LOCUS       NZ_CP116138             5775 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P649 plasmid pDETEC26, complete
            sequence.
ACCESSION   NZ_CP116138
VERSION     NZ_CP116138.1
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 5775)
  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  JOURNAL   Unpublished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 5775)
  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
            CP116138.1.
            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..5775
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-P649"
                     /isolation_source="ICU patient oral swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC26"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-09-05"
     gene            664..1182
                     /locus_tag="PIB66_RS24720"
                     /old_locus_tag="PIB66_24720"
     CDS             664..1182
                     /locus_tag="PIB66_RS24720"
                     /old_locus_tag="PIB66_24720"
                     /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="MbeB family mobilization protein"
                     /protein_id="WP_000067503.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVLFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     EKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            1189..1422
                     /locus_tag="PIB66_RS24725"
                     /old_locus_tag="PIB66_24725"
     CDS             1189..1422
                     /locus_tag="PIB66_RS24725"
                     /old_locus_tag="PIB66_24725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137441.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2093..2257
                     /locus_tag="PIB66_RS24730"
                     /old_locus_tag="PIB66_24730"
     CDS             2093..2257
                     /locus_tag="PIB66_RS24730"
                     /old_locus_tag="PIB66_24730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000968835.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000968835.1"
                     /translation="MMDKDTTTLKRTLAHNRAFSDNINRSGIAWCYNTEIVLAACEAIE
                     AELQRRGCL"
                     /name="hypothetical protein"
     gene            2628..3140
                     /locus_tag="PIB66_RS24735"
                     /old_locus_tag="PIB66_24735"
     CDS             2628..3140
                     /locus_tag="PIB66_RS24735"
                     /old_locus_tag="PIB66_24735"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001445155.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001276096.1"
                     /translation="MSARARKAGKRNQSERRQDLIEKLWEDDEIDTWHRLENDGYSTVP
                     RYLPLIGDLMDGLSKGSPLSTTYLALWFRVSDEGLIEIRDKAALAFESGFASERGVTTW
                     AGRMKKLKELGFISCREGSTGEFHYVLIVHPLVAVKKLLDEGIIPKGKTYNILSERVIE
                     VGASWEG"
                     /name="hypothetical protein"
     gene            3141..3635
                     /locus_tag="PIB66_RS24740"
                     /old_locus_tag="PIB66_24740"
     CDS             3141..3635
                     /locus_tag="PIB66_RS24740"
                     /old_locus_tag="PIB66_24740"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000929317.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000929317.1"
                     /translation="MAGTVWRDIRTGETVFPMGHLHPQRCCVDVNGTSVDIEISFGFHV
                     FTDEKQTGMLMKFKEEQRFFCRERYEGSKTIVHRILTAIENGEYITAFISKGQGQRYYH
                     LSHHDDFILMEIRKPQDRNNSLRIHVVTAYTLDEWGTVNKGRNLRFRYVLEQRLQGKKI
                     V"
                     /name="hypothetical protein"
     gene            complement(5182..5373)
                     /locus_tag="PIB66_RS24745"
                     /old_locus_tag="PIB66_24745"
     CDS             complement(5182..5373)
                     /locus_tag="PIB66_RS24745"
                     /old_locus_tag="PIB66_24745"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            5423..5761
                     /locus_tag="PIB66_RS24750"
                     /old_locus_tag="PIB66_24750"
     CDS             5423..5761
                     /locus_tag="PIB66_RS24750"
                     /old_locus_tag="PIB66_24750"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_271286765.1"
                     /translation="MKRERMLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSG
                     KLPTLAPPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVR
                     EHGARDDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          5007..5090
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.07e-36"
     Typing          4344..4565
                     /name="rep_cluster_2392"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.825"
                     /coverage="87.0"
                     /evalue="1.42e-85"
     Typing          4..1526
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.65"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          5409..5758
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.308"
                     /coverage="99.0"
                     /evalue="1.08e-63"
ORIGIN
        1 gaaaaggcgg tggcagtggt ccggttgatt acctgctggg aagggagcgt aaccgggaag
       61 gggcaacggt gcttcagggt aatccggaag aagtccggga actcatcgat gccacgccat
      121 ttgcgaagaa atacacgtca ggtgttctgt cgttcgcgga gaaggagctg ccgccgggag
      181 gacgtgaaaa ggtgatggcg agctttgagc gtgtactgat gcccggtctc gaaaaaaatc
      241 agtacagcat cctgtgggtg gagcaccagg acaagggacg gcttgagctg aattttgtca
      301 ttccgaacat ggagctacag agcggaaaac gcctccagcc gtactacgac cgggcagaca
      361 ggccgagaat tgatgcctgg cagacgctgg ttaatcacca ttacgggctg catgacccca
      421 acgccccgga gaaccgccgg atactgactc tccctgataa cctgccggaa acgaaacagg
      481 cgcttgcaga gagcgtcaca cgcgggatag acgctcttta tcatgtcggg gagataaaag
      541 gccgtcagga tgtgattcag gcgctcacag aggcagggct tgaagtggtc agggtgacgc
      601 gaagcagtat cagcattgca gacccgaacg gcgggaagaa tatcagactg aaaggagcat
      661 tctatgagca atcttttaca gacgggcgcg gagttcgaga aaaagctgaa agagagagcc
      721 gaatctacag agacaatgct gaacgacgag ttcagcaagc tcgaaaaatc tgtaagcaag
      781 gctgtgacat caaacgagac gaaaatcaaa gacgctatag ccctgttcac agcttcgaca
      841 gaggaatcac tgaaaaaaca ccgggaaggg gtgaaagagg cgatgatgca gcacaggaag
      901 gacgtgttaa agctggcagg gaatacgggc atgatgttac tggggatggt ccttttcctg
      961 tttaccgtga gtggcgggac gctctggtat cttggcgggc ggatacaggc gaacctggaa
     1021 gaaatcagga tacaggaaga aacattgcag aaactgaacg cgaagacatg gggcgtggag
     1081 tttgtgcagg acgggagaag gaaatttctg gtccttccgt acgggaaatc ggcaacggtg
     1141 attccctatc aggagaagga ctgggtacaa ctgacggagt gacacagagt gacggagctg
     1201 gaaagacatt tgctgaacgc cttagagcaa ctgcaacagg actatatgca gcggctgagc
     1261 gaatgggaga gcgccttcgt ggaattgcag aaaatgtttt cgcttacgca acgggacaac
     1321 gcgatgctga acgagcaggt catgcagttg agtcagcagg tgcagcactt gagcgagcgg
     1381 acagaacgct tgagccagtt atacagcgag aacaggagat aagggacgaa cggctgatac
     1441 aggagcgcga acatgagtta tccctggagc gtgagcgcca gctggaaata caggaacgga
     1501 cactggatgg cccttcgctg ggatggtaat cagagacagg ctaaaatgtt gtcagcgcgt
     1561 ttccggtgca ttttttggga taatggttgg ttcgggggca ccgggaacgc gcttcagtca
     1621 gaccttgctg aaaacacagg aacgcgttaa aacgcatacg ggcgcgattc tggtgtgtct
     1681 tttgttgctg tgttttgcct ctattgccag atcgcgctca ttcccctgaa cttctgtttt
     1741 cccgctccgg tccccgtctt cttcgcttcc gaaagcatga aaaaaatccg tttcagctgt
     1801 ctctggctgg caattcctgc gtgattcaca tggctgcata gctatgcatg tggttaaaat
     1861 ttaccgggtg cgatcgcggc agtttttcgg gtggtttgtt gccattttta cctgtctgct
     1921 gccgtgatcg caccgaacgc gtttctgcgg tgcgggcaac ggatgttatg gtaaatattg
     1981 gtgctctggg atgaagcgaa aataggcttt ttttcgctat tttagcctgt tcaggaacgg
     2041 caagagtaaa tatctgggag catgaagctc gttaacctga atggagatcc tgatgatgga
     2101 caaagatacc accaccctaa aacgcacttt ggctcataat cgagccttta gcgataatat
     2161 taaccgcagt ggcatagcct ggtgctataa cactgagatt gtactcgctg cttgtgaggc
     2221 gattgaagcc gaactacaac ggcgaggatg tttgtaacaa taagaaaacc cgcatcagcg
     2281 ggttttttag tctctgagac gcgctaccgc taaattattt ttctctctat ccgccctggc
     2341 ttgcccccta caaccccatg gagcacaagg agcacaggga gaaccatcga gcacaacgag
     2401 cacaatgagc accgccttcc tcttataaat cattattaat catataatta aacaacttca
     2461 ttgtaatata tattactttt tatgttttta aatgtaatgt ttattgcgat ttagcttgtt
     2521 tttaactcta ttttttcaga tgagaacaag ctgccagcaa tgaataacta tttgatttta
     2581 ttggtttttt caataaatta gtgtccatag acaaacggga gacgactatg tccgcaagag
     2641 caagaaaagc aggtaagaga aatcagtcag aacgacgtca ggatttgatt gaaaaattgt
     2701 gggaagacga cgaaatcgat acttggcatc gacttgaaaa tgatgggtac tcaacagttc
     2761 cacgttattt gcctttgata ggcgatctca tggatggtct gtcaaaagga tcaccattat
     2821 caacaaccta cttggcttta tggttcaggg tttctgatga ggggttgatt gaaataagag
     2881 ataaagcagc actggctttt gaatcagggt tcgctagtga aagaggcgta actacatggg
     2941 cagggagaat gaaaaagcta aaagaactgg ggttcatatc ctgtcgtgaa ggcagcaccg
     3001 gtgaatttca ttacgtgtta attgttcacc cattagttgc agtcaaaaag ctgcttgatg
     3061 aagggattat ccctaaagga aagacttata acattttgtc ggagcgtgta attgaggtgg
     3121 gagcctcttg ggagggttaa atggcgggca cagtatggcg tgacataaga acgggagaga
     3181 ctgtttttcc tatggggcac ctgcaccctc agaggtgctg tgttgatgta aacggtactt
     3241 ctgtagatat agaaattagt tttggttttc atgtttttac tgatgaaaaa caaaccggaa
     3301 tgctgatgaa atttaaggag gaacagaggt ttttttgtag ggaacgctat gagggcagca
     3361 aaactatcgt tcacagaata cttacagcga tagaaaacgg tgaatacatt acagcattta
     3421 tttcaaaggg gcaggggcag cggtattacc atcttagcca tcatgatgac ttcattttga
     3481 tggaaataag aaagcctcaa gatagaaata attctttgcg tattcatgtt gttacagctt
     3541 acacgcttga tgaatggggg actgtaaata aaggacgtaa cctgcggttt agatatgtgc
     3601 tggaacagcg actgcaggga aagaagattg tgtaaaaaac aaaaagcgcc taaggcgcct
     3661 ttgttttttg cagaatttcg gtctggcctt tcgttatccc gctcacaggc tgggagggtg
     3721 tgacccccgg catcagcacc cctctctcga ggttccggtt tgtgctgaca acattagtat
     3781 cctattccac atgttcgttg tcaaactagc gtactttttg gtgttcattg gtgtttatag
     3841 gttgtcattt accctctttg tggttataag tgtttatagg ttttcattgt tttttatagg
     3901 tgttcatatg aagttgcttg atagtaatga agtgtgtgag ctcttaggca tcagtaagtc
     3961 cactttgtat cgttggtgcg gggtgtctga ggatttttct ggcttgggtc taagtagcgg
     4021 tcttcctcag gctaacgcta ctcagaactc tttaggcagg gaaaataggc tcgttaggag
     4081 ggaattacag caaaacgctc tcggtgtcga agagacgcca agcgacttcc ctcgtccttt
     4141 caagatcggt cgttcgttta aatggaaaga cgccgaaatt atggcttggc ttgaaacgcg
     4201 acgcgtttga ttgatagatc ttcttgagat catttggatc tcgtcgtagt cttttgtcct
     4261 gtaaacgaaa aaaccaccat ggcaggtggt ttttcgaagg ttatttaatc ctggcagatt
     4321 gaataaccgt ggtaacagcc ttgtgcgaga cgtgtcacca aatctgtcct ttcagtgtag
     4381 cctcactaag gccaccactt caagaacttt gaatacatct ctcgcacatc ctgtttacca
     4441 atggctaccg ccactggcga tttttcgtgt ctgttccggg ttggactcaa gatgatagtt
     4501 accgggacaa cgtggtagtc gggctgaacg gggggttctt gcatacagcc cagcttggag
     4561 cgaactgtct aaacggaacg ggacgtggtg atttaggtaa agcttccacc acaacacgga
     4621 tgccgcagga cgggaacagg agagcgcaag agggagccgc cagggggaaa cgcctggtat
     4681 ctttaagtcc tgtcgggttt cgccacctct gacttgagcg tcgatttttg tgatgctcgt
     4741 caggggggcg gagcctatgg aaaaacgcca gcggcgtggc cttctctggg ttcttgtttt
     4801 ttgctcacat gtttcttttg gtgttatccc ctgattctgt ggataaccgc attaccgtct
     4861 ttgagtgagc tgataccgct cgccgcagcc gaacgaccga gcgtagcgag tcagtgagcg
     4921 aggaagcgga agagcgtcgg aagttgcatt ttctccttac acatctgtgc ggcatttcac
     4981 acccggcatg gcgcactttt catacaatcc gcactgatgc cgcatggtta agccagtata
     5041 cactccgcta tcgctacgtg actgggtcat ggctgcgccc cgacacccgc aaggtcaacg
     5101 gcctgacgcg ccctgacggg cttgtctgct cccggcatcc gctcacagac aagctgtgac
     5161 cgtctccggg agctgtatgt gtcagaggtt ttcaccgtca tccccgaagc gtgcgaggca
     5221 gctgcggtaa agctcatcgg cgtggtcgtg aagcgattca cagatgtctg cctgttcatc
     5281 cgcgtccagt tcgttgagct tttccagcag cgttaatgtc tggcttctga taaagcgggc
     5341 catgttaagg gcggtttttt cctgtttagt cactgatgcc tccgtgtaag gggggatttc
     5401 tgttcatggg gtaatgatac cgatgaaacg cgagaggatg ctcacgatac gggttactga
     5461 tgatgaacat gcacggttac tggaacgctg tgagggtaaa cagctggcgg tatggatgcg
     5521 gcgggtctgt ctgggtgagc cggttgcccg ttccgggaag ctgccgacac tggcaccgcc
     5581 gttactgcgc cagctggctg ccatcgggaa taatctgaat cagacggcga ggaaggtgaa
     5641 cagcgggcag tggtcttccg gtgaccgggt tcaggtggtg gccgcactga tggccatcga
     5701 gagagagttg cgcagcttac ggcaggtcgt cagggaacat ggagcgcggg atgatagtta
     5761 agtttcatgc caggg
//
