LOCUS       NZ_CP109882             3373 bp    DNA     circular CON 22-NOV-2023
DEFINITION  Escherichia coli strain EC488 plasmid pEC488-8, complete sequence.
ACCESSION   NZ_CP109882
VERSION     NZ_CP109882.1
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 3373)
  AUTHORS   He,X.
  TITLE     Carbapenemase - producing -Escherichia coli EC488
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3373)
  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
            CP109882.1.
            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..3373
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EC488"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEC488-8"
                     /geo_loc_name="China"
                     /lat_lon="27 N 110 E"
                     /collection_date="2021-08-04"
                     /collected_by="Xianhong He"
     gene            join(3280..3373,1..233)
                     /locus_tag="NQ150_RS27385"
                     /old_locus_tag="NQ150_27385"
     CDS             join(3280..3373,1..233)
                     /locus_tag="NQ150_RS27385"
                     /old_locus_tag="NQ150_27385"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000776994.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_161400506.1"
                     /translation="MKLSAPVAELSRVRSPSSQLPQPQTVFANTQASAKKGFFFGCLGG
                     CAAEKFLKNTESSCKLNELVSVATDNRLHRNIGEVANLNEPEEARLMAGFFRSTLPDEK
                     SQVK"
                     /name="hypothetical protein"
     gene            complement(507..740)
                     /locus_tag="NQ150_RS27390"
                     /old_locus_tag="NQ150_27390"
     CDS             complement(507..740)
                     /locus_tag="NQ150_RS27390"
                     /old_locus_tag="NQ150_27390"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(747..1307)
                     /locus_tag="NQ150_RS27395"
                     /old_locus_tag="NQ150_27395"
     CDS             complement(747..1307)
                     /locus_tag="NQ150_RS27395"
                     /old_locus_tag="NQ150_27395"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<1336..1995)
                     /locus_tag="NQ150_RS27400"
                     /old_locus_tag="NQ150_27400"
                     /pseudo=""
     CDS             complement(<1336..1995)
                     /locus_tag="NQ150_RS27400"
                     /old_locus_tag="NQ150_27400"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(1985..2308)
                     /locus_tag="NQ150_RS27405"
                     /old_locus_tag="NQ150_27405"
     CDS             complement(1985..2308)
                     /locus_tag="NQ150_RS27405"
                     /old_locus_tag="NQ150_27405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001696562.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     APPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2372..2563
                     /locus_tag="NQ150_RS27410"
                     /old_locus_tag="NQ150_27410"
     CDS             2372..2563
                     /locus_tag="NQ150_RS27410"
                     /old_locus_tag="NQ150_27410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_062914769.1"
                     /translation="MTKQEKTALNMARFIRNQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(2645..2725)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="89.024"
                     /coverage="93.0"
                     /evalue="1.87e-19"
     Typing          complement(425..1995)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.628"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 catctgcaaa aaaaggattt tttttcgggt gtctgggagg ctgtgcggcg gaaaaattct
       61 tgaagaatac agaaagttca tgcaaactga atgaactggt ttctgtcgcg actgacaaca
      121 gactccacag gaacattggg gaggtcgcaa acctcaatga acccgaagaa gctcgcctaa
      181 tggcgggctt ttttcgttct acgctccccg acgaaaaatc gcaagtgaaa taacgagatt
      241 tttcacgtct ttacgctcaa aaagcaaaaa aaccatgttt tcccctggct gaatccccaa
      301 aaacgcgtga aatgcgtttt caggatattg catagctatg cacaaatacg gcacacgatt
      361 tgtttcgctc gccccagccg tcgaacgggt caaaatggca agatttcgtc acttccccgg
      421 tcacatctcc attgatggcc cactccgaac ccgtgccgcg cgttcctgta cctcatgtct
      481 gtaccgggca cgctcctgtt catcccttag ctgttgttcg cgataaataa ccgactcaag
      541 cgatccactt gcccggctaa tctctgcacc tgctgactca atatcacgac gcgctcgttc
      601 agtatcgcgt tgttccgttg cgtaacctcg tgcatcttct gcaattccgc gaaggcgctc
      661 tcccactcgt tcagccgccg catatagtcc tgttgcaaat gctctaaggc gttcagcaaa
      721 tgcccttcca gttccgtcat actcgtttac tccctgacca gcctcacggc gttcttgtcg
      781 cccaccgtcc aggtgttttc ccctttcacc ccgtccggca acaccagaaa tttcccgttc
      841 tcgccattga cgaacgtcac cccccaggtt tttgcctcga gtttcgccag cgtgttttcc
      901 tgctctctga tagtcaggat atttttcgca atcttgcttt cctgccactc catcagcccc
      961 cagcacccca ggaaaatccc gcccgtgacg ctgagcgcgg tcagcgccgg aaacagtatc
     1021 cgccctttga tcacccgcca gagcagtttt ttctgctgcc gggacagttc ggcctctgtg
     1081 gtgctgaact gcatgctcac ggtggtgctc agcgtatcca gttgcttttt cacggatgtt
     1141 gtatgttcgc tgatagcgtc tctgattttc tgcctgttta agctcaatgc cttgtctaca
     1201 gactcttcga gcttcctgaa ctcgctgttc agcatgttct cggtagaagc ggctcgctct
     1261 ttcagtttct tctcgaagtc tgttcccatt tgtaaaagat tgctcataca gcgccccctt
     1321 tagcctgaga ttccgccccc cctccgggtc ggcaatactg atgctgcttt tggttgtcct
     1381 caccacctca aaacctgccg ctgtaagcgc ctctgtgaca tcctgacgcg tttttattgc
     1441 tccggcatgg taaagagcct caagaccccg tgtaatcgct tctgcggcct cctgtttcgc
     1501 ttttggcaga ttatttggcg tgacaagcgt ccgtctgttc tccggtgcgt tcgggtcacg
     1561 cagcccgtaa tgatgattaa ccagcgtctg ccaggcattt atcctcggcc tgtccgcacg
     1621 gtcgtagtac ggctggaggc gcttaccgct ctgtagctcc atgttcggga tgacaaaatt
     1681 cagttcgagc cgccccttat cctggtgttc cacccagaga atgctgtact ggtctttttc
     1741 gagaccgggc ataagaacac gctcaaagct cgtcatcact ctttcgcgtt cacccggtgg
     1801 tagctccttc tccgcgaacg acagaacgcc tgacgtgtat ttcttcgaaa atggcgtgga
     1861 atcaatgagt tcccgcactt cttccgggtt accccggagc accgttgcgc cttcgcggtt
     1921 acgctcccgc cccagcaggt aatcgaccgg gccacttcca ccgcctttcc ccctggcatg
     1981 aaatttaact atcatcccgt accccctgtt ccctgacagc ctgccgcaac tggcgcaatt
     2041 caccctcgat ggccatcagt gcggccacca catgaacccg gtcaatcgaa gaccactggc
     2101 cgctgttcac cttccgggct gtctggttca ggttgttccc gatggcagcc agatgccgca
     2161 gcaatggcgg tgccagtgtc ggcagttttc ctgtgcgtgc aaccggctcc cccagacaga
     2221 cccgccgcat ccattccgcc agtcgtttac cctcgcagcg ttccagtaac cgggcgtgct
     2281 cctcatcggt aacccgtatc gtgagcatct tctcgcgttt catcggtatc attcccccta
     2341 acaaatcccc catacaagga gccttaagac catgaccaaa caggaaaaaa cagcccttaa
     2401 catggctcgc tttatcagaa accagacgct aaccctgctg gaaaaactca acgatctgga
     2461 cgcggacgaa caggcagaca tctgcgaatc acttcacgac cacgccgacg aactctaccg
     2521 cagttgcctc gcacgcttcg gcgatgacgg tgaaagcaac tgaaacatgc agctcccgga
     2581 gacgttcaca gcttgcctgt gagcggatgc cgggagcaga caagcccgcc agggcgcgtc
     2641 agtgcgggtg tcggggcgca gccctgaccc agttcacaga gcgatagcga tgtgtatact
     2701 ggcttatctc attttgcatc agtgcagagt ggatggaaag tgcaccatgt caggagtaaa
     2761 aagccgcaca gatgcgtaaa aacagcgcac ccgataaaca gcacacatgc ggacacgggc
     2821 acaggcgcgt aagtgcacaa tgcttgcctc ggtgactctt ccgcttcctc gcccactcgc
     2881 tcactacgtt cggtcgctgg ggctgcggcg agcggtggga tcactctcgt tgtgatgcag
     2941 atccgttttt ttttttgcac tggagttatc aggagttgcg gtgcacatgg gatcgtgcga
     3001 tatgccggat ggtgaaaggt tggagggaac ggcaacaact cacccctccc agtgaaggga
     3061 cgggtagttt gccgctctcg atatgccgga cggagccaag gccatcgatc acggggcgcg
     3121 tcagtggaag aacccgcgcc tgcgtgacgt atgcgtcttc gccgcaccat ctcacccgtc
     3181 acgccaccac ataccgggaa ctgccgccaa ggtctaactc aaccaatcta gccgcgctac
     3241 atacggtttt tgtggcaact catcaggtgt ccgctgtcga tgaaactctc tgcgccggta
     3301 gcggaactct cacgcgtgcg gtcgccgtcg tcacagctcc cccaaccgca aacggtcttt
     3361 gcaaacacgc aag
//
