LOCUS       NZ_CP107239             4072 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain REF1 plasmid pREF1-18-5, complete sequence.
ACCESSION   NZ_CP107239
VERSION     NZ_CP107239.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31158898
            Assembly: GCF_036704625.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4072)
  AUTHORS   Karami,N., Sandberg,M., Yazdanshenas,S., KK,S., Jaen-Luchoro,D.,
            Westerlund,F. and Ahren,C.
  TITLE     Comparison of blaCTX-M-15 and blaCTX-M-27 carrying plasmids by
            combining ODM and CRISPR/Cas9 from different isolates
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4072)
  AUTHORS   Karami,N., Sandberg,M., Yazdanshenas,S., KK,S., Jaen-Luchoro,D.,
            Westerlund,F. and Ahren,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-OCT-2022) Infectious Diseases, University of
            Gothenburg - CCUG, Guldhedsgatan 10a, Box 7193, Gothenburg, Vastra
            Gotaland 40234, Sweden
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 437x
            Sequencing Technology :: Illumina NovaSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036704625.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 16:01:20
            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)                     :: 5,368
            CDSs (total)                      :: 5,250
            Genes (coding)                    :: 5,008
            CDSs (with protein)               :: 5,008
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 242
            CDSs (without protein)            :: 242
            Pseudo Genes (ambiguous residues) :: 0 of 242
            Pseudo Genes (frameshifted)       :: 91 of 242
            Pseudo Genes (incomplete)         :: 170 of 242
            Pseudo Genes (internal stop)      :: 43 of 242
            Pseudo Genes (multiple problems)  :: 56 of 242
            Pseudo Genes (short protein)      :: 3 of 242
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP107239.1.
            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..4072
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="REF1"
                     /isolation_source="human"
                     /db_xref="taxon:562"
                     /plasmid="pREF1-18-5"
                     /geo_loc_name="Sweden: Gothenburg"
                     /collection_date="2010"
     gene            468..1160
                     /locus_tag="OGY64_RS26825"
                     /old_locus_tag="OGY64_26710"
     CDS             468..1160
                     /locus_tag="OGY64_RS26825"
                     /old_locus_tag="OGY64_26710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_338540885.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKQGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1416..3575)
                     /gene="mobQ"
                     /locus_tag="OGY64_RS26830"
                     /old_locus_tag="OGY64_26715"
     CDS             complement(1416..3575)
                     /gene="mobQ"
                     /locus_tag="OGY64_RS26830"
                     /old_locus_tag="OGY64_26715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_001029353.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAECRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            3754..4008
                     /gene="mobC"
                     /locus_tag="OGY64_RS26835"
                     /old_locus_tag="OGY64_26720"
     CDS             3754..4008
                     /gene="mobC"
                     /locus_tag="OGY64_RS26835"
                     /old_locus_tag="OGY64_26720"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091747.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     Typing          complement(3218..3576)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.056"
                     /coverage="100.0"
                     /evalue="3.94e-177"
     Typing          3577..3753
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          469..1160
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.821"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1420..3662)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.332"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gaagtgaatc cgtcgccagg ttgagcacat acgcacggtt tttcggtagg tgatatgcgc
       61 tgaacccgca tgaatactgg atttccacag ggttggaagg ggagtattcg gaacttgcaa
      121 ttctgctttc ttgcaacaca ttgtttttat tggttttttg ttttcagcgc cccaagttat
      181 ccacaggctc gccgttaagt ttttagatct tgtttttaag atcttgtttt taatacttgt
      241 tttagggtca aaattcatta ataaaatcaa tatgttatag aggtatatgt ggaggaattt
      301 aaggtaaagg tggaggaatt taaggtgttt aggtggagga atttaaggta aaggtggagg
      361 aatttaaggt gttattcaca gaaatgtgag gatataaaaa aaaatattcc acatttctta
      421 tttgtggggc acattaaagc atcaccacat ttgaacggga tctttgtatg tcggacttga
      481 ttgcctacaa gtcgaatgct ttggttgagg ccagctacaa gttgacccta caggaacaac
      541 gttttctgtt gctgtgtatc agtcgattga aatctggtgc tgatgctgaa ttgcaaaaga
      601 caatgaccat taccgctgcg gaatattttg attcattccc tgacatgggg cggaaaaatg
      661 ccgaggttca gttacaggaa gcgatcgatc gtttatggga caggtcgatc attctcaaga
      721 atgacgagaa gcgtgaggag ttccgctgga tccagtatcg ggcacagtac gctaaaggtg
      781 aggccaaggc tcgaataacc ttttctgacg cggtaatgcc ttatctgacg caactgaagg
      841 ggcaattcac gcgcgttgtt ataaaaaaca tatcaggttt atcaagtagt tacagtataa
      901 gaatatacga gttcctccag caattccgca gtacgggaga gagaattatt gctcttaatg
      961 actttcgttc aatgttaggg attgaaaata aatacaaaca attcagagac ttaaataaaa
     1021 tactaataaa accctgtgtt gacgaactga acaaaaaaag cgacctggct gtaacggttg
     1081 agacgatcaa acaggggcgc acggttgtag ccctgcattt tcgcttcaag gaagacaaac
     1141 agatcaagat gacgatctaa aatcgatttt aaggcaccta aaacgctccc tgctgcgttt
     1201 tttttgtgtt agtagtgcga aggtactatt gaagtgaaaa attgcgtcaa aagcgctcta
     1261 atgcagcgaa aaaagaaccc ccaatttttg ggggcggaaa aacaaaacta tgcttgcatt
     1321 atgtgtgtgc ttcttgcatt catccctgtc gatgaacata gaagaacatc gacgaacata
     1381 acacgatgtt aaacaaaaca aaatattgtt cacattcact gtgaccaacc gcgatcatgt
     1441 ctcctctcgg tggtgtgtgt tcttgcatct tcctcgcgcc gccattcatc ccaggtacga
     1501 ttgaaaccta gagagcggaa cagatgatcc ggctgttttt ctggtgtgtt gacggcagca
     1561 aaaagcggtg cctcacgggt tttcagatga aactccataa gttccggcgc aggtgatatg
     1621 tggctgtctg catcgtgatt tacggcaaca ccataccctg cataccgtaa ccccttatcg
     1681 gtcagtgcac tgatgaccag ctggctgtta tcggctgagg gaacggcaaa cgcgggatac
     1741 agcgtaccat taagccggac aacaccgccc agagagtcat ccacgcccat gaccagcaaa
     1801 agctgaagct ggcgggtttc ccggtcgaca gaactcatta ccggcatcag cgtcggtagc
     1861 agacgtccct gcgtaaaatc caccttcctt gctgccagtg atggcatggc tggctggcgg
     1921 tcttctccaa gacagaaaga ctccggccat gtcttcggct ggcggagatt gcgggtatat
     1981 tgcggccatg tctggcaaac ctgcgtcaga agttgctcaa aggtcgcaga ggaataaaca
     2041 cgttgcagtg gtggatgttg accgatttcg cttcggtcac agatataacc actcctgtca
     2101 cgcattaaat caacacgctc aaagattctg gtgcggtatt tctccagctc gttcccccag
     2161 agcgtgtatt ctccgttccg gttgtgaagc agaaggtaac aggtcatttc cccgttacca
     2221 ggcatggggg cctcgccata ccccgtaacg actgcgctca gtacccctga atccataacg
     2281 gcattgtcat ttttcctgag ctgttccgct cgtcgctccg cgcgactacg ttctgtatcc
     2341 tcctgctcct tccggcgcaa ttcctcttca cgtttaagca actggactct gagagctgca
     2401 aggccggatg ccccccactg ctgccactgt ttttcaaatg ccgtctgact cgcgggaatg
     2461 tcctgtttct ccaccttccg gtaatgctgt cgcaattttt ccatttgctg gctcagcgac
     2521 tggatttttc cctgttcgct acggtattcc ggtgccgccc attgcatcag gggaatacgg
     2581 gaaaaaccgg acgaaaacgg cgatgatttt ttcaggctgg cagcatggct catcgcttcc
     2641 tttcgttcgg tgttcagctc ttcccagcgt ctgcgcgtcg cctgcatatc tgccatcatc
     2701 gacatggcat tactggtgag tttccatgcc gcattactgt ccttcggcaa cgcttcgatg
     2761 atgtcacgta gtgtgtacga agttgcgttg tcaggaagca cgatattcag aaggtcagcc
     2821 acacggcggg caggctctgt cagcccgctg ttcctgagtt cagtgcggga aatctgtatt
     2881 tccaggttaa gcctgttaat cagacgattc tgttcgccgc gttctgtttc gataccgcgt
     2941 gtttccatcg cacaggcaga ctttccgagg tgaataccag gcgttttctc aagcccctgt
     3001 cgctcgtatg aacgatggtc tatctcttcc tgataaccgg cgttcgccag tgctctgttt
     3061 gcatggtcag cccatgatgc acgccacgtc tcggcatgtg tccggtcgtt ccagtccctg
     3121 acctttccgc cgaacccagc aggtccgaca gccctcgtgg tcagcatgat gtgcgcatgg
     3181 ggatttgttt tatccatgtg atggaacgcc acatcagcaa tcatgccctg actgacaaag
     3241 ttttctctga caaaggcgag aacggtttcc cgtgcggcat cctgcggcag ttcacggggg
     3301 atagcgagtt caatttcccg cgcaagttgt gagttcttcc ggcattcggc cttctcaacg
     3361 gcattccaga gttcggcacg gttcgtacac caggcagggg ctgtcgcggg ggtcagaatc
     3421 acagcttcag ccacaccgct tttgcgggtg tagtcgtgag tcagtccggt acgctcatca
     3481 agcatcagtg aaccggaacg ataggcagcg gaagctacgg cgctgtagcc gctgcttctg
     3541 gagataattt tcatgctgag atgataaatc gccatttctg ccgtaatgcc tttttgtagt
     3601 tttctttcag ccccgcaggg cgcacacaat cgaaacggag tggagattgt ataagtgcgc
     3661 actttgtgat ttgtcgcgca ttatgccagc tcagttttta aactaccagt gacgcgctaa
     3721 aatgcgattt ttcatcgcgc acggagttac atcatgagca gaacgctcga acagaagatt
     3781 gctgatgctg aggcgagatt acagcgcctg aaggcgaaga gccggagcct ggacacagcg
     3841 cagaaggttg ttgtgggtgc agcattgctg gcaaaggtca gaaagccgga ggaggtgcag
     3901 ttgcgtgcct ggttactcca gttcctgaag gcagaggtga cacgacaggc tgatgtgacg
     3961 cgcatactgc cgctgattaa cgagctggag gcgctgccag gacagtgatt gtatcgtccg
     4021 ctcgccgcag ccccagcgac cgagcgttag cgagcgagtg ggcgaggaag cg
//
