LOCUS       NZ_CP107177             4073 bp    DNA     circular CON 14-AUG-2023
DEFINITION  Escherichia coli strain R7 plasmid pR7-S2K78-3, complete sequence.
ACCESSION   NZ_CP107177
VERSION     NZ_CP107177.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31158867
            Assembly: GCF_030707975.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4073)
  AUTHORS   Jaen-Luchoro,D., Kahnamouei,A., Yazdanshenas,S., Lindblom,A.,
            Samuelsson,E., Ahren,C. and Karami,N.
  TITLE     Comparative Genomic Analysis of ST131 Subclade C2 of ESBL-Producing
            E. coli Isolates from Patients with Recurrent and Sporadic Urinary
            Tract Infections
  JOURNAL   Microorganisms 11 (7), 1622 (2023)
   PUBMED   37512795
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 4073)
  AUTHORS   Jaen-Luchoro,D., Kahnamouei,A., Yazdanshenas,S., Lindblom,A.,
            Samuelsson,E., Ahren,C. and Karami,N.
  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                   :: 1474x
            Sequencing Technology :: Illumina NovaSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/11/2023 07:49:08
            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)                     :: 5,287
            CDSs (total)                      :: 5,170
            Genes (coding)                    :: 4,956
            CDSs (with protein)               :: 4,956
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 214
            CDSs (without protein)            :: 214
            Pseudo Genes (ambiguous residues) :: 0 of 214
            Pseudo Genes (frameshifted)       :: 78 of 214
            Pseudo Genes (incomplete)         :: 162 of 214
            Pseudo Genes (internal stop)      :: 40 of 214
            Pseudo Genes (multiple problems)  :: 58 of 214
            Pseudo Genes (short protein)      :: 3 of 214
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP107177.1.
            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..4073
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="R7"
                     /isolation_source="human"
                     /db_xref="taxon:562"
                     /plasmid="pR7-S2K78-3"
                     /geo_loc_name="Sweden: Gothenburg"
                     /collection_date="2018"
     gene            complement(383..637)
                     /gene="mobC"
                     /locus_tag="OGM36_RS26425"
                     /old_locus_tag="OGM36_26405"
     CDS             complement(383..637)
                     /gene="mobC"
                     /locus_tag="OGM36_RS26425"
                     /old_locus_tag="OGM36_26405"
                     /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_000091746.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     gene            816..2963
                     /gene="mobQ"
                     /locus_tag="OGM36_RS26430"
                     /old_locus_tag="OGM36_26410"
     CDS             816..2963
                     /gene="mobQ"
                     /locus_tag="OGM36_RS26430"
                     /old_locus_tag="OGM36_26410"
                     /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_001029354.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSPAARKVDFMQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVIRLNGTLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWEEW
                     QREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(3221..3922)
                     /locus_tag="OGM36_RS26435"
                     /old_locus_tag="OGM36_26415"
     CDS             complement(3221..3922)
                     /locus_tag="OGM36_RS26435"
                     /old_locus_tag="OGM36_26415"
                     /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_001281395.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVDITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(639..815)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          816..1174
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3222..3922)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          730..2960
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.989"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aagctccacc tttcaccccc aaaagctcca cttatcttgc cagaacatct ttaaaatcat
       61 ggtgttacaa gacctaaaaa ggttttaaaa aaaaagatct aaaaataaga tcttaaaaac
      121 ttaacggcga gcctgtggat aacttggggt gctgaaaaca aaaaaccaat aaaaacaatg
      181 cgttgcaata aagcagaatt gcaagtttcg aatacacccc ctccaaccct gtggaaaccc
      241 agtattcatg cgggttcagc gcatatcacc tgccgaaaaa ccgtgcgtat gtgctcaacc
      301 tggcgactga ttcacttccg cttcctcgcc cactcgctcg ctaacgctcg gtcgctgggg
      361 ctgcggcgag cggacgatac aatcactgtt ctggcagcgc ctccagctcg ttaatcagcg
      421 gcagtatgcg cgtcacatca gcctgtcgtg tcacctctgc cttcaggaac tggagtaacc
      481 aggcacgcaa ctgcacctcc tccggctttc tgacctttgc cagcaatgca gcacccacaa
      541 caaccttctg cgctgtgtcc aggctccggc tcttcgcctt caggcgctgt aatctcgcct
      601 cagcatcagc aatcttctgt tcgagcgttc tgctcatgat gtaactccgt gcgcgatgaa
      661 aaatcgcatt ttagcgcgtc actggtagtt taaaaactga gctggcataa tgcacggcaa
      721 atcacgaagt gcgcacttat acaatctcca ctccgtttcg attgtgtgcg ccctgcgggg
      781 ctgaaagaaa actacaaaaa ggcattacgg cagaaatggc gatttatcat ctcagcatga
      841 aaattatctc cagaagcagc ggctacagcg ccgtagcttc cgctgcctat cgttccggtt
      901 cactgatgct tgatgagcgt accggactga ctcacgacta cacccgcaaa agcggtgtgg
      961 ctgaggctgt gattctgacc cccgccaccg cccctgcctg gtgtacgaac cgtgccgaac
     1021 tctggaatgc cgttgagaag gccgaacgcc ggaagaactc acaacttgcg cgggaaattg
     1081 aactcgccat cccccacgaa ctgccgcagg atgccgcacg ggaaaccgtt ctcgcctttg
     1141 tcagagaaaa ctttgtcagt cagggcatga ttgctgatgt ggcgttccat cacatggata
     1201 aaacaaatcc ccatgcgcac atcatgctga ccacgagggc tatcggacct gctgggttca
     1261 gcggaaaggt cagggactgg aacgaccgga cacatgccga gacgtggcgg gcatcatggg
     1321 ctgaccatgc aaacagggca ctggcgaacg ccggttatca ggaagagata gaccatcgtt
     1381 catacgagcg acaggggctt gagaaaacgc ctggtattca cctcggaaag tctgcctgtg
     1441 cgatggaaac acgcggtatc gaaacagaac gcggcgaaca gaatcgtctg attaacaggc
     1501 ttaacctgga aatacagatt tcccgcaccg aactcaggaa cggagggctg acagagcctg
     1561 cccgccgtgt ggctgacctt ctgaatatcg ggcttcctga caacgcaact tcgtacacac
     1621 tacgtgacat tatcgaagcg ttgccgaagg acagtaactc ggcatggaaa ctcaccagta
     1681 atgccatgtc gatgatggca gatatgcagg cgacgcgcag acgctgggaa gagctgaaca
     1741 ccgaacgaaa ggaagcgatg agccatgctg ccagcctgaa aaaatcatcg ccgttttcgt
     1801 ccggtttttc ccgtattccc ctgatgcaat gggcggcacc ggaataccgt agtgagcagg
     1861 gaaaaatcca gtctctgagc cagcaaatgg aaaaattacg acagcattac cggaaggtgg
     1921 agaaacagga cattcccgcg agtcagatgg catttgaaaa acagtggcag cagtgggggg
     1981 aatccggcct tgcagctctc agagcccagt tgcttaaacg tgaagaggaa ttgcgccgga
     2041 aggaacagga agatactgaa cgtagtcgcg cggagcagct caggaaaaat gacaatgccg
     2101 ttatggattc aggggtgctg agagcagtcg ttacggggta tggcgaggct cccatgcctg
     2161 gtaacgggga aatgacctgt taccttctgc ttcacaaccg gaacggagaa tatacgctct
     2221 gggggaacga gctggagaaa taccgcacca gaatctttga gagtgttgat ttaatgcgtg
     2281 acaggagtgg ttatatctgt gaccgaagcg aaatcggcca acgtccgcca ctgcaacgtg
     2341 tttattcctc tgcaaccttt gagcaactgc tgacgcaggt ttgccagaca tggccgcaac
     2401 atacccgcaa tctccgccag ccgaagacat ggccggagtc tttctgtctt ggagaagacc
     2461 gccagccagc catgccatca ccagcggcaa ggaaggtgga ttttatgcag ggacgtctgc
     2521 caccgacgct gatgccggtc atgagttctg tcgaccggga aacccgccag cttcagcttt
     2581 tgctggtcat gggcgtggat gactctctgg gcggtgttat ccggcttaat ggtacgctgt
     2641 atcccgcgtt tgccgttccc tcagccgata acaggcatct ggtcatcagt gcgctgaccg
     2701 ataaggggtt acggtatgca gggtatggtg ttgccgtaaa tcacgatgca gacagccaca
     2761 tatcacctgc accagaactg atgcagtttc atctgaaaac ccgtgaggca ccgctttttg
     2821 ctgccgtcaa cacaccagaa aaacagccgg atcatctgtt ccgctcgctg ggttttaatc
     2881 gtacctggga ggaatggcag cgcgaggaag atgcacgaac acacaccacc gagaggagac
     2941 atgatcgcgg ttggtcacag tgaatgtgaa caatattttg ttttgtttaa catcgtgtta
     3001 tgttcgtcga tgttcttcga tgttcatcga cagggatgaa tgcaagaagc acactcacat
     3061 aacgcaagca tagttttgtt tttccgcccc caaaaattgg ggggtctttt ttcgctgcat
     3121 cagagcgttt ttgacgcaat ttttcacttc aatagtacct tcgcactact aacacaaaaa
     3181 aaacgcagca gggagcgttt taggtgcctt aaaatcgatt ttagatcgtc atcttgatct
     3241 gtttgtcttc cttgaagcga aaatgcaggg ctacaaccgt gcgccccttt ttgatcgtct
     3301 caacagttac aaccagatcg cttttttcgt tcagttcggc gatggctggc ttgattatca
     3361 tcttattcaa gtctttgaat tgttgatatt tatcttcaac ggcaagcatg gttcggaaat
     3421 catcgatagc tatcgttctg tcaccggtgc tgcggaactg ctggagcagc tcgtaaatgc
     3481 ggatgctgta ggtgctggaa aggctggaga cgttcttcac gactacccgc gtaaactgcc
     3541 ccttgagctg tgtcagatac ggcatgatgg catcggagaa ggtgatatct actttcgcct
     3601 cacctttgaa atactgcgcc cggtactgca cccagcggaa ctcttctcgt ttttcctcgt
     3661 tcttgatgat tactgacctg tcccagaggc gatctatcgc ttccttgagc ctagcttcag
     3721 cgtgctgccg tcccatgtca ggaaaggcat catgaaactc tgcagccgtg atggtcatgg
     3781 ttttttgttc atccggcgaa ggggaatctt ctccggattt taggcggctg atacagacca
     3841 gcaggaagcg ctgttcctgc aaagtgagct tgtagcttgc ctcgataagg gcgtttgatt
     3901 tgtaagctat cagatctgac atttcgcttg ctcgttgcta ttggtggcgt ttttttactg
     3961 tacgccactt atcatatggg tggaagtttt ttttttgcaa cccccttttt ctgtggatta
     4021 cacccccaaa agctccacct ttcaccccca aaagctccac ctttcacccc caa
//
