LOCUS       NZ_AP021966             5167 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain WP3-W18-CRE-03 plasmid pWP3-W18-CRE-03_3,
            complete sequence.
ACCESSION   NZ_AP021966
VERSION     NZ_AP021966.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194405
            Sequence Read Archive: DRR199241
            Assembly: GCF_014168775.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Sekizuka,T., Itokawa,K., Yatsu,K., Inamine,Y. and Kuroda,M.
  TITLE     complete genome sequences of Escherichia coli str. WP3-W18-CRE-03
            isolated from wastewater treatment plant effluent
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5167)
  AUTHORS   Sekizuka,T., Itokawa,K., Yatsu,K., Inamine,Y. and Kuroda,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-DEC-2019) Contact:Tsuyoshi Sekizuka National Institute
            of Infectious Diseases, Pathogen Genomics Center; 1-23-1 Toyama,
            Shinjuku-ku, Tokyo 162-8640, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: flye v2.5; minimap v0.2-r124; racon v1.1.0;
            circlator v1.5.3; Pilon v1.18; SPAdes v3.11.1; A5-miseq v20140604
            Genome Coverage                   :: 413x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 04:55:48
            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)                     :: 5,126
            CDSs (total)                      :: 5,007
            Genes (coding)                    :: 4,770
            CDSs (with protein)               :: 4,770
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 237
            CDSs (without protein)            :: 237
            Pseudo Genes (ambiguous residues) :: 0 of 237
            Pseudo Genes (frameshifted)       :: 90 of 237
            Pseudo Genes (incomplete)         :: 163 of 237
            Pseudo Genes (internal stop)      :: 41 of 237
            Pseudo Genes (multiple problems)  :: 52 of 237
            Pseudo Genes (short protein)      :: 4 of 237
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP021966.1.
            Annotated by DFAST v.1.2.3 (https://dfast.nig.ac.jp).
            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..5167
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WP3-W18-CRE-03"
                     /isolation_source="wastewater"
                     /db_xref="taxon:562"
                     /plasmid="pWP3-W18-CRE-03_3"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6684 N 139.4278 E"
                     /collection_date="2018-02-13"
     gene            101..310
                     /locus_tag="H7R02_RS25285"
                     /old_locus_tag="WP3W18C03_P30010"
     CDS             101..310
                     /locus_tag="H7R02_RS25285"
                     /old_locus_tag="WP3W18C03_P30010"
                     /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"
     gene            complement(376..909)
                     /locus_tag="H7R02_RS25290"
                     /old_locus_tag="WP3W18C03_P30020"
     CDS             complement(376..909)
                     /locus_tag="H7R02_RS25290"
                     /old_locus_tag="WP3W18C03_P30020"
                     /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_000168770.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            complement(912..1838)
                     /locus_tag="H7R02_RS25295"
                     /old_locus_tag="WP3W18C03_P30030"
     CDS             complement(912..1838)
                     /locus_tag="H7R02_RS25295"
                     /old_locus_tag="WP3W18C03_P30030"
                     /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_001331297.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTAPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            2015..2413
                     /locus_tag="H7R02_RS25300"
                     /old_locus_tag="WP3W18C03_P30040"
     CDS             2015..2413
                     /locus_tag="H7R02_RS25300"
                     /old_locus_tag="WP3W18C03_P30040"
                     /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_001222914.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLIDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKELKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            complement(2617..3531)
                     /locus_tag="H7R02_RS25305"
                     /old_locus_tag="WP3W18C03_P30050"
     CDS             complement(2617..3531)
                     /locus_tag="H7R02_RS25305"
                     /old_locus_tag="WP3W18C03_P30050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001738986.1"
                     /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_001271348.1"
                     /translation="MSAALQYFDENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRSTVATSARTL
                     KPWEALGISRAWYYQLKKRGLVE"
                     /name="replication initiation protein"
     Typing          complement(2757..3531)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.778"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(916..1838)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atccccctat gccaacgggg gattttttct ggttcactaa cgcataaata atagtgacac
       61 cctatcattc acaaaccgtg ataatataag gattatcatc atggcaaaat taggtgaaaa
      121 caccccacat attatcgatg ctactgtaga ttttatggca tcaagccagg catttcgtga
      181 gtatctgaaa aaacttcccc ctgataacac aataccgcca gctcttactg atgagcacgt
      241 accgttatat atacgaaggc tggaatacta tcgtctgctt tatcgaccaa agcagacaga
      301 atcatattga aaaaaacggt gaacggttcg cgaaattctt tcgcgggtcg tgaggcgttg
      361 gacaagcgaa gcgcgtcagt ttttccggct cttccccgtg acaggtttct ccaccagttt
      421 atcttccagt gtcacaactt tctgatacac cgccgctgtg gcgttgtagt tcctgtcgag
      481 tattgttttc attccccatc cgagcacaca gaacataacc agaaaagcca ctgacacccc
      541 acccagccat ttccagctat accctttaag ggtgttgtat tcctgcacga tattgctgtg
      601 aattgtcgca atatccctgt tcagggcatc cgcgtttgcc ttcatgtttg cgactgactc
      661 ttccagccgc tgaaaatcct ggctgatgcg ctcacctatc agtcctgcca cgtccagctt
      721 ctgcacctca tttctgactt catccctgac ctgttttgcc acaccgtcag aaatatcccg
      781 atatccgcga agagtttccc ttgccacagc cagagaatca gcaacagctt tctgttgctc
      841 cattgcggta tgttgcagat gctccaccga taacaggagc gtaagtaatt tttcttctgt
      901 gctggccatg ttcagaatcc catagaaaat ccacgtgacg gtgatttaac ccgttcaggt
      961 gcagttcggt tctgtctgct cactctgtct ctcatgtcaa agccatgctc ccgcgcaaca
     1021 tcatgttgca gccttctgac cagttcatgt tgcttaaccg gagtgtccag ccattccctg
     1081 atgtcatgcc cgaccgttcg cgcctgttca agatggcggg aatagtccgg ttcagaccgt
     1141 ttttgcatga tgtcatgacg ctgggcatca tcaagccgtc cggcagcttc aaaacccaga
     1201 tgcacttcgg gacgtcgttc aatgccctgt tctttcagcg tccggcagtc aatgaagccc
     1261 ctttcaaagc catgctttct catatgttcg ttgtgcttca cctcccagcg ttttcgcaat
     1321 tcccgcaact gctctttttg ctgagtgaga gtcaggcttc cggaatcctt tttcgcacct
     1381 ccccgctcgg gatacctggc gttatagcgc cggaaatact gttccggtgt acgttcaatg
     1441 ccatcattca cacgctgact catcatgata tgcgcatgag gctgttcgcc gccgtcaatg
     1501 ctcgctttcg gattgtgaat ggcaaaactc caggcgtgcc gttcgccagc ttcctgacgt
     1561 acaaaatcct gcaccagttc aaggcgctgt tccggtgtca gttcacgggg taatgcaatt
     1621 tcaagttccc tataggtcga accgttcgca cgttcaaact ggtcagccgc ctgccagaaa
     1681 tgggaaggat tatccctggc ccattccggc atgtttccgt gtgcggaata ttccaaatcc
     1741 tgacggtcgc ggtatttctc tttgcgctcg atgtaatcgg cgtggtttgc agcctgcccc
     1801 ttgccaccaa atttaacgct gaggtgatag gttgccacgg tttcagccct ctgcaggagc
     1861 gcactgtttc tcgacgaagg agagaaacat ataagtgcgc ttccttctaa ttttacgaat
     1921 tagcacggaa gataccccct gcacccgccg accgcaagcg atatactgca cgaccacaac
     1981 acaccgcaaa aaaacaccag ggagcatcac gaacatgcgc atcagcaaca tcgaatggct
     2041 gaagaaacgg atcggattca tcaggaagct cggagaacag accgcacgac agagacagat
     2101 tattgacctg atcgacaacg aagccggact cacagaacag gaacgcaaac ttctccacgt
     2161 actggcaaca gcggaaaaaa acgacttaca ggcacaggag agcgaacgaa aacaggcggt
     2221 ccaaaaacga atcgagggaa aaaaacaacg acgggaacgc aatcaccggc tctttctcgc
     2281 ggctgggcta ctgatcgaag caggactggt agacacaaaa acaggcgagc tatgctataa
     2341 aaaagacagg atattacaag cacttaagga acttaagtac gatctggaga catccccaaa
     2401 cccagacgcg taagtgcctc catccgtgtt ccgattccct ggtgcttcct cgctcattcg
     2461 ctcgctacgc tcggtcatga gactgcggcg agcactacca ccacaatcac gcggaaagcc
     2521 gcgccattgc agggctgaac ggggaaaaac ggcaaaaaac ctgctgctca aaaagacgcc
     2581 agaaaggcgc tgttatctga tataggctta tttggtctac tctacgagac ctcgtttttt
     2641 cagttggtaa taccaggcgc gactgatccc taatgcctcc cacggtttca gcgtgcgtgc
     2701 agatgtagct actgtgctgc gcttagactt agaaccgccc ttgcgaccgc gtgcagcctg
     2761 aatttctggc gtgtgcgtat cagccacata ctgtgcgaaa gtttccggcg tgaagttcct
     2821 gtgcgtgtat ttcgcaatgc tcttgccaat agcccgacat tcagccagtg aaagcggaac
     2881 gggaagcgat gcattgtaca tttcgacacg ctggatcacc gcttcaagcc actgtgagaa
     2941 cgctggccag ccctgacgaa tcgccctgta agcccatttg cgcgtcattt cgaacaggtg
     3001 gcagtttcgc cccatcccgt aatgtttatc gatgctacga cgctctgagg cgctcaaatc
     3061 gagataatca gccagttcat cgagggtata ggcttcctcg cgccactcca tcaccagcca
     3121 ttccaggtgg aacggatttt tgcaaatcag gccgctgtag ttcacatccg cacaaagttt
     3181 ctcacacagc gaacgttcaa ccgctgcggc atatttcagc gccttaaccg aggcatcagg
     3241 cgcggttctc acggcgatgt tgagtgcgta gagcaggtga gcgtgtccgt tcacaggatt
     3301 tttaacggtg atgttcggcg cgggagcgtt ccggtcgctc cagtcaatcg cagccccctc
     3361 gcggtcaacg tcaaaaacca gccagaactg cgcatgaggc tggttctgct gtatgtaccg
     3421 cgcaagaagc gcacgccctt tgccggagat gcgaagacca aaagcgagat catccgtgtg
     3481 atagggacga tggggtaaat tttcgtcgaa gtattgaagc gcggcgctca tgtgttacga
     3541 ttctctccgg gttatgcgac ctacacgccc tctgtatttc atgttgaatc ttgccggatc
     3601 tggacatgat ttcaggggcg tttgtttttc agtcgcttac actacaccca acggcaaatc
     3661 ctgtcgaacc ttcccgaaaa cccgatccat ttaccataac tcccgttgta cgcccccctt
     3721 aaaacgccct cagtcgcttt ctggcgcaaa aaacgcaaaa agacaagaaa acaccaggcc
     3781 aaaccagaaa aacgcgtcag aatcgttttc agggcgttgc ataactatgc acgaaagcga
     3841 tgtgcgatcg gtttcgtgcg ttctgaacac cgaacggctc aaaacgacaa gttttctccc
     3901 ctggtgcgtg gcgctctgac ggggtttcct gtttccaaac ttcacatctc gccaggacaa
     3961 aaaaaaaccg acctggggtc ggtggcaaga atcagagtct atgggaaata ttttagttat
     4021 cggatgctca atattcacaa acgcaaaaaa tgcctcagtg atgccctaaa acaacctttc
     4081 cagaaggagt ccgcgcttta cgatgcacgg aagagataaa aaaccccaca aaagtgggga
     4141 accaagagaa acaacaatta caggttgttg gttgtgttcg aacaacgatg aagtagctac
     4201 gctaaataat aattaccgta caggccctac atattcaaca ctaaatttaa gatcctgacg
     4261 aaggatttat aaatgcacga aaacacatag acagacaaat tcactaaatt catacacaaa
     4321 aacaagtgta gttttctaag taaattagat tcgacaacca attagtttat ccacatcgca
     4381 ttccactctt gctacaccaa tcacatttct tgatatgtaa tagcagaaaa aataaaacca
     4441 gacaccaata gaccaaaaaa caaacattca acaagaaaca ttttgaacaa tatcacaaaa
     4501 ctgtcacaac catcatcaga ctattgaaaa aaactggttg ctgttttata aaagcgactg
     4561 taacaacctc cactctatag ttccattagt ttaaagtgtc acacaaactg agcatccatt
     4621 tgttttcctt acttttgccc ctgtattcca aggggttttt ttataactta aagattagca
     4681 caccacacaa aaacaataaa aaaaaacgac aagttataca ataaaaccag tactatccat
     4741 acagctaatt acatataaat actattaaac catctggaca ttaaaaataa actcttataa
     4801 cataaaatta atgcggttcc ggtaccatat gtcagggata atgtgcaaat ggaggtatcg
     4861 gaactgcatt tcagttcatt attaattaat gacaaaaaaa acctctgcga gcgcagaggg
     4921 ggtaaggaat gttcccggtc ataatatgtc gatagtgttt atatacatac agaacaagaa
     4981 caacaaccag ccaactaata aatattttat tttttagagc tgaaacctta aagctcactt
     5041 ccattccata cattgttata aaccttatgt tgaaaactga aagtaagtac ggcagactta
     5101 ttaagttgcg tgcagtcttt tcacgttata caaacaagaa cacctgcgaa gttatttctc
     5161 cttacat
//
