LOCUS       NZ_CP063498             4237 bp    DNA     circular CON 17-JUN-2023
DEFINITION  Escherichia coli strain EF5-18-41 plasmid pEF5-18-41_6, complete
            sequence.
ACCESSION   NZ_CP063498
VERSION     NZ_CP063498.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16387482
            Assembly: GCF_016944675.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4237)
  AUTHORS   Moser,A.I., Campos-Madueno,E.I. and Endimiani,A.
  TITLE     Complete genome and plasmid sequences of MDR Escherichia coli from
            local people and environmental sources in Laos
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4237)
  AUTHORS   Moser,A.I., Campos-Madueno,E.I. and Endimiani,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-OCT-2020) Institute for Infectious Diseases,
            University of Bern, Friedbuehlstrasse 51, Bern 3001, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.7.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 694x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 06:48:23
            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)                     :: 5,747
            CDSs (total)                      :: 5,629
            Genes (coding)                    :: 5,357
            CDSs (with protein)               :: 5,357
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 272
            CDSs (without protein)            :: 272
            Pseudo Genes (ambiguous residues) :: 0 of 272
            Pseudo Genes (frameshifted)       :: 100 of 272
            Pseudo Genes (incomplete)         :: 199 of 272
            Pseudo Genes (internal stop)      :: 50 of 272
            Pseudo Genes (multiple problems)  :: 66 of 272
            Pseudo Genes (short protein)      :: 4 of 272
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP063498.1.
            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="EF5-18-41"
                     /isolation_source="chicken stool"
                     /host="Gallus gallus"
                     /db_xref="taxon:562"
                     /plasmid="pEF5-18-41_6"
                     /geo_loc_name="Laos"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            join(3135..4237,1..4)
                     /gene="mobQ"
                     /locus_tag="IQS14_RS29055"
     CDS             join(3135..4237,1..4)
                     /gene="mobQ"
                     /locus_tag="IQS14_RS29055"
                     /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="MobQ family relaxase"
                     /protein_id="WP_219892063.1"
                     /translation="MAIYHLSMKIISRKNGYSAVASAAYRSGSVIPDDRTGLIHDYTRK
                     RGVDDAVILTPANAPSWCGDRSVLWNAVEKAEQRRNSQLAREIELAIPREISREAAREA
                     VLAFVRENFVSRGMIADVAFHHMDRTNPHAHIMLTTRAVGETGFAGKVRDWNDRALAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKAPGLHLGKAACAMEKRGMETERGEQ
                     NRLINSLNLEIQVSRTRLAVIQVQENVRKRELSDAARRAAEALNLTIPAANASADTLRE
                     FIATLPQECGNAWEMTPEFVAMNGKANDIKREGNALVKERDILEKEMTGLRKARPVASI
                     LSELPLMTWAEPEYRKRQLRFWKLEKQI"
                     /name="mobQ"
     gene            30..1118
                     /locus_tag="IQS14_RS29060"
     CDS             30..1118
                     /locus_tag="IQS14_RS29060"
                     /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_285829311.1"
                     /translation="MKERDIPVRRQAFETQWNTWISPGMAELKEKLSAREAERRREEAE
                     AEARRKEQEYDARLKHHDNHRLSRETALAGVITELGRAREPGTGRITRYMMLSNRAGEF
                     TVWGDELAHYPQSVHDPVNVYLSPGGAVMVSDIREGMPESHETMARPERVRMYSGATVR
                     HVLEQMRQGWPSYGFPALPHHWPDNFYFSDDRRPAASPLPSAHRVDVTAYAAPEQLMPV
                     VFSTERNSRTLNLLLCKGPEEMLVGFVRLEDELRPVLALPSPDYSHLMVSIITENGIHL
                     AGYGEAINRDADTPYPPEPKLMQFRLKGCQDTLFAAINKPEEMPDYLFRQLGFNQTWHE
                     WKRDEQHRQQQRRPGHYRGMSM"
                     /name="hypothetical protein"
     gene            1567..2475
                     /locus_tag="IQS14_RS28440"
                     /old_locus_tag="IQS14_28445"
     CDS             1567..2475
                     /locus_tag="IQS14_RS28440"
                     /old_locus_tag="IQS14_28445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009440807.1"
                     /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_072656801.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAIERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRKFSPEGFSAVQAARGRKGGLAKGEAYEDKRFMALCMLENGYSQ
                     KAIAAMLDVHRNTIRNWAMHK"
                     /name="replication initiation protein"
     gene            complement(2681..2956)
                     /locus_tag="IQS14_RS28445"
                     /old_locus_tag="IQS14_28450"
     CDS             complement(2681..2956)
                     /locus_tag="IQS14_RS28445"
                     /old_locus_tag="IQS14_28450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091757.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_052995416.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVIVGAAMLARVRRP
                     EEAQLRAFLLQFLRKEVTRQADVNRLQPLINELEKLPRPPAKPQNG"
                     /name="hypothetical protein"
     Typing          complement(2961..3134)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.0"
                     /coverage="98.0"
                     /evalue="1.23e-74"
     Typing          complement(3135..3493)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1568..2295
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.982"
                     /coverage="91.0"
                     /evalue="0.0"
     Typing          4..1115
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.105"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3136..4235
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.095"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ttgaatctct tctccgcacc tacagggccg tgaaagaacg ggacattccc gtccgtcgtc
       61 aggcctttga aacgcagtgg aatacgtgga tttcgccggg aatggcagag ctgaaagaaa
      121 aactgtcagc acgggaagcg gagcggcgca gggaggaagc cgaagcggaa gcgcgccgga
      181 aggaacagga atatgacgca cggctgaaac accatgataa ccatcgcctg agccgagaaa
      241 cggcattagc cggggttatt acggagctgg ggcgtgccag agagccggga acgggcagga
      301 taacccgcta catgatgctg agtaacagag ccggagaatt cacggtatgg ggtgatgagc
      361 tggcgcatta cccccagagt gttcatgacc cggtgaatgt ttacctgtcg ccaggcgggg
      421 ctgtgatggt ctcggatata cgtgagggaa tgccagaatc tcatgagacg atggcgcggc
      481 ctgagcgtgt gagaatgtat tccggtgcga cggtccggca tgtactggaa cagatgcgcc
      541 aggggtggcc ctcttacggt tttccggcgc tgccgcatca ctggccggat aatttttatt
      601 tcagcgacga ccgcaggccc gcagcctctc cgctgccgtc agcgcaccgg gtggacgtca
      661 ccgcttatgc ggcaccggag caactcatgc ccgttgtctt ttcgacagag cgaaacagca
      721 ggacgctgaa tctgctgttg tgcaaagggc cggaggaaat gcttgtcggt tttgtgcgcc
      781 tggaggacga gctgcgtccc gttcttgcgc ttccgtcgcc ggattacagt catctgatgg
      841 taagcatcat cacagagaac gggatacacc tggcaggcta cggtgaggcc ataaaccgtg
      901 atgctgatac tccgtaccca ccggaaccga agctgatgca gttcaggctt aagggctgtc
      961 aggacacgct ttttgctgcc atcaacaaac cggaagagat gccggattat ctcttccgtc
     1021 aactcggatt taatcagacc tggcatgaat ggaagcggga cgaacagcac aggcaacaac
     1081 aacgacgccc cggacattac cggggcatga gtatgtgata tccggggctg caccccgaac
     1141 cccgccaacg tctcacggga cacgaaaaaa ttccgcgtcc cgtgaggcgt tttctggatg
     1201 agaaagtttg ccgttttgac ccgttcgcgc ttctgaacgg tcgaaaccga tcgcgcatcg
     1261 ctttcgtgca tagttatgca gcgccctaaa aacgattctg acgcattttt ctggttcagc
     1321 ctggtgtttc cttgtctttt tgcgtttttt gcgtcagaac gcgtctgaga gcgttttaga
     1381 gggtacgtac aacgggagtt atggtaaatg gatcgggttt tggggaagga tcgacagggt
     1441 ttggcgtttg ggtgtagggt aagcgccaga aaaaacaaac gcccctgaaa ttcgtgccta
     1501 tccggcaaga ctgtcacgaa aatacagggg cgatgtcggt cgataacctg gaaggaatcg
     1561 taacacatga gcgccgcgct tcaatacttc gaagaaaatt taccccaccg tccctatcac
     1621 acggatgatc tcgctttcgg ccttcgcatc tccggcaaag ggcgtgcgct tcttgcgcgg
     1681 tacatccagc agaaccagcc tcatgcgcag ttctggctgg tttttgacgt tgaccgcgag
     1741 ggggcagcga ttgactggag cgaccggaac gcccccgcgc cgaacatcac cgttaaaaat
     1801 cctgtgaacg gacacgctca cctgctctat gcactcaata tcgccgtgag aaccgcgcct
     1861 gatgcgtcgg ttaaggcgct gaaatatgct gccgcgattg aacgttcgct gtgtgagaaa
     1921 ctttgtgctg atgtgaacta cagcggactg atttgcaaaa atccgttcca cctggaatgg
     1981 caggtgatgg agtggcgcga ggaagcctat accctcgatg aactggcaga ttatctcgat
     2041 ttgagcgcct cagagcgtcg tagcatcgat aaacattacg ggatggggcg aaactgccac
     2101 ctgttcgaaa tgacgcgcaa atgggcttac agagcgattc gtcagggatg gccagcattc
     2161 tcacagtggc ttgatgccgt gatccagcgt gtcgaaatgt acaacgcatc gcttcccgtt
     2221 cctctttcac tggctgaatg ccgggctatt ggcaagagca ttgcgaaata cacgcacaga
     2281 aaattctcac cggaaggctt ttccgctgta caggccgctc gaggccggaa aggtggcctt
     2341 gctaaaggcg aagcctacga ggacaagcgt ttcatggcgc tatgtatgct ggagaatgga
     2401 tattctcaga aagctattgc ggcgatgctg gatgtacatc gaaatacgat ccgtaattgg
     2461 gcaatgcaca aatagcctta tcagataaca gcgccttttc ggcgcttttt tgagctgttg
     2521 gcgttcctgc ggtttttccg gttccgccca gcaatggcgc tggtttcctc gtgattgcgg
     2581 tggtagcgct cgccgcagcc tcatgaccga gcgtagcgag cgaatgtgcg aggaagcgca
     2641 aaggcgtccg gtggtgcatg tggcacttac gcgccggggc ttatccgttc tgcggtttcg
     2701 caggtggtct tggtagcttc tccagctcgt taatcagtgg ttgtagccgg ttcacatcgg
     2761 cctgtcttgt gacttccttt cgcaggaact ggagcaggaa cgcacgcagt tgcgcctctt
     2821 ccggcctccg taccctcgcc agcatggctg ctcccacaat gactttttgc gcagtgtcca
     2881 ggctccggct cttcgccttc aggcgctgca atctggcctc agcttcagca atcttctgtt
     2941 cgagtgttct gctcatttcg tgactccttg cgcggtgaaa aatcgcattt tagctcgtca
     3001 ctggtagttt aaaaactgag ctggcataat gcacggcata tcacgaagtg cgcacttata
     3061 caatcttcac ttcgtttcga ttgtgtgcgc cctgcggggc tgaaagaaaa cggcaaaaag
     3121 gcattacggc agaaatggcg atttatcatc tcagcatgaa aatcatttcg cgaaaaaacg
     3181 gctacagtgc cgttgcttct gctgcctacc gttccggctc tgtcataccc gatgaccgta
     3241 ccggattaat ccacgattac acccgtaaac gcggcgttga tgatgcggtc attctcaccc
     3301 ctgcgaatgc accgtcctgg tgtggtgacc gttccgttct ctggaatgcg gtcgagaaag
     3361 ccgaacagcg ccggaactcc cagctggcaa gggagattga actcgccatt ccccgtgaga
     3421 tttcccgcga ggccgcacgg gaggccgttc tcgcttttgt ccgggaaaac tttgtcagtc
     3481 ggggcatgat tgccgatgtg gcgttccatc atatggaccg gaccaacccc catgcacaca
     3541 tcatgctgac cacgagagct gtcggggaaa cgggattcgc aggaaaggtc agggactgga
     3601 acgaccgggc actcgccgag acgtggcgcg catcatgggc tgaccatgcg aacagagcgc
     3661 ttgcgaacgc cggctaccag gaagagatag accatcgttc atacgagcgt cagggactgg
     3721 agaaagcgcc gggccttcac ctcggaaagg ctgcctgtgc gatggaaaaa cggggcatgg
     3781 aaacagaacg cggtgagcag aaccgcctga ttaacagcct taacctggaa atacaggttt
     3841 cccgcacaag gctggcagtc atccaggtac aggagaacgt gcggaaacgg gaactcagcg
     3901 atgccgcacg tcgtgcagcg gaagccctta atctgaccat tcccgccgcg aatgcctcag
     3961 cggataccct gcgggaattc attgccacac tgccgcagga atgcgggaac gcatgggaga
     4021 tgacaccgga gttcgtggcg atgaacggga aggcaaacga catcaaacgt gaggggaatg
     4081 cgctggtgaa agagcgggat attctcgaaa aagagatgac cggactcaga aaagcccgtc
     4141 cggtagcgtc catcctgtca gagcttcccc tgatgacatg ggctgaaccg gaataccgca
     4201 aaagacaact ccgcttctgg aaactcgaga aacagat
//
