LOCUS       NZ_CP011066             3373 bp    DNA     circular CON 12-JUN-2024
DEFINITION  Escherichia coli str. Sanji plasmid pSJ_3, complete sequence.
ACCESSION   NZ_CP011066
VERSION     NZ_CP011066.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02580208
            Assembly: GCF_001610755.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli str. Sanji
  ORGANISM  Escherichia coli str. Sanji
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3373)
  AUTHORS   Ho,M., Zeng,X., Lambert,C., Hall,R., Baybayan,P. and Wilson,B.A.
  TITLE     Complete genome of antibiotic resistant Escherichia coli str. Sanji
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3373)
  AUTHORS   Ho,M., Zeng,X., Lambert,C., Hall,R., Baybayan,P. and Wilson,B.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-MAR-2015) Department of Microbiology, University of
            Illinois at Urbana-Champaign, 601 S. Goodwin Ave., Urbana, IL 61801,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 2.3
            Genome Coverage                   :: 135x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_001610755.1-RS_2024_06_12
            Annotation Date                   :: 06/12/2024 03:36:22
            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)                     :: 5,360
            CDSs (total)                      :: 5,238
            Genes (coding)                    :: 4,963
            CDSs (with protein)               :: 4,963
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 275
            CDSs (without protein)            :: 275
            Pseudo Genes (ambiguous residues) :: 0 of 275
            Pseudo Genes (frameshifted)       :: 101 of 275
            Pseudo Genes (incomplete)         :: 177 of 275
            Pseudo Genes (internal stop)      :: 62 of 275
            Pseudo Genes (multiple problems)  :: 60 of 275
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP011066.1.
            Bacteria available from Xiancheng Zeng, School of Animal Science,
            Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002,
            China (zxc206@163.com).
            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/
            This genome has a base modification file available.
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..3373
                     /organism="Escherichia coli str. Sanji"
                     /mol_type="genomic DNA"
                     /strain="Sanji"
                     /isolation_source="pheasant duodenum"
                     /host="pheasant"
                     /db_xref="taxon:1441627"
                     /plasmid="pSJ_3"
                     /geo_loc_name="China"
                     /lat_lon="26.2472 N 119.0831 E"
                     /collection_date="2011-10"
                     /collected_by="Xiancheng Zeng"
                     /note="highly drug-resistant strain"
     gene            complement(181..372)
                     /locus_tag="Y979_RS27105"
                     /old_locus_tag="Y979_27250"
     CDS             complement(181..372)
                     /locus_tag="Y979_RS27105"
                     /old_locus_tag="Y979_27250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_062914769.1"
                     /translation="MTKQEKTALNMARFIRNQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            436..759
                     /locus_tag="Y979_RS27110"
                     /old_locus_tag="Y979_27255"
     CDS             436..759
                     /locus_tag="Y979_RS27110"
                     /old_locus_tag="Y979_27255"
                     /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_001696562.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     APPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            968..>1405
                     /locus_tag="Y979_RS32035"
                     /pseudo=""
     CDS             968..>1405
                     /locus_tag="Y979_RS32035"
                     /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            1437..1997
                     /locus_tag="Y979_RS31360"
     CDS             1437..1997
                     /locus_tag="Y979_RS31360"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            2004..2237
                     /locus_tag="Y979_RS31365"
     CDS             2004..2237
                     /locus_tag="Y979_RS31365"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /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_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          17..100
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.882"
                     /coverage="95.0"
                     /evalue="4.11e-16"
     Typing          750..2320
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.628"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcacttccca tccactctgc accgatgcaa aatgaggaaa gccagtatac acatcgctat
       61 cgctctgtga actgggtcag ggctgcgccc cgacacccgc actgacgcgc cctggcgggc
      121 ttgtctgctc ccggcatccg ctcacaggca agctgtgaac gtctccggga gctgcatgtt
      181 tcagttgctt tcaccgtcat cgccgaagcg tgcgaggcaa ctgcggtaga gttcgtcggc
      241 gtggtcgtga agtgattcgc agatgtctgc ctgttcgtcc gcgtccagat cgttgagttt
      301 ttccagcagg gttagcgtct ggtttctgat aaagcgagcc atgttaaggg ctgttttttc
      361 ctgtttggtc atggtcttaa ggctccttgt atgggggatt tgttaggggg aatgataccg
      421 atgaaacgcg agaagatgct cacgatacgg gttaccgatg aggagcacgc ccggttactg
      481 gaacgctgcg agggtaaacg actggcggaa tggatgcggc gggtctgtct gggggagccg
      541 gttgcacgca caggaaaact gccgacactg gcaccgccat tgctgcggca tctggctgcc
      601 atcgggaaca acctgaacca gacagcccgg aaggtgaaca gcggccagtg gtcttcgatt
      661 gaccgggttc atgtggtggc cgcactgatg gccatcgagg gtgaattgcg ccagttgcgg
      721 caggctgtca gggaacaggg ggtacgggat gatagttaaa tttcatgcca gggggaaagg
      781 cggtggaagt ggcccggtcg attacctgct ggggcgggag cgtaaccgcg aaggcgcaac
      841 ggtgctccgg ggtaacccgg aagaagtgcg ggaactcatt gattccacgc cattttcgaa
      901 gaaatacacg tcaggcgttc tgtcgttcgc ggagaaggag ctaccaccgg gtgaacgcga
      961 aagagtgatg acgagctttg agcgtgttct tatgcccggt ctcgaaaaag accagtacag
     1021 cattctctgg gtggaacacc aggataaggg gcggctcgaa ctgaattttg tcatcccgaa
     1081 catggagcta cagagcggta agcgcctcca gccgtactac gaccgtgcgg acaggccgag
     1141 gataaatgcc tggcagacgc tggttaatca tcattacggg ctgcgtgacc cgaacgcacc
     1201 ggagaacaga cggacgcttg tcacgccaaa taatctgcca aaagcgaaac aggaggccgc
     1261 agaagcgatt acacggggtc ttgaggctct ttaccatgcc ggagcaataa aaacgcgtca
     1321 ggatgtcaca gaggcgctta cagcggcagg ttttgaggtg gtgaggacaa ccaaaagcag
     1381 catcagtatt gccgacccgg agggggggcg gaatctcagg ctaaaggggg cgctgtatga
     1441 gcaatctttt acaaatggga acagacttcg agaagaaact gaaagagcga gccgcttcta
     1501 ccgagaacat gctgaacagc gagttcagga agctcgaaga gtctgtagac aaggcattga
     1561 gcttaaacag gcagaaaatc agagacgcta tcagcgaaca tacaacatcc gtgaaaaagc
     1621 aactggatac gctgagcacc accgtgagca tgcagttcag caccacagag gccgaactgt
     1681 cccggcagca gaaaaaactg ctctggcggg tgatcaaagg gcggatactg tttccggcgc
     1741 tgaccgcgct cagcgtcacg ggcgggattt tcctggggtg ctgggggctg atggagtggc
     1801 aggaaagcaa gattgcgaaa aatatcctga ctatcagaga gcaggaaaac acgctggcga
     1861 aactcgaggc aaaaacctgg ggggtgacgt tcgtcaatgg cgagaacggg aaatttctgg
     1921 tgttgccgga cggggtgaaa ggggaaaaca cctggacggt gggcgacaag aacgccgtga
     1981 ggctggtcag ggagtaaacg agtatgacgg aactggaagg gcatttgctg aacgccttag
     2041 agcatttgca acaggactat atgcggcggc tgaacgagtg ggagagcgcc ttcgcggaat
     2101 tgcagaagat gcacgaggtt acgcaacgga acaacgcgat actgaacgag cgcgtcgtga
     2161 tattgagtca gcaggtgcag agattagccg ggcaagtgga tcgcttgagt cggttattta
     2221 tcgcgaacaa cagctaaggg atgaacagga gcgtgcccgg tacagacatg aggtacagga
     2281 acgcgcggca cgggttcgga gtgggccatc aatggagatg tgaccggaga agtgacgaaa
     2341 tcttgccatt ttgacccgtt cgacggctgg ggcgagcgaa acaaatcgtg tgccgtattt
     2401 gtgcatagct atgcaacatc ctgaaaacgc atttcacgcg tttttgggga ttcagccagg
     2461 ggaaaacatg gtttttttac tttttgagcg taaagacgtg aaaaatctcg ttattgcact
     2521 tgcgatcttt cgtcggtggg cgtagaacga aaacagctcg ccaggaaggc gagctgtttc
     2581 gggttcattg aggtctctga cctcctcaat gttcctgtgg aaactgttga gatccacaac
     2641 agaaaccagt tcattcagtt tgcatgagcc ttctgtattc ttcaagagtt tttcaacagc
     2701 acagtctccc aggaaccccg aaaaaaacct gtttttgcag atacttgcgt atttgcgaga
     2761 atcgtttgcg gttgggggag ctgtgacgac ggcgaccgca cgcgtgagag ttccgctacc
     2821 ggcgcagaga gtttcatcga cagcggacac ctgatgagtt gccacaaaaa ccgtatgtag
     2881 cgcggctaga ttggttgagt tagaccttgg cggcagttcc cggtatgtgg tggcgtgacg
     2941 ggtgagatgg tgcggcgaag acgcatacgt cacgcaggcg cgggttcttc cactgacgcg
     3001 ccccgtgatc gatggccttg gctccgtccg gcatatcgag agcggcaaac tacccgtccc
     3061 ttcactggga ggggtgagtt gttgccgttc cctccgacct tccaccatcc agcatatcgc
     3121 acgatcccat gtgcaccgct actcctgata actccagtgc aaaaaaaaaa acggatctgc
     3181 atcacaacga gagtgatccc accgctcgcc gcagccccag cgaccgaacg tagtgagcga
     3241 gtgggcgagg aagcggaaga gtcacagagg caagcattgt gcacttacgc gcctgtgcca
     3301 gtgtccgcgt gtgtgttgtt tatcgggcgc gctgttttta cgcatctgtg cggcttttta
     3361 ctcctgacat ggt
//
