LOCUS       NZ_CP116129             5775 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P666 plasmid pDETEC26, complete
            sequence.
ACCESSION   NZ_CP116129
VERSION     NZ_CP116129.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988472
            Assembly: GCF_027944795.1
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  JOURNAL   Unpublished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 02:06:33
            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)                     :: 5,170
            CDSs (total)                      :: 5,049
            Genes (coding)                    :: 4,837
            CDSs (with protein)               :: 4,837
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 212
            CDSs (without protein)            :: 212
            Pseudo Genes (ambiguous residues) :: 0 of 212
            Pseudo Genes (frameshifted)       :: 83 of 212
            Pseudo Genes (incomplete)         :: 145 of 212
            Pseudo Genes (internal stop)      :: 42 of 212
            Pseudo Genes (multiple problems)  :: 52 of 212
            Pseudo Genes (short protein)      :: 3 of 212
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116129.1.
            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-P666"
                     /isolation_source="ICU patient oral swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC26"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-09-10"
     gene            complement(join(5466..5775,1..14))
                     /locus_tag="PIB57_RS25645"
                     /old_locus_tag="PIB57_25650"
     CDS             complement(join(5466..5775,1..14))
                     /locus_tag="PIB57_RS25645"
                     /old_locus_tag="PIB57_25650"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_000955995.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="plasmid mobilization relaxosome protein MobC"
     gene            79..270
                     /locus_tag="PIB57_RS25650"
                     /old_locus_tag="PIB57_25655"
     CDS             79..270
                     /locus_tag="PIB57_RS25650"
                     /old_locus_tag="PIB57_25655"
                     /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            complement(1817..2311)
                     /locus_tag="PIB57_RS25655"
                     /old_locus_tag="PIB57_25660"
     CDS             complement(1817..2311)
                     /locus_tag="PIB57_RS25655"
                     /old_locus_tag="PIB57_25660"
                     /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(2312..2824)
                     /locus_tag="PIB57_RS25660"
                     /old_locus_tag="PIB57_25665"
     CDS             complement(2312..2824)
                     /locus_tag="PIB57_RS25660"
                     /old_locus_tag="PIB57_25665"
                     /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            complement(3195..3359)
                     /locus_tag="PIB57_RS25665"
                     /old_locus_tag="PIB57_25670"
     CDS             complement(3195..3359)
                     /locus_tag="PIB57_RS25665"
                     /old_locus_tag="PIB57_25670"
                     /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            complement(4030..4263)
                     /locus_tag="PIB57_RS25670"
                     /old_locus_tag="PIB57_25675"
     CDS             complement(4030..4263)
                     /locus_tag="PIB57_RS25670"
                     /old_locus_tag="PIB57_25675"
                     /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            complement(4270..4788)
                     /locus_tag="PIB57_RS25675"
                     /old_locus_tag="PIB57_25680"
     CDS             complement(4270..4788)
                     /locus_tag="PIB57_RS25675"
                     /old_locus_tag="PIB57_25680"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /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            complement(<4826..5488)
                     /locus_tag="PIB57_RS25680"
                     /old_locus_tag="PIB57_25685"
                     /pseudo=""
     CDS             complement(<4826..5488)
                     /locus_tag="PIB57_RS25680"
                     /old_locus_tag="PIB57_25685"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     Typing          complement(363..446)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.07e-36"
     Typing          complement(879..1109)
                     /name="rep_cluster_2392"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.81"
                     /coverage="91.0"
                     /evalue="1.42e-85"
     Typing          complement(3927..5476)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.794"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgtatcgtga gcatcctctc gcgtttcatc ggtatcatta ccccatgaac agaaatcccc
       61 ccttacacgg aggcatcagt gactaaacag gaaaaaaccg cccttaacat ggcccgcttt
      121 atcagaagcc agacattaac gctgctggaa aagctcaacg aactggacgc ggatgaacag
      181 gcagacatct gtgaatcgct tcacgaccac gccgatgagc tttaccgcag ctgcctcgca
      241 cgcttcgggg atgacggtga aaacctctga cacatacagc tcccggagac ggtcacagct
      301 tgtctgtgag cggatgccgg gagcagacaa gcccgtcagg gcgcgtcagg ccgttgacct
      361 tgcgggtgtc ggggcgcagc catgacccag tcacgtagcg atagcggagt gtatactggc
      421 ttaaccatgc ggcatcagtg cggattgtat gaaaagtgcg ccatgccggg tgtgaaatgc
      481 cgcacagatg tgtaaggaga aaatgcaact tccgacgctc ttccgcttcc tcgctcactg
      541 actcgctacg ctcggtcgtt cggctgcggc gagcggtatc agctcactca aagacggtaa
      601 tgcggttatc cacagaatca ggggataaca ccaaaagaaa catgtgagca aaaaacaaga
      661 acccagagaa ggccacgccg ctggcgtttt tccataggct ccgcccccct gacgagcatc
      721 acaaaaatcg acgctcaagt cagaggtggc gaaacccgac aggacttaaa gataccaggc
      781 gtttccccct ggcggctccc tcttgcgctc tcctgttccc gtcctgcggc atccgtgttg
      841 tggtggaagc tttacctaaa tcaccacgtc ccgttccgtt tagacagttc gctccaagct
      901 gggctgtatg caagaacccc ccgttcagcc cgactaccac gttgtcccgg taactatcat
      961 cttgagtcca acccggaaca gacacgaaaa atcgccagtg gcggtagcca ttggtaaaca
     1021 ggatgtgcga gagatgtatt caaagttctt gaagtggtgg ccttagtgag gctacactga
     1081 aaggacagat ttggtgacac gtctcgcaca aggctgttac cacggttatt caatctgcca
     1141 ggattaaata accttcgaaa aaccacctgc catggtggtt ttttcgttta caggacaaaa
     1201 gactacgacg agatccaaat gatctcaaga agatctatca atcaaacgcg tcgcgtttca
     1261 agccaagcca taatttcggc gtctttccat ttaaacgaac gaccgatctt gaaaggacga
     1321 gggaagtcgc ttggcgtctc ttcgacaccg agagcgtttt gctgtaattc cctcctaacg
     1381 agcctatttt ccctgcctaa agagttctga gtagcgttag cctgaggaag accgctactt
     1441 agacccaagc cagaaaaatc ctcagacacc ccgcaccaac gatacaaagt ggacttactg
     1501 atgcctaaga gctcacacac ttcattacta tcaagcaact tcatatgaac acctataaaa
     1561 aacaatgaaa acctataaac acttataacc acaaagaggg taaatgacaa cctataaaca
     1621 ccaatgaaca ccaaaaagta cgctagtttg acaacgaaca tgtggaatag gatactaatg
     1681 ttgtcagcac aaaccggaac ctcgagagag gggtgctgat gccgggggtc acaccctccc
     1741 agcctgtgag cgggataacg aaaggccaga ccgaaattct gcaaaaaaca aaggcgcctt
     1801 aggcgctttt tgttttttac acaatcttct ttccctgcag tcgctgttcc agcacatatc
     1861 taaaccgcag gttacgtcct ttatttacag tcccccattc atcaagcgtg taagctgtaa
     1921 caacatgaat acgcaaagaa ttatttctat cttgaggctt tcttatttcc atcaaaatga
     1981 agtcatcatg atggctaaga tggtaatacc gctgcccctg cccctttgaa ataaatgctg
     2041 taatgtattc accgttttct atcgctgtaa gtattctgtg aacgatagtt ttgctgccct
     2101 catagcgttc cctacaaaaa aacctctgtt cctccttaaa tttcatcagc attccggttt
     2161 gtttttcatc agtaaaaaca tgaaaaccaa aactaatttc tatatctaca gaagtaccgt
     2221 ttacatcaac acagcacctc tgagggtgca ggtgccccat aggaaaaaca gtctctcccg
     2281 ttcttatgtc acgccatact gtgcccgcca tttaaccctc ccaagaggct cccacctcaa
     2341 ttacacgctc cgacaaaatg ttataagtct ttcctttagg gataatccct tcatcaagca
     2401 gctttttgac tgcaactaat gggtgaacaa ttaacacgta atgaaattca ccggtgctgc
     2461 cttcacgaca ggatatgaac cccagttctt ttagcttttt cattctccct gcccatgtag
     2521 ttacgcctct ttcactagcg aaccctgatt caaaagccag tgctgcttta tctcttattt
     2581 caatcaaccc ctcatcagaa accctgaacc ataaagccaa gtaggttgtt gataatggtg
     2641 atccttttga cagaccatcc atgagatcgc ctatcaaagg caaataacgt ggaactgttg
     2701 agtacccatc attttcaagt cgatgccaag tatcgatttc gtcgtcttcc cacaattttt
     2761 caatcaaatc ctgacgtcgt tctgactgat ttctcttacc tgcttttctt gctcttgcgg
     2821 acatagtcgt ctcccgtttg tctatggaca ctaatttatt gaaaaaacca ataaaatcaa
     2881 atagttattc attgctggca gcttgttctc atctgaaaaa atagagttaa aaacaagcta
     2941 aatcgcaata aacattacat ttaaaaacat aaaaagtaat atatattaca atgaagttgt
     3001 ttaattatat gattaataat gatttataag aggaaggcgg tgctcattgt gctcgttgtg
     3061 ctcgatggtt ctccctgtgc tccttgtgct ccatggggtt gtagggggca agccagggcg
     3121 gatagagaga aaaataattt agcggtagcg cgtctcagag actaaaaaac ccgctgatgc
     3181 gggttttctt attgttacaa acatcctcgc cgttgtagtt cggcttcaat cgcctcacaa
     3241 gcagcgagta caatctcagt gttatagcac caggctatgc cactgcggtt aatattatcg
     3301 ctaaaggctc gattatgagc caaagtgcgt tttagggtgg tggtatcttt gtccatcatc
     3361 aggatctcca ttcaggttaa cgagcttcat gctcccagat atttactctt gccgttcctg
     3421 aacaggctaa aatagcgaaa aaaagcctat tttcgcttca tcccagagca ccaatattta
     3481 ccataacatc cgttgcccgc accgcagaaa cgcgttcggt gcgatcacgg cagcagacag
     3541 gtaaaaatgg caacaaacca cccgaaaaac tgccgcgatc gcacccggta aattttaacc
     3601 acatgcatag ctatgcagcc atgtgaatca cgcaggaatt gccagccaga gacagctgaa
     3661 acggattttt ttcatgcttt cggaagcgaa gaagacgggg accggagcgg gaaaacagaa
     3721 gttcagggga atgagcgcga tctggcaata gaggcaaaac acagcaacaa aagacacacc
     3781 agaatcgcgc ccgtatgcgt tttaacgcgt tcctgtgttt tcagcaaggt ctgactgaag
     3841 cgcgttcccg gtgcccccga accaaccatt atcccaaaaa atgcaccgga aacgcgctga
     3901 caacatttta gcctgtctct gattaccatc ccagcgaagg gccatccagt gtccgttcct
     3961 gtatttccag ctggcgctca cgctccaggg ataactcatg ttcgcgctcc tgtatcagcc
     4021 gttcgtccct tatctcctgt tctcgctgta taactggctc aagcgttctg tccgctcgct
     4081 caagtgctgc acctgctgac tcaactgcat gacctgctcg ttcagcatcg cgttgtcccg
     4141 ttgcgtaagc gaaaacattt tctgcaattc cacgaaggcg ctctcccatt cgctcagccg
     4201 ctgcatatag tcctgttgca gttgctctaa ggcgttcagc aaatgtcttt ccagctccgt
     4261 cactctgtgt cactccgtca gttgtaccca gtccttctcc tgatagggaa tcaccgttgc
     4321 cgatttcccg tacggaagga ccagaaattt ccttctcccg tcctgcacaa actccacgcc
     4381 ccatgtcttc gcgttcagtt tctgcaatgt ttcttcctgt atcctgattt cttccaggtt
     4441 cgcctgtatc cgcccgccaa gataccagag cgtcccgcca ctcacggtaa acaggaaaag
     4501 gaccatcccc agtaacatca tgcccgtatt ccctgccagc tttaacacgt ccttcctgtg
     4561 ctgcatcatc gcctctttca ccccttcccg gtgttttttc agtgattcct ctgtcgaagc
     4621 tgtgaacagg gctatagcgt ctttgatttt cgtctcgttt gatgtcacag ccttgcttac
     4681 agatttttcg agcttgctga actcgtcgtt cagcattgtc tctgtagatt cggctctctc
     4741 tttcagcttt ttctcgaact ccgcgcccgt ctgtaaaaga ttgctcatag aatgctcctt
     4801 tcagtctgat attcttcccg ccgttcgggt ctgcaatgct gatactgctt cgcgtcaccc
     4861 tgaccacttc aagccctgcc tctgtgagcg cctgaatcac atcctgacgg ccttttatct
     4921 ccccgacatg ataaagagcg tctatcccgc gtgtgacgct ctctgcaagc gcctgtttcg
     4981 tttccggcag gttatcaggg agagtcagta tccggcggtt ctccggggcg ttggggtcat
     5041 gcagcccgta atggtgatta accagcgtct gccaggcatc aattctcggc ctgtctgccc
     5101 ggtcgtagta cggctggagg cgttttccgc tctgtagctc catgttcgga atgacaaaat
     5161 tcagctcaag ccgtcccttg tcctggtgct ccacccacag gatgctgtac tgattttttt
     5221 cgagaccggg catcagtaca cgctcaaagc tcgccatcac cttttcacgt cctcccggcg
     5281 gcagctcctt ctccgcgaac gacagaacac ctgacgtgta tttcttcgca aatggcgtgg
     5341 catcgatgag ttcccggact tcttccggat taccctgaag caccgttgcc ccttcccggt
     5401 tacgctccct tcccagcagg taatcaaccg gaccactgcc accgcctttt cccctggcat
     5461 gaaacttaac tatcatcccg cgctccatgt tccctgacga cctgccgtaa gctgcgcaac
     5521 tctctctcga tggccatcag tgcggccacc acctgaaccc ggtcaccgga agaccactgc
     5581 ccgctgttca ccttcctcgc cgtctgattc agattattcc cgatggcagc cagctggcgc
     5641 agtaacggcg gtgccagtgt cggcagcttc ccggaacggg caaccggctc acccagacag
     5701 acccgccgca tccataccgc cagctgttta ccctcacagc gttccagtaa ccgtgcatgt
     5761 tcatcatcag taacc
//
