LOCUS       NZ_CP130709             3932 bp    DNA     linear   CON 08-AUG-2023
DEFINITION  Escherichia coli strain DDG220 plasmid pDDG220-3, complete sequence.
ACCESSION   NZ_CP130709
VERSION     NZ_CP130709.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36696312
            Assembly: GCF_030553115.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3932)
  AUTHORS   Wittum,T.
  TITLE     E.coli carrying blaNDM-5 recovered from dried distillers grains from
            feed mills
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3932)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-JUL-2023) CVM/OAS, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 317x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/01/2023 20:02:13
            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)                     :: 4,962
            CDSs (total)                      :: 4,843
            Genes (coding)                    :: 4,598
            CDSs (with protein)               :: 4,598
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 245
            CDSs (without protein)            :: 245
            Pseudo Genes (ambiguous residues) :: 0 of 245
            Pseudo Genes (frameshifted)       :: 84 of 245
            Pseudo Genes (incomplete)         :: 160 of 245
            Pseudo Genes (internal stop)      :: 55 of 245
            Pseudo Genes (multiple problems)  :: 52 of 245
            Pseudo Genes (short protein)      :: 4 of 245
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP130709.1.
            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..3932
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DDG220"
                     /isolation_source="dried distillers grain"
                     /db_xref="taxon:562"
                     /plasmid="pDDG220-3"
                     /geo_loc_name="USA:MN"
                     /collection_date="2021-07-23"
                     /collected_by="The Ohio State University"
     gene            complement(771..965)
                     /locus_tag="Q5R37_RS24790"
                     /old_locus_tag="Q5R37_24790"
     CDS             complement(771..965)
                     /locus_tag="Q5R37_RS24790"
                     /old_locus_tag="Q5R37_24790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_001485273.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENLTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1249..1572
                     /gene="mobA"
                     /locus_tag="Q5R37_RS24795"
                     /old_locus_tag="Q5R37_24795"
     CDS             1249..1572
                     /gene="mobA"
                     /locus_tag="Q5R37_RS24795"
                     /old_locus_tag="Q5R37_24795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_052584083.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQVIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            complement(1961..2389)
                     /locus_tag="Q5R37_RS24800"
                     /old_locus_tag="Q5R37_24800"
     CDS             complement(1961..2389)
                     /locus_tag="Q5R37_RS24800"
                     /old_locus_tag="Q5R37_24800"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000222531.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_000222531.1"
                     /translation="MTYSVKNKWKAGGLSLGWTAVPTVLFFIQNEKKLTSVAFNTLLNL
                     IVHWWSLQEWPHPSMESLAIRMGVSVRTVQRAINDLEKANLLDKKPTSKSDRRYGGRNI
                     YDLTKLVDYLDTMGPSVAEQVKKPRHKKPVYTVRKTTA"
                     /name="helix-turn-helix domain-containing protein"
     gene            2547..2717
                     /locus_tag="Q5R37_RS24805"
                     /old_locus_tag="Q5R37_24805"
     CDS             2547..2717
                     /locus_tag="Q5R37_RS24805"
                     /old_locus_tag="Q5R37_24805"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001531327.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001531327.1"
                     /translation="MKTEQRHDLVKDIEVFGVSLSLLISRANEKSVTMPSGLSREQRRA
                     WAAEQARKIHN"
                     /name="hypothetical protein"
     gene            2681..3109
                     /locus_tag="Q5R37_RS24810"
                     /old_locus_tag="Q5R37_24810"
     CDS             2681..3109
                     /locus_tag="Q5R37_RS24810"
                     /old_locus_tag="Q5R37_24810"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000534558.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000534558.1"
                     /translation="MGSGAGAQNPQLNIVSFSETFNLYYTSRYSAKTLDKIDDFIEHFE
                     KYNLFGDPLKGYPAWTGKVSPSWKVPDHYENKEAIEKYARANKLWHAHLGDPVFKDTFH
                     GKYKVSDWVIHFQRLTPNHIKLLELGYHDPMKLPQNFE"
                     /name="hypothetical protein"
     Typing          1001..1240
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          complement(211..736)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.03"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          complement(3385..3910)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.03"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          1250..1569
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.131"
                     /coverage="100.0"
                     /evalue="3.81e-61"
ORIGIN
        1 aacgaaaaaa ccaccctggc aggtggtttt tcgaaggtta gttaatcctg gcagattctc
       61 taaccgtggt aacagtcttg tgcgagacat gtcaccaaat actgtccttt cagtgtagcc
      121 tcagttaggc cgccacttca agaactctcg ttacatctct cgcacatcct gcttaccagt
      181 ggccgttgcc agtggcgtta agtcgtgtct taccgggttg gactcaagac gatagttacc
      241 ggataaggcg cagcggtcgg gctgaacggg gggttcgtgc acacagccca gcttggagcg
      301 aacgacctac accgaaccga gataccaaca gcgtgagcta tgagaaagcg ccacgcttcc
      361 cgaagggaga aaggcggaca ggtatccggt aagcggcagg gtcggaacag gagagcgcac
      421 gagggagctt ccagggggaa acgcctggta tctttatagt cctgtcgggt ttcgccacct
      481 ctgacttgag cgtcggtttt tgtgatgctc gtcagggggg cggagcctat ggaaaaacgc
      541 caacggcgcg gcctttgtcc ctggcttcgg ctttttgctc acatgttctt tccggcgtta
      601 tcccctgatt ctgtggataa ccgtattacc gcctttgagt gagctgacac cgctcgccgc
      661 agtcgaacga ccgagcgtag cgagtcagtg agcgaggaag cggaagagcg ccttatgtga
      721 cattttctcc ttacgctcct ctatgccgtt ctgcatcctg tccggatgcg ttatatcccg
      781 gtaagatttt ccgcttcaaa gcgtgtctgt atgctgttct gaagttcttc cgcgagttcg
      841 tgcagcttct cacacatggc ggcctgttcg tcagcatcaa gtgcgtccag tttttcgagc
      901 agcgtcaggc tctggctttt tatgaatcct gccatgttga gtacggtttg ctgctgcttg
      961 ttcatctttc tgttttctcc gttctttctg tcatctgcgt tgtgtgatta tatcgcgtac
     1021 cacttttcga ctgttttacc gtcggtattc tgctgtctga ctctttgacg ggcatttctg
     1081 tcagacaaca ctgtcactgc caaaaaactg ccgtgccttt gtcggtaatt cgaacttgct
     1141 gacaggacag gatgtgtaat tgttataccg cgcatacatg cacgctatta caattaccct
     1201 ggtcagggct ttgccccgac acccatgtca gatacggagc catgttttat gacaaaacga
     1261 agtggaagta atacgcgcag gcgggctatc agtcgccctg ttcgtctgac ggcagaagaa
     1321 gaccaggtaa tcagaaaaag ggctgctgaa tgcggcaaga ccgtttccgg ttttttacgg
     1381 gcggcagctc tcggtaagaa agttaactca ctgactgatg atcgggtact gaaagaagtt
     1441 atgagactgg gggcgttaca gaaaaaactc tttatcgacg gcaagcgtgt cggggacagg
     1501 gagtatgcgg aggtgctgat cgctattacg gagtatcacc gtgccctgtt atccaggctt
     1561 atggcagatt agcttcccgg agagaaaact gtcgaaaact gacggtatga acaccgtaag
     1621 ctcccaaagt gatcaccatt cgctttcatg catagctatg cagcgagctg aaaacgatcc
     1681 tgacgcatcc ttcctgtttt tccggggtaa aacatctctt tttgcggtgt ctgcgtcaga
     1741 atcgcgttca gcgcgtttca gtggtgcgta caattaaggg attatggtaa atatatgagc
     1801 tatgcgataa ctttaactgt gaagcgatga acccattaca ggcaaagcca attactcctg
     1861 acagtggttt agccagaagc agggctacca agaccaatgc aataagtaat atatcgtttt
     1921 gctatcgtgc atcgctcgcg ctcagttcca ttgtgctttt ttaagctgtc gtttttctta
     1981 cggtatatac cggtttttta tggcgtggtt tcttaacttg ttcagctact gatggaccca
     2041 ttgtatctag gtagtcaact agctttgtta gatcataaat attgcgacca ccatatcggc
     2101 gatcactctt cgatgttggt ttcttgtcca agagattagc tttttcaaga tcattgatag
     2161 ctctctgaac agtccgtaca gaaaccccca tacgtatggc tagactttcc attgacggat
     2221 gcggccactc ttgcaaactc caccagtgaa cgatcaggtt aagtagtgtg ttaaaggcca
     2281 ctgaagttag ctttttctcg ttttgtataa aaaacaatac ggtaggcact gctgtccagc
     2341 caagagacaa accgccagct ttccatttat tcttaacgga gtaagtcatt gattttccta
     2401 agccccaaaa tatttaaagt atatattata tggtatattc atatgaatag ggtgacacta
     2461 gcgccattat tgtgcaacca aaaaagacta ctctgaaaac gaggaaaaga ttttttcctg
     2521 cctgaattag atacggagtt agcgatatga aaaccgaaca acgtcatgat cttgttaaag
     2581 atattgaggt ttttggcgta tccttgtctc tgttgatttc cagagcgaat gagaagtctg
     2641 ttacaatgcc atctggtcta agtcgggagc agagaagagc atgggcagcg gagcaggcgc
     2701 gcaaaatcca caattgaata ttgtctcatt ctctgagacc ttcaaccttt attacacatc
     2761 cagatattct gcaaaaacac tcgataaaat cgatgatttc attgagcatt ttgaaaaata
     2821 caatctcttt ggcgatcctt taaaaggata tccagcttgg actggcaaag tatcgccatc
     2881 gtggaaagtg cctgatcatt acgaaaacaa agaagctatt gagaagtatg ctagagctaa
     2941 caaattatgg catgctcatt taggcgatcc ggtttttaaa gatacgtttc atgggaaata
     3001 caaggtttct gactgggtta ttcatttcca gcggctgaca ccgaaccata taaagctttt
     3061 agagcttgga taccatgacc caatgaagct acctcaaaac tttgaatgat cgagcggcag
     3121 gctaaatgaa atcttgagat tcattcagtc tcgtcgtaat ctcactattg taaaaacgaa
     3181 aaaaccaccc tggcaggtgg tttttcgaag gttagttaat cctggcagat tctctaaccg
     3241 tggtaacagt cttgtgcgag acatgtcacc aaatactgtc ctttcagtgt agcctcagtt
     3301 aggccgccac ttcaagaact ctcgttacat ctctcgcaca tcctgcttac cagtggccgt
     3361 tgccagtggc gttaagtcgt gtcttaccgg gttggactca agacgatagt taccggataa
     3421 ggcgcagcgg tcgggctgaa cggggggttc gtgcacacag cccagcttgg agcgaacgac
     3481 ctacaccgaa ccgagatacc aacagcgtga gctatgagaa agcgccacgc ttcccgaagg
     3541 gagaaaggcg gacaggtatc cggtaagcgg cagggtcgga acaggagagc gcacgaggga
     3601 gcttccaggg ggaaacgcct ggtatcttta tagtcctgtc gggtttcgcc acctctgact
     3661 tgagcgtcgg tttttgtgat gctcgtcagg ggggcggagc ctatggaaaa acgccaacgg
     3721 cgcggccttt gtccctggct tcggcttttt gctcacatgt tctttccggc gttatcccct
     3781 gattctgtgg ataaccgtat taccgccttt gagtgagctg acaccgctcg ccgcagtcga
     3841 acgaccgagc gtagcgagtc agtgagcgag gaagcggaag agcgccttat gtgacatttt
     3901 ctccttacgc tcctctatgc cgtcgcattc tg
//
