LOCUS       NZ_CP070927             4237 bp    DNA     linear   CON 17-JUN-2023
DEFINITION  Escherichia coli strain 40EC plasmid p40EC-7.
ACCESSION   NZ_CP070927
VERSION     NZ_CP070927.1
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 4237)
  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 4237)
  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
            CP070927.1.
            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..4237
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="40EC"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p40EC-7"
                     /geo_loc_name="Singapore"
                     /collection_date="2019-02"
     gene            complement(665..1378)
                     /locus_tag="JR909_RS25515"
                     /old_locus_tag="JR909_25515"
     CDS             complement(665..1378)
                     /locus_tag="JR909_RS25515"
                     /old_locus_tag="JR909_25515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001590713.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_001590713.1"
                     /translation="MNKKLIFSVLLCLFSFGSVAGIPVAIDASPEWAVEATRWTERLKQ
                     WSETARHYQSQIQAYKDQLATATGIRNIAAFTNELSNLQSELANIYKQGNSYISDFTSN
                     PEGALSSQAKNLFSKYGAFNMCSTGIESSDNLCKARIVSTAASIEQGNEINKQLSSAMS
                     QIQSLSNRIESSKDMKESQDLANALQAQSLKIQAIKMQYDVWDSKNRADAEMLKEQKYA
                     EYRLRQKNAKIPSFE"
                     /name="type IV secretion system protein"
     gene            complement(1375..2373)
                     /locus_tag="JR909_RS25520"
                     /old_locus_tag="JR909_25520"
     CDS             complement(1375..2373)
                     /locus_tag="JR909_RS25520"
                     /old_locus_tag="JR909_25520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000012467.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_052978250.1"
                     /translation="MSGFFEKFNSEVVSKIEEMTKPLQSQLGQDMLSLLSAGISVYILW
                     VGYQILAGKRQTPLQDLVWDLSKFAIILTFVSNADGYLTAAMDAIKSMKDGFLGKPVWA
                     TLDTMWSTTQLLADKVYAMDQSKYVSVEGGIGSMLVWGGSILIMSVAAVIYMLADVTMQ
                     LAILVAPIFIGCYMFGFTRVMFNNWLGILFSSVFTVIFAGVLVKIGTEFQTDMLSQISR
                     DANSTNILTMGAMAFVIGVLIAVFVWKSSSFAQQLAGAGVEGTLQGMALLGIGVAGMAV
                     EKTRNQMKRGTRTAAEWAGEKGEQKRASIGALGMEARRRASLEKARARNSA"
                     /name="type IV secretion system protein"
     gene            complement(2378..2641)
                     /locus_tag="JR909_RS25525"
                     /old_locus_tag="JR909_25525"
     CDS             complement(2378..2641)
                     /locus_tag="JR909_RS25525"
                     /old_locus_tag="JR909_25525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001677227.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EexN family lipoprotein"
                     /protein_id="WP_000717655.1"
                     /translation="MKKICTLLMSIFILSACGEDTKSSDWWLNHPKEATEKYKECKKSG
                     EDSVNCQNVKKVAGIIGRTYGPMLEILKAESAEYDKQHGLNR"
                     /name="EexN family lipoprotein"
     gene            complement(2729..3136)
                     /locus_tag="JR909_RS25530"
                     /old_locus_tag="JR909_25530"
     CDS             complement(2729..3136)
                     /locus_tag="JR909_RS25530"
                     /old_locus_tag="JR909_25530"
                     /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_126709166.1"
                     /translation="MSKNDVFACACRRLLEVVAGEQKWCFVRLLITTTWLEVFMTKHDA
                     IRISQLHQIFYDDDGLIDSEKNVTILYSIGFTVDEIAHFRNSTPNTVAAQLLNARVKLG
                     CASVSSLKPMILLRLLLNIKEIRFGFETDCK"
                     /name="hypothetical protein"
     gene            complement(3199..3714)
                     /locus_tag="JR909_RS25535"
                     /old_locus_tag="JR909_25535"
     CDS             complement(3199..3714)
                     /locus_tag="JR909_RS25535"
                     /old_locus_tag="JR909_25535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000097059.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_000097059.1"
                     /translation="MSSLSLQRYETNPFLELMTIPMKGKRIQVSRLGRDDNVLVNQNTG
                     EKFGTHVTTFKRVDSEQFVKLFTANIGLTFDLSSAGIKAFNVLLWAVQKQAFAKDQVLL
                     DSRALDDFLKSYDSLKLSYATLKRGINELEKAQIIAKTMRKGFYFINPNFVFNGDRIAF
                     TTLIERDC"
                     /name="replication/maintenance protein RepL"
     Typing          complement(1571..2373)
                     /name="MPF_T"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="89.552"
                     /coverage="91.0"
                     /evalue="1.41e-160"
ORIGIN
        1 aaccgcgcca gccccctgca aagcccatta gcacggaaca ggtagccaca cggttggtag
       61 gtggtcgtag accgtcgatg ttacagcgat gggggtctgg ggttctcccc agacggtttc
      121 cggttgcgct caaggcgctg ccggaaccgt ggcggctcgg tggttctaga gatcgggaaa
      181 caaaaacacg ctaggggttt tgaggtcggc aaaagagcaa tgcaggatag acaatcatgg
      241 tcaaaatgtt aacattttat ccatgattgt ccaaaaacga tgtttttgcc tgtgcctgcc
      301 gcaggctcta tatttagaat ttagaataga aaaggccatc tattcgatga cctttatttt
      361 ttacttcatt gaaaatcgca ttactattaa taacagaagt aaaatacaaa acagctttaa
      421 cgtaaaaagg agtctttctt ttataccacc gctgggaaca aacctctttt caattttatc
      481 agtgataaat tgcaatgtac cataatacat taaagcatta accagcttta acgtaagctc
      541 cacacttaaa acaataacta tgattggtag cgagattaac agtggcggcg gtgtagaacc
      601 ggtactattc aatctagacc aatgattatc tacccattct tttagcttat ttagctttat
      661 catatcattc gaaactcggt atctttgcat ttttctgacg caggcgatac tcagcatact
      721 tttgctcttt caacatttcc gcatcagccc tgtttttact atcccataca tcatactgca
      781 ttttaattgc ctgtattttt aacgactgcg cctgcaatgc gttagccaaa tcctgggatt
      841 ctttcatatc ctttgaagac tcaattcggt tacttaaact ctgaatctga gacattgcac
      901 ttgatagctg cttatttatc tcatttccct gttcaatgct agcggccgtt gaaactattc
      961 tggccttaca aaggttatca gaactttcaa tgcctgtaga acacatatta aaagcaccat
     1021 acttgctgaa cagatttttc gcctgactac ttaatgcacc ttcaggatta ctggtaaaat
     1081 cagaaatata actgttcccc tgcttataaa tgtttgccag ctctgattgt aggttactta
     1141 gttcatttgt gaatgccgca atattcctta tacctgttgc cgtggctaac tggtctttat
     1201 atgcctgaat ctgactttga taatgccgcg ctgtttcaga ccattgtttg agtcgttctg
     1261 tccatcttgt ggcttcaaca gcccattccg gactggcatc aatagcaacc ggaatacctg
     1321 cgacagaacc aaatgaaaat aagcacaaaa gtactgaaaa aattagtttt ttgttcatgc
     1381 tgaattcctc gcacgtgctt tttccaggga tgctcgtctt cttgcttcca ttcccaatgc
     1441 gcctattgaa gcccgtttct gctccccttt ttcacctgcc cattcggcgg ctgttcgcgt
     1501 tccacgtttc atctggtttc tcgttttctc tacggccatt ccagcaaccc caatccctaa
     1561 aagagccatt ccctgaagag taccttcaac acctgcaccg gcaagctgct gcgcgaaact
     1621 cgatgatttc cagacaaaga cagcaatcag aactccaatt acaaatgcca ttgcgcccat
     1681 tgttaaaata tttgttgagt tagcatctct cgatatctga ctaagcatat cagtttgaaa
     1741 ctcggtacca attttgacga gaactccagc aaaaataaca gtaaatacac tagaaaataa
     1801 tataccaagc cagttattaa acattactct agtgaatcca aacatataac aaccgataaa
     1861 tatcggagct acaagaatag ctaactgcat tgttacatcg gcaagcatgt aaataacagc
     1921 cgctacagac ataatcagga tacttcctcc ccaaaccaac attgacccga ttccaccttc
     1981 aactgacaca tatttggatt gatccatagc ataaactttg tcagccaaaa gctgagttgt
     2041 actccacatg gtatctagcg ttgcccatac aggtttacca aggaacccat ccttcataga
     2101 tttaatagca tccattgctg ccgtcagata gccatcagca ttgcttacga atgttaaaat
     2161 aatggcaaat tttgatagat cccagacgag atcttgtaat ggggtctggc gtttccctgc
     2221 caatatttga tagccaaccc agaggatata aacgctaata cctgcactta gaagagataa
     2281 catatcctga cctaattgac tttgaagtgg tttggtcatc tcttcgattt tactaacaac
     2341 ttcgctatta aacttttcaa agaaaccaga catgttatca cctgttcaat ccatgttgct
     2401 tatcatattc agctgactca gccttaagta tttcaagcat agggccatag gttctaccaa
     2461 taattccggc aactttttta acattttgac aattaacaga atcttcccct gactttttac
     2521 actccttata tttctccgtc gcttctttgg gatgattaag ccaccaatct gatgattttg
     2581 tatcttcacc acatgcggaa agaatgaaaa tagacattaa gagcgtacaa atttttttca
     2641 tctttgattc ctcgtatgga cattacaatt gctgatacaa tcagcaattg taattctagt
     2701 caagagcaaa aatacctatt gaactatatt atttgcaatc agtttcgaat ccaaaacgaa
     2761 tctcttttat gttcaaaagc aatcttaata agatcattgg ctttaaagat gaaaccgagg
     2821 cgcaacctaa tttaaccctt gcatttaata gctgagccgc aactgtgttt ggtgttgaat
     2881 ttctaaaatg agctatttca tcaactgtaa atcctatact gtataaaata gtcacgttct
     2941 tttctgaatc aattaatcca tcatcatcgt aaaaaatttg atgaagttga gaaatgcgta
     3001 tagcatcatg tttagtcata aaaacctcta gccaggttgt tgtgattagc aggcgaacaa
     3061 aacaccactt ttgttcgcct gcgactactt ctagtagcct gcggcaggca caggcaaaaa
     3121 catcgttttt ggacaatctg attcaaatgt taacatttga catcggattg tctatcctgc
     3181 attgtattgt tctatcgatt aacaatccct ctcaattagg gttgtaaatg ctattcgatc
     3241 tccattaaat acaaaattgg ggtttataaa ataaaatcct ttacgcattg tctttgctat
     3301 aatctgagct ttttctaact cgttaattcc tctctttaac gtagcataac taagttttaa
     3361 gctatcatag ctttttaaaa agtcatcaag agcccttgaa tccaaaagaa cctgatcctt
     3421 tgcaaaggct tgtttttgaa cagcccataa aagaacatta aaagctttaa ttcctgccga
     3481 tgataaatca aacgttaacc caatattcgc agtaaacaac ttaacaaatt gctcactatc
     3541 tacacgctta aaagtggtta catgtgttcc aaacttttct cccgtgtttt gattaaccaa
     3601 aacattgtca tcccgcccaa gacgagatac ttgtatccgt ttccctttca tcgggatcgt
     3661 cataagctct aaaaacgggt ttgtttcgta tctctgtaag cttagcgagc tcattattgc
     3721 atcctttttt gggctttgga gattcacaat aaatcctcat aagctcaaaa tcaagcaatt
     3781 tttgagcctg caaggtaccg gatctgagct tacaaggtac agatcctgat caccactttc
     3841 taggattcat gcgggttccg agaatttccc ttcttagttc ttaactaagg agcgtaggtg
     3901 ctcaattatg gctatcaatt ctcttccgct tcctcgccca ctcgctcact acgttcggtc
     3961 gctggggctg cggcgagcgg gatcacctct cgcatgttgt cagaaatgcc gttgctgttc
     4021 tgttcgaaaa tgcgttctgt gggccatcca gagcaccaga acgcgatttt caggtgttgg
     4081 taatgtttta gtcgtcttag ctcttaaaac gcgctcagac gcacgaaacg ggctttagat
     4141 gcccgtcagg gcatggaagg cgcgaaaaat gcttacagag ggtttcagga ggtcaggcgc
     4201 gccgataccc ctaaccaggg gctttcaggt cgccagg
//
