LOCUS       NZ_CP110981             6756 bp    DNA     circular CON 06-JAN-2024
DEFINITION  Escherichia coli strain XYEH3934 plasmid pYUXYEH3934-3, complete
            sequence.
ACCESSION   NZ_CP110981
VERSION     NZ_CP110981.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31720681
            Assembly: GCF_026248885.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6756)
  AUTHORS   Wang,J.
  TITLE     Complete sequence of E. coli XYEH3934
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6756)
  AUTHORS   Wang,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-NOV-2022) Key Laboratory of Prevention and Control of
            Biological Hazard Factors (Animal Origin) for Agrifood Safety and
            Quality, Ministry of Agriculture of China, Yangzhou University,
            No.48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: Nanopore MinIon
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/05/2024 18:38:27
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,800
            CDSs (total)                      :: 4,680
            Genes (coding)                    :: 4,479
            CDSs (with protein)               :: 4,479
            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)              :: 201
            CDSs (without protein)            :: 201
            Pseudo Genes (ambiguous residues) :: 0 of 201
            Pseudo Genes (frameshifted)       :: 67 of 201
            Pseudo Genes (incomplete)         :: 126 of 201
            Pseudo Genes (internal stop)      :: 45 of 201
            Pseudo Genes (multiple problems)  :: 34 of 201
            Pseudo Genes (short protein)      :: 3 of 201
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP110981.1.
            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..6756
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="XYEH3934"
                     /isolation_source="secretion"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pYUXYEH3934-3"
                     /geo_loc_name="China: Xuyi"
                     /lat_lon="33.01 N 118.54 E"
                     /collection_date="2021-09-19"
                     /collected_by="Guo-Zhuang Sun"
     gene            complement(596..>676)
                     /locus_tag="ORI33_RS23835"
                     /old_locus_tag="ORI33_23830"
                     /pseudo=""
     CDS             complement(596..>676)
                     /locus_tag="ORI33_RS23835"
                     /old_locus_tag="ORI33_23830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076612230.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0004803 - transposase activity [Evidence IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
                     /name="IS1 family transposase"
     gene            complement(728..1665)
                     /locus_tag="ORI33_RS23840"
                     /old_locus_tag="ORI33_23835"
                     /pseudo=""
     CDS             complement(728..1665)
                     /locus_tag="ORI33_RS23840"
                     /old_locus_tag="ORI33_23835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076611102.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS5 family transposase"
                     /name="IS5 family transposase"
     gene            complement(1859..3025)
                     /locus_tag="ORI33_RS23845"
                     /old_locus_tag="ORI33_23840"
     CDS             complement(1859..3025)
                     /locus_tag="ORI33_RS23845"
                     /old_locus_tag="ORI33_23840"
                     /inference="COORDINATES: protein motif:HMM:NF013080.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="phosphoethanolamine transferase"
                     /protein_id="WP_159145930.1"
                     /translation="MKIDPIRNRLYTLTVLSCYLVLTPNMLSKLAFNALHGMKEYISEL
                     IQFKKLNSLNSENNEWGEITNDSKYEINILFIGEMMRSDYLNVYGYNEKNTPFLSSVNG
                     TFVHNFYSADTHTVPSLRIMLTYQGENSKIEPNYPKSFINAANNAGYDTYWISNQGLIG
                     EYDTPISFIAKSATHKYFIKLHDNNAEDHDMLKVINYYISKPSKKKKLIVVHLFDSHGY
                     GSLCDQNKKFMTENKLLKYSETNKKDVECYSSAVTKTDKIISETYKTLNSKNIKFSIVY
                     FSDHGSSESTDNAGNIFYKHEDNDKAGYKIPLIRITSDDTEKKHIYTGYNGIDFTHGLL
                     NWLSIKSEKVNPSYNLFEYTEDFSSEKAKEKEKYINSLSDNFKPIELN"
                     /name="phosphoethanolamine transferase"
     gene            3587..4284
                     /locus_tag="ORI33_RS23850"
                     /old_locus_tag="ORI33_23845"
     CDS             join(3587..3836,3836..4284)
                     /locus_tag="ORI33_RS23850"
                     /old_locus_tag="ORI33_23845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558267.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
                     /protein_id="WP_223814698.1"
                     /translation="MASVSISCPSCSATEGVVRNGKSTAGHQRYLCSHCRKTWQLQFTY
                     TASQPGTHQKIIDMAMNGVGCRASARIMGVGLNTVLRHFKKLRPQSVTSRIQPGSDVIV
                     CAEMDEQWGYVGAKSRQRWLFYAYDRIRRTVVAHVFGERTLATLERLLGLLSAFEVVVW
                     MTDGWPLYESRLKGELHVISKRYTQRIERHNLNLRQHLARLGRKSLSFSKSVELHDKVI
                     GHYLNIKHYQ"
                     /name="IS1 family transposase"
     gene            4339..4494
                     /locus_tag="ORI33_RS23855"
                     /old_locus_tag="ORI33_23850"
     CDS             4339..4494
                     /locus_tag="ORI33_RS23855"
                     /old_locus_tag="ORI33_23850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008323621.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_053287134.1"
                     /translation="MKKLLFLGGVTVSVVLAACQVNNVRDTGGGAVSPSSTVTGVTLDS
                     GTNGNP"
                     /name="colicin release lysis protein"
     gene            5235..5426
                     /locus_tag="ORI33_RS23860"
                     /old_locus_tag="ORI33_23855"
     CDS             5235..5426
                     /locus_tag="ORI33_RS23860"
                     /old_locus_tag="ORI33_23855"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /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_042634516.1"
                     /translation="MNKQQKRAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            5897..6088
                     /locus_tag="ORI33_RS23865"
                     /old_locus_tag="ORI33_23860"
     CDS             5897..6088
                     /locus_tag="ORI33_RS23865"
                     /old_locus_tag="ORI33_23860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /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_000166328.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            6088..6510
                     /locus_tag="ORI33_RS23870"
                     /old_locus_tag="ORI33_23865"
     CDS             6088..6510
                     /locus_tag="ORI33_RS23870"
                     /old_locus_tag="ORI33_23865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_021314599.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKDIKVID
                     TSELIRVFGSLDGVIDAVKHDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     Typing          complement(4734..5360)
                     /name="rep_cluster_2327"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.627"
                     /coverage="99.0"
                     /evalue="3.3e-170"
ORIGIN
        1 tcatcgacga ctcactccac actatcagta acttatgacg acttgactct agcgtcgaat
       61 cgtcgctttg gcgtttttat gaccgtggtg actctagagt caagtcacga gtcgaatcgc
      121 cggtgaatcg tgtggtgagt cgtccggcga cttgccataa cgtgattgcc ggccgtcgac
      181 gaacccgatt cctgaacgtg ctgaaaaccg gttttccggc tgcgccggca acgcttcacg
      241 gccacgcaat aaattgcgca cccgttcacc gttttctgtt ggctttggtg cagattttaa
      301 gtcatccggc ctgaattcag gccaaaatcg cccgcgagtc agtccggtgc atagtcatgc
      361 atagggctga aaatctctca gcgcgtttct ggcgggtttt cgggtggttt gttgcctgtt
      421 ttaccggttt cccgtcagaa acgccctgag ggcgtctgag atggtgcacg caacggatgt
      481 tatggtaaat ccagctgatt ggcaggtaca aaaaaagccc cgtaggactt ttttgctatg
      541 agttagccat attttcgtgc gaatttttca tcggaatcgc ggtgatgact ccaacttact
      601 gatagtgttt tatgttcaga taatgcccga tgactttgtc atgcagctcc accgattttg
      661 agaacgacag tggctttgtt gaataaatca gatttcgggt aagtctcccc cgtagcgggt
      721 tgtgttttca ggcaatacgc acgctttcag gcatacctgc tttcgtcatt ttgttcagcg
      781 ctcgtaccag ggccatagcc tccgcaacct gaccatcgta gtcacgcagc gtcagtgaac
      841 ccccgaacag ctgttttacc cggtacatcg ccgtttccgc tatcgagcga cggttgtaat
      901 ctgttgtcca tttccaccgc gcattactcc cggtcattcg ctgattagcc actgcacggt
      961 tacggtctgc atattcaccg ggccagtaac ccgcaccttt tcggggagga ataagcgcgc
     1021 tgattttttt gcggcgcagt tcatcgtgac agagccgggt atcgtaagcc ccgtctgccg
     1081 gataaggccc gggaaggctt ctgagtccgt gacgttattc agcgacaggt ctgcacagac
     1141 aacttcatgt gtgttgctgt caacagcaag atgcaacttt cgccagatac gacggcgctc
     1201 tttgccgtga tttctgactt tccattcgcc ttcaccaaag accttcagcc cggtggaatc
     1261 aatcaccagg tgtgcgattt caccccgggt ggacgttttg aaactgacat taaccgactt
     1321 tgcccgctta ctgacactgg tgtaatccgg gcagcgcaac ggaacgttca tcagggcaaa
     1381 aatggaatca ataaaaccct gcgcagcccg cagggtcagc cggaatacgc gtttaatcac
     1441 cagaacggtg gtgatggcga gatcagaata gcgctggggc cttcctcgtg atgaaggcgt
     1501 tgccgactca taccaggcct gaatcgcctc atcatccagc cagaaagtga gggagccacg
     1561 gttgatgaga gctttgttgt aggtggacca gttggtgatt ctgaactttt gctttgccac
     1621 ggaatggtct gtgttgtcgg gaggatgcgt gatctgatcc ttcaactcag caaaagttcg
     1681 atttattcaa caaagccact ttcagtatgg atttgggtgt tacggggggg gggttggtgc
     1741 ttaaaatcgc gctgaggatt tctgatggtg ttaagcgggc ggttttgaga tgtaaactcg
     1801 cccgtttaac ataatgggta ttaagtgtag tgtgtttgtc tatcaataag agatttatct
     1861 aatttaattc aatgggttta aaattatcac ttaatgaatt gatatatttt tctttttctt
     1921 ttgctttttc agatgaaaaa tcctctgtgt attcgaataa gttatatgaa gggtttactt
     1981 tttctgattt aattgaaagc cagtttagca atccatgagt gaaatcaatg ccattataac
     2041 cagtgtaaat gtgttttttt tcagtgtcat cacttgttat tcttattaat ggtattttgt
     2101 atcctgcctt gtcattgtcc tcatgtttgt aaaatatatt tccagcgtta tcggttgatt
     2161 cggatgatcc atggtctgag aaataaacaa tggagaattt tatatttttt gaatttagtg
     2221 ttttatatgt ttcactaatt attttgtccg tttttgttac tgctgatgag tagcactcta
     2281 cgtctttttt attggtttca ctatatttca ataatttatt ttctgtcata aattttttat
     2341 tttggtcgca taaagagcca tatccatgcg aatcaaataa atgaacaact attagtttct
     2401 tttttttact aggttttgat atgtagtaat ttattacttt gagcatatca tggtcttcag
     2461 cgttattgtc gtgaagtttt ataaagtatt tgtgcgttgc acttttggct atgaatgata
     2521 ttggggtatc atactcacca attaaacctt gattactaat ccaatatgta tcatatcctg
     2581 cgttatttgc tgcatttatg aatgatttag gatagtttgg ttctatttta ctgttttctc
     2641 cttggtaagt tagcattatc cttagtgatg gaactgtgtg tgtatcagcg ctgtagaaat
     2701 tatgaacaaa tgttccgtta acggaagaca aaaatggagt gtttttttca ttgtatccat
     2761 aaacattgag gtagtcactt ctcatcattt ctccgatgaa aagaatgttt atttcatatt
     2821 tagagtcatt tgtaatttca ccccattcat tgttttcgct atttaatgaa ttgagttttt
     2881 taaattgaat tagttctgat atgtattctt tcatgccatg caatgcattg aatgccaatt
     2941 tagatagcat gtttggtgtc aggactaaat agcatgacag tacggttaat gtatatagcc
     3001 tatttcttat tgggtctatc ttcattgata tagatctgca ttttattatg aatataatag
     3061 ataaaatgct tattaataag cgctctttag gtattgattt aaaaaatgaa atggactcat
     3121 cttgagatgt gtttgctatc gctgcaatat agtcatattt tatcgggcct atatctatcc
     3181 cagtaataaa ataaatagag aaaaaagaaa gaaaaggaaa ggttaaaaac caataaataa
     3241 gtttatatct aaacgtaatt ggtagtatga ttgataaaag aaaagtgtat ctgatgttta
     3301 cttctttaaa aaaacaataa cttaacacta cagatataaa agtacataat aaaaaaagaa
     3361 ttatggcgta agaaaataca acggctttgc tttgcttcat ttgcttcatt tgctttattt
     3421 gatttatttg atttatttga ttcatttgat tcatttgatt tatttgattc atttgattta
     3481 tttgatttat ttgattcatt tgatttatta tgtcataaaa tacacctacc tggtaatggt
     3541 gccaacttac tgatttagtg tatgatggtg tttttgaggt gctccagtgg cttctgtttc
     3601 tatcagctgt ccctcctgtt cagctactga aggcgtggtg cgtaacggta aaagtactgc
     3661 cggacatcag cgctatctct gctctcactg ccgtaaaaca tggcagctac agttcactta
     3721 caccgcttct caacccggta cgcatcagaa aatcattgat atggccatga atggcgtcgg
     3781 atgtcgcgcc agtgcacgca ttatgggcgt tggcctcaac acggttttac gtcacttaaa
     3841 aaactcaggc cgcagtcggt aacctcgcgc atacaaccgg gcagtgatgt gattgtctgc
     3901 gctgaaatgg acgaacagtg gggctacgtc ggtgctaaat cacgccagcg ctggttgttt
     3961 tacgcgtatg acaggatacg gaggacggtt gtggcgcacg tattcggtga acgcacgctg
     4021 gccacgctgg agcgtcttct gggcctgctg tcggcctttg aggtcgtggt atggatgacg
     4081 gatggctggc cgctttatga atcacgcctg aagggagaac tgcacgttat cagcaagcga
     4141 tatacgcagc gcattgagcg gcataacctg aatctgaggc agcatctggc aaggctgggc
     4201 aggaagtcac tgtcgttctc aaaatcggtg gagctgcatg acaaagtcat cgggcattat
     4261 ctgaacataa aacactatca gtaagttgga gtcattacca ccccatttgc ctagaataat
     4321 aaaaataaaa ggtgatatat gaaaaaatta cttttcctgg ggggtgttac cgtttctgtg
     4381 gttctggcgg catgtcaggt caataatgtt cgtgacaccg gaggtggggc tgtttcacct
     4441 tcatcgacgg tgaccggagt tacgcttgat agcggtacga acggcaatcc gtaaaggatc
     4501 ttcttgagat cccatttgga tcgtcgtaat ctcttgctct gtaaacgaaa aaaccgcctt
     4561 ggcgggcggt tttttcgaag gttcgaggag ttggcgctct ttgaaccgag gtaactggct
     4621 ttcgcagagc acagaaacca aattagttat tacagtgtag ctgtacttca cctcacactt
     4681 caacacttct ttgttctgcg aatccgttac cagtggctgc tgccagtggc gataagtcgt
     4741 gtctttccgg attggactca agacgatagt taccggataa ggcgcagcgg tcggactgaa
     4801 cggggggttc gtgcatacag tccagcttgg agcgaactgc cttcccggaa ccgagtgtca
     4861 ggcgtggaat gagataaacg cggccataac agcggaatga caccggtaaa ccgaaaggca
     4921 ggaacaggag agcgcacgag ggagccacca gggggaaacg cctggtatct ttatagtcct
     4981 gtcgggtttc gccaccactg atttgagcgt cagatttcgt gatgcttgtc aggggggcgg
     5041 agcctatgga aaaacgcccc ggcggggcgt ggccttttcg cccttgtcct tagctttcgt
     5101 tatgcttacc gttacgttat ctgcttatct tccctccgct cgccgcagac tcatgaccga
     5161 acggagtgag cgaatgagcg aggaagcgga aaaccatcag aacctacagt aagcactttc
     5221 gcgccgggga cttcatgaac aaacaacaaa agagagccgt taacatggct aaattcatcc
     5281 aggatcagtc cctgcttctt ctggacaggc ttaatgagct ggatctggat catgaggctg
     5341 atttctgcga gaaactccat gaggatgcgg aacgccttta ccgaagcctg tcagcgcgcc
     5401 tgaatgagca gcaggacggt gcgtaatggc tctgttctgg gtattaccgg agtaataccg
     5461 gcatcgcctt aattttcatt gtcctggcgc ttaacattat tactccggta atacccagaa
     5521 tccctttatt ttttcttttt tatttatttt tcatgaagtt gcgatgaaaa tcgcggctgc
     5581 gttaggtgta tgaccatttt gaggttgaaa aataatcaac catggcgggt gatttacgca
     5641 ggttaagggg cgtcggtgac aaaaaaacgt cattaacgac ctcgttcatg ctcgcatgaa
     5701 cggattattt ttccggacta caggtaaact acagaaagac tacaaaagct gatgacttaa
     5761 tcctgatttt tagtgcgatg actacagata aactacaaaa taactacagg attacctcag
     5821 atccgttctc tgaaccattc gtacatccga cccccttacc ggttttacac tgagcactga
     5881 tgctctgagg tcccttatga cgaaacaaca gaaaacagcg ctgaacatgg ctaaattcat
     5941 ccagaatcag tctctgctcc tgctggagaa gcttaacgag cttgatctcg atgctgaggc
     6001 cgacctttgt gagaaactcc acgatgatgc ggagcatctt ttccgtacac tgtcctcgag
     6061 actggatgca ttacaggatg gtaactgatg gccagagtgt ctattagtga agcagcacgg
     6121 cttgttaagg ttagtcgccc tactatttac aagatgatta acagtggtaa gttaagttac
     6181 acctctgttg taaagcacgg gaaggatatt aaagttattg atacatcaga gcttattaga
     6241 gtgtttggtt ctcttgatgg tgtaatcgat gctgtaaaac atgatgtaaa aagtgacgca
     6301 gaatctacag gtattaacag cgttggttta catgatttac aacatagaat cgctttactt
     6361 gaagctgaaa acgatggtct taaaggggct gttaaggctc gagatgagca tattgattcc
     6421 cttcgtcagg ctatgcagct tctggagcac aagcacgaac cttcttcacc accccattcc
     6481 ccgtggtgga aattctggaa aaaatcctga tcccgccatg cttgagtttt cctctccggc
     6541 catgccgggg cgttcgtgaa ccttcccaaa aatcgccaga tctctgaacg ctcctcacac
     6601 taaaaatatc cacaccccac gcaaaattaa atttttgcag ataactcatt aatatcagtc
     6661 agttggttgt tattaaatta cgcagtatta ccttctgtaa ggtcaatcca agtcgtcggt
     6721 gattcgtgta cgacttgccg acgactcgtc atagag
//
