctgcctg gtgtacgaac cgtgccgaac
      301 tctggaatgc cgttgagaag gccgaacgcc ggaagaactc acaacttgcg cgggaaattg
      361 aactcgctat cccccgtgaa ctgccgcagg atgccgcacg ggaaaccgtt ctcgcctttg
      421 tcagagaaaa ctttgtcagt cagggcatga ttgctgatgt ggcgttccat cacatggata
      481 aaacaaatcc ccatgcgcac atcatgctga ccacgagggc tgtcggacct gctgggttcg
      541 gcggaaaggt cagggactgg aacgaccgga cacatgccga gacgtggcgt gcatcatggg
      601 ctgaccatgc aaacagagca ctggcgaacg ccggttatca ggaagagata gaccatcgtt
      661 catacgagcg acaggggctt gagaaaacgc ctggtattca cctcggaaag tctgcctgtg
      721 cgatggaaac acgcggtatc gaaacagaac gcggcgaaca gaatcgtctg attaacaggc
      781 ttaacctgga aatacagatt tcccgcactg aactcaggaa cagcgggctg acagagcctg
      841 cccgccgtgt ggctgacctt ctgaatatcg tgcttcctga caacgcaact tcgtacacac
      901 tacgtgacat catcgaagcg ttgccgaagg acagtaatgc ggcatggaaa ctcaccagta
      961 atgccatgtc gatgatggca gatatgcagg cgacgcgcag acgctgggaa gagctgaaca
     1021 ccgaacgaaa ggaagcgatg agccatgctg ccagcctgaa aaaatcatca ccgttttcgt
     1081 ccggtttttc ccgtattccc ctgatgcaat gggcggcacc ggaataccgt agcgaacagg
     1141 gaaaaattca gtcgctgagc cagcaaatgg aaaaattgcg acagcattac cggaaggtgg
     1201 agaaacagga cattcccgcg agtcagacgg catttgaaaa acagtggcag cagtgggggg
     1261 catccggcct tgcagctctc agagtccagt tgcttaaacg tgaagaggaa ttgcgccgga
     1321 aggagcagga ggatacagaa cgtagtcgca cggagcgacg agcggaacag ctcaggaaaa
     1381 atgacaatgc cgttatggat tcaggggtac tgagcgcagt cgttacgggg tatggcgagg
     1441 cccccatgcc tggtaacggg gaaatgacct gttaccttct gcttcacaac cggaacggag
     1501 aatacacgct ctgggggaac gagctggaga aataccgcac cagaatcttt gagcgtgttg
     1561 atttaatgcg tgacaggagt ggttatatct gtgaccgaag cgaaatcggt caacatccac
     1621 cactgcaacg tgtttattcc tctgcgacct ttgagcaact tctgacgcag gtttgccaga
     1681 catggccgca atatacccgc aatctccgcc agccgaagac atggccggag tctttctgtc
     1741 ttggagaaga ccgccagcca gccatgccat cactggcagc aaggaaggtg gattttacgc
     1801 agggacgtct gccaccgacg ctgatgccgg taatgagttc tgtcgaccgg gaaacccgcc
     1861 agcttcagct tttgctggtc atgggcgtgg atgactctct gggcggtgtt gtccggctta
     1921 atggtacgct gtatcccgcg tttgccgttc cctcagccga taacagccag ctggtcatca
     1981 gtgcactgac cgataagggg ttacggtatg cagggtatgg tgttgccgta aatcacgatg
     2041 cagacagcca catatcacct gcgccggaac ttatggagtt tcatctgaaa acccgtgagg
     2101 taccgctttt tgctgccgtc aacacaccag aaaaacagcc ggatcatctg ttccgctcgc
     2161 tgggtttcaa tcgtacctgg gacgaatggc ggcgcgagga agatgcaaga acacacacca
     2221 ccgagaggag acatgatcgc ggttggtcac agtgaatgtg aacaatattt tgttttgttt
     2281 aacatcgtgt tatgttcgtt gatgttcttc gatgttcatc gacagggatg aatgcaagaa
     2341 gcacactcac ataacgcaag catagttttg tttttccgcc cccaaaaatt gggggttctt
     2401 ttttcgctgc atcagagcgt ttttggcgca atttttcact tcaatagtac cttcgcacta
     2461 ctaacacaaa aaaaacgcag cagggagcgt tttaggtgcc ttaaaatcga ttttagatcg
     2521 tcatcttgat ctgtttgtct tccttgaagc gaaaatgcag ggctacaacc gtgcgcccct
     2581 ttttgatcgt ctcaaccgtt acagccaggt cgcttttttt gttcagttcg tcaacacagg
     2641 gttttattag tattttattt aagtctctga attgtttgta tttattttca atccctaaca
     2701 ttgaacgaaa gtcattaaga gcaataattc tctctcccgt actgcggaat tgctggagga
     2761 actcgtatat tcttatactg taactacttg ataaacctga tatgtttttt ataacaacgc
     2821 gcgtgaattg ccccttcagt tgcgtcagat aaggcattac cgcgtcagaa aaggttattc
     2881 gagccttggc ctcaccttta gcgtactgtg cccgatactg gatccagcgg aactcctcac
     2941 gcttctcgtc attcttgaga atgatcgacc tgtcccataa acgatcgatc gcttcctgta
     3001 actgaacctc ggcatttttc cgccccatgt cagggaatga atcaaaatat tccgcagcgg
     3061 taatggtcat tgtcttttgc aattcagcat cagcaccaga tttcaatcga ctgatacaca
     3121 gcaacagaaa acgttgttcc tgtagggtca acttgtagct ggcctcaacc aaagcattcg
     3181 acttgtaggc aatcaagtcc gacatacaaa gatcccgttc aaatgtggtg atgctttaat
     3241 gtgccccaca aataagaaat gtggaatatt tttttttata tcctcacatt tctgtgaata
     3301 acaccttaaa ttcctccacc tttaccttaa attcctccac ctaaacacct taaattcctc
     3361 cacatatacc ttaaattcct ccacatatac cactgcaaca tattgatttt attaatgaat
     3421 ttcgccccta aaacaagtat taaaaacaag atcttaaaaa caagatctaa aaacttaacg
     3481 gcgagcctgt ggataacttg gggtgctgaa aacaaaaaac aaataaaaac aatgtgttgc
     3541 aagaaagtag aattgcaagt tccgaatact ccccttccaa ccctgtggaa atccagtatt
     3601 catgcgggtt cagcgcatat cacctgccga aaaaccgtgc gtatgtgctc aacctggcga
     3661 cggattcact tccgcttcct cgcccactcg ctcgctaacg ctcggtcgct ggggctgcgg
     3721 cgagcggacg atacaatcac tgtcctggca gcgcctccag ctcgttaatc agcggcagta
     3781 tgcgcgtcac atcagcctgt cgtgtcacct ctgccttcag gaactggagt aaccaggcac
     3841 gcaactgcac ctcctccggc tttctgacct ttgccagcaa tgctgcaccc acaacaacct
     3901 tctgcgctgt gtccaagctc cggctcttcg ccttcaggcg ctgtaatctc gcctcagcat
     3961 cagcaatctt ctgttcgagc gttctgctca tgatgtaact ccgtgcgcga tgaaaaatcg
     4021 cattttagcg cgtcactggt agtttaaaaa ctgagctggc ataatgcacg gcaa
//
