LOCUS       NZ_CP086489             4237 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain Ec-050-T20-MAC plasmid pEc-050-T20-MAC_9,
            complete sequence.
ACCESSION   NZ_CP086489
VERSION     NZ_CP086489.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108724
            Assembly: GCF_022759765.1
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  JOURNAL   Unpublished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                   :: 308x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759765.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:40:39
            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)                     :: 5,280
            CDSs (total)                      :: 5,158
            Genes (coding)                    :: 4,886
            CDSs (with protein)               :: 4,886
            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)              :: 272
            CDSs (without protein)            :: 272
            Pseudo Genes (ambiguous residues) :: 0 of 272
            Pseudo Genes (frameshifted)       :: 108 of 272
            Pseudo Genes (incomplete)         :: 176 of 272
            Pseudo Genes (internal stop)      :: 53 of 272
            Pseudo Genes (multiple problems)  :: 57 of 272
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086489.1.
            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-MAC"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc-050-T20-MAC_9"
                     /geo_loc_name="Switzerland"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            join(3824..4237,1..585)
                     /locus_tag="LNN46_RS26210"
                     /old_locus_tag="LNN46_26210"
     CDS             join(3824..4237,1..585)
                     /locus_tag="LNN46_RS26210"
                     /old_locus_tag="LNN46_26210"
                     /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="type IV secretion system protein"
                     /protein_id="WP_000012467.1"
                     /translation="MSGFFEKFNSEVVSKIEEMTKPLQSQLGQDMLSLLSAGISVYILW
                     VGYQILAGKRQTPLQDLVWDLSKFAIILTFVSNADGYLTAAMDAIKSMKDGFLGKPVWA
                     TLDTMWSTTQLLADKVYAMDQSKYVSVEGGIGSMLVWGGSILIMSVAAVIYMLADVTMQ
                     LAILVAPIFIGCYMFGFTRVMFNNWLGILFSSVFTVIFAGVLVKIGTEFQTDMLSQISR
                     DANSTNILTMGAMAFVIGVLIAVFVWKSSSFAQQLAGAGVEGTLQGMALLGIGAAGMAV
                     EKTRNQMKRGTRTAAEWAGEKGEQKRASIGALGMEARRRASLEKARARNSA"
                     /name="type IV secretion system protein"
     gene            582..1295
                     /locus_tag="LNN46_RS26215"
                     /old_locus_tag="LNN46_26215"
     CDS             582..1295
                     /locus_tag="LNN46_RS26215"
                     /old_locus_tag="LNN46_26215"
                     /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"
     gene            2482..2997
                     /locus_tag="LNN46_RS26220"
                     /old_locus_tag="LNN46_26220"
     CDS             2482..2997
                     /locus_tag="LNN46_RS26220"
                     /old_locus_tag="LNN46_26220"
                     /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            3178..3468
                     /locus_tag="LNN46_RS26225"
                     /old_locus_tag="LNN46_26225"
     CDS             3178..3468
                     /locus_tag="LNN46_RS26225"
                     /old_locus_tag="LNN46_26225"
                     /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            3556..3819
                     /locus_tag="LNN46_RS26230"
                     /old_locus_tag="LNN46_26230"
     CDS             3556..3819
                     /locus_tag="LNN46_RS26230"
                     /old_locus_tag="LNN46_26230"
                     /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"
     Typing          2..390
                     /name="MPF_T"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="85.385"
                     /coverage="91.0"
                     /evalue="2.05e-64"
ORIGIN
        1 ttggtttggg gaggaagtat cctgattatg tctgtagcgg ctgttattta catgcttgcc
       61 gatgtaacaa tgcagttagc tattcttgta gctccgatat ttatcggttg ttatatgttt
      121 ggattcacta gagtaatgtt taataactgg cttggtatat tattttctag tgtatttact
      181 gttatttttg ctggagttct cgtcaaaatt ggtaccgagt ttcaaactga tatgcttagt
      241 cagatatcga gagatgctaa ctcaacaaat attttaacaa tgggcgcaat ggcatttgta
      301 attggagttc tgattgctgt ctttgtctgg aaatcatcga gtttcgcgca gcagcttgcc
      361 ggtgcaggtg ttgaaggtac tcttcaggga atggctcttt tagggattgg ggctgctgga
      421 atggccgtag agaaaacgag aaaccagatg aaacgtggaa cgcgaacagc cgccgaatgg
      481 gcaggtgaaa aaggggagca gaaacgggct tcaataggcg cattgggaat ggaagcaaga
      541 agacgagcat ccctggaaaa agcacgtgcg aggaattcag catgaacaaa aaactaattt
      601 tttcagtact tttgtgctta ttttcatttg gttctgtcgc aggtattccg gttgctattg
      661 atgccagtcc ggaatgggct gttgaagcca caagatggac agaacgactc aaacaatggt
      721 ctgaaacagc gcggcattat caaagtcaga ttcaggcata taaagaccag ttagccacgg
      781 caacaggtat aaggaatatt gcggcattca caaatgaact aagtaaccta caatcagagc
      841 tggcaaacat ttataagcag gggaacagtt atatttctga ttttaccagt aatcctgaag
      901 gtgcattaag tagtcaggcg aaaaatctgt tcagcaagta tggtgctttt aatatgtgtt
      961 ctacaggcat tgaaagttct gataaccttt gtaaggccag aatagtttca acggccgcta
     1021 gcattgaaca gggaaatgag ataaataagc agctatcaag tgcaatgtct cagattcaga
     1081 gtttaagtaa ccgaattgag tcttcaaagg atatgaaaga atcccaggat ttggctaacg
     1141 cattgcaggc gcagtcgtta aaaatacagg caattaaaat gcagtatgat gtatgggata
     1201 gtaaaaacag ggctgatgcg gaaatgttga aagagcaaaa gtatgctgag tatcgcctgc
     1261 gtcagaaaaa tgcaaagata ccgagtttcg aatgatatga taaagctaaa taagctaaaa
     1321 gaatgggtag ataatcattg gtctagattg aatagtaccg gttctacacc gccgccactg
     1381 ttaatctcgc taccaatcat agttattgtt ttaagtgtgg agcttacgtt aaagctgatt
     1441 aatgctttaa tgtattatgg tacattgcaa tttatcactg ataaaattga aaagaggttt
     1501 gttcccagcg gtggtataaa agaaagactc ctttttacgt taaagctgtt ttgtatttta
     1561 cttctgttat taatagtaat gcgattttca atgaagtaaa aaataaaggt catcgaatag
     1621 atggcctttt ctattctaaa ttctaaatat agagcctgcg gcaggcacag gcaaaaacat
     1681 cgtttttgga caatctgatt caaatgttaa catttgacat cggattgtct atcctgcatt
     1741 gctcttttgc cgacctcaaa acccctagcg tgtttttgtt tcccgatctc tagaaccacc
     1801 gagccgccac ggttccggca gcgccttgag cgcaaccgga aaccgtctgg ggagaacccc
     1861 agacccccat cgctgtaaca tcgacggtct acgaccacct accaaccgtg tggctacctg
     1921 ttccatgcta atgggctttg cagggggctg gcgcggttcc tggcgacctg aaagcccctg
     1981 gttaggggta tcggcgcgcc tgacctcctg aaaccctctg taagcatttt tcgcgccttt
     2041 catgccctga cgggcatcta aagcccgttt cgtgcgtctg agcgcgtttt aagagctaag
     2101 acgactaaaa cattaccaac acctgaaaat cgcgttctgg tgctctggat ggcccacaga
     2161 acgcattttc gaacagaaca gcaacggcat ttctgacaac atgcgagagg tgatcccgct
     2221 cgccgcagcc ccagcgaccg aacgtagtga gcgagtgggc gaggaagcgg aagagaattg
     2281 atagccataa ttgagcacct acgctcctta gttaagaact aagaagggaa attctcggaa
     2341 cccgcatgaa tcctagaaag tggtgatcag gatctgtacc ttgtaagctc agatccggta
     2401 ccttgcaggc tcaaaaattg cttgattttg agcttatgag gatttattgt gaatctccaa
     2461 agcccaaaaa aggatgcaat aatgagctcg ctaagcttac agagatacga aacaaacccg
     2521 tttttagagc ttatgacgat cccgatgaaa gggaaacgga tacaagtatc tcgtcttggg
     2581 cgggatgaca atgttttggt taatcaaaac acgggagaaa agtttggaac acatgtaacc
     2641 acttttaagc gtgtagatag tgagcaattt gttaagttgt ttactgcgaa tattgggtta
     2701 acgtttgatt tatcatcggc aggaattaaa gcttttaatg ttcttttatg ggctgttcaa
     2761 aaacaagcct ttgcaaagga tcaggttctt ttggattcaa gggctcttga tgacttttta
     2821 aaaagctatg atagcttaaa acttagttat gctacgttaa agagaggaat taacgagtta
     2881 gaaaaagctc agattatagc aaagacaatg cgtaaaggat tttattttat aaaccccaat
     2941 tttgtattta atggagatcg aatagcattt acaaccctaa ttgagaggga ttgttaatcg
     3001 atagaacaat acaatgcagg atagacaatc atggtcaaaa tgttaacatt ttatccatga
     3061 ttgtccaaaa acgatgtttt tgcctgtgcc tgccgcaggc tactagaagt agtcgcaggc
     3121 gaacaaaagt ggtgttttgt tcgcctgcta atcacaacaa cctggctaga ggtttttatg
     3181 actaaacatg atgctatacg catttctcaa cttcatcaaa ttttttacga tgatgatgga
     3241 ttaattgatt cagaaaagaa cgtgactatt ttatacagta taggatttac agttgatgaa
     3301 atagctcatt ttagaaattc aacaccaaac acagttgcga gtcagctatt aaatgcaagg
     3361 gttaaattag gttgcgcctc ggtttcatct ttaaagccaa tgatcttatt aagattgctt
     3421 ttgaacataa aagagattcg ttttggattc gaaactgatt gcaaataata tagttcaata
     3481 ggtatttttg ctcttgacta gaattacaat tgctgattgt atcagcaatt gtaatgtcca
     3541 tacgaggaat caaagatgaa aaaaatttgt acgctcttaa tgtctatttt cattctttcc
     3601 gcatgtggtg aagatacaaa atcatcagat tggtggctta atcatcccaa agaagcgacg
     3661 gagaaatata aggagtgtaa aaagtcaggg gaagattctg ttaattgtca aaatgttaaa
     3721 aaagttgccg gaattattgg tagaacctat ggccctatgc ttgaaatact taaggctgag
     3781 tcagctgaat atgataagca acatggattg aacaggtgat aacatgtctg gtttctttga
     3841 aaagtttaat agcgaagttg ttagtaaaat cgaagagatg accaaaccac ttcaaagtca
     3901 attaggtcag gatatgttat ctcttctaag tgcaggtatt agcgtttata tcctctgggt
     3961 tggctatcaa atattggcag ggaaacgcca gaccccatta caagatctcg tctgggatct
     4021 atcaaaattt gccattattt taacattcgt aagcaatgct gatggctatc tgacggcagc
     4081 aatggatgct attaaatcta tgaaggatgg gttccttggt aaacctgtat gggcaacgct
     4141 agataccatg tggagtacaa ctcagctttt ggctgacaaa gtttatgcta tggatcaatc
     4201 caaatatgtg tcagttgaag gtggaatcgg gtcaatg
//
