LOCUS       NZ_CP117233             3173 bp    DNA     circular CON 23-MAR-2024
DEFINITION  Escherichia coli strain ATCC 25922 plasmid pATCC25922_2, complete
            sequence.
ACCESSION   NZ_CP117233
VERSION     NZ_CP117233.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32977649
            Assembly: GCF_028596225.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3173)
  AUTHORS   Johnson,J.D., Blankenship,H. and Soehnlen,M.
  TITLE     Long read genome assemblers struggle with small plasmids
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3173)
  AUTHORS   Johnson,J.D.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-JAN-2023) Bureau of Laboratories, Michigan Department
            of Health and Human Services, 3350 N Martin Luther King Blvd.,
            Lansing, MI 48906, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2022
            Assembly Method                   :: Trycycler v. v0.5.3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 140x
            Sequencing Technology             :: Oxford Nanopore, Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_028596225.1-RS_2024_03_23
            Annotation Date                   :: 03/23/2024 03:31:35
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,067
            CDSs (total)                      :: 4,951
            Genes (coding)                    :: 4,722
            CDSs (with protein)               :: 4,722
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 229
            CDSs (without protein)            :: 229
            Pseudo Genes (ambiguous residues) :: 0 of 229
            Pseudo Genes (frameshifted)       :: 99 of 229
            Pseudo Genes (incomplete)         :: 139 of 229
            Pseudo Genes (internal stop)      :: 51 of 229
            Pseudo Genes (multiple problems)  :: 52 of 229
            Pseudo Genes (short protein)      :: 4 of 229
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP117233.1.
            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..3173
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ATCC 25922"
                     /db_xref="taxon:562"
                     /plasmid="pATCC25922_2"
                     /geo_loc_name="USA"
                     /collection_date="2022"
     gene            join(3108..3173,1..66)
                     /locus_tag="PQQ28_RS00345"
                     /old_locus_tag="PQQ28_00345"
     CDS             join(3108..3173,1..66)
                     /locus_tag="PQQ28_RS00345"
                     /old_locus_tag="PQQ28_00345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005019281.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023151671.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLATATGKQDVREM"
                     /name="hypothetical protein"
     gene            complement(282..710)
                     /locus_tag="PQQ28_RS00350"
                     /old_locus_tag="PQQ28_00350"
     CDS             complement(282..710)
                     /locus_tag="PQQ28_RS00350"
                     /old_locus_tag="PQQ28_00350"
                     /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"
     gene            complement(674..844)
                     /locus_tag="PQQ28_RS00355"
                     /old_locus_tag="PQQ28_00355"
     CDS             complement(674..844)
                     /locus_tag="PQQ28_RS00355"
                     /old_locus_tag="PQQ28_00355"
                     /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            1002..1430
                     /locus_tag="PQQ28_RS00360"
                     /old_locus_tag="PQQ28_00360"
     CDS             1002..1430
                     /locus_tag="PQQ28_RS00360"
                     /old_locus_tag="PQQ28_00360"
                     /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            complement(1819..2142)
                     /gene="mobA"
                     /locus_tag="PQQ28_RS00365"
                     /old_locus_tag="PQQ28_00365"
     CDS             complement(1819..2142)
                     /gene="mobA"
                     /locus_tag="PQQ28_RS00365"
                     /old_locus_tag="PQQ28_00365"
                     /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_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            2426..2620
                     /locus_tag="PQQ28_RS00370"
                     /old_locus_tag="PQQ28_00370"
     CDS             2426..2620
                     /locus_tag="PQQ28_RS00370"
                     /old_locus_tag="PQQ28_00370"
                     /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_001041622.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALNADEQAAMCEKLHELA
                     EELQNSIQTRFEAENLTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(2152..2388)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.49e-121"
     Typing          2656..3173
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.019"
                     /coverage="94.0"
                     /evalue="0.0"
     Typing          complement(1823..2142)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.23e-62"
ORIGIN
        1 ccggtaagac acgacttaac gccactggca acggccactg gtaagcagga tgtgcgagag
       61 atgtaacgag agttcttgaa gtggcggcct aactgaggct acactgaaag gacagtattt
      121 ggtgacatgt ctcgcacaag actgttacca cggttagaga atctgccagg attaactaac
      181 cttcgaaaaa ccacctgcca gggtggtttt ttcgttttta caatagtgag attacgacga
      241 gactgaatga atctcaagat ttcatttagc ctgccgctcg atcattcaaa gttttgaggt
      301 agcttcattg ggtcatggta tccaagctct aaaagcttta tatggttcgg tgtcagccgc
      361 tggaaatgaa taacccagtc agaaaccttg tatttcccat gaaacgtatc tttaaaaacc
      421 ggatcgccta aatgagcatg ccataatttg ttagctctag catacttctc aatagcttct
      481 ttgttttcgt aatgatcagg cactttccac gatggcgata ctttgccagt ccaagctgga
      541 tatcctttta aaggatcgcc aaagagattg tatttttcaa aatgctcaat gaaatcatcg
      601 attttatcga gtgtttttgc agaatatctg gatgtgtaat aaaggttgaa ggtctcagag
      661 aatgagacaa tattcaattg tggattttgc gcgcctgctc cgctgcccat gctcttctct
      721 gctcccgact tagaccagat ggcattgtaa cagacttctc attcgctctg gaaatcaaca
      781 gagacaagga tacgccaaaa acctcaatat ctttaacaag atcatgacgt tgttcggttt
      841 tcatatcgct aactccgtat ctaattcagg caggaaaaaa tcttttcctc gttttcagag
      901 tagtcttttt tggttgcaca ataatggcgc cagtgtcacc ctattcatat gaatatacca
      961 tataatatat actttaaata ttttggggct taggaaaatc aatgacttac tccgttaaga
     1021 ataaatggaa agctggcggt ttgtctcttg gctggacagc agtgcctacc gtattgtttt
     1081 ttatacaaaa cgagaaaaag ctaacttcag tggcctttaa cacactactt aacctgatcg
     1141 ttcactggtg gagtttgcaa gagtggccgc atccgtcaat ggaaagtcta gccatacgta
     1201 tgggggtttc tgtacggact gttcagagag ctatcaatga tcttgaaaaa gctaatctct
     1261 tggacaagaa accaacatcg aagagtgatc gccgatatgg tggtcgcaat atttatgatc
     1321 taacaaagct agttgactac ctagatacaa tgggtccatc agtagctgaa caagttaaga
     1381 aaccacgcca taaaaaaccg gtatataccg taagaaaaac gacagcttaa aaaagcacaa
     1441 tggaactgag cgcgagcgat gcacgatagc aaaacgatat attacttatt gcattggtct
     1501 tggtagccct gcttctggct aaaccactgt caggagtaat tggctttgcc tgtaatgggt
     1561 tcatcgcttc acagttaaag ttatcgcata gctcatatat ttaccataat cccttaattg
     1621 tacgcaccac tgaaacgcgc tgaacgcgat tctgacgcag acaccgcaaa aagagatgtt
     1681 ttaccccgga aaaacaggaa ggatgcgtca ggatcgtttt cagctcgctg catagctatg
     1741 catgaaagcg aatggtgatc actttgggag cttacggtgt tcataccgtc agttttcgac
     1801 agttttctct ccgggaagct aatctgccat aagcctggat aacagggcac ggtgatactc
     1861 cgtaatagcg atcagcacct ccgcatactc cctgtccccg acacgcttgc cgtcgataaa
     1921 gagttttttc tgtaacgccc ccagtctcat aacttctttc agtacccgat catcagtcag
     1981 tgagttaact ttcttaccga gagctgccgc ccgtaaaaaa ccggaaacgg tcttgccgca
     2041 ttcagcagcc ctttttctga tttcctggtc ttcttctgcc gtcagacgaa cagggcgact
     2101 gatagcccgc ctgcgcgtat tacttccact tcgttttgtc ataaaacatg gctccgtatc
     2161 tgacatgggt gtcggggcaa agccctgacc agggcaattg taatagcgtg catgtatgcg
     2221 cggtataaca attgcacatc ctgtcctgtc agcaagctcg aattaccgac aaaggcacgg
     2281 cagttttttg gcagtgacag tgttgtctga cagaaatgcc cgtcaaaaag ccaagcggca
     2341 gaatagcggc agcaaaacag tcgaaaagtg gtacgcgata taatcacaca acgcagatga
     2401 cagacagaac ggagaaaacg aaaagatgaa taagcagcag caagccgtac tcaacatggc
     2461 gggattcata aaaagtcaga gcctgacgct gctcgaaaaa ctggacgcac tcaatgccga
     2521 cgaacaggcc gccatgtgtg agaaactgca cgaactcgca gaagaactcc agaacagcat
     2581 acagacacgc tttgaagcgg aaaatcttac cgggatataa cgcatccgga caggatgcag
     2641 aacggcatag aggagcgtaa ggagaaaatg tcacataagg cgctcttccg cttcctcgct
     2701 cactgactcg ctacgctcgg tcgttcgact gcggcgagcg gtgtcagctc actcaaaggc
     2761 ggtaatacgg ttatccacag aatcggggga taaaaccgga aagaacatgt gagcaaaaga
     2821 caaagaccca gaagaagggc gcgcgggagg cgtttttcca taggctccgc ccccctgacg
     2881 agcatcacaa aaatcgacgc tcaagtcaga ggtggcgaaa cccgacagga ctataaagat
     2941 accaggcgtt tccccctgga agctccctcg tgcgctctcc tgttccgacc ctgccgctta
     3001 ccggatacct gtccgccttt ctcccttcgg gaagcgtggc gctttctcat agctcacgct
     3061 gttggtatct cggttcggtg taggtcgttc gctccaagct gggctgtgtg cacgaacccc
     3121 ccgttcagcc cgaccgctgc gccttatccg gtaactatcg tcttgagtcc aac
//
