LOCUS       NZ_CP086488             4773 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain Ec-050-T20-MAC plasmid pEc-050-T20-MAC_8,
            complete sequence.
ACCESSION   NZ_CP086488
VERSION     NZ_CP086488.1
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 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  JOURNAL   Unpublished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                   :: 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
            CP086488.1.
            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-T20-MAC"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc-050-T20-MAC_8"
                     /geo_loc_name="Switzerland"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            complement(<28..798)
                     /locus_tag="LNN46_RS26180"
                     /old_locus_tag="LNN46_26185"
                     /pseudo=""
     CDS             complement(<28..798)
                     /locus_tag="LNN46_RS26180"
                     /old_locus_tag="LNN46_26185"
                     /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            complement(737..1060)
                     /locus_tag="LNN46_RS26185"
                     /old_locus_tag="LNN46_26190"
     CDS             complement(737..1060)
                     /locus_tag="LNN46_RS26185"
                     /old_locus_tag="LNN46_26190"
                     /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            1698..1781
                     /locus_tag="LNN46_RS26495"
     CDS             1698..1781
                     /locus_tag="LNN46_RS26495"
                     /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"
     gene            complement(2375..2842)
                     /locus_tag="LNN46_RS26190"
                     /old_locus_tag="LNN46_26195"
     CDS             complement(2375..2842)
                     /locus_tag="LNN46_RS26190"
                     /old_locus_tag="LNN46_26195"
                     /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            3378..3929
                     /locus_tag="LNN46_RS26195"
                     /old_locus_tag="LNN46_26200"
     CDS             3378..3929
                     /locus_tag="LNN46_RS26195"
                     /old_locus_tag="LNN46_26200"
                     /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            complement(4128..4343)
                     /locus_tag="LNN46_RS26200"
                     /old_locus_tag="LNN46_26205"
     CDS             complement(4128..4343)
                     /locus_tag="LNN46_RS26200"
                     /old_locus_tag="LNN46_26205"
                     /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"
     Typing          complement(1162..1349)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.864"
                     /coverage="87.0"
                     /evalue="5.83e-49"
     Typing          1295..1807
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.829"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2..747)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.787"
                     /coverage="99.0"
                     /evalue="1.62e-159"
     Typing          complement(4025..4773)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="89.2"
                     /coverage="100.0"
                     /evalue="1.78e-136"
ORIGIN
        1 tgctgctgcg ctttcgattt ctgctctaag tccttcgcca gcgttaaaag actgttcata
       61 gatggctccc ttcagtcgga tgtttcgccc cccgtccggg tcggcaatgc tgatgctgct
      121 ttttgtggtg cgcaccacct caaaacctgc gctttctagc gcctcagtga cgtcctggcg
      181 ggttttcagc tccccggacg aggctaaggc cagtaaaccc cgtgtaattg cctgagcggc
      241 ttcctgcttc gttttcggca gcgcggacgg cgtgaccagc gcccgccggt tttcaggcgc
      301 gttcgggtca tgcagcccca gcctgccgtt cacgatggtc tgccaggcat caatgcgcgg
      361 acggtcggcg cggtcgtaat acggctggag acgcctgcct gtcagcagct ccatgttcgg
      421 gatcaggaag ttcagctcca gccgcccctt atcctggtgc tcaacccata gcacgctgta
      481 ctggtcttta tcgagtccgg gcatcagaac ccgttcaaag ctcgccatca gcttttcgcg
      541 ctgcccgggc ggtaaatcct tttcggcaaa ggacaggacg ccggatgtgt acttttttgc
      601 gtagggcgag gcgtcgataa gctccctgac ttcttccggc ttcccctgca gaacggtggc
      661 gccgtcgcgc tgtcggtctt tccccagcag ataatccacc ggaccggcgc caccgccgcg
      721 ccctcgcggg tgaaacttaa cgatcatcgt ctgcaccctt ttccagcacg gcatgccgca
      781 gccgctcgag tccggcatct atggccatca gcgcggcgac gacctgcacg cggtcgtgcc
      841 cgctgccgcc accggcgtta acctgccggg caatctggtt gaggttattc cccatgccgg
      901 caagctgacg aagcagcgcc ggcgagattg agggaagctt gccggcgcgg gcgggtttct
      961 cggccaggca cgtctggcgc atccaggctg caagctgttt accgtcgcag cgttccagca
     1021 gacggcggtg ctcatcttcg gtcacccaca tggtgagcat cttgttccgt ttctctgaca
     1081 aaccgatctc ctgataacgc cgggacgggc gggaaatctt ttcccggtcg gcgcggtgtt
     1141 ggacaagccg caggcgcgtc agtggtttta gcaggtttcg gggcgcagcc ctgaaccagt
     1201 cacgtagcgc tagcggagtg tatactggct caatatgtta cggcggagta acacgtaatg
     1261 aaagtgcttc atgtggcagg ggaaaaatgc agctgcaggg cgtacaggag aaaatggagg
     1321 ttacggtgat atgacgcctc ctcgctcact cggtcgcttc cgctcctgac gttcggctgc
     1381 ggcgggcgtt acctgcaaac ggataagagc aaaggcatac ggcatggcaa gcaggacagg
     1441 aaaaggatgc ggcgctgccg tttttccata ggctccgccc ccctgacaag catcacgaaa
     1501 tctgacgctc aaatcagtgg tggcgaaacc cgacaggact taaagatacc aggcgtttcc
     1561 ccctggtggc tccctcgtgc gctctcctgt tcctgccttt cggtttaccg gtgtcattcc
     1621 gctgttatgg ccgcgtttat ctcattccac gcctgacact cagttccggg taggcagttc
     1681 gctccaagct ggactgtatg cacgaacccc ccgttcagtc cgaccgctgc gccttgtccg
     1741 gtaactatcg tcttgagtcc aacccggata gacacgacta atcgccattg gcaacggcca
     1801 ctggtaagca ggatgtgcga gagatgtaac gagagttctt gaagtggcgg cctaactgag
     1861 gctacactga aaggacagta tttggtgaca tgtctcgcac aagactgtta ccacggttag
     1921 agaatctgcc aggattaact aaccttcgaa aaaaccacct gccagggtgg ttttttcgtt
     1981 tctgagcaag agactacgac gagccactga tgatctcaag tgttcatttc tgatattcac
     2041 agcagaataa ctgttaggat atagggtatc tatagccagg agcttcaaga aatccagaca
     2101 cagcaatgga ttccagggtt atcgaaaaaa attagtatat aggttgcaac caaaatgttg
     2161 gttgcaaatc tacatcacga tgtttatgat tattgtactg caagagcatt cgcagggggc
     2221 atcaaccagt aataggcctt ctgtgccggg cagtcagatg gctggtcatc tgccgggtag
     2281 ttacgacaag cgtcggtttc tgaaccctat gtgctaagga aatgctgcga ctaccaacga
     2341 attcataaag ggcgcttttt agcgccctat ttttttattc aatatgacca accaaagtac
     2401 cgtgcgccgt ccttcgtgtg tacgcagtca caacgacata gatccaacct gactcagttt
     2461 caggcgcttc tctgggctca agaattacga tgcctaccga cgactttagc actgcaggcc
     2521 gatgtttacc gcttgtactg ttgaactcgc aatatattgg tacgccacga cgaataatat
     2581 cccggacaaa acgagccaca tcattaacgg tcgtatatcc cagcttaacc agttcctgct
     2641 cgtgctcagc ccagatatgg cgaacaccaa agccccggtt agggccagta tgcctaccaa
     2701 cacgcaagaa gatgtcgcca gcaggaataa catcaccttt agaattaatt tcagggacac
     2761 ggccatagca atcaagccca tcagggtgag ctatagcgct gttaggtgaa ccagctacac
     2821 cgtaattgtt tggagcaggc acaaaacgat ccttattgag tagagtccgc atatggtacc
     2881 agagaggaaa caagcggaag gagcccaaga aaaaagcaga gacgataaaa agaatcctta
     2941 tggattattt ttttgtcctt tcatccttgg cgcataagga tatcacacct gaaaatgtga
     3001 cgtgcgaatc gccctagcag ctagatttac cataacatcc cttgcccgca ccgctccgga
     3061 cgggttcagc gtgaaagcgg cgttagcccg gtaaaaccgg cagtaaactc cccgctaaac
     3121 cgcgcattct gcgcctgata aatttcacgc ggctgcatag ccatgcagcc acgtgaatgg
     3181 ctcatgcttt caatgtatat cctcgtccaa gcccctgttt taaccggttt atcaaaaaaa
     3241 caaacaggaa gccttatcac taacaataaa agaggtaggg ggctgcattt tatcgcataa
     3301 aaaacattta caacacgaat tctatcgtat agatttcata aaaaaatgaa attgactcac
     3361 ctattaaggg tttctatatg aaagatatga aagctgttgt ggtttttacc gggaaggatt
     3421 tgaacataat gagaaccgag ggggggtcag gctactggca tgccagaaca gacaggctca
     3481 acgatgccga ttacctcata gcagtaagaa acagaaggga aacgtgggca gtaaaagacc
     3541 tggaacacgg cacagcattc ctgatcgcca aaattaccgg gtgttttaaa agccctgatt
     3601 acgacgacag gaacgtcata acctttgatg aatacgcaga aattcacact ccaaaagcat
     3661 ggaaaatgct aaccgatggt cagcgctatc cggttgctta cctgagcgca caggaagctt
     3721 ttttacgtat tggggtaaca ccggaacaac tggaatggaa gaaattccat ccttcatccc
     3781 catcggttcc taatacagtg attcctggtc tggctgaaga gaaaacagaa aaactctccc
     3841 ttaacgaggc aattgaaaga gccaaaaagg atattagcaa cgcaacaggg attgatagct
     3901 cagccataac aataagcatc aagatctgat gaagcgtgaa caacaagata gcagcctcat
     3961 gttctagaac tgaacctgtg cgccagaaac agcaagccca tgcttttccg gcgcacagat
     4021 tcaaagtgac ggaccgttgt acgttcgctg tcgctgagat cgttccagct ccagcgcttt
     4081 ctgatgctgc gccgcccgtt cctgctcacg atgtgcctct atcacgttca gccttgtgac
     4141 aaccggcgca gctgctcgct caaactctgc acctgcctgc tcaagcccgt gacgcgctcg
     4201 ctcagcgccg cgttctcccg ttgcataaga ccaaacatcg tccgccattc cgcgaaggcg
     4261 ttctcccact cgtccagcct tttcgagtag tcctgctgta gctgctctaa tgcgctcagc
     4321 aactgttttt ccagctccgt catgtgctat ttccccgcca gtatcatcca gctcgaatcc
     4381 tctccgaacc gtcccgcttc cgggttcacc ctcacgcagc gccgtctctg ctctccgcag
     4441 gtcgagagct gcacgccgct gttcctctcg gacagcatgg cctgcgtgct cttctgctcc
     4501 cggatgatcg tgtaattgtc gagtatctgc tgcccctgcc accatagaat gcttgcgccc
     4561 gatgctgtca gcagtgtaga caccaggacg atggtcagcc acgtctggct gaccatacgc
     4621 accatgcctt tcgtgcgctg gctcatggct gaggacagct tccggtcgtg gtcgaggatg
     4681 gcggcgctga ttctcttctc gctttcgctc agttccgctc tgacaaactt ctcgtgctcg
     4741 ctgaatgcga ctttcagcat ctcgccggta ctc
//
