Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103035
Name   oriT_pMR0516mcr in_silico
Organism   Escherichia coli strain MRSN388634
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KX276657 (189087..189344 [+], 258 nt)
oriT length   258 nt
IRs (inverted repeats)      234..241, 250..257  (ACCGCTAG..CTAGCGGT)
 172..177, 185..190  (ATAAAA..TTTTAT)
 118..126, 136..144  (GCGGTGTTG..CAACACCGC)
 19..26, 29..36  (GCAAAAAC..GTTTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 258 nt

>oriT_pMR0516mcr
AAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGACAAATTAGTTCTTCTTGCTCTCTTTGTGATATTTAAAAAAGCGGTGTCGGCGCGGTGTTGTAGCTGCGCCAACACCGCTTTTTAGGGGTGGTACTGACTATTTTCATAAAAAACATCATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2268 GenBank   WP_000986962
Name   traI_HTI35_RS01190_pMR0516mcr insolico UniProt ID   A0A0K2B7B9
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192018.92 Da        Isoelectric Point: 5.8722

>WP_000986962.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGRPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQDETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQIRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPRTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(575-626)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(633-712)


  Protein structure



No available structure.




Auxiliary protein

ID   929 GenBank   WP_001151524
Name   WP_001151524_pMR0516mcr insolico UniProt ID   A0A5W2DT22
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14517.48 Da        Isoelectric Point: 5.0516

>WP_001151524.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A5W2DT22

ID   930 GenBank   WP_000239828
Name   WP_000239828_pMR0516mcr insolico UniProt ID   B1P7U1
Length   119 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 119 a.a.        Molecular weight: 13861.82 Da        Isoelectric Point: 8.0399

>WP_000239828.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVKYLTMRLDDETNQLL
IAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(3-47)

TraY domain (TraY)

(58-105)


  Protein structure


Source ID Structure
AlphaFold DB B1P7U1


T4CP

ID   1965 GenBank   WP_001064245
Name   traC_HTI35_RS01085_pMR0516mcr insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99159.81 Da        Isoelectric Point: 5.8486

>WP_001064245.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNVADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

  Protein structure



No available structure.



ID   1966 GenBank   WP_000009324
Name   traD_HTI35_RS01175_pMR0516mcr insolico UniProt ID   _
Length   717 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 717 a.a.        Molecular weight: 81528.14 Da        Isoelectric Point: 5.1126

>WP_000009324.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIILYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEITGGRQLTDNPKEVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDAGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAVYEAWQREQNPDIQQKMQRREEVN
INVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 188495..214868

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTI35_RS00970 183948..184181 + 234 WP_000005987 DUF905 family protein -
HTI35_RS00975 184209..184406 + 198 Protein_196 hypothetical protein -
HTI35_RS00980 184461..184895 + 435 WP_064770609 conjugation system SOS inhibitor PsiB -
HTI35_RS00985 184892..185654 + 763 Protein_198 plasmid SOS inhibition protein A -
HTI35_RS01255 185833..185982 + 150 Protein_199 plasmid maintenance protein Mok -
HTI35_RS00990 185924..186049 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HTI35_RS01260 186269..186499 + 231 WP_001426396 hypothetical protein -
HTI35_RS01265 186497..186670 - 174 Protein_202 hypothetical protein -
HTI35_RS01000 186740..186946 + 207 WP_000547971 hypothetical protein -
HTI35_RS01005 186971..187258 + 288 WP_000107535 hypothetical protein -
HTI35_RS01010 187377..188198 + 822 WP_001234469 DUF932 domain-containing protein -
HTI35_RS01015 188495..189085 - 591 WP_186235717 transglycosylase SLT domain-containing protein -
HTI35_RS01020 189418..189801 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HTI35_RS01025 189988..190677 + 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
HTI35_RS01030 190776..191171 + 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HTI35_RS01035 191204..191569 + 366 WP_000994779 type IV conjugative transfer system pilin TraA -
HTI35_RS01040 191584..191895 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HTI35_RS01045 191917..192483 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HTI35_RS01050 192470..193198 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HTI35_RS01055 193198..194625 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
HTI35_RS01060 194615..195205 + 591 WP_001376242 conjugal transfer pilus-stabilizing protein TraP -
HTI35_RS01065 195192..195389 + 198 WP_001324648 conjugal transfer protein TrbD -
HTI35_RS01070 195401..195652 + 252 WP_001038342 conjugal transfer protein TrbG -
HTI35_RS01075 195649..196164 + 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
HTI35_RS01080 196299..196520 + 222 WP_001278689 conjugal transfer protein TraR -
HTI35_RS01085 196680..199307 + 2628 WP_001064245 type IV secretion system protein TraC virb4
HTI35_RS01090 199304..199690 + 387 WP_000099686 type-F conjugative transfer system protein TrbI -
HTI35_RS01095 199687..200319 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HTI35_RS01100 200316..201308 + 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
HTI35_RS01105 201317..201955 + 639 WP_000777700 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTI35_RS01110 201952..203760 + 1809 WP_000821841 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTI35_RS01115 203787..204044 + 258 WP_000864318 conjugal transfer protein TrbE -
HTI35_RS01120 204037..204780 + 744 WP_001030393 type-F conjugative transfer system pilin assembly protein TraF traF
HTI35_RS01125 204796..205143 + 348 WP_001287910 conjugal transfer protein TrbA -
HTI35_RS01130 205145..205459 - 315 WP_001324103 hypothetical protein -
HTI35_RS01135 205540..205824 + 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
HTI35_RS01140 205811..206356 + 546 WP_000059851 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTI35_RS01145 206286..206627 + 342 WP_001443031 P-type conjugative transfer protein TrbJ -
HTI35_RS01150 206614..206994 + 381 WP_001389370 F-type conjugal transfer protein TrbF -
HTI35_RS01155 206994..208367 + 1374 WP_001517790 conjugal transfer pilus assembly protein TraH traH
HTI35_RS01160 208364..211186 + 2823 WP_001007018 conjugal transfer mating-pair stabilization protein TraG traG
HTI35_RS01165 211202..211699 + 498 WP_000605857 entry exclusion protein -
HTI35_RS01170 211731..212462 + 732 WP_023565183 conjugal transfer complement resistance protein TraT -
HTI35_RS01175 212715..214868 + 2154 WP_000009324 type IV conjugative transfer system coupling protein TraD virb4
HTI35_RS01180 214877..215275 - 399 WP_000911313 type II toxin-antitoxin system VapC family toxin -
HTI35_RS01185 215275..215502 - 228 WP_000450520 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   3478 GenBank   NZ_KX276657
Plasmid name   pMR0516mcr Incompatibility group   IncN
Plasmid size   225069 bp Coordinate of oriT [Strand]   189087..189344 [+]
Host baterium   Escherichia coli strain MRSN388634

Cargo genes

Drug resistance gene   mcr-1.1, blaTEM-1B, aph(6)-Id, aph(3'')-Ib, sul2, dfrA14, tet(A), blaCTX-M-55, sitABCD
Virulence gene   iucA, iucB, iucC, iutA
Metal resistance gene   terE, terD, terC, terB, terA, terZ, terW
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -