LOCUS       NZ_CP086509             4237 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain Ec-050-T5-MAC plasmid pEc-050-T5-MAC_9,
            complete sequence.
ACCESSION   NZ_CP086509
VERSION     NZ_CP086509.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108722
            Assembly: GCF_022759725.1
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  JOURNAL   Unpublished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                   :: 275x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759725.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 05:24:20
            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)                    :: 4,888
            CDSs (with protein)               :: 4,888
            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)              :: 270
            CDSs (without protein)            :: 270
            Pseudo Genes (ambiguous residues) :: 0 of 270
            Pseudo Genes (frameshifted)       :: 108 of 270
            Pseudo Genes (incomplete)         :: 174 of 270
            Pseudo Genes (internal stop)      :: 53 of 270
            Pseudo Genes (multiple problems)  :: 57 of 270
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086509.1.
            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-T5-MAC"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc-050-T5-MAC_9"
                     /geo_loc_name="Switzerland"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            join(3741..4237,1..217)
                     /locus_tag="LNN49_RS26215"
                     /old_locus_tag="LNN49_26220"
     CDS             join(3741..4237,1..217)
                     /locus_tag="LNN49_RS26215"
                     /old_locus_tag="LNN49_26220"
                     /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            1404..1919
                     /locus_tag="LNN49_RS26220"
                     /old_locus_tag="LNN49_26225"
     CDS             1404..1919
                     /locus_tag="LNN49_RS26220"
                     /old_locus_tag="LNN49_26225"
                     /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            2100..2390
                     /locus_tag="LNN49_RS26225"
                     /old_locus_tag="LNN49_26230"
     CDS             2100..2390
                     /locus_tag="LNN49_RS26225"
                     /old_locus_tag="LNN49_26230"
                     /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            2478..2741
                     /locus_tag="LNN49_RS26230"
                     /old_locus_tag="LNN49_26235"
     CDS             2478..2741
                     /locus_tag="LNN49_RS26230"
                     /old_locus_tag="LNN49_26235"
                     /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            2746..3744
                     /locus_tag="LNN49_RS26235"
                     /old_locus_tag="LNN49_26240"
     CDS             2746..3744
                     /locus_tag="LNN49_RS26235"
                     /old_locus_tag="LNN49_26240"
                     /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"
     Typing          2747..3549
                     /name="MPF_T"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="89.552"
                     /coverage="91.0"
                     /evalue="1.15e-160"
ORIGIN
        1 gagtttaagt aaccgaattg agtcttcaaa ggatatgaaa gaatcccagg atttggctaa
       61 cgcattgcag gcgcagtcgt taaaaataca ggcaattaaa atgcagtatg atgtatggga
      121 tagtaaaaac agggctgatg cggaaatgtt gaaagagcaa aagtatgctg agtatcgcct
      181 gcgtcagaaa aatgcaaaga taccgagttt cgaatgatat gataaagcta aataagctaa
      241 aagaatgggt agataatcat tggtctagat tgaatagtac cggttctaca ccgccgccac
      301 tgttaatctc gctaccaatc atagttattg ttttaagtgt ggagcttacg ttaaagctga
      361 ttaatgcttt aatgtattat ggtacattgc aatttatcac tgataaaatt gaaaagaggt
      421 ttgttcccag cggtggtata aaagaaagac tcctttttac gttaaagctg ttttgtattt
      481 tacttctgtt attaatagta atgcgatttt caatgaagta aaaaataaag gtcatcgaat
      541 agatggcctt ttctattcta aattctaaat atagagcctg cggcaggcac aggcaaaaac
      601 atcgtttttg gacaatctga ttcaaatgtt aacatttgac atcggattgt ctatcctgca
      661 ttgctctttt gccgacctca aaacccctag cgtgtttttg tttcccgatc tctagaacca
      721 ccgagccgcc acggttccgg cagcgccttg agcgcaaccg gaaaccgtct ggggagaacc
      781 ccagaccccc atcgctgtaa catcgacggt ctacgaccac ctaccaaccg tgtggctacc
      841 tgttccatgc taatgggctt tgcagggggc tggcgcggtt cctggcgacc tgaaagcccc
      901 tggttagggg tatcggcgcg cctgacctcc tgaaaccctc tgtaagcatt tttcgcgcct
      961 ttcatgccct gacgggcatc taaagcccgt ttcgtgcgtc tgagcgcgtt ttaagagcta
     1021 agacgactaa aacattacca acacctgaaa atcgcgttct ggtgctctgg atggcccaca
     1081 gaacgcattt tcgaacagaa cagcaacggc atttctgaca acatgcgaga ggtgatcccg
     1141 ctcgccgcag ccccagcgac cgaacgtagt gagcgagtgg gcgaggaagc ggaagagaat
     1201 tgatagccat aattgagcac ctacgctcct tagttaagaa ctaagaaggg aaattctcgg
     1261 aacccgcatg aatcctagaa agtggtgatc aggatctgta ccttgtaagc tcagatccgg
     1321 taccttgcag gctcaaaaat tgcttgattt tgagcttatg aggatttatt gtgaatctcc
     1381 aaagcccaaa aaaggatgca ataatgagct cgctaagctt acagagatac gaaacaaacc
     1441 cgtttttaga gcttatgacg atcccgatga aagggaaacg gatacaagta tctcgtcttg
     1501 ggcgggatga caatgttttg gttaatcaaa acacgggaga aaagtttgga acacatgtaa
     1561 ccacttttaa gcgtgtagat agtgagcaat ttgttaagtt gtttactgcg aatattgggt
     1621 taacgtttga tttatcatcg gcaggaatta aagcttttaa tgttctttta tgggctgttc
     1681 aaaaacaagc ctttgcaaag gatcaggttc ttttggattc aagggctctt gatgactttt
     1741 taaaaagcta tgatagctta aaacttagtt atgctacgtt aaagagagga attaacgagt
     1801 tagaaaaagc tcagattata gcaaagacaa tgcgtaaagg attttatttt ataaacccca
     1861 attttgtatt taatggagat cgaatagcat ttacaaccct aattgagagg gattgttaat
     1921 cgatagaaca atacaatgca ggatagacaa tcatggtcaa aatgttaaca ttttatccat
     1981 gattgtccaa aaacgatgtt tttgcctgtg cctgccgcag gctactagaa gtagtcgcag
     2041 gcgaacaaaa gtggtgtttt gttcgcctgc taatcacaac aacctggcta gaggttttta
     2101 tgactaaaca tgatgctata cgcatttctc aacttcatca aattttttac gatgatgatg
     2161 gattaattga ttcagaaaag aacgtgacta ttttatacag tataggattt acagttgatg
     2221 aaatagctca ttttagaaat tcaacaccaa acacagttgc gagtcagcta ttaaatgcaa
     2281 gggttaaatt aggttgcgcc tcggtttcat ctttaaagcc aatgatctta ttaagattgc
     2341 ttttgaacat aaaagagatt cgttttggat tcgaaactga ttgcaaataa tatagttcaa
     2401 taggtatttt tgctcttgac tagaattaca attgctgatt gtatcagcaa ttgtaatgtc
     2461 catacgagga atcaaagatg aaaaaaattt gtacgctctt aatgtctatt ttcattcttt
     2521 ccgcatgtgg tgaagataca aaatcatcag attggtggct taatcatccc aaagaagcga
     2581 cggagaaata taaggagtgt aaaaagtcag gggaagattc tgttaattgt caaaatgtta
     2641 aaaaagttgc cggaattatt ggtagaacct atggccctat gcttgaaata cttaaggctg
     2701 agtcagctga atatgataag caacatggat tgaacaggtg ataacatgtc tggtttcttt
     2761 gaaaagttta atagcgaagt tgttagtaaa atcgaagaga tgaccaaacc acttcaaagt
     2821 caattaggtc aggatatgtt atctcttcta agtgcaggta ttagcgttta tatcctctgg
     2881 gttggctatc aaatattggc agggaaacgc cagaccccat tacaagatct cgtctgggat
     2941 ctatcaaaat ttgccattat tttaacattc gtaagcaatg ctgatggcta tctgacggca
     3001 gcaatggatg ctattaaatc tatgaaggat gggttccttg gtaaacctgt atgggcaacg
     3061 ctagatacca tgtggagtac aactcagctt ttggctgaca aagtttatgc tatggatcaa
     3121 tccaaatatg tgtcagttga aggtggaatc gggtcaatgt tggtttgggg aggaagtatc
     3181 ctgattatgt ctgtagcggc tgttatttac atgcttgccg atgtaacaat gcagttagct
     3241 attcttgtag ctccgatatt tatcggttgt tatatgtttg gattcactag agtaatgttt
     3301 aataactggc ttggtatatt attttctagt gtatttactg ttatttttgc tggagttctc
     3361 gtcaaaattg gtaccgagtt tcaaactgat atgcttagtc agatatcgag agatgctaac
     3421 tcaacaaata ttttaacaat gggcgcaatg gcatttgtaa ttggagttct gattgctgtc
     3481 tttgtctgga aatcatcgag tttcgcgcag cagcttgccg gtgcaggtgt tgaaggtact
     3541 cttcagggaa tggctctttt agggattggg gctgctggaa tggccgtaga gaaaacgaga
     3601 aaccagatga aacgtggaac gcgaacagcc gccgaatggg caggtgaaaa aggggagcag
     3661 aaacgggctt caataggcgc attgggaatg gaagcaagaa gacgagcatc cctggaaaaa
     3721 gcacgtgcga ggaattcagc atgaacaaaa aactaatttt ttcagtactt ttgtgcttat
     3781 tttcatttgg ttctgtcgca ggtattccgg ttgctattga tgccagtccg gaatgggctg
     3841 ttgaagccac aagatggaca gaacgactca aacaatggtc tgaaacagcg cggcattatc
     3901 aaagtcagat tcaggcatat aaagaccagt tagccacggc aacaggtata aggaatattg
     3961 cggcattcac aaatgaacta agtaacctac aatcagagct ggcaaacatt tataagcagg
     4021 ggaacagtta tatttctgat tttaccagta atcctgaagg tgcattaagt agtcaggcga
     4081 aaaatctgtt cagcaagtat ggtgctttta atatgtgttc tacaggcatt gaaagttctg
     4141 ataacctttg taaggccaga atagtttcaa cggccgctag cattgaacag ggaaatgaga
     4201 taaataagca gctatcaagt gcaatgtctc agattca
//
