LOCUS       NZ_CP148107             3173 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain Nissle plasmid pEcFELIX464.3, complete
            sequence.
ACCESSION   NZ_CP148107
VERSION     NZ_CP148107.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40298380
            Assembly: GCF_037744325.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3173)
  AUTHORS   Wan,K.H., Park,S., Neff,M., Lawrence,Q., Egbert,R., Booth,B.W. and
            Celniker,S.E.
  TITLE     Complete Genome Sequence of the Escherichia coli FELIX_MS464
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3173)
  AUTHORS   Wan,K.H., Park,S., Neff,M., Lawrence,Q., Egbert,R., Booth,B.W. and
            Celniker,S.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-MAR-2024) Life Sciences Division, Lawrence Berkeley
            National Lab, 717 Potter Street, Berkeley, CA 94720, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.9b
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 197.97x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_037744325.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 20:33:26
            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)                     :: 4,862
            CDSs (total)                      :: 4,748
            Genes (coding)                    :: 4,528
            CDSs (with protein)               :: 4,528
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 220
            CDSs (without protein)            :: 220
            Pseudo Genes (ambiguous residues) :: 0 of 220
            Pseudo Genes (frameshifted)       :: 93 of 220
            Pseudo Genes (incomplete)         :: 139 of 220
            Pseudo Genes (internal stop)      :: 51 of 220
            Pseudo Genes (multiple problems)  :: 54 of 220
            Pseudo Genes (short protein)      :: 4 of 220
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP148107.1.
            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="Nissle"
                     /db_xref="taxon:562"
                     /plasmid="pEcFELIX464.3"
     gene            join(2950..3173,1..100)
                     /gene="mobA"
                     /locus_tag="WHM01_RS24285"
     CDS             join(2950..3173,1..100)
                     /gene="mobA"
                     /locus_tag="WHM01_RS24285"
                     /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            complement(489..917)
                     /locus_tag="WHM01_RS24290"
     CDS             complement(489..917)
                     /locus_tag="WHM01_RS24290"
                     /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            1075..1245
                     /locus_tag="WHM01_RS24295"
     CDS             1075..1245
                     /locus_tag="WHM01_RS24295"
                     /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            1209..1637
                     /locus_tag="WHM01_RS24300"
     CDS             1209..1637
                     /locus_tag="WHM01_RS24300"
                     /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(1853..1984)
                     /locus_tag="WHM01_RS24305"
     CDS             complement(1853..1984)
                     /locus_tag="WHM01_RS24305"
                     /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(2472..2666)
                     /locus_tag="WHM01_RS24310"
     CDS             complement(2472..2666)
                     /locus_tag="WHM01_RS24310"
                     /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          2705..2941
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.49e-121"
     Typing          complement(1913..2437)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.085"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          2951..3171
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="5.8e-40"
ORIGIN
        1 tatcgacggc aagcgtgtcg gggacaggga gtatgcggag gtgctgatcg ctattacgga
       61 gtatcaccgt gccctgttat ccaggcttat ggcagattag cttcccggag agaaaactgt
      121 cgaaaactga cggtatgaac accgtaagct cccaaagtga tcaccattcg ctttcatgca
      181 tagctatgca gcgagctgaa aacgatcctg acgcatcctt cctgtttttc cggggtaaaa
      241 catctctttt tgcggtgtct gcgtcagaat cgcgttcagc gcgtttcagt ggtgcgtaca
      301 attaagggat tatggtaaat atatgagcta tgcgataact ttaactgtga agcgatgaac
      361 ccattacagg caaagccaat tactcctgac agtggtttag ccagaagcag ggctaccaag
      421 accaatgcaa taagtaatat atcgttttgc tatcgtgcat cgctcgcgct cagttccatt
      481 gtgctttttt aagctgtcgt ttttcttacg gtatataccg gttttttatg gcgtggtttc
      541 ttaacttgtt cagctactga tggacccatt gtatctaggt agtcaactag ctttgttaga
      601 tcataaatat tgcgaccacc atatcggcga tcactcttcg atgttggttt cttgtccaag
      661 agattagctt tttcaagatc attgatagct ctctgaacag tccgtacaga aacccccata
      721 cgtatggcta gactttccat tgacggatgc ggccactctt gcaaactcca ccagtgaacg
      781 atcaggttaa gtagtgtgtt aaaggccact gaagttagct ttttctcgtt ttgtataaaa
      841 aacaatacgg taggcactgc tgtccagcca agagacaaac cgccagcttt ccatttattc
      901 ttaacggagt aagtcattga ttttcctaag ccccaaaata tttaaagtat atattatatg
      961 gtatattcat atgaataggg tgacactggc gccattattg tgcaaccaaa aaagactact
     1021 ctgaaaacga ggaaaagatt ttttcctgcc tgaattagat acggagttag cgatatgaaa
     1081 accgaacaac gtcatgatct tgttaaagat attgaggttt ttggcgtatc cttgtctctg
     1141 ttgatttcca gagcgaatga gaagtctgtt acaatgccat ctggtctaag tcgggagcag
     1201 agaagagcat gggcagcgga gcaggcgcgc aaaatccaca attgaatatt gtctcattct
     1261 ctgagacctt caacctttat tacacatcca gatattctgc aaaaacactc gataaaatcg
     1321 atgatttcat tgagcatttt gaaaaataca atctctttgg cgatccttta aaaggatatc
     1381 cagcttggac tggcaaagta tcgccatcgt ggaaagtgcc tgatcattac gaaaacaaag
     1441 aagctattga gaagtatgct agagctaaca aattatggca tgctcattta ggcgatccgg
     1501 tttttaaaga tacgtttcat gggaaataca aggtttctga ctgggttatt catttccagc
     1561 ggctgacacc gaaccatata aagcttttag agcttggata ccatgaccca atgaagctac
     1621 ctcaaaactt tgaatgatcg agcggcaggc taaatgaaat cttgagattc attcagtctc
     1681 gtcgtaatct cactattgta aaaacgaaaa aaccaccctg gcaggtggtt tttcgaaggt
     1741 tagttaatcc tggcagattc tctaaccgtg gtaacagtct tgtgcgagac atgtcaccaa
     1801 atactgtcct ttcagtgtag cctcagttag gccgccactt caagaactct cgttacatct
     1861 ctcgcacatc ctgcttacca gtggccgttg ccagtggcgt taagtcgtgt cttaccgggt
     1921 tggactcaag acgatagtta ccggataagg cgcagcggtc gggctgaacg gggggttcgt
     1981 gcacacagcc cagcttggag cgaacgacct acaccgaacc gagataccaa cagcgtgagc
     2041 tatgagaaag cgccacgctt cccgaaggga gaaaggcgga caggtatccg gtaagcggca
     2101 gggtcggaac aggagagcgc acgagggagc ttccaggggg aaacgcctgg tatctttata
     2161 gtcctgtcgg gtttcgccac ctctgacttg agcgtcgatt tttgtgatgc tcgtcagggg
     2221 ggcggagcct atggaaaaac gcctcccgcg cgcccttctt ctgggtcttt gtcttttgct
     2281 cacatgttct ttccggtttt atcccccgat tctgtggata accgtattac cgcctttgag
     2341 tgagctgaca ccgctcgccg cagtcgaacg accgagcgta gcgagtcagt gagcgaggaa
     2401 gcggaagagc gccttatgtg acattttctc cttacgctcc tctatgccgt tctgcatcct
     2461 gtccggatgc gttatatccc ggtaagattt tccgcttcaa agcgtgtctg tatgctgttc
     2521 tggagttctt ctgcgagttc gtgcagtttc tcacacatgg cggcctgttc gtcggcattg
     2581 agtgcgtcca gtttttcgag cagcgtcagg ctctgacttt ttatgaatcc cgccatgttg
     2641 agtacggctt gctgctgctt attcatcttt tcgttttctc cgttctgtct gtcatctgcg
     2701 ttgtgtgatt atatcgcgta ccacttttcg actgttttgc tgccgctatt ctgccgcttg
     2761 gctttttgac gggcatttct gtcagacaac actgtcactg ccaaaaaact gccgtgcctt
     2821 tgtcggtaat tcgagcttgc tgacaggaca ggatgtgcaa ttgttatacc gcgcatacat
     2881 gcacgctatt acaattgccc tggtcagggc tttgccccga cacccatgtc agatacggag
     2941 ccatgtttta tgacaaaacg aagtggaagt aatacgcgca ggcgggctat cagtcgccct
     3001 gttcgtctga cggcagaaga agaccaggaa atcagaaaaa gggctgctga atgcggcaag
     3061 accgtttccg gttttttacg ggcggcagct ctcggtaaga aagttaactc actgactgat
     3121 gatcgggtac tgaaagaagt tatgagactg ggggcgttac agaaaaaact ctt
//
