LOCUS       NZ_CP116150             4087 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P622 plasmid pDETEC58, complete
            sequence.
ACCESSION   NZ_CP116150
VERSION     NZ_CP116150.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988467
            Assembly: GCF_027944835.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4087)
  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  JOURNAL   Unpublished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 4087)
  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 01:51:10
            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)                     :: 5,207
            CDSs (total)                      :: 5,096
            Genes (coding)                    :: 4,860
            CDSs (with protein)               :: 4,860
            Genes (RNA)                       :: 111
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 236
            CDSs (without protein)            :: 236
            Pseudo Genes (ambiguous residues) :: 0 of 236
            Pseudo Genes (frameshifted)       :: 76 of 236
            Pseudo Genes (incomplete)         :: 179 of 236
            Pseudo Genes (internal stop)      :: 36 of 236
            Pseudo Genes (multiple problems)  :: 49 of 236
            Pseudo Genes (short protein)      :: 3 of 236
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116150.1.
            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..4087
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-P622"
                     /isolation_source="ICU patient rectal swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC58"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-09-03"
     gene            complement(join(1999..4087,1..71))
                     /gene="mobQ"
                     /locus_tag="PIB88_RS25990"
                     /old_locus_tag="PIB88_25990"
     CDS             complement(join(1999..4087,1..71))
                     /gene="mobQ"
                     /locus_tag="PIB88_RS25990"
                     /old_locus_tag="PIB88_25990"
                     /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_023142279.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTEYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLATL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            250..504
                     /gene="mobC"
                     /locus_tag="PIB88_RS25995"
                     /old_locus_tag="PIB88_25995"
     CDS             250..504
                     /gene="mobC"
                     /locus_tag="PIB88_RS25995"
                     /old_locus_tag="PIB88_25995"
                     /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"
     gene            1036..1743
                     /locus_tag="PIB88_RS26000"
                     /old_locus_tag="PIB88_26000"
     CDS             1036..1743
                     /locus_tag="PIB88_RS26000"
                     /old_locus_tag="PIB88_26000"
                     /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_001296720.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          73..249
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          complement(3801..4087)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.83e-149"
     Typing          1037..1743
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2003..4086)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.712"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gcagcagaag caacggcgct gtagccgctg tttctggaga tgattttcat gctgagatga
       61 taaatcgcca tttctgccgt aatgcctttt tgtggttttc tttcagcccc gcagggcgca
      121 cacaatcgaa acggagtgga gattgtataa gtgcgcactt cgtgattttc cgtgcattat
      181 gccagctcag tttttaaact accagtgacg cgctaaaatg cgatttttca tcgcgcacgg
      241 agttacatca tgagcagaac actcgaacag aagattgctg atgctgaggc cagattacag
      301 cgcctgaagg cgaagagcag gagtctggac acagcgcaga aggtcattgt gggtgcagca
      361 ttgctggcaa aggtcagaaa gccggaggag gtgcagttgc gtgcctggtt actccagttc
      421 ctgaaggcag aggtgacacg acaggctgat gtgacgcgca tactgccgct gattaacgag
      481 ctggaagcgc tgccaggaca gtgattgtat cgtccgctcg ccgcagtccc agcgaccgag
      541 cgttagcgag cgagtgggcg aggaagcgga agtgaatccg tcgcctgatt gagcacatac
      601 gcacggtttt tcgggaggtg atatgcgctg aacccgcatg aatactggat ttccacaggg
      661 ttggaggggg tgtattcgga acttgcaatt ctgctttttt gcaacgcatt gtttttattg
      721 gttttttgtt ttcagcactc caagttatcc acaggctcgt cgttaagttt ttagatcttg
      781 tttttaagat cttgttttta atacttgttt tagcgccaaa attccttata gaaaacaaaa
      841 tgttacaacg ctataggtga tatgatttaa ggtaaaggtg atataattta aggtgcttgg
      901 gtgaggtaat ttaaggtaaa ggtgaggaga tttaaggtaa tattcacagg aaaatggggg
      961 gtgaaaatat aattgctcac caatgctaaa ggtgataggt ttttatttca cctcattttt
     1021 ggcctggtgg ttaaaatgac atcaaaccct ctgatagcct ataagtccaa tgcgctggtt
     1081 gaggccagtt acaagctaac tttacaagaa cagcgtttct tattgctctg cataagccga
     1141 cttaactccg gtactgacgt agcttcacct gaattgcaaa agacaatgac cattacagct
     1201 gcggaatatt ttgattcatt ccctgatatg gggcggaaaa atgccgaggt tcagctacag
     1261 gaagcgatcg atcgtttgtg ggacaggtcg atcattctca aggacgacga gaagcgcgag
     1321 gagttccgct ggattcagta tcgggcacag tacgcgaggg gagaggggaa agcacaaatc
     1381 actttttctg acgcggtaat gccttatctg acacagttga aggggcaatt caccagagtc
     1441 gtcattaaaa atatttctaa tttatcaaga agttacagca taagaatata cgaaattctc
     1501 cagcaattcc gcagtactgg ggaacgtatt atcgccctcg atgattttaa atcatcactg
     1561 atgcttgatg gtaaatataa agatttcaaa acgttaaaca gggatctaat aaaaccctgt
     1621 gttgacgaac tgaacaaaaa aagcgacctg gctgtaacgg ttgagacgat caaaaagggg
     1681 cgcacggttg tagccctgca ttttcgcttc aaggaagaca aacagatcaa gatgacgatc
     1741 tagaatcgat tttaaggcac ctaaaacgct ccctgctgcg ttttttttgt gttagtagtg
     1801 cgaaggtact attgaagtga aaaattgcgt caaaagcgct ctaatgcagc gaaaaaagaa
     1861 cccccatttt tcgggggcgg aaaaacaaaa ctatgcttgc attatgtgtg tgcttcttgc
     1921 attcatccct gtcgatgaac atcgaagaac atcgacgaac ataacacgat gttaaacaaa
     1981 acaaaatatt gttcacattc actgtgacca accgcgatca tgtctcctct cggtggcgtg
     2041 tgttcgtgca tcttcctcgc gccgccattc gtcccaggta cgattaaaac ccagcgagcg
     2101 gaacagatga tccggctgtt tttctggtgt gttgacggca gcaaaaagcg gtgcctcacg
     2161 ggttttcaga tgaaactcca taagttccgg cgcaggtgat atgtggctgt ctgcatcgtg
     2221 atttacggca acaccatacc ctgcataccg taacccctta tcggtcagtg cactgatgac
     2281 cagctggctg ttatcggctg agggaacggc aaacgcggga tacagcgtac cattaagccg
     2341 gacaacaccg cccagagagt catccacgcc catgaccagc aaaagctgaa gctggcgggt
     2401 ttcccggtcg acagaactca ttaccggcat cagcgtcgct agcagacgtc cctgcgtaaa
     2461 atccaccttc cttgctgcca gtgatggcat ggctggctgg cggtcttctc caagacagaa
     2521 agactccggc catgtcttcg gctggcggag attgcgggta tattgcggcc atgtctggca
     2581 aacctgcgtc agaagttgct caaaggtcgc agaggaataa acacgttgca gtggtggatg
     2641 ttgaccgatt tcgcttcggt cacagatata accactcctg tcacgcatta aatcaacacg
     2701 ctcaaagatt ctggtgcggt atttctccag ctcgttcccc cagagcgtgt attctccgtt
     2761 ccggttgtga agcagaaggt aacaggtcat ttccccgtta ccaggcatgg gggcctcgcc
     2821 atactccgta acgactgcgc tcagtacccc tgaatccata acggcattgt catttttcct
     2881 gagctgttcc gctcgtcgct ccgcgcgact acgttctgta tcctcctgct ccttccggcg
     2941 caattcctct tcacgtttaa gcaactggac tctgagagct gcaaggccgg atgcccccca
     3001 ctgctgccac tgtttttcaa atgccgtctg actcgcggga atgtcctgtt tctccacctt
     3061 ccggtaatgc tgtcgcaatt tttccatttg ctggctcagc gactggattt ttccctgttc
     3121 gctacggtat tccggtgccg cccattgcat caggggaata cgggaaaaac cggacgaaaa
     3181 cggcgatgat tttttcaggc tggcagcatg gctcatcgct tcctttcgtt cggtgttcag
     3241 ctcttcccag cgtctgcgcg tcgcctgcat atctgccatc atcgacatgg cattactggt
     3301 gagtttccat gccgcattac tgtccttcgg caacgcttcg atgatgtcac gtagtgtgta
     3361 cgaagttgcg ttgtcaggaa gcacgatatt cagaaggtca gccacacggc gggcaggctc
     3421 tgtcagcccg ctgtttctga gttcggtacg ggaaatctgt atttccaggt taagtctgtt
     3481 aatcagacga ttctgttcgc cgcgttctgt ttcgataccg cgtgtttcca tcgcacaggc
     3541 agactttccg aggtgaatac caggcgtttt ctcaagcccc tgtcgctcgt atgaacgatg
     3601 gtctatctct tcctgataac cggcgttcgc cagtgccctg ttcgcatggt cagcccatga
     3661 tgcacgccac gtctcggcat gtgtccggtc gttccagtcc ctgacctttc caccgaatcc
     3721 agcaggtccg acagctctcg tggtcagcat gatgtgcgca tggggatttg ttttatccat
     3781 gtgatggaac gccacatcag caatcatgcc ctgactgaca aagttttctc tgacaaaggc
     3841 gagaacggtt tcccgtgcgg catcctgcgg tagttcgcgg gggatggcga gttcaatttc
     3901 ccgcgcaagt tgtgagttct tccggcgttc ggccttctca acggcattcc agagttcggc
     3961 acggttcgta caccaggcag gggctgtcgc gggagtcaga atcacagctt cagccacacc
     4021 gcttttgcgg gtgtagtcgt gagtcagtcc ggtacgctca tcaagcatca gtgaaccgga
     4081 acgatag
//
