LOCUS       NZ_CP104684             4075 bp    DNA     circular CON 09-OCT-2023
DEFINITION  Escherichia coli strain 2022CK-00450 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP104684
VERSION     NZ_CP104684.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30655617
            Assembly: GCF_025398755.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4075)
  AUTHORS   Hergert,J., Casey,R., Wagner,J., Young,E.L. and Oakeson,K.F.
  TITLE     2022CK-00450
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4075)
  AUTHORS   Hergert,J., Casey,R., Wagner,J., Young,E.L. and Oakeson,K.F.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-SEP-2022) Utah Public Health Laboratory, Utah Public
            Health Laboratory Infectious Disease submission group, 4431 S 2700
            W, Salt Lake City, UT 84129, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 83.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/09/2023 03:52:08
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,192
            CDSs (total)                      :: 5,075
            Genes (coding)                    :: 4,823
            CDSs (with protein)               :: 4,823
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 252
            CDSs (without protein)            :: 252
            Pseudo Genes (ambiguous residues) :: 0 of 252
            Pseudo Genes (frameshifted)       :: 58 of 252
            Pseudo Genes (incomplete)         :: 183 of 252
            Pseudo Genes (internal stop)      :: 42 of 252
            Pseudo Genes (multiple problems)  :: 34 of 252
            Pseudo Genes (short protein)      :: 4 of 252
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP104684.1.
            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..4075
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="2022CK-00450"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed3"
                     /geo_loc_name="USA"
                     /collection_date="2022-07-20"
     gene            complement(901..2019)
                     /gene="wzz(fepE)"
                     /locus_tag="N5922_RS25735"
                     /old_locus_tag="N5922_25725"
     CDS             complement(901..2019)
                     /gene="wzz(fepE)"
                     /locus_tag="N5922_RS25735"
                     /old_locus_tag="N5922_25725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016243311.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WP_024191316.1"
                     /translation="MFSMKISKISDEHFSNYNMLPNGNEEIDLFDLIRVLWAAKIKIVG
                     VILFFACIGFLVSFVLPQKWTSSAVVTPAESVQWSELNKELSKLHVLGVDFDINRDSAF
                     ALFIKKFQSVNSLNEYMRSSPYVMEIIKKKNISALELHRAIVGLSENMKSVDDNASKKN
                     DKSSLYVSWTLSFTAPTSKEAHDVLSGYINYVSSLVVRDLMEDIRNELEVKTNVEKEIL
                     ALDEIKIRNQLNADIRRLNYSLEVANAAGIKKPVYSNGQIMKDDPDFPVALGSDGIATK
                     LNIKKSIKDVSELSGELRNRQYVVNQLVVAKVGDVDFMPFQYQLSPTLPVRKDGPSNAI
                     IVILSSVIGGMLACGYILLRHAMEARKMSVIE"
                     /name="wzz(fepE)"
     gene            complement(2829..3230)
                     /locus_tag="N5922_RS25740"
                     /old_locus_tag="N5922_25730"
     CDS             complement(2829..3230)
                     /locus_tag="N5922_RS25740"
                     /old_locus_tag="N5922_25730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /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_000135006.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVTRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3230..3421)
                     /locus_tag="N5922_RS25745"
                     /old_locus_tag="N5922_25735"
     CDS             complement(3230..3421)
                     /locus_tag="N5922_RS25745"
                     /old_locus_tag="N5922_25735"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /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_000166329.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCETLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(3890..4039)
                     /locus_tag="N5922_RS25750"
                     /old_locus_tag="N5922_25740"
     CDS             complement(3890..4039)
                     /locus_tag="N5922_RS25750"
                     /old_locus_tag="N5922_25740"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001515742.1"
                     /translation="MPSEYDEQPDATDALFPGEYDLFDLMAHVTEENLHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     Typing          complement(2..172)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="81.356"
                     /coverage="98.0"
                     /evalue="1.29e-29"
     Typing          153..681
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.545"
                     /coverage="89.0"
                     /evalue="1.2e-144"
ORIGIN
        1 ttcggggcgc agccctgaac cagtcacgta gcgctagcgg agtgcatact ggctaaatat
       61 tttaaaccga agtggtgatt tgccaaagtg cttcatgtgg caggagtgaa atgaggctta
      121 ccggcgtcag gagaagatgc tggttcaggt gatattccgc ttcctcgctc actgactcgc
      181 tgcgctcggt cgttcggctg cggcgagcgg tgcaggctta cgaatggggc ggaaatttat
      241 ttcctggtgg atgccaggaa gaaacttaac agggatacga taaggccgcg gcaaagccgt
      301 ttttccatag gctccgcccc cctgacaagc atcacgaaat ctgacgctca aatcagtggt
      361 ggcgaaaccc gacaggacta taaagatacc aggcgtttcc ccctggtggc tccctcttgc
      421 gctctcctgt tcccgtcctg cggcatccgt gtagtggtgg aagctttacc taaatcacca
      481 cgccccgttc cgtttagaca gttcgctcca agctgggctg tatgcaagaa ccccccgttc
      541 agcccgaccg ctgcgcctta tccggtaact atcgtcttga gtccaacccg gtaagacacg
      601 acttaacgcc attggcagcg gccactggta aacaggatgt gcgagagatg tattgagagt
      661 tcttgaagtg gcagccttac tgaggctaca ctagaaggac agatttggtg acatgtctcg
      721 cacaagactg ttaccacggt tcagaagttc cccaacttac tgaaccttcg aaaaaccacc
      781 tccccaggtg gttttttcgt tttctagagt agaagactac ggctgtaagg gaatgatctc
      841 aagaagatcc tttgaacttt ttataaaagt tgcttataaa atgatgcatc agcacaactt
      901 ttactcaatc acactcatct ttctggcctc catggcatga cgtaaaagta tatagccaca
      961 tgcaagcatc cctccaatga cagaagaaag aattacaatt atggcattac ttggcccatc
     1021 ctttctgacc ggtaacgttg ggctcaattg atactgaaac ggcataaaat caacatcccc
     1081 cactttcgcc acaaccaatt gattcacaac atattgacga tttcgcaact ccccactcaa
     1141 ttccgaaaca tccttgattg attttttgat gttcaattta gttgctatac catcagaacc
     1201 gagagccaca ggaaaatctg gatcatcctt cataatctga ccattgctgt atacaggttt
     1261 ttttattcca gccgcattag caacctccag tgaataattg aggcgtcgaa tatctgcatt
     1321 cagctggttt ctaattttta tctcatccag tgcaagaatt tctttttcaa cattagtttt
     1381 aacttctagt tcatttctta tatcttccat caaatccctt acaacaaggg aagaaacata
     1441 attaatatac ccagacaaca catcgtgagc ttctttactt gttggagcag taaaactcag
     1501 agtccatgat acatacaatg atgacttgtc gtttttctta ctggcattat catcaaccga
     1561 cttcatattt tcactcaacc caacaattgc acgatgcagt tcgagagcgc taatgttctt
     1621 ctttttaatt atctccataa cataaggaga tgatctcata tactcattca acgaattaac
     1681 ggactgaaat ttcttaataa acagagcaaa tgcgctatca cgattgatat caaaatccac
     1741 tcccagaaca tgaagcttgg aaagctcctt atttaattca ctccattgaa cagactcagc
     1801 aggagtaacc acagcagaac tagtccattt ttgtggcaaa acaaaagaaa caagaaagcc
     1861 aatacaagca aaaaatagaa tcaccccaac aatttttatt tttgctgccc ataaaactct
     1921 aatcaagtca aaaaggtcaa tttcttcatt accattcggc aacatgttgt aattagaaaa
     1981 atgttcgtca gatatctttg agattttcat tgaaaaaata caatatatta acatatggtt
     2041 tttttattct atcatatgtt aggaaaaatc ctaaaaacca ttcagcagac atttaacata
     2101 acattttaat tgtacgcacc actaaaacgg cctcagggcg tttctgacgg gaaaccggta
     2161 aaacaggcaa caaaccaccc gaaaacccgc cagaaacgcg caggctctgt ttttacggca
     2221 tgcatgagta tgcacgcaag tgcatagcgc gaaaattcac gccattcagc cagggtaagt
     2281 cctgtttccg gcgttcttcc tatccgaaaa cggtgaacgg ggacgcaatt tattgcgtgg
     2341 ccgtgaagcg ttgccggcgc agccggaaaa ccggttttca gcacgatcag gaatcgggtt
     2401 cgtcgacggc cggcaatcac gttatggcaa gtcgccggac gactcaccag acaattcacc
     2461 ggcgattcga ctcgtgactt gactctagag tcgtaaaggt caaaaaaaca ccaaaatgac
     2521 gattcaactc tagagtcaag tcatcataag ttactgatag tcttaagtga gtcgtcgatg
     2581 actctatgac gagtcgtcag caagtcgtac acgaatcgcc gacgacttgg attcacctta
     2641 cagaaagtaa tactgcgtaa tttaataacc cacaactaac tgatattaat gagttatctt
     2701 caaaatttta attttgcgta gggtgtgggt atttttagtg gtgaggagcg ttcagagatc
     2761 tgacgatttt tgggaaggtt caggaactcc ccgggatggc cggagaggaa aactgaagca
     2821 tgacggggtc aggatttttt ccagaatttc caccatggcg ccggggattc agttaatttt
     2881 gcctggtgat tttcaagaag gagcatagcc tgtttcaggc tgtcaatgtg cgaatccttg
     2941 gacaaaagta aggtgttcag gtgttcaatc tcctgtttca gatgacgagt cacctgttca
     3001 ctctggtcag cagaggctgt atcacgctgt tcagagacct gtccagaatg gtgttcaccc
     3061 ttcggttgtt caaagggacc aaagacacgt aaaagctctg aagtatctac catttttgca
     3121 ttgcgttcac cgctacaggt ggacaggtca cctgctttaa ttaacctgtg cagtgttgtt
     3181 ctactcttac ccgtcagtcg ggcagcctca ctaatagata ctctggccat cagttaccat
     3241 cctgtaatgc atccaatctc gaggacagtg tacggaaaag atgctccgca tcatcgtgga
     3301 gtgtctcaca aaggtccgcc tcaacatcga gatcaagctc gttaagcttc tccagcagga
     3361 gcagagactg attctggatg aatttagcca tgttcagcgc tgttttctgt tgtttcgtca
     3421 taagggccct cagagcatca gtgctcagta taaaccggta agggggtcgg atgtacgaat
     3481 ggttcagaga acggatctga ggttatcctg tagttatttt gtagtttatc tgtagtcatc
     3541 gcactaaaac gcaggattaa atcatcaact tttgtagtct tcctgtagtc tggaaaaata
     3601 atccgttcat gcaagcatga acgaagcagt taaagacgct ttttcgtcgc cgatgatcct
     3661 taacctgcgc agatcaccca gccagaatga taattttttg ccccttaaat ggtcatacac
     3721 ctaacgcagc cgcgattttt atcgcaactg catgaattaa atgaaaaaaa tggagttatt
     3781 tcgtgtatta gcgtaatacg caacgtatta caatcatctg taacaacatg aaaataaaca
     3841 aataacatgt aataccagcg tattacatgt acgctggcca gcgaaaaagc tataacgctt
     3901 cccggccgac aggcgggcca gaatccaccg gggcgtgcag gttctcttca gtaacatgag
     3961 ccattaagtc aaaaaggtca tattcgccgg gaaacagagc atcagtcgca tccggttgtt
     4021 catcatactc agatggcatg gtgtgatatc cagtagctga ggggtgttag cgggt
//
