LOCUS       NZ_CP130671             5772 bp    DNA     circular CON 01-AUG-2023
DEFINITION  Escherichia coli strain SM107 plasmid pSM107_2, complete sequence.
ACCESSION   NZ_CP130671
VERSION     NZ_CP130671.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36664847
            Assembly: GCF_030552915.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5772)
  AUTHORS   Bao,D.
  TITLE     Genomic characteristics of a carbapenem resistant Escherichia coli
            isolate
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5772)
  AUTHORS   Bao,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-JUL-2023) Department of Clinical laboratory, Sir Run
            Run Shaw Hospital, School of Medicine, Zhejiang University, 3
            Qingchun East Road, Hangzhou, Zhejiang 310016, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Oxford Nanopore GridION; Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/30/2023 16:45:42
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,424
            CDSs (total)                      :: 5,301
            Genes (coding)                    :: 5,066
            CDSs (with protein)               :: 5,066
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 235
            CDSs (without protein)            :: 235
            Pseudo Genes (ambiguous residues) :: 0 of 235
            Pseudo Genes (frameshifted)       :: 85 of 235
            Pseudo Genes (incomplete)         :: 168 of 235
            Pseudo Genes (internal stop)      :: 56 of 235
            Pseudo Genes (multiple problems)  :: 59 of 235
            Pseudo Genes (short protein)      :: 2 of 235
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP130671.1.
            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..5772
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SM107"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSM107_2"
                     /geo_loc_name="China: Sanmen"
                     /collection_date="2022-10-26"
                     /collected_by="Danni Bao"
     gene            complement(56..379)
                     /locus_tag="Q4S51_RS27075"
                     /old_locus_tag="Q4S51_27075"
     CDS             complement(56..379)
                     /locus_tag="Q4S51_RS27075"
                     /old_locus_tag="Q4S51_27075"
                     /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_001430281.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGRLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            443..634
                     /locus_tag="Q4S51_RS27080"
                     /old_locus_tag="Q4S51_27080"
     CDS             443..634
                     /locus_tag="Q4S51_RS27080"
                     /old_locus_tag="Q4S51_27080"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1698..1786)
                     /locus_tag="Q4S51_RS27085"
                     /old_locus_tag="Q4S51_27085"
     tRNA            complement(1698..1786)
                     /locus_tag="Q4S51_RS27085"
                     /old_locus_tag="Q4S51_27085"
                     /product="tRNA-Lys"
                     /inference="COORDINATES: profile:tRNAscan-SE:2.0.12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: tRNAscan-SE."
                     /anticodon=(pos:complement(1750..1752),aa:Lys,seq:ctt)
                     /name="tRNA-Lys"
     gene            1963..2853
                     /locus_tag="Q4S51_RS27090"
                     /old_locus_tag="Q4S51_27090"
     CDS             1963..2853
                     /locus_tag="Q4S51_RS27090"
                     /old_locus_tag="Q4S51_27090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015376142.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_021512263.1"
                     /translation="MPDLEIMPLQSPDFYKKNKRAIYEGYKCNCTKDWKKEDRFVVYKA
                     DCTGIDEIINTEISDDNIDTVIKLAEKYTSDKIIISGGHTVVNLNDRFSVSNEVEKSAK
                     FCIDYIIKSTHELNIKPDFLMEINDFYMEKSNGEDIDGGNIYRKLATSPYIIPEVINNY
                     IIEKQNQHNIKINCFYVSEKNMADRFKRHIKRKEKEKPFFKENNSVFMNVDGSSFEVIK
                     NNKPTCAAGNAATFRSIRYKISSNKTFDNYTSHIGVFPLCSMANVINGYKAAASFYSNF
                     NLPCLLIFFGTSCFK"
                     /name="hypothetical protein"
     gene            2865..3998
                     /locus_tag="Q4S51_RS27095"
                     /old_locus_tag="Q4S51_27095"
     CDS             2865..3998
                     /locus_tag="Q4S51_RS27095"
                     /old_locus_tag="Q4S51_27095"
                     /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_072647583.1"
                     /translation="MKINSIQWPVTFFATSFGAGIFFLPQTVGPKVIGTHGTITILILS
                     SLVSLLGQFTFYRFILITDKKEYVSSAILFIGKKAANAISIAFLLSMLLIAIINITTMI
                     NIICFSLSLNGSERIFVSLIISATLGSSFIFFNSKIEHLASGIAFPSLLIVLFLSIYFY
                     SHPAHPHSTEIQNISTSNLLTLFPVVLFSFNFSPCIQRFAQNKKDTAGDLRFFMFGILL
                     ILIFISFIVFSLSNIFSPSDIKNMREINSDALSYSANVTKNSFVAYISILTMILITSGA
                     YTGTLTGVVDTIVSLGFKNKTLIVFVVSVITFIAGEANFEIIKVIAALSTPIIAITVFI
                     IPSAFFLKTNCNSIFRKIMMTLNLLIGIGICFLAIIL"
                     /name="hypothetical protein"
     gene            complement(4392..4625)
                     /locus_tag="Q4S51_RS27100"
                     /old_locus_tag="Q4S51_27100"
     CDS             complement(4392..4625)
                     /locus_tag="Q4S51_RS27100"
                     /old_locus_tag="Q4S51_27100"
                     /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_004026237.1"
                     /translation="MTELEIHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(4632..5150)
                     /locus_tag="Q4S51_RS27105"
                     /old_locus_tag="Q4S51_27105"
     CDS             complement(4632..5150)
                     /locus_tag="Q4S51_RS27105"
                     /old_locus_tag="Q4S51_27105"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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_001749510.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQTNLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            complement(<5188..5619)
                     /locus_tag="Q4S51_RS27110"
                     /old_locus_tag="Q4S51_27110"
                     /pseudo=""
     CDS             complement(<5188..5619)
                     /locus_tag="Q4S51_RS27110"
                     /old_locus_tag="Q4S51_27110"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /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"
     Typing          complement(720..805)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.701"
                     /coverage="100.0"
                     /evalue="1.86e-34"
     Typing          827..1375
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.937"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(60..409)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.291"
                     /coverage="99.0"
                     /evalue="9.199999999999999e-69"
     Typing          complement(4289..5772)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.016"
                     /coverage="96.0"
                     /evalue="0.0"
ORIGIN
        1 ccccagcagg taatcaaccg gaccactgcc accacctttt cccctggcat gaaatttaac
       61 tatcatcccg cgccccctgt tccctgacgg ccagacgcag ccggcgcagc tcatccccga
      121 tggccatcag tgcggccacc acctgaaccc ggtcaccgga agaccactgc ccgctgttca
      181 ccttcctcgc tgtctgattc aggttatttc cgatggcggc cagctgacgc agtaacggcg
      241 gtgccagtgt cggcagcctc ccggaacggg caaccggctc ccccaggcag acccgccgca
      301 tccataccgc cagttgttta ccctcacagc gttcaagtaa ccgggcatgt tcatcatcag
      361 taacccgtat cgtgagcatc ctctcgcgtt tcatcggtat cattacccca tgaacagaaa
      421 tcccccttac acggaggcat cagtgactaa acaggaaaaa acagccctta acatggcgcg
      481 ctttatcaga agccagacat taacgctgct ggagaagctc aacgaactgg acgcggatga
      541 acaggcagac atctgtgaat cgcttcacga ccacgccgat gagctttacc gcagctgcct
      601 cgcacgcttc ggggatgacg gtgaaaacct ctgacacatg cagctcccgg agacggtcac
      661 agcttgtctg tgagcggatg ccgggagctg acaagcccgt cagggcgcgt cagcaggttt
      721 tagcgggtgt cggggcgcag ccctgaccca gtcacgtagc gatagcggag tgtatactgg
      781 cttaactatg cggcatcaga gcagattgta ctgagagtgc accatatgcg gtgtgaaata
      841 ccgcacagat gcgtaaggag aaaataccgc atcaggcgct cttccgcttc ctcgctcact
      901 gactcgctgc gctcggtcgt tcggctgcgg cgagcggtat cagctcactc aaagacggat
      961 atacggttat ccacagaatc aggggataac gccggaaaaa acatgtgagc aaaaaagagg
     1021 ccccgaaaaa aggccgcgcc ggtggcgttt ttccataggc tccgcccccc tgacgagcat
     1081 cacaaaaatc gacgctcaag tcagaggtgg cgaaacccga caggactata aagataccag
     1141 gcgtttcccc ctggaagctc cctcgtgcgc tctcctgttc cgaccctgcc gcttaccgga
     1201 tacctctccg cctttctccc ttcgggaagc gtggcgcttt ctcatagctc acgctgttgg
     1261 tatctcagtt cggtgtaggt cgttcgctcc aagctgggct gtgtgcacga accccccgtt
     1321 cagcccgacc gctgcgcctt atccggtaac tatcgtcttg agtccaaccc ggtaagacac
     1381 gccttaacgc cactggcagc agccattggt aactggacaa ggtggattga gatattaaga
     1441 gttcttgaag tggtggccta actgaggcta cactagaagg acagtatttg gtatctgcgc
     1501 tccaccaagc cagttacctt cgggaaaaag agttggtagc tcttgattcc ggcaaacgaa
     1561 ccaccgttgg tagcggtggt ttttttgttt acaggcagca gattacgcgc agaaaaaaag
     1621 gatctcaaga ggatcctttg atcttttttc aaaacccctc tcaattcaac aaatggtggg
     1681 ggaaacgatc aacaaaatgg cggagagggt aggattcgaa cctacgatac gcttgtcgca
     1741 tatggcctca agagagccct gacttagacc actcgcccac ctctccacaa aaaacaatac
     1801 atatttaaca aataacatcc aagacactat aagagaaaaa atagagacgc atcacataaa
     1861 taaaggagac atcaatgatc aaacactaac atgatctcta tcattgatat gtataagtca
     1921 taattagcaa aatattttct ttgtgacaaa ggaagcataa ctatgccaga cctagaaata
     1981 atgcccttac aaagtccaga tttttataaa aaaaacaaaa gagcaatata cgagggctat
     2041 aaatgtaatt gtacaaaaga ctggaaaaaa gaagacagat ttgttgtata caaagcagat
     2101 tgcacaggaa tcgatgagat aataaacaca gaaatatcag atgacaacat agatactgta
     2161 ataaaactag ccgaaaaata cacatcagac aagattatta tatctggtgg acatactgtt
     2221 gtgaatttga atgaccgttt ttcagttagt aatgaggttg aaaaatcggc taaattttgc
     2281 attgactaca taataaaatc aacacatgag ctaaatataa aacctgattt cctcatggaa
     2341 ataaatgatt tctacatgga aaaatcaaat ggcgaagata tcgatggtgg taatatttat
     2401 agaaaactag ccacatcacc ctatataata ccagaagtaa taaataacta tattatagag
     2461 aaacagaatc agcataatat aaaaataaat tgtttctatg ttagtgaaaa aaacatggca
     2521 gatcgtttta aacgacacat taaaagaaaa gaaaaagaaa agccattttt taaagaaaac
     2581 aactctgttt ttatgaatgt cgatggttca tcatttgaag tgataaaaaa taacaaaccg
     2641 acttgtgcag caggtaacgc agctacattt cgctcgattc gatataaaat ttcatcgaac
     2701 aagacatttg acaattacac atcacacata ggtgtattcc cattgtgctc aatggctaat
     2761 gtaattaatg gctataaagc agcagcatct ttttatagta attttaatct tccatgttta
     2821 cttattttct ttggaacatc atgcttcaaa tgaaaggttc aaaaatgaag ataaatagca
     2881 tccaatggcc agtaacattc tttgcaacat catttggggc agggattttt ttcctacccc
     2941 agactgtagg ccccaaagtc ataggaactc acggaacaat aacaatactg attttatcat
     3001 ctttggtatc tttattaggg caatttacat tttatagatt cattttaatt acagacaaaa
     3061 aagaatacgt tagttctgcc atattattta tcggaaaaaa agccgcaaat gctatcagta
     3121 ttgcattcct attatcaatg ctgttaatag caattataaa cataacaaca atgataaata
     3181 ttatttgctt tagcctaagt ctaaatggtt cagagcgaat atttgtgtca ctgattattt
     3241 ctgcaaccct tggttcttct tttatctttt ttaattcaaa gatagagcat ctcgcatcag
     3301 gaatagcatt tccatctttg cttattgtac tgttcttatc tatatatttc tattcacatc
     3361 cagcacatcc acattctaca gaaatacaaa atattagtac aagtaattta cttactctat
     3421 ttccagttgt tttatttagt tttaattttt caccatgtat acaacgcttt gctcaaaaca
     3481 aaaaagatac agccggtgat ttacgttttt tcatgtttgg gatactatta attttaatat
     3541 ttatctcatt catcgtgttc tcattaagca atatattctc accttcagac ataaaaaaca
     3601 tgcgcgagat taacagcgat gcattatcat atagcgccaa cgtaacaaaa aatagtttcg
     3661 ttgcttacat ttccatatta accatgattt taattaccag cggtgcatat acaggtacac
     3721 taacaggcgt tgttgataca atagtatccc ttggatttaa aaacaaaaca ttaatcgttt
     3781 ttgtcgtatc tgttatcaca tttatagcag gcgaagccaa tttcgaaatt ataaaagtta
     3841 ttgctgcatt atcaacccca attatagcaa taacagtatt cattatccca tcagcattct
     3901 ttttaaaaac aaattgtaac agtattttta gaaaaataat gatgacgttg aacctgctca
     3961 taggtattgg aatatgcttc ctagccatca tattatgatt attcctcacc caaatattct
     4021 gacgagttta tcttaatcgt cacaaccaaa tgtggaaaat ggggggatca tccaaaccat
     4081 ttaacataac gacaatattg tacgcaccgc taaaacgcgt tcagcgcgat cacggcagca
     4141 gacaggtaaa aatggcaaca aaccacccga aaaactgccg cgatcgcgcc tgataaattt
     4201 taaccgtatg aatacctatg caaccagatg gtacaggcca cattcccccc acttaatcca
     4261 ctgaagctgc catttttcat ggtttcacca tcccagcgaa gggccatcca gcgtgcgttc
     4321 ctgtatttcc ggctgacgct cccgttccag ggataacaca tgttcgcgct cctgtatcaa
     4381 ccgttcctct cttatctcca gttctcgctg tataactggc tcaagcgttc tgtctgctcg
     4441 ctcaagtgct gcacctgctg actcaactgc atgacccgct cgttcagcat cgcgttgtcc
     4501 cgttgtgtaa gcgaaaacat cttctgcaat tccacgaagg cgctctccca ttcgctcagc
     4561 cgctgcatat agtcctgttg cagctgctct aaggcgttca gcaaatgaat ttccagctct
     4621 gtcactctgt gtcactcctt cagatgtacc cactctttcc cctgaaaggg aatcacctcc
     4681 gctgatttcc cgtacggaag gacaaggaat ttcctgttcc cgtcctgcac aaactccacg
     4741 ccccatgtct tcgcgttcag tttctgcaat gtctcttcct gcttcctgat ttcttccagg
     4801 ttcgtctgta tccgtccgcc aagataccag agcgtcccgc cactcgcggt aaacaggaga
     4861 aagactatcc ccagtaacat catgcccgta ttccctgcca gctttaacac gtccttcctg
     4921 tgctgcatca tcgcctcttt caccccttcc cggtgttttt ccagcgattt ctctgtcgag
     4981 gctgtgaaca gggctatagc gtctctgatt ttcgtctcgt ttgaggtcac agcctcgctg
     5041 acagactcgc cgagcttcct gaactcgtcg ttcagcattt tctctgtaga ttcggctctc
     5101 tctttcagct ttttctcgaa ctccgcgccc gtctgtaaaa gattgctcat aaaatgctcc
     5161 tttcagcctg atattcctcc cgccgttcgg gtctgcaatg ctgatactgc ttcgcgtcac
     5221 cctgaccact tcaagccccg cctctgtgag cgcctgaatc acatcctgac ggccttttat
     5281 ctctccggca tggtaaagtg cgtctatacc gcgtgtaacg ctctcagcaa gtgcctgttt
     5341 cgtttccggc aggttatcag gaagggtcag cgtccggcgg ttctccgggg cgttggggtc
     5401 atgcagtccg taatggtgat tcaccagcgt ctgccaggca tcaattctcg gcctgtctgc
     5461 gcggtcgtag tacggctgga ggcgttttcc ggtctgtagc tccatgttcg gaatgacaaa
     5521 attcagctca agccgtccct tgtcctggtg ctccacccac aggatgctgt actgattttt
     5581 ttcgagaccg ggcatcagta cacgctcaaa gctcgccatc actttttcac gtcctcccgg
     5641 cggcagttcc ttctccgcga acgacagaac accggacgtg tatttcttcg caaatggcgt
     5701 ggcatcgatg agttcccgga cttcttccgg attaccctga agcaccgttg cgccttcgcg
     5761 gttacgctcc ct
//
