LOCUS       CP124973                4082 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KSE-D40 plasmid pKSE-D40_3, complete
            sequence.
ACCESSION   CP124973
VERSION     CP124973.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598759
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4082)
  AUTHORS   Gomi,R., Matsumura,Y., Yamamoto,M., Matsuda,T. and Harada,H.
  TITLE     Genomic surveillance of antimicrobial-resistant Escherichia coli in
            fecal sludge and sewage in Uganda
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4082)
  AUTHORS   Gomi,R., Matsumura,Y., Yamamoto,M., Matsuda,T. and Harada,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-MAY-2023) Department of environmental engineering,
            Kyoto University, KyotoDaigakuKatsura, Nishikyo-ku, Kyoto-city
            615-8540, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Illumina; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 05/09/2023 16:34:32
            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)                     :: 4,970
            CDSs (total)                      :: 4,850
            Genes (coding)                    :: 4,603
            CDSs (with protein)               :: 4,603
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 247
            CDSs (without protein)            :: 247
            Pseudo Genes (ambiguous residues) :: 0 of 247
            Pseudo Genes (frameshifted)       :: 91 of 247
            Pseudo Genes (incomplete)         :: 160 of 247
            Pseudo Genes (internal stop)      :: 55 of 247
            Pseudo Genes (multiple problems)  :: 55 of 247
            Pseudo Genes (short protein)      :: 4 of 247
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..4082
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KSE-D40"
                     /isolation_source="Sewage"
                     /db_xref="taxon:562"
                     /plasmid="pKSE-D40_3"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            complement(join(3524..4082,1..1601))
                     /gene="mobQ"
                     /locus_tag="QL152_24840"
     CDS             complement(join(3524..4082,1..1601))
                     /gene="mobQ"
                     /locus_tag="QL152_24840"
                     /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="WHJ22757.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDRERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            1780..2034
                     /gene="mobC"
                     /locus_tag="QL152_24845"
     CDS             1780..2034
                     /gene="mobC"
                     /locus_tag="QL152_24845"
                     /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="WHJ22758.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            2567..3268
                     /locus_tag="QL152_24850"
     CDS             2567..3268
                     /locus_tag="QL152_24850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0003887 - DNA-directed DNA polymerase activity [Evidence
                     IEA]; GO_process: GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WHJ22756.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGADAESPKL
                     QKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEARAQITFSDAVMPYLTQLQGQFTRVVIKNISRLSRSYSIRIYELLQQFRSTGERI
                     ITLDDFRSMLDIEHKYQTYKSLNQQLLRPCIDELNKKSDLAVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(1244..1602)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1603..1779
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2568..3268
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.858"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4..1688)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.644"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3528..4081)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="4.68e-117"
ORIGIN
        1 gtatattgcg gccatgtctg gcaaacctgc gtcagaagtt gctcaaaggt cgcagaggaa
       61 taaacacgtt gcagtggtgg atgttgaccg atttcgcttc ggtcacagat ataaccactc
      121 ctgtcacgca ttaaatcaac acgctcaaag attctggtgc ggtatttctc cagctcgttc
      181 ccccagagcg tgtattctcc gttccggttg tgaagcagaa ggtaacaggt catttccccg
      241 ttaccaggca tgggggcctc gccatacccc gtaacgactg cgctcagtac ccctgaatcc
      301 ataacggcat tgtcattttt cctgagctgt tccgctcgtc gctccgcgcg actacgttct
      361 ctatcctcct gctccttccg gcgcaattcc tcttcacgtt taagcaactg gactctgaga
      421 gctgcaaggc cggatgcccc ccactgctgc cactgttttt caaatgccgt ctgactcgcg
      481 ggaatgtcct gtttctccac cttccggtaa tgttgtcgca atttttccat ttgctggctc
      541 agcgactgga tttttccctg ttcgctacgg tattccggtg ccgcccattg catcagggga
      601 atacgggaaa aaccggacga aaacggcgat gattttttca ggctggcagc atggctcatc
      661 gcttcctttc gttcggtgtt cagctcttcc cagcgtctgc gcgtcgcctg catatctgcc
      721 atcatcgaca tggcattact ggtgagtttc catgccgcat tactgtcctt cggcaacgct
      781 tcgatgatgt cacgtagtgt gtacgaagtt gcgttgtcag gaagcacgat attcagaagg
      841 tcagccacac ggcgggcagg ctctgtcagc ccgctgtttc tgagttcggt acgggaaatc
      901 tgtatttcca ggttaagtct gttaatcaga cgattctgtt cgccgcgttc tgtttcgata
      961 ccgcgtgttt ccatcgcaca ggcagacttt ccgaggtgaa taccaggcgt tttctcaagc
     1021 ccctgtcgct cgtatgaacg atggtctatc tcttcctgat aaccggcgtt cgccagtgcc
     1081 ctgttcgcat ggtcagccca tgatgcacgc cacgtctcgg catgtgtccg gtcgttccag
     1141 tccctgacct ttccaccgaa tccagcaggt ccgacagctc tcgtggtcag catgatgtgc
     1201 gcatggggat ttgttttatc catgtgatgg aacgccacat cagcaatcat gccctgactg
     1261 acaaagtttt ctctgacaaa ggcgagaacg gtttcccgtg cggcatcctg cggtagttcg
     1321 cgggggatgg cgagttcaat ttcccgcgca agttgtgagt tcttccggcg ttcggccttc
     1381 tcaacggcat tccagagttc ggcacggttc gtacaccagg caggggctgt cgcgggagtc
     1441 agaatcacag cttcagccac accgcttttg cgggtgtagt cgtgagtcag tccggtacgc
     1501 tcatcaagca tcagtgaacc ggaacgatag gcagcagaag caacggcgct gtagccgctg
     1561 tttctggaga tgattttcat gctgagatga taaatcgcca tttctgccgt aatgcctttt
     1621 tgtggttttc tttcagcccc gcagggcgca cacaatcgaa acggagtgga gattgtataa
     1681 gtgcgcactt cgtgattttc cgtgcattat gccagctcag tttttaaact accagtgacg
     1741 cgctaaaatg cgatttttca tcgcgcacgg agttacatca tgagcagaac actcgaacag
     1801 aagattgctg atgctgaggc cagattacag cgcctgaagg cgaagagcag gagtctggac
     1861 acagcgcaga aggtcattgt gggtgcagca ttgctggcaa aggtcagaaa gccggaggag
     1921 gtgcagttgc gtgcctggtt actccagttc ctgaaggcag aggtgacacg acaggctgat
     1981 gtgacgcgca tactgccgct gattaacgag ctggaggcgc tgccaggaca gtgattgtat
     2041 cgtccgctcg ccgcagtccc agcgaccgag cgttagcgag cgagtgggcg aggaagcgga
     2101 agtgaatccg tcgcctgatt gagcacatac gcacggtttt tcgggaggtg atatgcgctg
     2161 aacccgcatg aatactggat ttccacaggg ttggaggggg tgtattcgga acttgcaatt
     2221 ctgctttttt gcaacgcatt gtttttattg gttttttgtt ttcagcactc caagttatcc
     2281 acaggctcgt cgttaagttt ttagatcttg tttttaagat cttgttttta atacttgttt
     2341 tagcgccaaa attccttata gaaaacaaaa tgttacaacg ctataggtaa tatgatttaa
     2401 ggtaaaggta atatgattta aggtgcttgg gtgaggtaat ttaaggtaaa ggcaatatga
     2461 tttaaggtaa tattcacaga aaaagggata ttaaaataaa aaggcattgc ctttcgttga
     2521 gggtatgttt atcttttatt cattaccttt tggggaggga tgctctatgt cggatctaat
     2581 tgcctataaa tccaatgcgc tggttgaagc cagttataaa ttgaccctac aggaacagcg
     2641 atttttgtta ctttgcatcg gtcgattgaa gtctggggct gatgcagaat ctccaaaatt
     2701 gcaaaagaca atgaccatta cagctgcgga atatttcgat tcattccctg acatggggcg
     2761 gaaaaatgcc gaggttcagt tacaggaagc aattgatcgt ttgtgggaca ggtcaatcat
     2821 tctcaaggat gacgagaaac gtgaggagtt ccgctggatc cagtatcggg cacagtacgc
     2881 taaaggcgag gccagagcac aaataacatt ttctgacgca gtaatgcctt atttgacaca
     2941 actacaaggg caatttacta gagttgtaat caagaatata tctagattat caagaagtta
     3001 cagtataagg atatacgaac tcctccagca gttccgcagt actggcgaac gtattatcac
     3061 tctcgatgat tttcgctcaa tgcttgatat agagcataaa tatcaaacat ataaatcact
     3121 taaccagcaa ttattaagac cctgcattga cgaactgaac aaaaaaagcg acctggctgt
     3181 aacggttgag acgatcaaaa aggggcgcac ggttgtagcc ctgcattttc gcttcaagga
     3241 agacaaacaa atcaagatga cgatctaaaa tcgattttaa ggcacctaaa acgctccctg
     3301 ccgcgttttt tttgtgttag tagtgcgaag gtactattga agtgaaaaat tgcgtcaaaa
     3361 gcgctctaat gcagcgaaaa aagaaccccc atttttgggg ggcggaaaaa caaaactatg
     3421 cttgcattat gtgtgtgctt cttgcattca tccctgtcga tgaacatcga agaacatcga
     3481 cgaacataac acgatgttaa acaaaacaaa atattgttca cattcactgt gaccaaccgc
     3541 gatcatgtct cctctcggtg gcgtgtgttc gtgcatcttc ctcgcgccgc cattcgtccc
     3601 aggtacgatt aaaacccagc gagcggaaca gatgatccgg ctgtttttct ggtgtgttga
     3661 cggcagcaaa aagcggtgcc tcacgggttt tcagatgaaa ctccataagt tccggcgcag
     3721 gtgatatgtg gctgtctgca tcgtgattta cggcaacacc ataccctgca taccgtaacc
     3781 ccttatcggt cagtgcactg atgaccagct ggctgttatc ggctgaggga acggcaaacg
     3841 cgggatacag cgtaccatta agccggacaa caccgcccag agagtcatcc acgcccatga
     3901 ccagcaaaag ctgaagctgg cgggtttccc ggtcgacaga actcattacc ggcatcagcg
     3961 tcggtagcag acgtccctgc gtaaaatcca ccttccttgc tgccagtgat ggcatggctg
     4021 gctggcggtc ttctccaaga cagaaagact ccggccatgt cttcggctgg cggagattgc
     4081 gg
//
