LOCUS       NZ_CP100507             4051 bp    DNA     circular CON 22-JUL-2023
DEFINITION  Escherichia coli strain LH50-c plasmid pLH50-c-G, complete sequence.
ACCESSION   NZ_CP100507
VERSION     NZ_CP100507.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29499317
            Assembly: GCF_024223415.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4051)
  AUTHORS   Biggel,M.
  TITLE     ESBL-producing Enterobacteriaceae from poultry
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4051)
  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 02:51:37
            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)                     :: 5,935
            CDSs (total)                      :: 5,818
            Genes (coding)                    :: 5,517
            CDSs (with protein)               :: 5,517
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 301
            CDSs (without protein)            :: 301
            Pseudo Genes (ambiguous residues) :: 1 of 301
            Pseudo Genes (frameshifted)       :: 131 of 301
            Pseudo Genes (incomplete)         :: 169 of 301
            Pseudo Genes (internal stop)      :: 69 of 301
            Pseudo Genes (multiple problems)  :: 59 of 301
            Pseudo Genes (short protein)      :: 4 of 301
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP100507.1.
            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..4051
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LH50-c"
                     /isolation_source="pooled poultry feces"
                     /host="Gallus gallus domesticus"
                     /db_xref="taxon:562"
                     /plasmid="pLH50-c-G"
                     /geo_loc_name="Switzerland"
                     /collection_date="2022"
                     /collected_by="Institute for Food Safety and Hygiene,
                     University of Zurich"
     gene            join(3799..4051,1..887)
                     /locus_tag="NLZ13_RS29535"
                     /old_locus_tag="NLZ13_29540"
     CDS             join(3799..4051,1..887)
                     /locus_tag="NLZ13_RS29535"
                     /old_locus_tag="NLZ13_29540"
                     /EC_number="2.7.7.49"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0003964 - RNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="reverse transcriptase family protein"
                     /protein_id="WP_005761319.1"
                     /translation="MNKPRFNGTPVASLDSLSAMLGIERKRLDWIVKSVSMSYKQFKVE
                     TGKNKKERQIFEPKRSLKGIQKKINKEIFEKIDYPHYLHGALSGRDYISNAAVHTRKRT
                     VICLDITNFYPSISKKDVCSIFKNLMRFSPDVSLCLTELVTLNNKVPQGGCCSSYIANL
                     LFFNSEYNLYNRLKSMGLSYSRLLDDITISSDKDLSSEEKTKVIKLVHGMVNQYRLSIN
                     ESKTTIEHSKDSSSKLSVTGLWVKHGVPKLTKENRRYIRYLVYICKKQGAYERHTKEYH
                     DLWNRCSGKVAQMSRLGHVQAVELRAILSEIMPVYDDYKISKLKLMAKHYLNKFTPPLT
                     DDQIRKIDRMLYDFDIVGRTNKNLAKLYRRKLVALLPDR"
                     /name="reverse transcriptase family protein"
     gene            892..1095
                     /locus_tag="NLZ13_RS29540"
                     /old_locus_tag="NLZ13_29545"
     CDS             892..1095
                     /locus_tag="NLZ13_RS29540"
                     /old_locus_tag="NLZ13_29545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000427298.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="retron Se72 family effector protein"
                     /protein_id="WP_000427298.1"
                     /translation="MENGFVNFYDHVKGYGFIRRERGRDVFFRYDDFLFLGHDVDICKG
                     ILVRFKLEKTDKGFKAVAIQKV"
                     /name="retron Se72 family effector protein"
     gene            complement(1933..2127)
                     /locus_tag="NLZ13_RS29545"
                     /old_locus_tag="NLZ13_29550"
     CDS             complement(1933..2127)
                     /locus_tag="NLZ13_RS29545"
                     /old_locus_tag="NLZ13_29550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041640.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2411..2734
                     /gene="mobA"
                     /locus_tag="NLZ13_RS29550"
                     /old_locus_tag="NLZ13_29555"
     CDS             2411..2734
                     /gene="mobA"
                     /locus_tag="NLZ13_RS29550"
                     /old_locus_tag="NLZ13_29555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            2959..3225
                     /locus_tag="NLZ13_RS29555"
                     /old_locus_tag="NLZ13_29560"
     CDS             2959..3225
                     /locus_tag="NLZ13_RS29555"
                     /old_locus_tag="NLZ13_29560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001243419.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_224471576.1"
                     /translation="MVKLLLVRNEYFNKNNDLKTVARFDGKTLRDAFSRKIATFDGKVL
                     RDASLKKVATFDGQNLRDASSKIILSADAEVGIVVMAFVAELI"
                     /name="hypothetical protein"
     Typing          2163..2402
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.755"
                     /coverage="100.0"
                     /evalue="7.66e-118"
     Typing          complement(1377..1898)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.476"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          2412..2731
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="3.08e-62"
ORIGIN
        1 gggcgttaag tggtcgcgat tatatatcta atgccgctgt tcatactagg aaaagaacag
       61 ttatatgtct tgatatcacc aatttttatc ccagcattag taaaaaagat gtttgttcta
      121 tttttaaaaa tttaatgcgt ttttctcctg atgtttcttt atgcttaacg gaacttgtga
      181 cgttgaataa taaggtccct cagggtgggt gctgttctag ttatattgca aatcttttat
      241 tttttaatag tgagtataat ctctataata gattgaagtc tatggggctt tcatattcaa
      301 ggcttttaga tgatattact atatcttctg ataaggatct ttcatcagag gaaaaaacaa
      361 aagtaataaa actcgttcac ggaatggtga atcagtacag actttcaata aatgaaagta
      421 agacaacgat agagcactca aaagattcgt cttctaaact tagtgtcact gggttgtggg
      481 taaagcatgg tgttcctaag ttaacaaaag aaaatagacg ttatatcagg tacttagttt
      541 atatatgtaa aaaacaaggt gcttatgaac gtcatacgaa agagtaccat gatttatgga
      601 atagatgctc tggcaaggtt gctcaaatgt cgaggcttgg gcatgtccag gcggttgaat
      661 tgagggcgat tctttctgag ataatgccag tttatgatga ttacaagata tctaaattaa
      721 agttgatggc taagcactat ctaaataagt ttacgccgcc tttaactgat gatcagatta
      781 ggaaaataga taggatgctc tatgattttg atatagtagg gcggactaat aagaatcttg
      841 caaaactata tagacgtaag ctcgtggcat tacttccaga taggtgatta tatggaaaat
      901 ggatttgtta atttttatga ccatgttaaa gggtatggct ttataaggcg tgagcgtgga
      961 cgtgatgttt tctttcggta tgatgatttt ttgtttttag ggcatgatgt cgatatatgt
     1021 aaaggtattt tagttaggtt taaattagaa aaaacagata aagggtttaa agctgtagcg
     1081 attcaaaagg tataacatcg tggatgtgtc agcttgtttt tatgatatga gaacttgaga
     1141 tcctttctat ctcgtcgtaa tctcttgctg tgtaaacgaa aaaaccgcct tgcagggcgg
     1201 tttttcgaag gttctcagag ctaccaactc tttgagccga ggtaactggc ttggaggagc
     1261 gcagtcacca aaacttgttc tttcagttta gccttaacag gcgcatgact tcaaggctaa
     1321 ctcctctaat tcggttacca gtggctgctg ccagtggcga taagtcgtgt cttctcggtt
     1381 tggattcaag tcgatagtta ccggataagg cgcagcggtc ggactgaacg gggggttcgt
     1441 gcatacagtc cagcttggag cgaacgacct acaccgggcc gagataccaa cagcgtgagc
     1501 tatgagaaag cgccacgttt cccgaaggga gaaaggcgga caggtatccg gtaagcggca
     1561 gggtcggaac aggagagcgc acgagggagc ttccaggggg aaacgcctgg tatctttata
     1621 gtcctgtcgg gtttcgccac ctctgacttg agcgtcggtt tttgtgatgc tcgtcagggg
     1681 ggcggagcct atggaaaaac gccatcggcg cggcctttgt ccctggcttc ggctttttgc
     1741 tcacatgttc tttccggcgt tatcccctga ttctgtggat aaccgtatta ccgcctttga
     1801 gtgagctgac accgctcgcc gcagtcgaac gaccgagcgt agcgagtcag tgagcgagga
     1861 agcggaagag cgccttatgt gacattttct ccttacgctc ctctatgccg ttctgcatcc
     1921 tgtccggatg cgttatatcc cggtgcgatt ttccgcttca aagcgtgtct gtatgctgtt
     1981 ctgaagttct tccgcgagtt cgtgcagctt ctcacacatg gcggcctgtt cgtcagcatc
     2041 aagtgcgtcc agtttttcga gcagcgtcag gctctggctt tttatgaatc ctgccatgtt
     2101 gagtacggtt tgctgctgct tgttcatctt tctgttttct ccgttctttc tgtcatctgc
     2161 gttgtgtgat tatatcgcgt accacttttc gactgtttta ccgtcggtat tctgctgtct
     2221 gactctttga cgggcatttc tgtcagacaa cactgtcact gccaaaaaac tgccgtgcct
     2281 ttgtcggtaa tttgagcttg ctgacaggac aggatgtgca attgttatac cgcgcataca
     2341 tgcacgctat tacaattacc ctggtcaggg ctttgccccg acacccatgt cagatacgga
     2401 gccatgtttt atgacaaaac gaagtggaag taatacgcgc aggcgggcta tcagtcgccc
     2461 tgttcgtctg acggcagaag aagaccagga aatcagaaaa agggctgctg aatgcggcaa
     2521 gaccgtttcc ggttttttac gggcggcagc tctcggtaag aaagttaact cactgactga
     2581 tgatcgggta ctgaaagaag ttatgagact gggggcgtta cagaaaaaac tctttatcga
     2641 cggcaagcgt gtcggggaca gggagtatgc ggaggtgctg atcgctatta cggagtatca
     2701 ccgtgccctg ttatccaggc ttatggcaga ttagcttcca ggggagaaaa ctgtcgaaaa
     2761 cagacggtat gaacactgta agctcccaaa gtgatcacca ctcgctttca tgcatagcta
     2821 tgcagcgagc tgaaaacgat cctgacgcat ttccccggtt ttcttagggt aaaacatctc
     2881 tttttgcagt gtctgtgtca gaatcgcgct gagcgcgatt ctgtggtgcg tacaattaag
     2941 ggattatggt aaatacaatt ggttaaatta ctattggtga gaaatgaata tttcaataaa
     3001 aacaatgact taaaaaccgt tgctcggttt gacggtaaaa ccttaagaga tgccttttcg
     3061 agaaaaatag cgacttttga tggcaaggtt ttaagggatg cctctttaaa aaaagtagca
     3121 acctttgacg gtcagaattt aagagatgct agttcaaaaa ttatcctgag tgccgatgct
     3181 gaggttggga ttgttgttat ggcctttgta gctgagttga tttgaatctc atgctgcata
     3241 ccttttagcc tatcgctggc aggataaggc gctttcttgt tggtgacaga aagataaaaa
     3301 actttataat aatcagcgaa gcgggcgaac cacgcctggc tctcgctctt taacaaatgg
     3361 ttacgtgtat gttgcgcaag gaaaccgatg ccttgttttt aaggcgatct cgcatgagat
     3421 catgaccggc ctggccgcta attaatggtg agaacgcccc tgagcgtgta tcagcactaa
     3481 aagaatagcg acgattgtct ggcaatgtga gttaaaagtc ccaaagagcc aatagagttt
     3541 ttccttgctt tcctactggt ctggcaaaat ttcataacca ataggagttg catcatgttt
     3601 attatcaaca tcaacattaa cgtaaccaag agctcttcat cttgttctgg agacggtcag
     3661 atgaagaaaa aaagagaggt tggctctctg gaggcactga aaaaaacaca gtttttgttt
     3721 tctatgtgct tgattatgtt taaagtaata gattacgtat cgaaactttt taactaatcg
     3781 acttttaact caaacatcat gaataaaccc aggtttaatg gaactcctgt tgcatctttg
     3841 gattctttat ctgcgatgtt aggcatagaa agaaaaagat tggactggat agtcaagtct
     3901 gtatcgatgt cgtacaagca gtttaaggtt gaaacaggga agaataaaaa agaaaggcaa
     3961 atttttgaac ccaagagatc tttgaaagga attcaaaaaa aaataaataa agagattttt
     4021 gagaaaattg attaccctca ttatttgcat g
//
