LOCUS       NZ_CP142962             4063 bp    DNA     circular CON 31-JAN-2024
DEFINITION  Escherichia coli strain EC200461 plasmid pEC200461_6, complete
            sequence.
ACCESSION   NZ_CP142962
VERSION     NZ_CP142962.1
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 4063)
  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  JOURNAL   Unpublished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 4063)
  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
            CP142962.1.
            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..4063
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EC200461"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEC200461_6"
                     /geo_loc_name="Ireland"
                     /collection_date="2020"
     gene            join(3728..4063,1..1812)
                     /gene="mobQ"
                     /locus_tag="VYI50_RS24950"
                     /old_locus_tag="VYI50_24950"
     CDS             join(3728..4063,1..1812)
                     /gene="mobQ"
                     /locus_tag="VYI50_RS24950"
                     /old_locus_tag="VYI50_24950"
                     /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_001029354.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSPAARKVDFMQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVIRLNGTLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWEEW
                     QREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(2060..2761)
                     /locus_tag="VYI50_RS24955"
                     /old_locus_tag="VYI50_24955"
     CDS             complement(2060..2761)
                     /locus_tag="VYI50_RS24955"
                     /old_locus_tag="VYI50_24955"
                     /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_001281395.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVDITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(3295..3549)
                     /gene="mobC"
                     /locus_tag="VYI50_RS24960"
                     /old_locus_tag="VYI50_24960"
     CDS             complement(3295..3549)
                     /gene="mobC"
                     /locus_tag="VYI50_RS24960"
                     /old_locus_tag="VYI50_24960"
                     /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"
     Typing          complement(3551..3727)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          3728..4063
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="94.0"
                     /evalue="5.09e-176"
     Typing          complement(2061..2761)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..1809
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.717"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tttgtcagtc agggcatgat tgctgatgtg gcgttccatc acatggataa aacaaatccc
       61 catgcgcaca tcatgctgac cacgagggct atcggacctg ctgggttcag cggaaaggtc
      121 agggactgga acgaccggac acatgccgag acgtggcggg catcatgggc tgaccatgca
      181 aacagggcac tggcgaacgc cggttatcag gaagagatag accatcgttc atacgagcga
      241 caggggcttg agaaaacgcc tggtattcac ctcggaaagt ctgcctgtgc gatggaaaca
      301 cgcggtatcg aaacagaacg cggcgaacag aatcgtctga ttaacaggct taacctggaa
      361 atacagattt cccgcaccga actcaggaac ggagggctga cagagcctgc ccgccgtgtg
      421 gctgaccttc tgaatatcgg gcttcctgac aacgcaactt cgtacacact acgtgacatt
      481 atcgaagcgt tgccgaagga cagtaactcg gcatggaaac tcaccagtaa tgccatgtcg
      541 atgatggcag atatgcaggc gacgcgcaga cgctgggaag agctgaacac cgaacgaaag
      601 gaagcgatga gccatgctgc cagcctgaaa aaatcatcgc cgttttcgtc cggtttttcc
      661 cgtattcccc tgatgcaatg ggcggcaccg gaataccgta gtgagcaggg aaaaatccag
      721 tctctgagcc agcaaatgga aaaattacga cagcattacc ggaaggtgga gaaacaggac
      781 attcccgcga gtcagatggc atttgaaaaa cagtggcagc agtgggggga atccggcctt
      841 gcagctctca gagcccagtt gcttaaacgt gaagaggaat tgcgccggaa ggaacaggaa
      901 gatactgaac gtagtcgcgc ggagcagctc aggaaaaatg acaatgccgt tatggattca
      961 ggggtgctga gagcagtcgt tacggggtat ggcgaggctc ccatgcctgg taacggggaa
     1021 atgacctgtt accttctgct tcacaaccgg aacggagaat atacgctctg ggggaacgag
     1081 ctggagaaat accgcaccag aatctttgag agtgttgatt taatgcgtga caggagtggt
     1141 tatatctgtg accgaagcga aatcggccaa cgtccgccac tgcaacgtgt ttattcctct
     1201 gcaacctttg agcaactgct gacgcaggtt tgccagacat ggccgcaaca tacccgcaat
     1261 ctccgccagc cgaagacatg gccggagtct ttctgtcttg gagaagaccg ccagccagcc
     1321 atgccatcac cagcggcaag gaaggtggat tttatgcagg gacgtctgcc accgacgctg
     1381 atgccggtca tgagttctgt cgaccgggaa acccgccagc ttcagctttt gctggtcatg
     1441 ggcgtggatg actctctggg cggtgttatc cggcttaatg gtacgctgta tcccgcgttt
     1501 gccgttccct cagccgataa caggcatctg gtcatcagtg cgctgaccga taaggggtta
     1561 cggtatgcag ggtatggtgt tgccgtaaat cacgatgcag acagccacat atcacctgca
     1621 ccagaactga tgcagtttca tctgaaaacc cgtgaggcac cgctttttgc tgccgtcaac
     1681 acaccagaaa aacagccgga tcatctgttc cgctcgctgg gttttaatcg tacctgggag
     1741 gaatggcagc gcgaggaaga tgcacgaaca cacaccaccg agaggagaca tgatcgcggt
     1801 tggtcacagt gaatgtgaac aatattttgt tttgtttaac atcgtgttat gttcgtcgat
     1861 gttcatcgac agggatgaat gcaagaagca cactcacata acgcaagcat agttttgttt
     1921 ttccgccccc aaaaattggg gggtcttttt tcgctgcatc agagcgtttt tgacgcaatt
     1981 tttcacttca atagtacctt cgcactacta acacaaaaaa aacgcagcag ggagcgtttt
     2041 aggtgcctta aaatcgattt tagatcgtca tcttgatctg tttgtcttcc ttgaagcgaa
     2101 aatgcagggc tacaaccgtg cgcccctttt tgatcgtctc aacagttaca accagatcgc
     2161 ttttttcgtt cagttcggcg atggctggct tgattatcat cttattcaag tctttgaatt
     2221 gttgatattt atcttcaacg gcaagcatgg ttcggaaatc atcgatagct atcgttctgt
     2281 caccggtgct gcggaactgc tggagcagct cgtaaatgcg gatgctgtag gtgctggaaa
     2341 ggctggagac gttcttcacg actacccgcg taaactgccc cttgagctgt gtcagatacg
     2401 gcatgatggc atcggagaag gtgatatcta ctttcgcctc acctttgaaa tactgcgccc
     2461 ggtactgcac ccagcggaac tcttctcgtt tttcctcgtt cttgatgatt actgacctgt
     2521 cccagaggcg atctatcgct tccttgagcc tagcttcagc gtgctgccgt cccatgtcag
     2581 gaaaggcatc atgaaactct gcagccgtga tggtcatggt tttttgttca tccggcgaag
     2641 gggaatcttc tccggatttt aggcggctga tacagaccag caggaagcgc tgttcctgca
     2701 aagtgagctt gtagcttgcc tcgataaggg cgtttgattt gtaagctatc agatctgaca
     2761 tttcgcttgc tcgttgctat tggtggcgtt tttttactgt acgccactta tcatatgggt
     2821 ggaagttttt tttttgcaac cccctttttc tgtggattac acccccaaaa gctccacctt
     2881 tcacccccaa aagctccacc tttcaccccc aaaagctcca cctttcaccc ccaaaagctc
     2941 cacttatctt gccagaacat ctttaaaatc atggtgttac aagacctaaa aaggttttaa
     3001 aaaaaaagat ctaaaaataa gatcttaaaa acttaacggc gagcctgtgg ataacttggg
     3061 gtgctgaaaa caaaaaacca ataaaaacaa tgcgttgcaa taaagcagaa ttgcaagttt
     3121 cgaatacacc ccctccaacc ctgtggaaac ccagtattca tgcgggttca gcgcatatca
     3181 cctgccgaaa aaccgtgcgt atgtgctcaa cctggcgact gattcacttc cgcttcctcg
     3241 cccactcgct cgctaacgct cggtcgctgg ggctgcggcg agcggacgat acaatcactg
     3301 ttctggcagc gcctccagct cgttaatcag cggcagtatg cgcgtcacat cagcctgtcg
     3361 tgtcacctct gccttcagga actggagtaa ccaggcacgc aactgcacct cctccggctt
     3421 tctgaccttt gccagcaatg cagcacccac aacaaccttc tgcgctgtgt ccaggctccg
     3481 gctcttcgcc ttcaggcgct gtaatctcgc ctcagcatca gcaatcttct gttcgagcgt
     3541 tctgctcatg atgtaactcc gtgcgcgatg aaaaatcgca ttttagcgcg tcactggtag
     3601 tttaaaaact gagctggcat aatgcacggc aaatcacgaa gtgcgcactt atacaatctc
     3661 cactccgttt cgattgtgtg cgccctgcgg ggctgaaaga aaactacaaa aaggcattac
     3721 ggcagaaatg gcgatttatc atctcagcat gaaaattatc tccagaagca gcggctacag
     3781 cgccgtagct tccgctgcct atcgttccgg ttcactgatg cttgatgagc gtaccggact
     3841 gactcacgac tacacccgca aaagcggtgt ggctgaggct gtgattctga cccccgccac
     3901 cgcccctgcc tggtgtacga accgtgccga actctggaat gccgttgaga aggccgaacg
     3961 ccggaagaac tcacaacttg cgcgggaaat tgaactcgcc atcccccacg aactgccgca
     4021 ggatgccgca cgggaaaccg ttctcgcctt tgtcagagaa aac
//
