LOCUS       CP125079                4074 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-B04 plasmid pKFS-B04_3, complete
            sequence.
ACCESSION   CP125079
VERSION     CP125079.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598738
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4074)
  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  JOURNAL   Unpublished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 4074)
  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                   :: Flye v. v2.9.1-b1780
            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 16:58:05
            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)                     :: 5,099
            CDSs (total)                      :: 4,986
            Genes (coding)                    :: 4,783
            CDSs (with protein)               :: 4,783
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 203
            CDSs (without protein)            :: 203
            Pseudo Genes (ambiguous residues) :: 0 of 203
            Pseudo Genes (frameshifted)       :: 76 of 203
            Pseudo Genes (incomplete)         :: 152 of 203
            Pseudo Genes (internal stop)      :: 36 of 203
            Pseudo Genes (multiple problems)  :: 54 of 203
            Pseudo Genes (short protein)      :: 3 of 203
            ##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..4074
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KFS-B04"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-B04_3"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            join(2227..4074,1..312)
                     /gene="mobQ"
                     /locus_tag="QL138_25475"
     CDS             join(2227..4074,1..312)
                     /gene="mobQ"
                     /locus_tag="QL138_25475"
                     /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="WHK12780.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(570..1262)
                     /locus_tag="QL138_25480"
     CDS             complement(570..1262)
                     /locus_tag="QL138_25480"
                     /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="WHK12781.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1794..2048)
                     /gene="mobC"
                     /locus_tag="QL138_25485"
     CDS             complement(1794..2048)
                     /gene="mobC"
                     /locus_tag="QL138_25485"
                     /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="WHK12782.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     Typing          complement(2050..2226)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2227..2585
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.056"
                     /coverage="100.0"
                     /evalue="3.94e-177"
     Typing          complement(571..1262)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2141..4074
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.38"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gccgttccct cagccgataa cagccagctg gtcatcagtg cactgaccga taaggggtta
       61 cggtatgcag ggtatggtgt tgccgtaaat cacgatgcag acagccacat atcacctgcg
      121 ccggaactta tggagtttca tctgaaaacc cgtgaggcac cgctttttgc tgccgtcaac
      181 acaccagaaa aacagccgga tcatctgttc cgctcgctgg gtttcaatcg tacctgggac
      241 gaatggcggc gcgaggaaga tgcaagaaca cacaccaccg agaggagaca tgatcgcggt
      301 tggtcacagt gaatgtgaac aatattttgt tttgtttaac atcgtgttat gttcgtcgat
      361 gttcttcgat gttcatcgac agggatgaat gcaagaagca cactcacata atgcaagcat
      421 agttttgttt ttccgccccc aaaaattggg ggttcttttt tcgctgcatc agagcgtttt
      481 tgacgcaatt tttcacttca atagtacctt cgcactacta acacaaaaaa aacgcagcag
      541 ggagcgtttt aggtgcctta aaatcgattt tagatcgtca tcttgatctg tttgtcttcc
      601 ttgaagcgaa aatgcagggc tacaaccgtg cgcccctttt tgatcgtctc aaccgttaca
      661 gccaggtcgc tttttttgtt cagttcgtca acacagggtt ttattagtat tttatttaag
      721 tctctgaatt gtttgtattt attttcaatc cctaacattg aacgaaagtc attaagagca
      781 ataattctct ctcccgtact gcggaattgc tggaggaact cgtatattct tatactgtaa
      841 ctacttgata aacctgatat gttttttata acaacgcgcg tgaattgccc cttcagttgc
      901 gtcagataag gcattaccgc gtcagaaaag gttattcgag ccttggcctc acctttagcg
      961 tactgtgccc gatactggat ccagcggaac tcctcacgct tctcgtcatt cttgagaatg
     1021 atcgacctgt cccataaacg atcgatcgct tcctgtaact gaacctcggc atttttccgc
     1081 cccatgtcag ggaatgaatc aaaatattcc gcagcggtaa tggtcattgt cttttgcaat
     1141 tcagcatcag caccagattt caatcgactg atacacagca acagaaaacg ttgttcctgt
     1201 agggtcaact tgtagctggc ctcaaccaaa gcattcgact tgtaggcaat caagtccgac
     1261 atacaaagat cccgttcaaa tgtggtgatg ctttaatgtg ccccacaaat aagaaatgtg
     1321 gaatgttttt ttttatatcc tcacatttct gtgaataaca ccttaaattc ctccaccttt
     1381 accttaaatt cctccaccta aacaccttaa attcctccac ctttacctta aattcctcca
     1441 catataccac tataacatat tgattttatt aatgaatttc acccctaaaa caagtattaa
     1501 aaacaagatc ttaaaaacaa gatctaaaaa cttaacggcg agcctgtgga taacttgggg
     1561 tgctgaaaac aaaaaaccaa taaaaacaat gtgttgcaag aaagcagaat tgcaagttcc
     1621 gaatactccc cttccaaccc tgtggaaatc cagtattcat gcgagttcag cgcatatcac
     1681 ctgccgaaaa accgtgcgta tgtgctcaac ctggcgacgg attcacttcc gcttcctcgc
     1741 ccactcgctc gctaacgctc ggtcgctggg gctgcggcga gcggacgata caatcactgt
     1801 cctggcagcg cctccagctc gttaatcagc ggcagtatgc gcgtcacatc agcctgtcgt
     1861 gtcacctctg ccttcaggaa ctggagtaac caggcacgca actgcacctc ctccggcttt
     1921 ctgacctttg ccagcaatgc tgcacccaca acaaccttct gcgctgtgtc caggctccgg
     1981 ctcttcgcct tcaggcgctg taatctcgcc tcagcatcag caatcttctg ttcgagcgtt
     2041 ctgctcatga tgtaactccg tgcgcgatga aaaatcgcat tttagcgcgt cactggtagt
     2101 ttaaaaactg agctggcata atgcacggca aatcacgaag tgcgcactta tacaatctcc
     2161 actccgtttc gattgtgtgc gccctgcggg gctgaaagaa aactacaaaa aggcattacg
     2221 gcagaaatgg cgatttatca tctcagcatg aaaattatct ccagaagcag cggctacagc
     2281 gccgtagctt ccgctgccta tcgttccggt tcactaatgc ttgatgagcg taccggactg
     2341 actcacgact acacccgcaa aagcggtgtg gctgaagctg tgattctgac ccccgcgaca
     2401 gcccctgcct ggtgtacgaa ccgtgccgaa ctctggaatg ccgttgagaa ggccgaacgc
     2461 cggaagaact cacaacttgc gcgggaaatt gaactcgcta tcccccgtga actgccgcag
     2521 gatgccgcac gggaaaccgt tctcgccttt gtcagagaaa actttgtcag tcagggcatg
     2581 attgctgatg tggcgttcca tcacatggat aaaacaaatc cccatgcgca catcatgctg
     2641 accacgaggg ctgtcggacc tgctgggttc ggcggaaagg tcagggactg gaacgaccgg
     2701 acacatgccg agacgtggcg tgcatcatgg gctgaccatg caaacagagc actggcgaac
     2761 gccggttatc aggaagagat agaccatcgt tcatacgagc gacaggggct tgagaaaacg
     2821 cctggtattc acctcggaaa gtctgcctgt gcgatggaaa cacgcggtat cgaaacagaa
     2881 cgcggcgaac agaatcgtct gattaacagg cttaacctgg aaatacagat ttcccgcact
     2941 gaactcagga acagcgggct gacagagcct gcccgccgtg tggctgacct tctgaatatc
     3001 gtgcttcctg acaacgcaac ttcgtacaca ctacgtgaca tcatcgaagc gttgccgaag
     3061 gacagtaatg cggcatggaa actcaccagt aatgccatgt cgatgatggc agatatgcag
     3121 gcgacgcgca gacgctggga agagctgaac accgaacgaa aggaagcgat gagccatgct
     3181 gccagcctga aaaaatcatc gccgttttcg tccggttttt cccgtattcc cctgatgcaa
     3241 tgggcggcac cggaataccg tagcgaacag ggaaaaatcc agtcgctgag ccagcaaatg
     3301 gaaaaattgc gacagcatta ccggaaggtg gagaaacagg acattcccgc gagtcagacg
     3361 gcatttgaaa aacagtggca gcagtggggg gcatccggcc ttgcagctct cagagtccag
     3421 ttgcttaaac gtgaagagga attgcgccgg aaggagcagg aggatacaga acgtagtcgc
     3481 gcggagcgac gagcggaaca gctcaggaaa aatgacaatg ccgttatgga ttcaggggta
     3541 ctgagcgcag tcgttacggg gtatggcgag gcccccatgc ctggtaacgg ggaaatgacc
     3601 tgttaccttc tgcttcacaa ccggaacgga gaatacacgc tctgggggaa cgagctggag
     3661 aaataccgca ccagaatctt tgagcgtgtt gatttaatgc gtgacaggag tggttatatc
     3721 tgtgaccgaa gcgaaatcgg tcaacatcca ccactgcaac gtgtttattc ctctgcgacc
     3781 tttgagcaac ttctgacgca ggtttgccag acatggccgc aatatacccg caatctccgc
     3841 cagccgaaga catggccgga gtctttctgt cttggagaag accgccagcc agccatgcca
     3901 tcactggcag caaggaaggt ggattttacg cagggacgtc tgccaccgac gctgatgccg
     3961 gtaatgagtt ctgtcgaccg ggaaacccgc cagcttcagc ttttgctggt catgggcgtg
     4021 gatgactctc tgggcggtgt tgtccggctt aatggtacgc tgtatcccgc gttt
//
