LOCUS       NZ_CP142040             2042 bp    DNA     circular CON 17-JAN-2024
DEFINITION  Escherichia coli strain HS4 plasmid pHS4_5, complete sequence.
ACCESSION   NZ_CP142040
VERSION     NZ_CP142040.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39202292
            Assembly: GCF_035666315.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2042)
  AUTHORS   Jiang,X., Li,D., Sun,Z., Lu,Y., Li,P., Li,W., Wang,D., Wei,L.,
            Xu,X., Yuan,Y. and Wang,M.
  TITLE     Type I BREX system defends against antibiotic-resistant plasmids in
            Escherichia coli
  JOURNAL   Antimicrobial agents and chemotherapy (2024) In press
REFERENCE   2  (bases 1 to 2042)
  AUTHORS   Jiang,X., Li,D., Sun,Z., Lu,Y., Li,P., Li,W., Wang,D., Wei,L.,
            Xu,X., Yuan,Y. and Wang,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-JAN-2024) Institute of Antibiotics, Huashan Hospital,
            Fudan University, middle wulumiqi road, Shanghai 200040, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Fyle v. V2.9.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 188x
            Sequencing Technology             :: Illumina NovaSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/17/2024 08:27:10
            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)                     :: 5,425
            CDSs (total)                      :: 5,306
            Genes (coding)                    :: 5,087
            CDSs (with protein)               :: 5,087
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 219
            CDSs (without protein)            :: 219
            Pseudo Genes (ambiguous residues) :: 0 of 219
            Pseudo Genes (frameshifted)       :: 78 of 219
            Pseudo Genes (incomplete)         :: 156 of 219
            Pseudo Genes (internal stop)      :: 34 of 219
            Pseudo Genes (multiple problems)  :: 43 of 219
            Pseudo Genes (short protein)      :: 4 of 219
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP142040.1.
            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..2042
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="HS4"
                     /isolation_source="bile"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pHS4_5"
                     /geo_loc_name="China: Shanghai"
                     /collection_date="2017"
                     /collected_by="Institute of Antibiotics, Huashan Hospital,
                     Fudan University"
     gene            106..432
                     /locus_tag="VJY30_RS27120"
                     /old_locus_tag="VJY30_27125"
     CDS             106..432
                     /locus_tag="VJY30_RS27120"
                     /old_locus_tag="VJY30_27125"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001614210.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_001070513.1"
                     /translation="MNQAALITIANELNHDQMRVLMALLAELDYENYIQVAQIDIAEAL
                     TMQKTNVSRAVKNLIDFGIILEGPKIGRSKTYRLNPQFGWKGTVSNHKKALKNGLSVIQ
                     GGRT"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(496..1464)
                     /gene="mobV"
                     /locus_tag="VJY30_RS27125"
                     /old_locus_tag="VJY30_27130"
     CDS             complement(496..1464)
                     /gene="mobV"
                     /locus_tag="VJY30_RS27125"
                     /old_locus_tag="VJY30_27130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000024818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobV family relaxase"
                     /protein_id="WP_025766223.1"
                     /translation="MANYAIMRCKKLTGMGSVASALQHCYRERETPNANAERTPENYCS
                     VSKSTDQAMGRVRELLPEKRRKDAVLAVEYVMTASPEWWKEATPRQQAEFFARSEQWLE
                     KKYGKDRVVAAVVHRDEATPHLSAFVVPLTQDGRLSAKEFIGGRSKMREDQSTYAESVK
                     KLGLERGIEGSRATHQTVQHYYESINRGTRSQVSISPEALEPRVLRKGIFTKDVEDQAA
                     IAKRLSHAVNDGFAGTIAMASQSAQNAKRARELQKTMDAQQKRLQSVTEPFKGLSREQM
                     TEILMMAQRFKQQNQEKEKQQRVEREKQRQMRSRGMGGMER"
                     /name="mobV"
     Typing          complement(500..1473)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.462"
                     /coverage="96.0"
                     /evalue="0.0"
ORIGIN
        1 atgcggagaa tcacgcaggt agaccaaagt acaggggagg aattaggtgg ttttgtagca
       61 gtgattcgtc ccaaacaaaa gtcatcattc cagaggcact ttactatgaa tcaagccgcg
      121 ctaattacca ttgccaatga gctaaaccat gaccagatgc gtgtactgat ggccttgctc
      181 gcagagctgg attacgagaa ctacatccag gtcgcgcaga tagatattgc agaagcgctg
      241 actatgcaaa aaacaaatgt cagtcgtgcg gtaaaaaacc tgattgattt cgggatcata
      301 ctggaaggac cgaagattgg gcggagcaaa acgtaccgcc taaatcccca gttcggctgg
      361 aaaggtactg tcagcaacca caaaaaagca ctgaaaaacg gcctcagcgt tatacagggc
      421 ggcagaacct gatctctgga atgccgcaaa tggcgtcatt ttgcggcgtt agccctatcc
      481 tgcatcgcat caaaactaac gctccatacc gcccatgcca cgcgatcgca tctgtcgctg
      541 tttctcacgt tcaacacgct gctgtttctc cttctcctgg ttttgctgct taaaccgctg
      601 agccatcatc aggatttcgg tcatctgctc tctggaaagc cccttaaaag gctctgtgac
      661 gctctgtagg cgtttctgct gcgcatccat agtcttctgt agctcacgcg ctctttttgc
      721 gttctgggcg ctctgagagg ccatagcgat ggttcctgca aagccatcgt tcactgcgtg
      781 gcttagacgt ttggctatgg ctgcctgatc ttccacgtct ttggtgaaaa tgcccttccg
      841 caatacacgc ggctccagcg cctccggcga gatcgatacc tggctacggg tgccacggtt
      901 tatcgattcg tagtagtgct gaactgtctg atgcgtggcg cggcttccct cgatgccgcg
      961 ctcaagaccc agttttttta ctgattcagc gtaggtgctc tgatcttcac gcatctttga
     1021 ccgcccgcca ataaactctt tcgcggacag ccgtccatcc tgcgtcaatg gcaccacgaa
     1081 cgcagacagg tgcggggtgg cctcgtcccg gtgaaccacc gccgccacaa cacgatcctt
     1141 cccgtatttc ttctccagcc attgctcaga gcgggcgaaa aactccgcct gctgccgtgg
     1201 tgtggcctct ttccaccact cagggcttgc tgtcataacg tattcaacgg ccagtaccgc
     1261 atctttacgg cgtttttccg gcagcagctc ccgcacacgc cccattgcct gatccgttga
     1321 tttggacaca gagcagtagt tttctggtgt ccgttcagcg ttagcgttcg gcgtctcacg
     1381 ctctcggtag cagtgctgca acgcgctggc cacgcttccc attcccgtca gctttttgca
     1441 gcgcattatc gcgtagttcg ccatgttccc ccctgattcc ggcattcatt cagccaggcg
     1501 ggggagcgca ttgcgatacc tccggcgggc cactatcaag atgatagtgt actcactaga
     1561 ctttgcttcg caaaatcgtt cgggaagctg cgcttccaaa ggtcaaaatc aacggcggtc
     1621 tggcaggtgg aaggcgtcgc tccgcgtcac ctcccaccac tgccaagcct gttttatccg
     1681 gtgagtcgtc aagggtaaat ggcactcgct acgctcgccc ttgacgaaat caggcaatga
     1741 atatcgtttt tgaaagagca ggaaccgctc gccgcaagaa cggattaggg agcggcatcg
     1801 ccgcgagtct gtccgttcga ggaagcggaa tttccacttc ccgtacatag aaattcgttc
     1861 gcaccgaacg ggcagaaaaa cgcctgattt tgccgatgta tgagtacgga gagtaataag
     1921 atacagaagg ggatgtctcg gaagccgcgc cacaagcgga aagtttttga caatagttat
     1981 ctctagagat aacttagtta tcttgagaga taactatttt tcctgaaatt ggagattttt
     2041 ag
//
