Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103279
Name   oriT_p1106-IncFIB in_silico
Organism   Escherichia coli strain 1106
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MG825372 (140433..140556 [-], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      101..106, 119..124  (TTTAAT..ATTAAA)
 91..99, 113..121  (AATAATGTA..TACATTATT)
 90..95, 107..112  (AAATAA..TTATTT)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
 3..10, 15..22  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_p1106-IncFIB
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2448 GenBank   WP_172692626
Name   traI_HTR02_RS00550_p1106-IncFIB 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: 191861.67 Da        Isoelectric Point: 6.0273

>WP_172692626.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDSPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGRPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIGLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(575-626)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(969-1156)

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   1046 GenBank   WP_001254386
Name   WP_001254386_p1106-IncFIB insolico UniProt ID   A0A3Z6KJB5
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9005.11 Da        Isoelectric Point: 10.1422

>WP_001254386.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A3Z6KJB5

ID   1047 GenBank   WP_000124981
Name   WP_000124981_p1106-IncFIB insolico UniProt ID   A0A630FTW9
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14542.59 Da        Isoelectric Point: 5.0278

>WP_000124981.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A630FTW9


T4CP

ID   2222 GenBank   WP_000009379
Name   traD_HTR02_RS00565_p1106-IncFIB 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: 81527.16 Da        Isoelectric Point: 5.1761

>WP_000009379.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKNMTQGGQIASMRIRMFSQIANIILYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEITGGRQLTDNPKEVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGREMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDAGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAVYEAWQREQNPDIQQKMQRREEVN
INVHRERGENVEPGDDF

  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   2223 GenBank   WP_072652432
Name   traC_HTR02_RS00650_p1106-IncFIB 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: 99282.99 Da        Isoelectric Point: 6.0801

>WP_072652432.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKNKARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(467-771)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 114987..141128

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTR02_RS00555 (NHKPALLO_00117) 114353..114580 + 228 WP_000450520 toxin-antitoxin system antitoxin VapB -
HTR02_RS00560 (NHKPALLO_00118) 114580..114978 + 399 WP_000911333 tRNA(fMet)-specific endonuclease VapC -
HTR02_RS00565 (NHKPALLO_00119) 114987..117140 - 2154 WP_000009379 type IV conjugative transfer system coupling protein TraD virb4
HTR02_RS00570 (NHKPALLO_00120) 117393..118124 - 732 WP_000850416 conjugal transfer complement resistance protein TraT -
HTR02_RS00575 (NHKPALLO_00121) 118138..118647 - 510 WP_000628105 conjugal transfer entry exclusion protein TraS -
HTR02_RS00580 (NHKPALLO_00122) 118644..121469 - 2826 WP_072652426 conjugal transfer mating-pair stabilization protein TraG traG
HTR02_RS00585 (NHKPALLO_00123) 121466..122839 - 1374 WP_000944319 conjugal transfer pilus assembly protein TraH traH
HTR02_RS01030 122826..123218 - 393 Protein_121 F-type conjugal transfer protein TrbF -
HTR02_RS00590 (NHKPALLO_00125) 123205..123546 - 342 WP_001442101 P-type conjugative transfer protein TrbJ -
HTR02_RS00595 (NHKPALLO_00126) 123476..124021 - 546 WP_000059833 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTR02_RS00600 (NHKPALLO_00127) 124008..124292 - 285 WP_000624108 type-F conjugative transfer system pilin chaperone TraQ -
HTR02_RS00605 (NHKPALLO_00128) 124373..124648 + 276 WP_001513501 hypothetical protein -
HTR02_RS00610 (NHKPALLO_00129) 124650..124997 - 348 WP_001287907 conjugal transfer protein TrbA -
HTR02_RS00615 (NHKPALLO_00130) 125013..125756 - 744 WP_001030378 type-F conjugative transfer system pilin assembly protein TraF traF
HTR02_RS00620 (NHKPALLO_00131) 125749..126006 - 258 WP_000864318 conjugal transfer protein TrbE -
HTR02_RS00625 (NHKPALLO_00132) 126033..127841 - 1809 WP_072645770 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTR02_RS00630 (NHKPALLO_00133) 127838..128476 - 639 WP_000777703 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTR02_RS00635 (NHKPALLO_00134) 128485..129477 - 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
HTR02_RS00640 (NHKPALLO_00135) 129474..130106 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HTR02_RS00645 (NHKPALLO_00136) 130103..130489 - 387 WP_000099688 type-F conjugative transfer system protein TrbI -
HTR02_RS00650 (NHKPALLO_00137) 130486..133113 - 2628 WP_072652432 type IV secretion system protein TraC virb4
HTR02_RS00655 (NHKPALLO_00139) 133273..133494 - 222 WP_001278690 conjugal transfer protein TraR -
HTR02_RS00660 (NHKPALLO_00140) 133629..134144 - 516 WP_000809834 type IV conjugative transfer system lipoprotein TraV traV
HTR02_RS00665 (NHKPALLO_00141) 134141..134392 - 252 WP_001038351 conjugal transfer protein TrbG -
HTR02_RS00670 (NHKPALLO_00142) 134404..134601 - 198 WP_001324648 conjugal transfer protein TrbD -
HTR02_RS00675 (NHKPALLO_00143) 134588..135178 - 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
HTR02_RS00680 (NHKPALLO_00144) 135168..136595 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
HTR02_RS00685 (NHKPALLO_00145) 136595..137323 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HTR02_RS00690 (NHKPALLO_00146) 137310..137876 - 567 WP_000399774 type IV conjugative transfer system protein TraE traE
HTR02_RS00695 (NHKPALLO_00147) 137898..138209 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HTR02_RS00700 (NHKPALLO_00148) 138224..138589 - 366 WP_000340276 type IV conjugative transfer system pilin TraA -
HTR02_RS00705 (NHKPALLO_00149) 138623..138850 - 228 WP_001254386 conjugal transfer relaxosome protein TraY -
HTR02_RS00710 (NHKPALLO_00150) 138944..139630 - 687 WP_001825184 PAS domain-containing protein -
HTR02_RS00715 (NHKPALLO_00151) 139821..140204 - 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
HTR02_RS00720 (NHKPALLO_00152) 140481..141128 + 648 WP_001825185 transglycosylase SLT domain-containing protein virB1
HTR02_RS00725 (NHKPALLO_00153) 141425..142246 - 822 WP_001234469 DUF932 domain-containing protein -
HTR02_RS01035 (NHKPALLO_00154) 142364..142651 - 288 WP_000107544 hypothetical protein -
HTR02_RS01040 142653..142974 + 322 Protein_151 hypothetical protein -
HTR02_RS00735 (NHKPALLO_00155) 143275..143397 - 123 WP_223195199 Hok/Gef family protein -
HTR02_RS01045 (NHKPALLO_00155) 143342..143494 - 153 Protein_153 DUF5431 family protein -
HTR02_RS00740 (NHKPALLO_00156) 143711..144430 - 720 WP_001276275 plasmid SOS inhibition protein A -
HTR02_RS00745 (NHKPALLO_00157) 144427..144861 - 435 WP_000845935 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   3722 GenBank   NZ_MG825372
Plasmid name   p1106-IncFIB Incompatibility group   IncFIB
Plasmid size   190401 bp Coordinate of oriT [Strand]   140433..140556 [-]
Host baterium   Escherichia coli strain 1106

Cargo genes

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