LOCUS       NZ_CP011067             2640 bp    DNA     circular CON 12-JUN-2024
DEFINITION  Escherichia coli str. Sanji plasmid pSJ_2, complete sequence.
ACCESSION   NZ_CP011067
VERSION     NZ_CP011067.1
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 2640)
  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  JOURNAL   Unpublished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 2640)
  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
            CP011067.1.
            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..2640
                     /organism="Escherichia coli str. Sanji"
                     /mol_type="genomic DNA"
                     /strain="Sanji"
                     /isolation_source="pheasant duodenum"
                     /host="pheasant"
                     /db_xref="taxon:1441627"
                     /plasmid="pSJ_2"
                     /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            197..397
                     /locus_tag="Y979_RS27120"
                     /old_locus_tag="Y979_27265"
     CDS             197..397
                     /locus_tag="Y979_RS27120"
                     /old_locus_tag="Y979_27265"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166333.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="antitoxin VbhA family protein"
                     /protein_id="WP_023139298.1"
                     /translation="MARSPDPRQRTEGFRKAEASLRLEGMDPAGTPLYENIKERVISGD
                     ITYEQGRAEILAHYQKRANGH"
                     /name="antitoxin VbhA family protein"
     gene            complement(973..1302)
                     /locus_tag="Y979_RS27130"
                     /old_locus_tag="Y979_27275"
     CDS             complement(973..1302)
                     /locus_tag="Y979_RS27130"
                     /old_locus_tag="Y979_27275"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_052909321.1"
                     /translation="MKILPAEPGLYFFASFESGAHVYKVVAWSENENGGLDPQCVLTAL
                     YDKSSSSQQWELHSTSASAYQHSNDGRPFMYFITYFTSNGGIPELYNAINTLAERWGYP
                     LIDLP"
                     /name="hypothetical protein"
     gene            complement(1386..1817)
                     /locus_tag="Y979_RS27135"
                     /old_locus_tag="Y979_27280"
     CDS             complement(1386..1817)
                     /locus_tag="Y979_RS27135"
                     /old_locus_tag="Y979_27280"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003511628.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF6530 family protein"
                     /protein_id="WP_001025244.1"
                     /translation="MNIPTHLKHKPIIAVENYDRIDGPYADDTDAMGLSVGIAQWNTPG
                     YTELSAKVWRNTGEKWSRQSEELPLHRVIDLATLICIAMDYSKHGRLSSSDDFPVSRSG
                     GNPELSRHIDLMKNELKENHEHLDESLKRLAAELKRLGY"
                     /name="DUF6530 family protein"
     Typing          complement(2135..2640)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.932"
                     /coverage="96.0"
                     /evalue="9.94e-175"
ORIGIN
        1 gatctgcgat gcctgattgg gctcgtgtcg cgccgtaccc tctctttacc gccggattac
       61 acagtttcct gcaatacttt ccttccggtt tacacattcg tctgcacgga taaacaacgg
      121 cagagtacgg gcaggatatg taaagtaggc ctactttacc gcctgcctta ttcgcttaca
      181 gctcaaagga acatcgatgg ccaggtcccc cgatccacga caacgtactg agggtttccg
      241 caaagcggaa gcgtcgctga ggcttgaagg catggacccc gccggaacgc cgctgtacga
      301 aaatatcaag gagcgggtta tttccgggga tatcacttac gaacagggac gggcagaaat
      361 tctggctcat taccagaagc gtgcgaacgg ccactgacac ggacaggaaa ctaggtacca
      421 tcgcttcctc aaaaaaacag gcgtggcctc tctccggcca ggcttttcct gtatttgcta
      481 tctgtttgct acttgtttgc tatctttttg ctatctgttt gctacttgtt tgctatctgt
      541 ttgctacttg tttgctaccg ctaccctctg ctgtgaaaag agtaaggcac gttagcgatg
      601 tatacatcgc cgcgccgcaa gggttcccct tccgaatccc gttcatcact gcgtgctgat
      661 tatccacgtt aaatccgacc tcctgcttgg tagtaaattc tgccatgcct gacggcctgg
      721 ccaacgcctc acggtcgcac agtaaactgt gcacccgttc accgttatcg ggggagttat
      781 gcgccggaaa gcaggctttc atgccagcat ccaccccaaa tcgaccgcca ttcacctgcg
      841 tgcatagcca tgcagccgcg cagaaatcat caggcgcgtt ttttcacgat atggacaggg
      901 aaagatgccg gaaataggca ggagggcgca gaaatgccct gagggcgtct gagatggtgc
      961 acgcaacgaa tgttatggta aatcaattaa tgggtatccc catcgttcgg ctagtgtgtt
     1021 tattgcgtta taaagttcag gtatcccgcc attgctggtg aagtaggtga taaaatacat
     1081 aaatggtctg ccgtcattgc tgtgctgata tgcagatgct gaagttgagt gaagttccca
     1141 ttgctggctg gaactgctct tgtcatataa ggccgttaac acacactgtg gatctaaacc
     1201 accattctca ttttctgacc aggccactac tttgtaaacg tgagcaccgg actcaaaaga
     1261 tgcgaaaaaa tataatcccg gttcagctgg taggatcttc attagctagc ttccttttgt
     1321 ttattctgtc tgagaggcaa taactaccta attccccgtg gtgggtataa aaaatcacgg
     1381 ggaggttaat aacctaaacg ttttagttct gctgctaaac gcttaagact ctcatctaaa
     1441 tgctcgtgat tctcttttag ctcgtttttc attaaatcaa tgtgacgaga taactcagga
     1501 ttgcctcctg aacgactgac cggaaagtcg tcgctggaag ataagcggcc atgtttactg
     1561 taatccattg ctatgcagat aagcgttgcc aagtcgataa cacgatgaag aggtaattct
     1621 tctgattgcc gtgaccactt ttctccggtg ttgcgccaca cttttgctga tagctcggta
     1681 tacccggggg tgttccattg agcaattcca acggaaagcc ccatagcatc agtgtcatca
     1741 gcataaggtc catcaattcg atcatagttt tctacagcga taatcggttt gtgtttcaga
     1801 tgagtaggga tgttcatatc attctctttt atgtgaattt aggttgttaa ttaacaaaat
     1861 aacaaaacag cttattttac taattagtaa gtgtaacatt ttgtgaattg atggatttga
     1921 agttgttggc gtggatcttc ttgagatcat ttatggcaga gcgtaatctc ttgctcagaa
     1981 aacgaaaaaa ccaccctggc aggtggtttt tcgaaggtta gttaatcctg gcagattctc
     2041 taaccgtggt aacagtcttg tgcgagacat gtcaccaaat ctgtcctttc agtgtagccg
     2101 cagtcaggcc accacttcaa gaactctcga tacatctctc gcacatcctg tttaccagtg
     2161 gctgctgcca gtggcgcttt gtcgtgtctt tccgggttgg actcaagttg atagttaccg
     2221 gaaaaggcgc agcagtcgga ctgaacgggg ggttcgtgca tacagtccag cttggagcga
     2281 actgccttcc cggaatcgag tgtcaggcgt ggaatgagat aaacgcggcc ataacagcgg
     2341 aatgacaccg gtaaaccgaa tggcaggaac aggagagcgc acgagggagc taccaggggg
     2401 aaacgcctgg gatctttata gtcctgtcgg gtttcgccac cactgatttg agcgtcagat
     2461 tctgtgatgc ttgtcagggg ggcgaagcct atggaaaaac ggcttcgccg cggccttttc
     2521 tgttcccctc tttctccttc cgctaccccc gaatctgtgg gtaactccag gtggactgcc
     2581 ggtaccgctc gccgcagccg aacggccgag cgtagcgagt cagtgagcga ggaagcggaa
//
