LOCUS       NZ_CP113491             4072 bp    DNA     circular CON 20-JAN-2024
DEFINITION  Escherichia coli strain GTEN_23 plasmid unnamed5, complete sequence.
ACCESSION   NZ_CP113491
VERSION     NZ_CP113491.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11875193
            Assembly: GCF_026689355.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4072)
  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  JOURNAL   Unpublished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 4072)
  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 (28-NOV-2022) 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
            Assembly Name                     :: GTEN_23
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 488.0x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/20/2024 06:31:39
            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)                     :: 5,428
            CDSs (total)                      :: 5,304
            Genes (coding)                    :: 5,082
            CDSs (with protein)               :: 5,082
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 222
            CDSs (without protein)            :: 222
            Pseudo Genes (ambiguous residues) :: 0 of 222
            Pseudo Genes (frameshifted)       :: 72 of 222
            Pseudo Genes (incomplete)         :: 153 of 222
            Pseudo Genes (internal stop)      :: 47 of 222
            Pseudo Genes (multiple problems)  :: 48 of 222
            Pseudo Genes (short protein)      :: 3 of 222
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP113491.1.
            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..4072
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="GTEN_23"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed5"
                     /geo_loc_name="USA: Massachusetts"
                     /collected_by="Massachusetts General Hospital"
     gene            complement(join(3733..4072,1..1820))
                     /gene="mobQ"
                     /locus_tag="FG550_RS27005"
     CDS             complement(join(3733..4072,1..1820))
                     /gene="mobQ"
                     /locus_tag="FG550_RS27005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_001029353.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAECRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            1999..2253
                     /gene="mobC"
                     /locus_tag="FG550_RS27010"
     CDS             1999..2253
                     /gene="mobC"
                     /locus_tag="FG550_RS27010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091747.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            2785..3477
                     /locus_tag="FG550_RS27015"
     CDS             2785..3477
                     /locus_tag="FG550_RS27015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001281403.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(1463..1821)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.056"
                     /coverage="100.0"
                     /evalue="3.94e-177"
     Typing          1822..1998
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2786..3477
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4..1907)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.37"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cggacaacac cgcccagaga gtcatccacg cccatgacca gcaaaagctg aagctggcgg
       61 gtttcccggt cgacagaact cattaccggc atcagcgtcg gtagcagacg tccctgcgta
      121 aaatccacct tccttgctgc cagtgatggc atggctggct ggcggtcttc tccaagacag
      181 aaagactccg gccatgtctt cggctggcgg agattgcggg tatattgcgg ccatgtctgg
      241 caaacctgcg tcagaagttg ctcaaaggtc gcagaggaat aaacacgttg cagtggtgga
      301 tgttgaccga tttcgcttcg gtcacagata taaccactcc tgtcacgcat taaatcaaca
      361 cgctcaaaga ttctggtgcg gtatttctcc agctcgttcc cccagagcgt gtattctccg
      421 ttccggttgt gaagcagaag gtaacaggtc atttccccgt taccaggcat gggggcctcg
      481 ccataccccg taacgactgc gctcagtacc cctgaatcca taacggcatt gtcatttttc
      541 ctgagctgtt ccgctcgtcg ctccgcgcga ctacgttctg tatcctcctg ctccttccgg
      601 cgcaattcct cttcacgttt aagcaactgg actctgagag ctgcaaggcc ggatgccccc
      661 cactgctgcc actgtttttc aaatgccgtc tgactcgcgg gaatgtcctg tttctccacc
      721 ttccggtaat gctgtcgcaa tttttccatt tgctggctca gcgactggat ttttccctgt
      781 tcgctacggt attccggtgc cgcccattgc atcaggggaa tacgggaaaa accggacgaa
      841 aacggcgatg attttttcag gctggcagca tggctcatcg cttcctttcg ttcggtgttc
      901 agctcttccc agcgtctgcg cgtcgcctgc atatctgcca tcatcgacat ggcattactg
      961 gtgagtttcc atgccgcatt actgtccttc ggcaacgctt cgatgatgtc acgtagtgtg
     1021 tacgaagttg cgttgtcagg aagcacgata ttcagaaggt cagccacacg gcgggcaggc
     1081 tctgtcagcc cgctgttcct gagttcagtg cgggaaatct gtatttccag gttaagcctg
     1141 ttaatcagac gattctgttc gccgcgttct gtttcgatac cgcgtgtttc catcgcacag
     1201 gcagactttc cgaggtgaat accaggcgtt ttctcaagcc cctgtcgctc gtatgaacga
     1261 tggtctatct cttcctgata accggcgttc gccagtgctc tgtttgcatg gtcagcccat
     1321 gatgcacgcc acgtctcggc atgtgtccgg tcgttccagt ccctgacctt tccgccgaac
     1381 ccagcaggtc cgacagccct cgtggtcagc atgatgtgcg catggggatt tgttttatcc
     1441 atgtgatgga acgccacatc agcaatcatg ccctgactga caaagttttc tctgacaaag
     1501 gcgagaacgg tttcccgtgc ggcatcctgc ggcagttcac gggggatagc gagttcaatt
     1561 tcccgcgcaa gttgtgagtt cttccggcat tcggccttct caacggcatt ccagagttcg
     1621 gcacggttcg tacaccaggc aggggctgtc gcgggggtca gaatcacagc ttcagccaca
     1681 ccgcttttgc gggtgtagtc gtgagtcagt ccggtacgct catcaagcat cagtgaaccg
     1741 gaacgatagg cagcggaagc tacggcgctg tagccgctgc ttctggagat aattttcatg
     1801 ctgagatgat aaatcgccat ttctgccgta atgccttttt gtagttttct ttcagccccg
     1861 cagggcgcac acaatcgaaa cggagtggag attgtataag tgcgcacttt gtgatttgtc
     1921 gcgcattatg ccagctcagt ttttaaacta ccagtgacgc gctaaaatgc gatttttcat
     1981 cgcgcacgga gttacatcat gagcagaacg ctcgaacaga agattgctga tgctgaggcg
     2041 agattacagc gcctgaaggc gaagagccgg agcctggaca cagcgcagaa ggttgttgtg
     2101 ggtgcagcat tgctggcaaa ggtcagaaag ccggaggagg tgcagttgcg tgcctggtta
     2161 ctccagttcc tgaaggcaga ggtgacacga caggctgatg tgacgcgcat actgccgctg
     2221 attaacgagc tggaggcgct gccaggacag tgattgtatc gtccgctcgc cgcagcccca
     2281 gcgaccgagc gttagcgagc gagtgggcga ggaagcggaa gtgaatccgt cgccaggttg
     2341 agcacatacg cacggttttt cggtaggtga tatgcgctga acccgcatga atactggatt
     2401 tccacagggt tggaagggga gtattcggaa cttgcaattc tgctttcttg caacacattg
     2461 tttttattgg ttttttgttt tcagcgcccc aagttatcca caggctcgcc gttaagtttt
     2521 tagatcttgt ttttaagatc ttgtttttaa tacttgtttt agggtcaaaa ttcattaata
     2581 aaatcaatat gttatagagg tatatgtgga ggaatttaag gtaaaggtgg aggaatttaa
     2641 ggtgtttagg tggaggaatt taaggtaaag gtggaggaat ttaaggtgtt attcacagaa
     2701 atgtgaggat ataaaaaaaa atattccaca tttcttattt gtggggcaca ttaaagcatc
     2761 accacatttg aacgggatct ttgtatgtcg gacttgattg cctacaagtc gaatgctttg
     2821 gttgaggcca gctacaagtt gaccctacag gaacaacgtt ttctgttgct gtgtatcagt
     2881 cgattgaaat ctggtgctga tgctgaattg caaaagacaa tgaccattac cgctgcggaa
     2941 tattttgatt cattccctga catggggcgg aaaaatgccg aggttcagtt acaggaagcg
     3001 atcgatcgtt tatgggacag gtcgatcatt ctcaagaatg acgagaagcg tgaggagttc
     3061 cgctggatcc agtatcgggc acagtacgct aaaggtgagg ccaaggctcg aataaccttt
     3121 tctgacgcgg taatgcctta tctgacgcaa ctgaaggggc aattcacgcg cgttgttata
     3181 aaaaacatat caggtttatc aagtagttac agtataagaa tatacgagtt cctccagcaa
     3241 ttccgcagta cgggagagag aattattgct cttaatgact ttcgttcaat gttagggatt
     3301 gaaaataaat acaaacaatt cagagactta aataaaatac taataaaacc ctgtgttgac
     3361 gaactgaaca aaaaaagcga cctggctgta acggttgaga cgatcaaaaa ggggcgcacg
     3421 gttgtagccc tgcattttcg cttcaaggaa gacaaacaga tcaagatgac gatctaaaat
     3481 cgattttaag gcacctaaaa cgctccctgc tgcgtttttt ttgtgttagt agtgcgaagg
     3541 tactattgaa gtgaaaaatt gcgtcaaaag cgctctaatg cagcgaaaaa agaaccccca
     3601 atttttgggg gcggaaaaac aaaactatgc ttgcattatg tgtgtgcttc ttgcattcat
     3661 ccctgtcgat gaacatagaa gaacatcgac gaacataaca cgatgttaaa caaaacaaaa
     3721 tattgttcac attcactgtg accaaccgcg atcatgtctc ctctcggtgg tgtgtgttct
     3781 tgcatcttcc tcgcgccgcc attcatccca ggtacgattg aaacccagag agcggaacag
     3841 atgatccggc tgtttttctg gtgtgttgac ggcagcaaaa agcggtgcct cacgggtttt
     3901 cagatgaaac tccataagtt ccggcgcagg tgatatgtgg ctgtctgcat cgtgatttac
     3961 ggcaacacca taccctgcat accgtaaccc cttatcggtc agtgcactga tgaccagctg
     4021 gctgttatcg gctgagggaa cggcaaacgc gggatacagc gtaccattaa gc
//
