LOCUS       NZ_CP128582             3555 bp    DNA     circular CON 05-JUL-2023
DEFINITION  Escherichia coli strain VG48B2 plasmid p48B2b, complete sequence.
ACCESSION   NZ_CP128582
VERSION     NZ_CP128582.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35722720
            Assembly: GCF_030384765.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3555)
  AUTHORS   Perreten,V., Collaud,A., Meylan,M. and Gosselin,V.
  TITLE     Hemolytic E. coli from farm environment
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3555)
  AUTHORS   Perreten,V., Collaud,A., Meylan,M. and Gosselin,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-JUN-2023) Institute of Veterinary Bacteriology,
            University of Bern, Laenggassstrasse 122, Bern 3012, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2023
            Assembly Method                   :: unicycler v. 0.4.8
            Assembly Name                     :: VG48B2.fasta
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 132x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/04/2023 08:14:30
            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)                     :: 4,878
            CDSs (total)                      :: 4,753
            Genes (coding)                    :: 4,521
            CDSs (with protein)               :: 4,521
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 232
            CDSs (without protein)            :: 232
            Pseudo Genes (ambiguous residues) :: 0 of 232
            Pseudo Genes (frameshifted)       :: 75 of 232
            Pseudo Genes (incomplete)         :: 171 of 232
            Pseudo Genes (internal stop)      :: 37 of 232
            Pseudo Genes (multiple problems)  :: 47 of 232
            Pseudo Genes (short protein)      :: 4 of 232
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP128582.1.
            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..3555
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="VG48B2"
                     /isolation_source="farm environment"
                     /db_xref="taxon:562"
                     /plasmid="p48B2b"
                     /geo_loc_name="Switzerland"
                     /lat_lon="46.948089 N 7.447439 E"
                     /collection_date="2021-09-08"
                     /collected_by="Lisa Windhofer"
     gene            complement(162..776)
                     /locus_tag="QUS02_RS00005"
                     /old_locus_tag="QUS02_00005"
     CDS             complement(162..776)
                     /locus_tag="QUS02_RS00005"
                     /old_locus_tag="QUS02_00005"
                     /inference="COORDINATES: protein motif:HMM:NF025107.2"
                     /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_052895292.1"
                     /translation="MSTKNAQKEQKKESLITTHWGDDATIHGWTAIPNSLLMLQGDLGI
                     GSTEMCILLNILMHQWPESGESISFPSIGTIASRIGVSKRTIQRGVSNLEALGILTRYQ
                     STRNDPLTNGANIFDSTPLKEYLNKKAKGITISNSNKKKERKKTGITPNIKLPRICPKC
                     LKTKATSHEEIVKFFGVRKTMAGEIINSYCKECRASEKDLF"
                     /name="helix-turn-helix domain-containing protein"
     gene            1097..1822
                     /locus_tag="QUS02_RS00010"
                     /old_locus_tag="QUS02_00010"
     CDS             1097..1822
                     /locus_tag="QUS02_RS00010"
                     /old_locus_tag="QUS02_00010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001307201.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="WP_001427890.1"
                     /translation="MASMETEQQPQQTTEQIEVKTKRVQCFIDGYNLYHAIEETGNKAL
                     HWVDLKSLCKRYLPKNASIDNVFWFSAKPSHLSRAINENYQNYTNALTECGVDVIGGRF
                     KKKNVTCEADNGCGGVFHKHEEKESDVNLAISLVSGACNDEYDIAIIITADSDLCPPIK
                     YVRERFPNKELWLVAPPGRIRRATDLCSLSSRSMEIKNDALRACCMRDEFYKDGVLVAR
                     RPQEWRAVANTRQRRARSR"
                     /name="NYN domain-containing protein"
     gene            complement(2628..2822)
                     /locus_tag="QUS02_RS00015"
                     /old_locus_tag="QUS02_00015"
     CDS             complement(2628..2822)
                     /locus_tag="QUS02_RS00015"
                     /old_locus_tag="QUS02_00015"
                     /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_001041640.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3106..3429
                     /gene="mobA"
                     /locus_tag="QUS02_RS00020"
                     /old_locus_tag="QUS02_00020"
     CDS             3106..3429
                     /gene="mobA"
                     /locus_tag="QUS02_RS00020"
                     /old_locus_tag="QUS02_00020"
                     /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"
     Typing          2858..3097
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          complement(2069..2593)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.274"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          3107..3426
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.86e-62"
ORIGIN
        1 accccgggga aaacatctct ttttgcggtg tttgcggcag aatcgcgttc agcgcgtttt
       61 agcggtgcgc gtaatgagac gttatggtaa atgggagcgt tagaaacagt cccatttact
      121 tgagtggggg gcagttggcc atataaaaaa tggtcaactg tttaaaatag atctttttca
      181 gaagctcggc attctttgca atatgaattt attatttccc cagccattgt ttttcgcacg
      241 ccaaaaaatt taacaatttc ttcgtggctg gttgctttag ttttcaaaca ttttgggcaa
      301 atgcgtggta attttatgtt gggtgtaatt ccggttttct ttctttcttt ctttttgttg
      361 ctgttgctaa ttgttatgcc tttagctttt ttgtttaaat attcttttag aggagttgag
      421 tcgaatatat tagcgccatt ggttagaggg tcattccttg ttgattggta tctagttaat
      481 atccccaatg cctctaggtt actaaccccg cgttgaattg ttcttttaga tacacctatt
      541 cttgatgcaa tggtaccaat tgacggaaaa gatattgact cccctgactc aggccattga
      601 tgcatcaata tattcagcag aatacacatc tcagtactcc caataccaag atcaccttgc
      661 agcataagga ggctatttgg tatagccgtc cacccatgta tggttgcatc atctccccag
      721 tgagtagtga ttaatgactc ttttttttgt tctttctgtg cgttttttgt gctcatagat
      781 gcttttctcg cgaaaaaaaa atcaaaatgt gaacagttac tacctaacta ctcttaatat
      841 aagagtagtt aggtagtaac atgtatcttt taggatgaca taaatgtcat ccatttgctc
      901 tttttttata tagaacttaa gttgagtcca ctacctaaga ggtatgctct tagtggctat
      961 ccaagtcgag gcttggaagc gcattgtaca aaattcttcc tgtattggat gcgtccatac
     1021 agtggtctgt taactgcggt taagagacgc aaaaaggcct gcatatgcag gcctttttgc
     1081 tatctagagg tcaaaaatgg caagtatgga aacagagcag caaccacaac aaactactga
     1141 gcaaatcgaa gtaaaaacaa agcgagtgca gtgctttatt gatgggtata atttatatca
     1201 tgcaattgaa gagactggta ataaagctct tcattgggtt gatcttaaat ctttatgcaa
     1261 gagatacctt cctaaaaatg catctattga taatgttttt tggttttccg ctaagccatc
     1321 acatttatca agagccataa atgaaaatta tcaaaattac accaacgctt taaccgaatg
     1381 tggtgttgat gttatcggtg ggcgttttaa aaaaaagaat gtaacgtgcg aagctgataa
     1441 tggatgtggt ggagttttcc ataagcatga agaaaaagag tccgatgtta atttggctat
     1501 aagtctagtg tctggtgcgt gtaatgatga gtatgatata gccattatta tcactgcgga
     1561 ttctgactta tgccccccta ttaaatacgt aagagagcga ttccctaata aagagctttg
     1621 gcttgtagct cctccgggga gaatcaggcg agcgacagat ctctgctctc tgtcatcgag
     1681 aagtatggag atcaagaatg atgctttgag agcctgctgt atgcgtgatg agttctacaa
     1741 agatggagta cttgtagcca gaaggcctca ggaatggcga gctgttgcca ataccaggca
     1801 aagaagggct agaagtcgtt aggctttgtt gacgcagcta gcgcaaggag attaatctaa
     1861 ctaggttgaa aacgaaaaaa ccgccttggc gggcggtttt tcgaaggttc atagagttgg
     1921 cgctctttga accgaggtaa ctggctttga ggagcacagt cgccaaaact tgttctttca
     1981 gtttagcctt atcaggtgca taacttcaag actcaactcc tctaaatcag ttaccaatgg
     2041 ctgctgccag tggcgttaag tcgtgtcttt ccgggttgga ctcaagacga tagttaccgg
     2101 ataaggcgca gcggtcgggc tgaacggggg gttcgtgcac acagcccagc ttggagcgaa
     2161 cgacctacac cgaactgaga taccaacagc gtgagctatg agaaagcgcc acgcttcccg
     2221 aagggagaaa ggcggacagg tatccggtaa gcggcagggt cggaacagga gagcgcacga
     2281 gggagcttcc agggggaaac gcctggtatc tttatagtcc tgtcgggttt cgccacctct
     2341 gacttgagcg tcgatttttg tgatgctcgt caggggggcg gagcctatgg aaaaacggca
     2401 tcggcgctgg cttgttccgg tgctttgctt tttgctcaca tgttctttcc ggcgttatcc
     2461 cctgattctg tggataaccg tattaccgcc tttgagtgag ctgacaccgc tcgccgcagt
     2521 cgaacgaccg agcgtagcga gtcagtgagc gaggaagcgg aagagcgtct gacgtggcat
     2581 tttctcctta cgctccgcta tgccgttctg catcctgtcc gggtgcgtta tatcccggtg
     2641 cgattttccg cttcaaagcg tgtctgtatg ctgttctgaa gttcttccgc gagttcgtgc
     2701 agcttctcac acatggcggc ctgttcgtca gcatcaagtg cgtccagttt ttcgagcagc
     2761 gtcaggctct ggctttttat gaatcccgcc atgttgagta cggtttgctg ctgcttgttc
     2821 atctttctgt tttctccgtt ctttctgtca tctgcgttgt gtgattatat cgagtaccac
     2881 ttttcgactg ttttaccgcc ggtattctgc tgtctgactc tttgacgggc atttctgtca
     2941 gacaacactg tcactgccaa aaaactgccg tgcttttgtc ggtaattcga gcttgctgac
     3001 aggacaggat gtgcaattgt tataccgcgc atacatgcac gctattacaa ttaccctggt
     3061 cagggctttg ccccgacacc catgtcagat acggagccat gttttatgac aaaacgaagt
     3121 ggaagtaata cgcgcaggcg ggctatcagt cgccctgttc gtctgacggc agaagaagac
     3181 caggaaatca gaaaaagggc tgctgaatgc ggcaagaccg tttctggttt tttacgggcg
     3241 gcagctctcg gtaagaaagt taattcactg actgatgacc gagtgctgaa agaagtcatg
     3301 cgactggggg cgttgcagaa aaaactcttt atcgacggca agcgtgtcgg ggacagagag
     3361 tatgcggagg tgctgatagc tattacggag tatcaccggg ccctgttatc caggcttatg
     3421 gcagattagc ttcccggagg gaaactgtcg aaaacagacg gtatgaacgc cgtaagtccc
     3481 caaaccgatc gccattcact ttcatgcata gctatgcagt gagctgaaag caatcctgac
     3541 gcatttttcc ggttt
//
