LOCUS       NZ_CP107169             4073 bp    DNA     circular CON 14-AUG-2023
DEFINITION  Escherichia coli strain R9 plasmid pR9-658-5, complete sequence.
ACCESSION   NZ_CP107169
VERSION     NZ_CP107169.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31158869
            Assembly: GCF_030707935.1
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                   :: 338x
            Sequencing Technology :: Illumina NovaSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/11/2023 07:51:19
            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)                     :: 5,176
            CDSs (total)                      :: 5,061
            Genes (coding)                    :: 4,871
            CDSs (with protein)               :: 4,871
            Genes (RNA)                       :: 115
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 190
            CDSs (without protein)            :: 190
            Pseudo Genes (ambiguous residues) :: 0 of 190
            Pseudo Genes (frameshifted)       :: 69 of 190
            Pseudo Genes (incomplete)         :: 138 of 190
            Pseudo Genes (internal stop)      :: 38 of 190
            Pseudo Genes (multiple problems)  :: 49 of 190
            Pseudo Genes (short protein)      :: 3 of 190
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP107169.1.
            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="R9"
                     /isolation_source="human"
                     /db_xref="taxon:562"
                     /plasmid="pR9-658-5"
                     /geo_loc_name="Sweden: Gothenburg"
                     /collection_date="2018"
     gene            complement(join(3404..4073,1..1478))
                     /gene="mobQ"
                     /locus_tag="OGM38_RS25835"
                     /old_locus_tag="OGM38_25805"
     CDS             complement(join(3404..4073,1..1478))
                     /gene="mobQ"
                     /locus_tag="OGM38_RS25835"
                     /old_locus_tag="OGM38_25805"
                     /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            1657..1911
                     /gene="mobC"
                     /locus_tag="OGM38_RS25840"
                     /old_locus_tag="OGM38_25810"
     CDS             1657..1911
                     /gene="mobC"
                     /locus_tag="OGM38_RS25840"
                     /old_locus_tag="OGM38_25810"
                     /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            2445..3146
                     /locus_tag="OGM38_RS25845"
                     /old_locus_tag="OGM38_25815"
     CDS             2445..3146
                     /locus_tag="OGM38_RS25845"
                     /old_locus_tag="OGM38_25815"
                     /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(1121..1479)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1480..1656
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2446..3146
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.858"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4..1565)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.571"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3408..4072)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.595"
                     /coverage="99.0"
                     /evalue="3.33e-138"
ORIGIN
        1 taaccactcc tgtcacgcat taaatcaaca ctctcaaaga ttctggtgcg gtatttctcc
       61 agctcgttcc cccagagcgt atattctccg ttccggttgt gaagcagaag gtaacaggtc
      121 atttccccgt taccaggcat gggagcctcg ccataccccg taacgactgc tctcagcacc
      181 cctgaatcca taacggcatt gtcatttttc ctgagctgct ccgcgcgact acgttcagta
      241 tcttcctgtt ccttccggcg caattcctct tcacgtttaa gcaactgggc tctgagagct
      301 gcaaggccgg attcccccca ctgctgccac tgtttttcaa atgccatctg actcgcggga
      361 atgtcctgtt tctccacctt ccggtaatgc tgtcgtaatt tttccatttg ctggctcaga
      421 gactggattt ttccctgctc actacggtat tccggtgccg cccattgcat caggggaata
      481 cgggaaaaac cggacgaaaa cggcgatgat tttttcaggc tggcagcatg gctcatcgct
      541 tcctttcgtt cggtgttcag ctcttcccag cgtctgcgcg tcgcctgcat atctgccatc
      601 atcgacatgg cattactggt gagtttccat gccgagttac tgtccttcgg caacgcttcg
      661 ataatgtcac gtagtgtgta cgaagttgcg ttgtcaggaa gcccgatatt cagaaggtca
      721 gccacacggc gggcaggctc tgtcagccct ccgttcctga gttcggtgcg ggaaatctgt
      781 atttccaggt taagcctgtt aatcagacga ttctgttcgc cgcgttctgt ttcgataccg
      841 cgtgtttcca tcgcacaggc agactttccg aggtgaatac caggcgtttt ctcaagcccc
      901 tgtcgctcgt atgaacgatg gtctatctct tcctgataac cggcgttcgc cagtgccctg
      961 tttgcatggt cagcccatga tgcccgccac gtctcggcat gtgtccggtc gttccagtcc
     1021 ctgacctttc cgctgaaccc agcaggtccg atagccctcg tggtcagcat gatgtgcgca
     1081 tggggatttg ttttatccat gtgatggaac gccacatcag caatcatgcc ctgactgaca
     1141 aagttttctc tgacaaaggc gagaacggtt tcccgtgcgg catcctgcgg cagttcgtgg
     1201 gggatggcga gttcaatttc ccgcgcaagt tgtgagttct tccggcgttc ggccttctca
     1261 acggcattcc agagttcggc acggttcgta caccaggcag gggcggtggc gggggtcaga
     1321 atcacagcct cagccacacc gcttttgcgg gtgtagtcgt gagtcagtcc ggtacgctca
     1381 tcaagcatca gtgaaccgga acgataggca gcggaagcta cggcgctgta gccgctgctt
     1441 ctggagataa ttttcatgct gagatgataa atcgccattt ctgccgtaat gcctttttgt
     1501 agttttcttt cagccccgca gggcgcacac aatcgaaacg gagtggagat tgtataagtg
     1561 cgcacttcgt gatttgccgt gcattatgcc agctcagttt ttaaactacc agtgacgcgc
     1621 taaaatgcga tttttcatcg cgcacggagt tacatcatga gcagaacgct cgaacagaag
     1681 attgctgatg ctgaggcgag attacagcgc ctgaaggcga agagccggag cctggacaca
     1741 gcgcagaagg ttgttgtggg tgctgcattg ctggcaaagg tcagaaagcc ggaggaggtg
     1801 cagttgcgtg cctggttact ccagttcctg aaggcagagg tgacacgaca ggctgatgtg
     1861 acgcgcatac tgccgctgat taacgagctg gaggcgctgc cagaacagtg attgtatcgt
     1921 ccgctcgccg cagccccagc gaccgagcgt tagcgagcga gtgggcgagg aagcggaagt
     1981 gaatcagtcg ccaggttgag cacatacgca cggtttttcg gcaggtgata tgcgctgaac
     2041 ccgcatgaat actgggtttc cacagggttg gagggggtgt attcgaaact tgcaattctg
     2101 ctttattgca acgcattgtt tttattggtt ttttgttttc agcaccccaa gttatccaca
     2161 ggctcgccgt taagttttta agatcttatt tttagatctt tttttttaaa acctttttag
     2221 gtcttgtaac accatgattt taaagatgtt ctggcaagat aagtggagct tttgggggtg
     2281 aaaggtggag cttttggggg tgaaaggtgg agcttttggg ggtgaaaggt ggagcttttg
     2341 ggggtgtaat ccacagaaaa agggggttgc aaaaaaaaaa cttccaccca tatgataagt
     2401 ggcgtacagt aaaaaaacgc caccaatagc aacgagcaag cgaaatgtca gatctgatag
     2461 cttacaaatc aaacgccctt atcgaggcaa gctacaagct cactttgcag gaacagcgct
     2521 tcctgctggt ctgtatcagc cgcctgaaat ccggagaaga ttccccttcg ccggatgaac
     2581 aaaaaaccat gaccatcacg gctgcagagt ttcatgatgc ctttcctgac atgggacggc
     2641 agcacgctga agctaggctc aaggaagcga tagatcgcct ctgggacagg tcagtaatca
     2701 tcaagaacga ggaaaaacga gaagagttcc gctgggtgca gtaccgggcg cagtatttca
     2761 aaggtgaggc gaaagtagat atcaccttct ccgatgccat catgccgtat ctgacacagc
     2821 tcaaggggca gtttacgcgg gtagtcgtga agaacgtctc cagcctttcc agcacctaca
     2881 gcatccgcat ttacgagctg ctccagcagt tccgcagcac cggtgacaga acgatagcta
     2941 tcgatgattt ccgaaccatg cttgccgttg aagataaata tcaacaattc aaagacttga
     3001 ataagatgat aatcaagcca gccatcgccg aactgaacga aaaaagcgat ctggttgtaa
     3061 ctgttgagac gatcaaaaag gggcgcacgg ttgtagccct gcattttcgc ttcaaggaag
     3121 acaaacagat caagatgacg atctaaaatc gattttaagg cacctaaaac gctccctgct
     3181 gcgttttttt tgtgttagta gtgcgaaggt actattgaag tgaaaaattg cgtcaaaaac
     3241 gctctgatgc agcgaaaaaa gaccccccaa tttttggggg cggaaaaaca aaactatgct
     3301 tgcgttatgt gagtgtgctt cttgcattca tccctgtcga tgaacatcga agaacatcga
     3361 cgaacataac acgatgttaa acaaaacaaa atattgttca cattcactgt gaccaaccgc
     3421 gatcatgtct cctctcggtg gtgtgtgttc gtgcatcttc ctcgcgctgc cattcctccc
     3481 aggtacgatt aaaacccagc gagcggaaca gatgatccgg ctgtttttct ggtgtgttga
     3541 cggcagcaaa aagcggtgcc tcacgggttt tcagatgaaa ctgcatcagt tctggtgcag
     3601 gtgatatgtg gctgtctgca tcgtgattta cggcaacacc ataccctgca taccgtaacc
     3661 ccttatcggt cagcgcactg atgaccagat gcctgttatc ggctgaggga acggcaaacg
     3721 cgggatacag cgtaccatta agccggataa caccgcccag agagtcatcc acgcccatga
     3781 ccagcaaaag ctgaagctgg cgggtttccc ggtcgacaga actcatgacc ggcatcagcg
     3841 tcggtggcag acgtccctgc ataaaatcca ccttccttgc cgctggtgat ggcatggctg
     3901 gctggcggtc ttctccaaga cagaaagact ccggccatgt cttcggctgg cggagattgc
     3961 gggtatgttg cggccatgtc tggcaaacct gcgtcagcag ttgctcaaag gttgcagagg
     4021 aataaacacg ttgcagtggc ggacgttggc cgatttcgct tcggtcacag ata
//
