LOCUS       NZ_AP022654             5164 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain 09-02E plasmid p4-09-02E, complete sequence.
ACCESSION   NZ_AP022654
VERSION     NZ_AP022654.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00198301
            Assembly: GCF_012149945.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Mohsin,M., Tanaka,K., Kawahara,R., Kondo,S., Noguchi,H., Motooka,D.,
            Nakamura,S., Khong,D.T., Nguyen,T.N., Tran,H.T. and Yamamoto,Y.
  TITLE     Whole-genome sequencing and comparative analysis of the genomes of
            Bacteroides thetaiotaomicron and Escherichia coli isolated from a
            healthy resident in Vietnam
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5164)
  AUTHORS   Mohsin,M., Tanaka,K. and Yamamoto,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-FEB-2020) Contact:Mashkoor Mohsin Institute of
            Microbiology; UAF main road 38000, Faisalabad, Punjab 38000,
            Pakistan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Platanus v. 1.2.4; Canu v. 1.7
            Genome Coverage                   :: 143X
            Sequencing Technology             :: illumina Miseq, Minion
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 02:15:49
            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)                     :: 5,204
            CDSs (total)                      :: 5,083
            Genes (coding)                    :: 4,862
            CDSs (with protein)               :: 4,862
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 221
            CDSs (without protein)            :: 221
            Pseudo Genes (ambiguous residues) :: 0 of 221
            Pseudo Genes (frameshifted)       :: 81 of 221
            Pseudo Genes (incomplete)         :: 153 of 221
            Pseudo Genes (internal stop)      :: 36 of 221
            Pseudo Genes (multiple problems)  :: 46 of 221
            Pseudo Genes (short protein)      :: 4 of 221
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022654.1.
            Annotated at DFAST 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..5164
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="09-02E"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p4-09-02E"
                     /geo_loc_name="Viet Nam:Thai Binh"
                     /lat_lon="20.445128 N 106.337870 E"
                     /collection_date="2018-10-10"
     gene            1..915
                     /locus_tag="HRS14_RS25630"
                     /old_locus_tag="Esc0902E_49750"
     CDS             1..915
                     /locus_tag="HRS14_RS25630"
                     /old_locus_tag="Esc0902E_49750"
                     /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_001271363.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRSTVATSARTL
                     KPWEALGISRAWYYQLKKRGLVE"
                     /name="replication initiation protein"
     gene            complement(1119..1517)
                     /locus_tag="HRS14_RS25635"
                     /old_locus_tag="Esc0902E_49760"
     CDS             complement(1119..1517)
                     /locus_tag="HRS14_RS25635"
                     /old_locus_tag="Esc0902E_49760"
                     /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            1694..2620
                     /locus_tag="HRS14_RS25640"
                     /old_locus_tag="Esc0902E_49770"
     CDS             1694..2620
                     /locus_tag="HRS14_RS25640"
                     /old_locus_tag="Esc0902E_49770"
                     /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_025732090.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     FTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTAPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            2623..3156
                     /locus_tag="HRS14_RS25645"
                     /old_locus_tag="Esc0902E_49780"
     CDS             2623..3156
                     /locus_tag="HRS14_RS25645"
                     /old_locus_tag="Esc0902E_49780"
                     /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(3222..3431)
                     /locus_tag="HRS14_RS25650"
                     /old_locus_tag="Esc0902E_49790"
     CDS             complement(3222..3431)
                     /locus_tag="HRS14_RS25650"
                     /old_locus_tag="Esc0902E_49790"
                     /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          2..915
                     /name="rep_cluster_2131"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.909"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1695..2617
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgagcgccg cgcttcaata cttcgaagaa aatttacccc accgtcccta tcacacggat
       61 gatctcgctt tcggccttcg tatctccggc aaagggcgcg cgcttcttgc acggtatatc
      121 cagcagaacc agcctcatgc acagttctgg ctggtttttg acgttgaccg cgagggggct
      181 gcgattgact ggagcgaccg gaacgctccc gcgccgaaca tcaccgttaa aaatcctgtg
      241 aacggacacg ctcacctgct ctacgcactc aacatcgccg tgagaaccgc gcctgatgcc
      301 tcggttaagg cgctgaaata tgccgcagcg gttgaacgtt cgctgtgtga gaaactttgt
      361 gcggatgtga actacagcgg cctgatttgc aaaaatccgt tccacctgga atggctggtg
      421 atggagtggc gcgaggaagc ctataccctc gatgaactgg ctgattatct cgatttgagc
      481 gcctcagagc gtcgtagcat cgataaacat tacgggatgg ggcgaaactg ccacctgttc
      541 gaaatgacgc gcaaatgggc ttacagggcg attcgtcagg gctggccagc gttctcacag
      601 tggcttgaag cggtgatcca gcgtgtcgaa atgtacaatg catcgcttcc cgttccgctt
      661 tcactggctg aatgtcgggc tattggcaag agcattgcga aatacacgca caggaacttc
      721 acgccggaaa ctttcgcaca gtatgtggct gatacgcaca cgccagaaat tcaggctgca
      781 cgcggtcgca agggcggttc taagtctaag cgcagcacag tagctacatc tgcacgcacg
      841 ctgaaaccgt gggaggcatt agggatcagt cgcgcctggt attaccaact gaaaaaacga
      901 ggtctcgtag agtagaccaa ataagcctat atcagataac agcgcctttc tggcgtcttt
      961 ttgagcagca ggttttttgc cgtttttccc cgttcagccc tgcaatggcg cggctttccg
     1021 cgtgattgtg gtggtagtgc tcgccgcagt ctcatgaccg agcgtagcga gcgaatgagc
     1081 gaggaagcac cagggaatcg gaacacggat ggaggcactt acgcgtctgg gtttggggat
     1141 gtctccagat cgtacttaag ttccttaagt gcttgtaata tcctgtcttt tttatagcat
     1201 agctcgcctg tttttgtgtc taccagtcct gcttcgatca gtagcccagc cgcgagaaag
     1261 agccggtgat tgcgttcccg tcgttgtttt tttccctcga ttcgtttttg gaccgcctgt
     1321 tttcgttcgc tctcctgtgc ctgtaagtcg tttttttccg ctgttgccag tacgtggaga
     1381 agtttgcgtt cctgttctgt gagtccggct tcgttgtcga tcaggtcaat aatctgtctc
     1441 tgtcgtgcgg tctgttctcc gagcttcctg atgaatccga tccgtttctt cagccattcg
     1501 atgttgctga tgcgcatgtt cgtgatgctc cctggtgttt ttttgcggtg tgttgtggtc
     1561 gtgcagtata tcgcttgcgg tcggcgggtg cagggggtat cttccgtgct aattcgtaaa
     1621 attagaagga agcgcactta tatgtttctc tccttcgtcg agaaacagtg cgctcctgca
     1681 gagggctgaa accgtggcaa cctatcacct cagcgttaaa tttggtggca aggggcaggc
     1741 tgcaaaccac gccgattaca tcgagcgcaa agagaaatac cgcgaccgtc aggatttgga
     1801 atattccgca cacggaaaca tgccggaatg ggccagggat aatccttccc atttctggca
     1861 ggcggctgac cagtttgaac gtgcgaacgg ttcgacctat agggaacttg aaattgcatt
     1921 accccgtgaa ctgacaccgg aacagcgcct tgaactggtg caggattttg tacgtcagga
     1981 agctggcgaa cggcacgcct ggagttttgc cattcacaat ccgaaagcga gcattgacgg
     2041 cggcgaacag cctcatgcgc atatcatgat gagtcagcgt gtgaatgatg gcattgaacg
     2101 tacaccggaa cagtatttcc ggcgctataa cgccaggtat cccgagcggg gaggtgcgaa
     2161 aaaggattcc ggaagcctga ctttcactca gcaaaaagag cagttgcggg aattgcgaaa
     2221 acgctgggag gtgaagcaca acgaacatat gagaaagcat ggctttgaaa ggggcttcat
     2281 tgactgccgg acgctgaaag aacagggcat tgaacgacgt cccgaagtgc atctgggttt
     2341 tgaagctgcc ggacggcttg atgatgccca gcgtcatgac atcatgcaaa aacggtctga
     2401 accggactat tcccgccatc ttgaacaggc gcgaacggtc gggcatgaca tcagggaatg
     2461 gctggacact ccggttaagc aacatgaact ggtcagaagg ctgcaacatg atgttgcgcg
     2521 ggagcatggc tttgacatga gagacagagt gagcagacag aaccgaactg cacctgaacg
     2581 ggttaaatca ccgtcacgtg gattttctat gggattctga acatggccag cacagaagaa
     2641 aaattactca cgctcctgtt atcggtggag catctgcaac ataccgcaat ggagcaacag
     2701 aaagctgttg ctgattctct ggctgtggca agggaaactc ttcgcggata tcgggatatt
     2761 tctgacggtg tggcaaaaca ggtcagggat gaagtcagaa atgaggtgca gaagctggac
     2821 gtggcaggac tgataggtga gcgcatcagc caggattttc agcggctgga agagtcagtc
     2881 gcaaacatga aggcaaacgc ggatgccctg aacagggata ttgcgacaat tcacagcaat
     2941 atcgtgcagg aatacaacac ccttaaaggg tatagctgga aatggctggg tggggtgtca
     3001 gtggcttttc tggttatgtt ctgtgtgctc ggatggggaa tgaaaacaat actcgacagg
     3061 aactacaacg ccacagcggc ggtgtatcag aaagttgtga cactggaaga taaactggtg
     3121 gagaaacctg tcacggggaa gagccggaaa aactgacgcg cttcgcttgt ccaacgcctc
     3181 acgacccgcg aaaggatttc gcgaaccgtt caccgttttt ttcaatatga ttctgtctgc
     3241 tttggtcgat aaagcagacg atagtattcc agccttcgta tatataacgg tacgtgctca
     3301 tcagtaagag ctggcggtat tgtgttatca gggggaagtt ttttcagata ctcacgaaat
     3361 gcctggcttg atgccataaa atctacagta gcatcgataa tatgtggggt gttttcacct
     3421 aattttgcca tgatgataat ccttatatta tcacggtttg tgaatgatag ggtgtcacta
     3481 ttatttatgc gttagtgaac cagaaaaaat cccccgttgg cataggggga tatgtaagga
     3541 gaaataactt cgcaggtgtt cttgtttgta taacgtgaaa agactgcacg caacttaata
     3601 agtctgccgt acttactttc agttttcaac ataaggttta taacaatgta tggaatggaa
     3661 gtgagcttta aggtttcagc tctaaaaaat aaaatattta ttagttggct ggttgttgtt
     3721 cttgttctgt atgtatataa acactatcga catattatga ccgggaacat tccttacccc
     3781 ctctgcgctc gcagaggttt tttttgtcat taattaataa tgaactgaaa tgcagttccg
     3841 atacctccat ttgcacatta tccctgacat atggtaccgg aaccgcatta attttatgtt
     3901 ataagagttt atttttaatg tccagatggt ttaatagtat ttatatgtaa ttagctgtat
     3961 ggatagtact ggttttattg tataacttgt cgtttttttt attgtttttg tgtggtgtgc
     4021 taatctttaa gttataaaaa aaccccttgg aatacagggg caaaagtaag gaaaacaaat
     4081 ggatgctcag tttgtgtgac actttaaact aatggaacta tagagtggag gttgttacag
     4141 tcgcttttat aaaacagcaa ccagtttttt tcaatagtct gatgatggtt gtgacagttt
     4201 tgtgatattg ttcaaaatgt ttcttgttga atgtttgttt tttggtctat tggtgtctgg
     4261 ttttattttt tctgctatta catatcaaga aatgtgattg gtgtagcaag agtggaatgc
     4321 gatgtggata aactaattgg ttgtcgaatc taatttactt agaaaactac acttgttttt
     4381 gtgtatgaat ttagtgaatt tgtctgtctg tgtgttttcg tgcatttata aatccttcgt
     4441 caggatctta aatttagtgt tgaatatgta gggcctgtac ggtaattatt atttagcgta
     4501 gctacttcat cgttgttcga acacaaccaa caacctgtaa ttgttgtttc tcttggttcc
     4561 ccacttttgt ggggtttttt atctcttccg tgcatcgtaa agcgcggact ccttctggaa
     4621 aggttgtttt agggcatcac tgaggcattt tttgcgtttg tgaatattga gcatccgata
     4681 actaaaatat ttcccataga ctctgattct tgccaccgac cccaggtcgg tttttttttg
     4741 tcctggcgag atgtgaagtt tggaaacagg aaaccccgtc agagcgccac gcaccagggg
     4801 agaaaacttg tcgttttgag ccgttcggtg ttcagaacgc acgaaaccga tcgcacatcg
     4861 ctttcgtgca tagttatgca acgccctgaa aacgattctg acgcgttttt ctggtttggc
     4921 ctggtgtttt cttgtctttt tgcgtttttt gcgccagaaa gcgattgatg gcgttttaca
     4981 tggtacgtac aacgggagtt atggtaaatg gatcggtttt tcgggaagga tcgacaggat
     5041 ttgccgttgg gtgtagtgta agcgactgaa aaacaaacgc ccctgaaatt cgtgtctatc
     5101 cgccaagact ttcacgaaaa tacaggggcg atgtcggtcg ataacctgga aggaatcgta
     5161 acac
//
