LOCUS       NZ_CP075468             4072 bp    DNA     circular CON 11-FEB-2024
DEFINITION  Escherichia coli strain NT1W22 plasmid pNT1W22-4k, complete
            sequence.
ACCESSION   NZ_CP075468
VERSION     NZ_CP075468.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16120651
            Assembly: GCF_014904185.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4072)
  AUTHORS   Li,R.
  TITLE     Distribution and genomic characterization of tigecycline-resistance
            tet(X4)-positive Escherichia coli of swine farm origin
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4072)
  AUTHORS   Li,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-MAY-2021) College of Veterinary Medicine, Yangzhou
            University, No. 88 South University Road, YangZhou, JiangSu 225000,
            China
REFERENCE   3  (bases 1 to 4072)
  AUTHORS   Li,Y. and Li,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-SEP-2020) College of Veterinary Medicine, Yangzhou
            University, Shuangqiao Street, YangZhou, JiangSu 225000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: unicycler v. v.0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 20.0x
            Sequencing Technology             :: Nanopore; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/11/2024 03:40:13
            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)                     :: 4,771
            CDSs (total)                      :: 4,653
            Genes (coding)                    :: 4,433
            CDSs (with protein)               :: 4,433
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 220
            CDSs (without protein)            :: 220
            Pseudo Genes (ambiguous residues) :: 0 of 220
            Pseudo Genes (frameshifted)       :: 62 of 220
            Pseudo Genes (incomplete)         :: 152 of 220
            Pseudo Genes (internal stop)      :: 42 of 220
            Pseudo Genes (multiple problems)  :: 33 of 220
            Pseudo Genes (short protein)      :: 4 of 220
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP075468.1.
            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..4072
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="NT1W22"
                     /isolation_source="pig farm"
                     /host="pig"
                     /db_xref="taxon:562"
                     /plasmid="pNT1W22-4k"
                     /geo_loc_name="China"
                     /lat_lon="32.01 N 120.86 E"
                     /collection_date="2018"
                     /collected_by="Yangzgou University"
     gene            join(3618..4072,1..1693)
                     /gene="mobQ"
                     /locus_tag="IGI32_RS00005"
     CDS             join(3618..4072,1..1693)
                     /gene="mobQ"
                     /locus_tag="IGI32_RS00005"
                     /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="WP_151140345.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLKIGLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGESGLAALRSQL
                     LKREEELRRKELEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQHPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGENRQPAMPSPVARRVDFTQGRLPPTLMPVM
                     SSVDRENRQLQLLLVMGVDDSLGGVVRLNGSLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADNHISPAPELMAFHLKTRETPLFAAVNTPEKQPDHLFRSLGFNHTWDEW
                     RREEHARTRVSGKKNDRDCSR"
                     /name="mobQ"
     gene            complement(1948..2655)
                     /locus_tag="IGI32_RS00010"
     CDS             complement(1948..2655)
                     /locus_tag="IGI32_RS00010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_001296720.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(3185..3439)
                     /gene="mobC"
                     /locus_tag="IGI32_RS00015"
     CDS             complement(3185..3439)
                     /gene="mobC"
                     /locus_tag="IGI32_RS00015"
                     /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="WP_000091746.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(3441..3617)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          3618..3976
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.722"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1949..2655)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.294"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3..1690
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.651"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cagggactgg aacgaccgga cacatgccga gacgtggcgg gcatcatggg ctgaccatgc
       61 aaacagggca ctggcgaacg ccggttatca ggaagagata gaccatcgtt catacgagcg
      121 acaggggctt gagaaaacgc ctggtattca cctcggaaag tctgcctgtg cgatggaaac
      181 acgcggtatc gaaacagaac gcggcgaaca gaatcgtctg attaacaggc ttaacctgga
      241 aatacagatt tcccgcaccg aactcaggaa cagcgggctg acagagcctg cccgccgtgt
      301 ggctgacctt ctgaagatcg ggcttcctga caacgcaact tcgtacacac tacgtgacat
      361 catcgaagcg ttgccgaagg acagtaacgc ggcatggaaa ctcaccagta acgccatgtc
      421 gatgatggca gatatgcagg cgacacgcag acgctgggaa gagctgaaca ccgaacgaaa
      481 ggaagcgatg agccatgctg ccagcctgaa aaaatcatcg ccgttttcgt ccggtttttc
      541 ccgtattccc ctgatgcaat gggctgcacc ggaataccgt agtgagcagg gaaaaatcca
      601 gtctctgagc cagcaaatgg aaaaattgcg acagcattac cggaaggtgg agaaacagga
      661 cattcccgcg agtcagacgg catttgaaaa acagtggcag cagtgggggg aatccggcct
      721 tgcagctctc agatcccagt tgcttaaacg tgaagaggaa ttgcgccgga aggagctgga
      781 ggatacagaa cgtagtcgcg cggagcagct caggaaaaat gacaatgccg ttatggattc
      841 aggggtgctg agagcagtcg ttacgggata tggcgaggct cccatgcctg gtaacgggga
      901 aatgacctgt taccttctgc ttcacaaccg gaacggagaa tatacgctct gggggaacga
      961 gctggagaaa taccgcacca ggatctttga gagtgttgat ttaatgcgtg acaggagtgg
     1021 ttatatctgt gaccgaagcg aaatcggtca acatccacca ctgcaacgtg tttattcctc
     1081 tgcgaccttt gagcaacttc tgacgcaggt ttgccagaca tggccgcaac atacccgcaa
     1141 tctccgccag ccgaagacat ggccggagtc tttctgtctt ggagaaaacc gccagccagc
     1201 catgccatca ccggtggcaa ggagggtgga ttttacgcag ggacgtctgc caccgacgct
     1261 gatgccggta atgagttctg tcgaccggga aaaccgacaa cttcagcttt tgctggtcat
     1321 gggcgtggat gactctctgg gcggtgttgt ccggcttaat ggttcgctgt atcccgcgtt
     1381 tgctgtcccc tccgccgata acaggcatct ggtcatcagt gcgctgaccg ataaggggtt
     1441 acgatatgca ggatatggtg ttgccgtaaa tcacgatgca gacaaccaca tttcacctgc
     1501 accggaactt atggcgtttc atcttaaaac ccgcgagaca ccgctttttg ctgccgtcaa
     1561 cacaccagaa aaacagccgg atcatctgtt ccgttcactg ggctttaatc acacctggga
     1621 tgaatggcgg cgcgaggagc atgcacgaac acgtgtctcc gggaagaaaa atgatcgcga
     1681 ctgttcacgg taactgctga tagtattttg ttttgtttta catcgtgtta tgttctctga
     1741 cattcatcgt aactggatga atgtcagatg cacacagatt gcacaaatcc aactttatcg
     1801 ttttcccgcc cccactaagt tgggggttct tttttttgaa cgccatagaa tcgattatga
     1861 agcaatttta tctcaccagt agtaccatcg catacctctc atggaaaaaa cgcaacagag
     1921 agcgttttag gtgccttaaa atcgattcta gatcgtcatc ttgatctgtt tgtcttcctt
     1981 gaagcgaaaa tgcagggcta caaccgtgcg cccctttttg atcgtctcaa ccgttacagc
     2041 caggtcgctt tttttgttca gttcgtcaac acagggtttt attagatccc tgtttaacgt
     2101 tttgaaatct ttatatttac catcaagcat cagtgatgat ttaaaatcat cgagggcgat
     2161 aatacgttcc ccagtactgc ggaattgctg gagaatctcg tatattctta tgctgtaact
     2221 tcttgataaa ttggagatat ttttaataac aactctggtg aattgcccct tcaactgtgt
     2281 cagataaggc attaccgcgt cagaaaaagt gatttgtgct ttcccctctc ccctcgcgta
     2341 ctgtgcccga tactgaatcc agcggaactc ctcgcgcttc tcgtcgtcct tgagaatgat
     2401 cgacctgtcc cacaaacgat cgatcgcttc ctgtagctga acctcggcat ttttccgccc
     2461 catatcaggg aatgaatcaa aatattccgc agctgtaatg gtcattgtct tttgcaattc
     2521 aggtgaagct acgtcagtac cggagttaag tcggcttatg cagagcaata agaaacgctg
     2581 ttcttgtaaa gttagcttgt aactggcctc aaccagcgca ttggacttat aggctatcag
     2641 agggtttgat gtcattttaa ccaccaggcc aaagatgagg tgagataaaa acctatcacc
     2701 tttagcattg gtgagcaatt atatttccac cccccatttt tctgtgaata ttaccttaaa
     2761 tctcctcacc tttaccttaa attacctcac ccaagaacct taaattatat cacctttacc
     2821 ttaaatttcc ccacctatac acgtgtaacg cattgttttt aatcaggaat ttcgacccta
     2881 aaacaagtat taaaaacaag tattaaaaac aagatctaaa aacttaacgg cgagcctgtg
     2941 gataacttgg agtgctgaaa ataaaaaccc aataaaaaca atgtgttgca aaaaatcagg
     3001 attggagatt ccgaataccc cccctccaac cctgtggaaa tccagtattc atgcgggttc
     3061 agcgcatatc acctgtcgaa aaaccgtgcg tatgtgctca acatggcgac tgattcactt
     3121 ccgcttcctc gcccactcgc tcgctaacgc tcggtcgctg ggctgcggcg agcggacgat
     3181 acaatcactg ttctggcagc gcctccagct cgttaatcag cggcagtatg cgcgtcacat
     3241 cagcctgtcg tgtcacctct gccttcagga actggagtaa ccaggcacgc aactgcacct
     3301 cctccggctt tctgaccttt gccagcaatg cagcacccac aacaaccttc tgcgctgtgt
     3361 ccaggctccg gctcttcgcc ttcaggcgct gtaatctcgc ctcagcatca gcaatcttct
     3421 gttcgagcgt tctgctcatg atgtaactcc gtgcgcgatg aaaaatcgca ttttagcgcg
     3481 tcactggtag tttaaaaact gagctggcat aatgcacggc aaatcacgaa gtgcgcactt
     3541 atacaatctc cactccgttt cgattgtgtg cgccctgcgg ggctgaaaga aaactacaaa
     3601 aaggcattac ggcagaaatg gcgatttatc atctcagcat gaaaattatc tccagaagca
     3661 gcggctacag cgccgtagct tccgctgcct atcgttccgg ttcactgatg cttgatgagc
     3721 gtaccggact gactcacgac tacacccgca aaagcggtgt ggctgaggct gtgattctga
     3781 cccccgccac cgcccctgcc tggtgtacga accgtgccga actctggaat gccgttgaga
     3841 aggccgaacg ccggaagaac tcacaacttg cgcgggaaat tgaactcgcc atcccccacg
     3901 aactgccgca ggatgccgcc cgggaaaccg ttctcgcctt tgtcagagaa aactttgtca
     3961 gtcagggcat gattgctgat gtggcgttcc atcacatgga taaaacaaat ccccatgcgc
     4021 acatcatgct gaccacgagg gctatcggac ctgctgggtt cagcggaaag gt
//
