LOCUS       NZ_AP025746             4612 bp    DNA     circular CON 24-JUN-2023
DEFINITION  Escherichia sp. 10290 plasmid pla5, complete sequence.
ACCESSION   NZ_AP025746
VERSION     NZ_AP025746.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00467134
            Sequence Read Archive: DRR360889
            Assembly: GCF_030295155.1
KEYWORDS    RefSeq.
SOURCE      Escherichia sp. 10290
  ORGANISM  Escherichia sp. 10290
            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  JOURNAL   Unpublished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 4612)
  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                   :: 61x
            Sequencing Technology             :: MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/22/2023 12:30:41
            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)                     :: 5,882
            CDSs (total)                      :: 5,747
            Genes (coding)                    :: 5,497
            CDSs (with protein)               :: 5,497
            Genes (RNA)                       :: 135
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 100
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 250
            CDSs (without protein)            :: 250
            Pseudo Genes (ambiguous residues) :: 0 of 250
            Pseudo Genes (frameshifted)       :: 87 of 250
            Pseudo Genes (incomplete)         :: 167 of 250
            Pseudo Genes (internal stop)      :: 44 of 250
            Pseudo Genes (multiple problems)  :: 43 of 250
            Pseudo Genes (short protein)      :: 3 of 250
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP025746.1.
            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..4612
                     /organism="Escherichia sp. 10290"
                     /mol_type="genomic DNA"
                     /strain="10290"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:2935450"
                     /plasmid="pla5"
                     /geo_loc_name="Japan"
                     /collection_date="2002"
     gene            34..357
                     /locus_tag="QUE74_RS29380"
                     /old_locus_tag="EsCdI10290_05827"
     CDS             34..357
                     /locus_tag="QUE74_RS29380"
                     /old_locus_tag="EsCdI10290_05827"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000956000.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            566..>997
                     /locus_tag="QUE74_RS29385"
                     /pseudo=""
     CDS             566..>997
                     /locus_tag="QUE74_RS29385"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial in the middle of a contig;
                     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            1035..1553
                     /locus_tag="QUE74_RS29390"
                     /old_locus_tag="EsCdI10290_05828"
     CDS             1035..1553
                     /locus_tag="QUE74_RS29390"
                     /old_locus_tag="EsCdI10290_05828"
                     /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="WP_072650569.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEESLEKHREGVKEAMMQHRRDVLKLAGNTGMMLLGIVFLLFTVSG
                     GTLWYLGGRIQANLEDIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVISFQ
                     GKEWVHLKG"
                     /name="MbeB family mobilization protein"
     gene            1560..1793
                     /locus_tag="QUE74_RS29395"
                     /old_locus_tag="EsCdI10290_05829"
     CDS             1560..1793
                     /locus_tag="QUE74_RS29395"
                     /old_locus_tag="EsCdI10290_05829"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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="WP_000137445.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2157..2393
                     /locus_tag="QUE74_RS29400"
     CDS             2157..2393
                     /locus_tag="QUE74_RS29400"
                     /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_125075503.1"
                     /translation="MSIIIDREKYTALMTLIQTSQGYVGSKVQPNGYTLKCSFDTGFAC
                     CISRNTRNSNLSVHFENESTDPATHFAILSAIS"
                     /name="hypothetical protein"
     gene            complement(2514..3257)
                     /locus_tag="QUE74_RS29405"
                     /old_locus_tag="EsCdI10290_05830"
     CDS             complement(2514..3257)
                     /locus_tag="QUE74_RS29405"
                     /old_locus_tag="EsCdI10290_05830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001423320.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="WP_286332283.1"
                     /translation="MASRRQTPLLRRAVGKKTADAVFFISKMELTPLKTIVYVDGFNFY
                     YRKLKDSNKKWLNIKAMVEKLLPDDEIIGINYYTARISGRIDSDAPRRQQIYFNALKSI
                     DNLSIHYGTFSVNESRMFLVQPLDFKHHLKNPNQKIKFANVLKTEEKGSDVNLGCHLVR
                     DGFQGKYEKAVIITNDTDLAEPMRVVKSELSLYIELLSPVNKPARTLSAICDKVTLISD
                     QSIADSQFEDVIVVGEKTVTKPAQW"
                     /name="NYN domain-containing protein"
     gene            complement(4390..4581)
                     /locus_tag="QUE74_RS29410"
     CDS             complement(4390..4581)
                     /locus_tag="QUE74_RS29410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          4220..4305
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.851"
                     /coverage="100.0"
                     /evalue="3.99e-36"
     Typing          complement(3666..4194)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.636"
                     /coverage="98.0"
                     /evalue="3.01e-155"
     Typing          348..1897
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.42"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgggggtaa tgataccgat gaaacgcgag aggatgctca cgatacgggt tactgatgat
       61 gaacatgccc ggttacttga acgctgtgag ggtaaacaac tggcggtatg gatgcggcgg
      121 gtctgcctgg gggagccggt tgcccgttcc gggaaactgc cgacactggc accgccgtta
      181 ctgcgtcagc tggccgccat cgggaataac ctgaatcaga cagcgaggaa ggtgaacagc
      241 gggcagtggt cttccggtga ccgggttcag gtggtggccg cactgatggc catcggggat
      301 gagctgcgcc ggctgcgtct ggccgtcagg gaacagggga cgcgggatga tagttaagtt
      361 tcatgccagg ggaaaaggcg gtggcagtgg tccggttgat tacctgctgg ggagggagcg
      421 taaccgggag ggcgcaaagg tgcttcaggg taacccggaa gaagtccggg aactcatcga
      481 tgccacgcca tttgcgaaga aatacacgtc cggtgttctg tcgttcgcgg agaaggaact
      541 gccgccggga ggacgtgaaa aagtgatggc gagttttgag cgtgtactga tgcccggtct
      601 cgaaaaaaat cagtacagca ttctgtgggt ggagcaccag gacaaggggc ggcttgagct
      661 taattttgtc attccgaaca tggagctaca gagcggaaaa cgcctccagc cgtactacga
      721 ccgcgcagac aggccgagaa ttgatgcctg gcagacgctg gtgaatcacc attacgggct
      781 gcatgacccc aacgccccgg agaaccgccg gatactgact ctccctgata acctgccgga
      841 aacgaaacag gcgcttgcag agagcgtcac acgcgggata gacgctcttt atcatgtcgg
      901 ggagataaaa ggccgtcagg atgtgattca ggcgctcaca gaggcagggc ttgaagtggt
      961 cagggtgacg cgaagcagta tcagcattgc agacccgaac ggtgggaaga atatcaggct
     1021 gaaaggagca ttttatgagc aatcttttgc agacgggcgc ggagttcgag aaaaagctga
     1081 aagagagagc cgaatctaca gagaaaatgc tgaacaacga gttcaggagg ctcggcgaat
     1141 ctgtaagcga ggctgtgaca tcaaacgaga cgaaaatcag agacgctata gccctgttca
     1201 cagcctcgac agaggaatct ctggaaaaac accgggaagg ggtgaaagag gcgatgatgc
     1261 agcacaggag ggacgtgtta aagctggcag ggaatacggg catgatgttg ctggggatag
     1321 tctttctcct gtttaccgtg agtggcggga cgctctggta tcttggcggg aggatacagg
     1381 cgaacctgga agatatcagg aagcaggaag agacattgca gaaactgaac gcgaagacat
     1441 ggggcgtgga gtttgtgcag gacgggaaca ggaaatttct ggtccttcct tacgggaagt
     1501 cagcagaggt gatttccttt caggggaagg aatgggtaca tctgaagggg tgacacagag
     1561 tgacagagct ggaaacacat ttgctgaacg ccttagagca gctgcaacag gactatatgc
     1621 agcggctgag cgaatgggag agcgccttcg tggaattgca gaagatgttt tcgcttacgc
     1681 aacgggacaa cgcgatgctg aacgagcggg tcatgcagtt gagtcagcag gtgcagcact
     1741 tgagcgagca gacagaacgc ttgagccagt tatacagcga gaactggaga taagagagga
     1801 acggttgata caggagcgcg aatatgcgtt atccctggaa cgggagcgtc agccggaaat
     1861 acaggaacgc acgctggatg gcccttcgct gggatggtga aactatgaaa aatggcaggt
     1921 tcagtggatt ttgacggact aatgtagtct gcaccatctt gttgcatagg tattcatgcg
     1981 gttaaaattt atcaggcgcg atcgcggcag tttttcggga ggtttgttgc ctgtttttcc
     2041 ggtttcccgt cagaaacgcg ctgagagcgt ctgaggcggt gcgggcaacg ggagttatgg
     2101 taaatagatt tattgctgag gtttaatgcc tgcagagtaa tactaatggg gatgtgatga
     2161 gtattattat tgatcgtgaa aaatatactg ctttgatgac gttgatccag acatctcaag
     2221 gatatgttgg ctcaaaagta caaccaaatg gatatacatt gaagtgttct ttcgacactg
     2281 gttttgcatg ttgtatctct agaaatacta gaaatagtaa cttatctgtt cattttgaaa
     2341 atgaaagtac agatcctgca actcactttg ctattttaag tgctattagc taatttttta
     2401 ttttctgcac atagctatag atttcatact ctttatattt gcctgaaggt ataatgcaaa
     2461 acataaaaag cccgggggac gggctttttt tcaacagaac gagtatgtag ccactaccac
     2521 tgtgctggtt ttgtcacggt tttctcacca actacaataa cgtcttcaaa ctggctatca
     2581 gctattgatt ggtcgcttat aagagtgacc ttatcgcata ttgcgctcag ggttcttgct
     2641 ggtttgttta caggagaaag tagttcaata taaaggctga gctctgattt gactactctc
     2701 attggttcag ccaaatctgt atcattagtt attattacag ccttctcgta tttcccttgg
     2761 aaaccatctc taaccaagtg gcaacctaaa ttaacgtcag aacccttttc ttctgtcttt
     2821 aagacgtttg caaactttat tttttgattc gggtttttta agtgatgttt gaaatcaaga
     2881 ggctgcacta aaaacattct gctttcattc accgaaaaag taccataatg gatacttagg
     2941 ttatctatgc ttttcagtgc attgaaatat atttgttgcc tacgaggtgc gtcagaatca
     3001 atccttcctg agatcctagc cgtgtaatag ttaattccta ttatttcatc atccggtagc
     3061 aatttttcga ccattgcttt tatgttcagc cactttttgt tggaatcttt cagcttacga
     3121 taataaaagt taaagccatc aacataaact attgttttca atggggttag ctccatttta
     3181 gatataaaaa aaaccgcatc tgcggttttt tttcctacgg cacgccgtag gaggggtgtt
     3241 tgcctgcggc tcgccacagg agggttgttt cttcgcctgc ggcacgccac aggggggttg
     3301 tttcttcgcc tgcggcacgc cacaggtctg taccaacatt attgcatttt ttttgtctag
     3361 tgcaaatgtt ttatatggtg acgaagtaag ccctacctaa aggagaaaag atcttcttga
     3421 gatccttttt ttctgcgcgt aatctcctgc tttgaaaacg aaaaaaccac cctggcaggt
     3481 ggtttttcga aggttagtta atcctggcag attctctaac cgcggtaacg gtcttgtgcg
     3541 agacatgtca ccaaatctgt cctttcagtg tagccgtagt caggccgcca cttcaagaac
     3601 tctcgataca tctctcgcac atcctgttta ccagtggccg ttgccaatgg cgattagtcg
     3661 tgtctttccg ggttggactc aagttgatag ttaccggata agacgcagcg gtcggactga
     3721 acggggggtt cgtgcataca gtccagcttg gagcgaactg ccttcccgga gccgagtgtc
     3781 aggcgtggaa tgagaaaccg cggccataac agcggaatga caccggtaca ccgaaaggca
     3841 ggaacaggag agcgcacgag ggagcttcca gggggaaacg cctggtatct ttatagtcct
     3901 gtcgggtttc gccacctctg acttgagcgt caatttttgt gatgctcgtc aggggggcgg
     3961 agcctatgga aaaacgcctg cggcgcggcc tttttccctg gttttgcctt tttgttcaca
     4021 tgttctttcc ggccttatcc cctgattctg tggataaccg cattaccgtc tttgcgtgag
     4081 ctgataccgc tcgccgcagc cgaacgaccg agcgtagcga gtcagtgagc gaggaagcgg
     4141 aagagcgcct gatgcggtat tttctcctta cgcatctgtg cggtatttca caccgcatat
     4201 ggtgctcttt tcttataatc tgcactgatg ccacatagtt aagccagtat acactccgct
     4261 atcgctacgt gactgggtca tggctgcgcc ccgacacccg ctaaaacccc ctgacgcgcc
     4321 ctgacgggct tgtctgctcc cggcatccgc tcacagacaa gctgtgaccg tctccgggag
     4381 ctgtatgtgt cagaggtttt caccgtcatc cccgaagcgt gcgaggcagc tgcggtaaag
     4441 ctcgtcggcg tggtcgtgaa gtgattcaca aatatcggcc tgttcatctg cgtccagttc
     4501 gttgagcttc tccagcagcg ttaatgtctg gcttcttata aagcgggcca tgttaagggc
     4561 ggttttttcc tgtttggtca ctgatgcctc cgtgtaaggg ggatttctgt tc
//
