LOCUS       NZ_CP116485             5604 bp    DNA     circular CON 27-FEB-2024
DEFINITION  Escherichia coli strain GTEN_24 plasmid unnamed5, complete sequence.
ACCESSION   NZ_CP116485
VERSION     NZ_CP116485.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11230615
            Assembly: GCF_028215995.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5604)
  AUTHORS   Yorki,S., Shea,T., Worby,C.J., Cuomo,C., LaRocque,R.C., Manson,A.L.
            and Earl,A.M.
  TITLE     Comparison of long and short read metagenomic assembly for
            low-abundance species and resistance genes
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5604)
  AUTHORS   Yorki,S., LaRocque,R.C., Worby,C.J., Shea,T., Earl,A.M.,
            Walker,B.J., Manson,A.L., Sridhar,S., Turbett,S., Becker,M.,
            Oliver,E., Bronson,R., Leung,D., Knouse,M., Hagmann,S., Kelly,P.,
            Harris,J. and Ryan,E.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-JAN-2023) Infectious Diseases & Microbiome, Broad
            Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/27/2024 02:21:11
            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)                     :: 4,977
            CDSs (total)                      :: 4,853
            Genes (coding)                    :: 4,676
            CDSs (with protein)               :: 4,676
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 177
            CDSs (without protein)            :: 177
            Pseudo Genes (ambiguous residues) :: 0 of 177
            Pseudo Genes (frameshifted)       :: 69 of 177
            Pseudo Genes (incomplete)         :: 118 of 177
            Pseudo Genes (internal stop)      :: 28 of 177
            Pseudo Genes (multiple problems)  :: 33 of 177
            Pseudo Genes (short protein)      :: 2 of 177
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116485.1.
            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..5604
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="GTEN_24"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed5"
                     /geo_loc_name="USA: Massachusetts"
                     /collection_date="2018"
                     /collected_by="Massachusetts General Hospital"
     gene            complement(join(5279..5604,1..508))
                     /locus_tag="E5Q65_RS24760"
     CDS             complement(join(5279..5604,1..508))
                     /locus_tag="E5Q65_RS24760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008196747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type-2 restriction enzyme EcoRI"
                     /protein_id="WP_001565219.1"
                     /translation="MSNKKQSNRLTEQHKLSQGVIGIFGDYAKAHDLAVGEVSKLVKKA
                     LSNEYPQLSFRYRDSIKKTEINEALKKIDPDLGGTLFVSNSSIKPDGGIVEVKDDYGEW
                     RVVLVAEAKHQGKDIINIRNGLLVGKRGDQDLMAAGNAIERSHKNISEIANFMLSESHF
                     PYVLFLEGSNFLTENISITRPDGRVVNLEYNSGILNRLDRLTAANYGMPINSNLCINKF
                     VNHKDKSIMLQAASIYTQGDGREWDSKIMFEIMFDISTTSLRVLGRDLFEQLTSK"
                     /name="type-2 restriction enzyme EcoRI"
     gene            complement(1126..1359)
                     /locus_tag="E5Q65_RS24765"
     CDS             complement(1126..1359)
                     /locus_tag="E5Q65_RS24765"
                     /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(1366..1896)
                     /locus_tag="E5Q65_RS24770"
     CDS             complement(1366..1896)
                     /locus_tag="E5Q65_RS24770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /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_146707920.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETILNDEFRKLEKSVSKAVTSNE
                     TKIKDAIALFTAWTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGMIQANLEEIRKQNENLEKLNAKTWGVRYHEGSNGRFLVLPEGMKAETNWTM
                     ENGKQNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(<1934..2632)
                     /locus_tag="E5Q65_RS24915"
                     /pseudo=""
     CDS             complement(<1934..2632)
                     /locus_tag="E5Q65_RS24915"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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(2574..2897)
                     /locus_tag="E5Q65_RS24780"
     CDS             complement(2574..2897)
                     /locus_tag="E5Q65_RS24780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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_000956005.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGRLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2962..3153
                     /locus_tag="E5Q65_RS24785"
     CDS             2962..3153
                     /locus_tag="E5Q65_RS24785"
                     /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            3821..3979
                     /locus_tag="E5Q65_RS24920"
     CDS             3821..3979
                     /locus_tag="E5Q65_RS24920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_071593719.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAATGNWTRWIEIL
                     RVLEVVA"
                     /name="replication initiation protein"
     gene            complement(4269..5249)
                     /locus_tag="E5Q65_RS24790"
     CDS             complement(4269..5249)
                     /locus_tag="E5Q65_RS24790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002670781.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="adenine-specific methyltransferase EcoRI family
                     protein"
                     /protein_id="WP_002670781.1"
                     /translation="MARNATNKLLHKAKKSKSDEFYTQYCDIENELQYYREHFSDKVVY
                     CNCDDPRVSNFFKYFAVNFDNLGLKKLIASCYVENKEGFSSSEAAKNGFYYEYHKENGK
                     KLVFDDISVSSFCGDGDFRSSESIDLLKKSDIVVTNPPFSLFREYLDQLIKYDKKFLII
                     ANVNSITYKEVFNLIKENKIWLGVHLGRGVSGFIVPEHYELYGTEARIDSNGNRIISPN
                     NCLWLTNLDVFIRHKDLPLTRKYFGNESSYPKYDNYDAINVNKTKDIPLDYNGVMGVPI
                     TFLHKFNPEQFELIKFRKGVDEKDLSINGKCPYFRILIKNKRLQK"
                     /name="adenine-specific methyltransferase EcoRI family
                     protein"
     Typing          complement(3239..3325)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="2.47e-38"
     Typing          3337..3893
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.566"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1023..2584)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.232"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctaagaaaag gacgtaagga aagtggctct cagagagcat aaaattcgct atctctgata
       61 tattcttatg agatctttcg atagcattac cagcagccat taaatcttga tctcctcttt
      121 tcccaactaa caaaccattc cttatattta taatatcttt accttggtgt ttggcttcag
      181 caacaagtac aactctccat tcaccataat catctttgac ctctacaatt ccaccatcag
      241 gtttgatgct ggaatttgaa acaaataaag taccgccaag atcagggtca atttttttta
      301 aagcttcatt tatttctgtt ttctttatac tatctctata tcgaaatgat aattgagggt
      361 attcgttgct aagagctttc tttactaatt ttgaaacctc accaacagcg agatcatgag
      421 cttttgcata atccccaaaa atcccaatta caccttgaga taacttatgt tgttcagtta
      481 gcctatttga ctgtttttta ttagacatga atccatgttt ccactgttat tttataaagt
      541 tacatatgtc gatagattaa catacgtttg atttaccata atcccttatt gtacgcaccg
      601 ctgaaacgcg ttcggcgcga tcacggcagc agacaggtaa aaatggcaac aaaccacccg
      661 aaaaactgcc gcgatcgcac ccggtaaatt ttaaccacat gcatagctat gcagctatgt
      721 gaatcatgca ggaattgcca gccagagaca gctgaaacgg atttttttca tgctttcgga
      781 agcgaagaag acggggaccg gagcgggaaa acagaagttc aggggaatga gcgcgatctg
      841 gcaatagagg caaaacacag caacaaaaga cacaccagaa tcgcgcccgt atgcgtttta
      901 acgcgttcct gtgttttcag caaggtctga ctgaagcgcg ttcccggtgc ccccgaacca
      961 accattatcc caaaaaatgc accggaaacg cgctgacaac attttagcct gtctctgatt
     1021 accatcccag cgaagggcca tccagtgtcc gttcctgtat ttccagctgg cgctcacgct
     1081 ccagggataa cgcatgttcg cgttcctgta tcagccgttc gtcccttatc tcctgttctc
     1141 gctgtataac tggctcaagc gttctgtctg ctcgctcaag tgctgcacct gctgactcaa
     1201 ctgcatgacc cgctcgttca gcatcgcgtt gtcccgttgc gtaagcgaaa acattttctg
     1261 caattccacg aaggcgctct cccattcgtt cagccgctgc atatagtcct gttgcagttg
     1321 ctctaatgcg ttcagcaaat gtctttccag ctccgtcatg ctctgttact cctgtaccag
     1381 ccttacggca ttctgtttcc cgttttccat cgtccagttc gtttcggctt tcatcccctc
     1441 gggcaacacc agaaaacgtc cgttgctccc ctcgtgataa cgcacgcccc atgtcttcgc
     1501 gttcagcttc tccagattct cgttctgctt cctgatttct tccaggttcg cctgtatcat
     1561 cccgccaaga taccagagcg tcccgccact cacggtaaac aggaaaatga ccatccccag
     1621 taacatcatg cccgtattcc ctgccagctt taacacgtcc ttcctgtgct gcatcatcgc
     1681 ctctttcacc ccttcccggt gttttttcag tgattcctct gtccaagctg tgaacagggc
     1741 tatagcgtct ttgattttcg tctcgtttga tgtcacagcc ttgcttacag atttttcgag
     1801 cttcctgaac tcgtcgttca gtattgtctc tgtagattcg gctctctctt tcagcttttt
     1861 ctcgaactcc gcgcccgtct gtaaaagatt gctcataaaa tgctcctttc agcctgatat
     1921 tcttcccacc gttcgggtct gcaatgctga tactgcttcg cgtcaccctg accactttaa
     1981 gccctgcctc tgtgagcgcc tgaatcacat cctgacggcc ttttatctcc ccgacatgat
     2041 aaagagcgtc tatcccgcgt gtgacgctct ctgcaagcgc ctgtttcgtt tccggcaggt
     2101 tatcagagag agtcagtatc cggcggttct ccggggcgtt ggggtcatgc agcccgtaat
     2161 ggtgattcac cagcgtctgc caggcatcaa ttctcggcct gtctgcccgg tcgtagtacg
     2221 gctggaggcg ttttccggtc tgtagctcca tgttcggaat gacaaaattc agctcaagcc
     2281 gtcccttgtc ctggtgctcc acccacagga tgctgtactg atttttttcg agaccgggca
     2341 tcagtacacg ctcaaagctc gccatcacct tttcacgtcc tcccggtggc agctccttct
     2401 ccgcgaacga cagcacaccg gacgtgtatt tcttcgcaaa tggcgtggca tcgatgagtt
     2461 cccgtacttc ttccggatta ccctgaagca ccgttgcccc ttcccggtta cgctcccttc
     2521 ccagcaggta atcaaccgga ccactgccac caccttttcc ccgggcatga aacttaacta
     2581 tcatcccgcg tcccctgttc cctgacggcc agacgcagcc ggcgcagctc atccccgatg
     2641 gccatcagtg cggccaccac ctgaacccgg tcaccggaag accactgccc gctgttcacc
     2701 ttcctcgctg tctgattcag gttattcccg atggcggcca gctgacgcag taacggcggt
     2761 gccagtgtcg gcagcctccc ggaacgggca accggctcac ccaggcagac ccgccgcatc
     2821 cataccgcca gctgtttacc ctcacagcgt tcaagtaacc gggcatgttc atcatcagta
     2881 acccgtattg tgagcatcct ctcgcgtttc atcggtatca ttatccccat gaacagaaat
     2941 cccccttaca cggaggcatc agtgaccaaa caggaaaaaa ccgcccttaa catggcccgc
     3001 tttataagaa gccagacatt aacgctgctg gagaagctca acgaactgga cgcggatgaa
     3061 caggcagata tctgtgaatc gcttcacgac cacgccgatg agctttaccg cagttgcctc
     3121 gctcgcttcg gggatgacgg tgaaaacctc tgacacatgc agctcccgga gacggtcaca
     3181 gcttgtctgt gagcggatgc cgggagctga caagcccgtc agggcacgtc agcgggtttt
     3241 agcgggtgtc ggggcgcagc cctgacccag tcacgtagcg atagcggagt gtatactggc
     3301 ttaaccatgc ggcatcagtg cggatggtat gaaaagtgcg ccataccggg tgtgaaatgc
     3361 cgcacagatg cgtaaggaga aaatgcacgt ccagccgctt ttccgcttcc tcgctcactg
     3421 actcgctacg ctcggtcgtt cgactgcggc gagcggtatc tactcactca aaaacgaaat
     3481 gctgttatcc acagaatcag gggataacac cggaaaaaac atgtgagcaa aagaccagga
     3541 acaggaagaa ggccgcgccg ctggcgtttt tccataggct ccgcccccct gacgagcatc
     3601 acaaaaatcg acgctcaagt cagaggtggc gaaacccgac aggacttaaa gataccaggc
     3661 gtttccccct ggtggctccc tcgtgcgctc tcctgttccg accctgccgc ttaccggata
     3721 cctgtccgcc tttctccctt cgggaagcgt ggcgctttct catagctcac gctgtaggta
     3781 tctcagttcg gtgtaggtcg ttcgctccaa gctgggctgt gtgcacgaac cccccgttca
     3841 gcccgaccgc tgcgccttat ccggtaacta tcgtcttgag tccaacccgg taagacacga
     3901 cttaacgcca ctggcagcag ccactggtaa ctggacaagg tggattgaga tattaagagt
     3961 tcttgaagtg gtggcctaac tgcggctaca ctagaaggac agtatttggt atctgcgctc
     4021 caccaagcca gttaccttcg gaaaaagagt tggtagctct tgatccggca aacaaaccac
     4081 cgttggtagc ggtggttttt ttgtttgcaa gcagcagatt acgcgcagaa aaaaaggatc
     4141 tcaagaagat cctttgatct tttctactga accttcgaaa aaaccaccag gagaggtggt
     4201 tttttcgttt ctggtaccga agcttacgac gaagctaatg atctcaagaa aaaactaaca
     4261 aacatcaatt acttttgtaa tcgtttgttt tttatcaaaa ttctgaaata agggcattta
     4321 ccatttatag acaaatcttt ttcatcaaca ccctttctaa attttattaa ctcaaattgc
     4381 tcagggttaa acttatgcaa gaatgtgata ggaaccccca taaccccatt gtaatctaat
     4441 ggaatatcct ttgttttgtt tacatttata gcatcataat tatcatattt tggatatgaa
     4501 ctttcattcc caaaatattt tcttgtaaga ggcaagtctt tatgcctaat aaagacatct
     4561 aggttagtta gccataagca gttgtttggc gagataattc tattaccatt agaatcaatt
     4621 ctcgcctcag taccatataa ttcataatgc tctggaacaa taaacccaga aacacctctc
     4681 ccgagatgaa ccccaagcca aatcttattt tccttaatta gattaaacac ctctttatat
     4741 gttattgaat taacattagc aattataagg aatttcttat catacttaat tagttgatca
     4801 agatactctc taaataacga gaatggagga ttcgtaacaa caatatctga tttttttagc
     4861 agatcaatgc tctccgaact gcgaaaatcg ccatcgccac agaaagaaga aacactaata
     4921 tcatcaaaaa ctaatttctt tccattttct ttatgatatt catagtaaaa tccgttcttc
     4981 gcggcttcgc tactagaaaa accttcttta ttctctacat agcaagatgc tattaacttt
     5041 ttcaagccaa gattatcaaa attcactgca aaatatttaa agaaattgct tactctagga
     5101 tcatcacaat tgcaataaac aaccttatca gagaagtgct ctctgtagta ttgcagttcg
     5161 ttctcaatat cacaatactg agtgtaaaat tcgtcgcttt tcgatttttt agctttgtgc
     5221 agtaacttgt ttgttgcatt tctagccatt aattaaaacc ttattaaaat aaaaaatatc
     5281 acttagatgt aagctgttca aacaagtcac gccccaacac tctgagcgaa gtcgttgata
     5341 tatcaaacat tatttcaaac ataattttcg aatcccactc cctcccatct ccttgagtat
     5401 atatagatgc tgcttgtagc ataatgcttt tgtctttatg atttacaaat ttgttaatac
     5461 atagattact atttataggc attccataat tagctgcagt tagtcgatct aacctattta
     5521 atataccaga attatactca agattaacaa cccttccatc tggtcttgtt attgagatat
     5581 tttctgttaa aaagttagac ccct
//
