LOCUS       NZ_CP116163             4073 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P351 plasmid pDETEC8, complete
            sequence.
ACCESSION   NZ_CP116163
VERSION     NZ_CP116163.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988454
            Assembly: GCF_027944875.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4073)
  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  JOURNAL   Unpublished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 4073)
  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 01:52:08
            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)                     :: 4,895
            CDSs (total)                      :: 4,775
            Genes (coding)                    :: 4,533
            CDSs (with protein)               :: 4,533
            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)              :: 242
            CDSs (without protein)            :: 242
            Pseudo Genes (ambiguous residues) :: 0 of 242
            Pseudo Genes (frameshifted)       :: 84 of 242
            Pseudo Genes (incomplete)         :: 155 of 242
            Pseudo Genes (internal stop)      :: 54 of 242
            Pseudo Genes (multiple problems)  :: 50 of 242
            Pseudo Genes (short protein)      :: 4 of 242
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116163.1.
            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..4073
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-P351"
                     /isolation_source="ICU patient rectal swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC8"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-08-13"
     gene            350..1051
                     /locus_tag="PIC26_RS24375"
                     /old_locus_tag="PIC26_24370"
     CDS             350..1051
                     /locus_tag="PIC26_RS24375"
                     /old_locus_tag="PIC26_24370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001281395.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVDITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1309..3456)
                     /gene="mobQ"
                     /locus_tag="PIC26_RS24380"
                     /old_locus_tag="PIC26_24375"
     CDS             complement(1309..3456)
                     /gene="mobQ"
                     /locus_tag="PIC26_RS24380"
                     /old_locus_tag="PIC26_24375"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /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_001029354.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSPAARKVDFMQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVIRLNGTLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWEEW
                     QREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            3635..3889
                     /gene="mobC"
                     /locus_tag="PIC26_RS24385"
                     /old_locus_tag="PIC26_24380"
     CDS             3635..3889
                     /gene="mobC"
                     /locus_tag="PIC26_RS24385"
                     /old_locus_tag="PIC26_24380"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091746.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(3099..3457)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3458..3634
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          351..1051
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1313..3543)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.989"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttctgcttta ttgcaacgca ttgtttttat tggttttttg ttttcagcac cccaagttat
       61 ccacaggctc gccgttaagt ttttaagatc ttatttttag atcttttttt ttaaaacctt
      121 tttaggtctt gtaacaccat gattttaaag atgttctggc aagataagtg gagcttttgg
      181 gggtgaaagg tggagctttt gggggtgaaa ggtggagctt ttgggggtga aaggtggagc
      241 ttttgggggt gtaatccaca gaaaaagggg gttgcaaaaa aaaaacttcc acccatatga
      301 taagtggcgt acagtaaaaa aacgccacca atagcaacga gcaagcgaaa tgtcagatct
      361 gatagcttac aaatcaaacg cccttatcga ggcaagctac aagctcactt tgcaggaaca
      421 gcgcttcctg ctggtctgta tcagccgcct aaaatccgga gaagattccc cttcgccgga
      481 tgaacaaaaa accatgacca tcacggctgc agagtttcat gatgcctttc ctgacatggg
      541 acggcagcac gctgaagcta ggctcaagga agcgatagat cgcctctggg acaggtcagt
      601 aatcatcaag aacgaggaaa aacgagaaga gttccgctgg gtgcagtacc gggcgcagta
      661 tttcaaaggt gaggcgaaag tagatatcac cttctccgat gccatcatgc cgtatctgac
      721 acagctcaag gggcagttta cgcgggtagt cgtgaagaac gtctccagcc tttccagcac
      781 ctacagcatc cgcatttacg agctgctcca gcagttccgc agcaccggtg acagaacgat
      841 agctatcgat gatttccgaa ccatgcttgc cgttgaagat aaatatcaac aattcaaaga
      901 cttgaataag atgataatca agccagccat cgccgaactg aacgaaaaaa gcgatctggt
      961 tgtaactgtt gagacgatca aaaaggggcg cacggttgta gccctgcatt ttcgcttcaa
     1021 ggaagacaaa cagatcaaga tgacgatcta aaatcgattt taaggcacct aaaacgctcc
     1081 ctgctgcgtt ttttttgtgt tagtagtgcg aaggtactat tgaagtgaaa aattgcgtca
     1141 aaaacgctct gatgcagcga aaaaagaccc cccaattttt gggggcggaa aaacaaaact
     1201 atgcttgcgt tatgtgagtg tgcttcttgc attcatccct gtcgatgaac atcgaagaac
     1261 atcgacgaac ataacacgat gttaaacaaa acaaaatatt gttcacattc actgtgacca
     1321 accgcgatca tgtctcctct cggtggtgtg tgttcgtgca tcttcctcgc gctgccattc
     1381 ctcccaggta cgattaaaac ccagcgagcg gaacagatga tccggctgtt tttctggtgt
     1441 gttgacggca gcaaaaagcg gtgcctcacg ggttttcaga tgaaactgca tcagttctgg
     1501 tgcaggtgat atgtggctgt ctgcatcgtg atttacggca acaccatacc ctgcataccg
     1561 taacccctta tcggtcagcg cactgatgac cagatgcctg ttatcggctg agggaacggc
     1621 aaacgcggga tacagcgtac cattaagccg gataacaccg cccagagagt catccacgcc
     1681 catgaccagc aaaagctgaa gctggcgggt ttcccggtcg acagaactca tgaccggcat
     1741 cagcgtcggt ggcagacgtc cctgcataaa atccaccttc cttgccgctg gtgatggcat
     1801 ggctggctgg cggtcttctc caagacagaa agactccggc catgtcttcg gctggcggag
     1861 attgcgggta tgttgcggcc atgtctggca aacctgcgtc agcagttgct caaaggttgc
     1921 agaggaataa acacgttgca gtggcggacg ttggccgatt tcgcttcggt cacagatata
     1981 accactcctg tcacgcatta aatcaacact ctcaaagatt ctggtgcggt atttctccag
     2041 ctcgttcccc cagagcgtat attctccgtt ccggttgtga agcagaaggt aacaggtcat
     2101 ttccccgtta ccaggcatgg gagcctcgcc ataccccgta acgactgctc tcagcacccc
     2161 tgaatccata acggcattgt catttttcct gagctgctcc gcgcgactac gttcagtatc
     2221 ttcctgttcc ttccggcgca attcctcttc acgtttaagc aactgggctc tgagagctgc
     2281 aaggccggat tccccccact gctgccactg tttttcaaat gccatctgac tcgcgggaat
     2341 gtcctgtttc tccaccttcc ggtaatgctg tcgtaatttt tccatttgct ggctcagaga
     2401 ctggattttt ccctgctcac tacggtattc cggtgccgcc cattgcatca ggggaatacg
     2461 ggaaaaaccg gacgaaaacg gcgatgattt tttcaggctg gcagcatggc tcatcgcttc
     2521 ctttcgttcg gtgttcagct cttcccagcg tctgcgcgtc gcctgcatat ctgccatcat
     2581 cgacatggca ttactggtga gtttccatgc cgagttactg tccttcggca acgcttcgat
     2641 aatgtcacgt agtgtgtacg aagttgcgtt gtcaggaagc ccgatattca gaaggtcagc
     2701 cacacggcgg gcaggctctg tcagccctcc gttcctgagt tcggtgcggg aaatctgtat
     2761 ttccaggtta agcctgttaa tcagacgatt ctgttcgccg cgttctgttt cgataccgcg
     2821 tgtttccatc gcacaggcag actttccgag gtgaatacca ggcgttttct caagcccctg
     2881 tcgctcgtat gaacgatggt ctatctcttc ctgataaccg gcgttcgcca gtgccctgtt
     2941 tgcatggtca gcccatgatg cccgccacgt ctcggcatgt gtccggtcgt tccagtccct
     3001 gacctttccg ctgaacccag caggtccgat agccctcgtg gtcagcatga tgtgcgcatg
     3061 gggatttgtt ttatccatgt gatggaacgc cacatcagca atcatgccct gactgacaaa
     3121 gttttctctg acaaaggcga gaacggtttc ccgtgcggca tcctgcggca gttcgtgggg
     3181 gatggcgagt tcaatttccc gcgcaagttg tgagttcttc cggcgttcgg ccttctcaac
     3241 ggcattccag agttcggcac ggttcgtaca ccaggcaggg gcggtggcgg gggtcagaat
     3301 cacagcctca gccacaccgc ttttgcgggt gtagtcgtga gtcagtccgg tacgctcatc
     3361 aagcatcagt gaaccggaac gataggcagc ggaagctacg gcgctgtagc cgctgcttct
     3421 ggagataatt ttcatgctga gatgataaat cgccatttct gccgtaatgc ctttttgtag
     3481 ttttctttca gccccgcagg gcgcacacaa tcgaaacgga gtggagattg tataagtgcg
     3541 cacttcgtga tttgccgtgc attatgccag ctcagttttt aaactaccag tgacgcgcta
     3601 aaatgcgatt tttcatcgcg cacggagtta catcatgagc agaacgctcg aacagaagat
     3661 tgctgatgct gaggcgagat tacagcgcct gaaggcgaag agccggagcc tggacacagc
     3721 gcagaaggtt gttgtgggtg ctgcattgct ggcaaaggtc agaaagccgg aggaggtgca
     3781 gttgcgtgcc tggttactcc agttcctgaa ggcagaggtg acacgacagg ctgatgtgac
     3841 gcgcatactg ccgctgatta acgagctgga ggcgctgcca gaacagtgat tgtatcgtcc
     3901 gctcgccgca gccccagcga ccgagcgtta gcgagcgagt gggcgaggaa gcggaagtga
     3961 atcagtcgcc aggttgagca catacgcacg gtttttcggc aggtgatatg cgctgaaccc
     4021 gcatgaatac tgggtttcca cagggttgga gggggtgtat tcgaaacttg caa
//
