LOCUS       NZ_CP086519             4237 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain Ec-050-T0 plasmid pEc-050-T0_9, complete
            sequence.
ACCESSION   NZ_CP086519
VERSION     NZ_CP086519.1
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 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  JOURNAL   Unpublished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                   :: 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
            CP086519.1.
            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-T0"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc-050-T0_9"
                     /geo_loc_name="Switzerland"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            complement(838..1551)
                     /locus_tag="LNN50_RS26190"
                     /old_locus_tag="LNN50_26195"
     CDS             complement(838..1551)
                     /locus_tag="LNN50_RS26190"
                     /old_locus_tag="LNN50_26195"
                     /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            complement(1548..2546)
                     /locus_tag="LNN50_RS26195"
                     /old_locus_tag="LNN50_26200"
     CDS             complement(1548..2546)
                     /locus_tag="LNN50_RS26195"
                     /old_locus_tag="LNN50_26200"
                     /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            complement(2551..2814)
                     /locus_tag="LNN50_RS26200"
                     /old_locus_tag="LNN50_26205"
     CDS             complement(2551..2814)
                     /locus_tag="LNN50_RS26200"
                     /old_locus_tag="LNN50_26205"
                     /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            complement(2902..3192)
                     /locus_tag="LNN50_RS26205"
                     /old_locus_tag="LNN50_26210"
     CDS             complement(2902..3192)
                     /locus_tag="LNN50_RS26205"
                     /old_locus_tag="LNN50_26210"
                     /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            complement(3373..3888)
                     /locus_tag="LNN50_RS26210"
                     /old_locus_tag="LNN50_26215"
     CDS             complement(3373..3888)
                     /locus_tag="LNN50_RS26210"
                     /old_locus_tag="LNN50_26215"
                     /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"
     Typing          complement(1744..2546)
                     /name="MPF_T"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="89.552"
                     /coverage="91.0"
                     /evalue="1.15e-160"
ORIGIN
        1 cgattttcag gtgttggtaa tgttttagtc gtcttagctc ttaaaacgcg ctcagacgca
       61 cgaaacgggc tttagatgcc cgtcagggca tgaaaggcgc gaaaaatgct tacagagggt
      121 ttcaggaggt caggcgcgcc gataccccta accaggggct ttcaggtcgc caggaaccgc
      181 gccagccccc tgcaaagccc attagcatgg aacaggtagc cacacggttg gtaggtggtc
      241 gtagaccgtc gatgttacag cgatgggggt ctggggttct ccccagacgg tttccggttg
      301 cgctcaaggc gctgccggaa ccgtggcggc tcggtggttc tagagatcgg gaaacaaaaa
      361 cacgctaggg gttttgaggt cggcaaaaga gcaatgcagg atagacaatc cgatgtcaaa
      421 tgttaacatt tgaatcagat tgtccaaaaa cgatgttttt gcctgtgcct gccgcaggct
      481 ctatatttag aatttagaat agaaaaggcc atctattcga tgacctttat tttttacttc
      541 attgaaaatc gcattactat taataacaga agtaaaatac aaaacagctt taacgtaaaa
      601 aggagtcttt cttttatacc accgctggga acaaacctct tttcaatttt atcagtgata
      661 aattgcaatg taccataata cattaaagca ttaatcagct ttaacgtaag ctccacactt
      721 aaaacaataa ctatgattgg tagcgagatt aacagtggcg gcggtgtaga accggtacta
      781 ttcaatctag accaatgatt atctacccat tcttttagct tatttagctt tatcatatca
      841 ttcgaaactc ggtatctttg catttttctg acgcaggcga tactcagcat acttttgctc
      901 tttcaacatt tccgcatcag ccctgttttt actatcccat acatcatact gcattttaat
      961 tgcctgtatt tttaacgact gcgcctgcaa tgcgttagcc aaatcctggg attctttcat
     1021 atcctttgaa gactcaattc ggttacttaa actctgaatc tgagacattg cacttgatag
     1081 ctgcttattt atctcatttc cctgttcaat gctagcggcc gttgaaacta ttctggcctt
     1141 acaaaggtta tcagaacttt caatgcctgt agaacacata ttaaaagcac catacttgct
     1201 gaacagattt ttcgcctgac tacttaatgc accttcagga ttactggtaa aatcagaaat
     1261 ataactgttc ccctgcttat aaatgtttgc cagctctgat tgtaggttac ttagttcatt
     1321 tgtgaatgcc gcaatattcc ttatacctgt tgccgtggct aactggtctt tatatgcctg
     1381 aatctgactt tgataatgcc gcgctgtttc agaccattgt ttgagtcgtt ctgtccatct
     1441 tgtggcttca acagcccatt ccggactggc atcaatagca accggaatac ctgcgacaga
     1501 accaaatgaa aataagcaca aaagtactga aaaaattagt tttttgttca tgctgaattc
     1561 ctcgcacgtg ctttttccag ggatgctcgt cttcttgctt ccattcccaa tgcgcctatt
     1621 gaagcccgtt tctgctcccc tttttcacct gcccattcgg cggctgttcg cgttccacgt
     1681 ttcatctggt ttctcgtttt ctctacggcc attccagcag ccccaatccc taaaagagcc
     1741 attccctgaa gagtaccttc aacacctgca ccggcaagct gctgcgcgaa actcgatgat
     1801 ttccagacaa agacagcaat cagaactcca attacaaatg ccattgcgcc cattgttaaa
     1861 atatttgttg agttagcatc tctcgatatc tgactaagca tatcagtttg aaactcggta
     1921 ccaattttga cgagaactcc agcaaaaata acagtaaata cactagaaaa taatatacca
     1981 agccagttat taaacattac tctagtgaat ccaaacatat aacaaccgat aaatatcgga
     2041 gctacaagaa tagctaactg cattgttaca tcggcaagca tgtaaataac agccgctaca
     2101 gacataatca ggatacttcc tccccaaacc aacattgacc cgattccacc ttcaactgac
     2161 acatatttgg attgatccat agcataaact ttgtcagcca aaagctgagt tgtactccac
     2221 atggtatcta gcgttgccca tacaggttta ccaaggaacc catccttcat agatttaata
     2281 gcatccattg ctgccgtcag atagccatca gcattgctta cgaatgttaa aataatggca
     2341 aattttgata gatcccagac gagatcttgt aatggggtct ggcgtttccc tgccaatatt
     2401 tgatagccaa cccagaggat ataaacgcta atacctgcac ttagaagaga taacatatcc
     2461 tgacctaatt gactttgaag tggtttggtc atctcttcga ttttactaac aacttcgcta
     2521 ttaaactttt caaagaaacc agacatgtta tcacctgttc aatccatgtt gcttatcata
     2581 ttcagctgac tcagccttaa gtatttcaag catagggcca taggttctac caataattcc
     2641 ggcaactttt ttaacatttt gacaattaac agaatcttcc cctgactttt tacactcctt
     2701 atatttctcc gtcgcttctt tgggatgatt aagccaccaa tctgatgatt ttgtatcttc
     2761 accacatgcg gaaagaatga aaatagacat taagagcgta caaatttttt tcatctttga
     2821 ttcctcgtat ggacattaca attgctgata caatcagcaa ttgtaattct agtcaagagc
     2881 aaaaatacct attgaactat attatttgca atcagtttcg aatccaaaac gaatctcttt
     2941 tatgttcaaa agcaatctta ataagatcat tggctttaaa gatgaaaccg aggcgcaacc
     3001 taatttaacc cttgcattta atagctgact cgcaactgtg tttggtgttg aatttctaaa
     3061 atgagctatt tcatcaactg taaatcctat actgtataaa atagtcacgt tcttttctga
     3121 atcaattaat ccatcatcat cgtaaaaaat ttgatgaagt tgagaaatgc gtatagcatc
     3181 atgtttagtc ataaaaacct ctagccaggt tgttgtgatt agcaggcgaa caaaacacca
     3241 cttttgttcg cctgcgacta cttctagtag cctgcggcag gcacaggcaa aaacatcgtt
     3301 tttggacaat catggataaa atgttaacat tttgaccatg attgtctatc ctgcattgta
     3361 ttgttctatc gattaacaat ccctctcaat tagggttgta aatgctattc gatctccatt
     3421 aaatacaaaa ttggggttta taaaataaaa tcctttacgc attgtctttg ctataatctg
     3481 agctttttct aactcgttaa ttcctctctt taacgtagca taactaagtt ttaagctatc
     3541 atagcttttt aaaaagtcat caagagccct tgaatccaaa agaacctgat cctttgcaaa
     3601 ggcttgtttt tgaacagccc ataaaagaac attaaaagct ttaattcctg ccgatgataa
     3661 atcaaacgtt aacccaatat tcgcagtaaa caacttaaca aattgctcac tatctacacg
     3721 cttaaaagtg gttacatgtg ttccaaactt ttctcccgtg ttttgattaa ccaaaacatt
     3781 gtcatcccgc ccaagacgag atacttgtat ccgtttccct ttcatcggga tcgtcataag
     3841 ctctaaaaac gggtttgttt cgtatctctg taagcttagc gagctcatta ttgcatcctt
     3901 ttttgggctt tggagattca caataaatcc tcataagctc aaaatcaagc aatttttgag
     3961 cctgcaaggt accggatctg agcttacaag gtacagatcc tgatcaccac tttctaggat
     4021 tcatgcgggt tccgagaatt tcccttctta gttcttaact aaggagcgta ggtgctcaat
     4081 tatggctatc aattctcttc cgcttcctcg cccactcgct cactacgttc ggtcgctggg
     4141 gctgcggcga gcgggatcac ctctcgcatg ttgtcagaaa tgccgttgct gttctgttcg
     4201 aaaatgcgtt ctgtgggcca tccagagcac cagaacg
//
