LOCUS       NZ_AP022653             5207 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain 09-02E plasmid p3-09-02E, complete sequence.
ACCESSION   NZ_AP022653
VERSION     NZ_AP022653.1
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  JOURNAL   Unpublished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 5207)
  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
            AP022653.1.
            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..5207
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="09-02E"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p3-09-02E"
                     /geo_loc_name="Viet Nam:Thai Binh"
                     /lat_lon="20.445128 N 106.337870 E"
                     /collection_date="2018-10-10"
     gene            558..1076
                     /locus_tag="HRS14_RS25590"
                     /old_locus_tag="Esc0902E_49650"
     CDS             558..1076
                     /locus_tag="HRS14_RS25590"
                     /old_locus_tag="Esc0902E_49650"
                     /function="mobilization protein"
                     /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="MbeB family mobilization protein"
                     /protein_id="WP_032491136.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVLFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVIPQGKSATVIPYQ
                     GKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            1083..1316
                     /locus_tag="HRS14_RS25595"
                     /old_locus_tag="Esc0902E_49660"
     CDS             1083..1316
                     /locus_tag="HRS14_RS25595"
                     /old_locus_tag="Esc0902E_49660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137439.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1861..2157)
                     /locus_tag="HRS14_RS25600"
                     /old_locus_tag="Esc0902E_49680"
     CDS             complement(1861..2157)
                     /locus_tag="HRS14_RS25600"
                     /old_locus_tag="Esc0902E_49680"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679964.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000047647.1"
                     /translation="MSKTKSGRHRLSKTDKRLLAALIAAGYEERTARDLIQKHVYTLTQ
                     ADLRHLVSEISNGVGQSQAYDAIYQARRIRLARKFLNGKKPEEGLNAWKGDLP"
                     /name="hypothetical protein"
     gene            2369..2566
                     /locus_tag="HRS14_RS25605"
                     /old_locus_tag="Esc0902E_49690"
     CDS             2369..2566
                     /locus_tag="HRS14_RS25605"
                     /old_locus_tag="Esc0902E_49690"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335786.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001335786.1"
                     /translation="MKEEKVLLHRFLFVVRNKNGCELSCSADLMGTRDDVYKYFSDSVS
                     GLDVELIDVSCESEWEEHSH"
                     /name="hypothetical protein"
     gene            2584..2868
                     /locus_tag="HRS14_RS25610"
                     /old_locus_tag="Esc0902E_49700"
     CDS             2584..2868
                     /locus_tag="HRS14_RS25610"
                     /old_locus_tag="Esc0902E_49700"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000625497.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin Z C-terminal domain-related protein"
                     /protein_id="WP_000625497.1"
                     /translation="MISQNVWAPPFFFGPWVELENHTGDIAYTVYFDTLSNVPGPFIAF
                     IWYAPNGPRTVNVIGPASYQISCKGAGVDKIKFKSVSGTGQIIHVYTTL"
                     /name="colicin Z C-terminal domain-related protein"
     gene            complement(2932..3321)
                     /locus_tag="HRS14_RS25615"
                     /old_locus_tag="Esc0902E_49710"
     CDS             complement(2932..3321)
                     /locus_tag="HRS14_RS25615"
                     /old_locus_tag="Esc0902E_49710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679965.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000477210.1"
                     /translation="MFKSSVKSITSSTILTLLIGCSSTETNKNIVYKVGGDSIILNKYC
                     ILKMYPSQSEKNKGVIIEVNTDSLCKKKLNEITSKNIGKPLISYFDGKVISQPAIIHSA
                     LNPTHYYQPVNDETTVMEIIKAYSK"
                     /name="hypothetical protein"
     gene            complement(4508..4699)
                     /locus_tag="HRS14_RS25620"
                     /old_locus_tag="Esc0902E_49730"
     CDS             complement(4508..4699)
                     /locus_tag="HRS14_RS25620"
                     /old_locus_tag="Esc0902E_49730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4764..5087
                     /locus_tag="HRS14_RS25625"
                     /old_locus_tag="Esc0902E_49740"
     CDS             4764..5087
                     /locus_tag="HRS14_RS25625"
                     /old_locus_tag="Esc0902E_49740"
                     /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="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_000955995.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="plasmid mobilization relaxosome protein MobC"
     Typing          4336..4422
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          complement(3769..4325)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.821"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3..1420
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.776"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          4735..5084
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.308"
                     /coverage="99.0"
                     /evalue="1.08e-63"
ORIGIN
        1 cgatgccacg ccatttgcga agaaatacac gtccggtgtt ctgtcgttcg cggagaagga
       61 gctgccgccg ggaggacgtg aaaaagtgat ggcgagcttt gagcgtgtac tgatgcccgg
      121 tctcgaaaaa aatcagtaca gcatcctgtg ggtggagcac caggacaagg gacggcttga
      181 gctgaatttt gtcattccga acatggagct acagagcgga aaacgcctcc agccgtacta
      241 cgaccgggca gacaggccga gaattgatgc ctggcagacg ctggttaatc accattacgg
      301 gctgcatgac cccaacgccc cggagaaccg ccggatactg actctccctg ataacctgcc
      361 ggaaacgaaa caggcgcttg cagagagcgt cacacgcggg atagacgctc tttatcatgt
      421 cggggagata aaaggccgtc aggatgtgat tcaggcgctc acagaggcag ggcttgaagt
      481 ggtcagggtg acgcgaagca gtatcagcat tgcagacccg aacggtggga agaatatcag
      541 gctgaaagga gcattttatg agcaatcttt tacagacggg cgcggagttc gagaaaaagc
      601 tgaaagagag agccgaatct acagagacaa tgctgaacga cgagttcagc aagctcgaaa
      661 aatctgtaag caaggctgtg acatcaaacg agacgaaaat caaagacgct atagccctgt
      721 tcacagcttc gacagaggaa tcactgaaaa aacaccggga aggggtgaaa gaggcgatga
      781 tgcagcacag gaaggacgtg ttaaagctgg cagggaatac gggcatgatg ttactgggga
      841 tggtcctttt cctgtttacc gtgagtggcg ggacgctctg gtatcttggc gggcggatac
      901 aggcgaacct ggaagaaatc aggatacagg aagaaacatt gcagaaactg aacgcgaaga
      961 catggggcgt ggagtttgtg caggacggga gaaggaaatt tctggtcatc ccgcagggga
     1021 aatcggcaac ggtgattccc tatcagggga aggactgggt acaactgacg gagtgacaca
     1081 gagtgacgga gctggaaaga catttgctga acgcattaga gcaactgcaa caggactata
     1141 tgcagcggct gaacgaatgg gagagcgcct tcgtggaatt gcagaaaatg ttttcgctta
     1201 cgcaacggga caacgcgatg ctgaacgagc gggtcatgca gttgagtcag caggtgcagc
     1261 acttgagcga gcagacagaa cgcttgagcc agttatacag cgagaacagg agataaggga
     1321 cgaacggctg atacaggaac gcgaacatgc gttatccctg gagcgtgagc gccagctgga
     1381 aatacaggaa cggacactgg atggcccttc gctgggatgg taatcagaga caggctaaaa
     1441 tgttgtcagc gcgtttccgg tgcatttttt gggataatgg ttggttcggg ggcaccggga
     1501 acgcgcttca gtcagacctt gctgaaaaca caggaacgcg ttaaaacgca tacgggcgcg
     1561 attctggtgt gtcttttgtt gctgtgtttt gcctctattg ccagatcgcg ctcattcccc
     1621 tgaacttctg ttttcccgct ccggtccccg tcttcttcgc ttccgaaagc atgaaaaaaa
     1681 tccgtttcag ctgtctctgg ctggcaattc ctgcatgatt cacatggctg catagctatg
     1741 catgtggtta aaatttaccg ggtgcgatcg cggcagtttt tcgggtggtt tgttgccatt
     1801 tttacctgtc tgctgccgtg atcgcgccga acgcgtttca gcggtgcgta caataagtga
     1861 ttatggtaaa tcacccttcc aggcgttcag cccttcttcc ggtttttttc cgttcaggaa
     1921 tttacgggcg agacgaatgc gtcttgcctg gtaaatcgca tcgtaggcct gtgactgtcc
     1981 cacaccgtta ctgatttcac tgaccagatg gcgcaggtcg gcctgtgtca gtgtgtaaac
     2041 gtgtttctgg atgaggtcac gggctgtccg ctcttcgtat ccggcagcga taagtgcagc
     2101 cagcaggcgt ttgtctgttt tgctcagtcg gtggcgacca gattttgttt tgctcacgtt
     2161 atctcctctc tgttttttct cctgatgtta tccggtgctg tttttctgct gcgaatcttc
     2221 ccttcctgat ttttataagg gtgattcaga tcacaaaaat gaaaattcat atcattgaca
     2281 ggaaaaataa tgcggcgtaa tttatactgt atataaaact agtatttata tatacagtat
     2341 attctgtgta aataaaggga gggataaaat gaaagaagaa aaagtattgc ttcaccgttt
     2401 cttatttgta gttaggaata agaatggttg tgaactatca tgttcggcag accttatggg
     2461 aacaagggat gatgtttata agtatttctc tgattctgtt agtgggctag atgttgagct
     2521 tatagatgtt tcttgcgaga gtgaatggga agaacattcg cattgaacta atcaggagat
     2581 tatatgattt ctcaaaatgt ttgggctcct cctttctttt ttggtccttg ggttgaactt
     2641 gaaaatcata ctggtgatat cgcgtacact gtctattttg atacattgtc taatgtaccc
     2701 ggtccattta ttgcttttat ctggtatgcc cctaatgggc caagaacagt taacgttatt
     2761 ggtccagcat cttatcagat ctcttgcaag ggcgctggtg ttgataaaat taaatttaaa
     2821 agtgtcagtg ggacagggca gattattcat gtatacacta ccttataata agagctgaat
     2881 aaatataatc ctgcctaagc tataccttaa gcaggattat atctattaat attattttga
     2941 atatgctttt atgatttcca tcactgttgt ttcatcgttc acaggttgat aataatgggt
     3001 tggatttagt gcagaatgaa tgattgcagg ttgggatatt acttttccat caaaatatga
     3061 aatcaggggt ttccctatat ttttactagt tatttcgttt agttttttct tacataaact
     3121 atctgtgttt acttctatta tgacgccttt gtttttttct gattgggaag ggtacatttt
     3181 aagtatgcaa tatttattca gaatgatgct gtcaccacca actttgtaaa caatgttttt
     3241 gtttgtttca gtacttgaac atcctataag taaggtcagt atagtactcg atgttattga
     3301 ctttactgat gatttgaaca tattaactcc attttatttt gttaaaattc caatctataa
     3361 atacatatac acgtaaaaat aaacaatgcg aacgttttca cttatattat ccccatgatg
     3421 tgattgaatg gtggttccat ataagagagg gcaattatac tatctttctc tcctgaactg
     3481 atgggattgc agtttagaga aaaaagatca aaggatcttc ttgagatcct ttttttctgc
     3541 gcgtaatctg ctgcctgtaa acgaaaaaac caccctggca ggtggttttt cgaaggttag
     3601 ctaatcctgg cagattacct aaccgggtag ctggcttaag tggagcacag ataccaaaag
     3661 atgtcctttc agtgtagccg ctataaggct tcaacttcaa gagttctgcg tatctaaatc
     3721 cactttttag ttaccaatgg ctgctgccag tggcgttaag tcgtgtctta ccgggttgga
     3781 ctcaagacga tagttaccgg ataaggcgca gcggtcgggc tgaacggggg gttcgtgcac
     3841 acagcccagc ttggagcgaa cgacctacac cgaactgaga tacctacagc gtgagctatg
     3901 agaaagcgcc acgcttcccg aagggagaaa ggcggacagg tatccggtaa acggtaaggt
     3961 cggaacagga gagcgcacga gggagcttcc ggggggaaac gcctggtatc tttaagtcct
     4021 gtcgggtttc gccacctctg acttgagcgt cgatttttgt gatgctcgtc aggggggcgg
     4081 agcctatgga aaaacgccag cggcgcggcc ttcttcctgt tcctggtctt ttgctcacat
     4141 gttttttccg gtgttatccc ctgattctgt ggataacagc atttcgtttt tgagtgagta
     4201 gataccgctc gccgcagtcg aacgaccgag cgtagcgagt cagtgagcga ggaagcggaa
     4261 aagcgcctgg acgtgcattt tctccttacg catctgtgcg gcatttcaca cccggtatgg
     4321 cgcacgtttc atacaatccg cactgatgcc gcatggttaa gccagtatac actccgctat
     4381 cgctacgtga ctgggtcatg gctgcgcccc gacacccgct aaaacccgct gacgcgccct
     4441 gacgggcttg tctgctcccg gcatccgctc acagacaagc tgtgaccgtc tccgggagct
     4501 gtatgtgtca gaggttttca ccgtcatccc cgaagcgtgc gaggcagctg cggtaaagct
     4561 catcggcgtg gtcgtgaagc gattcacaga tgtctgcctg ttcatccgcg tccagttcgt
     4621 tgagcttttc cagcagcgtt aatgtctggc ttctgataaa gcgggccatg ttaagggcgg
     4681 ttttttcctg tttagtcact gatgcctccg tgtaaggggg gatttctgtt catggggtaa
     4741 tgataccgat gaaacgcgag aggatgctca cgatacgggt tactgatgat gaacatgccc
     4801 ggttactgga acgctgtgag ggtaaacagc tggcggtatg gatgcggcgg gtctgtctgg
     4861 gtgagccggt tgcccgttcc gggaagctgc cgacactggc accgccgtta ctgcgccagc
     4921 tggctgccat cgggaataac ctgaatcaga cggcgaggaa ggtgaacagc gggcagtggt
     4981 cttccggtga ccgggttcag gtggtggccg cactgatggc catcgagaga gagttgcgca
     5041 gcttacggca ggtcgtcagg gaacatggag cgcgggatga tagttaagtt tcatgccagg
     5101 ggaaaaggcg gtggcagtgg tccggttgat tacctgctgg gaagggagcg taaccgggaa
     5161 ggggcaacgg tgcttcaggg taatccggaa gaagtccggg aactcat
//
