Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102923
Name   oriT_p1540-4 in_silico
Organism   Escherichia coli strain CRE1540
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP019055 (153353..153704 [+], 352 nt)
oriT length   352 nt
IRs (inverted repeats)      255..262, 271..278  (ACCGCTAG..CTAGCGGT)
 192..198, 206..212  (TATAAAA..TTTTATA)
 40..47, 50..57  (GCAAAAAC..GTTTTTGC)
 4..11, 16..23  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 352 nt

>oriT_p1540-4
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGAGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGCAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2194 GenBank   WP_001611029
Name   traI_BVL39_RS28675_p1540-4 insolico UniProt ID   A0A075MCD1
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191983.83 Da        Isoelectric Point: 5.9594

>WP_001611029.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGLPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTSFIDLGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRECGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMTGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPRTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

AAA domain (AAA_30)

(969-1156)

TrwC relaxase (TrwC)

(10-283)

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

(575-625)

DNA helicase TraI (TraI_C)

(1434-1557)


  Protein structure



No available structure.




Auxiliary protein

ID   897 GenBank   WP_001151524
Name   WP_001151524_p1540-4 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   898 GenBank   WP_001369361
Name   WP_001369361_p1540-4 insolico UniProt ID   B7LI64
Length   133 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 133 a.a.        Molecular weight: 15409.70 Da        Isoelectric Point: 9.9240

>WP_001369361.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MLLKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVK
YLTMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(18-61)

TraY domain (TraY)

(72-119)


  Protein structure


Source ID Structure
AlphaFold DB B7LI64


T4CP

ID   1870 GenBank   WP_021526192
Name   traD_BVL39_RS28660_p1540-4 insolico UniProt ID   _
Length   735 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 735 a.a.        Molecular weight: 83648.41 Da        Isoelectric Point: 5.1126

>WP_021526192.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIILYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEITGGRQLTDNPKEVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPVSPAINDKKSDAGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAVYEAWQ
REQNPDIQQKMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

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

(173-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 152782..165375

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BVL39_RS28555 (BVL39_29035) 147932..149473 - 1542 WP_001298859 IS21-like element ISEc12 family transposase -
BVL39_RS28560 (BVL39_29040) 149666..150236 + 571 Protein_158 plasmid SOS inhibition protein A -
BVL39_RS29815 150415..150564 + 150 Protein_159 plasmid maintenance protein Mok -
BVL39_RS28565 (BVL39_29050) 150506..150631 + 126 WP_096937776 type I toxin-antitoxin system Hok family toxin -
BVL39_RS29820 150932..151205 - 274 Protein_161 hypothetical protein -
BVL39_RS28575 (BVL39_29060) 151257..151553 + 297 WP_001272245 hypothetical protein -
BVL39_RS28580 (BVL39_29065) 151664..152485 + 822 WP_001234487 DUF932 domain-containing protein -
BVL39_RS28585 (BVL39_29070) 152782..153372 - 591 WP_279947734 transglycosylase SLT domain-containing protein -
BVL39_RS28590 (BVL39_29075) 153705..154088 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
BVL39_RS28595 (BVL39_29080) 154275..154964 + 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
BVL39_RS28600 (BVL39_29085) 155063..155458 + 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
BVL39_RS28605 (BVL39_29090) 155491..155856 + 366 WP_000994779 type IV conjugative transfer system pilin TraA -
BVL39_RS28610 (BVL39_29095) 155871..156182 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
BVL39_RS28615 (BVL39_29100) 156204..156770 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
BVL39_RS28620 (BVL39_29105) 156757..157485 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
BVL39_RS28625 (BVL39_29110) 157485..158912 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
BVL39_RS28630 (BVL39_29115) 158902..159492 + 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
BVL39_RS28635 (BVL39_29120) 159479..159676 + 198 WP_001324648 conjugal transfer protein TrbD -
BVL39_RS28640 (BVL39_29125) 159688..159939 + 252 WP_001038342 conjugal transfer protein TrbG -
BVL39_RS29375 159936..160370 + 435 Protein_176 type IV conjugative transfer system lipoprotein TraV -
BVL39_RS28645 (BVL39_29130) 160371..161639 + 1269 Protein_177 conjugal transfer protein TraG -
BVL39_RS28650 (BVL39_29135) 161655..162152 + 498 WP_000605857 entry exclusion protein -
BVL39_RS28655 (BVL39_29140) 162184..162915 + 732 WP_023565183 conjugal transfer complement resistance protein TraT -
BVL39_RS28660 (BVL39_29145) 163168..165375 + 2208 WP_021526192 type IV conjugative transfer system coupling protein TraD virb4
BVL39_RS28665 (BVL39_29150) 165384..165782 - 399 WP_000911313 type II toxin-antitoxin system VapC family toxin -
BVL39_RS28670 (BVL39_29155) 165782..166009 - 228 WP_000450520 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   3366 GenBank   NZ_CP019055
Plasmid name   p1540-4 Incompatibility group   IncFIB
Plasmid size   184166 bp Coordinate of oriT [Strand]   153353..153704 [+]
Host baterium   Escherichia coli strain CRE1540

Cargo genes

Drug resistance gene   sitABCD
Virulence gene   vat, iroN, iroE, iroD, iroC, iroB, iucA, iucB, iucC, iutA
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -