LOCUS       NZ_CP100490             5328 bp    DNA     circular CON 22-JUL-2023
DEFINITION  Escherichia coli strain LH85-a plasmid pLH85-a-D, complete sequence.
ACCESSION   NZ_CP100490
VERSION     NZ_CP100490.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29499321
            Assembly: GCF_024224055.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5328)
  AUTHORS   Biggel,M.
  TITLE     ESBL-producing Enterobacteriaceae from poultry
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5328)
  AUTHORS   Biggel,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-JUL-2022) Institute for Food Safety and Hygiene,
            University of Zurich, Winterthurerstrasse 272, Zurich 8057,
            Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x, 100x
            Sequencing Technology :: Illumina MiniSeq, Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/22/2023 02:47:25
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,168
            CDSs (total)                      :: 5,047
            Genes (coding)                    :: 4,895
            CDSs (with protein)               :: 4,895
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 152
            CDSs (without protein)            :: 152
            Pseudo Genes (ambiguous residues) :: 0 of 152
            Pseudo Genes (frameshifted)       :: 45 of 152
            Pseudo Genes (incomplete)         :: 114 of 152
            Pseudo Genes (internal stop)      :: 27 of 152
            Pseudo Genes (multiple problems)  :: 30 of 152
            Pseudo Genes (short protein)      :: 3 of 152
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP100490.1.
            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..5328
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LH85-a"
                     /isolation_source="pooled poultry feces"
                     /host="Gallus gallus domesticus"
                     /db_xref="taxon:562"
                     /plasmid="pLH85-a-D"
                     /geo_loc_name="Switzerland"
                     /collection_date="2022"
                     /collected_by="Institute for Food Safety and Hygiene,
                     University of Zurich"
     gene            join(4451..5328,1..142)
                     /locus_tag="NLZ16_RS25735"
                     /old_locus_tag="NLZ16_25730"
     CDS             join(4451..5328,1..142)
                     /locus_tag="NLZ16_RS25735"
                     /old_locus_tag="NLZ16_25730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221104.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_113977129.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALFARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREDAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDNSGEWLTKKQIIKC"
                     /name="replication initiation protein"
     gene            complement(403..801)
                     /locus_tag="NLZ16_RS25740"
                     /old_locus_tag="NLZ16_25735"
     CDS             complement(403..801)
                     /locus_tag="NLZ16_RS25740"
                     /old_locus_tag="NLZ16_25735"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_113977128.1"
                     /translation="MRISNIEWLKKRIEFIRKLGKQTARQRQIIDLLDNEDRLTEQERK
                     LLHVLATAEKNDLQAQESERKQAIQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDMILQRLKPIKHDLDTCPNPDA"
                     /name="hypothetical protein"
     gene            978..1904
                     /locus_tag="NLZ16_RS25745"
                     /old_locus_tag="NLZ16_25740"
     CDS             978..1904
                     /locus_tag="NLZ16_RS25745"
                     /old_locus_tag="NLZ16_25740"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_049595749.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPDRGGAKKDSGNLT
                     PTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYYRHLEQARMVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDGVSRQNRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            1907..2440
                     /locus_tag="NLZ16_RS25750"
                     /old_locus_tag="NLZ16_25745"
     CDS             1907..2440
                     /locus_tag="NLZ16_RS25750"
                     /old_locus_tag="NLZ16_25745"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_113977127.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTMLDRNYNATAAVYQKIVTLED
                     KLAEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            complement(2506..2715)
                     /locus_tag="NLZ16_RS25755"
                     /old_locus_tag="NLZ16_25750"
     CDS             complement(2506..2715)
                     /locus_tag="NLZ16_RS25755"
                     /old_locus_tag="NLZ16_25750"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001618649.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001096196.1"
                     /translation="MAKLGENTPHIIDATVDFMASSQAFREYLKKLPPDNTIPPALTDE
                     HVPLYIRRLEYYRLLYRPKQTESY"
                     /name="hypothetical protein"
     Typing          4452..5226
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.165"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          979..1901
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.377"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcgtagggcg cttgatatgt atatcttggg agcgtcaacg gaagatattg cagtggcggt
       61 tggtgttagc agccggacta ttcgacgctg gatggataat tctggagaat ggctaaccaa
      121 gaaacaaata attaaatgtt agttaacaaa gaagcaacac taccccccgt tttttgttaa
      181 tggttggtta aattcgcgga catgaacaag cctatatcag ataacagcgc ctttcggcgt
      241 ctttttgagc agcgggcttt ccggcggttt tctcctctca gcccagcaat ggtgcggctt
      301 accgcatgat tgaggtggta gtgctcgccg cagtctcatg accgagcgta gcgagcgaat
      361 gagcgaggaa gcaccagggc accggaacgt gaacgggaac acttacgcgt ctgggtttgg
      421 gcatgtgtct agatcgtgct taatgggttt aagtctttgt aatatcatat cttttttata
      481 gcatagctcg cctgtttttg tgtccaccag tcctgcttcg atcagtagcc ccgctgctag
      541 aaagagccgg tgattgcgtt cccgtcgttg tttcttcccc tcgattcgtt tctggatcgc
      601 ctgttttcgt tcgctctcct gtgcctgtaa gtcgtttttt tcggctgttg ccagtacgtg
      661 gagaagtttg cgttcctgtt ctgtgagtct gtcctcgttg tcgagcaggt caatgatctg
      721 tctctgtcgt gcggtctgtt ttccgagctt cctgatgaac tcgatccgtt tcttcagcca
      781 ttcgatgttg ctgatgcgca tgttggtggt gctccctggt gtttttttgc ggtgtgttgt
      841 ggtcgtgcag tatatcgctt gcggttggtg ggtgcagggg ttaccttccg tactaattcg
      901 aaaaattaga aggaagcgca cttatatgtt tctctccttc gtcgagaaac agtgcgctcc
      961 tgcagagggc tgaaaccgtg gcaacctatc acctcagcgt taaatttggt ggcaaggggc
     1021 aggctgcaaa ccacgccgat tacatcgagc gcaaagagaa ataccgcgac cgtcaggatt
     1081 tggaatattc cgcacacgga aacatgccgg aatgggccag ggataatcct tcccatttct
     1141 ggcaggcggc tgaccagttt gaacgtgcga acggttcgac ctatagggaa cttgaaattg
     1201 cattaccccg tgaactgaca ccggaacagc gccttgaact ggtgcaggat tttgtacgtc
     1261 aggaagctgg cgaacggcac gcctggagtt ttgccattca caatccgaaa gcgagcattg
     1321 acggcggcga acagcctcat gcgcatatca tgatgagtca gcgtgtgaat gatggcattg
     1381 aacgtacacc ggaacagtat ttccggcgct ataacgccag gtatcccgac cggggaggtg
     1441 cgaaaaagga ttccggaaac ctgaccccca ctcagcaaaa agagcagttg cgggaattgc
     1501 gaaaacgctg ggaggtgaag cacaacgaac atatgagaaa gcatggcttt gaaaggggct
     1561 tcattgactg ccggacactg aaagaacagg gcattgaacg acgtcccgaa gtgcatctgg
     1621 gttttgaagc tgccggacga cttgatgatg cccagcgtca tgacatcatg caaaaacggt
     1681 ctgaaccgga ctattaccgc catcttgaac aggcgcgaat ggtcgggcat gacatcaggg
     1741 aatggctgga tacaccggtt aagcaacatg aactggtcag aaggctgcaa catgatgttg
     1801 cgcgggagca tggctttgac atgagagacg gagtgagcag acagaaccga actgaacctg
     1861 aacgggttaa atcaccgtca cgtggatttt ctatgggatt ctgaacatgg ccagcacaga
     1921 agaaaaatta ctcacgctcc tgttatcggt ggagcatctg caacataccg caatggagca
     1981 acagaaagct gttgctgatt ctctggctgt ggcaagggaa actcttcgcg gatatcggga
     2041 tatttctgac ggtgtggcaa aacaggtcag ggatgaagtc agaaatgagg tgcagaagct
     2101 ggacgtggca ggactgatag gtgagcgcat cagccaggat tttcagcggc tggaagagtc
     2161 agtcgcaaac atgaaggcaa acgcggatgc cctgaacagg gatattgcga caattcacag
     2221 caatatcgtg caggaataca acacccttaa agggtatagc tggaaatggc tgggtggggt
     2281 gtcagtggct tttctggtta tgttctgtgt gctcggatgg ggaatgaaaa caatgctcga
     2341 caggaactac aacgccacag cggcggtgta tcagaaaatt gtgacactgg aagataaact
     2401 ggcggagaaa cctgtcacgg gtaagagccg gaaaaactga cgcgcttcgc ttgtccaacg
     2461 cctcacggag cgcgaaagga tttcgcgaac cgttcaccgt ttttttcaat atgattctgt
     2521 ctgctttggt cgataaagca gacgatagta ttccagcctt cgtatatata acggtacgtg
     2581 ctcatcagta agagctggcg gtattgtgtt atcaggggga agttttttca gatactcacg
     2641 aaatgcctgg cttgatgcca taaaatctac agtagcatcg ataatatgtg gggtgttttc
     2701 acctaatttt gccatgatga taatccttat attatcacgg ttcgtgaatg atagggtgtc
     2761 actattattt atgcgttagt aaaccagaaa aaatcccccg ttggcatagg gggatgtata
     2821 aggagaaata acttcgcagg tgttcttgtt tgtataacgt gaaaagactg cacgcaactg
     2881 aataaatctg ccgtacttac tttcagtttt caacataagg tttataacaa tgtatggaat
     2941 ggaagtgagc tttaaggttt cagctctaaa aaataaaata tttattagtt ggttggttgt
     3001 tgttcttgtt ctgtatgtat ataaacacta gcgacatatt atgaccggga aattccttac
     3061 cccctctgcg ctctcagagg gttttttttt gtcattaatt aataatgagc tgaaatgcag
     3121 ttccgatacc tccaattgca cactatccct gacatatggt accggaaccg cattaatttt
     3181 atgttataag agtttatttt taatgtccag atggtttaat aagtatttat atgtaattag
     3241 ctgtatgaat aatactggtt ttgttgtata acttgttgtt ttttttattg tttttatgtg
     3301 gtgtactaat ctttaagtta taaaaaaacc ccttggaaca caggggcaaa agtaaggaaa
     3361 acaaatggat gctcagtttg tgtgacactt taaactaatg gaactataga gtggaggttg
     3421 ttacattcgt ttttataaat cagcaaactg tttttttcta tatcctgatg ataaatggtg
     3481 acaattttgt gatattattc aaaatgcttt gagtaaaatg tttgtttttt agtctattgg
     3541 tcagtttttt gttagctcca tcaagaagtg tgattgatgt cgcaagagtg gaatgtggtg
     3601 aatataaact gattgtttag taaatctaac ttgtttagca aaatattctt gttttgtttg
     3661 tgagtttggt gaatttatct gtctttgtgt ttgtttgttt ttataaattc atgcacaatg
     3721 atcttaaatt gattgttgag gccggattac ctgtgcggta attattattt ataacgtaac
     3781 agcttcatct tcatcgttgt tcgaacacaa caaacaacct gtaattgttg tttctcttgg
     3841 ttccccactt ttgtggggtt tttttatctc ttccgtgcat cgtaaagcgc ggactccttc
     3901 tggaaaggtt gttttagggc atcactgagg aattttttgc gtttgtgaat attgagcatc
     3961 cgataactaa aatatttccc atagactctg attcttgcca ccgaccccag gtcggttttt
     4021 ttttgtcctg gcgagatgtg aagtttggaa acaggaaacc ccgtcagagc gccacgcacc
     4081 aggggagaaa acttgtcatt ttgacccgtc cggtgttctg aacggtcgaa accgatcgcg
     4141 catcgctttc gtgaatagtt atgcaaggcc tctaaaaacg attctggcgc gtttttctgg
     4201 tttaccctgg cgttttcttg tctttttgtg ttttttgcgt cagagagcgt ctgagagcgt
     4261 tttaaggggt gcgtacaacg ggagttatgg taaatggatc gggttttcgg gaaggttcga
     4321 caggatttgc cgttgggtgt agtgtaagcg actgaaaaac aaacgcccct gaaattcgtg
     4381 tctctccgcc aagattgtca cgagaataca ggggcgaggt cggtcgataa cctggaagga
     4441 atcgtaacac atgagcgccg cgcttcaata cttcgaagaa aatttacccc accgccccta
     4501 tcacacggat gatctcgctt tcggccttcg catctccggc aaagggcgtg cgctttttgc
     4561 gcggtacatc cagcagaacc agcctcatgc gcagttctgg ctggtttttg acgttgaccg
     4621 cgagggggct gcgattgact ggagcgaccg gaacgccccc gcgccgaaca tcaccgttaa
     4681 aaatcctgtg aacggacacg ctcacctgct ctacgcactc aacatcgccg tgagaaccgc
     4741 gcctgatgcc tcggttaagg cgctgaaata tgccgcagcg gttgaacgtt cgctgtgtga
     4801 gaaactttgt gctgatgtga actacagcgg cctgatttgc aaaaatccgt tccacctgga
     4861 atggcaggtg atggagtggc gcgaggacgc ctataccctc gatgaactgg cagattatct
     4921 cgatttgagc gcctcagagc gtcgtagcat cgataaacat tacgggatgg ggcgaaactg
     4981 ccacctgttc gaaatgacgc gcaaatgggc ttacagggcg attcgtcagg gatggccagc
     5041 attctcacag tggcttgatg ccgtgattca gcgtgtcgaa atgtacaatg catcgcttcc
     5101 cgttccgctt tcaccgcctg aatgtcgggc tattggcaag agtattgcga aatacacgca
     5161 caggaacttc acgccggaaa ctttcgcaca gtatgtggct gatacgcaca caccagaaat
     5221 tcaggcagca cgcggtcgca agggcgggaa ggccaattcg tcagaaaatc agtcggacaa
     5281 agggaaaaaa agcgccgctg ttcggtggac tgctaacgac gacaaacg
//
