LOCUS       NZ_CP109880             4072 bp    DNA     circular CON 22-NOV-2023
DEFINITION  Escherichia coli strain EC488 plasmid pEC488-6, complete sequence.
ACCESSION   NZ_CP109880
VERSION     NZ_CP109880.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30088785
            Assembly: GCF_025946585.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4072)
  AUTHORS   He,X.
  TITLE     Carbapenemase - producing -Escherichia coli EC488
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4072)
  AUTHORS   He,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-AUG-2022) Clinical Laboratory, Sir Run Run Shaw
            Hospital, Zhejiang University School of Medicine, Qingchun,
            Hangzhou, Zhejiang 310000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SPAdes v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/22/2023 18:08:23
            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)                     :: 5,510
            CDSs (total)                      :: 5,391
            Genes (coding)                    :: 5,160
            CDSs (with protein)               :: 5,160
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 231
            CDSs (without protein)            :: 231
            Pseudo Genes (ambiguous residues) :: 0 of 231
            Pseudo Genes (frameshifted)       :: 78 of 231
            Pseudo Genes (incomplete)         :: 160 of 231
            Pseudo Genes (internal stop)      :: 44 of 231
            Pseudo Genes (multiple problems)  :: 46 of 231
            Pseudo Genes (short protein)      :: 5 of 231
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP109880.1.
            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..4072
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EC488"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEC488-6"
                     /geo_loc_name="China"
                     /lat_lon="27 N 110 E"
                     /collection_date="2021-08-04"
                     /collected_by="Xianhong He"
     gene            join(3554..4072,1..1629)
                     /gene="mobQ"
                     /locus_tag="NQ150_RS27355"
                     /old_locus_tag="NQ150_27355"
     CDS             join(3554..4072,1..1629)
                     /gene="mobQ"
                     /locus_tag="NQ150_RS27355"
                     /old_locus_tag="NQ150_27355"
                     /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_264403884.1"
                     /translation="MAIYHLSMKIISRSNGYSAVASAAYRSSSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLKIGLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGESGLAALRSQL
                     LKREEELRRKELEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQHPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGENRQPAMPSPVARRVDFTQGRLPPTLMPVM
                     SSVDRENRQLQLLLVMGVDDSLGGVVRLNGSLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADNHISPAPELMAFHLKTRETPLFAAVNTPEKQPDHLFRSLGFNHTWDEW
                     RREEHARTRVSGKKNDRDCSR"
                     /name="mobQ"
     gene            complement(1884..2591)
                     /locus_tag="NQ150_RS27360"
                     /old_locus_tag="NQ150_27360"
     CDS             complement(1884..2591)
                     /locus_tag="NQ150_RS27360"
                     /old_locus_tag="NQ150_27360"
                     /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"
     gene            complement(3121..3375)
                     /gene="mobC"
                     /locus_tag="NQ150_RS27365"
                     /old_locus_tag="NQ150_27365"
     CDS             complement(3121..3375)
                     /gene="mobC"
                     /locus_tag="NQ150_RS27365"
                     /old_locus_tag="NQ150_27365"
                     /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_000091744.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(3377..3553)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.315"
                     /coverage="100.0"
                     /evalue="5.65e-83"
     Typing          3554..3912
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.667"
                     /coverage="100.0"
                     /evalue="8.58e-169"
     Typing          complement(1885..2591)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.294"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..1626
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="86.347"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3468..4072
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.545"
                     /coverage="100.0"
                     /evalue="1.64e-123"
ORIGIN
        1 agggcactgg cgaacgccgg ttatcaggaa gagatagacc atcgttcata cgagcgacag
       61 gggcttgaga aaacgcctgg tattcacctc ggaaagtctg cctgtgcgat ggaaacacgc
      121 ggtatcgaaa cagaacgcgg cgaacagaat cgtctgatta acaggcttaa cctggaaata
      181 cagatttccc gcaccgaact caggaacagc gggctgacag agcctgcccg ccgtgtggct
      241 gaccttctga agatcggact tcctgacaac gcaacttcgt acacactacg tgacatcatc
      301 gaagcgttgc cgaaggacag taacgcggca tggaaactca ccagtaacgc catgtcgatg
      361 atggcagata tgcaggcgac acgcagacgc tgggaagagc tgaacaccga acgaaaggaa
      421 gcgatgagcc atgctgccag cctgaaaaaa tcatcgccgt tttcgtccgg tttttcccgt
      481 attcccctga tgcaatgggc tgcaccggaa taccgtagtg agcagggaaa aatccagtct
      541 ctgagccagc aaatggaaaa attgcgacag cattaccgga aggtggagaa acaggacatt
      601 cccgcgagtc agacggcatt tgaaaaacag tggcagcagt ggggggaatc cggccttgca
      661 gctctcagat cccagttgct taaacgtgaa gaggaattgc gccggaagga gctggaggat
      721 acagaacgta gtcgcgcgga gcagctcagg aaaaatgaca atgccgttat ggattcaggg
      781 gtgctgagag cagtcgttac gggatatggc gaggctccca tgcctggtaa cggggaaatg
      841 acctgttacc ttctgcttca caaccggaac ggagaatata cgctctgggg gaacgagctg
      901 gagaaatacc gcaccaggat ctttgagagt gttgatttaa tgcgtgacag gagtggttat
      961 atctgtgacc gaagcgaaat cggtcaacat ccaccactgc aacgtgttta ttcctctgcg
     1021 acctttgagc aacttctgac gcaggtttgc cagacatggc cgcaacatac ccgcaatctc
     1081 cgccagccga agacatggcc ggagtctttc tgtcttggag aaaaccgcca gccagccatg
     1141 ccatcaccgg tggcaaggag ggtggatttt acgcagggac gtctgccacc gacgctgatg
     1201 ccggtaatga gttctgtcga ccgggaaaac cgacaacttc agcttttgct ggtcatgggc
     1261 gtggatgact ctctgggcgg tgttgtccgg cttaatggtt cgctgtatcc cgcgtttgct
     1321 gtcccctccg ccgataacag gcatctggtc atcagtgcgc tgaccgataa ggggttacga
     1381 tatgcaggat atggtgttgc cgtaaatcac gatgcagaca accacatttc acctgcaccg
     1441 gaacttatgg cgtttcatct taaaacccgc gagacaccgc tttttgctgc cgtcaacaca
     1501 ccagaaaaac agccggatca tctgttccgt tcactgggct ttaatcacac ctgggatgaa
     1561 tggcggcgcg aggagcatgc acgaacacgt gtctccggga agaagaatga tcgcgactgt
     1621 tcacggtaac tgctgatagt attttgtttt gttttacatc gtgttatgtt ctctgacatt
     1681 catcgtaact ggatgaatgt cagatgcaca cagattgcac aaatccaact ttatcgtttt
     1741 cccgccccca ctaagttggg ggttcttttt tttgaacgcc atagaatcga ttatgaagca
     1801 attttatctc accagtagta ccatcgcata cctctcatgg aaaaaacgca acagagagcg
     1861 ttttaggtgc cttaaaatcg attctagatc gtcatcttga tctgtttgtc ttccttgaag
     1921 cgaaaatgca gggctacaac cgtgcgcccc tttttgatcg tctcaaccgt tacagccagg
     1981 tcgctttttt tgttcagttc gtcaacacag ggttttatta gatccctgtt taacgttttg
     2041 aaatctttat atttaccatc aagcatcagt gatgatttaa aatcatcgag ggcgataata
     2101 cgttccccag tactgcggaa ttgctggaga atctcgtata ttcttatgct gtaacttctt
     2161 gataaattgg agatattttt aataacaact ctggtgaatt gccccttcaa ctgtgtcaga
     2221 taaggcatta ccgcgtcaga aaaagtgatt tgtgctttcc cctctcccct cgcgtactgt
     2281 gcccgatact gaatccagcg gaactcctcg cgcttctcgt cgtccttgag aatgatcgac
     2341 ctgtcccaca aacgatcgat cgcttcctgt agctgaacct cggcattttt ccgccccata
     2401 tcagggaatg aatcaaaata ttccgcagct gtaatggtca ttgtcttttg caattcaggt
     2461 gaagctacgt cagtaccgga gttaagtcgg cttatgcaga gcaataagaa acgctgttct
     2521 tgtaaagtta gcttgtaact ggcctcaacc agcgcattgg acttataggc tatcagaggg
     2581 tttgatgtca ttttaaccac caggccaaag atgaggtgag ataaaaacct atcaccttta
     2641 gcattggtga gcaattatat ttccaccccc catttttctg tgaatattac cttaaatctc
     2701 ctcaccttta ccttaaatta cctcacccaa gaaccttaaa ttatatcacc tttaccttaa
     2761 atttccccac ctatacacgt gtaacgcatt gtttttaatc aggaatttcg accctaaaac
     2821 aagtattaaa aacaagtatt aaaaacaaga tctaaaaact taacggcgag cctgtggata
     2881 acttggagtg ctgaaaataa aaacccaata aaaacaatgc gttgcaaaaa atcaggattg
     2941 gagattccga ataccccccc tccaaccctg tggaaatcca gtattcatgc gggttcagcg
     3001 catatcacct gtcgaaaaac cgtgcgtatg tgctcaacat ggcgactgat tcacttccgc
     3061 ttcctcgccc actcgctcgc taacgctcgg tcgctgggct gcggcgagcg gacgatacaa
     3121 tcactgctct ggcagcgcct ccagctcgtt aatcagcggc agtattcgcg tcacatcagc
     3181 ctgccgtgtc acctctgcct tcaggaactg gagtaaccaa gctcgcaact gcacttcctc
     3241 cggctttctg acctttgcca gcaatgctgc acccacaatg accttctgcg ctgtgtccag
     3301 gctccggctc ttcgccttca ggcgctgtaa tctcgcctca gcatcagcaa tcttctgttc
     3361 gagcgttctg ctcatgatgt aactccatgc gcaatgaaaa atcgcatttt agcgcgtcac
     3421 tggtagttta aaaactgagc tggcataatg cacggcaaat cacgaagtgc gcacttatac
     3481 aatttccact ccgtttcaat tgtgtgcgcc ctgcggggct gaaagaaaac tgcaaaaagg
     3541 cattacggca gaaatggcaa tttatcatct cagtatgaaa atcatctcca gaagcaacgg
     3601 ctacagcgcc gttgcttctg ctgcctatcg ttctagttca ctaatgcttg atgagcgtac
     3661 cggactgact cacgactaca cccgcaaaag cggtgtggct gaggctgtga ttctgacccc
     3721 cgcgacagcc cctgcctggt gtacgaatcg tgccgaactc tggaatgccg ttgagaaggc
     3781 cgaacgccgg aagaactcac aacttgcgcg ggaaattgaa ctcgccatcc cccacgaact
     3841 gccgcaggat gccgcacggg aaaccgttct cgcctttgtc agagaaaact ttgtcagtca
     3901 gggcatgatt gctgatgtgg cgttccatca catggataaa acaaatcccc atgcgcacat
     3961 catgctgacc acgagggcta tcggacctgc tgggttcagc ggaaaggtca gggactggaa
     4021 cgaccggaca catgccgaga cgtggcgggc atcatgggct gaccatgcaa ac
//
