LOCUS       NZ_CP059842             5218 bp    DNA     circular CON 13-SEP-2023
DEFINITION  Escherichia coli strain E2348/69 plasmid p5217, complete sequence.
ACCESSION   NZ_CP059842
VERSION     NZ_CP059842.2
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13901561
            Assembly: GCF_014117345.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5218)
  AUTHORS   Tvedte,E.S., Gasser,M., Sparklin,B.C., Michalski,J., Zhao,X.,
            Bromley,R., Tallon,L.J., Sadzewicz,L., Rasko,D.A. and Dunning
            Hotopp,J.C.
  TITLE     Comparison of long read sequencing technologies in resolving
            bacteria and fly genomes
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5218)
  AUTHORS   Tvedte,E.S., Gasser,M., Sparklin,B.C., Michalski,J., Zhao,X.,
            Bromley,R., Tallon,L.J., Sadzewicz,L., Rasko,D.A. and Dunning
            Hotopp,J.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-MAY-2021) Institute for Genome Sciences, University of
            Maryland, School of Medicine, 670 W Baltimore St, Baltimore, MD
            21201, USA
  REMARK    Nucleotide sequence updated by submitter
REFERENCE   3  (bases 1 to 5218)
  AUTHORS   Tvedte,E.S., Gasser,M., Sparklin,B.C., Michalski,J., Zhao,X.,
            Bromley,R., Tallon,L.J., Sadzewicz,L., Rasko,D.A. and Dunning
            Hotopp,J.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (29-JUL-2020) Institute for Genome Sciences, University of
            Maryland, School of Medicine, 670 W Baltimore St, Baltimore, MD
            21201, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Coverage                   :: 2000x
            Sequencing Technology :: Illumina HiSeq 4000; Pacbio Sequel II
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/13/2023 03:36:50
            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)                     :: 5,095
            CDSs (total)                      :: 4,976
            Genes (coding)                    :: 4,691
            CDSs (with protein)               :: 4,691
            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)              :: 286
            CDSs (without protein)            :: 285
            Pseudo Genes (ambiguous residues) :: 0 of 286
            Pseudo Genes (frameshifted)       :: 120 of 286
            Pseudo Genes (incomplete)         :: 191 of 286
            Pseudo Genes (internal stop)      :: 64 of 286
            Pseudo Genes (multiple problems)  :: 78 of 286
            Pseudo Genes (short protein)      :: 2 of 286
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059842.2.
            On Aug 11, 2021 this sequence version replaced NZ_CP059842.1.
            Bacteria and source DNA available from Source DNA is available from
            the authors.
            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..5218
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="E2348/69"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p5217"
                     /geo_loc_name="United Kingdom: Taunton"
                     /lat_lon="51.0153 N 3.1068 W"
                     /collection_date="1969"
     gene            354..500
                     /locus_tag="H4J01_RS25615"
     CDS             354..500
                     /locus_tag="H4J01_RS25615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /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_230905658.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPERHDKTPLAAAIGKRVYKRLLM
                     QSS"
                     /name="replication initiation protein"
     gene            complement(858..1367)
                     /locus_tag="H4J01_RS25210"
     CDS             complement(858..1367)
                     /locus_tag="H4J01_RS25210"
                     /inference="COORDINATES: protein motif:HMM:NF014505.3"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system PemK/MazF family
                     toxin"
                     /protein_id="WP_012615286.1"
                     /translation="MAITFHPKKKQILICDFKGSVSPEINQCRPVLILREEIVGSQKLV
                     VVVPISNTEPNPLCSFHHELDDASLSGHMMGKKHWAKCDLVSTVSVDRLDRIRSRDPRT
                     GKNYFHVGVMTDDDFDAVRDKVMYGIGFDDFLDVKNEGVPDGAAASVVIAAEVNVAEVE
                     KQKKAI"
                     /name="type II toxin-antitoxin system PemK/MazF family
                     toxin"
     gene            complement(1383..1631)
                     /locus_tag="H4J01_RS25215"
     CDS             complement(1383..1631)
                     /locus_tag="H4J01_RS25215"
                     /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_000372772.1"
                     /translation="MDQREKAKLLAYVLKTEWNAKQKHIALVLQVSEGTISLWVKEMSL
                     KHQIYKLSQELQEVRALAQGLVSSGQIEQNPGFLPSF"
                     /name="hypothetical protein"
     gene            1851..2282
                     /locus_tag="H4J01_RS25220"
     CDS             1851..2282
                     /locus_tag="H4J01_RS25220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019535530.1"
                     /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_012615289.1"
                     /translation="MKIPTHLKHKPVIQVENYDRIDGPYAEDTDAMGLSVGIAQWNTPG
                     WTELSAKVWRNTGEKWSRQSEELPLHRVIDLATLICITMDYSKNGRLSSSDDFPVSRSS
                     DNQELAHHTELMKKELKENQEYLDESLKRLSAELKRLGY"
                     /name="DUF6530 family protein"
     gene            complement(2885..3118)
                     /locus_tag="H4J01_RS25225"
     CDS             complement(2885..3118)
                     /locus_tag="H4J01_RS25225"
                     /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_000137441.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3125..3643)
                     /locus_tag="H4J01_RS25230"
     CDS             complement(3125..3643)
                     /locus_tag="H4J01_RS25230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_012615288.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVIPQGKSATVIPYQ
                     GKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(<3681..4331)
                     /locus_tag="H4J01_RS25620"
                     /pseudo=""
     CDS             complement(<3681..4331)
                     /locus_tag="H4J01_RS25620"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(4321..4644)
                     /locus_tag="H4J01_RS25240"
     CDS             complement(4321..4644)
                     /locus_tag="H4J01_RS25240"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000955993.1"
                     /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_000955990.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     ALPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVLAALMAIGEELRRLRLAVREQGAR
                     DDC"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4708..4899
                     /locus_tag="H4J01_RS25245"
     CDS             4708..4899
                     /locus_tag="H4J01_RS25245"
                     /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"
     Typing          complement(4992..5075)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.07e-36"
     Typing          56..486
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.769"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2782..4331)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.171"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4328..4674)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.828"
                     /coverage="98.0"
                     /evalue="1.61e-65"
ORIGIN
        1 aaagacggta atgcggttat ccacagaatc aggggataag gccggaaaga acatgtgagc
       61 aaaagaccaa gagccggaaa aaggccacgc cgatggcgtt tttccatagg ctccgccccc
      121 ctgacgagca tcacaaaaac agacgctcaa gtcagaggtg gcgaaacccg acaggactat
      181 aaagatacca ggcgtttccc cctggaagct ccctcgtgcg ctctcctgtt ccgaccctgc
      241 cgcttaccgg atacctctcc gcctttctcc cttcgggaag cgtggcgctt tctcatagct
      301 cacgctgtag gtatctcggc tcggtgtagg tcgttcgctc caagctgggc tgtgtgcacg
      361 aaccccccgt tcagcccgac cgctgcgcct tatccggtaa ctatcgtctt gagtccaacc
      421 cggaaagaca cgacaaaacg ccactggcag cagccattgg taagagggtg tacaagagat
      481 tactgatgca gagttcttga agtctgagcc aaactacagc taaactggaa ggacgatttt
      541 ggtggcagcg gtcttgtaca ccctgttacc acggttcaga agttccccaa cttactgacc
      601 cctcgaaaaa accacctccc caggtggttt tttcgtttac aggacaggag attacctcca
      661 acccctaatg atctcaagaa gaagcagatg ctcgatctta taactattga taattaaaat
      721 atcgacacta taattactag tgttccctta ggggcttgta agtccgcttt atgcggctag
      781 ttgtaaaaga ttgaccaact tttagactat gactccgtga aaacggcttg ggtcaaaaaa
      841 aagccatttg atgaaaatca gatggctttt ttttgttttt ctacttcagc aacgttcact
      901 tcggcagcaa ttaccactga agctgctgcc ccatcaggaa caccttcatt ttttacatcc
      961 aaaaagtcat caaatccgat accgtacatg actttatctc ttactgcgtc aaagtcatca
     1021 tcagtcatga ctcctacatg aaagtaattt ttacccgttc tcggatcccg gcttctaatt
     1081 cgatctaaac ggtcaacaga cactgttgat accagatcac atttagccca atgctttttc
     1141 cccatcatgt ggccgctaag tgaagcatca tctaactcat gatgaaagct gcaaagggga
     1201 ttaggttcag tattgctaat aggaacaaca acaacgagct tctgactgcc aacaatctct
     1261 tctcttaaaa tcaacactgg tcggcattgg ttaatttctg gagataccga acctttaaaa
     1321 tcacatatca agatctgctt ttttttaggg tgaaaggtta tagccatgta gcatccattt
     1381 atttagaaac taggtaaaaa accagggttt tgctcaatct gcccagaact taccagcccc
     1441 tgagctaaag ccctaacctc ttgtaattct tgactaagtt tataaatctg atgttttaaa
     1501 gacatctctt tcacccacaa agagatagtt ccttctgata cctgtagtac taaagcgatg
     1561 tgtttttgct ttgcgttcca ctcggttttt aatacataag ccaacaattt ggccttttct
     1621 cgctgatcca taaacagccc catcaaacat ttaaaatatt ttaaatgttt taaagaaacg
     1681 agacaaagct gtcaacgcag cggtaaatta aaaaccagat gcactataaa taatgcatta
     1741 aaaatcaaat atatataatc aaaataatat ttacttacat ttagtaaatt tactaatcaa
     1801 taaattttgt tattttgtta ataacaaaaa aacaacaatc ggttctatca atgaaaatac
     1861 caactcattt aaaacataag cctgtaattc aagttgaaaa ctatgaccgc atagatggtc
     1921 catatgcaga agatacagat gccatgggac tatccgttgg tattgctcaa tggaacactc
     1981 caggatggac agagctttcg gcaaaggttt ggcgaaatac cggcgaaaag tggtctcggc
     2041 agtctgagga gcttccactt caccgcgtaa tagaccttgc tactctgatc tgcataacga
     2101 tggattacag caaaaatggg cggttatcat ctagtgatga tttcccggtc agtcgttctt
     2161 cagacaacca agaactcgct catcacactg agctcatgaa aaaagaacta aaagaaaacc
     2221 aggaatacct cgatgagagc ttaaaacgtc tgtcggctga gttgaaacgt cttggttact
     2281 aaaaaagccg cccacagggg cggctttttc ataccatcac acctgtaata tttaccataa
     2341 catctctatt gtacgcacca ctgaaacgcg ttcggtgcga tcacggcagc agactggtaa
     2401 aaatggcaac aaaccacccg aaaaactgcc gcgatcgcac ccgataaatt ttaaccacat
     2461 gcatagctat gcagccatgt gaatcacgca ggaattgcca gccagagact gctgaaacgg
     2521 atttttttca tactttcgga aaggcagaag acggaaccgg agcggaaaaa cagaagttca
     2581 ggggaatgag cgcgatctgg caatagaggc aaaacacagc aacaaaagat acaccagaat
     2641 cgcgcccgta tgcgttttaa cgcgttcctg tgttttcagc aaggtctgac agaagcgcgt
     2701 tcccggaacc cccgaaccaa ccattatccc aaaaaatgca ccggaaacgc gctgacaaca
     2761 ttttagcctg tctctgatta ccatcccagc gaagggccat ccagtgtgcg ttcctgtatt
     2821 tccggctggc gctcacgctc cagggataac gcatgttcgc gctcctgtat cagccgttcg
     2881 tcccttatct cctgttctcg ctgtataact ggctcaagcg ttctgtccgc tcgctcaagt
     2941 gctgcacctg ctgactcaac tgcatgacct gctcgttcag catcgcgttg tcccgttgcg
     3001 taagcgaaaa catcttctgc aattccacga aggcgctctc ccattcgctc agccgctgca
     3061 tatagtcctg ttgcagttgc tctaatgcgt tcagcaaatg tctttccagc tccgtcactc
     3121 tgtgtcactc cgtcagttgt acccagtcct tcccctgata gggaatcacc gttgccgatt
     3181 tcccctgcgg gatgaccaga aatttccttc tcccgtcctg cacaaactcc acgccccatg
     3241 tcttcgcgtt cagtttctgc aatgtttctt cctgtatcct gatttcttcc aggttcgcct
     3301 gtatccgccc gccaagatac cagagcgtcc cgccactcac ggtaaacagg aaaatgacca
     3361 tccccagtaa catcatgccc gtattccctg ccagctttaa cacgtccttc ctgtgctgca
     3421 tcatcgcctc tttcacccct tcccggtgtt ttttcagtga ttcctctgtc gaagctgtga
     3481 acagggctat agcgtctttg attttcgtct cgtttgatgt cacagccttg cttacagatt
     3541 tttcgagctt gctgaactcg tcgttcagca ttgtctctgt agattcggct ctctctttca
     3601 gctttttctc gaactccgcg cccgtctgta aaagattgct catagaatgc tcctttcagc
     3661 ctgatattct tcccaccgtt cgggtctgca atgctgatac tgcttcgcgt caccctgacc
     3721 acttcaagcc ctgcctctgt gagcgcctga atcacatcct gacggccttt tatctccccg
     3781 acatgataaa gagcgtctat cccgcgtgtg acgctctctg caagcgcctg tttcgtttcc
     3841 ggcaggttat cagggagagt cagtatccgg cggttctccg gggcgttggg gtcatgcagc
     3901 ccgtaatggt gattcaccag cgtctgccag gcatcaattc tcggcctgtc tgcccggtcg
     3961 tagtacggct ggaggcgttt tccggtctgt agctccatgt tcggaatgac aaaattcagc
     4021 tcaagccgtc ccttgtcctg gtgctccacc cacaggatgc tgtactgatt cttttcgaga
     4081 ccgggcatca gtacacgctc aaagctcgcc atcacctttt cacgtcctcc cggcggcagc
     4141 tccttctccg cgaacgacag aacacctgac gtgtatttct tcgcaaatgg cgtggcatcg
     4201 atgagttccc ggacttcttc cggattaccc tgaagcaccg ttgccccttc ccggtttcgc
     4261 tcccttccca gcaggtaatc aaccggacca ctgccaccgc cttttcccct ggcatgaaat
     4321 ttaacaatca tcccgcgcgc cctgttccct gacggccaga cgcagccgac gcagctcctc
     4381 cccgatggcc atcagcgcag ccaacacctg aacccgatca ccggaagacc actgcccgct
     4441 gttcaccttc ctcgctgtct gattcaggtt attcccgatg gcggccagct gacgcagtaa
     4501 cggcagtgcc agtgtcggca gtttcccgga acgggcaacc ggctccccca ggcagacccg
     4561 ccgcatccat accgccagtt gtttaccctc acagcgttca agtaaccggg catgttcatc
     4621 atcagtaacc cgtattgtga gcatcctctc gcgtttcatc ggtatcatta ccccatgaac
     4681 agaaatcccc cttacacgga ggcatcagtg accaaacagg aaaaaaccgc ccttaacatg
     4741 gcccgcttta taagaagcca gacattaacg ctgctggaga agctcaacga actggacgca
     4801 gatgaacagg ccgatatttg tgaatcactt cacgaccacg ccgacgagct ttaccgcagc
     4861 tgcctcgcac gcttcgggga tgacggtgaa aacctctgac acatacagct cccggagacg
     4921 gtcacagctt gtctgtgagc ggatgccggg agcagacaag cccgtcaggg cgcgtcaggc
     4981 cgttgacctt gcgggtgtcg gggcgcagcc atgacccagt cacgtagcga tagcggagtg
     5041 tatactggct taaccatgcg gcatcagtgc ggattgtatg aaaagtgcgc catgccgggt
     5101 gtgaaatgcc gcacagatgt gtaaggagaa aatgcaactt ccgacgctct tccgcttcct
     5161 cgctcactga ctcgctacgc tcggtcgttc ggctgcggcg agcggtatca gctcactc
//
