LOCUS       NZ_CP116132             4396 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P666 plasmid pDETEC29, complete
            sequence.
ACCESSION   NZ_CP116132
VERSION     NZ_CP116132.1
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 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  JOURNAL   Unpublished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 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
            CP116132.1.
            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-P666"
                     /isolation_source="ICU patient oral swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC29"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-09-10"
     gene            join(4134..4396,1..25)
                     /locus_tag="PIB57_RS25745"
                     /old_locus_tag="PIB57_25750"
     CDS             join(4134..4396,1..25)
                     /locus_tag="PIB57_RS25745"
                     /old_locus_tag="PIB57_25750"
                     /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="EexN family lipoprotein"
                     /protein_id="WP_061089808.1"
                     /translation="MKSLKYILIGTISLTAAVCNAEPEVKTAEWYMQHHDEVLSKYKEC
                     KAAQDKSYGGTGYSDDCKNVLKASLRIKDPDFIKSLNKIRLESINEILNK"
                     /name="EexN family lipoprotein"
     gene            35..1084
                     /locus_tag="PIB57_RS25750"
                     /old_locus_tag="PIB57_25755"
     CDS             35..1084
                     /locus_tag="PIB57_RS25750"
                     /old_locus_tag="PIB57_25755"
                     /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"
     gene            1426..2133
                     /locus_tag="PIB57_RS25755"
                     /old_locus_tag="PIB57_25760"
     CDS             1426..2133
                     /locus_tag="PIB57_RS25755"
                     /old_locus_tag="PIB57_25760"
                     /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            3182..3709
                     /locus_tag="PIB57_RS25760"
                     /old_locus_tag="PIB57_25765"
     CDS             3182..3709
                     /locus_tag="PIB57_RS25760"
                     /old_locus_tag="PIB57_25765"
                     /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            3795..4079
                     /locus_tag="PIB57_RS25765"
                     /old_locus_tag="PIB57_25770"
     CDS             3795..4079
                     /locus_tag="PIB57_RS25765"
                     /old_locus_tag="PIB57_25770"
                     /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"
ORIGIN
        1 tattaatgag attttaaata agtaaggtga ttgtatggct ggcttttttg aaaaaatgaa
       61 tgaaaagatt gatagtctgt tgactgcaac atcagaaggt atgtcaggta aatactcaga
      121 cagtatttca ttaattgccg cttctgctct ggttctgtat ggagtaatcc ttgcgtttta
      181 tataatggga gggaaaaaga aaatagagga tgtaggatct acttttttcc atgcaatgat
      241 tgtttatgtt tttgtaacta atgcaggagg gtatttaaat attttaagtg acggtataaa
      301 aggacttaat gatggtcttg ctactgttgg cggtgctggc agctctgcat ggagtttgct
      361 tgataaacaa tgggaagtaa cacaacgact agcggagaca gtgaaatctt tagatacaga
      421 ctatttttcc ataacaggag ctattgcttc attaatgata tggattggta caggagtagt
      481 tttggttata tcaagtctgg ttttattaat cgctaaaatc gctctgacac ttcttttaac
      541 cactgcccct gtttttattt attgtcttac attcccattt ttacggcaga ccttcaataa
      601 ctgggtacaa aacgttttat cgtccattct aacggtaatg tttgcctcgc tggtgattaa
      661 ttttggttta gaattttata acgacatact tagccagtta acggcaaacg tagataatgc
      721 aagcctcatg acaaccggcg ctatagcggt tgtttgcgga attgtcgccg gtgctattgt
      781 ccttgtgtcc gcaaaacttg cgcaaagtat ttctggtgca ggcattgatg cagctattca
      841 gggtgctgcc gctatgggga taggcgggag tattttagct gccagcaaaa cagcaggaac
      901 agcaaaaaat attggcaccg gagcttatga aggggcgagc gggaaaaact ggaaggagcg
      961 cgaatcaaaa ggcgttacac ctgcaatcgc atatggtagc gggcgtatcg gcagagctgc
     1021 tattcagaaa gtgatagcca gcaattcacg cagcgaacgg agcatcccga cagcacgaaa
     1081 ttaaacatga cgcaggatag gcatagccac tacaaatgtg cacatttgag tatctacgcc
     1141 agaaagtttt ttaaactttc tcctgccgct gcacggggcc attttaaaaa caaataacct
     1201 aagtatgaaa atcatattag ttatgctaac tgtaatttct acagtaagta tctttctgtt
     1261 ttctatgtat ctcacagtta tttttcttca cagaaaagtt tcaccgtaca tagaccatat
     1321 tttaaaaaag tatattttta ctgaaaaacc atccttaagg cgaataatta ttatctattg
     1381 ttcgatattt atttttttac gttttatagt attaaggagc gttcaatgaa tttaaataaa
     1441 tacttattgg tcattgctat tgcttattcc tcatctgttt tttctgccgg gattcctgta
     1501 gttgatactg ttggtaacgc acaggaactg gcgcactgga cagaaaagct gaaacaatgg
     1561 acagagacag tacagcatta caaaaaccag ttacaggctt ataaagatca actggcaacg
     1621 tctacaggtc ttagagatat acaaggttta gtatctcagg ggaaaagcct taagaatgac
     1681 attatcagcc ttcagaaaca aggaatcagc ctggatagtc ttttaacatc gagcagcgca
     1741 ccatcaggaa ctctcgatac actgtataaa aagtttaaag attttgatat ctgcgatgaa
     1801 aaacaggcag aatcatatat caatatttgc aaacaggaga cagtaaacaa agcttgggcg
     1861 atagaacaaa cagcagacgt acaggagaaa ataagtgatg ccctcaacga tatctcagac
     1921 cttaccgatc gcatggcgaa cgccaaagat ataaaagaaa gtcaggactt ggctaatgcg
     1981 atccaggcta aaagtatcca gctaaatatt ctctctcaac agtgggaaat taatatgaaa
     2041 tcatcagaac agcgtgataa acttctagca gagaaacgcc ggaaggcttt cagggaaagt
     2101 cagattacag cacctgtacc gcaatttaat tagcatcggg gttatccgag ttaaaagagc
     2161 gggtggtaat aaatatcttt gaatcaatta tattcttgaa accaactgta ggtcaccggg
     2221 caaacgttgc ggaatggcgt cattttgcgg tgtttgccct atcctgcatc ggagttaaac
     2281 cacgaagatt tttattcccc gttcttcaga acgaccgagc ctccacggtt ccggcagcgc
     2341 cttgagcgca accggaaacc gtctggggag aaccccagac ccccatcgct gtaataccga
     2401 cggtctacga ccacctacca cccgaatagc tgcctgtacc gtgcaaatgg gctttgcagg
     2461 gggctgacgc agttcctggc gacctgaaaa cccctagtta ggggtatcgg cgcgcctgac
     2521 cttctgaaac cctctgtaag cgtttttcgc gccttccatg ccctgacggg catttaaaac
     2581 ctgtttcgtg cgtctgagag cgtctgagcg cgtttgaggg gctatctggc gactcatccc
     2641 cgaaagaaca acaacggaat caccgacaac atgtgagagg tggcaccgct cgccgcagcc
     2701 ccagcgaccg aacggagtga gcgagtgggc gaggaagcgg aagagaacag gtcgaaaaat
     2761 aagcaattac gctctgattt aagccctgat ttaagccctc gcgcacgcgt taaaataaag
     2821 atatagatct ggcaaaccag atacagcaag gcctagcggc gagaatcgta ctcacctcga
     2881 gtactaatcg tactcacctc gagtactaat cgtactcacc tcgggtacta atcgtacttg
     2941 aggaaaagta tttgcaaagg gtagagaacc gctagttagg tgatcacatt tgcacctgat
     3001 cagatataga ataaagaaat tatcaagtaa ttgattttat ttgatttttt ttaaaaccga
     3061 gtgcaatagc ttattgcact caccagtgca gtagctaatt gcactcactt gcactggtag
     3121 tgttgattgg ctgcatgggt tgtgtaatta tgttgctcac ttaatgcaaa ggattacacc
     3181 gatgagtgca acgattgaaa atgatgaatc tctgccatca acaccagcga acaatcacaa
     3241 cttcgtgcag gtttcacgcg cttatctgaa agcatggaga ggcttgatcc gaaaaagtgg
     3301 tttagctgcc gagatccttt tttatcttgt tgaaaggatg gggaaaacaa cgaatgctgt
     3361 tgtttgtagc tatgcaactt taactgaggt tacaggctat agtcggcgaa gtgttgctac
     3421 ggccataaaa atcctcaaag aggataattg gatacaggtc gttaaaattg gaaatgctag
     3481 tgcttattgt gttaacgaga aggttatttg gcaggctgga agaaatcagc gcaaatatgc
     3541 gattttcagc gccacagtcg ttgccagcga atctgagcag gaaagtgatt accatctaaa
     3601 agcaaaagaa aaactaactt acattccgtt tgttgaacgt actgaaagga tggttatcgg
     3661 ggaagaagaa ttacccccac cagaccaaaa agatttggat ctatcgtagt accgcatgaa
     3721 tgctttaacg cagtcagtag gagcttggac cctcctaccg accgctaacc aaaacaacct
     3781 ggattggagg ctgtatggct gggtgtattg tgccagaaag cagcggcgag aagaattctt
     3841 tcttcaggct tctgctcgat ttggaaaacc gtggttattt tatccgtggt gtatacgcag
     3901 aacatcaaaa cgttcgtggg cgtgatattc atcttaaact tatatcctca aacggggata
     3961 tcaagtatct cgctgttaaa aaattccgta ctaatgctcc tcacgaagtt acacattacg
     4021 caatcgacaa ataccgacgt tggctgagac aatataagcg ccagccagtt aaatcatgaa
     4081 aaaatacacg ggttcggcat tcgagcccgt ttttacacaa aaaaggaaat gttatgaaga
     4141 gtcttaagta tatcctcata ggaactatct ctctgacggc tgcggtttgc aacgcagaac
     4201 cagaagttaa aaccgcagaa tggtatatgc agcaccatga tgaggtctta tctaaatata
     4261 aagaatgtaa ggccgcacaa gataagtctt atggcggcac tggatattca gatgattgta
     4321 aaaacgtatt aaaagcatcc ctcagaatta aagacccgga ttttattaaa tcactaaata
     4381 aaatcagact tgagag
//
