LOCUS       NZ_CP086518             4773 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain Ec-050-T0 plasmid pEc-050-T0_8, complete
            sequence.
ACCESSION   NZ_CP086518
VERSION     NZ_CP086518.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108721
            Assembly: GCF_022759805.1
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  JOURNAL   Unpublished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                   :: 271x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759805.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:49:50
            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)                     :: 5,277
            CDSs (total)                      :: 5,155
            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)              :: 269
            CDSs (without protein)            :: 269
            Pseudo Genes (ambiguous residues) :: 0 of 269
            Pseudo Genes (frameshifted)       :: 109 of 269
            Pseudo Genes (incomplete)         :: 173 of 269
            Pseudo Genes (internal stop)      :: 53 of 269
            Pseudo Genes (multiple problems)  :: 58 of 269
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086518.1.
            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-T0"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc-050-T0_8"
                     /geo_loc_name="Switzerland"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            complement(join(4606..4773,1..156))
                     /locus_tag="LNN50_RS26160"
                     /old_locus_tag="LNN50_26165"
     CDS             complement(join(4606..4773,1..156))
                     /locus_tag="LNN50_RS26160"
                     /old_locus_tag="LNN50_26165"
                     /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            794..877
                     /locus_tag="LNN50_RS26480"
     CDS             794..877
                     /locus_tag="LNN50_RS26480"
                     /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(1471..1938)
                     /locus_tag="LNN50_RS26165"
                     /old_locus_tag="LNN50_26170"
     CDS             complement(1471..1938)
                     /locus_tag="LNN50_RS26165"
                     /old_locus_tag="LNN50_26170"
                     /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            2474..3025
                     /locus_tag="LNN50_RS26170"
                     /old_locus_tag="LNN50_26175"
     CDS             2474..3025
                     /locus_tag="LNN50_RS26170"
                     /old_locus_tag="LNN50_26175"
                     /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(3224..3439)
                     /locus_tag="LNN50_RS26175"
                     /old_locus_tag="LNN50_26180"
     CDS             complement(3224..3439)
                     /locus_tag="LNN50_RS26175"
                     /old_locus_tag="LNN50_26180"
                     /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"
     gene            complement(3443..3928)
                     /locus_tag="LNN50_RS26180"
                     /old_locus_tag="LNN50_26185"
     CDS             complement(3443..3928)
                     /locus_tag="LNN50_RS26180"
                     /old_locus_tag="LNN50_26185"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_079967943.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKVAFSEHEKFVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSTLLTASGASILWWQGQQIL
                     DNYTIIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(<3963..4667)
                     /locus_tag="LNN50_RS26485"
                     /old_locus_tag="LNN50_26190"
                     /pseudo=""
     CDS             complement(<3963..4667)
                     /locus_tag="LNN50_RS26485"
                     /old_locus_tag="LNN50_26190"
                     /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"
     Typing          complement(258..445)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.864"
                     /coverage="87.0"
                     /evalue="5.83e-49"
     Typing          391..903
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.829"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2..156)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.154"
                     /coverage="100.0"
                     /evalue="2.63e-26"
     Typing          complement(3121..4616)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.385"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctgacgaagc agcgccggcg agattgaggg aagcttgccg gcgcgggcgg gtttctcggc
       61 caggcacgtc tggcgcatcc aggctgcaag ctgtttaccg tcgcagcgtt ccagcagacg
      121 gcggtgctca tcttcggtca cccacatggt gagcatcttg ttccgtttct ctgacaaacc
      181 gatctcctga taacgccggg acgggcggga aatcttttcc cggtcggcgc ggtgttggac
      241 aagccgcagg cgcgtcagtg gttttagcag gtttcggggc gcagccctga accagtcacg
      301 tagcgctagc ggagtgtata ctggctcaat atgttacggc ggagtaacac gtaatgaaag
      361 tgcttcatgt ggcaggggaa aaatgcagct gcagggcgta caggagaaaa tggaggttac
      421 ggtgatatga cgcctcctcg ctcactcggt cgcttccgct cctgacgttc ggctgcggcg
      481 ggcgttacct gcaaacggat aagagcaaag gcatacggca tggcaagcag gacaggaaaa
      541 ggatgcggcg ctgccgtttt tccataggct ccgcccccct gacaagcatc acgaaatctg
      601 acgctcaaat cagtggtggc gaaacccgac aggacttaaa gataccaggc gtttccccct
      661 ggtggctccc tcgtgcgctc tcctgttcct gcctttcggt ttaccggtgt cattccgctg
      721 ttatggccgc gtttatctca ttccacgcct gacactcagt tccgggtagg cagttcgctc
      781 caagctggac tgtatgcacg aaccccccgt tcagtccgac cgctgcgcct tgtccggtaa
      841 ctatcgtctt gagtccaacc cggatagaca cgactaatcg ccattggcaa cggccactgg
      901 taagcaggat gtgcgagaga tgtaacgaga gttcttgaag tggcggccta actgaggcta
      961 cactgaaagg acagtatttg gtgacatgtc tcgcacaaga ctgttaccac ggttagagaa
     1021 tctgccagga ttaactaacc ttcgaaaaaa ccacctgcca gggtggtttt ttcgtttctg
     1081 agcaagagac tacgacgagc cactgatgat ctcaagtgtt catttctgat attcacagca
     1141 gaataactgt taggatatag ggtatctata gccaggagct tcaagaaatc cagacacagc
     1201 aatggattcc agggttatcg aaaaaaatta gtatataggt tgcaaccaaa atgttggttg
     1261 caaatctaca tcacgatgtt tatgattatt gtactgcaag agcattcgca gggggcatca
     1321 accagtaata ggccttctgt gccgggcagt cagatggctg gtcatctgcc gggtagttac
     1381 gacaagcgtc ggtttctgaa ccctatgtgc taaggaaatg ctgcgactac caacgaattc
     1441 ataaagggcg ctttttagcg ccctattttt ttattcaata tgaccaacca aagtaccgtg
     1501 cgccgtcctt cgtgtgtacg cagtcacaac gacatagatc caacctgact cagtttcagg
     1561 cgcttctctg ggctcaagaa ttacgatgcc taccgacgac tttagcactg caggccgatg
     1621 tttaccgctt gtactgttga actcgcaata tattggtacg ccacgacgaa taatatcccg
     1681 gacaaaacga gccacatcat taacggtcgt atatcccagc ttaaccagtt cctgctcgtg
     1741 ctcagcccag atatggcgaa caccaaagcc ccggttaggg ccagtatgcc taccaacacg
     1801 caagaagatg tcgccagcag gaataacatc acctttagaa ttaatttcag ggacacggcc
     1861 atagcaatca agcccatcag ggtgagctat agcgctgtta ggtgaaccag ctacaccgta
     1921 attgtttgga gcaggcacaa aacgatcctt attgagtaga gtccgcatat ggtaccagag
     1981 aggaaacaag cggaaggagc ccaagaaaaa agcagagacg ataaaaagaa tccttatgga
     2041 ttattttttt gtcctttcat ccttggcgca taaggatatc acacctgaaa atgtgacgtg
     2101 cgaatcgccc tagcagctag atttaccata acatcccttg cccgcaccgc tccggacggg
     2161 ttcagcgtga aagcggcgtt agcccggtaa aaccggcagt aaactccccg ctaaaccgcg
     2221 cattctgcgc ctgataaatt tcacgcggct gcatagccat gcagccacgt gaatggctca
     2281 tgctttcaat gtatatcctc gtccaagccc ctgttttaac cggtttatca aaaaaacaaa
     2341 caggaagcct tatcactaac aataaaagag gtagggggct gcattttatc gcataaaaaa
     2401 catttacaac acgaattcta tcgtatagat ttcataaaaa aatgaaattg actcacctat
     2461 taagggtttc tatatgaaag atatgaaagc tgttgtggtt tttaccggga aggatttgaa
     2521 cataatgaga accgaggggg ggtcaggcta ctggcatgcc agaacagaca ggctcaacga
     2581 tgccgattac ctcatagcag taagaaacag aagggaaacg tgggcagtaa aagacctgga
     2641 acacggcaca gcattcctga tcgccaaaat taccgggtgt tttaaaagcc ctgattacga
     2701 cgacaggaac gtcataacct ttgatgaata cgcagaaatt cacactccaa aagcatggaa
     2761 aatgctaacc gatggtcagc gctatccggt tgcttacctg agcgcacagg aagctttttt
     2821 acgtattggg gtaacaccgg aacaactgga atggaagaaa ttccatcctt catccccatc
     2881 ggttcctaat acagtgattc ctggtctggc tgaagagaaa acagaaaaac tctcccttaa
     2941 cgaggcaatt gaaagagcca aaaaggatat tagcaacgca acagggattg atagctcagc
     3001 cataacaata agcatcaaga tctgatgaag cgtgaacaac aagatagcag cctcatgttc
     3061 tagaactgaa cctgtgcgcc agaaacagca agcccatgct tttccggcgc acagattcaa
     3121 agtgacggac cgttgtacgt tcgctgtcgc tgagatcgtt ccagctccag cgctttctga
     3181 tgctgcgccg cccgttcctg ctcacgatgt gcctctatca cgttcagcct tgtgacaacc
     3241 ggcgcagctg ctcgctcaaa ctctgcacct gcctgctcaa gcccgtgacg cgctcgctca
     3301 gcgccgcgtt ctcccgttgc ataagaccaa acatcgtccg ccattccgcg aaggcgttct
     3361 cccactcgtc cagccttttc gagtagtcct gctgtagctg ctctaatgcg ctcagcaact
     3421 gtttttccag ctccgtcatg tgctatttcc ccgccagtat catccagctc gaatcctctc
     3481 cgaaccgtcc cgcttccggg ttcaccctca cgcagcgccg tctctgctct ccgcaggtcg
     3541 agagctgcac gccgctgttc ctctcggaca gcatggcctg cgtgctcttc tgctcccgga
     3601 tgatcgtgta attgtcgagt atctgctgcc cctgccacca tagaatgctt gcgcccgatg
     3661 ctgtcagcag tgtagacacc aggacgatgg tcagccacgt ctggctgacc atacgcacca
     3721 tgcctttcgt gcgctggctc atggctgagg acagcttccg gtcgtggtcg aggatggcgg
     3781 cgctgattct cttctcgctt tcgctcagtt ccgctctgac aaacttctcg tgctcgctga
     3841 atgcgacttt cagcatctcg ccggtactct gctgctgcgc tttcgatttc tgctctaagt
     3901 ccttcgccag cgttaaaaga ctgttcatag atggctccct tcagtcggat gtttcgcccc
     3961 ccgtccgggt cggcaatgct gatgctgctt tttgtggtgc gcaccacctc aaaacctgcg
     4021 ctttctagcg cctcagtgac gtcctggcgg gttttcagct ccccggacga ggctaaggcc
     4081 agtaaacccc gtgtaattgc ctgagcggct tcctgcttcg ttttcggcag cgcggacggc
     4141 gtgaccagcg cccgccggtt ttcaggcgcg ttcgggtcat gcagccccag cctgccgttc
     4201 acgatggtct gccaggcatc aatgcgcgga cggtcggcgc ggtcgtaata cggctggaga
     4261 cgcctgcctg tcagcagctc catgttcggg atcaggaagt tcagctccag ccgcccctta
     4321 tcctggtgct caacccatag cacgctgtac tggtctttat cgagtccggg catcagaacc
     4381 cgttcaaagc tcgccatcag cttttcgcgc tgcccgggcg gtaaatcctt ttcggcaaag
     4441 gacaggacgc cggatgtgta cttttttgcg tagggcgagg cgtcgataag ctccctgact
     4501 tcttccggct tcccctgcag aacggtggcg ccgtcgcgct gtcggtcttt ccccagcaga
     4561 taatccaccg gaccggcgcc accgccgcgc cctcgcgggt gaaacttaac gatcatcgtc
     4621 tgcacccttt tccagcacgg catgccgcag ccgctcgagt ccggcatcta tggccatcag
     4681 cgcggcgacg acctgcacgc ggtcgtgccc gctgccgcca ccggcgttaa cctgccgggc
     4741 aatctggttg aggttattcc ccatgccggc aag
//
