LOCUS       NZ_CP107146             4073 bp    DNA     circular CON 14-AUG-2023
DEFINITION  Escherichia coli strain S2 plasmid pS2-S1K81-3, complete sequence.
ACCESSION   NZ_CP107146
VERSION     NZ_CP107146.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31158875
            Assembly: GCF_030708335.1
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                   :: 1581x
            Sequencing Technology :: Illumina NovaSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/11/2023 07:59:10
            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)                     :: 5,290
            CDSs (total)                      :: 5,173
            Genes (coding)                    :: 4,959
            CDSs (with protein)               :: 4,959
            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
            CP107146.1.
            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="S2"
                     /isolation_source="human"
                     /db_xref="taxon:562"
                     /plasmid="pS2-S1K81-3"
                     /geo_loc_name="Sweden: Gothenburg"
                     /collection_date="2017"
     gene            complement(252..2399)
                     /gene="mobQ"
                     /locus_tag="OGM44_RS26440"
                     /old_locus_tag="OGM44_26420"
     CDS             complement(252..2399)
                     /gene="mobQ"
                     /locus_tag="OGM44_RS26440"
                     /old_locus_tag="OGM44_26420"
                     /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            2578..2832
                     /gene="mobC"
                     /locus_tag="OGM44_RS26445"
                     /old_locus_tag="OGM44_26425"
     CDS             2578..2832
                     /gene="mobC"
                     /locus_tag="OGM44_RS26445"
                     /old_locus_tag="OGM44_26425"
                     /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            3366..4067
                     /locus_tag="OGM44_RS26450"
                     /old_locus_tag="OGM44_26430"
     CDS             3366..4067
                     /locus_tag="OGM44_RS26450"
                     /old_locus_tag="OGM44_26430"
                     /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(2042..2400)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2401..2577
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          3367..4067
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(256..2486)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.989"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttttaaggca cctaaaacgc tccctgctgc gttttttttg tgttagtagt gcgaaggtac
       61 tattgaagtg aaaaattgcg tcaaaaacgc tctgatgcag cgaaaaaaga ccccccaatt
      121 tttgggggcg gaaaaacaaa actatgcttg cgttatgtga gtgtgcttct tgcattcatc
      181 cctgtcgatg aacatcgaag aacatcgacg aacataacac gatgttaaac aaaacaaaat
      241 attgttcaca ttcactgtga ccaaccgcga tcatgtctcc tctcggtggt gtgtgttcgt
      301 gcatcttcct cgcgctgcca ttcctcccag gtacgattaa aacccagcga gcggaacaga
      361 tgatccggct gtttttctgg tgtgttgacg gcagcaaaaa gcggtgcctc acgggttttc
      421 agatgaaact gcatcagttc tggtgcaggt gatatgtggc tgtctgcatc gtgatttacg
      481 gcaacaccat accctgcata ccgtaacccc ttatcggtca gcgcactgat gaccagatgc
      541 ctgttatcgg ctgagggaac ggcaaacgcg ggatacagcg taccattaag ccggataaca
      601 ccgcccagag agtcatccac gcccatgacc agcaaaagct gaagctggcg ggtttcccgg
      661 tcgacagaac tcatgaccgg catcagcgtc ggtggcagac gtccctgcat aaaatccacc
      721 ttccttgccg ctggtgatgg catggctggc tggcggtctt ctccaagaca gaaagactcc
      781 ggccatgtct tcggctggcg gagattgcgg gtatgttgcg gccatgtctg gcaaacctgc
      841 gtcagcagtt gctcaaaggt tgcagaggaa taaacacgtt gcagtggcgg acgttggccg
      901 atttcgcttc ggtcacagat ataaccactc ctgtcacgca ttaaatcaac actctcaaag
      961 attctggtgc ggtatttctc cagctcgttc ccccagagcg tatattctcc gttccggttg
     1021 tgaagcagaa ggtaacaggt catttccccg ttaccaggca tgggagcctc gccatacccc
     1081 gtaacgactg ctctcagcac ccctgaatcc ataacggcat tgtcattttt cctgagctgc
     1141 tccgcgcgac tacgttcagt atcttcctgt tccttccggc gcaattcctc ttcacgttta
     1201 agcaactggg ctctgagagc tgcaaggccg gattcccccc actgctgcca ctgtttttca
     1261 aatgccatct gactcgcggg aatgtcctgt ttctccacct tccggtaatg ctgtcgtaat
     1321 ttttccattt gctggctcag agactggatt tttccctgct cactacggta ttccggtgcc
     1381 gcccattgca tcaggggaat acgggaaaaa ccggacgaaa acggcgatga ttttttcagg
     1441 ctggcagcat ggctcatcgc ttcctttcgt tcggtgttca gctcttccca gcgtctgcgc
     1501 gtcgcctgca tatctgccat catcgacatg gcattactgg tgagtttcca tgccgagtta
     1561 ctgtccttcg gcaacgcttc gataatgtca cgtagtgtgt acgaagttgc gttgtcagga
     1621 agcccgatat tcagaaggtc agccacacgg cgggcaggct ctgtcagccc tccgttcctg
     1681 agttcggtgc gggaaatctg tatttccagg ttaagcctgt taatcagacg attctgttcg
     1741 ccgcgttctg tttcgatacc gcgtgtttcc atcgcacagg cagactttcc gaggtgaata
     1801 ccaggcgttt tctcaagccc ctgtcgctcg tatgaacgat ggtctatctc ttcctgataa
     1861 ccggcgttcg ccagtgccct gtttgcatgg tcagcccatg atgcccgcca cgtctcggca
     1921 tgtgtccggt cgttccagtc cctgaccttt ccgctgaacc cagcaggtcc gatagccctc
     1981 gtggtcagca tgatgtgcgc atggggattt gttttatcca tgtgatggaa cgccacatca
     2041 gcaatcatgc cctgactgac aaagttttct ctgacaaagg cgagaacggt ttcccgtgcg
     2101 gcatcctgcg gcagttcgtg ggggatggcg agttcaattt cccgcgcaag ttgtgagttc
     2161 ttccggcgtt cggccttctc aacggcattc cagagttcgg cacggttcgt acaccaggca
     2221 ggggcggtgg cgggggtcag aatcacagcc tcagccacac cgcttttgcg ggtgtagtcg
     2281 tgagtcagtc cggtacgctc atcaagcatc agtgaaccgg aacgataggc agcggaagct
     2341 acggcgctgt agccgctgct tctggagata attttcatgc tgagatgata aatcgccatt
     2401 tctgccgtaa tgcctttttg tagttttctt tcagccccgc agggcgcaca caatcgaaac
     2461 ggagtggaga ttgtataagt gcgcacttcg tgatttgccg tgcattatgc cagctcagtt
     2521 tttaaactac cagtgacgcg ctaaaatgcg atttttcatc gcgcacggag ttacatcatg
     2581 agcagaacgc tcgaacagaa gattgctgat gctgaggcga gattacagcg cctgaaggcg
     2641 aagagccgga gcctggacac agcgcagaag gttgttgtgg gtgctgcatt gctggcaaag
     2701 gtcagaaagc cggaggaggt gcagttgcgt gcctggttac tccagttcct gaaggcagag
     2761 gtgacacgac aggctgatgt gacgcgcata ctgccgctga ttaacgagct ggaggcgctg
     2821 ccagaacagt gattgtatcg tccgctcgcc gcagccccag cgaccgagcg ttagcgagcg
     2881 agtgggcgag gaagcggaag tgaatcagtc gccaggttga gcacatacgc acggtttttc
     2941 ggcaggtgat atgcgctgaa cccgcatgaa tactgggttt ccacagggtt ggagggggtg
     3001 tattcgaaac ttgcaattct gctttattgc aacgcattgt ttttattggt tttttgtttt
     3061 cagcacccca agttatccac aggctcgccg ttaagttttt aagatcttat ttttagatct
     3121 ttttttttaa aaccttttta ggtcttgtaa caccatgatt ttaaagatgt tctggcaaga
     3181 taagtggagc ttttgggggt gaaaggtgga gcttttgggg gtgaaaggtg gagcttttgg
     3241 gggtgaaagg tggagctttt gggggtgtaa tccacagaaa aagggggttg caaaaaaaaa
     3301 acttccaccc atatgataag tggcgtacag taaaaaaacg ccaccaatag caacgagcaa
     3361 gcgaaatgtc agatctgata gcttacaaat caaacgccct tatcgaggca agctacaagc
     3421 tcactttgca ggaacagcgc ttcctgctgg tctgtatcag ccgcctaaaa tccggagaag
     3481 attccccttc gccggatgaa caaaaaacca tgaccatcac ggctgcagag tttcatgatg
     3541 cctttcctga catgggacgg cagcacgctg aagctaggct caaggaagcg atagatcgcc
     3601 tctgggacag gtcagtaatc atcaagaacg aggaaaaacg agaagagttc cgctgggtgc
     3661 agtaccgggc gcagtatttc aaaggtgagg cgaaagtaga tatcaccttc tccgatgcca
     3721 tcatgccgta tctgacacag ctcaaggggc agtttacgcg ggtagtcgtg aagaacgtct
     3781 ccagcctttc cagcacctac agcatccgca tttacgagct gctccagcag ttccgcagca
     3841 ccggtgacag aacgatagct atcgatgatt tccgaaccat gcttgccgtt gaagataaat
     3901 atcaacaatt caaagacttg aataagatga taatcaagcc agccatcgcc gaactgaacg
     3961 aaaaaagcga tctggttgta actgttgaga cgatcaaaaa ggggcgcacg gttgtagccc
     4021 tgcattttcg cttcaaggaa gacaaacaga tcaagatgac gatctaaaat cga
//
