LOCUS       NZ_LR898872             3838 bp    DNA     circular CON 25-JUN-2023
DEFINITION  Escherichia coli strain MSB1_1D isolate MSB1_1D plasmid 5, complete
            sequence.
ACCESSION   NZ_LR898872
VERSION     NZ_LR898872.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMEA3357393
            Assembly: GCF_905071865.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Hawkey,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-NOV-2020) THE UNIVERSITY OF MELBOURNE, 30 Flemington
            Rd, Australia
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/25/2023 10:31:24
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,672
            CDSs (total)                      :: 4,553
            Genes (coding)                    :: 4,302
            CDSs (with protein)               :: 4,302
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 251
            CDSs (without protein)            :: 251
            Pseudo Genes (ambiguous residues) :: 0 of 251
            Pseudo Genes (frameshifted)       :: 58 of 251
            Pseudo Genes (incomplete)         :: 185 of 251
            Pseudo Genes (internal stop)      :: 46 of 251
            Pseudo Genes (multiple problems)  :: 35 of 251
            Pseudo Genes (short protein)      :: 4 of 251
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            LR898872.1.
            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..3838
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MSB1_1D"
                     /isolate="MSB1_1D"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="5"
                     /geo_loc_name="Australia"
                     /collection_date="2014-01"
     gene            370..516
                     /locus_tag="JMX26_RS23400"
     CDS             370..516
                     /locus_tag="JMX26_RS23400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001487656.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_063922569.1"
                     /translation="MHEPPVQSDRCASSGNFQLDSNPERHDKAPLAAATGKRVYKRLLI
                     QSS"
                     /name="hypothetical protein"
     gene            943..1605
                     /locus_tag="JMX26_RS23025"
     CDS             943..1605
                     /locus_tag="JMX26_RS23025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000430080.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="GNVR domain-containing protein"
                     /protein_id="WP_130053517.1"
                     /translation="MEKNSSDIDVIELFLFLKNKIMSIILFVIFSLILSSIFLLINKNK
                     ISVKYELNMITNSPGMIINCEDDFYCKANMIQSIIKNKSNSITSNIDERGKKINLSWAG
                     DDRYKPSVTAEVNAIHKAINDWYIQDYKTYKSIVNNQDSNYINGTETYAKIALLTKTNT
                     SGERNFISINNETVNKKYKPALIMTLTLIMAIIFSSSYHIIKRSVLDYKNKSNRSFY"
                     /name="GNVR domain-containing protein"
     gene            1757..>1933
                     /locus_tag="JMX26_RS23030"
                     /pseudo=""
     CDS             1757..>1933
                     /locus_tag="JMX26_RS23030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012477181.1"
                     /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="IS1-like element transposase"
                     /name="IS1-like element transposase"
     gene            complement(1948..2645)
                     /locus_tag="JMX26_RS23035"
     CDS             complement(join(1948..2396,2396..2645))
                     /locus_tag="JMX26_RS23035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558153.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
                     /protein_id="WP_251123150.1"
                     /translation="MASISIRCPSCSTTEGVVRNGKSTAGHQRYLCSHCRKTWQLQFTY
                     TASQPGTHQKIIDMAMNGVGCRASARIMGVGPNTVLRHFKKLRPQSVTSRIQPGSDVIV
                     CAEMDEQWGYVGAKSRQRWLFYAYDRIRRTVVAHVFGERTLATLERLLSLLSAFEVVVW
                     MTDGWPLYEPRLKGKLHVISKRYTQRIERHNLNLRQHLARLGRKSLSFSKSVELHDKVI
                     GHYLNIKHYQ"
                     /name="IS1 family transposase"
     gene            complement(3489..3638)
                     /locus_tag="JMX26_RS23040"
     CDS             complement(3489..3638)
                     /locus_tag="JMX26_RS23040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023282155.1"
                     /translation="MPSEYDEQLGSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGPPVG
                     REAL"
                     /name="hypothetical protein"
     Typing          complement(3675..3838)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.182"
                     /coverage="95.0"
                     /evalue="9.27e-76"
     Typing          2..539
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.878"
                     /coverage="89.0"
                     /evalue="0.0"
ORIGIN
        1 tcgctcactg actcgctgcg ctcggtcgtt cggctgcggc gagcggtacc ggcttacagg
       61 cggggcggaa atttcctggg agatgccaga aagaagctta acagggaagc gataaggccg
      121 cggcgaagcc gtttttccat aggctccgcc cccctgacaa gcatcacgaa atctgacgct
      181 caaatcagtg gtggcgaaac ccgacaggac tataaagata ccaggcgttt ccccctggtg
      241 gctccctcgt gcgctctcct gttcctgcct ttcggtttac cggtgtcatt ccgctgttat
      301 ggccgcgttt gtctcattcc acgcctgaca ctcagttccg ggaaggcagt tcgctccaag
      361 ctggactgta tgcacgaacc ccccgttcag tccgaccgct gcgcctcctc cggtaacttt
      421 caacttgatt ccaacccgga aaggcacgac aaagcgccac tggcagcagc cactggtaag
      481 agggtgtaca agagattact gatacagagt tcttgaagtc agagccaaac tacggctaaa
      541 ctggaaggac gaatttggtg gcagcggtct tgtacaccct gttaccacgg ttcagaagtt
      601 ccccaactta ctgaaccttc gaaaaaccac ctccccaggt ggttttttcg ttttcagagc
      661 aagagattac ggctgtaacg caaggatctc aagaagatct taaaatatgt tgaaaggata
      721 caggctaaca acaactccct ccatagacat gaccgaacaa aaaagaaaca aaaaaaatga
      781 ttttaggagt tttttcacac ctaaatagta ggtaaaatgt tcttttattc gattggcttt
      841 taaaatgaaa tacactaaat ccgcaaaaat attcatcaca gcctttttaa ttttatttat
      901 ttatttaacc catactttaa taaatattat tggtatataa aaatggaaaa aaattcatct
      961 gatattgatg ttatcgagtt atttctcttt ctcaaaaaca aaataatgag tattattttg
     1021 tttgttattt tctcattgat tttgtcatct atttttttgt taataaacaa aaacaaaata
     1081 agtgtaaagt acgaattaaa tatgatcact aattcgccag gtatgattat taactgtgag
     1141 gatgactttt attgcaaagc gaacatgata caatcaataa taaaaaacaa aagcaattct
     1201 ataacatcaa atatagatga aagaggaaaa aaaataaacc tgtcatgggc tggtgatgac
     1261 cgttacaaac cctcggttac cgctgaagta aacgctatcc ataaagctat taatgactgg
     1321 tacatccaag attataaaac ttataaaagc atagttaaca accaggatag caactatata
     1381 aatggcactg aaacatatgc aaaaattgca ttattaacta aaacaaacac ttccggagaa
     1441 agaaacttta tttcaatcaa taatgaaaca gtaaataaaa agtataaacc agctttaatt
     1501 atgactctaa cgttaattat ggctattatc ttttcctcct cgtaccatat aataaaaaga
     1561 tctgtacttg actataaaaa taagtcaaat aggtcttttt attagcctgt aacgattaat
     1621 aaccgtattc tagcaacatc cgttacacgc ctgatgcaga aaagcccgct aatagcgggc
     1681 ctcccgacaa atctcactgg gtgatgcctc taattagttg aatctgatgt ataatacggg
     1741 cttttgaggt tatctcatag ccagcgttaa tattcattgt ccccgttgtc agtcagctcg
     1801 ggtttaccgc catggtcaga accctaaagg ccgtgacaga tttcgctgcc gtgactgcca
     1861 ccgtgtattt cagctcactt atacttatca agcacgtaag ccgggtatga aagagctgat
     1921 cactgaaatg gcggtaatga ctccaactta ctgatagtgt tttatgttca gataatgccc
     1981 gatgaccttg tcatgcagct ccaccgattt tgagaacgac agtgacttcc gtcccagcct
     2041 tgccagatgt tgtctcagat tcaggttatg tcgctcaatg cgctgagtgt aacgcttgct
     2101 gataacgtgc agctttccct tcaggcgggg ttcatacagc ggccagccat ccgtcatcca
     2161 taccacgacc tcaaaggccg acagcaggct cagaagacgc tccagtgtgg ccagagtgcg
     2221 ttcaccgaag acgtgcgcca caaccgtcct ccgtatcctg tcatacgcgt aaaacagcca
     2281 gcgctgacgt gatttagcac cgacgtagcc ccactgttcg tccatttcag cgcagacaat
     2341 cacatcactg cccggttgta tgcgcgaggt taccgactgc ggcctgagtt ttttaagtga
     2401 cgtaaaaccg tgttggggcc aacgcccata atgcgtgcac tggcgcgaca tccgacgcca
     2461 ttcatggcca tatcaatgat tttctggtgc gtaccgggct gagaggcggt gtaagtgaac
     2521 tgtagttgcc atgttttacg gcaatgagag cagagatagc gctgatgtcc ggcagtgctt
     2581 ttgccgttac gcaccacgcc ttcagtagtg gagcaggaag gacatctgat ggaaatggaa
     2641 gccacgcaag caccttaaaa tcaccatcat acactaaatc agtaagttgg cagcattacc
     2701 tgtatttcag cttcatcaat cccgtttttt ttactgaatc catttaccaa tatcctgtcc
     2761 atacgttact aaagaaaata atatatacgg aatgagttat catgcgccta atttaccata
     2821 acatccgttg cccgcaccgc ctgagaggct ctgagagcgt ttttacgccc tcacccgcaa
     2881 aagaacacgt cttaccccat caaaaccgtt caaaatcgtt ctgatacgtt ttacgaatgt
     2941 gaatgactat gcaccggaat gaacgccccg gtctttcagg taaaaatcat cgtgtaatct
     3001 acgaaaacag gacaaattgg taacggtgaa cgggtgggca attcattgac caactgttag
     3061 gcatggcaga ctgaggctgg attcaaaggt ccgttctgta gtaattctgt agtgtttctg
     3121 tagtctcccc cctccggttt gtagtaaatc agtagtaaat cagtagtgac gctgtagttt
     3181 attagtagtc aggaggaata agctgttcat acaagtatga acgagctagt tatggacgtt
     3241 ttttttcaca gatctcctca gaataggcaa agctcagccc ggtaaggaga tgattcttta
     3301 tcccttaaat ggccatacac catacgcaac cgcgattttc atcgcaattg catgaattaa
     3361 aaggtaaaaa ctgaagttcc cgtttattta tgtaatacgc aacgtattac aaccacctgt
     3421 aatcacatga aaataaagaa ataagatgta ataccggcgt attacacgta cgggggtaag
     3481 cgaaaaagct ataacgcttc acggccgaca ggtggcccaa aatccaccgg ggcgtgcagg
     3541 ttctcttcag taacctgcgc cattaaatca aaaaggtcat attcgccggg aagctgcgta
     3601 tcagtcgaac ccagttgttc atcatattca gatggcatgg ggtgatatcc aatagctgag
     3661 aggttgttag agtgtttcaa ggcgcagccc tgaaccagtc acgtagcgct agcggagcgt
     3721 atactggctt actatgttgg cacggatgcg aatatcagtg aagtgcttca tgtggcagga
     3781 gaaaaatgca gcagcggagc gtcagcagaa tatgcgatac aggatatatt ccgcttcc
//
