LOCUS       NZ_CP116114             4692 bp    DNA     circular CON 11-MAR-2024
DEFINITION  Escherichia coli strain DETEC-P80 plasmid pDETEC22, complete
            sequence.
ACCESSION   NZ_CP116114
VERSION     NZ_CP116114.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988479
            Assembly: GCF_028551585.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4692)
  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  JOURNAL   Unpublished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 4692)
  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                   :: 03/11/2024 05:23:25
            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)                     :: 5,036
            CDSs (total)                      :: 4,915
            Genes (coding)                    :: 4,640
            CDSs (with protein)               :: 4,640
            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)              :: 275
            CDSs (without protein)            :: 275
            Pseudo Genes (ambiguous residues) :: 0 of 275
            Pseudo Genes (frameshifted)       :: 82 of 275
            Pseudo Genes (incomplete)         :: 193 of 275
            Pseudo Genes (internal stop)      :: 52 of 275
            Pseudo Genes (multiple problems)  :: 51 of 275
            Pseudo Genes (short protein)      :: 4 of 275
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116114.1.
            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..4692
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-P80"
                     /isolation_source="ICU patient rectal swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC22"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-08-01"
     gene            131..1024
                     /locus_tag="PIC84_RS25115"
                     /old_locus_tag="PIC84_25115"
     CDS             131..1024
                     /locus_tag="PIC84_RS25115"
                     /old_locus_tag="PIC84_25115"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016237866.1"
                     /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_001277133.1"
                     /translation="MSAVLQRFREKLPHKPYCTNDFAYGVRILPKNIAILARFIQQNQP
                     HALYWLPFDVDRTGASIDWSDRNCPAPNITVKNPRNGHAHLLYALALPVRTAPDASASA
                     LRYAAAIERALCEKLGADVNYSGLICKNPCHPEWQEVEWREEPYTLDELADYLDLSASA
                     RRSVDKNYGLGRNYHLFEKVRKWAYRAIRQGWPVFSQWLDAVIQRVEMYNASLPVPLSP
                     AECRAIGKSIAKYTHRKFSPEGFSAVQAARGRKGGTKSKRAAVPTSARSLKPWEALGIS
                     RATYYRKLKCDPDLAK"
                     /name="replication initiation protein"
     gene            complement(1240..1515)
                     /locus_tag="PIC84_RS25120"
                     /old_locus_tag="PIC84_25120"
     CDS             complement(1240..1515)
                     /locus_tag="PIC84_RS25120"
                     /old_locus_tag="PIC84_25120"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091757.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /protein_id="WP_272756117.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVIVGAAMLARVRRP
                     EEAQLRAFLLQFLRKEVTRQADVNRLQPLINELEKLPGPPAKPQNH"
                     /name="mobilization protein"
     gene            1694..3913
                     /gene="mobQ"
                     /locus_tag="PIC84_RS25125"
                     /old_locus_tag="PIC84_25125"
     CDS             1694..3913
                     /gene="mobQ"
                     /locus_tag="PIC84_RS25125"
                     /old_locus_tag="PIC84_25125"
                     /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"
     gene            4216..4491
                     /locus_tag="PIC84_RS25130"
                     /old_locus_tag="PIC84_25130"
     CDS             4216..4491
                     /locus_tag="PIC84_RS25130"
                     /old_locus_tag="PIC84_25130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001419705.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_052977602.1"
                     /translation="MAYDEHSIRVMSADEIEQRFDWLRLENLAKEHRLPVDWVRRGFEA
                     CWRLGIEPDYFIDRYIFKRDVPLVPEFEVVFREIVNENRYRDRMRF"
                     /name="hypothetical protein"
     Typing          complement(1520..1693)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.857"
                     /coverage="100.0"
                     /evalue="5.54e-83"
     Typing          complement(1694..2052)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.444"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          132..1024
                     /name="rep_cluster_2150"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.275"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1695..3910
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.61"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaaaacaaac gccccgtaaa tcgtgctctc accgccaaga ttgatcacga aattacaggg
       61 cgccgggttc cgcgtttccc gatgggaaag cgcggttagt taaactgtgt accgagagaa
      121 atcgtatcac atgagcgccg tacttcaacg cttcagggaa aaattaccgc acaaaccgta
      181 ctgtacgaac gatttcgcgt acggcgttcg cattctgccg aaaaacattg ccattcttgc
      241 ccgtttcatc cagcagaacc agccacatgc actgtactgg cttccctttg acgtggaccg
      301 gacgggggca tcaatcgact ggagcgaccg gaattgtccg gccccgaaca tcaccgtaaa
      361 aaatccccgt aacgggcacg cgcatctgct ctacgcgctc gcccttcctg tgagaactgc
      421 gccggatgca tcggcttcgg cgctcagata cgctgccgct attgagcgtg cgttgtgtga
      481 aaaactgggc gcggatgtga attacagcgg cctgatctgc aaaaatccgt gccaccctga
      541 atggcaggaa gtggaatggc gcgaggaacc ctacactctc gacgaactgg ctgattatct
      601 cgatttgagc gcctcagcgc gccgtagcgt cgataaaaat tacgggctgg ggcgaaacta
      661 ccatctgttc gaaaaggtcc gtaaatgggc ctacagagcg attcgtcagg gctggcctgt
      721 attctcacaa tggcttgatg ccgtgatcca gcgtgtcgaa atgtacaacg catcgcttcc
      781 cgttccgctt tctccggctg aatgtcgggc tattggcaag agcattgcga aatatacaca
      841 caggaaattc tcaccagagg gattttccgc tgtacaggcc gctcgaggtc gcaagggcgg
      901 aactaaatct aagcgcgcag cagttcctac atcagcacgt tcgctgaagc cgtgggaggc
      961 attagggatc agtcgagcga cgtactaccg aaaattaaaa tgtgatccag atctcgcaaa
     1021 atgagaccag ataagcctta tcagataaca gcgccctttt ggcgtctttt tgagcagtga
     1081 tctttcttgc gatttcctcc gttttgcccc gtaatggcgt ggctttccgc atgattgagg
     1141 tggtagcgct cgccgcagtc tcatgaccga gcgtagcgag cgaatgagcg aggaagcgca
     1201 aaggcgtccg gtggtgcatg ggcacttacg cgccggggct tagtggttct gcggtttcgc
     1261 cggtggtccg ggtagcttct ccagctcgtt aatcagcggt tgtagtcggt tcacatccgc
     1321 ctgtcttgtg acttcctttc gcagaaactg gagcaggaac gcacgcagtt gcgcttcttc
     1381 cggcctccgt accctcgcca gcatggcagc ccccacaatg actttttgcg ccgtgtccag
     1441 gctccggctc ttcgccttca ggcgctgtaa tctggcctca gcttcggcaa tcttctgttc
     1501 gagtgttctg ctcatttcgt gactccgtgc gcggtgaaaa atcgtatttt agcgcgtcac
     1561 tggtagttgc aaaactgaac tggcataatg cacggcacat cacgaagtgc gcacttatac
     1621 aatcttcact tcgtttcgat tgtgtgcggt ctgcgacgct aaaagaaaac ggcaaaaagg
     1681 cattacggca gaaatggcga tttatcatct cagcatgaaa atcatttcgc gaaaaaacgg
     1741 ctacagtgcc gttgcttctg ctgcctaccg ttccggctct gtcatacccg atgaccgtac
     1801 cggattaacc cacgattaca cccgtaaacg cggcgttgat gatgcggtca ttctcacccc
     1861 tgtgaatgca ccgtcctggt gtggtgaccg ttccgttctc tggaatgcgg tcgagaaagc
     1921 cgaacagcgc cggaactccc agctggcaag ggagattgaa ctcgccattc cccgtgagat
     1981 ttcccgcgag gccgcacggg aggccgttct cgcttttgtc cgggaaaact ttgtcagtcg
     2041 gggcatgatt gccgatgtgg cgttccatca tatggaccgg accaaccccc atgcacacat
     2101 catgctgacc acgagagctg tcggggaaac gggattcgca ggaaaggtca gggactggaa
     2161 cgaccgggca ctcgccgaga cgtggcgcgc atcatgggct gaccatgcga acagagcgct
     2221 tgcgaacgcc ggctaccagg aagagataga ccatcgttca tacgagcgtc agggactgga
     2281 gaaagcgccg ggccttcacc tcggaaaggc tgcctgtgcg atggaaaaac ggggcatgga
     2341 aacagaacgc ggtgagcaga accgcctgat taacagcctt aacctggaaa tacaggtttc
     2401 ccgcacaagg ctggcagtca tccaggtaca ggagaacgtg cggaaacggg aactcagcga
     2461 tgccgcacgt cgtgcagcgg aagcccttaa tctgaccatt cccgccgcga atgcctcagc
     2521 ggataccctg cgggaattca ttgccacact gccgcaggaa tgcgggaacg catgggagat
     2581 gacaccggag ttcgtggcga tgaacgggaa ggcaaacgac atcaaacgtg aggggaatgc
     2641 gctggtgaaa gagcgggata ttctcgaaaa agagatgacc ggactcagaa aagcccgtcc
     2701 ggtagcgtcc atcctgtcag agcttcccct gatgacatgg gctgaaccgg aataccgcaa
     2761 aagacaactc cgcttctgga aactcgagaa acagattgaa tctcttcgcc gcacctacag
     2821 ggccgtgaaa gaacgggaca ttcccgcccg tcgtcaggcc tttgaaacgc agtggaatac
     2881 gtggatttcg ccgggaatgg cagagctgaa agaaaaactg tcagcacggg aagcggagcg
     2941 gcgcagggag gaagccgaag cggaagcgcg ccggaaggaa caggaatatg acgcacggct
     3001 gaaacaccat gataaccatc gcctgagccg tgaaacggca ttagccgggg ttattacggg
     3061 gctggggcgt gccagagagc cgggaacggg catgataacc cgctacatga tactgagtaa
     3121 cagagccgga gaattcacgg tatggggtga tgaactggcg gattatcccc agagtgttca
     3181 tgaccaggtg aatgtttatc tgtcgccagg tggggccgtg atggtcacgg atatacattc
     3241 ggggctgtca gaatctcatg agacgctggc ccggcctgag cgtgtgagaa tgtattccgg
     3301 tgcgacggtc cggcatgtac tggaacagat gcgccagggg tggccctctt acggttttcc
     3361 ggcgctgccg catcactggc cggataattt ttatttcagc gatgaccgca ggcccgcagc
     3421 ctctccgctg ccgtcagcgc accgggtgga cgtcaccgct tatgcggcac cggagcaact
     3481 catgcccgtt gtcttttcga cagagcgaaa cagcaggacg ctgaatctgc tgttgtgcaa
     3541 agggccggag gaaatgcttg tcggttttgt gcgcctggag gacgagctgc gtcccgttct
     3601 tgcgcttccg tcgccggatt acagtcatct gatggtaagc atcatcacag agaacgggat
     3661 acacctggca ggctacggtg aggccataaa ccgtgatgct gatactccgt acccaccgga
     3721 accgaagctg atgcagttca ggcttaaggg ctgtcaggac acgctttttg ctgccatcaa
     3781 caaaccggaa gagatgccgg attatctctt ccgtcaactc ggatttaatc agacctggca
     3841 tgaatggaag cgggacgaac agcacaggca acaacaacga cgccccggac attaccgggg
     3901 catgagtatg tgatatccgg ggctgcaccc cgaaccccgc caacgtctca cgggacacga
     3961 aaaaattccg cgtcccgtga ggcgttttct ggatgagaaa gtttgccgtt ttgacccgtt
     4021 cgcgcttctg aacggtcgaa accgatcgcg catcgctttc gtgaatagtt atgcagaccc
     4081 ctaaaaacga ttctgacgcg tttttctggt ttggcctggt gttttcttgt ctttttgtgt
     4141 tttttgcgtc agaacgcgtc tgagagcgtt ttaaggggta cgcacaacag gagttatggt
     4201 aaatcggagg tgtttatggc ttacgacgaa cattcgattc gcgtgatgtc tgctgacgag
     4261 atcgagcaac gttttgactg gttgcgcctg gagaacctgg cgaaggagca tcgcctaccc
     4321 gttgactggg tccgacgggg atttgaagcc tgctggcgac tgggtatcga gccggattat
     4381 ttcatcgaca ggtatatctt caaacgggat gtgccactgg tgccggagtt tgaggtcgtg
     4441 ttcagggaga tcgtgaacga aaaccgatac agggatcgga tgcgtttctg atatgcctct
     4501 aaaaacgcct gtaagcgatt ctgacgcgtt tttctgattt gggtgaggtt ttttacgtcc
     4561 atatccactt ttttgcgtca cagagcgatt gagagcgttt tagagggtac gtacaacggg
     4621 agttatggta aatggatcgg gttttcggga aggttcgaca ggatttgccg ttgggtgtag
     4681 tgtaagcgac tg
//
