LOCUS       NZ_CP116099             2678 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-S560 plasmid pDETEC71, complete
            sequence.
ACCESSION   NZ_CP116099
VERSION     NZ_CP116099.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988492
            Assembly: GCF_027944675.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2678)
  AUTHORS   Moran,R.A., Baomo,L., Doughty,E.L., Guo,Y., Ba,X., van Schaik,W.,
            Zhuo,C. and McNally,A.
  TITLE     Extended-spectrum beta-lactamase genes traverse the Escherichia coli
            populations of ICU patients, staff and environment
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2678)
  AUTHORS   Moran,R.A., Baomo,L., Doughty,E.L., Guo,Y., Ba,X., van Schaik,W.,
            Zhuo,C. and McNally,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-JAN-2023) Institute of Microbiology and Infection,
            University of Birmingham, Institute of Microbiology and Infection,
            Birmingham B15 2TT, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 10x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/25/2024 02:00:16
            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)                     :: 5,033
            CDSs (total)                      :: 4,912
            Genes (coding)                    :: 4,656
            CDSs (with protein)               :: 4,656
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 256
            CDSs (without protein)            :: 256
            Pseudo Genes (ambiguous residues) :: 0 of 256
            Pseudo Genes (frameshifted)       :: 82 of 256
            Pseudo Genes (incomplete)         :: 173 of 256
            Pseudo Genes (internal stop)      :: 52 of 256
            Pseudo Genes (multiple problems)  :: 48 of 256
            Pseudo Genes (short protein)      :: 4 of 256
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116099.1.
            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..2678
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-S560"
                     /isolation_source="ICU staff rectal swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC71"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-09-01"
     gene            228..500
                     /locus_tag="PIC78_RS25115"
                     /old_locus_tag="PIC78_25110"
     CDS             228..500
                     /locus_tag="PIC78_RS25115"
                     /old_locus_tag="PIC78_25110"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001286144.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001286144.1"
                     /translation="MSDVKSDQIIKYLSEKWGGSKCPLCKKGRWNVSDKIFELREFHEG
                     NVVIGAGPIVPIIPVTCDNCGNVVLVNAIISGCLSADNKQDGGSK"
                     /name="hypothetical protein"
     gene            497..901
                     /locus_tag="PIC78_RS25120"
                     /old_locus_tag="PIC78_25115"
     CDS             497..901
                     /locus_tag="PIC78_RS25120"
                     /old_locus_tag="PIC78_25115"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000014067.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000014067.1"
                     /translation="MSGGNNFKMSQDYEIAQPKKKMAYPILVEEWDFLIGKIESISDDE
                     NIYHTIGSIFLGVAGSALIAALTLDLPSDDGYMPRQILISWYVFWASLICGVLSMFFGR
                     KNKKINRTSAKDIVQQMRLIEKRYEQGSMD"
                     /name="hypothetical protein"
     gene            complement(1115..1276)
                     /locus_tag="PIC78_RS25225"
     CDS             complement(1115..1276)
                     /locus_tag="PIC78_RS25225"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001318243.1"
                     /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_071527578.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPERHDLSPLAAATGNRIRGVSLE
                     VMRLLRLN"
                     /name="replication initiation protein"
     gene            complement(1746..1940)
                     /locus_tag="PIC78_RS25125"
                     /old_locus_tag="PIC78_25120"
     CDS             complement(1746..1940)
                     /locus_tag="PIC78_RS25125"
                     /old_locus_tag="PIC78_25120"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_001041622.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALNADEQAAMCEKLHELA
                     EELQNSIQTRFEAENLTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2224..2547
                     /gene="mobA"
                     /locus_tag="PIC78_RS25130"
                     /old_locus_tag="PIC78_25125"
     CDS             2224..2547
                     /gene="mobA"
                     /locus_tag="PIC78_RS25130"
                     /old_locus_tag="PIC78_25125"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     Typing          1979..2215
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.49e-121"
     Typing          complement(1205..1712)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.441"
                     /coverage="95.0"
                     /evalue="2.2999999999999997e-156"
     Typing          2225..2544
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="9.47e-63"
ORIGIN
        1 ggggtaaaac atctcttttt gcggtgtctg cgtcagaatc gcgttcagcg cgtttcagcg
       61 gtgcgtacaa tactggtatt atggtaaatg taagatttta tatttatgtt tttttgcgca
      121 caaaacagat atggatgtac tctataaagt tacttgatca ataaattatt gagtgatgtg
      181 attgttcgct aataaatata tgagtataag gaatgcttgg agggaatatg agtgatgtta
      241 agtcagatca aataattaaa tatttgtctg aaaagtgggg agggagcaaa tgtcccttgt
      301 gtaaaaaagg gcgttggaat gtttctgaca aaatttttga actaagagaa tttcatgaag
      361 gtaatgttgt tattggggca ggtccgatag tcccaattat tcctgtaact tgtgataatt
      421 gcgggaatgt tgttcttgtt aatgccatta tctcagggtg cttatctgct gacaataagc
      481 aagatggagg ctcaaagtga gtggtggtaa taattttaaa atgtctcagg actatgaaat
      541 tgctcaacca aaaaagaaaa tggcttaccc tattcttgtt gaagaatggg attttttaat
      601 agggaaaata gaaagtatta gtgatgatga aaatatatac catacgattg gttctatatt
      661 tttaggtgtg gctggctcgg cattgatagc agcattaact ttagatttgc catcagatga
      721 tggttatatg ccaaggcaga tattaatttc atggtacgta ttttgggcaa gccttatttg
      781 tggagtgctt tctatgtttt ttggtagaaa gaataaaaag attaatagaa cttctgcgaa
      841 ggatattgtg caacaaatga gattgataga gaaacgttac gagcaaggta gtatggatta
      901 actggatgct gaacgtttag cgaggttacg gcgtgccaag ggggggggca taatgtaagg
      961 atcttcttga gatccttgtc ttgtcgtcgt agtctcttgt ctatgaaacg aaaaaaccac
     1021 ccggcaaggt ggtttttcga aggttctcag agctaccaac tctttgagcc gaggtaactg
     1081 gcttggagga gcgcagtcac caaaacttgt tctttcagtt tagccttaac aggcgcatga
     1141 cttcaaggct aactcctcta attcggttac cagtggctgc tgccagtggc gataagtcgt
     1201 gtctttccgg gttggattca agtcgatagt taccggataa ggcgcagcgg tcggactgaa
     1261 cggggggttc gtgcatacag tccagcttgg agcgaactgc ctacccggaa ctgagtgtca
     1321 ggcgtggaat gagataaacg cggccataac tgcggaatga cattggtaaa ccgaaaggca
     1381 ggaacaggag agcgcacgag ggagcttcca gggggaaacg cctggtatct ttatagtcct
     1441 gtcgggtttc gccacctctg acttgagcgt cggtttttat gatgctcgtc aggggggcgg
     1501 agcctatgga aaaacgcctc ccgcgcgccc ttcttctgag tctttgtctt ttgctcacat
     1561 gttctttccg gttttatccc ccgattctgt ggataaccgt attaccgcct ttgagtgagc
     1621 tgacaccgct cgccgcagtc gaacgaccga gcgtagcgag tcagtgagcg aggaagcgga
     1681 agagcgcctt atgtgacatt ttctccttac gctcctctat gccgttctgc atcctgtctg
     1741 gagcgttata tcccggtaag attttccgct tcaaagcgtg tctgtatgct gttctggagt
     1801 tcttctgcga gttcgtgcag tttctcacac atggcggcct gttcgtcggc attgagtgcg
     1861 tccagttttt cgagcagcgt caggctctga ctttttatga atcccgccat gttgagtacg
     1921 gcttgctgct gcttgttcat cttttcgttt tctccgttct gtctgtcatc tgcgttgtgt
     1981 gattatatcg cgtaccactt ttcgactgtt ttgctgccgc tattctgccg cttggctttt
     2041 tgacgggcat ttctgtcaga caacactgtc actgccaaaa aactgccgtg cctttgtcgg
     2101 taattcgagc ttgctgacag gacaggatgt gcaattgtta taccgcgcat acatgcacgc
     2161 tattacaatt gccctggtca gggctttgcc ccgacaccca tgtcagatac ggagccatgt
     2221 tttatgacaa aacgaagtgg aagtaatacg cgcaggcggg ctatcagtcg ccctgttcgc
     2281 ctgacggcag aagaagacca ggaaatcaga aaaagggctg ctgaatgcgg caagaccgtt
     2341 tccggttttt tacgggcggc agctctcggt aagaaagtta actcactgac tgatgatcgg
     2401 gtactgaaag aagttatgag actgggggcg ttacagaaaa aactctttat cgacggcaag
     2461 cgtgtcgggg acagggagta tgcggaggtg ctgatcgcta ttacggagta tcaccgtgcc
     2521 ctgttatcca gacttatggc agattagctt cccggagaga aaactgtcga aaacagacgg
     2581 tatgaacacc gtaagctccc aaagtgatca ccattcgctt tcatgcatag ctatgcagcg
     2641 agctgaaaac gatcctgacg catccttcct gttttccc
//
