Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101551
Name   oriT_pL1M1-01a in_silico
Organism   Escherichia coli strain L1M1-01
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAPZDR010000002 (112798..112883 [+], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      61..68, 73..80  (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: 86 nt

>oriT_pL1M1-01a
AATTACATGATTTAAAACACAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1374 GenBank   WP_275038887
Name   traI_O8D02_RS24050_pL1M1-01a 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: 192034.92 Da        Isoelectric Point: 5.8722

>WP_275038887.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGRPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQDETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPVRFIAPGRKYPQPYVALPAFDRNGKSAG
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)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)


  Protein structure



No available structure.




Auxiliary protein

ID   492 GenBank   WP_001352842
Name   WP_001352842_pL1M1-01a insolico UniProt ID   A0A6Y3H4U0
Length   71 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 71 a.a.        Molecular weight: 8117.19 Da        Isoelectric Point: 9.9216

>WP_001352842.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacteriaceae]
MSRGRTRAAPGNKVLLILDETTNQKLLAARDRSGRTKTNEVFIRLKDHLNRFPDFYNASLVKEEAESIDD
I

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-60)


  Protein structure


Source ID Structure
AlphaFold DB A0A6Y3H4U0

ID   493 GenBank   WP_001063020
Name   WP_001063020_pL1M1-01a 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


T4CP

ID   1007 GenBank   WP_000009324
Name   traD_O8D02_RS24065_pL1M1-01a 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.



ID   1008 GenBank   WP_001064245
Name   traC_O8D02_RS24155_pL1M1-01a 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 87230..113451

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
O8D02_RS24055 (O8D02_24015) 86596..86823 + 228 WP_000450520 toxin-antitoxin system antitoxin VapB -
O8D02_RS24060 (O8D02_24020) 86823..87221 + 399 WP_000911313 type II toxin-antitoxin system VapC family toxin -
O8D02_RS24065 (O8D02_24025) 87230..89383 - 2154 WP_000009324 type IV conjugative transfer system coupling protein TraD virb4
O8D02_RS24070 (O8D02_24030) 89636..90367 - 732 WP_023565183 conjugal transfer complement resistance protein TraT -
O8D02_RS24075 (O8D02_24035) 90399..90896 - 498 WP_000605857 entry exclusion protein -
O8D02_RS24080 (O8D02_24040) 90912..93734 - 2823 WP_001007018 conjugal transfer mating-pair stabilization protein TraG traG
O8D02_RS24085 (O8D02_24045) 93731..95104 - 1374 WP_001517790 conjugal transfer pilus assembly protein TraH traH
O8D02_RS24090 (O8D02_24050) 95104..95484 - 381 WP_001389370 F-type conjugal transfer protein TrbF -
O8D02_RS24095 (O8D02_24055) 95471..95812 - 342 WP_001443031 P-type conjugative transfer protein TrbJ -
O8D02_RS24100 (O8D02_24060) 95742..96287 - 546 WP_000059851 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
O8D02_RS24105 (O8D02_24065) 96274..96558 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
O8D02_RS24110 (O8D02_24070) 96639..96953 + 315 WP_001324103 hypothetical protein -
O8D02_RS24115 (O8D02_24075) 96955..97302 - 348 WP_001287910 conjugal transfer protein TrbA -
O8D02_RS24120 (O8D02_24080) 97318..98061 - 744 WP_001030377 type-F conjugative transfer system pilin assembly protein TraF traF
O8D02_RS24125 (O8D02_24085) 98054..98311 - 258 WP_000864318 conjugal transfer protein TrbE -
O8D02_RS24130 (O8D02_24090) 98338..100146 - 1809 WP_000821838 type-F conjugative transfer system mating-pair stabilization protein TraN traN
O8D02_RS24135 (O8D02_24095) 100143..100781 - 639 WP_000777695 type-F conjugative transfer system pilin assembly protein TrbC trbC
O8D02_RS24140 (O8D02_24100) 100790..101782 - 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
O8D02_RS24145 (O8D02_24105) 101779..102411 - 633 WP_001203717 type-F conjugative transfer system protein TraW traW
O8D02_RS24150 (O8D02_24110) 102408..102794 - 387 WP_000099691 type-F conjugative transfer system protein TrbI -
O8D02_RS24155 (O8D02_24115) 102791..105418 - 2628 WP_001064245 type IV secretion system protein TraC virb4
O8D02_RS24160 (O8D02_24120) 105578..105799 - 222 WP_001278689 conjugal transfer protein TraR -
O8D02_RS24165 (O8D02_24125) 105934..106449 - 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
O8D02_RS24170 (O8D02_24130) 106446..106697 - 252 WP_001038342 conjugal transfer protein TrbG -
O8D02_RS24175 (O8D02_24135) 106709..106906 - 198 WP_024179215 conjugal transfer protein TrbD -
O8D02_RS24180 (O8D02_24140) 106893..107483 - 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
O8D02_RS24185 (O8D02_24145) 107473..108900 - 1428 WP_000146676 F-type conjugal transfer pilus assembly protein TraB traB
O8D02_RS24190 (O8D02_24150) 108900..109628 - 729 WP_001230813 type-F conjugative transfer system secretin TraK traK
O8D02_RS24195 (O8D02_24155) 109615..110181 - 567 WP_000399790 type IV conjugative transfer system protein TraE traE
O8D02_RS24200 (O8D02_24160) 110203..110514 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
O8D02_RS24205 (O8D02_24165) 110529..110894 - 366 WP_000340282 type IV conjugative transfer system pilin TraA -
O8D02_RS24210 (O8D02_24170) 110937..111152 - 216 WP_001352842 conjugal transfer relaxosome protein TraY -
O8D02_RS24215 (O8D02_24175) 111288..111935 - 648 WP_000332520 conjugal transfer transcriptional regulator TraJ -
O8D02_RS24220 (O8D02_24180) 112127..112510 - 384 WP_001063020 conjugal transfer relaxosome DNA-binding protein TraM -
O8D02_RS24225 (O8D02_24185) 112849..113451 + 603 WP_077248356 transglycosylase SLT domain-containing protein virB1
O8D02_RS24230 (O8D02_24190) 113746..114567 - 822 WP_001234475 DUF932 domain-containing protein -
O8D02_RS24235 (O8D02_24195) 114686..114973 - 288 WP_000107546 hypothetical protein -
O8D02_RS24240 (O8D02_24200) 114998..115204 - 207 WP_000547965 hypothetical protein -
O8D02_RS24245 (O8D02_24205) 115274..115570 + 297 Protein_115 hypothetical protein -
O8D02_RS24250 (O8D02_24210) 115871..115996 - 126 WP_096937776 type I toxin-antitoxin system Hok family toxin -
O8D02_RS24255 (O8D02_24215) 115938..116087 - 150 Protein_117 DUF5431 family protein -
O8D02_RS24260 (O8D02_24220) 116261..117023 - 763 Protein_118 plasmid SOS inhibition protein A -
O8D02_RS24265 (O8D02_24225) 117020..117454 - 435 WP_000845928 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   1995 GenBank   NZ_JAPZDR010000002
Plasmid name   pL1M1-01a Incompatibility group   IncFIB
Plasmid size   166362 bp Coordinate of oriT [Strand]   112798..112883 [+]
Host baterium   Escherichia coli strain L1M1-01

Cargo genes

Drug resistance gene   tet(A), blaTEM-1B, sitABCD
Virulence gene   iroB, iroC, iroD, iroE, iroN, vat, iutA, iucC, iucB, iucA
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -