LOCUS       CP048292                7010 bp    DNA     linear   BCT 07-FEB-2022
DEFINITION  Escherichia coli strain CVM N18EC0432 plasmid pN18EC0432-5, complete
            sequence.
ACCESSION   CP048292
VERSION     CP048292.1
DBLINK      BioProject: PRJNA292663
            BioSample: SAMN12359680
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 7010)
  AUTHORS   Tyson,G.H., Li,C., Hsu,C.H., Ayers,S., Borenstein,S., Mukherjee,S.,
            Tran,T.T., McDermott,P.F. and Zhao,S.
  TITLE     The mcr-9 Gene of Salmonella and E. coli is Not Associated with
            Colistin Resistance in the United States
  JOURNAL   Antimicrob. Agents Chemother. (2020) In press
   PUBMED   32513803
  REMARK    Publication Status: Available-Online prior to print
REFERENCE   2  (bases 1 to 7010)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-JAN-2020) CVM/OR, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: DEC-2019
            Assembly Method                   :: HGAP v. 4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 921x
            Sequencing Technology             :: PacBio RS
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 02/03/2020 14:12:39
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.11
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 5,340
            CDSs (total)                      :: 5,222
            Genes (coding)                    :: 5,030
            CDSs (with protein)               :: 5,030
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 192
            CDSs (without protein)            :: 192
            Pseudo Genes (ambiguous residues) :: 0 of 192
            Pseudo Genes (frameshifted)       :: 83 of 192
            Pseudo Genes (incomplete)         :: 112 of 192
            Pseudo Genes (internal stop)      :: 37 of 192
            Pseudo Genes (multiple problems)  :: 39 of 192
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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..7010
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="CVM N18EC0432"
                     /isolation_source="Chicken Wings"
                     /db_xref="taxon:562"
                     /plasmid="pN18EC0432-5"
                     /geo_loc_name="USA:CA-UC Davis"
                     /collection_date="2018"
                     /collected_by="FDA"
     gene            1..821
                     /locus_tag="GZ082_23920"
                     /pseudo=""
     CDS             1..821
                     /locus_tag="GZ082_23920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001632669.1"
                     /note="frameshifted; incomplete; partial on complete
                     genome; missing N-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=3
                     /transl_table=11
                     /product="rhsE core protein with extension"
                     /name="rhsE core protein with extension"
     gene            821..1048
                     /locus_tag="GZ082_23925"
     CDS             821..1048
                     /locus_tag="GZ082_23925"
                     /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="QJH52202.1"
                     /translation="MHDPEYPENLPAAPLVCYDWTPRGELAAVYDRSGTQMRHFTYDDK
                     YRGRMVGHRYAGRPEMRYRLRRCGAGGGAT"
                     /name="hypothetical protein"
     gene            1361..1999
                     /locus_tag="GZ082_23930"
     CDS             1361..1999
                     /locus_tag="GZ082_23930"
                     /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="RHS repeat protein"
                     /protein_id="QJH52203.1"
                     /translation="MVSPDGLESRRAYDEPGRLVSETSRSGDVIRYAYDNPHSELPATT
                     TDATGSTRQMTWSRYGQLLAFTDCSGYQTRYEYDRFGQMTAVHREEGISLYRHYDNRGR
                     LTSVKDAQGRETQYEYNAAGDLTAVITPDGNRSETQYDAWGKAVSTTQGGLTRSMEYDA
                     AGRVISLTNENGSHSDFSYDALDRLVQQGGFDGRTQRYHYDLTGKTHAE"
                     /name="RHS repeat protein"
     gene            2202..2513
                     /locus_tag="GZ082_23935"
     CDS             2202..2513
                     /locus_tag="GZ082_23935"
                     /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="RHS repeat protein"
                     /protein_id="QJH52204.1"
                     /translation="MENPETGELLWQHETKHAYNEQGLANRVTPDSLPPVEWLTYGSGY
                     LAGMKLGGTPLVEYTRDRLHRETVRSFGSMAGSNAAYELTSTYTPRPVTEPAPEQPGV"
                     /name="RHS repeat protein"
     gene            2506..4127
                     /locus_tag="GZ082_23940"
                     /pseudo=""
     CDS             2506..4127
                     /locus_tag="GZ082_23940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004022383.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="RHS repeat protein"
                     /name="RHS repeat protein"
     gene            4323..4555
                     /locus_tag="GZ082_23945"
                     /pseudo=""
     CDS             4323..4555
                     /locus_tag="GZ082_23945"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001702891.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(4552..4662)
                     /locus_tag="GZ082_23950"
                     /pseudo=""
     CDS             complement(4552..4662)
                     /locus_tag="GZ082_23950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012477181.1"
                     /note="internal stop; incomplete; partial on complete
                     genome; missing N-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            5094..5210
                     /locus_tag="GZ082_23955"
     CDS             5094..5210
                     /locus_tag="GZ082_23955"
                     /inference="COORDINATES: protein motif:HMM:NF025180.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="transposase family protein"
                     /protein_id="QJH52205.1"
                     /translation="MNINYRIILLLTICAVISGAEGWEDIEDFGKHIRDVLK"
                     /name="transposase family protein"
     gene            5310..5483
                     /locus_tag="GZ082_23960"
     CDS             5310..5483
                     /locus_tag="GZ082_23960"
                     /inference="COORDINATES: protein motif:HMM:NF033564.0"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="transposase"
                     /protein_id="QJH52206.1"
                     /translation="MRDCHSSDDKDVIAIDGKTLRHSYDKSRRRGAIHVISAFSTMHSL
                     VLGQIKTDEKIQ"
                     /name="transposase"
     gene            complement(6218..6970)
                     /locus_tag="GZ082_23965"
                     /pseudo=""
     CDS             complement(6218..6970)
                     /locus_tag="GZ082_23965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_414754.1"
                     /note="frameshifted; incomplete; partial on complete
                     genome; missing C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="amidohydrolase"
                     /name="amidohydrolase"
ORIGIN
        1 ccggcgtggc gtgctcggtg tgtccgggcg ggatgacttc gggcaacccg gtaaatccgc
       61 tgctgggggc gaaggtgctg cccggcgaga cggaccttgc gctgccccgc ccgctgccgt
      121 ttcattctct cccgcaccta acagcagcta ccggacgaaa gacgcctgca ccggtgggcg
      181 ttttcggccc cggctggaaa gcgccttctg atatccgctt acagatacgc gatgatgcac
      241 tggtactcaa cgacaacggc gggcggagca ttcactttga gccgctgctg ccgggggagg
      301 cggtgtacag ccgcagtgag tcaatgtggc tggtgcgtgg cggtaaggca gtgcagccgg
      361 acggccacac gctggcacgg ctgtgggcgt cgctgccgcc ggatatccgg ttaagcccgc
      421 atctttacct ggcgaccaac agcgcacagg ggccgtggtg gatactgggg tggtctgagg
      481 gggtgccggg tgctgaggac gtactgccag cgccgctgcc gccgtaccgg gtgcttaccg
      541 ggatggcgga ccgcttcgga cggacgctgg cgtaccggtg tgaggccgcc ggtgacctgg
      601 ccggggaaat caccggcgtg acggacggtg ccgggcggga gtttccgtct ggtactgacc
      661 accacaggca cagcgggcgg aagaggcccg taaaccgcca ccgcttcgtt atcttcccct
      721 gaacagtccc cgccctctct cagctccttc cttccccgac acactgcccg gtacggaata
      781 cggcgctgac agcggtatcc gtctttcggc ggtgtggctg atgcacgacc cggaataccc
      841 ggaaaattta cctgccgcgc cactggtgtg ctacgactgg acgccacgcg gtgagctggc
      901 ggcggtgtat gaccgcagcg gtacgcagat gcgccacttt acttacgatg ataaataccg
      961 gggccggatg gtggggcacc gttatgcagg caggccggag atgcgctacc gcttacgacg
     1021 atgcggggcg ggtggtggag caacttaacc ggcaggcctg agttaccgat accagttatg
     1081 agcaggaccg catcacgtca ccgacagcct gaaccggcgt gaggtgctgc atcagaaggc
     1141 ggggccgggc tgaagcgggt ggtgaaaaaa gaaactggcg gacggcagcg tcacgcacag
     1201 gggtatgacg cggcaggaag gctaacggcg cagacggagc gcggcgggac ggcggacaga
     1261 gtacggtctg aatgtggtgt ccggcgatat cacggacatc acacaccgga cgggcgggag
     1321 gacgaaattt tactataacg acgggaacca gctgacggcg gtggtgtccc cggacgggct
     1381 ggagagccgc cgggcatatg atgaaccggg caggctggta tcggagacat cgcgcagtgg
     1441 ggacgtcatc cggtatgctt atgataatcc gcacagtgaa ttaccggcca cgacaacaga
     1501 tgcgacgggc agcacccggc agatgacgtg gagccgctac gggcagttgc tggcgttcac
     1561 tgactgctcg ggctaccaga cccgctatga atacgaccgc ttcggccaga tgacggcggt
     1621 tcaccgcgag gaaggtatca gcctttaccg ccactatgac aaccgtggcc ggttaacctc
     1681 ggtgaaagac gcacagggcc gtgaaacgca gtatgagtac aacgccgcag gcgacctgac
     1741 tgccgttatc accccggacg gcaaccggag cgagacacag tacgatgcgt ggggaaaggc
     1801 ggtcagcacc acgcagggcg ggctgacgcg cagcatggaa tacgatgctg ccggacgtgt
     1861 catcagtctg actaacgaga acggcagcca cagcgacttc agctacgatg cgctggaccg
     1921 gttggtacag cagggcggct ttgacgggcg gacgcaacgt tatcattatg acctgaccgg
     1981 aaaaactcac gcagagtgaa gatgaggggc ttgtcaccct ctggtactac gatgaatcgg
     2041 accgtatcac tcaccgcacg gtgaacggcg aaccggcaga gcagtggcag tatgatgacc
     2101 acggctggct gacagacatc agccacctga gcgaaggcca ccgtgtcgct gtccactacg
     2161 gctacgacga taagggccgc ctgaccggcg aacggcagac ggtggagaac ccggagacgg
     2221 gggaactgct gtggcagcat gagacgaaac acgcctacaa cgaacagggg ctggcaaacc
     2281 gcgtcacgcc ggacagcctg ccgccggtgg agtggctgac ctacggcagc ggttacctgg
     2341 cgggcatgaa gctgggcggg acgccgctgg tcgagtatac gcgggacagg ctgcaccgtg
     2401 agacggtgcg cagcttcggc agcatggcag gcagtaatgc cgcatatgaa ctgaccagca
     2461 catacacccc caggccagtt acagagccag cacctgaaca gcctggtgta tgaccgtgac
     2521 tacgggtgga atgacaacgg cgacctggtg cgcatcagcg gtccgcgaca gacgcgggaa
     2581 tacggctaca gcgccacggg caggctggag agcgtgcgca ccctcgcacc ggacctggac
     2641 atccgcatcc cgtatgccac cgacccggcg ggaaaccgcc tgccggaccc ggagctgcac
     2701 ccggacagta ccctcacggc gtggccggat aaccgcatcg cagaggatgc gcactatgtt
     2761 taccactatg atgaatacgg cagactgacg gagaagacgg accttatccc ggcgggtgtt
     2821 atccggacgg acgacgagcg gacccaccac taccactacg acagccagca ccgtctggtg
     2881 ttccacacgc ggatacagca tggcgagcca ctggtcgaga gccgctacct ctacgacccg
     2941 ctgggacggc gaatggcgaa acgggtatgg cggcgggagc gtgacctgac ggggtggatg
     3001 tcgctgtcgc gtaaaccgga gatgacgtgg tacaggtggg acggcgaccg gctgacgacg
     3061 gtacagaccg acaccacgcg tatccagacg gtatatcagc cggggagctt cgcgccgctc
     3121 atccgcatcg aaacagacaa cggcgagcgg gagaaagcgc agcgccgcag cctggcggag
     3181 aagctgcagc aggaagggag cgaggacggg cacggcgtgg tatttccggc tgaactggtg
     3241 cggctgctgg acaggctgga ggaagaaatc cgggcagacc gcgtgagcag tgaaagccgg
     3301 gcgtggcttg cgcagtgcgg gctgacggtg gagcaactgg ccagacaggt ggagccggaa
     3361 tacacaccgg cgcgaaaagt tcatttttac cactgcgacc accggggcct gccgctggcg
     3421 ctcatcagcg aagacggcaa tacggcgtgg cgcggggagt atgatgaatg gggcaaccag
     3481 cttaatgaag agaacccgta ttacctgcac cagccatacc gtctgccggg gcagcagcat
     3541 gatgaggaat cagggctgta ctataaccgg aaccggtact atgacccgct acaggggagg
     3601 tatattacac aagaccccat tgggctggcg gggggatgga acctgtataa ttacccactg
     3661 aatccgataa taaggatgga tcctttgggt ttgtataatt tatatcaatt attatatgat
     3721 gtttggcatg atgattcata tggaacatca tcaattgata ttactggcag tggagatcta
     3781 atatcattag gtggtcatgc aggacttggc gttgcgtttg ctaaaaagaa aggtgaaatg
     3841 ttatctgata tttgtattta tgctacagca tgcggacatg caggaattgg tggtgggata
     3901 aatgcggcta tcacatattc tgagaccaag tctttaccta catcgggagt cagcaattca
     3961 gtaggtgtaa cggttggcgg cggagttggg gggcattttg cgtatactta tgtagtggat
     4021 gttgataatc cagaatcatc gacagaatct gttggtatcg gtgcaggtgt tgacgcttca
     4081 gttatgactc tggcttgtaa acgtggcaag aatgctgggt caattaacag gaggaaatat
     4141 gaaaaaatat atatttttag ttttattttt attgtgtggt tgttctccag tggacataga
     4201 gccagctaga caagaagtta atatctttcg tggtttatat cagacaggaa atacagtgat
     4261 atatataaaa tcacttcaag tgattttcag actgccacat ctgaaaaaaa tttatcgaca
     4321 taatgaacga agcaaaagaa aaagatcttg ggacttataa aaaatcaacc cttaaaactg
     4381 aaaaaatcac tcgcggatta ttttcaaacg atgaaattac attgatatat ttctcagata
     4441 ttcaaaaaga attgtccaag aggtttttgt gtttaatgtt gaagacaaaa aagtaaaatt
     4501 aaaaggttat aggtatgatt cgattattaa attttttgat gatgacttca attagtagaa
     4561 catgtatttt tcgataaaag caccgatgac tttttcatga agttctacag agcgcgagaa
     4621 acagatggtt ctgcgagtca gacgtttgat tcaggttctc aggggcgatt cagggaaaga
     4681 tcacagggaa agatcatcgt gtgccgtagg cacaaagatg caaacgggac gttttgcatg
     4741 taataagcat aagcttgtga agagatggtg gcaggcccac cgggatctgc tgtcggaagt
     4801 cggtcccaaa caaccccggc tgctgtggta aagagccatg gtagtgagcg caggggaacg
     4861 atcagacgag atctgatcct atgtgagtta gggaaagatc atcaaaagtt cactttttgt
     4921 actaaataat tcgcatttta tgtttaaaaa ttgagatatt cctcattacc tgaagctgtt
     4981 ttttattgct tatacatgat caaatactcc ttacatatta aggagaacaa aatggaactt
     5041 aaaaaattga tggaacatat ttctattatc ccgattacag acaagcctgg aaagtgaaca
     5101 taaattatcg gattattcta ctgttgacta tttgtgccgt tatttctggt gcagaaggct
     5161 gggaagatat agaggatttt gggaaacaca tccgcgatgt tttgaagtga tatggtgatt
     5221 ttgaaaaatg gtattcctgt tcacgatatc attgccagag ttgtatcctg tatcagtcct
     5281 gcaaaatttc acgagtgctt tataactgga tgcgtgactg ccattcttca gatgataaag
     5341 acgtcatcgc aattgatgga aaaacgctcc ggcactctta tgacaagagt cgtcgcaggg
     5401 gagcgattca tgtcattagt gcgttctcaa caatgcatag tctggtcctc ggacagatca
     5461 agacggatga gaaaatccaa tgagattaca gccattcctg aacttcttaa catgatggat
     5521 taaaggaaaa atcatcacaa ctgatgcgat gggctgccag aaagatattg cagaaaagat
     5581 acaaaaacag ggaggtgatt atttatttcg cggtaaaagg aaaccagggg cggctaaata
     5641 aagccttgag gaaaaatttc gctgaaagaa ttaaaataat cagagcatga cagttacgca
     5701 atgagtgaaa agagtcacgg cagagaagaa atccgtcttc atattgtttg cgatgtccct
     5761 gatgaactta ttgatttcac gtttgaatgg aaagggctga gaattatgcg tggcagtctc
     5821 ctttcggtcc ataatagcag aacaaaagaa gagccagaaa tgacggtcca gatattatat
     5881 cagttctgct gatttaaccg cagagaagtt cgccacagca atccgaaaca ctggcacgtg
     5941 agaataagct gcactggcgt ctggacgtgg taatgaatga agacgactgc aaaataagaa
     6001 aaggaaatgc agcagaatta ttttcaggga tacggcacat tgctattaat attttgacga
     6061 atgataaggt attcaaggca gggttaagac gtaagatgcg aaatgcagct atggacagaa
     6121 aactatctgg cgtcagtcct tgcggagagc gggcttttcg tagtcttacc ccgactctcc
     6181 ccagccttaa acacaacccc cactcaccgc aacctaactc atccgcatcc cgccatgccg
     6241 gaaacttatc gcgatattcc cttaacaccg ccatcgacag ctcggcatca agcgcgttgc
     6301 ctgatgcgcg gtcggcagta gcgataatct cgccttgtgg attaatcacc cggctgtcac
     6361 cgcgataatg gcagccgttg ccatcgctgc cgacgcgatt gcatcccgcc acatacgcct
     6421 gattctcaat cgcgcgggcc gtcagcaatg cctgccagtg cagagagcgc ggagcaggcc
     6481 agttggcgac tacagggcga ggtcataatc gttgagattg cgcgaaccac acaggaaacg
     6541 taagtcgtag cacaccagcg gccaaaatac gccagccgcg ccattccaca atcactcgcg
     6601 cattgcccgc tttataatgt agatgctcat ctgccatgcg gaaacagatg acgcttatca
     6661 taaaaatgta ccgtgccgcc cggctcaacc agcaaaagcg gttaaccgaa ccagactccg
     6721 tttgtaatgc aacactgcct gcaatcagcg cattgcactg gcgccttagc tgtcatccag
     6781 ttcactacgt catcttgtgc tagcgacgaa gctgccgctt ccatggcaaa gccgctggta
     6841 aacatctccg gtagaacgat cacatcgcgc ccggtaatac cttccagttg acgatcaaaa
     6901 tgagcaggtt ggcagggcca tccatccaca ccagtggttg ctgcaaaagc gtaatcttca
     6961 aaccaggcac ggtgtacaac tcctttatgc gaagggtttt ataactttaa
//
