LOCUS       NZ_CP086498             4773 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain Ec-050-T5-ESBL plasmid pEc-050-T5-ESBL_8,
            complete sequence.
ACCESSION   NZ_CP086498
VERSION     NZ_CP086498.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108723
            Assembly: GCF_022759745.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4773)
  AUTHORS   Moser,A.I., Endimiani,A., Campos-Madueno,E.I. and Vallone,A.
  TITLE     Genome plasticity in E. coli and K. pneumoniae: SNV accumulation
            over time
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4773)
  AUTHORS   Moser,A.I., Endimiani,A., Campos-Madueno,E.I. and Vallone,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-NOV-2021) Institute for Infectious Diseases,
            University of Bern, Friedbuehlstrasse 51, Bern 3001, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 225x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759745.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:58:31
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,273
            CDSs (total)                      :: 5,151
            Genes (coding)                    :: 4,884
            CDSs (with protein)               :: 4,884
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 267
            CDSs (without protein)            :: 267
            Pseudo Genes (ambiguous residues) :: 0 of 267
            Pseudo Genes (frameshifted)       :: 107 of 267
            Pseudo Genes (incomplete)         :: 174 of 267
            Pseudo Genes (internal stop)      :: 53 of 267
            Pseudo Genes (multiple problems)  :: 59 of 267
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086498.1.
            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..4773
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="Ec-050-T5-ESBL"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc-050-T5-ESBL_8"
                     /geo_loc_name="Switzerland"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            458..781
                     /locus_tag="LNN51_RS26155"
                     /old_locus_tag="LNN51_26160"
     CDS             458..781
                     /locus_tag="LNN51_RS26155"
                     /old_locus_tag="LNN51_26160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_000957080.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLAEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            990..>1424
                     /locus_tag="LNN51_RS26160"
                     /pseudo=""
     CDS             990..>1424
                     /locus_tag="LNN51_RS26160"
                     /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            1459..1944
                     /locus_tag="LNN51_RS26165"
                     /old_locus_tag="LNN51_26170"
     CDS             1459..1944
                     /locus_tag="LNN51_RS26165"
                     /old_locus_tag="LNN51_26170"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /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_079967943.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKVAFSEHEKFVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSTLLTASGASILWWQGQQIL
                     DNYTIIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            1948..2163
                     /locus_tag="LNN51_RS26170"
                     /old_locus_tag="LNN51_26175"
     CDS             1948..2163
                     /locus_tag="LNN51_RS26170"
                     /old_locus_tag="LNN51_26175"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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_000137420.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMFGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2362..2913)
                     /locus_tag="LNN51_RS26175"
                     /old_locus_tag="LNN51_26180"
     CDS             complement(2362..2913)
                     /locus_tag="LNN51_RS26175"
                     /old_locus_tag="LNN51_26180"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000654246.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000654246.1"
                     /translation="MKDMKAVVVFTGKDLNIMRTEGGSGYWHARTDRLNDADYLIAVRN
                     RRETWAVKDLEHGTAFLIAKITGCFKSPDYDDRNVITFDEYAEIHTPKAWKMLTDGQRY
                     PVAYLSAQEAFLRIGVTPEQLEWKKFHPSSPSVPNTVIPGLAEEKTEKLSLNEAIERAK
                     KDISNATGIDSSAITISIKI"
                     /name="hypothetical protein"
     gene            3449..3916
                     /locus_tag="LNN51_RS26180"
                     /old_locus_tag="LNN51_26185"
     CDS             3449..3916
                     /locus_tag="LNN51_RS26180"
                     /old_locus_tag="LNN51_26185"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011899450.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_157186121.1"
                     /translation="MPAPNNYGVAGSPNSAIAHPDGLDCYGRVPEINSKGDVIPAGDIF
                     LRVGRHTGPNRGFGVRHIWAEHEQELVKLGYTTVNDVARFVRDIIRRGVPIYCEFNSTS
                     GKHRPAVLKSSVGIVILEPREAPETESGWIYVVVTAYTRRTAHGTLVGHIE"
                     /name="hypothetical protein"
     gene            complement(4510..4593)
                     /locus_tag="LNN51_RS26465"
     CDS             complement(4510..4593)
                     /locus_tag="LNN51_RS26465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_058652899.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPDRHD"
                     /name="hypothetical protein"
     Typing          170..354
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.17"
                     /coverage="86.0"
                     /evalue="5.83e-49"
     Typing          complement(2..224)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.625"
                     /coverage="99.0"
                     /evalue="1.87e-77"
     Typing          complement(4294..4773)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.481"
                     /coverage="94.0"
                     /evalue="2.23e-146"
     Typing          772..2267
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.385"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctgatttgag cgtcagattt cgtgatgctt gtcagggggg cggagcctat ggaaaaacgg
       61 cagcgccgca tccttttcct gtcctgcttg ccatgccgta tgcctttgct cttatccgtt
      121 tgcaggtaac gcccgccgca gccgaacgtc aggagcggaa gcgaccgagt gagcgaggag
      181 gcgtcatatc accgtaacct ccattttctc ctgtacgccc tgcagctgca tttttcccct
      241 gccacatgaa gcactttcat tacgtgttac tccgccgtaa catattgagc cagtatacac
      301 tccgctagcg ctacgtgact ggttcagggc tgcgccccga aacctgctaa aaccactgac
      361 gcgcctgcgg cttgtccaac accgcgccga ccgggaaaag atttcccgcc cgtcccggcg
      421 ttatcaggag atcggtttgt cagagaaacg gaacaagatg ctcaccatgt gggtgaccga
      481 agatgagcac cgccgtctgc tggaacgctg cgacggtaaa cagcttgcag cctggatgcg
      541 ccagacgtgc ctggccgaga aacccgcccg cgccggcaag cttccctcaa tctcgccggc
      601 gctgcttcgt cagcttgccg gcatggggaa taacctcaac cagattgccc ggcaggttaa
      661 cgccggtggc ggcagcgggc acgaccgcgt gcaggtcgtc gccgcgctga tggccataga
      721 tgccggactc gagcggctgc ggcatgccgt gctggaaaag ggtgcagacg atgatcgtta
      781 agtttcaccc gcgagggcgc ggcggtggcg ccggtccggt ggattatctg ctggggaaag
      841 accgacagcg cgacggcgcc accgttctgc aggggaagcc ggaagaagtc agggagctta
      901 tcgacgcctc gccctacgca aaaaagtaca catccggcgt cctgtccttt gccgaaaagg
      961 atttaccgcc cgggcagcgc gaaaagctga tggcgagctt tgaacgggtt ctgatgcccg
     1021 gactcgataa agaccagtac agcgtgctat gggttgagca ccaggataag gggcggctgg
     1081 agctgaactt cctgatcccg aacatggagc tgctgacagg caggcgtctc cagccgtatt
     1141 acgaccgcgc cgaccgtccg cgcattgatg cctggcagac catcgtgaac ggcaggctgg
     1201 ggctgcatga cccgaacgcg cctgaaaacc ggcgggcgct ggtcacgccg tccgcgctgc
     1261 cgaaaacgaa gcaggaagcc gctcaggcaa ttacacgggg tttactggcc ttagcctcgt
     1321 ccggggagct gaaaacccgc caggacgtca ctgaggcgct agaaagcgca ggttttgagg
     1381 tggtgcgcac cacaaaaagc agcatcagca ttgccgaccc ggacgggggg cgaaacatcc
     1441 gactgaaggg agccatctat gaacagtctt ttaacgctgg cgaaggactt agagcagaaa
     1501 tcgaaagcgc agcagcagag taccggcgag atgctgaaag tcgcattcag cgagcacgag
     1561 aagtttgtca gagcggaact gagcgaaagc gagaagagaa tcagcgccgc catcctcgac
     1621 cacgaccgga agctgtcctc agccatgagc cagcgcacga aaggcatggt gcgtatggtc
     1681 agccagacgt ggctgaccat cgtcctggtg tctacactgc tgacagcatc gggcgcaagc
     1741 attctatggt ggcaggggca gcagatactc gacaattaca cgatcatccg ggagcagaag
     1801 agcacgcagg ccatgctgtc cgagaggaac agcggcgtgc agctctcgac ctgcggagag
     1861 cagagacggc gctgcgtgag ggtgaacccg gaagcgggac ggttcggaga ggattcgagc
     1921 tggatgatac tggcggggaa atagcacatg acggagctgg aaaaacagtt gctgagcgca
     1981 ttagagcagc tacagcagga ctactcgaaa aggctggacg agtgggagaa cgccttcgcg
     2041 gaatggcgga cgatgtttgg tcttatgcaa cgggagaacg cggcgctgag cgagcgcgtc
     2101 acgggcttga gcaggcaggt gcagagtttg agcgagcagc tgcgccggtt gtcacaaggc
     2161 tgaacgtgat agaggcacat cgtgagcagg aacgggcggc gcagcatcag aaagcgctgg
     2221 agctggaacg atctcagcga cagcgaacgt acaacggtcc gtcactttga atctgtgcgc
     2281 cggaaaagca tgggcttgct gtttctggcg cacaggttca gttctagaac atgaggctgc
     2341 tatcttgttg ttcacgcttc atcagatctt gatgcttatt gttatggctg agctatcaat
     2401 ccctgttgcg ttgctaatat cctttttggc tctttcaatt gcctcgttaa gggagagttt
     2461 ttctgttttc tcttcagcca gaccaggaat cactgtatta ggaaccgatg gggatgaagg
     2521 atggaatttc ttccattcca gttgttccgg tgttacccca atacgtaaaa aagcttcctg
     2581 tgcgctcagg taagcaaccg gatagcgctg accatcggtt agcattttcc atgcttttgg
     2641 agtgtgaatt tctgcgtatt catcaaaggt tatgacgttc ctgtcgtcgt aatcagggct
     2701 tttaaaacac ccggtaattt tggcgatcag gaatgctgtg ccgtgttcca ggtcttttac
     2761 tgcccacgtt tcccttctgt ttcttactgc tatgaggtaa tcggcatcgt tgagcctgtc
     2821 tgttctggca tgccagtagc ctgacccccc ctcggttctc attatgttca aatccttccc
     2881 ggtaaaaacc acaacagctt tcatatcttt catatagaaa cccttaatag gtgagtcaat
     2941 ttcatttttt tatgaaatct atacgataga attcgtgttg taaatgtttt ttatgcgata
     3001 aaatgcagcc ccctacctct tttattgtta gtgataaggc ttcctgtttg tttttttgat
     3061 aaaccggtta aaacaggggc ttggacgagg atatacattg aaagcatgag ccattcacgt
     3121 ggctgcatgg ctatgcagcc gcgtgaaatt tatcaggcgc agaatgcgcg gtttagcggg
     3181 gagtttactg ccggttttac cgggctaacg ccgctttcac gctgaacccg tccggagcgg
     3241 tgcgggcaag ggatgttatg gtaaatctag ctgctagggc gattcgcacg tcacattttc
     3301 aggtgtgata tccttatgcg ccaaggatga aaggacaaaa aaataatcca taaggattct
     3361 ttttatcgtc tctgcttttt tcttgggctc cttccgcttg tttcctctct ggtaccatat
     3421 gcggactcta ctcaataagg atcgttttgt gcctgctcca aacaattacg gtgtagctgg
     3481 ttcacctaac agcgctatag ctcaccctga tgggcttgat tgctatggcc gtgtccctga
     3541 aattaattct aaaggtgatg ttattcctgc tggcgacatc ttcttgcgtg ttggtaggca
     3601 tactggccct aaccggggct ttggtgttcg ccatatctgg gctgagcacg agcaggaact
     3661 ggttaagctg ggatatacga ccgttaatga tgtggctcgt tttgtccggg atattattcg
     3721 tcgtggcgta ccaatatatt gcgagttcaa cagtacaagc ggtaaacatc ggcctgcagt
     3781 gctaaagtcg tcggtaggca tcgtaattct tgagcccaga gaagcgcctg aaactgagtc
     3841 aggttggatc tatgtcgttg tgactgcgta cacacgaagg acggcgcacg gtactttggt
     3901 tggtcatatt gaataaaaaa atagggcgct aaaaagcgcc ctttatgaat tcgttggtag
     3961 tcgcagcatt tccttagcac atagggttca gaaaccgacg cttgtcgtaa ctacccggca
     4021 gatgaccagc catctgactg cccggcacag aaggcctatt actggttgat gccccctgcg
     4081 aatgctcttg cagtacaata atcataaaca tcgtgatgta gatttgcaac caacattttg
     4141 gttgcaacct atatactaat ttttttcgat aaccctggaa tccattgctg tgtctggatt
     4201 tcttgaagct cctggctata gataccctat atcctaacag ttattctgct gtgaatatca
     4261 gaaatgaaca cttgagatca tcagtggctc gtcgtagtct cttgctcaga aacgaaaaaa
     4321 ccaccctggc aggtggtttt ttcgaaggtt agttaatcct ggcagattct ctaaccgtgg
     4381 taacagtctt gtgcgagaca tgtcaccaaa tactgtcctt tcagtgtagc ctcagttagg
     4441 ccgccacttc aagaactctc gttacatctc tcgcacatcc tgcttaccag tggccgttgc
     4501 caatggcgat tagtcgtgtc tatccgggtt ggactcaaga cgatagttac cggacaaggc
     4561 gcagcggtcg gactgaacgg ggggttcgtg catacagtcc agcttggagc gaactgccta
     4621 cccggaactg agtgtcaggc gtggaatgag ataaacgcgg ccataacagc ggaatgacac
     4681 cggtaaaccg aaaggcagga acaggagagc gcacgaggga gccaccaggg ggaaacgcct
     4741 ggtatcttta agtcctgtcg ggtttcgcca cca
//
