LOCUS       NZ_CP035127             4991 bp    DNA     circular CON 18-JUN-2024
DEFINITION  Escherichia coli strain EC25 plasmid pEC25-4, complete sequence.
ACCESSION   NZ_CP035127
VERSION     NZ_CP035127.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10743440
            Assembly: GCF_004088295.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4991)
  AUTHORS   He,F.
  TITLE     Carbapenem-resistant Escherichia coli strain harboring blaNDM-7 in
            China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4991)
  AUTHORS   He,F.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-JAN-2019) Department of Clinical laboratory, Sir Run
            Run Shaw Hospital, School of Medicine, Zhejiang University, 3
            Qingchun East Road, Hangzhou, Zhejiang 310016, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Oxford Nanopore GridION; Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_004088295.1-RS_2024_06_18
            Annotation Date                   :: 06/18/2024 04:29:28
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,001
            CDSs (total)                      :: 4,881
            Genes (coding)                    :: 4,618
            CDSs (with protein)               :: 4,618
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 263
            CDSs (without protein)            :: 263
            Pseudo Genes (ambiguous residues) :: 0 of 263
            Pseudo Genes (frameshifted)       :: 85 of 263
            Pseudo Genes (incomplete)         :: 176 of 263
            Pseudo Genes (internal stop)      :: 47 of 263
            Pseudo Genes (multiple problems)  :: 38 of 263
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP035127.1.
            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..4991
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EC25"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEC25-4"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2017-08-17"
                     /collected_by="Fang He"
     gene            13..417
                     /locus_tag="EQK40_RS25320"
                     /old_locus_tag="EQK40_25320"
     CDS             13..417
                     /locus_tag="EQK40_RS25320"
                     /old_locus_tag="EQK40_25320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016529521.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF2251 domain-containing protein"
                     /protein_id="WP_008321396.1"
                     /translation="MTILVTIQAQLVVGEEQVIKSLAPEGMLAAVFEDDGRTGYFYALD
                     ESVEGNPIMDAVHIYNAEDVSDGHIPSDVKIGWSEDSQKCVLLINGYPHGAFDFVGKNG
                     YCRSGYPPPINKVWSLSGHEWSDSVDDFFR"
                     /name="DUF2251 domain-containing protein"
     gene            complement(511..942)
                     /locus_tag="EQK40_RS25325"
                     /old_locus_tag="EQK40_25325"
     CDS             complement(511..942)
                     /locus_tag="EQK40_RS25325"
                     /old_locus_tag="EQK40_25325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001025244.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF6530 family protein"
                     /protein_id="WP_042109831.1"
                     /translation="MKIPAHLKHKPIIQVENYDRIDGPHADDTDAMGLSVGIAQWNTPG
                     WTELSAKVWRNTGEKWSRQSEELPLHRVIDLATLICITMDYSKNGRLSSSDDFPVTRST
                     DNPELAHHTEFMKKELKQNKSNLDVSLKRLSTELKRLGY"
                     /name="DUF6530 family protein"
     gene            1360..1617
                     /locus_tag="EQK40_RS25330"
                     /old_locus_tag="EQK40_25330"
     CDS             1360..1617
                     /locus_tag="EQK40_RS25330"
                     /old_locus_tag="EQK40_25330"
                     /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_042109830.1"
                     /translation="MGSNNNQNKDLQDKQADLLDQTYTLGWMDGYAEGYDDAIEDTQNA
                     LNKLENENELLTEVVESKDNVIKELASSAGRALQAVKKNK"
                     /name="hypothetical protein"
     gene            complement(1647..2705)
                     /locus_tag="EQK40_RS25335"
                     /old_locus_tag="EQK40_25335"
     CDS             complement(1647..2705)
                     /locus_tag="EQK40_RS25335"
                     /old_locus_tag="EQK40_25335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012508929.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ParA family protein"
                     /protein_id="WP_042109829.1"
                     /translation="MAIYAVWNNKGGVGKSYLTFQLASEYARQNPTKKVLVVDLCPQAN
                     SSSMLLGGMINGENTLNQIHSAIQRKTISGYIEDRIRSPYIPTNTGSSYVINVSTHNSK
                     VPNNLYLVTGDEQLELQASRVVGASFPGPHDAWRTVHLWINDLISDICNSWNNEDSCVF
                     IDCNPSFSIYTELALTAAERLLIPFSADGSSKRAVKAVLSLVYGERRHQNEPQSDFYLN
                     SNRYSMSLPQIYMYVGNRLTQMNNSSASAFKTVVTEIGDEIWKVWQTKPSLFCIHPNGS
                     STPNNKRSFRNMFQYEVNDANTASVVSGALGIPIATLTAGNKTVSGKIIKVNQTQLDKQ
                     VPNIVALAGMIE"
                     /name="ParA family protein"
     gene            complement(3035..3201)
                     /locus_tag="EQK40_RS26290"
                     /old_locus_tag="EQK40_25340"
                     /pseudo=""
     CDS             complement(3035..3201)
                     /locus_tag="EQK40_RS26290"
                     /old_locus_tag="EQK40_25340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505258.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            3617..3808
                     /locus_tag="EQK40_RS25350"
                     /old_locus_tag="EQK40_25350"
     CDS             3617..3808
                     /locus_tag="EQK40_RS25350"
                     /old_locus_tag="EQK40_25350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /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_032489493.1"
                     /translation="MTKQQKTALNMAKFIQHQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3808..4209
                     /locus_tag="EQK40_RS25355"
                     /old_locus_tag="EQK40_25355"
     CDS             3808..4209
                     /locus_tag="EQK40_RS25355"
                     /old_locus_tag="EQK40_25355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_032489494.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQLKGEHHSGQVSEQRDTASVDQCEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     Typing          complement(3094..3496)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.857"
                     /coverage="99.0"
                     /evalue="7.72e-165"
ORIGIN
        1 agaacagacc tgatgaccat tttagtgacg atacaggccc agctcgttgt cggggaggaa
       61 caggttataa agagcctcgc tcctgagggc atgctggccg ccgtgttcga agacgatggc
      121 cggaccgggt atttctatgc gctcgatgag tccgtcgagg gaaacccgat tatggacgca
      181 gtacacatct acaatgccga agacgtttca gacggtcaca ttccttctga tgttaaaatt
      241 ggctggtcag aagacagtca gaagtgcgta ctcctgatca atggataccc gcacggggca
      301 ttcgatttcg tgggaaaaaa cgggtactgc aggagtggtt atcctccccc tataaacaag
      361 gtgtggtctc tttccgggca tgagtggagc gactctgtgg atgatttttt ccggtgaatt
      421 acggcaggct atagcctgcc attatggttc gaaaaacgga tgttatggta aattcgtctg
      481 tgaagtaggt agacatttct aaagctagtt ttaatagcca agtctcttca attcagtcga
      541 gaggcgtttg aggcttacat caagattgct tttattttgt tttaactctt ttttcataaa
      601 ctcagtgtga tgtgctagct cagggttatc agttgagcga gtcacgggaa aatcatcact
      661 ggatgaaagt cgcccatttt tactgtagtc catggtgata cagatcagag ttgcaaggtc
      721 gattacccgg tgaagaggca gctcttctga ttgtcttgac catttttctc ctgtgtttcg
      781 ccaaaccttt gccgaaagct cagtccatcc aggagtgttc cattgagcaa tacctacaga
      841 tagccccata gcatcagtgt catcggcatg tgggccgtca atgcggtcgt aattttcgac
      901 ttgaataatt ggtttatgct tcaaatgcgc gggtattttc atcagttcgt ccttaggtaa
      961 tgtttgtgat tattaaatta cattgttttt ctaattataa aactcactaa atgtaagtaa
     1021 atattaatat ctattgttat catgtgcttg tgattttgtt tttccaattt tatgtttttt
     1081 gcttggagag tagcggtgtt tttttgtgtc aagtgttatg ataagccgta cgtttttttt
     1141 ctggtttata gttcggttat tcacagcaat gggcgtggtt ttctatgact acagataacg
     1201 ttaggaatat tggcgactat aaaaagaaag atgtcggggt ggatgctgac tgtaatccag
     1261 tctcaggaaa cacaccacca gtcagactaa gtgagaaact tagaaatgga attcctcctg
     1321 gtttgaaaac tcagatgcgc caacaaatga ggaaaaaaca tgggctctaa caataatcag
     1381 aataaagatc tgcaggataa gcaagctgat cttttggacc aaacgtatac tcttggttgg
     1441 atggatggct atgccgaagg gtatgatgat gctattgaag atactcagaa cgctttgaat
     1501 aaactggaaa acgaaaacga gttgcttact gaggttgttg aaagtaaaga taatgtaatc
     1561 aaagagttgg cctctagtgc tggcagggcg ctgcaagcag taaagaaaaa caaataaaaa
     1621 aaggcccttt taagggcctt gctattttat tcgatcatac cagcgagagc tacaatgttg
     1681 gggacttgtt tatctagctg cgtctgatta acctttatta tttttcctga aacagtttta
     1741 tttcctgcag ttaatgtcgc gattggaata cctaaggctc cagatacgac agatgctgtg
     1801 tttgcatcat ttacttcata ctgaaacata ttcctgaaag atcttttatt atttggcgtt
     1861 gagctcccat ttgggtgaat acaaaacaga cttggttttg tttgccatac tttccaaatt
     1921 tcatcaccaa tttcggttac taccgtctta aatgcactgg cagatgaatt gttcatttgc
     1981 gttaatctat ttccaacata catatatatt tgtggtagcg acatagaata acgattgcta
     2041 ttaagataga aatctgattg tggttcattc tgatggcgac gctcaccata aactaaagaa
     2101 agtacagcct taactgctct ctttgatgaa ccatcggcag agaaaggaat taaaaggcgc
     2161 tctgctgcgg ttaaagctaa ctctgtataa atagagaagc tagggttgca gtcaatgaat
     2221 acgcagctat cttcattatt ccatgagttg caaatgtcac tgattaaatc attaatccag
     2281 aggtgaacag tacgccatgc atcatgggga cctggaaatg atgccccaac aactcttgat
     2341 gcttggagtt ctaattgttc atcgccagtg acaagatata gattatttgg aactttacta
     2401 ttgtgtgtag atacatttat tacatagcta gaaccagtgt tggtaggaat atatggactt
     2461 ctgatcctat cctcaatata tccagatatt gtctttctct gtattgctga atgaatctgg
     2521 tttagtgtgt tttcgccatt tatcattcca ccaagtaaca tagaggacga gttcgcttgt
     2581 gggcacaggt caaccaccag gaccttttta gtagggttct gtctggcata ttcagaggct
     2641 aactgaaaag taaggtaact tttccctaca ccacccttgt tattccatac ggcatagatc
     2701 gccatctata actcctaatc tagttttgtt gttagcttag attcagggta ctagagatta
     2761 ttgttctact gttagtttct ttcagctgac tgcctttttt tggaacgata ttcagtcgaa
     2821 ggggttggct ggctcaccat gacttatctg gagttgtcga attccgatta aaaggatctt
     2881 cttgagatcc taacctgcgg gatgtaatct tttgctctgt aaacgaaaaa accacctggg
     2941 gaggtggttt ttcgaaggat cagtaagttg gggaacttct gaaccgtggt aacagggtgt
     3001 acaagaccgc tgccaccaaa tctgtccttt cagtttagct gtagttaggc tgtaacttca
     3061 agaactctgc accagtaatt cttgtacacc ccttaccagt ggctgctgcc agtggcgttt
     3121 tgtcgtgcct tccgggttgg actcaagtcg aaagttaccg gaacaggcgc agcagtcgga
     3181 ctgaacgggg ggttcgtgca tacagtccag cttggagcga actgcctacc cggaactgag
     3241 tgtcaggcgt ggaatgagac aaacgcggcc ataacagcgg aatgacaccg gtaaaccgaa
     3301 aggcaggaac aggagagcgc acgagggagc catcaggggg aaacgcctga tatctttata
     3361 gtcctgtcgg gtttcgccac cactgatttg agcgtccgtt tctgtgatgc ttgtcagggg
     3421 ggcggagcct atggaaaaac ggccgctgtg cggccttccc ttttctaaat tacgtgatcg
     3481 ctcggttttc tcgagctttc atacgcatgc tcctgccgct cgccgcagcc gaacggcagg
     3541 agcgtagcga ctgagtgagc gaggaagcgg aaaagagaac atccctacac tgagcactga
     3601 cgctctgagg cctcttatga cgaaacaaca gaaaacagcg ctgaacatgg ctaaattcat
     3661 ccagcatcaa tctctgctcc tgctggagaa gcttaacgag cttgatcttg atgtcgaggc
     3721 cgacctttgt gagaaactcc acgatgatgc ggagcatctt ttccgtacac tgtcctcgag
     3781 actggatgca ttacaggatg gtaactgatg gccagagtgt ctattagtga ggcagcccga
     3841 ctgacgggta agagtagaac aacactgcac aggttaatta aagcaggtga cctgtccacc
     3901 tgtagcggtg agcgcaatgc aaaaatggta gatacttcag agcttttacg tgtctttggt
     3961 ccctttgaac aactgaaggg tgaacaccat tctggacagg tctctgaaca gcgcgataca
     4021 gcctctgttg accagtgtga acaggtgatt cgtcatctga aacaggagat tgaacacctg
     4081 aacactttac ttttgtccaa agattcgcac attgacagcc tgaaacaggc catgctcctt
     4141 cttgaaaatc accaggcaaa attaactgaa tccccggcgc catggtggaa attctggaaa
     4201 aaatcctgac cctgtcatgc ttcagttttc ctctccggcc atcccgggga gttcctgaac
     4261 cttcccaaaa atagtcagat ctctgaacgc tcctcaccac taaaaatacc cacaccccac
     4321 gcaaaattaa aattttgcag atttgtattt aatatcagta gtttactttc ctgagatttc
     4381 gttttttaaa ttttatttat atagatccga ctctatgacg actcgtcata gagtccccgg
     4441 cgagtcgtca tagagtcggt aacgactcag ggctataaaa acaatgagtt aataacgacc
     4501 cgactctaga cccgactccc cgtttggttg ttttttagtc gcggcgactc taggtacgac
     4561 tctagtgcag agtcgccggt gaatcgtgtg gtgagtcgtc cggcgacttg ccataacgtg
     4621 attgccggcc gtcgacgaac ccgattcctg aacgtgctga aaaccggttt tccggctgcg
     4681 ccggcaacgc ttcacggcca cgcaataaat tgcgtccccg ttcaccgttt tcggatggga
     4741 agaacgccgg aaacaggact taccctgtct gaatggcgtg aatattcgcg ctatgcactt
     4801 gcgtgcatac tcatgcatgc cataaaaaca gagcctgcgc gtttctggcg ggttttcggg
     4861 tggtttgttg cctgttttac cggtttcccg tcagaaacgc cctcagcgcg tttctgacga
     4921 tgctgataac ggatgttatg gtaaattatc cgcttgtctg aaagctggct gccgaagcaa
     4981 ccaaggaaag g
//
