LOCUS       CP124983                4773 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KSE-D31 plasmid pKSE-D31_6, complete
            sequence.
ACCESSION   CP124983
VERSION     CP124983.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598758
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4773)
  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  JOURNAL   Unpublished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 4773)
  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 16:43:15
            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)                     :: 5,034
            CDSs (total)                      :: 4,910
            Genes (coding)                    :: 4,652
            CDSs (with protein)               :: 4,652
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 258
            CDSs (without protein)            :: 258
            Pseudo Genes (ambiguous residues) :: 0 of 258
            Pseudo Genes (frameshifted)       :: 82 of 258
            Pseudo Genes (incomplete)         :: 177 of 258
            Pseudo Genes (internal stop)      :: 54 of 258
            Pseudo Genes (multiple problems)  :: 49 of 258
            Pseudo Genes (short protein)      :: 4 of 258
            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..4773
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KSE-D31"
                     /isolation_source="Sewage"
                     /db_xref="taxon:562"
                     /plasmid="pKSE-D31_6"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            join(4608..4773,1..179)
                     /locus_tag="QL154_25130"
     CDS             join(4608..4773,1..179)
                     /locus_tag="QL154_25130"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WHJ27404.1"
                     /translation="MSEKRNKMLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLAEKPAR
                     AGKLPSISPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHA
                     VLEKGADDDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            388..822
                     /locus_tag="QL154_25135"
                     /pseudo=""
     CDS             388..822
                     /locus_tag="QL154_25135"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial on complete genome; missing
                     C-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            857..1342
                     /locus_tag="QL154_25140"
     CDS             857..1342
                     /locus_tag="QL154_25140"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WHJ27405.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKVAFSEHEKFVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSTLLTASGASILWWQGQQIL
                     DNYTIIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            1346..1561
                     /locus_tag="QL154_25145"
     CDS             1346..1561
                     /locus_tag="QL154_25145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WHJ27406.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMFGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1760..2311)
                     /locus_tag="QL154_25150"
     CDS             complement(1760..2311)
                     /locus_tag="QL154_25150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000654246.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WHJ27407.1"
                     /translation="MKDMKAVVVFTGKDLNIMRTEGGSGYWHARTDRLNDADYLIAVRN
                     RRETWAVKDLEHGTAFLIAKITGCFKSPDYDDRNVITFDEYAEIHTPKAWKMLTDGQRY
                     PVAYLSAQEAFLRIGVTPEQLEWKKFHPSSPSVPNTVIPGLAEEKTEKLSLNEAIERAK
                     KDISNATGIDSSAITISIKI"
                     /name="hypothetical protein"
     gene            2847..3314
                     /locus_tag="QL154_25155"
     CDS             2847..3314
                     /locus_tag="QL154_25155"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011899450.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WHJ27403.1"
                     /translation="MPAPNNYGVAGSPNSAIAHPDGLDCYGRVPEINSKGDVIPAGDIF
                     LRVGRHTGPNRGFGVRHIWAEHEQELVKLGYTTVNDVARFVRDIIRRGVPIYCEFNSTS
                     GKHRPAVLKSSVGIVILEPREAPETESGWIYVVVTAYTRRTAHGTLVGHIE"
                     /name="hypothetical protein"
     Typing          4341..4525
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.17"
                     /coverage="86.0"
                     /evalue="5.83e-49"
     Typing          complement(3883..4395)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.829"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          170..1665
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.385"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4630..4772
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.833"
                     /coverage="99.0"
                     /evalue="6.4199999999999995e-24"
ORIGIN
        1 tgcttcgtca gcttgccggc atggggaata acctcaacca gattgcccgg caggttaacg
       61 ccggtggcgg cagcgggcac gaccgcgtgc aggtcgtcgc cgcgctgatg gccatagatg
      121 ccggactcga gcggctgcgg catgccgtgc tggaaaaggg tgcagacgat gatcgttaag
      181 tttcacccgc gagggcgcgg cggtggcgcc ggtccggtgg attatctgct ggggaaagac
      241 cgacagcgcg acggcgccac cgttctgcag gggaagccgg aagaagtcag ggagcttatc
      301 gacgcctcgc cctacgcaaa aaagtacaca tccggcgtcc tgtcctttgc cgaaaaggat
      361 ttaccgcccg ggcagcgcga aaagctgatg gcgagctttg aacgggttct gatgcccgga
      421 ctcgataaag accagtacag cgtgctatgg gttgagcacc aggataaggg gcggctggag
      481 ctgaacttcc tgatcccgaa catggagctg ctgacaggca ggcgtctcca gccgtattac
      541 gaccgcgccg accgtccgcg cattgatgcc tggcagacca tcgtgaacgg caggctgggg
      601 ctgcatgacc cgaacgcgcc tgaaaaccgg cgggcgctgg tcacgccgtc cgcgctgccg
      661 aaaacgaagc aggaagccgc tcaggcaatt acacggggtt tactggcctt agcctcgtcc
      721 ggggagctga aaacccgcca ggacgtcact gaggcgctag aaagcgcagg ttttgaggtg
      781 gtgcgcacca caaaaagcag catcagcatt gccgacccgg acggggggcg aaacatccga
      841 ctgaagggag ccatctatga acagtctttt aacgctggcg aaggacttag agcagaaatc
      901 gaaagcgcag cagcagagta ccggcgagat gctgaaagtc gcattcagcg agcacgagaa
      961 gtttgtcaga gcggaactga gcgaaagcga gaagagaatc agcgccgcca tcctcgacca
     1021 cgaccggaag ctgtcctcag ccatgagcca gcgcacgaaa ggcatggtgc gtatggtcag
     1081 ccagacgtgg ctgaccatcg tcctggtgtc tacactgctg acagcatcgg gcgcaagcat
     1141 tctatggtgg caggggcagc agatactcga caattacacg atcatccggg agcagaagag
     1201 cacgcaggcc atgctgtccg agaggaacag cggcgtgcag ctctcgacct gcggagagca
     1261 gagacggcgc tgcgtgaggg tgaacccgga agcgggacgg ttcggagagg attcgagctg
     1321 gatgatactg gcggggaaat agcacatgac ggagctggaa aaacagttgc tgagcgcatt
     1381 agagcagcta cagcaggact actcgaaaag gctggacgag tgggagaacg ccttcgcgga
     1441 atggcggacg atgtttggtc ttatgcaacg ggagaacgcg gcgctgagcg agcgcgtcac
     1501 gggcttgagc aggcaggtgc agagtttgag cgagcagctg cgccggttgt cacaaggctg
     1561 aacgtgatag aggcacatcg tgagcaggaa cgggcggcgc agcatcagaa agcgctggag
     1621 ctggaacgat ctcagcgaca gcgaacgtac aacggtccgt cactttgaat ctgtgcgccg
     1681 gaaaagcatg ggcttgctgt ttctggcgca caggttcagt tctagaacat gaggctgcta
     1741 tcttgttgtt cacgcttcat cagatcttga tgcttattgt tatggctgag ctatcaatcc
     1801 ctgttgcgtt gctaatatcc tttttggctc tttcaattgc ctcgttaagg gagagttttt
     1861 ctgttttctc ttcagccaga ccaggaatca ctgtattagg aaccgatggg gatgaaggat
     1921 ggaatttctt ccattccagt tgttccggtg ttaccccaat acgtaaaaaa gcttcctgtg
     1981 cgctcaggta agcaaccgga tagcgctgac catcggttag cattttccat gcttttggag
     2041 tgtgaatttc tgcgtattca tcaaaggtta tgacgttcct gtcgtcgtaa tcagggcttt
     2101 taaaacaccc ggtaattttg gcgatcagga atgctgtgcc gtgttccagg tcttttactg
     2161 cccacgtttc ccttctgttt cttactgcta tgaggtaatc ggcatcgttg agcctgtctg
     2221 ttctggcatg ccagtagcct gaccccccct cggttctcat tatgttcaaa tccttcccgg
     2281 taaaaaccac aacagctttc atatctttca tatagaaacc cttaataggt gagtcaattt
     2341 cattttttta tgaaatctat acgatagaat tcgtgttgta aatgtttttt atgcgataaa
     2401 atgcagcccc ctacctcttt tattgttagt gataaggctt cctgtttgtt tttttgataa
     2461 accggttaaa acaggggctt ggacgaggat atacattgaa agcatgagcc attcacgtgg
     2521 ctgcatggct atgcagccgc gtgaaattta tcaggcgcag aatgcgcggt ttagcgggga
     2581 gtttactgcc ggttttaccg ggctaacgcc gctttcacgc tgaacccgtc cggagcggtg
     2641 cgggcaaggg atgttatggt aaatctagct gctagggcga ttcgcacgtc acattttcag
     2701 gtgtgatatc cttatgcgcc aaggatgaaa ggacaaaaaa ataatccata aggattcttt
     2761 ttatcgtctc tgcttttttc ttgggctcct tccgcttgtt tcctctctgg taccatatgc
     2821 ggactctact caataaggat cgttttgtgc ctgctccaaa caattacggt gtagctggtt
     2881 cacctaacag cgctatagct caccctgatg ggcttgattg ctatggccgt gtccctgaaa
     2941 ttaattctaa aggtgatgtt attcctgctg gcgacatctt cttgcgtgtt ggtaggcata
     3001 ctggccctaa ccggggcttt ggtgttcgcc atatctgggc tgagcacgag caggaactgg
     3061 ttaagctggg atatacgacc gttaatgatg tggctcgttt tgtccgggat attattcgtc
     3121 gtggcgtacc aatatattgc gagttcaaca gtacaagcgg taaacatcgg cctgcagtgc
     3181 taaagtcgtc ggtaggcatc gtaattcttg agcccagaga agcgcctgaa actgagtcag
     3241 gttggatcta tgtcgttgtg actgcgtaca cacgaaggac ggcgcacggt actttggttg
     3301 gtcatattga ataaaaaaat agggcgctaa aaagcgccct ttatgaattc gttggtagtc
     3361 gcagcatttc cttagcacat agggttcaga aaccgacgct tgtcgtaact acccggcaga
     3421 tgaccagcca tctgactgcc cggcacagaa ggcctattac tggttgatgc cccctgcgaa
     3481 tgctcttgca gtacaataat cataaacatc gtgatgtaga tttgcaacca acattttggt
     3541 tgcaacctat atactaattt ttttcgataa ccctggaatc cattgctgtg tctggatttc
     3601 ttgaagctcc tggctataga taccctatat cctaacagtt attctgctgt gaatatcaga
     3661 aatgaacact tgagatcatc agtggctcgt cgtagtctct tgctcagaaa cgaaaaaacc
     3721 accctggcag gtggtttttt cgaaggttag ttaatcctgg cagattctct aaccgtggta
     3781 acagtcttgt gcgagacatg tcaccaaata ctgtcctttc agtgtagcct cagttaggcc
     3841 gccacttcaa gaactctcgt tacatctctc gcacatcctg cttaccagtg gccgttgcca
     3901 atggcgatta gtcgtgtcta tccgggttgg actcaagacg atagttaccg gacaaggcgc
     3961 agcggtcgga ctgaacgggg ggttcgtgca tacagtccag cttggagcga actgcctacc
     4021 cggaactgag tgtcaggcgt ggaatgagat aaacgcggcc ataacagcgg aatgacaccg
     4081 gtaaaccgaa aggcaggaac aggagagcgc acgagggagc caccaggggg aaacgcctgg
     4141 tatctttaag tcctgtcggg tttcgccacc actgatttga gcgtcagatt tcgtgatgct
     4201 tgtcaggggg gcggagccta tggaaaaacg gcagcgccgc atccttttcc tgtcctgctt
     4261 gccatgccgt atgcctttgc tcttatccgt ttgcaggtaa cgcccgccgc agccgaacgt
     4321 caggagcgga agcgaccgag tgagcgagga ggcgtcatat caccgtaacc tccattttct
     4381 cctgtacgcc ctgcagctgc atttttcccc tgccacatga agcactttca ttacgtgtta
     4441 ctccgccgta acatattgag ccagtataca ctccgctagc gctacgtgac tggttcaggg
     4501 ctgcgccccg aaacctgcta aaaccactga cgcgcctgcg gcttgtccaa caccgcgccg
     4561 accgggaaaa gatttcccgc ccgtcccggc gttatcagga gatcggtttg tcagagaaac
     4621 ggaacaagat gctcaccatg tgggtgaccg aagatgagca ccgccgtctg ctggaacgct
     4681 gcgacggtaa acagcttgca gcctggatgc gccagacgtg cctggccgag aaacccgccc
     4741 gcgccggcaa gcttccctca atctcgccgg cgc
//
