LOCUS       NZ_CP142960             4107 bp    DNA     circular CON 31-JAN-2024
DEFINITION  Escherichia coli strain EC200461 plasmid pEC200461_4, complete
            sequence.
ACCESSION   NZ_CP142960
VERSION     NZ_CP142960.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39501436
            Assembly: GCF_036287745.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4107)
  AUTHORS   Maguire,M.
  TITLE     Spatiotemporal and genomic analysis of carbapenem resistance
            elements in Enterobacterales from hospital inpatients and natural
            water ecosystems of an Irish city
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4107)
  AUTHORS   Maguire,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-JAN-2024) Bacteriology, University of Galway,
            University Road, Galway, Galway 000000, Ireland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 84.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/30/2024 20:05:42
            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)                     :: 4,998
            CDSs (total)                      :: 4,885
            Genes (coding)                    :: 4,693
            CDSs (with protein)               :: 4,693
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 192
            CDSs (without protein)            :: 192
            Pseudo Genes (ambiguous residues) :: 0 of 192
            Pseudo Genes (frameshifted)       :: 79 of 192
            Pseudo Genes (incomplete)         :: 124 of 192
            Pseudo Genes (internal stop)      :: 43 of 192
            Pseudo Genes (multiple problems)  :: 49 of 192
            Pseudo Genes (short protein)      :: 4 of 192
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP142960.1.
            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..4107
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EC200461"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEC200461_4"
                     /geo_loc_name="Ireland"
                     /collection_date="2020"
     gene            169..561
                     /locus_tag="VYI50_RS24900"
                     /old_locus_tag="VYI50_24900"
     CDS             169..561
                     /locus_tag="VYI50_RS24900"
                     /old_locus_tag="VYI50_24900"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_241565387.1"
                     /translation="MALSACFRQQLNPVVNSLLKERIIHSPKELEHDNAVIRALQKLQI
                     QEVCNSTLWETAKQQLLQKSDGRYFAINSKHLSFPGPGESHAFCCIKYKNAIGINGNNA
                     ETQSTHYQPYPYDKVSIWGPFPHNLT"
                     /name="hypothetical protein"
     gene            complement(1106..1339)
                     /locus_tag="VYI50_RS24905"
                     /old_locus_tag="VYI50_24905"
     CDS             complement(1106..1339)
                     /locus_tag="VYI50_RS24905"
                     /old_locus_tag="VYI50_24905"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_000137439.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1346..1876)
                     /locus_tag="VYI50_RS24910"
                     /old_locus_tag="VYI50_24910"
     CDS             complement(1346..1876)
                     /locus_tag="VYI50_RS24910"
                     /old_locus_tag="VYI50_24910"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /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_000067495.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTSALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPEGMKAETNWTM
                     ENGKQNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(<1917..2564)
                     /locus_tag="VYI50_RS24915"
                     /old_locus_tag="VYI50_24915"
                     /pseudo=""
     CDS             complement(<1917..2564)
                     /locus_tag="VYI50_RS24915"
                     /old_locus_tag="VYI50_24915"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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(2554..2877)
                     /locus_tag="VYI50_RS24920"
                     /old_locus_tag="VYI50_24920"
     CDS             complement(2554..2877)
                     /locus_tag="VYI50_RS24920"
                     /old_locus_tag="VYI50_24920"
                     /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_000956003.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGNRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2941..3132
                     /locus_tag="VYI50_RS24925"
                     /old_locus_tag="VYI50_24925"
     CDS             2941..3132
                     /locus_tag="VYI50_RS24925"
                     /old_locus_tag="VYI50_24925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3801..3959
                     /locus_tag="VYI50_RS24930"
                     /old_locus_tag="VYI50_24930"
     CDS             3801..3959
                     /locus_tag="VYI50_RS24930"
                     /old_locus_tag="VYI50_24930"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005093880.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAIGNWTRWIEIL
                     RVLEVVA"
                     /name="hypothetical protein"
     Typing          complement(3218..3303)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          3316..3873
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.853"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1003..2564)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.202"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccgcaaaaaa ggatctcaag aagatcttga atcactctat gaaaattttg ttttatagcc
       61 gtatttgttg atgctataag ccagagacct tctatgagaa tagacatatc acatcaaaca
      121 cggcataccc cgccaaacat gcttcctcgg gaacaaaatt gtgtagcaat ggcattatct
      181 gcgtgcttta gacaacaact aaaccctgtg gtaaacagct tattaaaaga gagaataata
      241 cactccccta aagaattgga acatgacaac gcagtaataa gagccctgca aaaactacaa
      301 attcaagaag tttgtaacag caccctttgg gagacagcca aacaacaact acttcaaaaa
      361 tcggacggaa gatattttgc catcaattct aaacacttat cctttccagg cccaggagaa
      421 tctcacgcct tctgttgcat caaatacaaa aatgcaattg gcattaacgg aaacaatgcc
      481 gaaacccaat cgacccacta ccaaccctat ccctatgata aagtcagtat atggggacca
      541 ttccctcaca atttaacgta atatcttatt atcagcaccg ctgaaacgcg ttcggcgcga
      601 tcacggcagc agacaggtaa aaatggcaac aaaccacccg aaaaactgcc gcgatcgcac
      661 ccggtaaatt ttaaccacat gcatagctat gcagccatgt gaatcacgca ggaattgcca
      721 gccagagaca gctgaaacgg atttttttca tgctttcgga agcgaagaag acggggacct
      781 gagcgggaaa acagaagttc aggggaatga gcgcgatctg gcaatagagg caaaacacag
      841 caacaaaaga cacaccagaa tcgcgcccgt atgcgtttta acgcgttcct atgttttcag
      901 caaggtctga ctgaagcgcg ttcccggtgc ccccgaacca accattatcc caaaaaatgc
      961 accggaaacg cgctgacaac attttagcct gtctctgatt accatcccag cgaagggcca
     1021 tccagtgtcc gttcctgtat ttccagctgg cgctcacgct ccagggataa cgcatgttcg
     1081 cattcctgta tcagccgttc gtcccttatc tcctgttctc gctgtataac tggctcaagc
     1141 gttctgtctg ctcgctcaag tgctgcacct gctgactcaa ctgcatgacc cgctcgttca
     1201 gcatcgcgtt gtcccgttgc gtaagcgaaa acattttctg caattccacg aaggcgctct
     1261 cccattcgtt cagccgctgc atatagtcct gttgcagttg ctctaatgcg ttcagcaaat
     1321 gtctttccag ctccgtcatg ctctgttact cctgtaccag ccttacggca ttctgtttcc
     1381 cgttttccat cgtccagttc gtttcggctt tcatcccctc gggcaacacc agaaaacgtc
     1441 cgttgctgtc ctcgtgataa cgcacgcccc atgtcttcgc gttcagcttc tccagactct
     1501 ctttctgctc gcggagaata ttcatgttcg cgtttatctt catgccctgg taccacagca
     1561 ggctcccggt cgtggcaaac atcagtactg agacgataat cagccacagc cagcgtttca
     1621 cgctcatttt cagtacggtt ttccagtgtg cgtccatcgt atcgacggtc gttttctgat
     1681 acctctccag aagttctttc agggctgatg tatggtcgtt gatagcgttc ctgattaaag
     1741 attcgtttga ggtcagttcc ctgtttacag attcttcgag cttcctgaac tcgtcgttca
     1801 gcattttctc tgtagattcg gctctctctt tcagcttttt ctcgaactcc gcacccgtct
     1861 gtaaaagatt gctcataaaa cgctcctttc agtctgatat tcttcccgcc gttcgggtct
     1921 gcaatgctga tactgcttcg cgtcaccctg accacgtcaa tccctgcctc tgtgagcgcc
     1981 tgaatcacat cctgacggcc ttttatctct ccggcatggt aaagcgcgtc tatcccgcgt
     2041 gtaacgccct cagcaatcgc ctgtttcgtt tccggcagat tatcagggag tgtcagcgtc
     2101 ctgcggttct ccggggcgtt cgggtcatgc agcccgtaat ggtgattaac cagcgtctgc
     2161 caggcatcaa ttctaggcct gtctgcgcgg tcgtagtacg gctggaggcg ttttccggtc
     2221 tgtagctcca tgttcggaat gacaaaattc agctcaagcc gtcccttgtc ctggtgctcc
     2281 acccacagga tgctgtactg atttttttcg agaccgggca tcagtacacg ctcaaagctc
     2341 gccatcactt tttcacgtcc tcccggcgtc agctccttct ccgcgaacga cagaacaccg
     2401 gacgtgtatt tcttcgcaaa tggcgtggca tcgatgagtt cccggacttc ttccggatta
     2461 ccctgaagca ccgttgcccc ttcccggtta cgctcccttc ccagcaggta atcaaccgga
     2521 ccactgccac caccttttcc ccgggcatga aacttaacta tcatcccgcg tcccctgttc
     2581 cctgacggcc agacgcagcc ggcgcagctc gtccccgatg gccatcagtg cggccaccac
     2641 ctgaacccgg ttaccggaag accactgccc gctgttcacc ttcctcgctg tctgattcag
     2701 gttattcccg atggcagcca gctgacgcag taacggcggt gccagtgtcg gcagtttccc
     2761 ggaacgggca accggctccc ccaggcagac ccgccgcatc cataccgcca gctgtttacc
     2821 ctcacagcgt tccagtaacc gggcatgttc atcatcagta acccgtatcg tgagcatcct
     2881 ctcgcgtttc atcggtatca ttacctcctg aacagaaatc ccccttacac ggaggcatca
     2941 gtgactaaac aggaaaaaac cgcccttaac atggcccgct ttatcagaag ccagacatta
     3001 acgctgctgg agaagctcaa cgaactggac gcggatgaac aggctgatat ctgtgaatcg
     3061 cttcacgacc acgccgatga gctttaccgc agctgcctcg cacgtttcgg ggatgacggt
     3121 gaaaacctct gacatatgca gctcccggag acggtcacag cttgtctgtg agcggatgcc
     3181 gggagcagac aagcccgtca gggcgcgtca gcaggtttta gcgggtgtcg gggcgcagcc
     3241 atgacccagt cacgtagcga tagcggagtg tatactggct taaccatgcg gcatcagtgc
     3301 agattgtatg aaaagtgcgc cataccgggt gtgaaatgca gcacagatgc gtaaggagaa
     3361 aatgcacgtc caggcgcttt tccgcttcct cgctcactga ctcgctacgc tcggtcgttc
     3421 gactgcggcg agcggtatct actcactcaa aaacgaaatg ctgttatcca cagaatcagg
     3481 ggataacgcc ggaaagaaca tgtgagcaaa agaccaggaa caggaagaag gccgcgccga
     3541 tggcgttttt ccataggctc cgcccccctg acgagcatca caaaaaccga cgctcaagtc
     3601 agaggtggcg aaacccgaca ggactataaa gataccaggc gtttccccct ggaagctccc
     3661 tcgtgcgctc tcctgttccg accctgccgc ttaccggata cctgtccgcc tttctccctt
     3721 cgggaagcgt ggcgctttct catagctcac gctgttggta tctcagttcg gtgtaggtcg
     3781 ttcgctccaa gctgggctgt gtgcacgaac cccccgttca gcccgaccgc tgcgccttat
     3841 ccggtaacta tcgtcttgag tccaacccgg taagacacga cttaacgcca ctggcagcag
     3901 ccattggtaa ctggacaagg tggattgaga tattaagagt tcttgaagtg gtggcctaac
     3961 tgcggctaca ctagaaggac agcatttggt atctgtgctc caccaagcca gttaccttcg
     4021 gaagaaagag ttggtagctc tagattccgg caaacaaacc accgttggta gcggtggttt
     4081 ttttgtttgc aggcagcaga ttacgcg
//
