LOCUS       NZ_JAEFCJ010000001      6262 bp    DNA     linear   CON 26-DEC-2024
DEFINITION  Escherichia coli strain 8178 8-78_1, whole genome shotgun sequence.
ACCESSION   NZ_JAEFCJ010000001 REGION: 3865119..3871380
VERSION     NZ_JAEFCJ010000001.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17073774
            Assembly: GCF_016433265.1
KEYWORDS    WGS; RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6262)
  AUTHORS   Benz,F., Huisman,J.S., Bakkeren,E., Herter,J.A., Stadler,T.,
            Ackermann,M., Diard,M., Egli,A., Hall,A.R., Hardt,W.D. and
            Bonhoeffer,S.
  TITLE     Plasmid- and strain-specific factors drive variation in
            ESBL-plasmid spread in vitro and in vivo
  JOURNAL   ISME J 15 (3), 862-878 (2021)
   PUBMED   33149210
REFERENCE   2  (bases 1 to 6262)
  AUTHORS   Benz,F., Huisman,J.S., Bakkeren,E., Herter,J.A., Stadler,T.,
            Ackermann,M., Diard,M., Egli,A., Hall,A.R., Hardt,W.D. and
            Bonhoeffer,S.
  TITLE     Plasmid- and strain-specific factors drive variation in
            ESBL-plasmid spread in vitro and in vivo
  JOURNAL   ISME J 15 (3), 862-878 (2021)
   PUBMED   33149210
REFERENCE   3  (bases 1 to 6262)
  AUTHORS   Huisman,J.S., Tschudin-Sutter,S., Egli,A., Neher,R., Bonhoeffer,S.
            and Stadler,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-DEC-2020) Environmental Systems Science, ETH Zurich,
            Universitaetstrasse 16, Zurich 8092, Switzerland
REFERENCE   4  (bases 1 to 6262)
  AUTHORS   Huisman,J.S., Tschudin-Sutter,S., Egli,A., Neher,R., Bonhoeffer,S.
            and Stadler,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-DEC-2020) Environmental Systems Science, ETH Zurich,
            Universitaetstrasse 16, Zurich 8092, Switzerland
COMMENT     REFSEQ INFORMATION: The reference sequence is identical to
            JAEFCJ010000001.1.
            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/
            
            ##Genome-Assembly-Data-START##
            Assembly Method        :: Unicycler v. 0.4.7
            Genome Representation  :: Full
            Expected Final Version :: Yes
            Genome Coverage        :: 80x
            Sequencing Technology  :: Illumina MiSeq; Pacbio Sequel
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_016433265.1-RS_2024_12_26
            Annotation Date                   :: 12/26/2024 02:13:21
            Annotation Pipeline               :: NCBI Prokaryotic Genome
                                                 Annotation Pipeline (PGAP)
            Annotation Method                 :: Best-placed reference protein
                                                 set; GeneMarkS-2+
            Annotation Software revision      :: 6.9
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,168
            CDSs (total)                      :: 5,050
            Genes (coding)                    :: 4,836
            CDSs (with protein)               :: 4,836
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 214
            CDSs (without protein)            :: 214
            Pseudo Genes (ambiguous residues) :: 0 of 214
            Pseudo Genes (frameshifted)       :: 104 of 214
            Pseudo Genes (incomplete)         :: 123 of 214
            Pseudo Genes (internal stop)      :: 39 of 214
            Pseudo Genes (multiple problems)  :: 46 of 214
            Pseudo Genes (short protein)      :: 1 of 214
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..6262
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /submitter_seqid="8-78_1"
                     /strain="8178"
                     /isolation_source="feces"
                     /host="Mus musculus"
                     /db_xref="taxon:562"
                     /geo_loc_name="Switzerland: Zurich"
                     /lat_lon="47.38 N 8.54 E"
                     /collection_date="2007-06-17"
                     /collected_by="Hardt group, ETH"
     gene            1..1083
                     /gene="lacI"
                     /locus_tag="JDA82_RS18815"
                     /old_locus_tag="JDA82_18820"
     CDS             1..1083
                     /gene="lacI"
                     /locus_tag="JDA82_RS18815"
                     /old_locus_tag="JDA82_18820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_414879.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA-binding transcriptional repressor LacI"
                     /protein_id="WP_000805859.1"
                     /translation="MKPVTLYDVAEYAGVSYQTVSRVVNQACHVSAKTREKVEAAMAE
                     LNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERS
                     GVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACANVPALFLDVSDQTPINSII
                     FSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREG
                     DWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDT
                     EDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLPPNT
                     QTASPRALADSLMQLARQVSRLESGQ"
     gene            1206..4280
                     /gene="lacZ"
                     /locus_tag="JDA82_RS18820"
                     /old_locus_tag="JDA82_18825"
     CDS             1206..4280
                     /gene="lacZ"
                     /locus_tag="JDA82_RS18820"
                     /old_locus_tag="JDA82_18825"
                     /EC_number="3.2.1.23"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_414878.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="beta-galactosidase"
                     /protein_id="WP_033559648.1"
                     /translation="MTMITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEAR
                     TDRPSQQLRSLNGEWRFAWFPAPEAVPESWLERDLPDADTVVVPSNWQMHGYDAPIYT
                     NVTYPITVNPPFVPAENPTGCYSLTFNIDESWLQEGQTRIIFDGVNSAFHLWCNGRWV
                     GYGQDSRLPSEFDLSAFLHAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDVSLLHK
                     PTTQISDFQVTTRFNDDFSRAVLEAEVQMYGELRDELRVTVSLWQGETQVASGTAPFG
                     GEIIDERGGYADRVTLRLNVENPELWSAEIPNLYRAVVELHTADGTLIEAEACDVGFR
                     EVRIENGLLLLNGKPLLIRGVNRHEHHPLHGQVMDEQTMVQDILLMKQNNFNAVRCSH
                     YPNHPLWYTLCDRYGLYVVDEANIETHGMVPMNRLTDDPRWLPAMSERVTRMVQRDRN
                     HPSVIIWSLGNESGHGANHDALYRWIKSVDPSRPVQYEGGGADTSATDIICPMYARVD
                     EDQPFPAVPKWSIKKWLSLPGEMRPLILCEYAHAMGNSLGGFAKYWQAFRQYPRLQGG
                     FVWDWVDQSLIKYDENGNPWSAYGGDFGDTPNDRQFCMNGLVFADRTPHPALTEAKHQ
                     QQYFQFRLSGRIIEVTSEYLFRHSDNEFLHWMVALDGKPLASGEVPLDVGPQGKQLIE
                     LPELPQPESAGQLWLTVRVVQPNATAWSEAGHISAWQQWRLAENLSVTLPSASHAIPQ
                     LTTSGTDFCIELGNKRWQFNRQSGFLSQMWIGDEKQLLTPLRDQFTRAPLDNDIGVSE
                     ATRIDPNAWVERWKAAGHYQAEAALLQCTADTLADAVLITTAHAWQHQGKTLFISRKT
                     YRIDGHGEMVINVDVAVASDTPHPARIGLTCQLAQVSERVNWLGLGPQENYPDRLTAA
                     CFDRWDLPLSDMYTPYVFPSENGLRCGTRELNYGPHQWRGDFQFNISRYSQQQLMETS
                     HRHLLHAEEGTWLNIDGFHMGIGGDDSWSPSVSAEFQLSAGRYHYQLVWCQK"
     gene            4332..5585
                     /gene="lacY"
                     /locus_tag="JDA82_RS18825"
                     /old_locus_tag="JDA82_18830"
     CDS             4332..5585
                     /gene="lacY"
                     /locus_tag="JDA82_RS18825"
                     /old_locus_tag="JDA82_18830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_414877.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="lactose permease"
                     /protein_id="WP_000291549.1"
                     /translation="MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSD
                     TGIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYN
                     ILVGSIVGGIYLGFCFNAGAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGI
                     MFTINNQFVFWLGSGCALILAVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFR
                     QPKLWFLSLYVIGVSCTYDVFDQQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIM
                     FFAPLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCF
                     KYITSQFEVRFSATIYLVCFCFFKQLAMIFMSVLAGNMYESIGFQGAYLVLGLVALGF
                     TLISVFTLSGPGPLSLLRRQVNEVA"
     gene            5651..6262
                     /gene="lacA"
                     /locus_tag="JDA82_RS18830"
                     /old_locus_tag="JDA82_18835"
     CDS             5651..6262
                     /gene="lacA"
                     /locus_tag="JDA82_RS18830"
                     /old_locus_tag="JDA82_18835"
                     /EC_number="2.3.1.18"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_308422.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="galactoside O-acetyltransferase"
                     /protein_id="WP_001350624.1"
                     /translation="MNMSMTERIKAGKLFTDMCEGLPEKRLRGKTLMYEFNHSHPSEV
                     DKRESLIKEMFATVGENAWVEPPVYFSYGSNIYIGRNFYANFNLTIVDDYTVTIGDNV
                     LIAPNVTLSVTGHPVHHELRKNGEMYSFPITIGNNVWIGSHVVINPGVTIGDNSVIGA
                     GSVVTKDIPPNVVAAGVPCRVIREINDRDKQYYFKDFKVESSV"
ORIGIN      
        1 gtgaaaccag taacgctata cgatgtcgca gagtatgccg gtgtctctta tcagaccgtt
       61 tcccgcgtgg tgaaccaggc ctgccacgtt tctgcgaaaa cgcgggaaaa agtggaagcg
      121 gcgatggcgg agctgaatta cattcccaac cgcgtggcac aacaactggc gggcaaacag
      181 tcgttgctga ttggcgttgc cacctccagt ctggccctgc acgcgccgtc gcaaattgtt
      241 gcggcgataa aatctcgcgc cgatcaactg ggtgccagcg tggtggtgtc gatggtagaa
      301 cgaagcggcg tcgaagcctg taaagcggcg gtgcacaatc ttctcgcgca acgcgtcagt
      361 gggctgatca ttaactatcc gctggatgac caggatgcca ttgctgtgga agctgcctgc
      421 gctaatgttc cggcgttatt tcttgatgtc tctgaccaga ctcccatcaa cagtattatt
      481 ttctcccatg aagacggtac gcgactgggc gtggagcacc tggtcgcatt gggtcatcag
      541 caaatcgcgc tgttagcagg cccattaagt tctgtctcgg cgcgtctgcg tctggcaggc
      601 tggcataaat atctcacacg caatcaaatt cagccgatag cggaacggga aggcgactgg
      661 agtgccatgt ccggttttca acaaaccatg caaatgctaa atgagggcat cgttcccact
      721 gcgatgctgg ttgccaacga tcagatggcg ctgggcgcaa tgcgcgccat taccgagtcc
      781 gggctgcgcg ttggtgcgga tatctcggta gtgggatacg acgataccga agacagctcg
      841 tgttatatcc cgccgttaac caccatcaaa caggattttc gcctgctggg gcaaaccagc
      901 gtggaccgct tgctgcaact ctctcagggc caggcggtga agggcaatca gctgttgccc
      961 gtctcactgg tgaaaagaaa aaccaccctt ccgcccaata cgcaaaccgc ctctccccgc
     1021 gcgttggccg attcattaat gcagctggca cgacaagttt cccgactgga aagcgggcag
     1081 tgagcgcaac acaattaatg tgagtcagct cactcattag gcaccccagt ctttacactc
     1141 tatgtgtccg gctcgtatgt tgtgtgaaat tgtgagcgga taacaatttc acacaggata
     1201 cagctatgac tatgattacg gattctctgg ccgtcgtatt acaacgtcgt gactgggaaa
     1261 accctggcgt tacccaactt aatcgccttg cggcacatcc ccctttcgcc agctggcgta
     1321 atagcgaaga ggcccgcacc gatcgccctt cccaacagtt gcgcagcctg aatggcgaat
     1381 ggcgctttgc ctggtttccg gcaccagaag cggtgccgga aagctggctg gagcgcgatc
     1441 ttcctgacgc cgatactgtc gtcgtcccct caaactggca gatgcacggt tacgatgcgc
     1501 ctatctacac caacgtgacc tatcccatta cggtcaatcc gccgtttgtt cccgcggaga
     1561 atccgacagg ttgttactcg ctcacattta atattgatga aagctggcta caggaaggcc
     1621 agacgcgaat tatttttgat ggcgttaact cggcgtttca tctgtggtgc aacgggcgct
     1681 gggtcggtta cggccaggac agccgtttgc cgtctgaatt tgacctgagc gcatttttac
     1741 acgccggaga aaaccgcctc gcggtgatgg tgctgcgctg gagtgacggc agttatctgg
     1801 aagatcagga tatgtggcgg atgagcggca ttttccgtga cgtctcgttg ctgcataaac
     1861 cgaccacgca aatcagcgat ttccaagtta ccactcgctt taatgatgat ttcagccgcg
     1921 cagtactgga ggcagaagtt cagatgtacg gcgagctgcg cgatgaactg cgggtgacgg
     1981 tttctttgtg gcagggtgaa acgcaggtcg ccagcggcac cgcgcctttc ggcggtgaaa
     2041 ttatcgatga gcgtggcggt tatgccgatc gcgtcacgct acgcctgaac gttgaaaatc
     2101 cggaactgtg gagcgccgaa atcccgaatc tctatcgtgc ggtggttgaa ctgcacaccg
     2161 ccgacggcac gctgattgaa gcagaagcct gcgatgtcgg tttccgcgag gtgcggattg
     2221 aaaatggtct gctgctgctg aacggcaagc cgttgctgat tcgcggcgtt aaccgtcacg
     2281 agcatcatcc tctgcatggt caggtcatgg atgagcagac gatggtgcag gatatcctgc
     2341 tgatgaagca gaacaacttt aacgccgtgc gctgttcgca ttatccgaac catccgctgt
     2401 ggtacacgct gtgcgaccgc tacggcctgt atgtggtgga tgaagccaat attgaaaccc
     2461 acggcatggt gccaatgaat cgtctgaccg atgatccgcg ctggctaccc gcgatgagcg
     2521 aacgcgtaac gcggatggtg cagcgcgatc gtaatcaccc gagtgtgatc atctggtcgc
     2581 tggggaatga atcaggccac ggcgctaatc acgacgcact ctatcgctgg atcaaatctg
     2641 tcgatccttc ccgcccggta cagtatgaag gcggcggagc cgacacctcc gcaaccgata
     2701 ttatttgccc gatgtacgcg cgcgtggatg aagaccagcc cttcccggcg gtgccgaaat
     2761 ggtccattaa aaaatggctt tcgctgcctg gagaaatgcg cccgctgatc ctttgcgaat
     2821 atgcccacgc gatgggtaac agtcttggcg gcttcgctaa atactggcag gcgtttcgtc
     2881 agtacccccg tttacagggc ggcttcgtct gggactgggt ggatcagtcg ctgattaaat
     2941 atgatgaaaa cggcaacccg tggtcggctt acggcggtga ttttggcgat acgccgaacg
     3001 atcgccagtt ctgtatgaac ggtctggtct ttgccgaccg cacgccgcat ccggcgctga
     3061 cggaagcaaa acaccaacag cagtatttcc agttccgttt atccgggcga atcatcgaag
     3121 tgaccagcga atacctgttc cgtcatagcg ataacgagtt cctgcactgg atggtggcgc
     3181 tggatggcaa gccgctggca agcggtgaag tgcctctgga tgttggcccg caaggtaagc
     3241 agttgattga actgcctgaa ctgccgcagc cggagagcgc cggacaactc tggctaacgg
     3301 tacgcgtagt gcaaccaaac gcgaccgcat ggtcagaagc cggacacatc agcgcctggc
     3361 agcaatggcg tctggcggaa aacctcagcg tgacactccc ctccgcgtcc cacgccatcc
     3421 ctcaactgac caccagcgga acggattttt gcatcgagct gggtaataag cgttggcaat
     3481 ttaaccgcca gtcaggcttt ctttcacaga tgtggattgg cgatgaaaaa caactgctga
     3541 ccccgctgcg cgatcagttc acccgtgcgc cgctggataa cgacattggc gtaagtgaag
     3601 cgacccgcat tgaccctaac gcctgggtcg aacgctggaa ggcggcgggc cattaccagg
     3661 ccgaagcggc gttgttgcag tgcacggcag atacacttgc cgacgcggtg ctgattacga
     3721 ccgcccacgc gtggcagcat caggggaaaa ccttatttat cagccggaaa acctaccgga
     3781 ttgatgggca cggtgagatg gtcatcaatg tggatgttgc ggtggcaagc gatacaccgc
     3841 atccggcgcg gattggcctg acctgccagc tggcgcaggt ctcagagcgg gtaaactggc
     3901 tcggcctggg gccgcaagaa aactatcccg accgccttac tgcagcctgt tttgaccgct
     3961 gggatctgcc attgtcagac atgtataccc cgtacgtctt cccgagcgaa aacggtctgc
     4021 gctgcgggac gcgcgaattg aattatggcc cacaccagtg gcgcggcgac ttccagttca
     4081 acatcagccg ctacagccaa caacaactga tggaaaccag ccatcgccat ctgctgcacg
     4141 cggaagaagg cacatggctg aatatcgacg gtttccatat ggggattggt ggcgacgact
     4201 cctggagccc gtcagtatcg gcggaattcc agctgagcgc cggtcgctac cattaccagt
     4261 tggtctggtg tcaaaaataa taataaccgg gcaggctatg tctgcccgta tttcgcgtaa
     4321 ggaaatccat tatgtactat ttaaaaaaca caaacttttg gatgttcggt ttattctttt
     4381 tcttttactt ttttatcatg ggggcctact tcccgttttt cccgatttgg ctacatgaca
     4441 tcaaccatat cagcaaaagt gatacgggta ttatttttgc cgctatttct ctgttctcgc
     4501 tattattcca accgctgttt ggtctgcttt ctgacaaact cgggctgcgc aaatacctgc
     4561 tgtggattat taccggcatg ttagtgatgt ttgcgccgtt ctttattttt atcttcggac
     4621 cactgttaca atacaacatt ttagtaggat cgattgttgg tggtatttat cttggctttt
     4681 gttttaacgc cggtgcgcca gcagtagagg catttatcga gaaagtcagc cgtcgcagta
     4741 atttcgaatt tggtcgcgcg cggatgtttg gctgtgttgg ctgggcgctg tgtgcctcga
     4801 ttgtcggcat catgttcacc atcaataatc agtttgtttt ctggctgggt tctggctgtg
     4861 cactcatcct cgccgtttta ctctttttcg ccaaaacgga tgcgccctct tcagccacgg
     4921 ttgccaatgc ggtaggtgcc aaccattcgg catttagcct taagctggcg ctggaactgt
     4981 tcagacagcc aaaactgtgg tttttgtcac tgtatgttat tggcgtttcc tgcacctacg
     5041 atgtttttga ccaacagttt gctaatttct ttacttcgtt ttttgctacc ggtgaacagg
     5101 gtacgcgggt atttggctac gtaacgacaa tgggcgaatt acttaatgcc tcgattatgt
     5161 tctttgcgcc actgatcatt aatcgcatcg gtgggaaaaa tgccctgctg ctggctggca
     5221 ctattatgtc tgtacgtatt attggctcat cgttcgccac ctcagcgctg gaagtagtta
     5281 ttctgaaaac gctgcatatg tttgaagtac cgttcctgct ggtgggctgc tttaaatata
     5341 ttaccagcca gtttgaagtg cgtttttcag cgacgattta tctggtctgt ttctgcttct
     5401 ttaagcaact ggcgatgatt tttatgtctg tactggcggg caatatgtat gaaagcatcg
     5461 gtttccaggg cgcttatctg gtgctgggtc tggtggcgct gggcttcacc ttaatttccg
     5521 tgttcacgct tagcggcccc ggcccgcttt ccttgctgcg tcgccaggtg aatgaagtcg
     5581 cttaagcaat taatgtcgga tgcggcgcga gcgccttatc cgaccaacat atcagggcgg
     5641 aatgatcgca atgaacatgt cgatgacaga aagaataaaa gcaggcaagc tatttaccga
     5701 tatgtgcgaa ggcttacctg aaaaaagact tcgtggaaaa acgttaatgt atgagtttaa
     5761 tcactcgcat ccatcagaag ttgataaaag agaaagtctg attaaagaaa tgtttgccac
     5821 ggtaggggaa aacgcctggg tagaaccccc cgtctatttc tcttacggtt ccaacatcta
     5881 tataggccgc aatttttatg caaatttcaa tttaaccatt gtcgacgact acacggtaac
     5941 gatcggtgat aacgtactga ttgcacccaa cgttactctt tccgttacgg gacacccggt
     6001 acaccatgaa ttgagaaaaa acggagagat gtactctttt ccgataacga ttggcaataa
     6061 cgtctggatc ggaagtcatg tggttattaa tccaggcgtc accatcgggg ataattctgt
     6121 tattggcgcg ggtagtgtcg tcacaaaaga cattccacca aacgtcgtgg ctgctggcgt
     6181 tccttgtcgg gttattcgcg aaataaacga ccgggataag caatattatt tcaaagattt
     6241 taaagttgag tcttcagttt aa
//
