LOCUS       NZ_CP040072             5221 bp    DNA     circular CON 20-JUN-2024
DEFINITION  Escherichia coli strain A1_181 plasmid p_unnamed5, complete
            sequence.
ACCESSION   NZ_CP040072
VERSION     NZ_CP040072.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10887807
            Assembly: GCF_006352265.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5221)
  AUTHORS   Ahlstrom,C.A., Ramey,A.M., Woksepp,H. and Bonnedahl,J.
  TITLE     Repeated detection of carbapenemase-producing Escherichia coli in
            gulls inhabiting Alaska, USA
  JOURNAL   Antimicrob. Agents Chemother. (2019) In press
  REMARK    Publication Status: Available-Online prior to print DOI:
            10.1128/AAC.00758-19
REFERENCE   2  (bases 1 to 5221)
  AUTHORS   Ahlstrom,C.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-MAY-2019) Alaska Science Center, USGS, 4210 University
            Drive, Anchorage, AK 99508, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. NOV-2018
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 127.0x
            Sequencing Technology             :: Illumina HiSeq; PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_006352265.1-RS_2024_06_20
            Annotation Date                   :: 06/20/2024 02:46:44
            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)                     :: 5,130
            CDSs (total)                      :: 5,006
            Genes (coding)                    :: 4,741
            CDSs (with protein)               :: 4,741
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 265
            CDSs (without protein)            :: 265
            Pseudo Genes (ambiguous residues) :: 0 of 265
            Pseudo Genes (frameshifted)       :: 80 of 265
            Pseudo Genes (incomplete)         :: 175 of 265
            Pseudo Genes (internal stop)      :: 50 of 265
            Pseudo Genes (multiple problems)  :: 36 of 265
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP040072.1.
            Bacteria and source DNA available from USGS Alaska Science Center.
            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..5221
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="A1_181"
                     /isolation_source="feces"
                     /host="Larus sp."
                     /db_xref="taxon:562"
                     /plasmid="p_unnamed5"
                     /geo_loc_name="USA: Alaska, Anchorage mudflats"
                     /collection_date="2016-08-09"
     gene            complement(join(5050..5221,1..125))
                     /locus_tag="FDP43_RS25810"
                     /old_locus_tag="FDP43_25820"
     CDS             complement(join(5050..5221,1..125))
                     /locus_tag="FDP43_RS25810"
                     /old_locus_tag="FDP43_25820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679964.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001679964.1"
                     /translation="MSKTKSGRHRLSKTDKRLLAALIAAGYEERTARDLIQKHVYTLTQ
                     ADLRHLVSEISNGVGQSQAYDAIYQARRIRLARKYLNGKKPEEGLNAWKGDLP"
                     /name="hypothetical protein"
     gene            337..534
                     /locus_tag="FDP43_RS25815"
                     /old_locus_tag="FDP43_25825"
     CDS             337..534
                     /locus_tag="FDP43_RS25815"
                     /old_locus_tag="FDP43_25825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335786.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001335786.1"
                     /translation="MKEEKVLLHRFLFVVRNKNGCELSCSADLMGTRDDVYKYFSDSVS
                     GLDVELIDVSCESEWEEHSH"
                     /name="hypothetical protein"
     gene            552..836
                     /locus_tag="FDP43_RS25820"
                     /old_locus_tag="FDP43_25830"
     CDS             552..836
                     /locus_tag="FDP43_RS25820"
                     /old_locus_tag="FDP43_25830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000625497.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin Z C-terminal domain-related protein"
                     /protein_id="WP_000625497.1"
                     /translation="MISQNVWAPPFFFGPWVELENHTGDIAYTVYFDTLSNVPGPFIAF
                     IWYAPNGPRTVNVIGPASYQISCKGAGVDKIKFKSVSGTGQIIHVYTTL"
                     /name="colicin Z C-terminal domain-related protein"
     gene            complement(900..1289)
                     /locus_tag="FDP43_RS25825"
                     /old_locus_tag="FDP43_25835"
     CDS             complement(900..1289)
                     /locus_tag="FDP43_RS25825"
                     /old_locus_tag="FDP43_25835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679965.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001679965.1"
                     /translation="MFKSSVKSITSSTILTLLIGCSSTETNKNIVYKVGGDSIILNKYC
                     ILKMYPSQSEKNKGVIIEVNTDSLCKKKLNEITSKNIGKPLISYFDGKVISQPAIIHSA
                     LNLTHYYQPVNDETTVMEIIKAYSK"
                     /name="hypothetical protein"
     gene            complement(1695..1808)
                     /locus_tag="FDP43_RS26875"
     CDS             complement(1695..1808)
                     /locus_tag="FDP43_RS26875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001427889.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAIGN"
                     /name="hypothetical protein"
     gene            2138..2326
                     /locus_tag="FDP43_RS25830"
                     /old_locus_tag="FDP43_25840"
     CDS             2138..2326
                     /locus_tag="FDP43_RS25830"
                     /old_locus_tag="FDP43_25840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001441803.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_249489876.1"
                     /translation="MDNRITAFECADTARRSRTTERSESVSEEAEEHRHLHVLLTHLCD
                     ISHPAWCTFHTIRTDAA"
                     /name="hypothetical protein"
     gene            complement(2479..2670)
                     /locus_tag="FDP43_RS25835"
                     /old_locus_tag="FDP43_25845"
     CDS             complement(2479..2670)
                     /locus_tag="FDP43_RS25835"
                     /old_locus_tag="FDP43_25845"
                     /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_116965635.1"
                     /translation="MTKQERTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2734..3057
                     /locus_tag="FDP43_RS25840"
                     /old_locus_tag="FDP43_25850"
     CDS             2734..3057
                     /locus_tag="FDP43_RS25840"
                     /old_locus_tag="FDP43_25850"
                     /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_000956005.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGRLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3266..>3697
                     /locus_tag="FDP43_RS26690"
                     /pseudo=""
     CDS             3266..>3697
                     /locus_tag="FDP43_RS26690"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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            3735..4265
                     /locus_tag="FDP43_RS25850"
                     /old_locus_tag="FDP43_25860"
     CDS             3735..4265
                     /locus_tag="FDP43_RS25850"
                     /old_locus_tag="FDP43_25860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /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_117014864.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLGESVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGMIQANLEEIRKQNESLEKLNAKTWGVRYHEGSNGRFLVLPEGMKAETNWTM
                     ENGKQNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            4272..4505
                     /locus_tag="FDP43_RS25855"
                     /old_locus_tag="FDP43_25865"
     CDS             4272..4505
                     /locus_tag="FDP43_RS25855"
                     /old_locus_tag="FDP43_25865"
                     /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_000137439.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          2306..2393
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.876"
                     /coverage="100.0"
                     /evalue="3.19e-37"
     Typing          complement(1737..2290)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.705"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3048..4609
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.505"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtgtaaacgt gtttctggat gaggtcacgg gctgtccgct cttcgtatcc ggcagcgata
       61 agtgcagcca gcaggcgttt gtctgttttg ctcagtcggt ggcgaccaga ttttgttttg
      121 ctcacgttat ctcctctctg ttttttctcc tgatgttatc cggtgctgtt tttctgctgc
      181 gaatcttccc ttcctgattt ttataagggt gattcagatc acaaaaatga aaattcatat
      241 cattgacagg aaaaataatg cggcgtaatt tatgctgtat ataaaactag tgtttatata
      301 tacagtatat tctgtgtaaa taaagggagg gataaaatga aagaagaaaa agtattgctt
      361 caccgtttct tatttgtagt taggaataag aatggttgtg aactatcatg ttcggcagac
      421 cttatgggaa caagggatga tgtttataag tatttctctg attctgttag tgggctagat
      481 gttgagctta tagatgtttc ttgcgagagt gaatgggaag aacattcgca ttgaactaat
      541 caggagatta tatgatttct caaaatgttt gggctcctcc tttctttttt ggtccttggg
      601 ttgaacttga aaatcatact ggtgatatcg cgtacactgt ctattttgat acattgtcta
      661 atgtacccgg tccatttatt gcttttatct ggtatgcccc taatgggcca agaacagtta
      721 acgttattgg tccagcatct tatcagatct cttgcaaggg cgctggtgtt gataaaatta
      781 aatttaaaag tgtcagtggg acagggcaga ttattcatgt atacactacc ttataataag
      841 agctgaatag atataatcct gcctaagcta taccttaagc aggattatat ctattaatat
      901 tattttgaat atgcttttat gatttccatc actgttgttt catcgttcac aggttgataa
      961 taatgggtta gatttagtgc agaatgaatg attgcaggtt gggatattac ttttccatca
     1021 aaatatgaaa tcaggggttt ccctatattt ttactagtta tttcgtttag ttttttctta
     1081 cataaactat ctgtgtttac ttctattatg acgcctttgt ttttttctga ttgggaaggg
     1141 tacattttaa gtatgcaata tttattcaga atgatgctgt cacctccaac tttgtaaaca
     1201 atgtttttgt ttgtttcagt acttgaacat cctataagta aggtcagtat agtactcgat
     1261 gttattgact ttactgatga tttgaacata ttaactccat tttattttgt taaaattcca
     1321 atctataaat acatatacac gtaaaaataa acaatgcgaa cgttttcact tatattatcc
     1381 ccatgatgtg attgaatggt ggttccatat aagagagggc aattatacta tctttctctc
     1441 ctgaactgat gggattgcag tttagagaaa aaagatcaaa ggatcttctt gagatccttt
     1501 ttttctgcgc gtaatctgct gcctgtaaac gaaaaaacca ccctggcagg tggtttttcg
     1561 aaggttagct aatcctggca gattacctaa ccgggtagct ggcttaagtg gagcacagat
     1621 accaaaagat gtcctttcag tgtagccgct ataaggcttc aacttcaaga gttctgcgta
     1681 tctaaatcca ctttttagtt accaatggct gctgccagtg gcgttaagtc gtgtcttacc
     1741 gggttggact caagacgata gttaccggat aaggcgcagc ggtcgggctg aacggggggt
     1801 tcgtgcacac agcccagctt ggagcgaacg acctacaccg aactgagata cctacagcgt
     1861 gagctatgag aaagcgccac gcttcccgaa gggagaaagg cggacaggta tccggtaaac
     1921 ggtaaggtcg gaacaggaga gcgcacgagg gagcttccgg ggggaaacgc ctggtatctt
     1981 taagtcctgt cgggtttcgc cacctctgac ttgagcgtcg atttttgtga tgctcgtcag
     2041 gggggcggag cctatggaaa aagcgcctcc ggcgcggcct tttccggggt ttttgttttt
     2101 tgctcacatg ttctttccgg cgttatctcc tgattgtgtg gataaccgta tcaccgcttt
     2161 tgagtgcgca gacaccgctc gccgcagccg aacgaccgag cgcagcgagt cagtgagcga
     2221 ggaagcggaa gagcaccggc atttgcatgt tctccttacg catctgtgcg acatttcaca
     2281 ccctgcatgg tgtacttttc atacaatccg cactgatgcc gcatgactaa gccagtatac
     2341 actccgctgt cgctacgtga ctgggtcatg gctgcgcccc gacacccgct aaaaccccgc
     2401 tgacgcgccc tgacgggctt gtcggctccc ggcatccgct cacagacaag ctgtgaccgt
     2461 ctccgggagc tgcatgtgtc agaggttttc accgtcatcc ccgaagcgag cgaggcagct
     2521 gcggtaaagc tcatcggcgt ggtcgtgaag cgattcacag atgtctgcct gttcatccgc
     2581 gtccagttcg ttgagctttt ccagcagtgt taatgtctgg cttctgataa agcgcgccat
     2641 gttaagggcg gttctttcct gtttagtcac tgatgcctcc gtgtaagggg gatttctgtt
     2701 catggggtaa tgataccgat gaaacgcgag aggatgctca cgatacgggt tactgatgat
     2761 gaacatgccc ggttactgga acgctgtgag ggtaaacagc tggcggtatg gatgcggcgg
     2821 gtctgcctgg gtgagcctgt cgcccgttcc gggaggctgc cgacactggc accgccgtta
     2881 ctgcgtcagc tggccgctat cggaaataac ctgaatcaga cagcgaggaa ggtaaacagc
     2941 gggcagtggt cttccggtga ccgggttcag gtggtggctg cactgatggc catcggggat
     3001 gagctgcgcc ggctgcgtct ggccgtcagg gaacagggga cgcgggatga tagttaagtt
     3061 tcatgcccgg ggaaaaggcg gtggcagtgg tccggttgat tacctgctgg gaagggagcg
     3121 aaaccgggaa ggggcaacgg tgcttcaggg taatccggaa gaagtccggg aactcatcga
     3181 tgccacgcca tttgcgaaga aatacacgtc cggtgttctc tcgttcgcgg agaaggcgct
     3241 gccagcggga ggacgtgaaa aagtgatggc gagttttgag cgtgtactga tgcccggtct
     3301 cgaaaaaaat cagtacagca tcctgtgggt ggagcaccag gacaagggac ggcttgagct
     3361 gaattttgtc attccgaaca tggagctaca gagcggaaaa cgcctccagc cgtactacga
     3421 ccgggcagac aggccgagaa ttgatgcctg gcagacgctg gttaatcacc attacgggct
     3481 gcatgacccc aacgccccgg agaaccgccg gatactgact ctccctgata acctgccgga
     3541 aacgaaacag gcgtttgctg agggcgtcac acgcgggata gacgcgcttt accatgccgg
     3601 agagataaaa ggccgtcagg atgtgattca ggcgctcatg gaagcaggga ttgaagtggt
     3661 cagggtgacg cgaagcagta tcagcattgc agacccgaac ggcgggaaga atatcagact
     3721 gaaaggagca ttctatgagc aatcttttac agacgggcgc ggagttcgag aaaaagctga
     3781 aagagagagc cgaatctaca gagaaaatgc tgaacgacga gttcaggaag ctcggcgaat
     3841 ctgtaagcaa ggctgtgaca tcaaacgaga cgaaaatcaa agacgctata gccctgttca
     3901 cagcttcgac agaggaatca ctgaaaaaac accgggaagg ggtgaaagag gcgatgatgc
     3961 agcacaggaa ggacgtgtta aagctggcag ggaatacggg catgatgtta ctggggatgg
     4021 tcattttcct gtttaccgtg agtggcggga cgctctggta tcttggcggg atgatacagg
     4081 cgaacctgga agaaatcaga aagcagaacg agagtctgga gaagctgaac gcgaagacat
     4141 ggggcgtgcg ttatcacgag gggagcaacg gacgttttct ggtgttgccc gaggggatga
     4201 aagccgaaac gaactggacg atggaaaacg ggaaacagaa tgccgtaagg ctggtacagg
     4261 agtaacagag catgacggag ctggaaagac atttgctgaa cgccttagag caactgcaac
     4321 aggactatat gcagcggctg aacgaatggg agagcgcctt cgtggaattg cagaaaatgt
     4381 tttcgcttac gcaacgggac aacgcgatgc tgaacgagcg ggtcatgcag ttgagtcagc
     4441 aggtgcagca cttgagcgag cagacagaac gcttgagcca gttatacagc gagaacagga
     4501 gataagggac gaacggctga tacaggaacg cgaacatgcg ttatccctgg agcgtgagcg
     4561 ccagccggaa atacaggaac ggacactgga tggcccttcg ctgggatggt aatcagagac
     4621 aggctaaaat gttgtcagcg cgtttccggt gcattttttg ggataatggt tggttcgggg
     4681 gcaccgggaa cgcgcttcag tcagaccttg ctgaaaacac aggaacgcgt taaaacgcat
     4741 acgggcgcga ttctggtgtg tcttttgttg ctgtgttttg cctctattgc cagatcgcgc
     4801 tcattcccct gaacttctgt tttcccgctc cggtccccgt cttcttcgct tccgaaagca
     4861 tgaaaaaaat ccgtttcagc tgtctctggc tggcaattcc tgcgtgattc acatggctgc
     4921 atagctatgc atgtggttaa aatttaccgg gtgcgatcgc ggcagttttt cggggggttt
     4981 gttgccattt ttacctgtct gctgccgtga tcgcgccgaa cgcgtttcag cggtgcgtac
     5041 aatgagacgt tatggtaaat cacccttcca ggcgttcagc ccttcttccg gtttttttcc
     5101 gttcaggtat ttacgggcga gacgaatgcg tcttgcctgg taaatcgcat cgtaggcctg
     5161 tgactgtccc acaccgttac tgatttcact gaccagatgg cgcaggtcgg cctgtgtcag
     5221 t
//
