LOCUS       NZ_CP116084             4059 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-S586 plasmid pDETEC54, complete
            sequence.
ACCESSION   NZ_CP116084
VERSION     NZ_CP116084.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988516
            Assembly: GCF_027944615.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4059)
  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  JOURNAL   Unpublished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 4059)
  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 01:50:10
            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)                     :: 5,261
            CDSs (total)                      :: 5,142
            Genes (coding)                    :: 4,937
            CDSs (with protein)               :: 4,937
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 205
            CDSs (without protein)            :: 205
            Pseudo Genes (ambiguous residues) :: 0 of 205
            Pseudo Genes (frameshifted)       :: 65 of 205
            Pseudo Genes (incomplete)         :: 145 of 205
            Pseudo Genes (internal stop)      :: 38 of 205
            Pseudo Genes (multiple problems)  :: 43 of 205
            Pseudo Genes (short protein)      :: 5 of 205
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116084.1.
            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..4059
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-S586"
                     /isolation_source="ICU staff rectal swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC54"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-09-01"
     gene            complement(join(2844..4059,1..932))
                     /gene="mobQ"
                     /locus_tag="PIC49_RS26220"
                     /old_locus_tag="PIC49_26225"
     CDS             complement(join(2844..4059,1..932))
                     /gene="mobQ"
                     /locus_tag="PIC49_RS26220"
                     /old_locus_tag="PIC49_26225"
                     /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_050963243.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTMRAVGPAGFGGKVRDWNDRTHAEA
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRSSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHATSLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAEQLGKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQLPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSVDNSQLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWEEW
                     QLEEDARTHATVRRHDRGWSQ"
                     /name="mobQ"
     gene            1110..1364
                     /gene="mobC"
                     /locus_tag="PIC49_RS26225"
                     /old_locus_tag="PIC49_26230"
     CDS             1110..1364
                     /gene="mobC"
                     /locus_tag="PIC49_RS26225"
                     /old_locus_tag="PIC49_26230"
                     /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            1897..2598
                     /locus_tag="PIC49_RS26230"
                     /old_locus_tag="PIC49_26235"
     CDS             1897..2598
                     /locus_tag="PIC49_RS26230"
                     /old_locus_tag="PIC49_26235"
                     /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_001281397.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGADAESPKL
                     QKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEARAQITFSDAVMPYLTQLQGQFTRVVIKNISRLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCIDELNKKSDLAVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(575..933)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.611"
                     /coverage="100.0"
                     /evalue="1.82e-180"
     Typing          934..1109
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.82"
                     /coverage="100.0"
                     /evalue="4.47e-69"
     Typing          1899..2597
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.857"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(4..1019)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.935"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2848..4058)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.569"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cgttcggtgt tcagctcttc ccagcgtctg cgcgtcgcct gcatatctgc catcatcgac
       61 atggcattac tggtgagttt ccatgccgca ttactgtcct tcggcaacgc ttcgatgatg
      121 tcacgtagtg tgtacgaagt tgcgttgtca ggaagcacga tattcagaag gtcagccaca
      181 cggcgggcag gctctgtcag cccgctgctc ctgagttcag tgcgggaaat ctgtatttcc
      241 aggttaagcc tgttaatcag acgattctgt tcgccgcgtt ctgtttcgat accgcgtgtt
      301 tccatcgcac aggcagactt tccgaggtga ataccaggcg ttttctcaag cccctgtcgc
      361 tcgtatgaac gatggtctat ctcttcctga taaccggcgt tcgccagtgc cctgtttgca
      421 tggtcagccc atgatgcccg ccacgcctcg gcgtgtgtcc ggtcgttcca gtccctgacc
      481 tttccgccga acccagcagg tccgacagcc ctcatggtca gcatgatgtg cgcatgggga
      541 tttgttttat ccatgtgatg gaacgccaca tcagcaatca tgccctgact gacaaagttt
      601 tctctgacaa aggcgagaac ggtttcccgt gcggcatcct gcggcagttc gcgggggatg
      661 gcgagttcaa tttcccgcgc aagttgtgag ttcttccggc gttcggcctt ctcaacggca
      721 ttccagagtt cggcacggtt cgtacaccag gcaggggctg tcgcgggggt cagaatcaca
      781 gcttcagcca caccgctttt gcgggtgtag tcatgagtca gtcctgtacg ctcatcaagc
      841 atcagtgaac cggaacgata ggcggcagaa gcaacggcgc tgtagccgct gtttctggag
      901 atgattttca tgctgagatg ataaatcgcc atttctgccg taatgccttt ttgtcgtgtt
      961 ctttcagccc cgcagggcgc acacaatcga aacggagtga agattgtata agtgcgcact
     1021 tcgtggtttt ttcgcattat gccagttcag tttttaaact gccagtgacg cgctaaaatg
     1081 cgatttttca tcacgcacgg agttacatca tgagcagaac gctcgaacag aagattgctg
     1141 acgctgaggc gagattacag cgcctgaagg cgaagagccg gagcctggac acagcgcaga
     1201 aggtcgttgt gggtgcagca ttgctggcaa aggtcagaaa gccggaggag gtgcagttgc
     1261 gtgcctggtt actccagttc ctgaaggcag aggtgacacg acaggctgat gtgacgcgaa
     1321 tactgccgct gattaacgag ctggaggcac tgccagaaca gtgattgtat cgtccgctcg
     1381 ccgcagcccc agcgaccgag cgttagcgag cgagtgggcg aggaagtgga agtgaatccg
     1441 tcgcctgatt gagcacatac gcacggtttt tcggcaggtg atatgcgctg aacccgcatg
     1501 aatactggat ttccacaggg ttggaggggg agtattcgga acttgcaatt ctgctttttt
     1561 gcaaggcatt gtttttattg tttttttgtt tttagcaccc caagttatcc acaggctcgt
     1621 cgttaagttt ttagatcttg tttttaagat cttgttttta atacttgttt taggggcaaa
     1681 attccttata aaaaacaaaa tgttacaacg ctataggtaa tataatttaa ggtaaaggta
     1741 atatgattta aggtgtttag gtaatataat ttaaggtaaa ggtaatatga tttaaggtaa
     1801 tatccacagg aaaagggata ttaaaaaaaa aaggcattgc ctttcgttga gggtatgttt
     1861 atcttttatt cattaccttt tggggaggga tgctctgtgt cggatctaat tgcctataaa
     1921 tccaatgcgc tggttgaagc cagttataaa ttgaccctac aggaacagcg atttttgtta
     1981 ctttgcatcg gtcgattgaa gtctggggct gatgcagaat ctccaaaatt gcaaaagaca
     2041 atgaccatta cagctgcgga atatttcgat tcattccctg acatggggcg gaaaaatgcc
     2101 gaggttcagt tacaggaagc aattgatcgt ttgtgggaca ggtcaatcat tctcaaggat
     2161 gacgagaaac gtgaggagtt ccgctggatc cagtatcggg cacagtacgc taaaggcgag
     2221 gccagagcac aaataacatt ttctgacgca gtaatgcctt atttgacaca actacaaggg
     2281 caatttacta gagttgtaat caagaatata tctagattat caagaagtta cagtataagg
     2341 atatacgaac tcctccagca gttccgcagt actggcgaac gtattatcgc tctcgatgat
     2401 tttcgctcaa tgcttgatat agagcataaa tatcaaacat ataaatcact taaccagcaa
     2461 ttattaagac cctgcattga cgaactgaac aaaaaaagcg acctggctgt aacggttgag
     2521 acgatcaaaa aggggcgcac ggttgtagcc ctgcattttc gcttcaagga agacaaacag
     2581 atcaagatga cgatctagga tcgattttaa ggcatctaaa acgttctctg gtgtgctttt
     2641 ttagtgtcag gtatgcgatg gtactgcttt ggcaataaat tgcgtcagaa ttgatttgag
     2701 aggtcaaaaa agaaccccca attttttggg ggcgggaaaa cgataaagtt gatttgtgtt
     2761 atgtgtgctt cttgcattca tccctgtcga tgaacatcga cgaacataac acgatgttaa
     2821 acaaaacaaa atattgttca cattcactgt gaccaaccgc gatcatgtct cctcacggtg
     2881 gcgtgtgttc gtgcatcttc ctcgagctgc cattcctccc aggtacgatt aaaacccagc
     2941 gagcggaaca gatgatccgg ctgtttttct ggtgtgttga cggcagcaaa aagcggtgcc
     3001 tcacgggttt tcagatgaaa ctccataagt tccggcgcag gtgatatgtg gctgtctgca
     3061 tcgtgattta cggcaacacc ataccctgca taccgtaacc ccttatcggt cagtgcactg
     3121 atgaccagct ggctgttatc gactgaggga acggcaaacg cgggatacag cgtaccatta
     3181 agccggacaa caccgcccag agagtcatcc acgcccatga ccagcaaaag ctgaagctgg
     3241 cgggtttccc ggtcgacaga actcattacc ggcatcagcg tcggtggcag acgtccctgc
     3301 gtaaaatcca ccttccttgc tgccagtgat ggcatggctg gctggcggtc ttctccaaga
     3361 cagaaagact ccggccatgt cttcggctgg cggagattgc gggtatgttg cggccatgtc
     3421 tggcaaacct gcgtcagcag ttgctcaaag gtcgcagagg aataaacacg ttgcagtggc
     3481 ggaagttggc cgatttcgct tcggtcacag atataaccac tcctgtcacg cattaaatca
     3541 acacgctcaa agattctggt gcggtatttc tccagctcgt taccccagag cgtatattct
     3601 ccgttccggt tgtgaagcag aaggtaacag gtcatttccc cgttaccagg catgggggcc
     3661 tcgccatacc ccgtaacgac tgcgctcagt acccctgaat ccataacggc attgtcattt
     3721 ttcccgagct gctccgcgcg actacgttct gtatcctcct gctccttccg gcgcaattcc
     3781 tcttcacgtt taagcaattg gactctgaga gctgcaaggc cggatgcccc ccactgctgc
     3841 cactgttttt caaatgccgt ctgactcgcg ggaatgtcct gtttctccac cttccggtaa
     3901 tgctgtcgca atttttccat ttgctggctc agcgactgga tttttccctg ctcactacgg
     3961 tattccggtg ccgcccattg catcagggga atacgggaaa aaccggacga aaacggcgat
     4021 gattttttca ggctggtagc atggctcatc gcttccttt
//
