LOCUS       NZ_CP086479             4237 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain Ec-050-T20-ESBL plasmid pEc-050-T20-ESBL_9,
            complete sequence.
ACCESSION   NZ_CP086479
VERSION     NZ_CP086479.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108725
            Assembly: GCF_022759785.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4237)
  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  JOURNAL   Unpublished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 4237)
  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                   :: 390x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759785.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:58:40
            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)                     :: 5,279
            CDSs (total)                      :: 5,157
            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)              :: 273
            CDSs (without protein)            :: 273
            Pseudo Genes (ambiguous residues) :: 0 of 273
            Pseudo Genes (frameshifted)       :: 109 of 273
            Pseudo Genes (incomplete)         :: 176 of 273
            Pseudo Genes (internal stop)      :: 53 of 273
            Pseudo Genes (multiple problems)  :: 57 of 273
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086479.1.
            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..4237
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="Ec-050-T20-ESBL"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc-050-T20-ESBL_9"
                     /geo_loc_name="Switzerland"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            945..1460
                     /locus_tag="LNN47_RS26195"
                     /old_locus_tag="LNN47_26200"
     CDS             945..1460
                     /locus_tag="LNN47_RS26195"
                     /old_locus_tag="LNN47_26200"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000097059.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_000097059.1"
                     /translation="MSSLSLQRYETNPFLELMTIPMKGKRIQVSRLGRDDNVLVNQNTG
                     EKFGTHVTTFKRVDSEQFVKLFTANIGLTFDLSSAGIKAFNVLLWAVQKQAFAKDQVLL
                     DSRALDDFLKSYDSLKLSYATLKRGINELEKAQIIAKTMRKGFYFINPNFVFNGDRIAF
                     TTLIERDC"
                     /name="replication/maintenance protein RepL"
     gene            1641..1931
                     /locus_tag="LNN47_RS26200"
                     /old_locus_tag="LNN47_26205"
     CDS             1641..1931
                     /locus_tag="LNN47_RS26200"
                     /old_locus_tag="LNN47_26205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000160396.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="transcriptional regulator"
                     /protein_id="WP_024241218.1"
                     /translation="MTKHDAIRISQLHQIFYDDDGLIDSEKNVTILYSIGFTVDEIAHF
                     RNSTPNTVASQLLNARVKLGCASVSSLKPMILLRLLLNIKEIRFGFETDCK"
                     /name="transcriptional regulator"
     gene            2019..2282
                     /locus_tag="LNN47_RS26205"
                     /old_locus_tag="LNN47_26210"
     CDS             2019..2282
                     /locus_tag="LNN47_RS26205"
                     /old_locus_tag="LNN47_26210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001677227.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EexN family lipoprotein"
                     /protein_id="WP_000717655.1"
                     /translation="MKKICTLLMSIFILSACGEDTKSSDWWLNHPKEATEKYKECKKSG
                     EDSVNCQNVKKVAGIIGRTYGPMLEILKAESAEYDKQHGLNR"
                     /name="EexN family lipoprotein"
     gene            2287..3285
                     /locus_tag="LNN47_RS26210"
                     /old_locus_tag="LNN47_26215"
     CDS             2287..3285
                     /locus_tag="LNN47_RS26210"
                     /old_locus_tag="LNN47_26215"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000012467.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_000012467.1"
                     /translation="MSGFFEKFNSEVVSKIEEMTKPLQSQLGQDMLSLLSAGISVYILW
                     VGYQILAGKRQTPLQDLVWDLSKFAIILTFVSNADGYLTAAMDAIKSMKDGFLGKPVWA
                     TLDTMWSTTQLLADKVYAMDQSKYVSVEGGIGSMLVWGGSILIMSVAAVIYMLADVTMQ
                     LAILVAPIFIGCYMFGFTRVMFNNWLGILFSSVFTVIFAGVLVKIGTEFQTDMLSQISR
                     DANSTNILTMGAMAFVIGVLIAVFVWKSSSFAQQLAGAGVEGTLQGMALLGIGAAGMAV
                     EKTRNQMKRGTRTAAEWAGEKGEQKRASIGALGMEARRRASLEKARARNSA"
                     /name="type IV secretion system protein"
     gene            3282..3995
                     /locus_tag="LNN47_RS26215"
                     /old_locus_tag="LNN47_26220"
     CDS             3282..3995
                     /locus_tag="LNN47_RS26215"
                     /old_locus_tag="LNN47_26220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001590713.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_001590713.1"
                     /translation="MNKKLIFSVLLCLFSFGSVAGIPVAIDASPEWAVEATRWTERLKQ
                     WSETARHYQSQIQAYKDQLATATGIRNIAAFTNELSNLQSELANIYKQGNSYISDFTSN
                     PEGALSSQAKNLFSKYGAFNMCSTGIESSDNLCKARIVSTAASIEQGNEINKQLSSAMS
                     QIQSLSNRIESSKDMKESQDLANALQAQSLKIQAIKMQYDVWDSKNRADAEMLKEQKYA
                     EYRLRQKNAKIPSFE"
                     /name="type IV secretion system protein"
     Typing          2288..3090
                     /name="MPF_T"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="89.552"
                     /coverage="91.0"
                     /evalue="1.15e-160"
ORIGIN
        1 cgttaaagct gttttgtatt ttacttctgt tattaatagt aatgcgattt tcaatgaagt
       61 aaaaaataaa ggtcatcgaa tagatggcct tttctattct aaattctaaa tatagagcct
      121 gcggcaggca caggcaaaaa catcgttttt ggacaatctg attcaaatgt taacatttga
      181 catcggattg tctatcctgc attgctcttt tgccgacctc aaaaccccta gcgtgttttt
      241 gtttcccgat ctctagaacc accgagccgc cacggttccg gcagcgcctt gagcgcaacc
      301 ggaaaccgtc tggggagaac cccagacccc catcgctgta acatcgacgg tctacgacca
      361 cctaccaacc gtgtggctac ctgttccatg ctaatgggct ttgcaggggg ctggcgcggt
      421 tcctggcgac ctgaaagccc ctggttaggg gtatcggcgc gcctgacctc ctgaaaccct
      481 ctgtaagcat ttttcgcgcc tttcatgccc tgacgggcat ctaaagcccg tttcgtgcgt
      541 ctgagcgcgt tttaagagct aagacgacta aaacattacc aacacctgaa aatcgcgttc
      601 tggtgctctg gatggcccac agaacgcatt ttcgaacaga acagcaacgg catttctgac
      661 aacatgcgag aggtgatccc gctcgccgca gccccagcga ccgaacgtag tgagcgagtg
      721 ggcgaggaag cggaagagaa ttgatagcca taattgagca cctacgctcc ttagttaaga
      781 actaagaagg gaaattctcg gaacccgcat gaatcctaga aagtggtgat caggatctgt
      841 accttgtaag ctcagatccg gtaccttgca ggctcaaaaa ttgcttgatt ttgagcttat
      901 gaggatttat tgtgaatctc caaagcccaa aaaaggatgc aataatgagc tcgctaagct
      961 tacagagata cgaaacaaac ccgtttttag agcttatgac gatcccgatg aaagggaaac
     1021 ggatacaagt atctcgtctt gggcgggatg acaatgtttt ggttaatcaa aacacgggag
     1081 aaaagtttgg aacacatgta accactttta agcgtgtaga tagtgagcaa tttgttaagt
     1141 tgtttactgc gaatattggg ttaacgtttg atttatcatc ggcaggaatt aaagctttta
     1201 atgttctttt atgggctgtt caaaaacaag cctttgcaaa ggatcaggtt cttttggatt
     1261 caagggctct tgatgacttt ttaaaaagct atgatagctt aaaacttagt tatgctacgt
     1321 taaagagagg aattaacgag ttagaaaaag ctcagattat agcaaagaca atgcgtaaag
     1381 gattttattt tataaacccc aattttgtat ttaatggaga tcgaatagca tttacaaccc
     1441 taattgagag ggattgttaa tcgatagaac aatacaatgc aggatagaca atcatggtca
     1501 aaatgttaac attttatcca tgattgtcca aaaacgatgt ttttgcctgt gcctgccgca
     1561 ggctactaga agtagtcgca ggcgaacaaa agtggtgttt tgttcgcctg ctaatcacaa
     1621 caacctggct agaggttttt atgactaaac atgatgctat acgcatttct caacttcatc
     1681 aaatttttta cgatgatgat ggattaattg attcagaaaa gaacgtgact attttataca
     1741 gtataggatt tacagttgat gaaatagctc attttagaaa ttcaacacca aacacagttg
     1801 cgagtcagct attaaatgca agggttaaat taggttgcgc ctcggtttca tctttaaagc
     1861 caatgatctt attaagattg cttttgaaca taaaagagat tcgttttgga ttcgaaactg
     1921 attgcaaata atatagttca ataggtattt ttgctcttga ctagaattac aattgctgat
     1981 tgtatcagca attgtaatgt ccatacgagg aatcaaagat gaaaaaaatt tgtacgctct
     2041 taatgtctat tttcattctt tccgcatgtg gtgaagatac aaaatcatca gattggtggc
     2101 ttaatcatcc caaagaagcg acggagaaat ataaggagtg taaaaagtca ggggaagatt
     2161 ctgttaattg tcaaaatgtt aaaaaagttg ccggaattat tggtagaacc tatggcccta
     2221 tgcttgaaat acttaaggct gagtcagctg aatatgataa gcaacatgga ttgaacaggt
     2281 gataacatgt ctggtttctt tgaaaagttt aatagcgaag ttgttagtaa aatcgaagag
     2341 atgaccaaac cacttcaaag tcaattaggt caggatatgt tatctcttct aagtgcaggt
     2401 attagcgttt atatcctctg ggttggctat caaatattgg cagggaaacg ccagacccca
     2461 ttacaagatc tcgtctggga tctatcaaaa tttgccatta ttttaacatt cgtaagcaat
     2521 gctgatggct atctgacggc agcaatggat gctattaaat ctatgaagga tgggttcctt
     2581 ggtaaacctg tatgggcaac gctagatacc atgtggagta caactcagct tttggctgac
     2641 aaagtttatg ctatggatca atccaaatat gtgtcagttg aaggtggaat cgggtcaatg
     2701 ttggtttggg gaggaagtat cctgattatg tctgtagcgg ctgttattta catgcttgcc
     2761 gatgtaacaa tgcagttagc tattcttgta gctccgatat ttatcggttg ttatatgttt
     2821 ggattcacta gagtaatgtt taataactgg cttggtatat tattttctag tgtatttact
     2881 gttatttttg ctggagttct cgtcaaaatt ggtaccgagt ttcaaactga tatgcttagt
     2941 cagatatcga gagatgctaa ctcaacaaat attttaacaa tgggcgcaat ggcatttgta
     3001 attggagttc tgattgctgt ctttgtctgg aaatcatcga gtttcgcgca gcagcttgcc
     3061 ggtgcaggtg ttgaaggtac tcttcaggga atggctcttt tagggattgg ggctgctgga
     3121 atggccgtag agaaaacgag aaaccagatg aaacgtggaa cgcgaacagc cgccgaatgg
     3181 gcaggtgaaa aaggggagca gaaacgggct tcaataggcg cattgggaat ggaagcaaga
     3241 agacgagcat ccctggaaaa agcacgtgcg aggaattcag catgaacaaa aaactaattt
     3301 tttcagtact tttgtgctta ttttcatttg gttctgtcgc aggtattccg gttgctattg
     3361 atgccagtcc ggaatgggct gttgaagcca caagatggac agaacgactc aaacaatggt
     3421 ctgaaacagc gcggcattat caaagtcaga ttcaggcata taaagaccag ttagccacgg
     3481 caacaggtat aaggaatatt gcggcattca caaatgaact aagtaaccta caatcagagc
     3541 tggcaaacat ttataagcag gggaacagtt atatttctga ttttaccagt aatcctgaag
     3601 gtgcattaag tagtcaggcg aaaaatctgt tcagcaagta tggtgctttt aatatgtgtt
     3661 ctacaggcat tgaaagttct gataaccttt gtaaggccag aatagtttca acggccgcta
     3721 gcattgaaca gggaaatgag ataaataagc agctatcaag tgcaatgtct cagattcaga
     3781 gtttaagtaa ccgaattgag tcttcaaagg atatgaaaga atcccaggat ttggctaacg
     3841 cattgcaggc gcagtcgtta aaaatacagg caattaaaat gcagtatgat gtatgggata
     3901 gtaaaaacag ggctgatgcg gaaatgttga aagagcaaaa gtatgctgag tatcgcctgc
     3961 gtcagaaaaa tgcaaagata ccgagtttcg aatgatatga taaagctaaa taagctaaaa
     4021 gaatgggtag ataatcattg gtctagattg aatagtaccg gttctacacc gccgccactg
     4081 ttaatctcgc taccaatcat agttattgtt ttaagtgtgg agcttacgtt aaagctgatt
     4141 aatgctttaa tgtattatgg tacattgcaa tttatcactg ataaaattga aaagaggttt
     4201 gttcccagcg gtggtataaa agaaagactc cttttta
//
