LOCUS       NZ_CP116121             4060 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P793 plasmid pDETEC18, complete
            sequence.
ACCESSION   NZ_CP116121
VERSION     NZ_CP116121.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988477
            Assembly: GCF_027944775.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4060)
  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  JOURNAL   Unpublished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 4060)
  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 01:55:41
            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)                     :: 5,351
            CDSs (total)                      :: 5,234
            Genes (coding)                    :: 4,997
            CDSs (with protein)               :: 4,997
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 237
            CDSs (without protein)            :: 237
            Pseudo Genes (ambiguous residues) :: 0 of 237
            Pseudo Genes (frameshifted)       :: 84 of 237
            Pseudo Genes (incomplete)         :: 166 of 237
            Pseudo Genes (internal stop)      :: 38 of 237
            Pseudo Genes (multiple problems)  :: 48 of 237
            Pseudo Genes (short protein)      :: 4 of 237
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116121.1.
            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..4060
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-P793"
                     /isolation_source="ICU patient rectal swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC18"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-09-12"
     gene            complement(join(2359..4060,1..446))
                     /gene="mobQ"
                     /locus_tag="PIC92_RS26665"
                     /old_locus_tag="PIC92_26670"
     CDS             complement(join(2359..4060,1..446))
                     /gene="mobQ"
                     /locus_tag="PIC92_RS26665"
                     /old_locus_tag="PIC92_26670"
                     /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_171874286.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGKSGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSPAARKVDFMQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVIRLNGTLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWDEW
                     RREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            625..879
                     /gene="mobC"
                     /locus_tag="PIC92_RS26670"
                     /old_locus_tag="PIC92_26675"
     CDS             625..879
                     /gene="mobC"
                     /locus_tag="PIC92_RS26670"
                     /old_locus_tag="PIC92_26675"
                     /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"
     gene            1412..2113
                     /locus_tag="PIC92_RS26675"
                     /old_locus_tag="PIC92_26680"
     CDS             1412..2113
                     /locus_tag="PIC92_RS26675"
                     /old_locus_tag="PIC92_26680"
                     /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"
     Typing          complement(89..447)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          448..624
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          1413..2113
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2363..4059)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.316"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ctgaacccag caggtccgat agccctcgtg gtcagcatga tgtgcgcatg gggatttgtt
       61 ttatccatgt gatggaacgc cacatcagca atcatgccct gactgacaaa gttttctctg
      121 acaaaggcga gaacggtttc ccgtgcggca tcctgcggca gttcgtgggg gatggcgagt
      181 tcaatttccc gcgcaagttg tgagttcttc cggcgttcgg ccttctcaac ggcattccag
      241 agttcggcac ggttcgtaca ccaggcaggg gcggtggcgg gggtcagaat cacagcctca
      301 gccacaccgc ttttgcgggt gtagtcgtga gtcagtccgg tacgctcatc aagcatcagt
      361 gaaccggaac gataggcagc ggaagctacg gcgctgtagc cgctgcttct ggagataatt
      421 ttcatgctga gatgataaat cgccatttct gccgtaatgc ctttttgtag ttttctttca
      481 gccccgcagg gcgcacacaa tcgaaacgga gtggagattg tataagtgcg cacttcgtga
      541 tttgccgtgc attatgccag ctcagttttt aaactaccag tgacgcgcta aaatgcgatt
      601 tttcatcgcg cacggagtta catcatgagc agaacgctcg aacagaagat tgctgatgct
      661 gaggccagat tacagcgcct gaaggcgaag agccggagcc tggacacagc gcagaaggtt
      721 gttgtgggtg ctgcattgct ggcaaaggtc agaaagccgg aggaggtgca gttgcgtgcc
      781 tggttactcc agttcctgaa ggcagaggtg acacgacagg ctgatgtgac gcgcatactg
      841 ccgctgatta acgagctgga ggcgctgcca gaacagtgat tgtatcgtcc gctcgccgca
      901 gccccagcga ccgagcgtta gcgagcgagt gggcgaggaa gcggaagtga atcagtcgcc
      961 aggttgagca catacgcacg gtttttcggc aggtgatatg cgctgaaccc gcatgaatac
     1021 tgggtttcca cagggttgga gggggtgtat tcgaaacttg caattctgct ttattgcaac
     1081 gcattgtttt tattggtttt ttgttttcag caccccaagt tatccacagg ctcgccgtta
     1141 agtttttaag atcttatttt tagatctttt ttttaaaacc tttttaggtc ttgtaacacc
     1201 atgattttaa agatgttctg gcaagataag tggagctttt gggggtgaaa ggtggagctt
     1261 ttgggggtga aaggtggagc ttttgggggt gaaaggtgga gcttttgggg gtgtaatcca
     1321 cagaaaaagg gggttgcaaa aaaaaaactt ccacccatat gataagtggc gtacagtaaa
     1381 aaaacgccac caatagcaac gagcaagcga aatgtcagat ctgatagctt acaaatcaaa
     1441 cgcccttatc gaggcaagct acaagctcac tttgcaggaa cagcgcttcc tgctggtctg
     1501 tatcagccgc ctaaaatccg gagaagattc cccttcgccg gatgaacaaa aaaccatgac
     1561 catcacggct gcagagtttc atgatgcctt tcctgacatg ggacggcagc acgctgaagc
     1621 taggctcaag gaagcgatag atcgcctctg ggacaggtca gtaatcatca agaacgagga
     1681 aaaacgagaa gagttccgct gggtgcagta ccgggcgcag tatttcaaag gtgaggcgaa
     1741 agtagatatc accttctccg atgccatcat gccgtatctg acacagctca aggggcagtt
     1801 tacgcgggta gtcgtgaaga acgtctccag cctttccagc acctacagca tccgcattta
     1861 cgagctgctc cagcagttcc gcagcaccgg tgacagaacg atagctatcg atgatttccg
     1921 aaccatgctt gccgttgaag ataaatatca acaattcaaa gacttgaata agatgataat
     1981 caagccagcc atcgccgaac tgaacgaaaa aagcgatctg gttgtaactg ttgagacgat
     2041 caaaaagggg cgcacggttg tagccctgca ttttcgcttc aaggaagaca aacagatcaa
     2101 gatgacgatc taaaatcgat tttaaggcac ctaaaacgct ccctgctgcg ttttttttgt
     2161 gttagtagtg cgaaggtact attgaagtga aaaattgcgt caaaagcgct ctaatgcagc
     2221 gaaaaaagaa cccccatttt ttgggggcgg aaaaacaaaa ctatgcttgc attatgtgtg
     2281 tgcttcttgc attcatccct gtcgatgaac atcgaagaac ataacacgat gttaaacaaa
     2341 acaaaatatt gttcacattc actgtgacca accgcgatca tgtctcctct cggtggcgtg
     2401 tgttcgtgca tcttcctcgc gccgccattc gtcccaggta cgattaaaac ccagcgagcg
     2461 gaacagatga tccggctgtt tttctggtgt gttgacggca gcaaaaagcg gtgcctcacg
     2521 ggttttcaga tgaaactgca tcagttctgg tgcaggtgat atgtggctgt ctgcatcgtg
     2581 atttacggca acaccatacc ctgcataccg taacccctta tcggtcagcg cactgatgac
     2641 cagatgcctg ttatcggctg agggaacggc aaacgcggga tacagcgtac cattaagccg
     2701 gataacaccg cccagagagt catccacgcc catgaccagc aaaagctgaa gctggcgggt
     2761 ttcccggtcg acagaactca tgaccggcat cagcgtcggt ggcagacgtc cctgcataaa
     2821 atccaccttc cttgccgctg gtgatggcat ggctggctgg cggtcttctc caagacagaa
     2881 agactccggc catgtcttcg gctggcggag attgcgggta tgttgcggcc atgtctggca
     2941 aacctgcgtc agcagttgct caaaggttgc agaggaataa acacgttgca gtggcggacg
     3001 ttggccgatt tcgcttcggt cacagatata accactcctg tcacgcatta aatcaacact
     3061 ctcaaagatt ctggtgcggt atttctccag ctcgttcccc cagagcgtat attctccgtt
     3121 ccggttgtga agcagaaggt aacaggtcat ttccccgtta ccaggcatgg gagcctcgcc
     3181 ataccccgta acgactgctc tcagcacccc tgaatccata acggcattgt catttttcct
     3241 gagctgctcc gcgcgactac gttcagtatc ttcctgttcc ttccggcgca attcctcttc
     3301 acgtttaagc aactgggctc tgagagctgc aaggccggat ttcccccact gctgccactg
     3361 tttttcaaat gccatctgac tcgcgggaat gtcctgtttc tccaccttcc ggtaatgctg
     3421 tcgtaatttt tccatttgct ggctcagaga ctggattttt ccctgctcac tacggtattc
     3481 cggtgccgcc cattgcatca ggggaatacg ggaaaaaccg gacgaaaacg gcgatgattt
     3541 tttcaggctg gcagcatggc tcatcgcttc ctttcgttcg gtgttcagct cttcccagcg
     3601 tctgcgcgtc gcctgcatat ctgccatcat cgacatggca ttactggtga gtttccatgc
     3661 cgagttactg tccttcggca acgcttcgat aatgtcacgt agtgtgtacg aagttgcgtt
     3721 gtcaggaagc ccgatattca gaaggtcagc cacacggcgg gcaggctctg tcagccctcc
     3781 gttcctgagt tcggtgcggg aaatctgtat ttccaggtta agcctgttaa tcagacgatt
     3841 ctgttcgccg cgttctgttt cgataccgcg tgtttccatc gcacaggcag actttccgag
     3901 gtgaatacca ggcgttttct caagcccctg tcgctcgtat gaacgatggt ctatctcttc
     3961 ctgataaccg gcgttcgcca gtgccctgtt tgcatggtca gcccatgatg cccgccacgt
     4021 ctcggcatgt gtccggtcgt tccagtccct gacctttccg
//
