LOCUS       NZ_CP116142             4069 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P649 plasmid pDETEC30, complete
            sequence.
ACCESSION   NZ_CP116142
VERSION     NZ_CP116142.1
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 4069)
  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  JOURNAL   Unpublished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 4069)
  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
            CP116142.1.
            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..4069
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-P649"
                     /isolation_source="ICU patient oral swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC30"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-09-05"
     gene            join(3588..4069,1..1678)
                     /gene="mobQ"
                     /locus_tag="PIB66_RS24840"
                     /old_locus_tag="PIB66_24840"
     CDS             join(3588..4069,1..1678)
                     /gene="mobQ"
                     /locus_tag="PIB66_RS24840"
                     /old_locus_tag="PIB66_24840"
                     /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_029976510.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAEHRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(1916..2623)
                     /locus_tag="PIB66_RS24845"
                     /old_locus_tag="PIB66_24845"
     CDS             complement(1916..2623)
                     /locus_tag="PIB66_RS24845"
                     /old_locus_tag="PIB66_24845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /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_024623342.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIQPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(3155..3409)
                     /gene="mobC"
                     /locus_tag="PIB66_RS24850"
                     /old_locus_tag="PIB66_24850"
     CDS             complement(3155..3409)
                     /gene="mobC"
                     /locus_tag="PIB66_RS24850"
                     /old_locus_tag="PIB66_24850"
                     /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_000091745.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     Typing          complement(3411..3587)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          3588..3946
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.444"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1917..2623)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.859"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3..1675
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3502..4067
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.942"
                     /coverage="99.0"
                     /evalue="1.9600000000000001e-118"
ORIGIN
        1 cgagacgtgg cgtgcatcat gggctgacca tgcgaacagg gcactggcga acgccggtta
       61 tcaggaagag atagaccatc gttcatacga gcgacagggg cttgagaaaa cgcctggtat
      121 tcacctcgga aagtctgcct gtgcgatgga aacacgcggt atcgaaacag aacgcggcga
      181 acagaatcgt ctgattaaca gacttaacct ggaaatacag atttcccgta ccgaactcag
      241 aaacagcggg ctgacagagc ctgcccgccg tgtggctgac cttctgaata tcgtgcttcc
      301 tgacaacgca acttcgtaca cactacgtga catcatcgaa gcgttgccga aggacagtaa
      361 tgcggcatgg aaactcacca gtaatgccat gtcgatgatg gcagatatgc aggcgacgcg
      421 cagacgctgg gaagagctga acaccgaacg aaaggaagcg atgagccatg ctgccagcct
      481 gaaaaaatca tcgccgtttt cgtccggttt ttcccgtatt cccctgatgc aatgggcggc
      541 accggaatac cgtagcgaac agggaaaaat ccagtcgctg agccagcaaa tggaaaaatt
      601 gcgacagcat taccggaagg tggagaaaca ggacattccc gcgagtcaga cggcatttga
      661 aaaacagtgg cagcagtggg gggcatccgg ccttgcagct ctcagagtcc agttgcttaa
      721 acgtgaagag gaattgcgcc ggaaggagca ggaggataca gaacgtagtc gcgcggagcg
      781 acgagcggaa cagctcagga aaaatgacaa tgccgttatg gattcagggg tactgagcgc
      841 agtcgttacg gggtatggcg aggcccccat gcctggtaac ggggaaatga cctgttacct
      901 tctgcttcac aaccggaacg gagaatacac gctctggggg aacgagctgg agaaataccg
      961 caccagaatc tttgagcgtg ttgatttaat gcgtgacagg agtggttata tctgtgaccg
     1021 aagcgaaatc ggtcaacatc caccactgca acgtgtttat tcctctgcga cctttgagca
     1081 acttctgacg caggtttgcc agacatggcc gcaatatacc cgcaatctcc gccagccgaa
     1141 gacatggccg gagtctttct gtcttggaga agaccgccag ccagccatgc catcactggc
     1201 agcaaggaag gtggatttta cgcagggacg tctgctaccg acgctgatgc cggtaatgag
     1261 ttctgtcgac cgggaaaccc gccagcttca gcttttgctg gtcatgggcg tggatgactc
     1321 tctgggcggt gttgtccggc ttaatggtac gctgtatccc gcgtttgccg ttccctcagc
     1381 cgataacagc cagctggtca tcagtgcact gaccgataag gggttacggt atgcagggta
     1441 tggtgttgcc gtaaatcacg atgcagacag ccacatatca cctgcgccgg aacttatgga
     1501 gtttcatctg aaaacccgtg aggcaccgct ttttgctgcc gtcaacacac cagaaaaaca
     1561 gccggatcat ctgttccgct cgctgggttt taatcgtacc tgggacgaat ggcggcgcga
     1621 ggaagatgca cgaacacacg ccaccgagag gagacatgat cgcggttggt cacagtgaat
     1681 gtgaacaata ttttgttttg tttaacatcg tgttatgttc gtcgatgttc atcgacaggg
     1741 atgaatgcaa gaagcacaca cagcatagtt ttgtttttcc gcccccaaaa attgggggtt
     1801 cttttttcgc tgcattagag cgcttttgac gcaatttttc acttcaatag taccttcgca
     1861 ctactaacac aaaaaaaacg cagcagggag cgttttaggt gccttaaaat cgattctaga
     1921 tcgtcatctt gatctgtttg tcttccttga agcgaaaatg cagggctaca accgtgcgcc
     1981 cctttttgat cgtctcaacc gttacagcca ggtcgctttt tttgttcagt tcgtcaacac
     2041 agggttgtat tagatccctg tttaacgttt tgaaatcttt atatttacca tcaagcatca
     2101 gtgatgattt aaaatcatcg agggcgataa tacgttcccc agtactgcgg aattgctgga
     2161 gaatttcgta tattcttatg ctgtaacttc ttgataaatt agaaatattt ttaatgacga
     2221 ctctggtgaa ttgccccttc aactgtgtca gataaggcat taccgcgtca gaaaaagtga
     2281 tttgtgcttt cccctctccc ctcgcgtact gtgcccgata ctgaatccag cggaactcct
     2341 cgcgcttctc gtcgtccttg agaatgatcg acctgtccca caaacgatcg atcgcttcct
     2401 gtagctgaac ctcggcattt ttccgcccca tatcagggaa tgaatcaaaa tattccgcag
     2461 ctgtaatggt cattgtcttt tgcaattcag gtgaagctac gtcagtaccg gagttaagtc
     2521 ggcttatgca gagcaataag aaacgctgtt cttgtaaagt tagcttgtaa ctggcctcaa
     2581 ccagcgcatt ggacttatag gctatcagag ggtttgatgt cattttaacc accaggccaa
     2641 aaatgaggtg aaataaaaac ctatcacctt tagcattggt gagcaattat attttcaccc
     2701 cccattttcc tgtgaatatt accttaaatc tcctcacctt taccttaaat tacctcaccc
     2761 aagcacctta aattatatca cctttacctt aaatcatatc acctatagcg ttgtaacatt
     2821 ttgttttcta taaggaattt tggcgctaaa acaagtatta aaaacaagat cttaaaaaca
     2881 agatctaaaa acttaacgac gagcctgtgg ataacttgga gtgctgaaaa caaaaaacca
     2941 ataaaaacaa tgcgttgcaa aaaagcagaa ttgcaagttc cgaatacacc ccctccaacc
     3001 ctgtggaaat ccagtattca tgcgggttca gcgcatatca cctcccgaaa aaccgtgcgt
     3061 atgtgctcaa tcaggcgacg gattcacttc cgcttcctcg cccactcgct cgctaacgct
     3121 cggtcgctgg gactgcggcg agcggacgat acaatcactg tcctggcagc gcttccagct
     3181 cgttaatcag cggcagtatg cgcgtcacat cagcctgtcg tgtcacctct gccttcagga
     3241 actggagtaa ccaggcacgc aactgcacct cctccggctt tctgaccttt gccagcaatg
     3301 ctgcacccac aatgaccttc tgcgctgtgt ccagactcct gctcttcgcc ttcaggcgct
     3361 gtaatctggc ctcagcatca gcaatcttct gttcgagtgt tctgctcatg atgtaactcc
     3421 gtgcgcgatg aaaaatcgca ttttagcgcg tcactggtag tttaaaaact gagctggcat
     3481 aatgcacgga aaatcacgaa gtgcgcactt atacaatctc cactccgttt cgattgtgtg
     3541 cgccctgcgg ggctgaaaga aaaccacaaa aaggcattac ggcagaaatg gcgatttatc
     3601 atctcagcat gaaaatcatc tccagaaaca gcggctacag cgccgttgct tctgctgcct
     3661 atcgttccgg ttcactgatg cttgatgagc gtaccggact gactcacgac tacacccgca
     3721 aaagcggtgt ggctgaagct gtgattctga ctcccgcgac agcccctgcc tggtgtacga
     3781 accgtgccga actctggaat gccgttgaga aggccgaaca ccggaagaac tcacaacttg
     3841 cgcgggaaat tgaactcgcc atcccccgcg aactgccgca ggatgccgca cgggaaaccg
     3901 ttctcgcctt tgtcagagaa aactttgtca gtcagggcat gattgctgat gtggcgttcc
     3961 atcacatgga taaaacaaat ccccatgcgc acatcatgct gaccacgaga gctgtcggac
     4021 ctgctggatt cggtggaaag gtcagggact ggaacgaccg gacacatgc
//
