LOCUS       NZ_CP079890             5488 bp    DNA     circular CON 02-NOV-2023
DEFINITION  Escherichia fergusonii strain 6S41-1 plasmid p6-6S41-1, complete
            sequence.
ACCESSION   NZ_CP079890
VERSION     NZ_CP079890.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN20239770
            Assembly: GCF_020002285.1
KEYWORDS    RefSeq.
SOURCE      Escherichia fergusonii
  ORGANISM  Escherichia fergusonii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5488)
  AUTHORS   Liu,R.
  TITLE     Genomic of Escherichia fergusonii
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5488)
  AUTHORS   Liu,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-JUL-2021) Zhejiang University, State Key Laboratory
            for Diagnosis and Treatment of Infectious Disease, No. 79 Qingchun
            Road, Hangzhou, Zhejiang 310003, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SPAdes v. 3.10.0
            Assembly Name                     :: 6S41-1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200.0x
            Sequencing Technology :: Oxford Nanopore; Illumina NovaSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/02/2023 04:16:04
            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)                     :: 4,919
            CDSs (total)                      :: 4,804
            Genes (coding)                    :: 4,637
            CDSs (with protein)               :: 4,637
            Genes (RNA)                       :: 115
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 167
            CDSs (without protein)            :: 167
            Pseudo Genes (ambiguous residues) :: 0 of 167
            Pseudo Genes (frameshifted)       :: 35 of 167
            Pseudo Genes (incomplete)         :: 118 of 167
            Pseudo Genes (internal stop)      :: 32 of 167
            Pseudo Genes (multiple problems)  :: 18 of 167
            Pseudo Genes (short protein)      :: 1 of 167
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP079890.1.
            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..5488
                     /organism="Escherichia fergusonii"
                     /mol_type="genomic DNA"
                     /strain="6S41-1"
                     /isolation_source="soil"
                     /db_xref="taxon:564"
                     /plasmid="p6-6S41-1"
                     /geo_loc_name="China:Zhejiang"
                     /collection_date="2019-05"
     gene            complement(join(5335..5488,1..1046))
                     /gene="tet(A)"
                     /locus_tag="KYC43_RS24500"
                     /old_locus_tag="KYC43_24385"
     CDS             complement(join(5335..5488,1..1046))
                     /gene="tet(A)"
                     /locus_tag="KYC43_RS24500"
                     /old_locus_tag="KYC43_24385"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000804064.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="tetracycline efflux MFS transporter Tet(A)"
                     /protein_id="WP_001493765.1"
                     /translation="MKPNRPLIVILSTVALDAVGIGLIMPVLPGLLRDLVHSNDVTAHY
                     GILLALYALMQFACAPVLGALSDRFGRRPVLLVSLAGAAVDYAIMATTPFLWVLYIGRI
                     VAGITGATGAVAGAYIADITDGDERARHFGFMSACFGFGMVAGPVLGGLMGGFSPHAPF
                     FAAAALNGLNFLTGCFLLPESHKGERRPLRREALNPLASFRWARGMTVVAALMAVFFIM
                     QLVGQVPAALWVIFGEDRFHWDATTIGISLAAFGILHSLAQAMITGPVAARLGERRALM
                     LGMIADGTGYILLAFATRGWMAFPIMVLLASGGIGMPALQAMLSRQVDEERQGQLQGSL
                     AALTSLTSIVGPLLFTAIYAASITTWNGWAWIAGAALYLLCLPALRRGLWSGAGQRADR
                     "
                     /name="tet(A)"
     gene            1152..1802
                     /gene="tetR(A)"
                     /locus_tag="KYC43_RS24505"
                     /old_locus_tag="KYC43_24390"
     CDS             1152..1802
                     /gene="tetR(A)"
                     /locus_tag="KYC43_RS24505"
                     /old_locus_tag="KYC43_24390"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000164043.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="tetracycline resistance transcriptional repressor
                     TetR(A)"
                     /protein_id="WP_001493764.1"
                     /translation="MTKLQPNTVIRAALDLLNEVGVDGLTTRKLAERLGVQQPALYWHF
                     RNKRALLDALAEAMLAENHTHSVPRADDDWRSFLIGNARSFRQALLAYRDGARIHAGTR
                     PGAPQMETADAQLRFLCEAGFSAGDAVNALMTISYFTVGAVLEEQAGDSDAGERGGTVE
                     QAPLSPLLRAAIDAFDEADPDAAFEQGLAVIVDGLAKRRLVVRNVEGPRKGDD"
                     /name="tetR(A)"
     gene            complement(1834..2076)
                     /locus_tag="KYC43_RS24510"
                     /old_locus_tag="KYC43_24395"
     CDS             complement(1834..2076)
                     /locus_tag="KYC43_RS24510"
                     /old_locus_tag="KYC43_24395"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000844627.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="transposase"
                     /protein_id="WP_000844627.1"
                     /translation="MKTAALDLARERQAHEAGARTRATAHERTPQQERQKAAREAERGR
                     EAWTLGQGMKKPVAGCYGRLTRWKGGGDVVYMALL"
                     /name="transposase"
     gene            complement(2134..>3885)
                     /locus_tag="KYC43_RS24515"
                     /old_locus_tag="KYC43_24400"
                     /pseudo=""
     CDS             complement(2134..>3885)
                     /locus_tag="KYC43_RS24515"
                     /old_locus_tag="KYC43_24400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001138014.1"
                     /GO_function="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="Tn3-like element TnAs1 family transposase"
                     /name="Tn3-like element TnAs1 family transposase"
     gene            3889..4281
                     /locus_tag="KYC43_RS24520"
                     /old_locus_tag="KYC43_24405"
     CDS             3889..4281
                     /locus_tag="KYC43_RS24520"
                     /old_locus_tag="KYC43_24405"
                     /EC_number="3.-.-.-"
                     /inference="COORDINATES: protein motif:HMM:NF013053.3"
                     /GO_function="GO:0016787 - hydrolase activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="isochorismatase family cysteine hydrolase"
                     /protein_id="WP_001351729.1"
                     /translation="MLFPNFSLGEEYEHAPPATNRQISPYLPSGRFRTGLPVEGLAIER
                     GDLFYACPRASVFYGTALDADLRTRGVSTLVMAGISTTGVVLSSVAWASDADYDVRLVQ
                     DCCYDPDRDAHEALLRSGFGGRVQVV"
                     /name="isochorismatase family cysteine hydrolase"
     gene            4419..5303
                     /locus_tag="KYC43_RS24525"
                     /old_locus_tag="KYC43_24410"
     CDS             4419..5303
                     /locus_tag="KYC43_RS24525"
                     /old_locus_tag="KYC43_24410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000058717.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EamA family transporter"
                     /protein_id="WP_000058717.1"
                     /translation="MSLRTPDLLFTAIAPAIWGSTYIVTTQYLPNFSPMTVAMLRALPA
                     GLLLVMIVRQIPTGIWWMRIFILGALNISLFWSLLFISVYRLPGGVAATVGAVQPLMVV
                     FISAALLGSPIRLMAVLGAICGTAGVALLVLTPNAALDPVGVAAGLAGAVSMAFGTVLT
                     RKWQPPVPLLTFTAWQLAAGGLLLVPVALVFDPPIPMPTGTNVLGLAWLGLIGAGLTYF
                     LWFRGISRLEPTVVSLLGFLSPGTAVLLGWLFLDQTLSALQIIGVLLVIGSIWLGQRSN
                     RTPRARIACRKSP"
                     /name="EamA family transporter"
     ARG             complement(4..1046)
                     /name="tet(C)"
                     /gene="tet(C)"
                     /gene_name="major facilitator superfamily (MFS) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="tetracycline antibiotic"
                     /identity="79.89"
                     /coverage="87.88"
ORIGIN
        1 atcgaggtca ggctggtgag cgccgccagt gagccttgca gctgcccctg acgttcctca
       61 tccacctgcc tggacaacat tgcttgcagc gccggcattc cgatgccacc cgaagcaagc
      121 aggaccatga tcgggaacgc catccatccc cgtgtcgcga aggcaagcag gatgtagcct
      181 gtgccgtcgg caatcattcc gagcatgagt gcccgccttt cgccgagccg ggcggctaca
      241 gggccggtga tcattgcctg ggcgagtgaa tgcagaatgc caaatgcggc aagcgaaatg
      301 ccgatcgtgg tcgcgtccca gtgaaagcga tcctcgccga aaatgaccca aagcgcggcc
      361 ggcacctgtc cgacaagttg catgatgaag aagaccgcca tcagggcggc gacgacggtc
      421 atgccccggg cccaccggaa cgaagcgagc gggttgagag cctcccggcg taacggccgg
      481 cgttcgcctt tgtgcgactc cggcaaaagg aaacagcccg tcaggaaatt gaggccgttc
      541 aaggctgccg cggcgaagaa cggagcgtgg ggggagaaac cgcccatcag cccaccgagc
      601 acaggtcccg cgaccatccc gaacccgaaa caggcgctca tgaagccgaa gtgccgcgcg
      661 cgctcatcgc catcagtgat atcggcaata taagcgccgg ctaccgcccc agtcgccccg
      721 gtgatgccgg ccacgatccg cccgatatag agaacccaaa ggaaaggcgt cgtcgccatg
      781 atggcgtagt cgacagcagc gccggccagc gagacgagca agaccggccg ccgcccgaaa
      841 cgatccgaca gcgcgcccag cacaggtgcg caggcaaatt gcatcaacgc atacagcgcc
      901 agcagaatgc catagtgggc ggtgacgtcg ttcgagtgaa ccagatcgcg caggaggccc
      961 ggcagcaccg gcataatcag gccgatgccg acagcgtcga gcgcgacagt gctcagaatt
     1021 acgatcaggg gtctgttggg tttcacgtct ggcctccgga ccagcctccg ctggtccgat
     1081 tgaacgcgcg gattctttat cactgataag ttggtggaca tattatgttt atcagtgata
     1141 aagtgtcaag catgacaaag ttgcagccga atacagtgat ccgtgccgcc ctggacctgt
     1201 tgaacgaggt cggcgtagac ggtctgacga cacgcaaact ggcggaacgg ttgggggttc
     1261 agcagccggc gctttactgg cacttcagga acaagcgggc gctgctcgac gcactggccg
     1321 aagccatgct ggcggagaat catacgcatt cggtgccgag agccgacgac gactggcgct
     1381 catttctgat cgggaatgcc cgcagcttca ggcaggcgct gctcgcctac cgcgatggcg
     1441 cgcgcatcca tgccggcacg cgaccgggcg caccgcagat ggaaacggcc gacgcgcagc
     1501 ttcgcttcct ctgcgaggcg ggtttttcgg ccggggacgc cgtcaatgcg ctgatgacaa
     1561 tcagctactt cactgttggg gccgtgcttg aggagcaggc cggcgacagc gatgccggcg
     1621 agcgcggcgg caccgttgaa caggctccgc tctcgccgct gttgcgggcc gcgatagacg
     1681 ccttcgacga agccgatccg gacgcagcgt tcgagcaggg actcgcggtg attgtcgatg
     1741 gattggcgaa aaggaggctc gttgtcagga acgttgaagg accgagaaag ggtgacgatt
     1801 gatcaggacc gctgccggag cgcaacccac tcactacagc agagccatgt agacaacatc
     1861 ccctccccct ttccaccgcg tcagacgccc gtagcagccc gctacgggct ttttcatgcc
     1921 ctgccctagc gtccaagcct cacggccgcg ctcggcctct ctggcggcct tctggcgctc
     1981 ctgctgcggc gtccgctcgt gggccgtggc gcgggtccgc gcgccggcct cgtgcgcctg
     2041 gcgctcgcgg gcgaggtcca gggcggccgt cttcacgttc tgccttgcgc agatgagata
     2101 ggggagcccg cagaattcgg aaaaaatcgt acgctaaggt tttccgggca tccgtaaggg
     2161 ccgaaacttc ccgtcttcca gtctgcggct ctgccgccag acgtaatcgc cggttaggtt
     2221 gatgtgctcc cagcccagcg gcgacaggaa ttgcagcagc tcgccgtcca ccggcttgcc
     2281 ggcctcgacc aacccctggg tggcgcgttc caggtacacc gtgttccaca gcacgatagc
     2341 cgccgtcacc aggttgaggc cgctggcccg gtagcgctgc tgctcgaagc tccgatccct
     2401 gatttcccca aggcggttga agaacaccgc cctggccagc gagttgcgcg cctcaccttt
     2461 gttcaggccg gcatgcacgc ggcggcgcag ttcaacactt tgcagccagt ccaggatgaa
     2521 cagcgtgcgc tcgatccggc ccagctcgcg cagggccacg gccagtccgt tctggcgcgg
     2581 gtagctgccg agcttgcgca gcatcagcga ggcggtgacg gtgccctgct tgatcgagct
     2641 ggccaggcgc aggatgtcgt cccagtgggc acgcacgtgc ttgatgttca gggtgccgcc
     2701 gatcagcggg cgcaacgtcg ggtaggcttg cacgccctgc ggcacgtaca gcttggtttc
     2761 gccgaggtcg cggatgcgcg gcgcgaagcg gaagcctagc aggtgcatca gggcaaagac
     2821 gtgatcggtg aagccggccg tgtcggtgta gtgctcctcg atccgcaggt cggactcgtg
     2881 gtacagcagg ccgtcgagca cataggtgga atcgcggacg ccgacattca ccacgcgggt
     2941 gctgaacggc gcgtactggt cggagatatg ggtatagaac agccgtcccg gctcgctacc
     3001 gtacttcggg ttgacgtgcc cggtgctctc gccccggcca cccgcgcgga agcgctggcc
     3061 atcggaggat gaggtcgtgc cgtcgcccca gtgggcggca aaggcgtggc gatactggtg
     3121 gttgaccagc tcggccaagg ccgccgaata ggtttcgtcg cggatgtgcc aggcttgcag
     3181 ccaggacagc ttggcgtagg tcaggccggg gctcgactcg gccatcttgg tcagcccgag
     3241 gttgatcgca tcaccgagga ttgcggacag cagcaacgtc ctgtctttgg cctcggcccc
     3301 gtccttcaag tgggtgaagt ggcggctgaa gcccgtccag tcgtccacgt ccatcagcag
     3361 ttcggtgatc ttgatgcgcg gcagtaactg gctggtttgg tcgatcagcg cctgcgcccg
     3421 atccggcacc gccgcatcca gcggggtgat tttcagccct gactcggtga ggatggcatc
     3481 gggcagctcg ttgtccttgg ccaggcgggt gacggtggcc aactgctcgt ccagcagctg
     3541 caaacgctct tccaggtact ggtcgctgtt cgggttgatc gccaggggca gggcctgctc
     3601 gcgcttgagt gcggcgaact tctcggccgg cagcaggtag tcgtcgaagt cgcggaactg
     3661 ccgcgagccc ttgacccaga tgtcgccgga gcgcagggcg ttcttcagct cggacagggc
     3721 gcagatttcg tagaatttcc ggtcgaggcc ttccggggtg atcaccagcg gcttccagcg
     3781 cggcttgatg aaggccgtgg gtgcatcggc cggcaccttg cgcaggttgt cggcgttcat
     3841 ctcacgcagg gtctgcacgg ctgccagcac gccttgcgcg gccggcccgt gctgttcccc
     3901 aacttttcgc tcggcgaaga gtatgaacat gcgccgccgg cgacgaatcg ccaaatctca
     3961 ccgtatctcc cgagcggacg atttcgcacc ggtctgcccg tcgaagggct tgcgatcgaa
     4021 cggggcgacc ttttctatgc atgtccgcga gccagcgtct tttatggcac ggcgctcgac
     4081 gccgaccttc ggacgcgcgg cgtaagcacg cttgtcatgg ccgggataag caccaccggc
     4141 gttgttcttt caagcgtcgc ctgggctagt gatgcggact acgacgtgcg tttggtccag
     4201 gactgctgct acgacccgga tcgggatgcc cacgaagctc tgttgcgttc cgggttcggc
     4261 ggacgtgtac aggtcgtgta attttcgggc ctcgcatgat cgcggccata gccgcaggtg
     4321 gattggtgcg aggcagggcc agtccaagtc agggtgcggt catcgcggcg cctgcaactc
     4381 tcaaaaaccc atcgccgtag cggaggtctt gtaatcgcat gtcattacgc acgcccgatt
     4441 tattgttcac agcgatagca cctgccattt ggggcagcac ctacattgtc accacccaat
     4501 acctgccgaa cttctcaccg atgacggtcg cgatgctgcg ggcgttgccg gcgggtttat
     4561 tgctcgtgat gatcgtccga cagattccaa cgggaatctg gtggatgcgc atcttcatcc
     4621 tcggcgcact taatatttcg ctattctgga gcttgttgtt tatttcggtc taccgcctgc
     4681 cgggcggggt cgcggcgacg gtaggcgctg tgcagccgct gatggtcgtg ttcatctctg
     4741 ccgctctgct aggtagcccg atacgattga tggcggtcct gggggctatt tgcggaactg
     4801 cgggcgtggc gctgttggtg ttgacaccaa acgcagcgct agatcctgtc ggcgtcgcag
     4861 cgggcctggc gggggcggtt tccatggcgt tcggaaccgt gctgacccgc aagtggcaac
     4921 ctcccgtgcc tctgctcacc tttaccgcct ggcaactggc ggccggagga cttctgctcg
     4981 ttccagtagc tttagtgttt gatccgccaa tcccgatgcc tacaggaacc aatgttctcg
     5041 gcctggcgtg gctcggcctg atcggagcgg gtttaaccta cttcctttgg ttccggggga
     5101 tctcgcgact cgaacctaca gttgtttcct tactgggctt tctcagcccg gggaccgccg
     5161 tgttgctagg atggttgttc ttggatcaga cgctgagtgc gcttcaaatc atcggcgtcc
     5221 tgctcgtgat cgggagtatc tggctgggcc aacgttccaa ccgcactcct agggcgcgta
     5281 tagcttgccg gaagtcgcct tgacccgcat ggcataggcc tatcgtttcc acgatcagcg
     5341 atcggctcgt tgccctgcgc cgctccaaag cccgcgacgc agcgccggca ggcagagcaa
     5401 gtagagggca gcgcctgcaa tccatgccca cccgttccac gttgttatag aagccgcata
     5461 gatcgccgtg aagaggaggg gtccgacg
//
