LOCUS       NZ_CP086499             4237 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain Ec-050-T5-ESBL plasmid pEc-050-T5-ESBL_9,
            complete sequence.
ACCESSION   NZ_CP086499
VERSION     NZ_CP086499.1
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 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  JOURNAL   Unpublished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                   :: 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
            CP086499.1.
            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-T5-ESBL"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc-050-T5-ESBL_9"
                     /geo_loc_name="Switzerland"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            join(3981..4237,1..259)
                     /locus_tag="LNN51_RS26185"
                     /old_locus_tag="LNN51_26190"
     CDS             join(3981..4237,1..259)
                     /locus_tag="LNN51_RS26185"
                     /old_locus_tag="LNN51_26190"
                     /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            440..730
                     /locus_tag="LNN51_RS26190"
                     /old_locus_tag="LNN51_26195"
     CDS             440..730
                     /locus_tag="LNN51_RS26190"
                     /old_locus_tag="LNN51_26195"
                     /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            818..1081
                     /locus_tag="LNN51_RS26195"
                     /old_locus_tag="LNN51_26200"
     CDS             818..1081
                     /locus_tag="LNN51_RS26195"
                     /old_locus_tag="LNN51_26200"
                     /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            1086..2084
                     /locus_tag="LNN51_RS26200"
                     /old_locus_tag="LNN51_26205"
     CDS             1086..2084
                     /locus_tag="LNN51_RS26200"
                     /old_locus_tag="LNN51_26205"
                     /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            2081..2794
                     /locus_tag="LNN51_RS26205"
                     /old_locus_tag="LNN51_26210"
     CDS             2081..2794
                     /locus_tag="LNN51_RS26205"
                     /old_locus_tag="LNN51_26210"
                     /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          1087..1889
                     /name="MPF_T"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="89.552"
                     /coverage="91.0"
                     /evalue="1.15e-160"
ORIGIN
        1 tgttctttta tgggctgttc aaaaacaagc ctttgcaaag gatcaggttc ttttggattc
       61 aagggctctt gatgactttt taaaaagcta tgatagctta aaacttagtt atgctacgtt
      121 aaagagagga attaacgagt tagaaaaagc tcagattata gcaaagacaa tgcgtaaagg
      181 attttatttt ataaacccca attttgtatt taatggagat cgaatagcat ttacaaccct
      241 aattgagagg gattgttaat cgatagaaca atacaatgca ggatagacaa tcatggtcaa
      301 aatgttaaca ttttatccat gattgtccaa aaacgatgtt tttgcctgtg cctgccgcag
      361 gctactagaa gtagtcgcag gcgaacaaaa gtggtgtttt gttcgcctgc taatcacaac
      421 aacctggcta gaggttttta tgactaaaca tgatgctata cgcatttctc aacttcatca
      481 aattttttac gatgatgatg gattaattga ttcagaaaag aacgtgacta ttttatacag
      541 tataggattt acagttgatg aaatagctca ttttagaaat tcaacaccaa acacagttgc
      601 gagtcagcta ttaaatgcaa gggttaaatt aggttgcgcc tcggtttcat ctttaaagcc
      661 aatgatctta ttaagattgc ttttgaacat aaaagagatt cgttttggat tcgaaactga
      721 ttgcaaataa tatagttcaa taggtatttt tgctcttgac tagaattaca attgctgatt
      781 gtatcagcaa ttgtaatgtc catacgagga atcaaagatg aaaaaaattt gtacgctctt
      841 aatgtctatt ttcattcttt ccgcatgtgg tgaagataca aaatcatcag attggtggct
      901 taatcatccc aaagaagcga cggagaaata taaggagtgt aaaaagtcag gggaagattc
      961 tgttaattgt caaaatgtta aaaaagttgc cggaattatt ggtagaacct atggccctat
     1021 gcttgaaata cttaaggctg agtcagctga atatgataag caacatggat tgaacaggtg
     1081 ataacatgtc tggtttcttt gaaaagttta atagcgaagt tgttagtaaa atcgaagaga
     1141 tgaccaaacc acttcaaagt caattaggtc aggatatgtt atctcttcta agtgcaggta
     1201 ttagcgttta tatcctctgg gttggctatc aaatattggc agggaaacgc cagaccccat
     1261 tacaagatct cgtctgggat ctatcaaaat ttgccattat tttaacattc gtaagcaatg
     1321 ctgatggcta tctgacggca gcaatggatg ctattaaatc tatgaaggat gggttccttg
     1381 gtaaacctgt atgggcaacg ctagatacca tgtggagtac aactcagctt ttggctgaca
     1441 aagtttatgc tatggatcaa tccaaatatg tgtcagttga aggtggaatc gggtcaatgt
     1501 tggtttgggg aggaagtatc ctgattatgt ctgtagcggc tgttatttac atgcttgccg
     1561 atgtaacaat gcagttagct attcttgtag ctccgatatt tatcggttgt tatatgtttg
     1621 gattcactag agtaatgttt aataactggc ttggtatatt attttctagt gtatttactg
     1681 ttatttttgc tggagttctc gtcaaaattg gtaccgagtt tcaaactgat atgcttagtc
     1741 agatatcgag agatgctaac tcaacaaata ttttaacaat gggcgcaatg gcatttgtaa
     1801 ttggagttct gattgctgtc tttgtctgga aatcatcgag tttcgcgcag cagcttgccg
     1861 gtgcaggtgt tgaaggtact cttcagggaa tggctctttt agggattggg gctgctggaa
     1921 tggccgtaga gaaaacgaga aaccagatga aacgtggaac gcgaacagcc gccgaatggg
     1981 caggtgaaaa aggggagcag aaacgggctt caataggcgc attgggaatg gaagcaagaa
     2041 gacgagcatc cctggaaaaa gcacgtgcga ggaattcagc atgaacaaaa aactaatttt
     2101 ttcagtactt ttgtgcttat tttcatttgg ttctgtcgca ggtattccgg ttgctattga
     2161 tgccagtccg gaatgggctg ttgaagccac aagatggaca gaacgactca aacaatggtc
     2221 tgaaacagcg cggcattatc aaagtcagat tcaggcatat aaagaccagt tagccacggc
     2281 aacaggtata aggaatattg cggcattcac aaatgaacta agtaacctac aatcagagct
     2341 ggcaaacatt tataagcagg ggaacagtta tatttctgat tttaccagta atcctgaagg
     2401 tgcattaagt agtcaggcga aaaatctgtt cagcaagtat ggtgctttta atatgtgttc
     2461 tacaggcatt gaaagttctg ataacctttg taaggccaga atagtttcaa cggccgctag
     2521 cattgaacag ggaaatgaga taaataagca gctatcaagt gcaatgtctc agattcagag
     2581 tttaagtaac cgaattgagt cttcaaagga tatgaaagaa tcccaggatt tggctaacgc
     2641 attgcaggcg cagtcgttaa aaatacaggc aattaaaatg cagtatgatg tatgggatag
     2701 taaaaacagg gctgatgcgg aaatgttgaa agagcaaaag tatgctgagt atcgcctgcg
     2761 tcagaaaaat gcaaagatac cgagtttcga atgatatgat aaagctaaat aagctaaaag
     2821 aatgggtaga taatcattgg tctagattga atagtaccgg ttctacaccg ccgccactgt
     2881 taatctcgct accaatcata gttattgttt taagtgtgga gcttacgtta aagctgatta
     2941 atgctttaat gtattatggt acattgcaat ttatcactga taaaattgaa aagaggtttg
     3001 ttcccagcgg tggtataaaa gaaagactcc tttttacgtt aaagctgttt tgtattttac
     3061 ttctgttatt aatagtaatg cgattttcaa tgaagtaaaa aataaaggtc atcgaataga
     3121 tggccttttc tattctaaat tctaaatata gagcctgcgg caggcacagg caaaaacatc
     3181 gtttttggac aatctgattc aaatgttaac atttgacatc ggattgtcta tcctgcattg
     3241 ctcttttgcc gacctcaaaa cccctagcgt gtttttgttt cccgatctct agaaccaccg
     3301 agccgccacg gttccggcag cgccttgagc gcaaccggaa accgtctggg gagaacccca
     3361 gacccccatc gctgtaacat cgacggtcta cgaccaccta ccaaccgtgt ggctacctgt
     3421 tccatgctaa tgggctttgc agggggctgg cgcggttcct ggcgacctga aagcccctgg
     3481 ttaggggtat cggcgcgcct gacctcctga aaccctctgt aagcattttt cgcgcctttc
     3541 atgccctgac gggcatctaa agcccgtttc gtgcgtctga gcgcgtttta agagctaaga
     3601 cgactaaaac attaccaaca cctgaaaatc gcgttctggt gctctggatg gcccacagaa
     3661 cgcattttcg aacagaacag caacggcatt tctgacaaca tgcgagaggt gatcccgctc
     3721 gccgcagccc cagcgaccga acgtagtgag cgagtgggcg aggaagcgga agagaattga
     3781 tagccataat tgagcaccta cgctccttag ttaagaacta agaagggaaa ttctcggaac
     3841 ccgcatgaat cctagaaagt ggtgatcagg atctgtacct tgtaagctca gatccggtac
     3901 cttgcaggct caaaaattgc ttgattttga gcttatgagg atttattgtg aatctccaaa
     3961 gcccaaaaaa ggatgcaata atgagctcgc taagcttaca gagatacgaa acaaacccgt
     4021 ttttagagct tatgacgatc ccgatgaaag ggaaacggat acaagtatct cgtcttgggc
     4081 gggatgacaa tgttttggtt aatcaaaaca cgggagaaaa gtttggaaca catgtaacca
     4141 cttttaagcg tgtagatagt gagcaatttg ttaagttgtt tactgcgaat attgggttaa
     4201 cgtttgattt atcatcggca ggaattaaag cttttaa
//
