LOCUS       NZ_CP116174             4296 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P1056 plasmid pDETEC85, complete
            sequence.
ACCESSION   NZ_CP116174
VERSION     NZ_CP116174.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988445
            Assembly: GCF_027944915.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4296)
  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  JOURNAL   Unpublished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 4296)
  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 01:49:26
            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)                     :: 4,863
            CDSs (total)                      :: 4,743
            Genes (coding)                    :: 4,559
            CDSs (with protein)               :: 4,559
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 184
            CDSs (without protein)            :: 184
            Pseudo Genes (ambiguous residues) :: 0 of 184
            Pseudo Genes (frameshifted)       :: 64 of 184
            Pseudo Genes (incomplete)         :: 109 of 184
            Pseudo Genes (internal stop)      :: 47 of 184
            Pseudo Genes (multiple problems)  :: 37 of 184
            Pseudo Genes (short protein)      :: 3 of 184
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116174.1.
            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..4296
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-P1056"
                     /isolation_source="ICU patient rectal swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC85"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-10-22"
     gene            240..1175
                     /locus_tag="PIC86_RS24255"
                     /old_locus_tag="PIC86_24250"
     CDS             240..1175
                     /locus_tag="PIC86_RS24255"
                     /old_locus_tag="PIC86_24250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011666805.1"
                     /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_089577255.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDIDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDSSVKA
                     LKYAAAIERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASA
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSL
                     PECRAIGKSIAKYTHRNFTPETFAQYVATTHTPEIQAARGRKGGIAKGAGYEDKRSTAL
                     EMLANGCTQKAIAEMLGVSDRSIRNWKSGK"
                     /name="replication initiation protein"
     gene            complement(1391..1657)
                     /locus_tag="PIC86_RS24260"
                     /old_locus_tag="PIC86_24255"
     CDS             complement(1391..1657)
                     /locus_tag="PIC86_RS24260"
                     /old_locus_tag="PIC86_24255"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091750.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /protein_id="WP_089577256.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVIVGAAMLARVRRP
                     EEAQLRAFLLQFLRKEVTRQADVNRIQPLINELEKLPRPPAKP"
                     /name="mobilization protein"
     gene            1836..4055
                     /gene="mobQ"
                     /locus_tag="PIC86_RS24265"
                     /old_locus_tag="PIC86_24260"
     CDS             1836..4055
                     /gene="mobQ"
                     /locus_tag="PIC86_RS24265"
                     /old_locus_tag="PIC86_24260"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001029330.1"
                     /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_154074701.1"
                     /translation="MAIYHLSMKIISRKNGYSAVASAAYRSGSVIPDDRTGLTHDYTRK
                     RGVDDAVILTPVNAPSWCGDRSVLWNAVEKAEQRRNSQLAREIELAIPREISREAAREA
                     VLAFVRENFVSRGMIADVAFHHMDRTNPHAHIMLTTRAVGETGFAGKVRDWNDRALAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKAPGLHLGKAACAMEKRGMETERGEQ
                     NRLINSLNLEIQVSRTRLAVIQVQENVRKRELSDAARRAAEALNLTIPAANASADTLRE
                     FIATLPQECGNAWEMTPEFVAMNGKANDIKREGNALVKERDILEKEMTGLRKARPVASI
                     LSELPLMTWAEPEYRKRQLRFWKLEKQIESLRRTYRAVKERDIPARRQAFETQWNTWIS
                     PGMAELKEKLSAREAERRREEAEAEARRKEQEYDARLKHHDNHRLSRETALAGVITGLG
                     RAREPGTGMITRYMILSNRAGEFTVWGDELADYPQSVHDQVNVYLSPGGAVMVTDIHSG
                     LSESHETLARPERVRMYSGATVRHVLEQMRQGWPSYGFPALPHHWPDNFYFSDDRRPAA
                     SPLPSAHRVDVTAYAAPEQLMPVVFSTERNSRTLNLLLCKGPEEMLVGFVRLEDELRPV
                     LALPSPDYSHLMVSIITENGIHLAGYGEAINRDADTPYPPEPKLMQFRLKGCQDTLFAA
                     INKPEEMPDYLFRQLGFNQTWHEWKRDEQHRQQQRRPGHYRGMSM"
                     /name="mobQ"
     Typing          complement(1662..1835)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          complement(1836..2194)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.444"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          241..1175
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.502"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1837..4052
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.61"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgcgtctgag agcgttttaa ggggtacgca caacgggagt tatggtaaat ggatcgggtt
       61 ttggggaata atcgacaggg tttgccgttg ggtgtagtgt aagcgactga aaaacaaacg
      121 ccccgtaaat cgtgctctca ccgccaagat tgatcacgaa attacagggc gccgggttcc
      181 gcgtctcccg atgggaaagc gcggttagtt aaactgtgta ccgagaggaa tcgtaacaca
      241 tgagcgccgc gcttcaatac ttcgaagaaa atttacctca tcgtccctat cacacggatg
      301 atctcgcttt cggccttcgc atctctggca aagggcgcgc tcttcttgcg cgctacatcc
      361 agcagaacca gccacatgcg cagttctggc tggtttttga cattgaccgc gagggggctg
      421 cgattgactg gagcgaccgg aatgctcccg cgccgaacat caccgtaaaa aatcctgtga
      481 acggtcatgc tcacctgctc tacgcgctca atatcgccgt gagaaccgcg ccggacagct
      541 cggttaaggc gctgaaatac gccgctgcga ttgaacgttc gctgtgtgag aaactttgtg
      601 ctgatgtgaa ctacagcgga ctgatttgca aaaacccgtt tcacctggaa tggcaggtga
      661 tggagtggcg agaggaagcc tataccctcg atgaactggc tgattatctc gatttgagtg
      721 cctcagcgcg ccgtagcatt gataaacatt acgggatggg gcgaaactgc cacctgttcg
      781 aaatgacgcg caaatgggct tacagggcga ttcgtcaggg ctggccagca ttctcacagt
      841 ggcttgatgc cgtgattcag cgtgtcgaaa tgtacaacgc atcgcttccc gttccgcttt
      901 cacttcctga atgtcgggct attggcaaga gtattgcgaa atacacgcac aggaacttca
      961 cgccggaaac tttcgcacag tatgtggcga caacgcacac gccggaaatt caggccgccc
     1021 gaggccggaa aggtggtata gccaaagggg ctggctatga ggataagcgc agcaccgcgc
     1081 tggaaatgtt agcgaatgga tgtactcaaa aggctatagc tgaaatgtta ggtgtttccg
     1141 atcgctctat tcgaaactgg aaaagcggaa aatagcctat atcagataac agcgcctttt
     1201 tggcgtcttt ttgagcggct tggtttgttg ctatttccct cgttgaatcc cgcaatggcg
     1261 cggctttccg catgattgag gtggtagcgc tcgccgcagt ctcatgaccg agcgtagcga
     1321 gcgaatgagc gaggaagcgc aaaggtgtcc ggtggtgcat gtggcactta cgcgccgggg
     1381 tttctccgtt ctacggtttc gcaggtggtc tgggtagctt ctccagctcg ttaatcagcg
     1441 gttgtatccg gttcacatcc gcctgtcttg tgacttcctt tcgcagaaac tggagcagga
     1501 acgcacgcag ttgcgcctct tccggcctcc gtaccctcgc cagcatggca gcccccacaa
     1561 tgactttttg cgccgtgtcc aggctccggc tcttcgcctt caggcgctgt aatctggcct
     1621 cagcttcggc aatcttctgt tcgagtgttc tgctcatttt gtgactccgt gcgcggtgaa
     1681 aaatcgcatt ttagcgcgtc actggtagtt gcaaaactga actggcataa tgcacggcac
     1741 atcacgaagt gcgcacttat acaatcttca cttcgtttcg attgtgtgcg gtctgcgacg
     1801 ctaaaagaaa acggcaaaaa ggcattacgg cagaaatggc gatttatcat ctcagcatga
     1861 aaatcatttc gcgaaaaaac ggctacagtg ccgttgcttc tgctgcctac cgttccggct
     1921 ctgtcatacc cgatgaccgt accggattaa cccacgatta cacccgtaaa cgcggcgttg
     1981 atgatgcggt cattctcacc cctgtgaatg caccgtcctg gtgtggtgac cgttccgttc
     2041 tctggaatgc ggtcgagaaa gccgaacagc gccggaactc ccagctggca agggagattg
     2101 aactcgccat tccccgtgag atttcccgcg aggccgcacg ggaggccgtt ctcgcttttg
     2161 tccgggaaaa ctttgtcagt cggggcatga ttgccgatgt ggcgttccat catatggacc
     2221 ggaccaaccc ccatgcacac atcatgctga ccacgagagc tgtcggggaa acgggattcg
     2281 caggaaaggt cagggactgg aacgaccggg cactcgccga gacgtggcgc gcatcatggg
     2341 ctgaccatgc gaacagagcg cttgcgaacg ccggctacca ggaagagata gaccatcgtt
     2401 catacgagcg tcagggactg gagaaagcgc cgggccttca cctcggaaag gctgcctgtg
     2461 cgatggaaaa acggggcatg gaaacagaac gcggtgagca gaaccgcctg attaacagcc
     2521 ttaacctgga aatacaggtt tcccgcacaa ggctggcagt catccaggta caggagaacg
     2581 tgcggaaacg ggaactcagc gatgccgcac gtcgtgcagc ggaagccctt aatctgacca
     2641 ttcccgccgc gaatgcctca gcggataccc tgcgggaatt cattgccaca ctgccgcagg
     2701 aatgcgggaa cgcatgggag atgacaccgg agttcgtggc gatgaacggg aaggcaaacg
     2761 acatcaaacg tgaggggaat gcgctggtga aagagcggga tattctcgaa aaagagatga
     2821 ccggactcag aaaagcccgt ccggtagcgt ccatcctgtc agagcttccc ctgatgacat
     2881 gggctgaacc ggaataccgc aaaagacaac tccgcttctg gaaactcgag aaacagattg
     2941 aatctcttcg ccgcacctac agggccgtga aagaacggga cattcccgcc cgtcgtcagg
     3001 cctttgaaac gcagtggaat acgtggattt cgccgggaat ggcagagctg aaagaaaaac
     3061 tgtcagcacg ggaagcggag cggcgcaggg aggaagccga agcggaagcg cgccggaagg
     3121 aacaggaata tgacgcacgg ctgaaacacc atgataacca tcgcctgagc cgtgaaacgg
     3181 cattagccgg ggttattacg gggctggggc gtgccagaga gccgggaacg ggcatgataa
     3241 cccgctacat gatactgagt aacagagccg gagaattcac ggtatggggt gatgaactgg
     3301 cggattatcc ccagagtgtt catgaccagg tgaatgttta tctgtcgcca ggtggggccg
     3361 tgatggtcac ggatatacat tcggggctgt cagaatctca tgagacgctg gcccggcctg
     3421 agcgtgtgag aatgtattcc ggtgcgacgg tccggcatgt actggaacag atgcgccagg
     3481 ggtggccctc ttacggtttt ccggcgctgc cgcatcactg gccggataat ttttatttca
     3541 gcgatgaccg caggcccgca gcctctccgc tgccgtcagc gcaccgggtg gacgtcaccg
     3601 cttatgcggc accggagcaa ctcatgcccg ttgtcttttc gacagagcga aacagcagga
     3661 cgctgaatct gctgttgtgc aaagggccgg aggaaatgct tgtcggtttt gtgcgcctgg
     3721 aggacgagct gcgtcccgtt cttgcgcttc cgtcgccgga ttacagtcat ctgatggtaa
     3781 gcatcatcac agagaacggg atacacctgg caggctacgg tgaggccata aaccgtgatg
     3841 ctgatactcc gtacccaccg gaaccgaagc tgatgcagtt caggcttaag ggctgtcagg
     3901 acacgctttt tgctgccatc aacaaaccgg aagagatgcc ggattatctc ttccgtcaac
     3961 tcggatttaa tcagacctgg catgaatgga agcgggacga acagcacagg caacaacaac
     4021 gacgccccgg acattaccgg ggcatgagta tgtgatatcc ggggctgcac cccgaacccc
     4081 gccaacgtct cacgggacac gaaaaaattc cgcgtcccgt gaggcgtttt ctggatgaga
     4141 aagtttgccg ttttgacccg ttcgcgcttc tgaacggtcg aaaccgatcg cgcatcgctt
     4201 tcgtgaatag ttatgcagac ccctaaaaac gattctgacg cgtttttctg gtttggcctg
     4261 gtgttttctt gtctttttgt gttttttgcg tcagaa
//
