LOCUS       NZ_CP070926             4980 bp    DNA     linear   CON 17-JUN-2023
DEFINITION  Escherichia coli strain 40EC plasmid p40EC-6.
ACCESSION   NZ_CP070926
VERSION     NZ_CP070926.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17807534
            Assembly: GCF_017088445.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4980)
  AUTHORS   Ding,Y., Saw,W.-Y., Tan,L.W.L., Moong,D.K.N., Nagarajan,N., Teo,Y.Y.
            and Seedorf,H.
  TITLE     Whole-genome analysis of antimicrobial-resistant Escherichia coli in
            human gut microbiota reveals its origin and flexibility in
            transmitting mcr-1
  JOURNAL   bioRxiv (2021)
REFERENCE   2  (bases 1 to 4980)
  AUTHORS   Ding,Y. and Seedorf,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-FEB-2021) Henning Seedorf Group, Temasek Life Sciences
            Laboratory Limited, 1 Research Link National University of Singapore
            Singapore, Singapore 117604, Singapore
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 378x
            Sequencing Technology :: Illumina NovaSeq Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 06:58:43
            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)                     :: 5,165
            CDSs (total)                      :: 5,048
            Genes (coding)                    :: 4,866
            CDSs (with protein)               :: 4,866
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 182
            CDSs (without protein)            :: 182
            Pseudo Genes (ambiguous residues) :: 0 of 182
            Pseudo Genes (frameshifted)       :: 66 of 182
            Pseudo Genes (incomplete)         :: 118 of 182
            Pseudo Genes (internal stop)      :: 38 of 182
            Pseudo Genes (multiple problems)  :: 39 of 182
            Pseudo Genes (short protein)      :: 3 of 182
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP070926.1.
            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/
FEATURES             Location/Qualifiers
     source          1..4980
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="40EC"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p40EC-6"
                     /geo_loc_name="Singapore"
                     /collection_date="2019-02"
     gene            <1..852
                     /locus_tag="JR909_RS25485"
                     /old_locus_tag="JR909_25485"
     CDS             <1..852
                     /locus_tag="JR909_RS25485"
                     /old_locus_tag="JR909_25485"
                     /inference="COORDINATES: protein motif:HMM:NF013211.2"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA];
                     GO:0050829 - defense response to Gram-negative bacterium
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like pore-forming protein"
                     /protein_id="WP_205899306.1"
                     /translation="NHDNNITAVNAVSPETRASDMEKSSKMVSALIDEKQNQKNQIAAQ
                     ISEKNKKIEEMKKIFKHHSYHGITDLERDVDELQRKSNQLDADISKLYDYKNTLKSDVD
                     KIKDAVAYTATFYEKVTEKYGEKAELLAKSLADKANGKTIRGVDDALAAFDRYRSSLGD
                     KFNSADRAAIVAGIQALDATNTANSLAKYSKAFGYLGNAIDLADILVELKNALTTDNWR
                     PVLVKLEIITANRAAVAISAIVFSIITGVPMGIVGFGVLVALAGSFFDEQLVNEINSQL
                     GI"
                     /name="colicin-like pore-forming protein"
     gene            1246..1386
                     /locus_tag="JR909_RS25490"
                     /old_locus_tag="JR909_25490"
     CDS             1246..1386
                     /locus_tag="JR909_RS25490"
                     /old_locus_tag="JR909_25490"
                     /inference="COORDINATES: protein motif:HMM:NF014457.2"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_153276082.1"
                     /translation="MKKMFFVGVVIISFCLVACQMNNIKGNSGGSFSSSNSGVGIQVKK
                     S"
                     /name="colicin release lysis protein"
     gene            complement(2374..2565)
                     /locus_tag="JR909_RS25495"
                     /old_locus_tag="JR909_25495"
     CDS             complement(2374..2565)
                     /locus_tag="JR909_RS25495"
                     /old_locus_tag="JR909_25495"
                     /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_001401730.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGEAL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(3400..3828)
                     /locus_tag="JR909_RS25500"
                     /old_locus_tag="JR909_25500"
     CDS             complement(3400..3828)
                     /locus_tag="JR909_RS25500"
                     /old_locus_tag="JR909_25500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000830439.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="WP_042089515.1"
                     /translation="MKRSGGTRYMYLSALITVAAALTACTPKTSLEQHTRHYVYASDDG
                     FDPNFYTKKADTTRMMIPFFQQFREMGVKDKAAGVSAETAQQRIKEFHSEEFLQSLRTT
                     TTFAGRKYTNGDMPSPEKMKLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            complement(3909..4346)
                     /locus_tag="JR909_RS25505"
                     /old_locus_tag="JR909_25505"
     CDS             complement(3909..4346)
                     /locus_tag="JR909_RS25505"
                     /old_locus_tag="JR909_25505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405929.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="entry exclusion protein 1"
                     /protein_id="WP_170981958.1"
                     /translation="MGHCHFMAWHTLQDALKMTGRSRSQFYRDMRAGLVSYRTSQDGRR
                     EFETSELIRAYGELKRNETPERHTAGQAEKPHDQQTERILRELNELKQCLTLMLEDKQA
                     QDTERQRQEAEREQLQNEIAQLRQALEQEKKRGVWSRLFGR"
                     /name="entry exclusion protein 1"
     gene            4606..>4980
                     /locus_tag="JR909_RS25510"
                     /old_locus_tag="JR909_25510"
                     /pseudo=""
     CDS             4606..>4980
                     /locus_tag="JR909_RS25510"
                     /old_locus_tag="JR909_25510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_159420795.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     Typing          complement(1672..2216)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.698"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aatcacgata ataacatcac tgctgttaat gcagtatctc cagaaactcg agccagtgat
       61 atggagaaaa gttctaagat ggtgagtgct ctgattgatg aaaagcagaa ccagaaaaat
      121 cagattgctg cgcagattag tgaaaaaaat aaaaaaatag aggagatgaa aaaaatattc
      181 aagcatcact cctatcatgg aattactgat cttgaaaggg atgttgatga gttacaaaga
      241 aaatctaatc agttggatgc tgatattagc aagttatatg attacaaaaa cacattgaaa
      301 agcgatgtgg ataaaataaa ggatgctgtt gcctatacag ctactttcta tgaaaaagta
      361 acagaaaagt atggtgagaa agctgaatta ttagcgaaaa gtttggctga taaagctaat
      421 ggaaaaacta ttcgtggtgt tgatgatgct ttggctgcat ttgatcggta tagaagttct
      481 ttgggtgata agtttaattc tgctgatcgt gccgctattg tcgcaggaat tcaggcatta
      541 gatgctacga atacagcaaa cagtttagct aaatatagta aagcatttgg ttatttagga
      601 aatgctattg atctggctga tattcttgtt gaacttaaaa atgcattgac aacagataat
      661 tggcgacctg ttcttgttaa actagaaatt attaccgcaa atcgtgcagc cgtggctatt
      721 tctgcaattg ttttttctat tattacagga gttcctatgg ggattgttgg ttttggtgtc
      781 cttgtggctt tagcaggctc tttttttgat gagcagttag ttaatgaaat taactcgcaa
      841 ctaggtattt aatggttgtt aagctggtca ttttttttga ccagcttgtc cttatctata
      901 aaaagataaa taatgctgaa tgggattgcg aaaataacac aaaaaaacac atatataacg
      961 taaaatcgat taaccccatt ggagtttaac caagtggggt tccaaaactg tattgatgta
     1021 tatcttaatg ctactgtttt tacagtgtac atagatacag gaagaagtat tccgctgagt
     1081 atatatatga ttgatatttg tattgttttt gatgtcaatg gttcgtggaa taagttatat
     1141 attgcgataa gtataggaaa tagaccccat aataaacgag agaaatagaa tttcttgttc
     1201 atatgttaat gtctcactat cttgttttta tataaaggag tatacatgaa gaaaatgttt
     1261 tttgtaggtg ttgtaatcat atcattttgt ttggttgcat gtcagatgaa taatattaaa
     1321 ggtaattcag gtggttcatt ttcgtcatct aactcaggtg tcggtatcca agtgaagaaa
     1381 tcgtgagttt gcatcactga tcctcttgtg atccttttct tctgcgcgta atctgctgct
     1441 tgcaaacaaa aaaaccaccg ctaccaacgg tggtttgttt gccggatcaa gagctaccaa
     1501 ctctttttcc gaaggtaact ggcttcagca gagcgcagat accaaatact gtccttccag
     1561 tgtagccgca gtcgggccac aacttcaaga actctgtagc accatttgtg ccatcatcgc
     1621 tctgctaatc cggttaccag tggctgctgc cagtggcgtt aagtcgtgtc ttaccgggtt
     1681 ggactcaaga cgatagttac cggataaggc gcagcggtcg ggctgaacgg ggggttcgtg
     1741 cacacagccc agcttggagc gaacgaccta caccgagccg agataccaac agcgtgagct
     1801 atgagaaagc gccacgcttc ccgaagggag aaaggcggac aggtatccgg taagcggcag
     1861 ggtcggaaca ggagagcgca cgagggagct tccaggggga aacgcctggt atctttatag
     1921 tcctgtcggg gttcgccacc tctgacttga gcgtcaattt ttgtgatgct cgtcaggggg
     1981 gcggagccta tggaaaaacg ccagtggtgc ggctttcttc cggttcttgg tcttttgctc
     2041 acatgttctt tccggcgtta tcccctgatt ctgtggataa ttgtattaca gcttttgagt
     2101 gagtggactc cgctcgccgc agccgaacga ccgagcgcag cgagtcagtg agcgaggaag
     2161 cggaagagcg cctgaactgg cattttctcc ttacgcatct gtgcggcatt tcacactgga
     2221 catgccgcat ggttaagccc gtatacactc cgctatcgct acgtgactgg gtcatggctg
     2281 cgccccgaca cccgctaaaa cccgttgacg ggcttgtctg ctcccggtat ccgctcacag
     2341 gcaagctgtg accgtctccg ggagctgcat gtgtcagagg gcttcaccgt catccccgaa
     2401 acgtgcgagg caactgcggt aaagctcatc ggcgtggtcg tgaagcgatt cacagatatc
     2461 tgcctgttca tctgcgtcca gttcgttgag cttctccagc agcgttaatg tctggcttct
     2521 gatgaagcgc gccatgttca gagcggtttt ttcctgtttg gtcactggtc tgatgtctcc
     2581 gtgtaaggga atttctgttc atgggagcat gataactgtg acgcaggcga gagtgataaa
     2641 gctgagtgag cggttagtca ggggcgcaaa cattcgaacg cggccagtgc gatgcaggat
     2701 agggaaaacg ccgtaaaacg acgtcccttt cggcaatagc aatatcatgg cacggcatat
     2761 caactgataa ataattcctg tgcagtacag ccgctgttgc ataaaatctc gctctgcggt
     2821 gagtattgtt taatcaaaaa tccccgcagt tcttccagaa aaacgcgagt ctgttctcat
     2881 gcctgaaatg cccacacccc acgcaaaacc aactttttgc tgatttgctt tttaaatcat
     2941 gttgttatgg ttttaaaaat gtattttctt attcagattt atacaaaagc acgtcgtcga
     3001 cgaccctatg gcgacgctat gacgacccta cttagggtca gtactgacta tctgtagaaa
     3061 aaacagttaa ttaatgtagg ggcgccccta ggggcgcgtc gcctttttta catcacaccc
     3121 ctgggggcgc tgccaggggt gtctgcccgg atatgtagca atgagccagg gattcacgaa
     3181 ctgaaaatgt ccgaaaatgt gcctcatggg caccgtatgc gcccaaacag atcgctattc
     3241 agtttcgtgc atagtcatgc aacgccctga aaacgatcct gacgcatttt tccggttttc
     3301 ctgggggtaa gcatttcttt ttgcggtgcc tgcgtcagaa tcgcgctcaa cgcgttttaa
     3361 tggtgcgtac aattaaggga ttatggtaaa tgtctccctt tactgcctgc cctcgtagcc
     3421 atcaagataa accgcagaaa tcgtgtcagc cagcagcttc attttttccg gtgatggcat
     3481 atcaccgttc gtgtattttc tgcccgcaaa ggtggttgtg gttctcagtg actgaaggaa
     3541 ttcttcagag tggaattctt ttatgcgttg ctgtgccgtt tctgctgata ctccagctgc
     3601 tttgtctttc acccccatct cccggaactg ctgaaagaac ggaatcatca tccgtgtggt
     3661 gtcagctttc ttggtgtaga agttaggatc aaacccatca tctgaagcat aaacataatg
     3721 ccgggtatgt tgttccaggc tggtttttgg ggtacaggcc gtgagggctg ctgccacagt
     3781 tatcagggcg ctaagataca tatagcgtgt gccgccagaa cgtttcatgc gagtctcctt
     3841 accttaaagt atttattttc ggtgagttat tatctgatgg ctatcttatc atcagtctct
     3901 gagtgcgttc agcgaccgaa caacctggac cagactcccc gtttcttttc ctgctccagc
     3961 gcctgcctga gctgggctat ctcattctgt agctgttccc gttctgcttc ctggcgctgg
     4021 cgctccgtat cctgagcttg tttatcctca agcatcagcg tcaggcattg tttcagctcg
     4081 ttcagctccc ggagaatgcg ttctgtctgc tgatcatgag gtttttctgc ctgtcccgca
     4141 gtgtgccttt ctggtgtctc attccgcttt aattcgccgt atgcccggat cagttcactg
     4201 gtttcaaact cccgtcgtcc gtcctggctt gtacggtaac tgacaaggcc tgcgcgcata
     4261 tcacggtaaa actgtgaacg cgatctgccc gtcattttca gtgcgtcctg gagtgtgtgc
     4321 catgccataa agtgacagtg tcccataggt gtctcatatc atggtttcag taaaacatac
     4381 tgaggccgga gaacggtaat gtttgtgctg gtttttgtgg catcgggcgg gaatagctcg
     4441 tggtgtgggg ggcttttttt ttgaacgttt tcacaaaaat gaaaatccac agggttgaca
     4501 gggaaaacgc agcggcgtaa ttttaagctg tatataaaac cagtggttat atatacagta
     4561 ttatggtttt aactatttat ttttaatgtc aaagaggtat tttttatggc gaaagaactt
     4621 ggtggatatg gcccaactgc cggtgaatct atggggggaa caggggcgaa tttgaatcag
     4681 caaggtggac ataataatag tggtgttcac tgggggggag gctccggaca cggtaataat
     4741 ggtggtcagg gtaatacaag ctcatcgaat tcaacatcga cagtgatgaa gccaggtgag
     4801 tcatatctaa ccccgtgggg agatgttgtt attaataaag atggtctccc ggtgatgaat
     4861 ggtgttgtta tgacagaaga taattcttct ttggttgata atccattagg gggggtctcc
     4921 agagttctta actctttaat tagtgatatg ccatcacttt ttaccaaggc gacaggaaat
//
