LOCUS       NZ_CP086530             4440 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain Ec-042-T20-MAC plasmid pEc-042-T20-MAC_4,
            complete sequence.
ACCESSION   NZ_CP086530
VERSION     NZ_CP086530.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108719
            Assembly: GCF_022759865.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4440)
  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  JOURNAL   Unpublished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 4440)
  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                   :: 290x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759865.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:47:49
            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)                     :: 4,723
            CDSs (total)                      :: 4,602
            Genes (coding)                    :: 4,369
            CDSs (with protein)               :: 4,369
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 233
            CDSs (without protein)            :: 233
            Pseudo Genes (ambiguous residues) :: 0 of 233
            Pseudo Genes (frameshifted)       :: 64 of 233
            Pseudo Genes (incomplete)         :: 156 of 233
            Pseudo Genes (internal stop)      :: 41 of 233
            Pseudo Genes (multiple problems)  :: 25 of 233
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086530.1.
            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..4440
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="Ec-042-T20-MAC"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc-042-T20-MAC_4"
                     /geo_loc_name="Switzerland"
                     /collection_date="2019"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            complement(803..1225)
                     /locus_tag="LNN58_RS23455"
                     /old_locus_tag="LNN58_23450"
     CDS             complement(803..1225)
                     /locus_tag="LNN58_RS23455"
                     /old_locus_tag="LNN58_23450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_004216558.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKGIKVID
                     TSELIRVFGSLDGVIDAVKYDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1225..1416)
                     /locus_tag="LNN58_RS23460"
                     /old_locus_tag="LNN58_23455"
     CDS             complement(1225..1416)
                     /locus_tag="LNN58_RS23460"
                     /old_locus_tag="LNN58_23455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000166328.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1897..2046)
                     /locus_tag="LNN58_RS23465"
                     /old_locus_tag="LNN58_23460"
     CDS             complement(1897..2046)
                     /locus_tag="LNN58_RS23465"
                     /old_locus_tag="LNN58_23460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_017880354.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            2953..3867
                     /locus_tag="LNN58_RS23470"
                     /old_locus_tag="LNN58_23465"
     CDS             2953..3867
                     /locus_tag="LNN58_RS23470"
                     /old_locus_tag="LNN58_23465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001448734.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Abi family protein"
                     /protein_id="WP_017880353.1"
                     /translation="MPNTVNYPQIIPFISKGKMDAIKNTFGNTLTDRECYGIYIWSQKA
                     SAAIYPLLQQLEVTLRNSIDKEATNVMGLNWWDGVYTDKTKPKWDDFIFNINKGRDRYK
                     KNYKKNNPSVLSSLIVVPHDDAIAHTDFYTWQAVLSDTFHTQNRKHVNKSLWPRLTYKV
                     LKGLDRKKTEKAARLDFINELNEIRNYRNRLSHNDCIWIKMNSNNLQSAVETVREKINK
                     IEDLIKTINPQIHSTLVKWGVFYHARRICSQREVEHHMGKNIVNCTNPTMSSILATIYS
                     WTDDGKLTSVVNDGKNDLAIHKF"
                     /name="Abi family protein"
     Typing          2202..2713
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.686"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ctactcgaaa cggtaatttt aacgaagccc tccccccccc ctcaatacaa acccgaatat
       61 taagctattt accataacat cccttgcgtg caccacctga gaggccctca gggcgtttct
      121 gacgggaaac cggcaaaaca gacaacaaac cacccgaaaa cccgccagaa acgcgcaggc
      181 tctgttttta cggcatgcat gagtatgcgc gcaagtgcat agcgcggaaa ttcacgccat
      241 tcagccgggg taagtcctgt ttccggcgtt cttcccatcc gaaaacggtg aacggggacg
      301 caatttattg cgtggccgtg aagcgttgcc ggcgcagccg gaaaaccggt tttcagcacg
      361 ttcaggaatc gggttcgtcg acggccggca atcacgttat ggcaagtcgc cggacgactc
      421 accacacgat tcaccggcga ttcgactcgt gacttgactc tagagtcacc acggtcaaaa
      481 aaacgccaaa tcgacgattc gactctagag tcaagtcgtc ataagttact gatagtgtgg
      541 agtgagtcgt cgatgactct atgacgagtc gtcggcaagt cgtacacgaa tcaccgacga
      601 cttggattga ccttacagaa ggtaatactg cgtaatttaa taacaaccaa ctaactgata
      661 ttaatgaatt atctgcaaaa atttaatttt gcgtggggtg tggatatttt tagtgtgagg
      721 agcgttcaga ggtctgacga tttttgggaa ggttcacgaa cgccccggca tggccggaga
      781 ggaaaactca agcatggcgg gatcaggatt ttttccagaa tttccaccac ggggaatggg
      841 gtggtgaaga aggttcgtgc ttgtgctcca gaagctgcat agcctgacga agggaatcaa
      901 tatgctcatc tcgagcctta acagcccctt taagaccatc gttttcagct tcaagtaaag
      961 cgattctatg ttgtaaatca tgtaaaccaa cgctgttaat acctgtagat tctgcgtcac
     1021 tttttacatc atattttaca gcatcgatta caccatcaag agaaccaaac actctaataa
     1081 gctctgatgt atcaataact ttaataccct tcccgtgctt tacaacagag gtgtaactta
     1141 acttaccact gttaatcatc ttgtaaatag tagggcgact aaccttaaca agccgtgctg
     1201 cttcactaat agacactctg gccatcagtt accatcctgt aatgcatcca gtctcgagga
     1261 cagtgtacgg aaaagatgct ccgcatcatc gtggagtttc tcacaaaggt cggcctcagc
     1321 atcgagatca agctcgttaa gcttctccag caggagcaga gactgattct ggatgaattt
     1381 agccatgttc agcgcagttt tctgttgttt cgtcataagg gacctcagag catcagtgct
     1441 cagtgtaaaa ccggtaaggg ggtcggatgt acgaatggtt cagagaacgg atctgaggta
     1501 atcctgtagt tattttgtag tttatctgta gtcatcgcac taaaaatcag gattaagtca
     1561 tcagcttttg tagtctttct gtagtttacc tgtagtccgg aaaaataatc cgttcatgcg
     1621 agcatgaacg aggtcgttaa tgacgttttt ttgtcaccga cgccccttaa cctccgcaga
     1681 tcacccggcc agaatgataa ttgtttggcc cttaaatggt catacaccta acgcagccgc
     1741 gattttcatc gcaactgcat gaattaaaag gtaaaaattg aaacctccgt ttatttatgt
     1801 aatacgcaac gtattacaat cacctgtaac cacatgaaaa taaagaaata aaatgtaata
     1861 ccggcgtatt accacgtacg cgggcaagcg aaaaagctat aacgcttccc ggccgacagg
     1921 tggcccggaa tccacagggg cgtgcaggtt ctcttcagta acctgcgcca ttaaatcaaa
     1981 aaggtcatat tcgccgggaa gctgcgtatc agtcgaatcc agttgttcat catattcaga
     2041 tggcatgggg tgatatccag tagctgagag gttgttagcg ggtttcgggg cgcagccctg
     2101 aaccagtcaa atagcacgtg cggagtgtat acgggctcaa tatgctacgg tggagtaaca
     2161 cgttatgaga gtgcgtcatg tgacagagga aagtgcagcg gcggggcgta cgggagaaaa
     2221 tggaaacccg gggatatgac gcctcctcgc tcactcagtc gctgccgctc ctgccgttcg
     2281 gctgcggcgg gcgttacctg cacacggata agagcaaaga catacggcat gacaagcggg
     2341 gcagcaaaag aatgcgccgc tgccgttttt ccataggctc cgcccccctg acaagcatca
     2401 cagaatcgga cgctcaaatc agtggtggcg aaacccgaca ggactataaa gatatcaggc
     2461 gtttccccct gatggctccc tcgtgcgctc tcctgttcct gcctttcggt ttaccggtgt
     2521 cattccgctg ttatggccgc gtttgtctca ttccacgcct gacactcagt tccgggtagg
     2581 cagttcgctc caagctggac tgtatgcacg acccccccgt tcagtccgac cgctgcgcct
     2641 tatccggtaa ctatcgtctt gagtccaacc cggatagacg tgcaaatgcg ccactggcaa
     2701 cggccactgg taagcaggat gtgcgagaga tgtatcgaga gttcttgaag tggaggcctt
     2761 agtgaggcta cactggaagg acagatttgg tgacatgtct cgcacaagac tgttaccacg
     2821 gttcagaaac ttgccggtta atgaaccttc gaaaaaccac cttgccgggt ggttttttcg
     2881 tttcatactc tacaactatg ctgagccata tggcaacatc aattcatacc tacatatgaa
     2941 gaagcgatgc ccatgcctaa caccgttaat tatccgcaaa taatcccgtt catatcgaaa
     3001 gggaaaatgg atgctataaa aaacactttc ggtaatacct taacagacag ggaatgctac
     3061 gggatatata tatggtcgca aaaagcgtct gctgcaatat accctctcct acagcagtta
     3121 gaggtaacgc ttaggaactc aatagataaa gaagcaacaa atgttatggg tctgaactgg
     3181 tgggatggag tctatacaga taaaaccaaa cctaaatggg atgattttat tttcaacata
     3241 aacaaaggcc gagatagata taagaagaat tataaaaaaa acaacccatc tgtactcagc
     3301 tctttgattg tcgttccgca tgatgacgct atagctcata ctgactttta cacatggcaa
     3361 gcggtcctaa gtgacacatt tcacacgcaa aatagaaaac acgtaaataa atctctctgg
     3421 ccaaggctta cttacaaggt gctaaaaggt ctagacagaa aaaaaacaga gaaagcagca
     3481 aggcttgatt ttatcaacga actaaatgag ataagaaatt acagaaacag attatcgcac
     3541 aatgactgta tatggataaa aatgaactcc aataacttac agtccgcagt ggaaacagtt
     3601 agagaaaaaa taaataaaat tgaagactta ataaaaacaa ttaaccctca aatacattcg
     3661 accctggtta aatggggagt tttctaccat gcgagaagaa tttgctctca aagagaggtt
     3721 gagcatcata tggggaaaaa catagtaaac tgcaccaacc caactatgag ctctatttta
     3781 gcaaccattt actcatggac ggacgatgga aagctaacca gcgtcgtgaa tgacggtaaa
     3841 aacgaccttg cgatacataa gttctagaag gagaaaaggc ccgacatgct aagcatgtcg
     3901 agccttttcc aagtcttttg ccaatatcac cttacggcgg agcgtggcct ttattccatt
     3961 ataaataatg cataaaagcg aaagctctag gcttcattaa aaatgattct acatcactta
     4021 ctcaaaaaag agcaagacct tatgtcacaa gggatcacac gagcagccgt aaatgactta
     4081 acttgatgaa aaaaaacgtt tttaatctaa ctaaacttac ctgcctggct ttaataaaga
     4141 gcttaaaaat ggtacaatca accatccaag caattgtttt ataaagtcaa ttagcgttcc
     4201 atcagacaaa aaataatgga gagaaaggag aatgaaaaca atgaaaacgt tctttaaggt
     4261 taaaaatctt ttaaaatcaa tgagatactt aaagcgtttc ctgtcactga atgcgacagt
     4321 gaaacgcgag tgcgcggtgg tgtgtaacac cttcgctgtc gcattcagtg acaggcacta
     4381 gtttatcaca aaaaacgata aaagtcaata taaccaacac tttaaaacca aacattttag
//
