LOCUS       NZ_AP025758             4238 bp    DNA     circular CON 24-JUN-2023
DEFINITION  Escherichia sp. KS167_9B strain KS-P079 plasmid pla4, complete
            sequence.
ACCESSION   NZ_AP025758
VERSION     NZ_AP025758.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00159532
            Sequence Read Archive: DRR168433
            Assembly: GCF_030295215.1
KEYWORDS    RefSeq.
SOURCE      Escherichia sp. KS167_9B
  ORGANISM  Escherichia sp. KS167_9B
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Ogura,Y. and Okuno,M.
  TITLE     Escherichia cryptic clade I strains
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4238)
  AUTHORS   Ogura,Y. and Okuno,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-MAY-2022) Contact:Yoshitoshi Ogura Kurume University
            School of Medicine, Department of Infectious Medicine; Asahi-machi
            67, Kurume, Fukuoka 830-0011, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.4
            Genome Coverage                   :: 117x
            Sequencing Technology             :: MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/22/2023 11:55:43
            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)                     :: 5,675
            CDSs (total)                      :: 5,544
            Genes (coding)                    :: 5,294
            CDSs (with protein)               :: 5,294
            Genes (RNA)                       :: 131
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 100
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 250
            CDSs (without protein)            :: 250
            Pseudo Genes (ambiguous residues) :: 0 of 250
            Pseudo Genes (frameshifted)       :: 104 of 250
            Pseudo Genes (incomplete)         :: 164 of 250
            Pseudo Genes (internal stop)      :: 45 of 250
            Pseudo Genes (multiple problems)  :: 59 of 250
            Pseudo Genes (short protein)      :: 3 of 250
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP025758.1.
            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..4238
                     /organism="Escherichia sp. KS167_9B"
                     /mol_type="genomic DNA"
                     /strain="KS-P079"
                     /isolation_source="feces"
                     /host="Bos taurus"
                     /db_xref="taxon:2509666"
                     /plasmid="pla4"
                     /geo_loc_name="Japan"
                     /collection_date="2013"
     gene            1..516
                     /locus_tag="QUE34_RS28355"
                     /old_locus_tag="EsCd1KSP079_05624"
     CDS             1..516
                     /locus_tag="QUE34_RS28355"
                     /old_locus_tag="EsCd1KSP079_05624"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000097059.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_000097059.1"
                     /translation="MSSLSLQRYETNPFLELMTIPMKGKRIQVSRLGRDDNVLVNQNTG
                     EKFGTHVTTFKRVDSEQFVKLFTANIGLTFDLSSAGIKAFNVLLWAVQKQAFAKDQVLL
                     DSRALDDFLKSYDSLKLSYATLKRGINELEKAQIIAKTMRKGFYFINPNFVFNGDRIAF
                     TTLIERDC"
                     /name="replication/maintenance protein RepL"
     gene            580..987
                     /locus_tag="QUE34_RS28360"
                     /old_locus_tag="EsCd1KSP079_05625"
     CDS             580..987
                     /locus_tag="QUE34_RS28360"
                     /old_locus_tag="EsCd1KSP079_05625"
                     /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="hypothetical protein"
                     /protein_id="WP_133299398.1"
                     /translation="MSKNDVFACACRRLLEVVAGEQKWCFVRLLITTTWLEVFMTKHDA
                     IRISQLHQIFYDDDGLIDSEKNVTILYSIGFTVDEIAHFRNSTPNTVAGQLLNARVKLG
                     CASVSSLKPMILLRLLLNIKEIRFGFETDCK"
                     /name="hypothetical protein"
     gene            1075..1338
                     /locus_tag="QUE34_RS28365"
                     /old_locus_tag="EsCd1KSP079_05626"
     CDS             1075..1338
                     /locus_tag="QUE34_RS28365"
                     /old_locus_tag="EsCd1KSP079_05626"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001677227.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EexN family lipoprotein"
                     /protein_id="WP_000717655.1"
                     /translation="MKKICTLLMSIFILSACGEDTKSSDWWLNHPKEATEKYKECKKSG
                     EDSVNCQNVKKVAGIIGRTYGPMLEILKAESAEYDKQHGLNR"
                     /name="EexN family lipoprotein"
     gene            1343..2341
                     /locus_tag="QUE34_RS28370"
                     /old_locus_tag="EsCd1KSP079_05627"
     CDS             1343..2341
                     /locus_tag="QUE34_RS28370"
                     /old_locus_tag="EsCd1KSP079_05627"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000012467.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_000012467.1"
                     /translation="MSGFFEKFNSEVVSKIEEMTKPLQSQLGQDMLSLLSAGISVYILW
                     VGYQILAGKRQTPLQDLVWDLSKFAIILTFVSNADGYLTAAMDAIKSMKDGFLGKPVWA
                     TLDTMWSTTQLLADKVYAMDQSKYVSVEGGIGSMLVWGGSILIMSVAAVIYMLADVTMQ
                     LAILVAPIFIGCYMFGFTRVMFNNWLGILFSSVFTVIFAGVLVKIGTEFQTDMLSQISR
                     DANSTNILTMGAMAFVIGVLIAVFVWKSSSFAQQLAGAGVEGTLQGMALLGIGAAGMAV
                     EKTRNQMKRGTRTAAEWAGEKGEQKRASIGALGMEARRRASLEKARARNSA"
                     /name="type IV secretion system protein"
     gene            2338..3051
                     /locus_tag="QUE34_RS28375"
                     /old_locus_tag="EsCd1KSP079_05628"
     CDS             2338..3051
                     /locus_tag="QUE34_RS28375"
                     /old_locus_tag="EsCd1KSP079_05628"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001590713.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_001590713.1"
                     /translation="MNKKLIFSVLLCLFSFGSVAGIPVAIDASPEWAVEATRWTERLKQ
                     WSETARHYQSQIQAYKDQLATATGIRNIAAFTNELSNLQSELANIYKQGNSYISDFTSN
                     PEGALSSQAKNLFSKYGAFNMCSTGIESSDNLCKARIVSTAASIEQGNEINKQLSSAMS
                     QIQSLSNRIESSKDMKESQDLANALQAQSLKIQAIKMQYDVWDSKNRADAEMLKEQKYA
                     EYRLRQKNAKIPSFE"
                     /name="type IV secretion system protein"
     Typing          1344..2146
                     /name="MPF_T"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="89.552"
                     /coverage="91.0"
                     /evalue="1.15e-160"
ORIGIN
        1 atgagctcgc taagcttaca gagatacgaa acaaacccgt ttttagagct tatgacgatc
       61 ccgatgaaag ggaaacggat acaagtatct cgtcttgggc gggatgacaa tgttttggtt
      121 aatcaaaaca cgggagaaaa gtttggaaca catgtaacca cttttaagcg tgtagatagt
      181 gagcaatttg ttaagttgtt tactgcgaat attgggttaa cgtttgattt atcatcggca
      241 ggaattaaag cttttaatgt tcttttatgg gctgttcaaa aacaagcctt tgcaaaggat
      301 caggttcttt tggattcaag ggctcttgat gactttttaa aaagctatga tagcttaaaa
      361 cttagttatg ctacgttaaa gagaggaatt aacgagttag aaaaagctca gattatagca
      421 aagacaatgc gtaaaggatt ttattttata aaccccaatt ttgtatttaa tggagatcga
      481 atagcattta caaccctaat tgagagggat tgttaatcga tagaacaata caatgcagga
      541 tagacaatcc actagaaatt gcatgcaatt ttcagtggat tgtccaaaaa cgatgttttt
      601 gcctgtgcct gccgcaggct actagaagta gtcgcaggcg aacaaaagtg gtgttttgtt
      661 cgcctgctaa tcacaacaac ctggctagag gtttttatga ctaaacatga tgctatacgc
      721 atttctcaac ttcatcaaat tttttacgat gatgatggat taattgattc agaaaagaac
      781 gtgactattt tatacagtat aggatttaca gttgatgaaa tagctcattt tagaaattca
      841 acaccaaaca cagttgcggg tcagctatta aatgcaaggg ttaaattagg ttgcgcctcg
      901 gtttcatctt taaagccaat gatcttatta agattgcttt tgaacataaa agagattcgt
      961 tttggattcg aaactgattg caaataatat agttcaatag gtatttttgc tcttgactag
     1021 aattacaatt gctgattgta tcagcaattg taatgtccat acgaggaatc aaagatgaaa
     1081 aaaatttgta cgctcttaat gtctattttc attctttccg catgtggtga agatacaaaa
     1141 tcatcagatt ggtggcttaa tcatcccaaa gaagcgacgg agaaatataa ggagtgtaaa
     1201 aagtcagggg aagattctgt taattgtcaa aatgttaaaa aagttgccgg aattattggt
     1261 agaacctatg gccctatgct tgaaatactt aaggctgagt cagctgaata tgataagcaa
     1321 catggattga acaggtgata atatgtctgg tttctttgaa aagtttaata gcgaagttgt
     1381 tagtaaaatc gaagagatga ccaaaccact tcaaagtcaa ttaggtcagg atatgttatc
     1441 tcttctaagt gcaggtatta gcgtttatat cctctgggtt ggctatcaaa tattggcagg
     1501 gaaacgccag accccattac aagatctcgt ctgggatcta tcaaaatttg ccattatttt
     1561 aacattcgta agcaatgctg atggctatct gacggcagca atggatgcta ttaaatctat
     1621 gaaggatggg ttccttggta aacctgtatg ggcaacgcta gataccatgt ggagtacaac
     1681 tcagcttttg gctgacaaag tttatgctat ggatcaatcc aaatatgtgt cagttgaagg
     1741 tggaatcggg tcaatgttgg tttggggagg aagtatcctg attatgtctg tagcggctgt
     1801 tatttacatg cttgccgatg taacaatgca gttagctatt cttgtagctc cgatatttat
     1861 cggttgttat atgtttggat tcactagagt aatgtttaat aactggcttg gtatattatt
     1921 ttctagtgta tttactgtta tttttgctgg agttctcgtc aaaattggta ccgagtttca
     1981 aactgatatg cttagtcaga tatcgagaga tgctaactca acaaatattt taacaatggg
     2041 cgcaatggca tttgtaattg gagttctgat tgctgtcttt gtctggaaat catcgagttt
     2101 cgcgcagcag cttgccggtg caggtgttga aggtactctt cagggaatgg ctcttttagg
     2161 gattggggct gctggaatgg ccgtagagaa aacgagaaac cagatgaaac gtggaacgcg
     2221 aacagccgcc gaatgggcag gtgaaaaagg ggagcagaaa cgggcttcaa taggcgcatt
     2281 gggaatggaa gcaagaagac gagcatccct ggaaaaagca cgtgcgagga attcagcatg
     2341 aacaaaaaac taattttttc agtacttttg tgcttatttt catttggttc tgtcgcaggt
     2401 attccggttg ctattgatgc cagtccggaa tgggctgttg aagccacaag atggacagaa
     2461 cgactcaaac aatggtctga aacagcgcgg cattatcaaa gtcagattca ggcatataaa
     2521 gaccagttag ccacggcaac aggtataagg aatattgcgg cattcacaaa tgaactaagt
     2581 aacctacaat cagagctggc aaacatttat aagcagggga acagttatat ttctgatttt
     2641 accagtaatc ctgaaggtgc attaagtagt caggcgaaaa atctgttcag caagtatggt
     2701 gcttttaata tgtgttctac aggcattgaa agttctgata acctttgtaa ggccagaata
     2761 gtttcaacgg ccgctagcat tgaacaggga aatgagataa ataagcagct atcaagtgca
     2821 atgtctcaga ttcagagttt aagtaaccga attgagtctt caaaggatat gaaagaatcc
     2881 caggatttgg ctaacgcatt gcaggcgcag tcgttaaaaa tacaggcaat taaaatgcag
     2941 tatgatgtat gggatagtaa aaacagggct gatgcggaaa tgttgaaaga gcaaaagtat
     3001 gctgagtatc gcctgcgtca gaaaaatgca aagataccga gtttcgaatg atatgataaa
     3061 gctaaataag ctaaaagaat gggtagataa tcattggtct agattgaata gtaccggttc
     3121 tacaccgccg ccactgttaa tctcgctacc aatcatagtt attgttttaa gtgtggagct
     3181 tacgttaaag ctgattaatg ctttaatgta ttatggtaca ttgcaattta tcactgataa
     3241 aattgaaaag aggtttgttc ccagcggtgg tataaaagaa agactccttt ttacgttaaa
     3301 gctgttttgt attttacttc tgttattaat agtaatgcga ttttcaatga agtaaaaaat
     3361 aaaggtcatc gaatagatgg ccttttctat tctaaattct aaatatagag cctgcggcag
     3421 gcacaggcaa aaacatcgtt tttggacaat catggataaa atgttaacat tttgaccatg
     3481 attgtctatc ctgcattgct cttttgccga cctcaaaacc cctagcgtgt ttttgtttcc
     3541 cgatctctag aaccaccgag ccgccacggt tccggcagcg ccttgagcgc aaccggaaac
     3601 cgtctgggga gaaccccaga cccccatcgc tgtaacatcg acggtctacg accacctacc
     3661 aaccgtgtgg ctacctgttc cgtgctaatg ggctttgcag ggggctggcg cggttcctgg
     3721 cgacctgaaa gcccctggtt aggggtatcg gcgcgcctga cctcctgaaa ccctctgtaa
     3781 gcatttttcg cgccttccat gccctgacgg gcatctaaag cccgtttcgt gcgtctgagc
     3841 gcgttttaag agctaagacg actaaaacat taccaacacc tgaaaatcgc gttctggtgc
     3901 tctggatggc ccacagaacg cattttcgaa cagaacagca acggcatttc tgacaacatg
     3961 cgagaggtga tcccgctcgc cgcagcccca gcgaccgaac gtagtgagcg agtgggcgag
     4021 gaagcggaag agaattgata gccataattg agcacctacg ctccttagtt aagaactaag
     4081 aagggaaatt ctcggaaccc gcatgaatcc tagaaagtgg tgatcaggat ctgtaccttg
     4141 taagctcaga tccgatacct tgcaggctca aaaattgctt gattttgagc tcatgaggat
     4201 ttattgtgaa tctccaaagc ccaaaaaagg atgcaata
//
