Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120194
Name   oriT_6S-65-1|p1 in_silico
Organism   Escherichia albertii strain 6S-65-1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP141902 (67772..67862 [-], 91 nt)
oriT length   91 nt
IRs (inverted repeats)      66..73, 78..85  (TTGGTGGT..ACCACCAA)
 27..34, 37..44  (GCAAAAAC..GTTTTTGC)
 8..13, 21..26  (TGATTT..AAATCA)
Location of nic site      53..54
Conserved sequence flanking the
  nic site    		  GGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 91 nt

>oriT_6S-65-1|p1
AATTACATGATTTAAAACACAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12705 GenBank   WP_324649223
Name   traI_VK940_RS24750_6S-65-1|p1 insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192342.96 Da        Isoelectric Point: 6.0786

>WP_324649223.1 conjugative transfer relaxase/helicase TraI [Escherichia albertii]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEGASLKSRDVAALDTRKSKQHVDPEIRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQDGMTFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQILITDSGQRTGTGSALMSMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQSIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARNPSFTVVSEQI
KARAGETLLETAISHQKSALHTPAQQAIHLALPVVESKNLAFSQVDLLTEAKSFAAEGTSFVDLGREIDA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDHTGRTPETREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQKTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGRTEQAVREIAWQERERAVTSEREAALPESVLREPQREREAVREVVRENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(575-626)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(969-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   7158 GenBank   WP_001063020
Name   WP_001063020_6S-65-1|p1 insolico UniProt ID   A0A6Y3HD60
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14442.54 Da        Isoelectric Point: 5.3125

>WP_001063020.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Bacteria]
MAKIQVYVNDHVSEKINAIAVQRRAEGAKEKDVSYSSIASMLLELGLRVYEAQMERKESAFNQAEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGKPKFEYANMVEDIREKVSVEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A6Y3HD60

ID   7159 GenBank   WP_024226173
Name   WP_024226173_6S-65-1|p1 insolico UniProt ID   _
Length   71 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 71 a.a.        Molecular weight: 8131.22 Da        Isoelectric Point: 9.9216

>WP_024226173.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Escherichia]
MSRGRTRAAPGNKVLLILDETTNQKLLAARDRSGRTKTNEVFIRLKDHLNRFPDFYNASLIKEEAESIDD
I

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-60)


  Protein structure



No available structure.




T4CP

ID   14911 GenBank   WP_024226180
Name   traC_VK940_RS24655_6S-65-1|p1 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: 99211.87 Da        Isoelectric Point: 5.7326

>WP_024226180.1 MULTISPECIES: type IV secretion system protein TraC [Escherichia]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQMVGDRIEYGLREFSWSGEQAERFNAITQAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVTDNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 67204..89122

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
VK940_RS24545 (VK940_24545) 63200..63634 + 435 WP_000845950 conjugation system SOS inhibitor PsiB -
VK940_RS24550 (VK940_24550) 63631..64393 + 763 Protein_69 plasmid SOS inhibition protein A -
VK940_RS24555 (VK940_24555) 64567..64716 + 150 Protein_70 DUF5431 family protein -
VK940_RS24560 (VK940_24560) 64658..64783 + 126 WP_231822392 type I toxin-antitoxin system Hok family toxin -
VK940_RS24565 (VK940_24565) 65084..65380 - 297 Protein_72 hypothetical protein -
VK940_RS24570 (VK940_24570) 65450..65656 + 207 WP_000547965 hypothetical protein -
VK940_RS24575 (VK940_24575) 65681..65968 + 288 WP_000107542 hypothetical protein -
VK940_RS24580 (VK940_24580) 66087..66908 + 822 WP_324649237 DUF932 domain-containing protein -
VK940_RS24585 (VK940_24585) 67204..67794 - 591 WP_001375132 transglycosylase SLT domain-containing protein virB1
VK940_RS24590 (VK940_24590) 68150..68533 + 384 WP_001063020 conjugal transfer relaxosome DNA-binding protein TraM -
VK940_RS24595 (VK940_24595) 68724..69370 + 647 Protein_78 conjugal transfer transcriptional regulator TraJ -
VK940_RS24600 (VK940_24600) 69506..69721 + 216 WP_024226173 conjugal transfer relaxosome protein TraY -
VK940_RS24605 (VK940_24605) 69764..70129 + 366 WP_000340282 type IV conjugative transfer system pilin TraA -
VK940_RS24610 (VK940_24610) 70144..70455 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
VK940_RS24615 (VK940_24615) 70477..71043 + 567 WP_096306498 type IV conjugative transfer system protein TraE traE
VK940_RS24620 (VK940_24620) 71030..71758 + 729 WP_024226175 type-F conjugative transfer system secretin TraK traK
VK940_RS24625 (VK940_24625) 71758..73185 + 1428 WP_324649238 F-type conjugal transfer pilus assembly protein TraB traB
VK940_RS24630 (VK940_24630) 73175..73765 + 591 WP_324649239 conjugal transfer pilus-stabilizing protein TraP -
VK940_RS24635 (VK940_24635) 73752..73949 + 198 WP_024226177 conjugal transfer protein TrbD -
VK940_RS24640 (VK940_24640) 73961..74212 + 252 WP_001038342 conjugal transfer protein TrbG -
VK940_RS24645 (VK940_24645) 74209..74724 + 516 WP_024226179 type IV conjugative transfer system lipoprotein TraV traV
VK940_RS24650 (VK940_24650) 74859..75080 + 222 WP_001278692 conjugal transfer protein TraR -
VK940_RS24655 (VK940_24655) 75240..77867 + 2628 WP_024226180 type IV secretion system protein TraC virb4
VK940_RS24660 (VK940_24660) 77864..78250 + 387 WP_000099690 type-F conjugative transfer system protein TrbI -
VK940_RS24665 (VK940_24665) 78247..78879 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
VK940_RS24670 (VK940_24670) 78876..79868 + 993 WP_024226181 conjugal transfer pilus assembly protein TraU traU
VK940_RS24675 (VK940_24675) 79877..80515 + 639 WP_324649244 type-F conjugative transfer system pilin assembly protein TrbC trbC
VK940_RS24680 (VK940_24680) 80512..82320 + 1809 WP_097412160 type-F conjugative transfer system mating-pair stabilization protein TraN traN
VK940_RS24685 (VK940_24685) 82347..82559 + 213 WP_029785264 conjugal transfer protein TrbE -
VK940_RS24690 (VK940_24690) 82597..83340 + 744 WP_024226183 type-F conjugative transfer system pilin assembly protein TraF traF
VK940_RS24695 (VK940_24695) 83356..83703 + 348 WP_024226184 conjugal transfer protein TrbA -
VK940_RS24700 (VK940_24700) 83822..84106 + 285 WP_096245929 type-F conjugative transfer system pilin chaperone TraQ -
VK940_RS24705 (VK940_24705) 84093..84638 + 546 WP_016236310 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
VK940_RS24710 (VK940_24710) 84568..84930 + 363 WP_071587080 P-type conjugative transfer protein TrbJ -
VK940_RS24715 (VK940_24715) 84930..86303 + 1374 WP_000944322 conjugal transfer pilus assembly protein TraH traH
VK940_RS24720 (VK940_24720) 86300..89122 + 2823 WP_262930124 conjugal transfer mating-pair stabilization protein TraG traG
VK940_RS24725 (VK940_24725) 89137..89622 + 486 WP_324649240 surface exclusion protein -
VK940_RS24730 (VK940_24730) 89685..90847 + 1163 WP_085947598 IS3-like element IS3 family transposase -
VK940_RS24735 (VK940_24735) 90933..91664 + 732 WP_000850424 conjugal transfer complement resistance protein TraT -
VK940_RS24740 (VK940_24740) 92064..93038 - 975 WP_012478345 IS30-like element ISApl1 family transposase -

Host bacterium

ID   20623 GenBank   NZ_CP141902
Plasmid name   6S-65-1|p1 Incompatibility group   IncFIB
Plasmid size   180516 bp Coordinate of oriT [Strand]   67772..67862 [-]
Host baterium   Escherichia albertii strain 6S-65-1

Cargo genes

Drug resistance gene   tet(A), sitABCD
Virulence gene   iucA, iucB, iucC, iutA
Metal resistance gene   merP, merT, merR, pcoD, pcoC, pcoB, pcoA, silP, silA, silB, silF, silC, silR, silS, silE, yfeC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -