LOCUS       NZ_CP116141             4396 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P649 plasmid pDETEC29, complete
            sequence.
ACCESSION   NZ_CP116141
VERSION     NZ_CP116141.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988469
            Assembly: GCF_027944815.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4396)
  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  JOURNAL   Unpublished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 4396)
  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 01:50:27
            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)                     :: 4,984
            CDSs (total)                      :: 4,864
            Genes (coding)                    :: 4,648
            CDSs (with protein)               :: 4,648
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 216
            CDSs (without protein)            :: 216
            Pseudo Genes (ambiguous residues) :: 0 of 216
            Pseudo Genes (frameshifted)       :: 82 of 216
            Pseudo Genes (incomplete)         :: 150 of 216
            Pseudo Genes (internal stop)      :: 41 of 216
            Pseudo Genes (multiple problems)  :: 52 of 216
            Pseudo Genes (short protein)      :: 3 of 216
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116141.1.
            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..4396
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-P649"
                     /isolation_source="ICU patient oral swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC29"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-09-05"
     gene            join(3907..4396,1..218)
                     /locus_tag="PIB66_RS24815"
                     /old_locus_tag="PIB66_24815"
     CDS             join(3907..4396,1..218)
                     /locus_tag="PIB66_RS24815"
                     /old_locus_tag="PIB66_24815"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016537130.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_047662918.1"
                     /translation="MNLNKYLLVIAIAYSSSVFSAGIPVVDTVGNAQELAHWTEKLKQW
                     TETVQHYKNQLQAYKDQLATSTGLRDIQGLVSQGKSLKNDIISLQKQGISLDSLLTSSS
                     APSGTLDTLYKKFKDFDICDEKQAESYINICKQETVNKAWAIEQTADVQEKISDALNDI
                     SDLTDRMANAKDIKESQDLANAIQAKSIQLNILSQQWEINMKSSEQRDKLLAEKRRKAF
                     RESQITAPVPQFN"
                     /name="type IV secretion system protein"
     gene            1267..1794
                     /locus_tag="PIB66_RS24820"
                     /old_locus_tag="PIB66_24820"
     CDS             1267..1794
                     /locus_tag="PIB66_RS24820"
                     /old_locus_tag="PIB66_24820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001271729.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_021533607.1"
                     /translation="MSATIENDESLPSTPANNHNFVQVSRAYLKAWRGLIRKSGLAAEI
                     LFYLVERMGKTTNAVVCSYATLTEVTGYSRRSVATAIKILKEDNWIQVVKIGNASAYCV
                     NEKVIWQAGRNQRKYAIFSATVVASESEQESDYHLKAKEKLTYIPFVERTERMVIGEEE
                     LPPPDQKDLDLS"
                     /name="replication/maintenance protein RepL"
     gene            1880..2164
                     /locus_tag="PIB66_RS24825"
                     /old_locus_tag="PIB66_24825"
     CDS             1880..2164
                     /locus_tag="PIB66_RS24825"
                     /old_locus_tag="PIB66_24825"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_061089809.1"
                     /translation="MAGCIVPESSGEKNSFFRLLLDLENRGYFIRGVYAEHQNVRGRDI
                     HLKLISSNGDIKYLAVKKFRTNAPHEVTHYAIDKYRRWLRQYKRQPVKS"
                     /name="hypothetical protein"
     gene            2219..2506
                     /locus_tag="PIB66_RS24830"
                     /old_locus_tag="PIB66_24830"
     CDS             2219..2506
                     /locus_tag="PIB66_RS24830"
                     /old_locus_tag="PIB66_24830"
                     /inference="COORDINATES: protein motif:HMM:NF033894.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EexN family lipoprotein"
                     /protein_id="WP_061089808.1"
                     /translation="MKSLKYILIGTISLTAAVCNAEPEVKTAEWYMQHHDEVLSKYKEC
                     KAAQDKSYGGTGYSDDCKNVLKASLRIKDPDFIKSLNKIRLESINEILNK"
                     /name="EexN family lipoprotein"
     gene            2516..3565
                     /locus_tag="PIB66_RS24835"
                     /old_locus_tag="PIB66_24835"
     CDS             2516..3565
                     /locus_tag="PIB66_RS24835"
                     /old_locus_tag="PIB66_24835"
                     /inference="COORDINATES: protein motif:HMM:NF016491.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_061089807.1"
                     /translation="MAGFFEKMNEKIDSLLTATSEGMSGKYSDSISLIAASALVLYGVI
                     LAFYIMGGKKKIEDVGSTFFHAMIVYVFVTNAGGYLNILSDGIKGLNDGLATVGGAGSS
                     AWSLLDKQWEVTQRLAETVKSLDTDYFSITGAIASLMIWIGTGVVLVISSLVLLIAKIA
                     LTLLLTTAPVFIYCLTFPFLRQTFNNWVQNVLSSILTVMFASLVINFGLEFYNDILSQL
                     TANVDNASLMTTGAIAVVCGIVAGAIVLVSAKLAQSISGAGIDAAIQGAAAMGIGGSIL
                     AASKTAGTAKNIGTGAYEGASGKNWKERESKGVTPAIAYGSGRIGRAAIQKVIASNSRS
                     ERSIPTARN"
                     /name="type IV secretion system protein"
ORIGIN
        1 cagaccttac cgatcgcatg gcgaacgcca aagatataaa agaaagtcag gacttggcta
       61 atgcgatcca ggctaaaagt atccagctaa atattctctc tcaacagtgg gaaattaata
      121 tgaaatcatc agaacagcgt gataaacttc tagcagagaa acgccggaag gctttcaggg
      181 aaagtcagat tacagcacct gtaccgcaat ttaattagca tcggggttat ccgagttaaa
      241 agagcgggtg gtaataaata tctttgaatc aattatattc ttgaaaccaa ctgtaggtca
      301 ccgggcaaac gttgcggaat ggcgtcattt tgcggtgttt gccctatcct gcatcggagt
      361 taaaccacga agatttttat tccccgttct tcagaacgac cgagcctcca cggttccggc
      421 agcgccttga gcgcaaccgg aaaccgtctg gggagaaccc cagaccccca tcgctgtaat
      481 accgacggtc tacgaccacc taccacccga atagctgcct gtaccgtgca aatgggcttt
      541 gcagggggct gacgcagttc ctggcgacct gaaaacccct agttaggggt atcggcgcgc
      601 ctgaccttct gaaaccctct gtaagcgttt ttcgcgcctt ccatgccctg acgggcattt
      661 aaaacctgtt tcgtgcgtct gagagcgtct gagcgcgttt gaggggctat ctggcgactc
      721 atccccgaaa gaacaacaac ggaatcaccg acaacatgtg agaggtggca ccgctcgccg
      781 cagccccagc gaccgaacgg agtgagcgag tgggcgagga agcggaagag aacaggtcga
      841 aaaataagca attacgctct gatttaagcc ctgatttaag ccctcgcgca cgcgttaaaa
      901 taaagatata gatctggcaa accagataca gcaaggccta gcggcgagaa tcgtactcac
      961 ctcgagtact aatcgtactc acctcgagta ctaatcgtac tcacctcggg tactaatcgt
     1021 acttgaggaa aagtatttgc aaagggtaga gaaccgctag ttaggtgatc acatttgcac
     1081 ctgatcagat atagaataaa gaaattatca agtaattgat tttatttgat tttttttaaa
     1141 accgagtgca atagcttatt gcactcacca gtgcagtagc taattgcact cacttgcact
     1201 ggtagtgttg attggctgca tgggttgtgt aattatgttg ctcacttaat gcaaaggatt
     1261 acaccgatga gtgcaacgat tgaaaatgat gaatctctgc catcaacacc agcgaacaat
     1321 cacaacttcg tgcaggtttc acgcgcttat ctgaaagcat ggagaggctt gatccgaaaa
     1381 agtggtttag ctgccgagat ccttttttat cttgttgaaa ggatggggaa aacaacgaat
     1441 gctgttgttt gtagctatgc aactttaact gaggttacag gctatagtcg gcgaagtgtt
     1501 gctacggcca taaaaatcct caaagaggat aattggatac aggtcgttaa aattggaaat
     1561 gctagtgctt attgtgttaa cgagaaggtt atttggcagg ctggaagaaa tcagcgcaaa
     1621 tatgcgattt tcagcgccac agtcgttgcc agcgaatctg agcaggaaag tgattaccat
     1681 ctaaaagcaa aagaaaaact aacttacatt ccgtttgttg aacgtactga aaggatggtt
     1741 atcggggaag aagaattacc cccaccagac caaaaagatt tggatctatc gtagtaccgc
     1801 atgaatgctt taacgcagtc agtaggagct tggaccctcc taccgaccgc taaccaaaac
     1861 aacctggatt ggaggctgta tggctgggtg tattgtgcca gaaagcagcg gcgagaagaa
     1921 ttctttcttc aggcttctgc tcgatttgga aaaccgtggt tattttatcc gtggtgtata
     1981 cgcagaacat caaaacgttc gtgggcgtga tattcatctt aaacttatat cctcaaacgg
     2041 ggatatcaag tatctcgctg ttaaaaaatt ccgtactaat gctcctcacg aagttacaca
     2101 ttacgcaatc gacaaatacc gacgttggct gagacaatat aagcgccagc cagttaaatc
     2161 atgaaaaaat acacgggttc ggcattcgag cccgttttta cacaaaaaag gaaatgttat
     2221 gaagagtctt aagtatatcc tcataggaac tatctctctg acggctgcgg tttgcaacgc
     2281 agaaccagaa gttaaaaccg cagaatggta tatgcagcac catgatgagg tcttatctaa
     2341 atataaagaa tgtaaggccg cacaagataa gtcttatggc ggcactggat attcagatga
     2401 ttgtaaaaac gtattaaaag catccctcag aattaaagac ccggatttta ttaaatcact
     2461 aaataaaatc agacttgaga gtattaatga gattttaaat aagtaaggtg attgtatggc
     2521 tggctttttt gaaaaaatga atgaaaagat tgatagtctg ttgactgcaa catcagaagg
     2581 tatgtcaggt aaatactcag acagtatttc attaattgcc gcttctgctc tggttctgta
     2641 tggagtaatc cttgcgtttt atataatggg agggaaaaag aaaatagagg atgtaggatc
     2701 tacttttttc catgcaatga ttgtttatgt ttttgtaact aatgcaggag ggtatttaaa
     2761 tattttaagt gacggtataa aaggacttaa tgatggtctt gctactgttg gcggtgctgg
     2821 cagctctgca tggagtttgc ttgataaaca atgggaagta acacaacgac tagcggagac
     2881 agtgaaatct ttagatacag actatttttc cataacagga gctattgctt cattaatgat
     2941 atggattggt acaggagtag ttttggttat atcaagtctg gttttattaa tcgctaaaat
     3001 cgctctgaca cttcttttaa ccactgcccc tgtttttatt tattgtctta cattcccatt
     3061 tttacggcag accttcaata actgggtaca aaacgtttta tcgtccattc taacggtaat
     3121 gtttgcctcg ctggtgatta attttggttt agaattttat aacgacatac ttagccagtt
     3181 aacggcaaac gtagataatg caagcctcat gacaaccggc gctatagcgg ttgtttgcgg
     3241 aattgtcgcc ggtgctattg tccttgtgtc cgcaaaactt gcgcaaagta tttctggtgc
     3301 aggcattgat gcagctattc agggtgctgc cgctatgggg ataggcggga gtattttagc
     3361 tgccagcaaa acagcaggaa cagcaaaaaa tattggcacc ggagcttatg aaggggcgag
     3421 cgggaaaaac tggaaggagc gcgaatcaaa aggcgttaca cctgcaatcg catatggtag
     3481 cgggcgtatc ggcagagctg ctattcagaa agtgatagcc agcaattcac gcagcgaacg
     3541 gagcatcccg acagcacgaa attaaacatg acgcaggata ggcatagcca ctacaaatgt
     3601 gcacatttga gtatctacgc cagaaagttt tttaaacttt ctcctgccgc tgcacggggc
     3661 cattttaaaa acaaataacc taagtatgaa aatcatatta gttatgctaa ctgtaatttc
     3721 tacagtaagt atctttctgt tttctatgta tctcacagtt atttttcttc acagaaaagt
     3781 ttcaccgtac atagaccata ttttaaaaaa gtatattttt actgaaaaac catccttaag
     3841 gcgaataatt attatctatt gttcgatatt tattttttta cgttttatag tattaaggag
     3901 cgttcaatga atttaaataa atacttattg gtcattgcta ttgcttattc ctcatctgtt
     3961 ttttctgccg ggattcctgt agttgatact gttggtaacg cacaggaact ggcgcactgg
     4021 acagaaaagc tgaaacaatg gacagagaca gtacagcatt acaaaaacca gttacaggct
     4081 tataaagatc aactggcaac gtctacaggt cttagagata tacaaggttt agtatctcag
     4141 gggaaaagcc ttaagaatga cattatcagc cttcagaaac aaggaatcag cctggatagt
     4201 cttttaacat cgagcagcgc accatcagga actctcgata cactgtataa aaagtttaaa
     4261 gattttgata tctgcgatga aaaacaggca gaatcatata tcaatatttg caaacaggag
     4321 acagtaaaca aagcttgggc gatagaacaa acagcagacg tacaggagaa aataagtgat
     4381 gccctcaacg atatct
//
