LOCUS       NZ_CP115828             4658 bp    DNA     circular CON 07-JAN-2024
DEFINITION  Escherichia coli strain E1 plasmid pE1-Col1, complete sequence.
ACCESSION   NZ_CP115828
VERSION     NZ_CP115828.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32542048
            Assembly: GCF_034089005.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4658)
  AUTHORS   Dong,N.
  TITLE     Characterization of E. coli strain E1 from bloodstream infection
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4658)
  AUTHORS   Dong,N.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-JAN-2023) Department of Medical Microbiology, Soochow
            University, Ren'ai, Suzhou 215123, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: unicycler v. v0.5.0
            Assembly Name                     :: E1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200.0x
            Sequencing Technology :: Illumina; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/06/2024 23:26:36
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,530
            CDSs (total)                      :: 5,407
            Genes (coding)                    :: 5,198
            CDSs (with protein)               :: 5,198
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 209
            CDSs (without protein)            :: 209
            Pseudo Genes (ambiguous residues) :: 0 of 209
            Pseudo Genes (frameshifted)       :: 76 of 209
            Pseudo Genes (incomplete)         :: 152 of 209
            Pseudo Genes (internal stop)      :: 37 of 209
            Pseudo Genes (multiple problems)  :: 51 of 209
            Pseudo Genes (short protein)      :: 3 of 209
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP115828.1.
            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..4658
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="E1"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pE1-Col1"
                     /geo_loc_name="China"
                     /collection_date="2019"
     gene            complement(join(3785..4658,1..626))
                     /locus_tag="PBU98_RS27605"
     CDS             complement(join(3785..4658,1..626))
                     /locus_tag="PBU98_RS27605"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_062980410.1"
                     /translation="MIVKFHPRGRGGGAGPVDYLLGKDRQRDGATVLQGKPEEVRELID
                     ASPYAKKYTSGVLSFAEKDLPPGQREKLMASFERVLMPGLDKDQYSVLWVEHQDKGRLE
                     LNFLIPNTELLTGKRLQPYYDRADRPRIDAWQTIVNGRLGLHDPNAPENRRALVTPSAL
                     PETKQEAAQAITRGLLALASSGELKTRQDVTEALESAGFEVVRTTKSSISIADPDGGRN
                     IRLKGAIYEQSFNAGEGLRAEIESAAAEYRRDAESRIQRAREVCQSGTERKREENQRRH
                     PRPRQEAVRCHEPAHERYAADGQPDVADHRLGVYTADSIGRKHSVVAGAADTRQLHDHP
                     GAEAHAGHAVREEQRCAALDLRRAETPLREGEPGSGTVRRGFELDDTGGEIAHDGAGKT
                     VAERIRAATAGLLEKAGRVGERLRGMADDVWSYATGERGAERARYGLEQAGAEFERAAA
                     PVVTRLNVIEAHREQERAAQHQKALELERSQRQRTYNGPSL"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(616..939)
                     /locus_tag="PBU98_RS27610"
     CDS             complement(616..939)
                     /locus_tag="PBU98_RS27610"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_171944688.1"
                     /translation="MLTMWVTEDEHRRLLERCNGKQLAAWMRQTCLDEKPARAGKLPSL
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            complement(1168..1347)
                     /locus_tag="PBU98_RS27615"
     CDS             complement(1168..1347)
                     /locus_tag="PBU98_RS27615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001347451.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_223203143.1"
                     /translation="MEKRQRRILFSFILDLSAIHLVILEQVTPAAASRQERSDRVSEEA
                     SFHRLQHFALTPHS"
                     /name="hypothetical protein"
     gene            complement(2186..2665)
                     /locus_tag="PBU98_RS27620"
     CDS             complement(2186..2665)
                     /locus_tag="PBU98_RS27620"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001050742.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001050742.1"
                     /translation="MNLLLPRDIVEAVLNDKKTKNARVAKCDGSEFFLELPSMNADFPA
                     GKIILKLGDSGFYNKRTKSLEGAYGLRHIWDKHRVEIGATSAEDIVIFLESILLAGAEV
                     LIDPKKGQNKAIVVESGTGMMILELKKPNGEDPYYSIITAYDRKSHPGTKLHTLI"
                     /name="hypothetical protein"
     gene            3142..3693
                     /locus_tag="PBU98_RS27625"
     CDS             3142..3693
                     /locus_tag="PBU98_RS27625"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000654246.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000654246.1"
                     /translation="MKDMKAVVVFTGKDLNIMRTEGGSGYWHARTDRLNDADYLIAVRN
                     RRETWAVKDLEHGTAFLIAKITGCFKSPDYDDRNVITFDEYAEIHTPKAWKMLTDGQRY
                     PVAYLSAQEAFLRIGVTPEQLEWKKFHPSSPSVPNTVIPGLAEEKTEKLSLNEAIERAK
                     KDISNATGIDSSAITISIKI"
                     /name="hypothetical protein"
     Typing          complement(1041..1227)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.263"
                     /coverage="87.0"
                     /evalue="2.7100000000000003e-47"
     Typing          1207..1686
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.164"
                     /coverage="93.0"
                     /evalue="7.55e-176"
     Typing          complement(4..626)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.596"
                     /coverage="99.0"
                     /evalue="4.25e-131"
     Typing          complement(3789..4657)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="88.276"
                     /coverage="99.0"
                     /evalue="5.87e-159"
ORIGIN
        1 tttgtggtgc gtaccacctc aaaacctgcg ctttccagcg cctcagtgac gtcctggcgg
       61 gttttcagct ccccggacga ggctaaggcc agtaaacccc gtgtaattgc ctgagcggct
      121 tcctgcttcg tttccggcag cgcggacggc gtgaccagcg cccgccggtt ttcaggcgcg
      181 ttcgggtcat gcagccccag cctgccgttc acgatggtct gccaggcatc aatgcgcgga
      241 cggtcggcgc ggtcgtaata cggctggaga cgcttgccgg tcagcagctc cgtgttcggg
      301 atcaggaagt tcagctccag ccgcccctta tcctggtgct caacccacag cacgctgtac
      361 tggtctttat cgagtccggg catcagaacc cgttcaaagc tcgccatcag cttttcgcgc
      421 tgcccgggcg gtaaatcctt ttcggcaaag gacaggacgc cggatgtgta cttttttgcg
      481 tagggcgagg cgtcgataag ctccctgact tcttccggct tcccctgcag aacggtggcg
      541 ccgtcgcgct gtcggtcttt ccccagcaga taatccaccg gaccggcgcc accgccgcgc
      601 cctcgcgggt gaaacttaac gatcatcgtc tgcacccttt tccagcacgg catgccgcag
      661 ccgctcgagt ccggcatcta tggccatcag cgcggcgacg acctgcacgc ggtcgtgccc
      721 gctgccacca ccggcgttaa cctgccgggc aatctggttg aggttgttcc ccataccggc
      781 aagctgacga agcagcgccg gcgagagcga gggaagcttg ccggcgcggg cgggtttctc
      841 gtccaggcac gtctggcgca tccaggctgc aagctgttta ccgttgcagc gctccagcag
      901 acggcggtgc tcatcttcgg tcacccacat cgtgagcatt ttgctgcgtt tatctgccaa
      961 tccggcctcc tgataacgcc gggacgggcg ggaaatcttt tcccggtcgg cgcggtgttg
     1021 gacaagccgc aggcgcgtca gtggttttag cgggtttcgg ggcgcagccc tgaaccagtc
     1081 acgtagcgct agcggagtgt atactggctt agtatggtaa atcgaagtgg aaattcaggg
     1141 aagtgcttca tgtggcaggt aaaaaattca gctgtggggc gtaagtgcga aatgctggag
     1201 acgatgaaat gacgcctcct cgctcactcg gtcgctacgc tcctgccgtg aggctgcggc
     1261 gggcgttacc tgctcaagaa tgacgagatg aatagcgctc aaatcaagaa tgaaggagaa
     1321 aaggatccgg cgttgccgtt tttccatagg ctccgccccc ctgacaagca tcacgaaatc
     1381 tgacgctcaa atcagtggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc
     1441 cctggtggct ccctcgtgcg ctctcctgtt cctgcctttc ggtttaccgg tgtcattccg
     1501 ctgttatggc cgcgtttatc tcattccacg cctgacactc agttccgggt aggcagttcg
     1561 ctccaagctg gactgtatgc acgaaccccc cgttcagtcc gaccgctgcg ccttatccgg
     1621 taactatcgt cttgagtcca acccgaaaag acacgactta acgccactgg cagcggccac
     1681 tggtaagcag gatgtgcgag agatgtatcg agagttcttg aagtggaggc cttagtgagg
     1741 ctacactgga aggacagtat ttggtgacat gtctcgcaca agactgttac cacggttcag
     1801 aaacttgccg gtttactgaa ccttcgaaaa accaccttgc cgggtggttt tttcgtttac
     1861 agggagagag attacgacga gagtaaaacg atcacaagga gatctgaccg tttaccagtg
     1921 atttggcttc gttttggttt ccactgaaca ccaaaatagc actttttgca aaaagatgag
     1981 cagtgataga gttgtattct gtatgtgtag aagggcttgg tatgtaacct gaactctgga
     2041 ttggttacat atttgtaggc tacttgtcgg aaaccagatt tcgacaatgc gttgttaagg
     2101 tcaaagacct gtcccgaacc gaaatgctaa gggaatgcca cgaacaacac tattacgaag
     2161 aagtcggcta tttagccggc ttttttcata ttagggtatg aagttttgta cctggatggc
     2221 tcttcctatc ataagcagta atgatgctgt agtacgggtc ttcgccgttt ggttttttca
     2281 attctagtat catcatcccc gttcctgact ctacaacaat cgctttgttt tggccttttt
     2341 taggatctat gagcacttct gccccagcta ataatatgct ctccaaaaag atgacaatat
     2401 cctcagcgga agtagctcct atctcgacac gatgcttgtc ccatatatgc ctaaggccat
     2461 aggctccctc gagacttttt gtccttttgt tgtaaaaacc ggaatctcct agcttgagga
     2521 tgattttccc tgcgggaaag tctgcattca tgcttggcag ttctagaaaa aattcacttc
     2581 catcacactt agccactcgt gcattttttg ttttcttatc attaagaaca gcttcaacta
     2641 tatcgcgtgg aagtaacaag ttcacaaact acacctctat agccttcact attatgttta
     2701 ggcgttaaat ccctttttga agggctgatt ctaacactga cgtaatgagc aatttccagt
     2761 aaatcttgat agaaaaaacc agttgtattt accataacat tccttgcccg caccgctccg
     2821 gacgggttca gcgtgaaagc ggcgttagcc cggtaaaacc ggcagtaaac tccccgctaa
     2881 accgcgcatt ctgcgcctga taaatttcac gtggctgcat agccatgcag ccacgtgaat
     2941 tgctcatgct ttcaatgtat atcctcgtcc aagcccctgt tttaaccggt ttatcaaaaa
     3001 accaaacaga aagccttacc actaacaata aaagaggtag gaggactgta ttttatcgca
     3061 taaaaaacat ttacaacacg atttttatcg tatagattcc ataaaaaaaa tgaaattcac
     3121 tcacctatta agggtttcta tatgaaagat atgaaagctg ttgtggtttt taccgggaag
     3181 gatttgaaca taatgagaac tgaggggggg tcaggctact ggcatgccag aacagacagg
     3241 ctcaacgatg ccgattacct catagcagta agaaacagaa gggaaacgtg ggcagtaaaa
     3301 gacctggaac acggcacagc attcctgatc gccaaaatta ccgggtgttt taaaagccct
     3361 gattacgacg acaggaacgt cataaccttt gatgaatacg cagaaattca cacgccaaaa
     3421 gcatggaaaa tgctaaccga tggtcagcgc tatccggttg cttacctgag cgcacaggaa
     3481 gcttttttac gtattggggt aacaccggaa caactggaat ggaagaaatt ccatccttca
     3541 tccccatcgg ttcctaatac agtgattcct ggtctggctg aagagaaaac agaaaaactc
     3601 tcccttaacg aggcaattga aagagccaaa aaggatatta gcaacgcaac agggattgat
     3661 agctcagcca taacaataag catcaagatc tgatgaagcg tgaacaacaa gatagcagcc
     3721 tcatgttcta gaactgaacc tgtacgccag aaacagcaag cccatgcttt tccggcgcac
     3781 agattcaaag tgacggaccg ttgtacgttc gctgtcgctg agatcgttcc agctccagcg
     3841 ctttctgatg ctgcgccgcc cgttcctgct cacgatgtgc ctctatcacg ttcagccttg
     3901 tgacaaccgg cgcagctgct cgctcaaact ctgcacctgc ctgctcaagc ccgtaacgcg
     3961 ctcgctcagc gccgcgttct cccgttgcat aagaccagac atcgtccgcc attccgcgaa
     4021 ggcgttctcc cactcgtcca gccttttcga gtagtcctgc tgtagctgct ctaatgcgct
     4081 cagcaactgt ttttccagct ccgtcatgtg ctatttcccc gccagtatca tccagctcga
     4141 atcctctccg aaccgtcccg cttccgggtt caccctcacg cagcggcgtc tctgctctcc
     4201 gcaggtcgag agctgcacac cgctgttcct ctcggacagc atggcctgcg tgcgcttctg
     4261 ctcccggatg gtcgtgtaat tgtcgagtat ctgctgcccc tgccaccaca gaatgcttgc
     4321 gcccgatgct gtcagcagtg tagacaccaa gacgatggtc agccacgtct ggctgaccat
     4381 ccgcagcata cctttcgtgc gctggctcat ggcagcggac agcttcctgt cgtggtcgag
     4441 gatggcggcg ctgattctct tctcgctttc gctcagttcc gctctgacag acttctcgtg
     4501 ctcgctgaat gcggctttca gcatctcgcc ggtactctgc tgctgcgctt tcgatttctg
     4561 ctctaagtcc ttcgccagcg ttaaaagact gttcatagat ggctcccttc agtcggatgt
     4621 ttcgcccccc gtccgggtcg gcaatgctga tgctgctt
//
