LOCUS       NZ_AP027671             3916 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain PSS-04 plasmid pPSS-04_5, complete sequence.
ACCESSION   NZ_AP027671
VERSION     NZ_AP027671.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562521
            Assembly: GCF_036500705.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Hoang,H.T.T., Yamamoto,M., Calvopina,M., Bastidas-Caldes,C.,
            Khong,D.T., Nguyen,T.N. and Yamamoto,Y.
  TITLE     Comparative genome analysis of colistin-resistant Escherichia coli
            strains possessing mcr isolated in Ecuador and Vietnam
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3916)
  AUTHORS   Yamamoto,Y. and Hoang,H.T.T.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-MAR-2023) Contact:Yoshimasa Yamamoto The United
            Graduate School of Drug Discovery and Medical Information Sciences,
            Gifu University; Yanagido 1-1, Gifu 501-1194, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Coverage                   :: 150x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036500705.1-RS_2024_04_03
            Annotation Date                   :: 04/03/2024 23:58:23
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,746
            CDSs (total)                      :: 4,625
            Genes (coding)                    :: 4,365
            CDSs (with protein)               :: 4,365
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 260
            CDSs (without protein)            :: 260
            Pseudo Genes (ambiguous residues) :: 0 of 260
            Pseudo Genes (frameshifted)       :: 56 of 260
            Pseudo Genes (incomplete)         :: 189 of 260
            Pseudo Genes (internal stop)      :: 54 of 260
            Pseudo Genes (multiple problems)  :: 38 of 260
            Pseudo Genes (short protein)      :: 3 of 260
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027671.1.
            Annotated by DFAST https://dfast.ddbj.nig.ac.jp/
            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..3916
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PSS-04"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pPSS-04_5"
                     /geo_loc_name="Ecuador:Puyo"
                     /collection_date="2019"
     gene            join(3738..3916,1..145)
                     /gene="mobA"
                     /locus_tag="AABJ69_RS23700"
     CDS             join(3738..3916,1..145)
                     /gene="mobA"
                     /locus_tag="AABJ69_RS23700"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            493..1848
                     /locus_tag="AABJ69_RS23705"
                     /old_locus_tag="VEE17_45550"
     CDS             493..1848
                     /locus_tag="AABJ69_RS23705"
                     /old_locus_tag="VEE17_45550"
                     /inference="COORDINATES: protein motif:HMM:NF024700.4"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0016887 - ATP hydrolysis activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ATP-binding protein"
                     /protein_id="WP_000498067.1"
                     /translation="MFVRLTIENFRSVKENFTLDLSASGSNSHLVNHIYKNAEMSVGTL
                     MSAGIYGANASGKSNVLMAFEAIKYIATDSGDLKEGTRIPCYEPYALSLATNESPVRFV
                     ADFYSVEGNRFNYEVKYIKDRIIFESLDYYPSRVKANLFTRDEGDTWETIKFGGHYRGG
                     VKKIPFFPNNSYLAKAGNNAASPDIIKEAYDFFRKGIRHIGLNEKIRISSFGKREEVVS
                     ETAEVLCMVDTGVAGISVREVESDLPIRMDDDIPPEIKEMIEEDYKYRYLFSHATEEGG
                     SVSFPMSRESEGTQKLFEIIPLIRSAFNNSMVVIIDELDNSLHPHIADLIVKLFNDPDV
                     NKKGSQLIFSTHNMQLMTPEKMRRDQIWFCEKNKGASALYSLDDFDKKKVKTTTPYASW
                     YDEGRFGGVPDINYLKVAKFLSGNAMTAIHDIDVDALAGDFFEEFNEDLSND"
                     /name="ATP-binding protein"
     gene            1841..2458
                     /locus_tag="AABJ69_RS23710"
                     /old_locus_tag="VEE17_45560"
     CDS             1841..2458
                     /locus_tag="AABJ69_RS23710"
                     /old_locus_tag="VEE17_45560"
                     /inference="COORDINATES: protein motif:HMM:NF025084.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="RloB family protein"
                     /protein_id="WP_071345274.1"
                     /translation="MTKRKGGRNVPRVMYIYCEGEKTEPLYLESYISENSRRTLSVFKI
                     PKTRKNTPEQLVDEAIKKKNSSSTADGDEFWVVYDQEHLTTQSVLCHQRAWNKANRHGI
                     NIAISCVCFELWLLLHFGYTTRSFSSYENLMSASPFKGLLPNYNKGSSSTYDVLKNRIG
                     KARKNAAQLEIFAKSDNENIHEPYKFPCYTSFHKLLDAIDNF"
                     /name="RloB family protein"
     gene            complement(3258..3452)
                     /locus_tag="AABJ69_RS23715"
                     /old_locus_tag="VEE17_45570"
     CDS             complement(3258..3452)
                     /locus_tag="AABJ69_RS23715"
                     /old_locus_tag="VEE17_45570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_001041643.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEVENSTEI"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          3488..3729
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.9300000000000005e-124"
     Typing          complement(2700..3229)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.413"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          3..142
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.872"
                     /coverage="99.0"
                     /evalue="7.9e-21"
     Typing          3739..3914
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="3.62e-30"
ORIGIN
        1 actgaaagaa gttatgagac tgggggcgtt acagaaaaaa ctctttatcg acggcaagcg
       61 tgtcggggac agggagtatg cggaggtgct gatcgctatt acggagtatc accgtgccct
      121 gttatccagg cttatggcag attagcttcc cggagagaaa actgtcgaaa actgacggta
      181 tgaacaccgt aagctcccaa agtgatcacc attcgctttc atgcatagct atgcagcgag
      241 ctgaaaacga tcctgacgca tccttcctgt tttcccgggg taaaacatct ctttttgcgg
      301 tgtctgcgtc agaatcgcgt tcagcgcgtt tcagtggtgc gtacaattta taggttatgt
      361 taaatgttgt gtggtgaatg gtcgtacaag attctttatg atgatgttgt ttcaaattta
      421 aagcatgtgc tgtatcttgt ttattgcttt tttttcgctt ttttggcgaa aaaactcatt
      481 taggagttgc ctatgtttgt tcgtttgact attgaaaatt ttagatccgt aaaggaaaac
      541 tttacgcttg atttaagtgc gtctggctca aatagccatt tagttaatca tatttataaa
      601 aacgccgaga tgtctgttgg aacacttatg agtgctggga tttatggggc gaatgcgtca
      661 ggtaagtcca acgttctcat ggcttttgag gctattaaat atattgctac agatagcggg
      721 gatctgaagg aaggaactcg aattccatgc tacgaaccgt atgccctctc gttggctacg
      781 aatgagtcac cagttcggtt tgtggctgat ttttactctg ttgaggggaa tcgttttaat
      841 tatgaggtta aatatattaa agatcgaatt atattcgagt cattggatta ctatccgtct
      901 agggtaaagg ctaatttgtt tactagggat gaaggcgata catgggaaac aattaagttt
      961 ggtggtcatt atagaggtgg ggtgaaaaaa ataccattct tccctaataa ctcatatttg
     1021 gccaaggccg gtaataatgc ggcatctcca gatataatta aagaagctta tgactttttt
     1081 aggaaaggga taaggcatat aggtcttaat gaaaaaataa gaatctcatc ttttggtaaa
     1141 agagaggaag tagtaagtga aactgctgag gttctgtgca tggttgatac aggtgttgct
     1201 ggaatatccg tgcgagaagt agaatctgat ttaccaataa gaatggatga tgatattcct
     1261 ccagaaataa aagaaatgat agaggaggat tataagtatc gatatttgtt ttctcatgct
     1321 actgaggagg gcgggagtgt ttcttttcct atgtccagag agtctgaagg cactcagaag
     1381 ttatttgaaa taataccttt aattagaagt gcatttaata acagcatggt tgtgattatc
     1441 gatgaactag ataatagttt gcatccacat attgcagatc taattgttaa gctatttaat
     1501 gatcctgatg ttaacaaaaa gggatctcag ctaatattct ctacgcataa tatgcagttg
     1561 atgactcctg aaaaaatgag aagggatcag atatggtttt gcgaaaaaaa caaaggtgct
     1621 tcggcattat acagtttaga tgattttgat aagaaaaaag taaaaacaac aacaccttat
     1681 gctagttggt atgatgaggg ccggtttggc ggcgttcctg atattaatta tttgaaagta
     1741 gctaaattcc tatcaggaaa tgctatgact gctattcatg atattgatgt tgatgctctt
     1801 gctggtgatt ttttcgaaga gtttaacgag gatctttcta atgactaaaa ggaagggagg
     1861 gagaaatgtt cctcgagtga tgtatatata ttgtgaaggg gagaagacgg agccgttgta
     1921 tcttgaatct tatatatctg aaaattcaag aagaacgttg agtgtgttta aaatacctaa
     1981 aacaaggaaa aatacaccag agcagctagt agatgaggcg ataaagaaaa agaattcatc
     2041 atccactgcg gatggtgatg agttttgggt cgtttatgat caagagcatt tgactacgca
     2101 gtctgttttg tgccatcaaa gggcgtggaa caaagctaat aggcacggta taaatatagc
     2161 tatatcttgt gtttgttttg aactgtggtt gttgttgcac tttggttata caacaagatc
     2221 tttttcatct tatgaaaatt taatgtctgc ctctccgttt aagggtctgt tgccaaatta
     2281 taataaaggt agtagttcaa catatgatgt tttgaagaat aggattggga aggcgagaaa
     2341 aaatgcggca caactagaga ttttcgctaa atcagataac gaaaatatac atgagccata
     2401 taaatttcca tgttatacat catttcataa gttacttgat gcgattgata acttttgaat
     2461 taatccattg accatggctt attgctggtt gtaatctata gaaaataaaa accaccgcta
     2521 ccaacggtgg tttttagaag gtacatgagc taccaactta tgtaccgggt aactggctta
     2581 gaggagcgca gtcaccaaaa cttgtccttt tagtttagcc ttaactggcg catgacttca
     2641 agactaactc ctctaaatcg gttaccagtg gctgctgcca gtggcgttaa gtcgtgtctt
     2701 accgggttgg actcaagacg atagttaccg gataagacgc agcggtcggg ctgaacgggg
     2761 ggttcgtgca cacagcccag cttggagcga acgacctaca ccgggccgag atacctacag
     2821 cgtgagctat gagaaagcgc cacgcttccc gaagggagaa aggcggacag gtatccggta
     2881 agcggcaggg tcggaacagg agagcgcacg agggagcttc cagggggaaa cgcctggtat
     2941 ctttatagtc ctgtcgggtt tcgccacctc tgacttgagc gtcgattttt gtgatgctcg
     3001 tcaggggggc ggagcctatg gaaaaacgcc tgcggtgctg gcttcttccg gtgctttgct
     3061 ttttgctcac atgttctttc cggctttatc ccctgattct gtggataacc gtattaccgc
     3121 ctttgagtga gctgacaccg ctcgccgcag tcgaacgacc gagcgtagcg agtcagtgag
     3181 cgaggaagcg gaagagcgcc ttatgtgaca ttttctcctt acgctctgtt gtgccgttcg
     3241 gcatcctgcc ctgagcgtta tatctctgtg ctattttcta cttcaaagcg tgtctgtatg
     3301 ctgttctgga gttcttccgc gagttcgtgc agcttctcac acatggcggc ctgttcgtcg
     3361 gcatcgagtg cgtccagctt ttcgagcagt gtcaggctct ggctttttat gaagcccgcc
     3421 atgttgagta cagtttgctg ctgcttgttc atctttctgt tttctccgtt ctgtctgtca
     3481 tctgcgttat gtgattatat cgcgtaccac ttttcgacag ttttgccgcc ggtattctgc
     3541 cgtctgactc tttgacgggc atttctgcct gacaatactg tcactgccaa aaaaactgcc
     3601 gtgcctttgt cggtaattcg aacttgctga caggacagga tgtgtaattg ttataccgcg
     3661 catacatgca cgctattaca attaccctgg tcagggcttc gccccgacac cccatgtcag
     3721 atacggagcc atgttttatg acaaaacgaa gtggaagtaa tacgcgcagg cgggctatca
     3781 gtcgccctgt tcgtctgacg gcagaagaag accaggaaat cagaaaaagg gctgctgaat
     3841 gcggcaagac cgtttccggt tttttacggg cggcagctct cggtaagaaa gttaactcac
     3901 tgactgatga tcgggt
//
