LOCUS       NZ_LR898871             4710 bp    DNA     circular CON 25-JUN-2023
DEFINITION  Escherichia coli strain MSB1_1D isolate MSB1_1D plasmid 4, complete
            sequence.
ACCESSION   NZ_LR898871
VERSION     NZ_LR898871.1
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
            LR898871.1.
            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..4710
                     /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="4"
                     /geo_loc_name="Australia"
                     /collection_date="2014-01"
     gene            join(4274..4710,1..199)
                     /locus_tag="JMX26_RS22995"
     CDS             join(4274..4710,1..199)
                     /locus_tag="JMX26_RS22995"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016236519.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_113403431.1"
                     /translation="MNDIFSLIESSRKIKKESIASTVRMPESLHTFIETLACDLELSKQ
                     EIMLKLLEQGARSAQEALAEIEKKELVELGAVEQLEPQTAVGFHILNTNKAHSDEDSEW
                     MLDKGIAAAFYDPWKWNINRIKPNEVVFLYENGKGIVAYGRGTGEVKIRDYHGDKDECH
                     YQELEGFKILENPLSAAQIKKILERNVVFLRTMSAMPDGQKVLNLIEG"
                     /name="hypothetical protein"
     gene            complement(303..611)
                     /locus_tag="JMX26_RS23000"
     CDS             complement(303..611)
                     /locus_tag="JMX26_RS23000"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012564913.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_113403432.1"
                     /translation="MTDKLKGTASVLNQTKTYEELVQKHSPEVANGLLANAINNALPNA
                     GITSNDVVGFSKVTTALRTGEVDLAKTAEEANADAEAVSANILAGLTAKQKSTDEIK"
                     /name="hypothetical protein"
     gene            complement(922..1035)
                     /locus_tag="JMX26_RS23005"
     CDS             complement(922..1035)
                     /locus_tag="JMX26_RS23005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_072003743.1"
                     /translation="MHEPPVQSDYHARSGNYRLESNPERHDKSPLAVATGN"
                     /name="replication initiation protein"
     gene            1496..>1954
                     /locus_tag="JMX26_RS23010"
                     /pseudo=""
     CDS             1496..>1954
                     /locus_tag="JMX26_RS23010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076612230.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="frameshifted; 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 family transposase"
                     /name="IS1 family transposase"
     gene            2304..2690
                     /locus_tag="JMX26_RS23015"
     CDS             2304..2690
                     /locus_tag="JMX26_RS23015"
                     /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_038988600.1"
                     /translation="MFFYRFITLIFGAVYIATTLTLGESALSSSLYAIGIAKTPSSASG
                     ILTLLLMLWVLVASVMMPKSWKVFAGIYLCLGLSGFLMPKSMHYGAGVYPLINSLTLLS
                     YLAFTLAIKLRDKYISKINQKTAW"
                     /name="hypothetical protein"
     gene            2741..3438
                     /locus_tag="JMX26_RS23020"
     CDS             join(2741..2990,2990..3438)
                     /locus_tag="JMX26_RS23020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001743396.1"
                     /ribosomal_slippage=""
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS1-like element IS1A family transposase"
                     /protein_id="WP_237158192.1"
                     /translation="MASVSISCPSCSATDGVVRNGKSTAGHQRYLCSHCRKTWQLQFTY
                     TASQPGTHQKIIDMAMNGVGCRATARIMGVGLNTILRHFKKLRPQSVTSRIQPGSDVIV
                     CAEMDEQWGYVGAKSRQRWLFYAYDSLRKTVVAHVFGERTMATLGRLMSLLSPFDVVIW
                     MTDGWPLYESRLKGKLHVISKRYTQRIERHNLNLRQHLARLGRKSLSFSKSVELHDKVI
                     GHYLNIKHHQ"
                     /name="IS1-like element IS1A family transposase"
     Typing          complement(919..1305)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.373"
                     /coverage="90.0"
                     /evalue="2.89e-174"
ORIGIN
        1 tactggtgag gttaaaattc gcgattatca tggcgataaa gacgaatgcc actaccaaga
       61 gctggaaggg tttaaaattc ttgaaaatcc gctatcggct gctcaaatta agaagatatt
      121 ggagcggaat gttgtgtttt tgagaacaat gtcggctatg ccagatggtc aaaaggtgct
      181 gaaccttatc gaaggttaag ccgagcactt gatggggttg agtgcggtta aaattttttt
      241 ataagtaatt acatacgaaa ccttggcccg tctagttcgg gcttttttgt acctgcggga
      301 aattatttta tttcatctgt acttttttgt tttgctgtca ggccagcaag aatatttgct
      361 gaaacggctt ccgcatcggc attggcttct tcggctgttt ttgctagatc aacttctcct
      421 gtacgcaagg ccgtcgtcac tttgctgaat ccaacgacgt cattcgaagt tattcctgcg
      481 ttaggcaaag cattattgat agcatttgcc agcaagccgt tagctacttc aggtgaatgc
      541 ttctgaacca attcctcata agttttggtt tgattaagaa cgctagctgt tcctttgagt
      601 ttgtctgtca tgtaaacctc tagtctgtga tgagtcagga gtagaaaatt ttatgtacaa
      661 gactcgcgtt aggcgggcac tcatactgaa gcaaaatcac tgctaaacag ccggatcttc
      721 ttgtgatcct tttactctcg tcgtaatctc attccctgta aacaaaaaaa ccaccgctac
      781 caacggtggt tcgtttgccg gaatcaagag ctaccaactc tttcttccga aggtaactgg
      841 cttggaggag cgcagtcacc aaaactgtcc tttcagtgta gctgcatcgc accaggaact
      901 tcaagactct cctcctctaa atcagttacc agtggctacc gccaatggcg atttatcgtg
      961 tctttccggg ttggactcaa gtcgatagtt accggaacgg gcgtggtagt cggactgaac
     1021 ggggggttcg tgcatacagt ccagcttgga gcgaactgcc ttcccggaac tgagtgtcag
     1081 gcgtggaatg agataaacgc ggccataaca gcggaatgac accggtaaac cgaaaggcag
     1141 gaacaggaga gcgcacgagg gagccaccag ggggaaacgc ctgggatctt tatagtcctg
     1201 tcgggtttcg ccaccactga tttgagcgtc agattctgtg atgcttgtca ggggggcgga
     1261 gcctatggaa aaccggcaac gccgcggcct tttcttttgc ctctcgatcc tctctcattg
     1321 cctgtgcctt aatgtctccg ttccctccgc tcgccgcagc cgaacgaccg agcgtagcga
     1381 gtcagtgagc gaggaagcgg aatatctcct gtattgcatc ttctgctgac gcgccggtgc
     1441 ggtgatgctg ccaacttact gatttagtgt atgatggtgt ttttgaggtg ctccagtggc
     1501 ttctgtttct atcagctgtc cctcctgttc agctactgac gggggtggtg cgtaacggca
     1561 aaagcaccgc cggacatcag cgttatctct gctctcactg ccgtaaaaca tggcaactgc
     1621 agttcactta caccgcttct caacccggta cgcaccagaa aatcattgat atggccatga
     1681 atggcgttgg atgccgggca actgcacgca ttatgggcgt tagcctcaac acgattttac
     1741 gtcacttaaa aaactcaggc cgcagtcggt aacctcgcgc atacagccgg gcagtgacgt
     1801 catcgtctgc gcggaaatgg acgaacagtg gggctatgtc ggggctaaat cgcgccagcg
     1861 ctggctgttt tacgcgtatg acagtctccg gaagacggtt gttgcgcacg tattcggtga
     1921 acgcactatg gcgacgctgg ggcgtgtcat ttcgtttcgg ctccccctgt ttttcccttt
     1981 cttcgctgga cgctcatcag gataaaaaca aaaagactac cgccctcgtt ttactcggtt
     2041 ggtcaaatcg cttcttgcca caaacttgtt ttgtggcaag aagcgatttc gcatcgtttt
     2101 acttgtcagt ttgaatgatg ttaaaaacgc actcagaagc tcgcaaaacc gttctaaact
     2161 ttcagcgtag atttggtttt gaggggcttt aatggggatg aacgggcggt tttcgctaac
     2221 taactcgccc gtttaacata aaagggatta gaagaaccta tgtttatgta aaatctacaa
     2281 ttatttaata taggcgggct attatgtttt tctatcgatt tatcacttta atttttgggg
     2341 ctgtgtatat tgctacaact ctaacattgg gagagtcggc gttatcctct tcgctttatg
     2401 caatagggat tgctaaaacc cctagctccg cttctggtat tttgactctt ttgttgatgt
     2461 tgtgggtttt agttgcttcg gtcatgatgc ctaaatcttg gaaagttttt gctggcattt
     2521 atctatgctt gggtttgtca gggttcctta tgccgaaaag catgcattat ggtgccggtg
     2581 tttacccatt gataaactct ttaacacttc ttagttatct ggcctttacc cttgcaataa
     2641 agctaagaga caaatacatc tccaaaataa atcaaaaaac tgcctggtga tgctgccaac
     2701 ttactgattt agtgtatgat ggtgtttttg aggtgctcca gtggcttctg tttctatcag
     2761 ctgtccctcc tgttcagcta ctgacggggt ggtgcgtaac ggcaaaagca ccgccggaca
     2821 tcagcgctat ctctgctctc actgccgtaa aacatggcaa ctgcagttca cttacaccgc
     2881 ttctcaaccc ggtacgcacc agaaaatcat tgatatggcc atgaatggcg ttggatgccg
     2941 ggcaactgcc cgcattatgg gcgttggcct caacacgatt ttacgtcact taaaaaactc
     3001 aggccgcagt cggtaacctc gcgcatacag ccgggcagtg acgtcatcgt ctgcgcggaa
     3061 atggacgaac agtggggcta tgtcggggct aaatcgcgcc agcgctggct gttttacgcg
     3121 tatgacagtc tccggaagac ggttgttgcg cacgtattcg gtgaacgcac tatggcgacg
     3181 ctggggcgtc ttatgagcct gctgtcaccc tttgacgtgg tgatatggat gacggatggc
     3241 tggccgctgt atgaatcccg cctgaaggga aagctgcacg taatcagcaa gcgatatacg
     3301 cagcgaattg agcggcataa cctgaatctg aggcagcacc tggcacggct gggacggaag
     3361 tcgctgtcgt tctcaaaatc ggtggagctg catgacaaag tcatcgggca ttatctgaac
     3421 ataaaacacc atcaataagt tggagtcatt acccgttata gctttttcgc ttacccgcgt
     3481 acgtggtaat acgccggtat tacatcttat ttctttattt tcatgtaatt acaggtggtt
     3541 gtaatacgtt gcgtattaca taaataaacg gggaattcag tttttacctt ttaattcatg
     3601 caattgcgat gaaaatcgcg gttgcgtatg gtgtatggcc atttaaggga taaagaatca
     3661 tctccttacc gggctgagct ttgcctattc tgaggagatc tgtgaaaaaa aacgtccata
     3721 actagctcgt tcatacttgt atgaacagct tattcctcct gactactaat aaactacagc
     3781 gtcactactg atttactact gatttactac aaaccggagg ggggagacta cagaaacact
     3841 acagaattac tacagaacgg acctttgaat ccagcctcag tctgccatgc ctaacagttg
     3901 gtcaatgaat tgcccacccg ttcaccgtta ccaatttgtc ctgttttcgt agattacacg
     3961 atgattttta cctgaaagac cggggcgttc attccggtgc atagtcattc acattcgtaa
     4021 aacgtatcag aacgattttg aacggttttg atggggtaag acgtgttctt ttgcgggtga
     4081 gggcgtaaaa acgctctcag agcctctcag gcggtgcggg caacggatgt tatggtaaat
     4141 acacatcgta atgactattc gtgcatacgc catcatctat cacttggagt tagaatctat
     4201 tttgattcaa ttattgcatc gttttttgat tcactatatg cttctataac aaaaccaatt
     4261 taaggttcat aaaatgaatg atattttttc tttaatcgaa agctccagaa aaattaaaaa
     4321 agaatcgata gcttccacag tgcgaatgcc cgagtcgttg catacgttta tcgaaacgct
     4381 ggcctgcgat ctcgaacttt caaagcaaga gatcatgctt aaactccttg agcaaggagc
     4441 caggagtgct caagaggcgt tagctgagat tgaaaagaag gagttggttg agttaggcgc
     4501 tgtagaacaa ctcgagccgc agacagccgt tggcttccat attttgaata caaacaaagc
     4561 tcatagcgat gaagactctg aatggatgct tgacaaagga atcgctgctg ctttttatga
     4621 tccatggaaa tggaacatca atcgaatcaa gcccaatgaa gtagtgtttc tgtatgaaaa
     4681 cggtaaaggc atagttgcct atggtagggg
//
