Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101418
Name   oriT_pB-9428-3 in_silico
Organism   Escherichia coli strain SCPM-O-B-9428
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAJIZO010000009 (12298..12421 [+], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      92..99, 113..120  (ATAATGTA..TACATTAT)
 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_pB-9428-3
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTATTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1290 GenBank   WP_086210984
Name   traI_LMH83_RS26670_pB-9428-3 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: 191844.60 Da        Isoelectric Point: 5.8942

>WP_086210984.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRIMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFVASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLESAISHQKSALHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWEKNPDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(575-626)

AAA domain (AAA_30)

(968-1156)

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   457 GenBank   WP_001151564
Name   WP_001151564_pB-9428-3 insolico UniProt ID   A0AA36PD43
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14446.39 Da        Isoelectric Point: 4.7197

>WP_001151564.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacterales]
MAKVQAYVSDEIVYKINKIVERRRAEGAKSTDVSFSSISTMLLELGLRVYEAQMERKESAFNQAEFNKVL
LECAVKTQSTVAKILGIESLSPHVSGNPKFEYANMVEDIRDKVSSEMERFFPENDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure



No available structure.



ID   458 GenBank   WP_001254390
Name   WP_001254390_pB-9428-3 insolico UniProt ID   A0A7H9SGQ1
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9033.12 Da        Isoelectric Point: 10.2071

>WP_001254390.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacteriaceae]
MRRRNARGGISRTVSVYLDEDTNNRLIRAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A7H9SGQ1


T4CP

ID   903 GenBank   WP_000069752
Name   traC_LMH83_RS26560_pB-9428-3 insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 99572.55 Da        Isoelectric Point: 6.6265

>WP_000069752.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASFHGAKITTQTVDAQAFIEIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKKKQARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQY
TANGTYGRYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGW
RLLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREG
MSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(39-277)

Family of unknown function (DUF5934) (DUF5934)

(291-447)

TraG P-loop domain (P-loop_TraG)

(468-772)

  Protein structure



No available structure.



ID   904 GenBank   WP_228355618
Name   traD_LMH83_RS26665_pB-9428-3 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: 83595.27 Da        Isoelectric Point: 5.1083

>WP_228355618.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
KRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQ
QENHPDTQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 11726..41629

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LMH83_RS26425 (LMH83_26410) 7088..7342 + 255 WP_001230709 hypothetical protein -
LMH83_RS26430 (LMH83_26415) 7339..7581 + 243 WP_000151456 hypothetical protein -
LMH83_RS26435 (LMH83_26420) 7854..8036 + 183 WP_001744154 hypothetical protein -
LMH83_RS26440 (LMH83_26425) 8152..8445 + 294 WP_000673431 hypothetical protein -
LMH83_RS26445 (LMH83_26430) 8750..9037 + 288 WP_000606467 hypothetical protein -
LMH83_RS26450 (LMH83_26435) 9465..9698 + 234 WP_000093745 hypothetical protein -
LMH83_RS26455 (LMH83_26440) 9774..10076 + 303 WP_106504554 CcgAII protein -
LMH83_RS26460 (LMH83_26445) 10348..10497 + 150 WP_000903193 hypothetical protein -
LMH83_RS26465 (LMH83_26450) 10608..11429 + 822 WP_032283064 DUF932 domain-containing protein -
LMH83_RS26470 (LMH83_26455) 11726..12373 - 648 WP_000614287 transglycosylase SLT domain-containing protein virB1
LMH83_RS26475 (LMH83_26460) 12659..13042 + 384 WP_001151564 conjugal transfer relaxosome DNA-binding protein TraM -
LMH83_RS26480 (LMH83_26465) 13236..13922 + 687 WP_000332487 PAS domain-containing protein -
LMH83_RS26485 (LMH83_26470) 14016..14243 + 228 WP_001254390 conjugal transfer relaxosome protein TraY -
LMH83_RS26490 (LMH83_26475) 14277..14642 + 366 WP_228355623 type IV conjugative transfer system pilin TraA -
LMH83_RS26495 (LMH83_26480) 14657..14968 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
LMH83_RS26500 (LMH83_26485) 14990..15556 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
LMH83_RS26505 (LMH83_26490) 15543..16271 + 729 WP_001230809 type-F conjugative transfer system secretin TraK traK
LMH83_RS26510 (LMH83_26495) 16271..17698 + 1428 WP_000146638 F-type conjugal transfer pilus assembly protein TraB traB
LMH83_RS26515 (LMH83_26500) 17688..18260 + 573 WP_023063811 conjugal transfer pilus-stabilizing protein TraP -
LMH83_RS26520 (LMH83_26505) 18257..18577 + 321 WP_001462162 conjugal transfer protein TrbD virb4
LMH83_RS26525 (LMH83_26510) 18570..18821 + 252 WP_001038342 conjugal transfer protein TrbG -
LMH83_RS26530 (LMH83_26515) 18818..19333 + 516 WP_001462163 type IV conjugative transfer system lipoprotein TraV traV
LMH83_RS26535 (LMH83_26520) 19468..19689 + 222 WP_001278978 conjugal transfer protein TraR -
LMH83_RS26540 (LMH83_26525) 19682..20155 + 474 WP_000549598 hypothetical protein -
LMH83_RS26545 (LMH83_26530) 20234..20452 + 219 WP_001377841 hypothetical protein -
LMH83_RS26550 (LMH83_26535) 20480..20827 + 348 WP_000836682 hypothetical protein -
LMH83_RS26555 (LMH83_26540) 20953..21582 + 630 Protein_36 TraC family protein -
LMH83_RS26560 (LMH83_26545) 21747..24377 + 2631 WP_000069752 type IV secretion system protein TraC virb4
LMH83_RS26565 (LMH83_26550) 24374..24760 + 387 WP_000214082 type-F conjugative transfer system protein TrbI -
LMH83_RS26570 (LMH83_26555) 24757..25389 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
LMH83_RS26575 (LMH83_26560) 25386..26378 + 993 WP_000830190 conjugal transfer pilus assembly protein TraU traU
LMH83_RS26580 (LMH83_26565) 26408..26713 + 306 WP_000224411 hypothetical protein -
LMH83_RS26585 (LMH83_26570) 26722..27360 + 639 WP_032299189 type-F conjugative transfer system pilin assembly protein TrbC trbC
LMH83_RS26590 (LMH83_26575) 27357..27728 + 372 WP_000056340 hypothetical protein -
LMH83_RS26595 (LMH83_26580) 27753..28175 + 423 WP_001229306 HNH endonuclease signature motif containing protein -
LMH83_RS26600 (LMH83_26585) 28172..29980 + 1809 WP_228355617 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LMH83_RS26605 (LMH83_26590) 30007..30264 + 258 WP_000864319 conjugal transfer protein TrbE -
LMH83_RS26610 (LMH83_26595) 30257..31000 + 744 WP_001462109 type-F conjugative transfer system pilin assembly protein TraF traF
LMH83_RS26615 (LMH83_26600) 31016..31354 + 339 WP_001287905 conjugal transfer protein TrbA -
LMH83_RS26620 (LMH83_26605) 31481..31765 + 285 WP_000623730 type-F conjugative transfer system pilin chaperone TraQ -
LMH83_RS26625 (LMH83_26610) 31752..32297 + 546 WP_000059832 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LMH83_RS26630 (LMH83_26615) 32287..32569 + 283 Protein_51 P-type conjugative transfer protein TrbJ -
LMH83_RS26635 (LMH83_26620) 32556..32948 + 393 WP_000662236 F-type conjugal transfer protein TrbF -
LMH83_RS26640 (LMH83_26625) 32935..34308 + 1374 WP_021501421 conjugal transfer pilus assembly protein TraH traH
LMH83_RS26645 (LMH83_26630) 34305..37121 + 2817 WP_001007075 conjugal transfer mating-pair stabilization protein TraG traG
LMH83_RS26650 (LMH83_26635) 37154..37675 + 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
LMH83_RS26655 (LMH83_26640) 37700..38431 + 732 WP_000850422 conjugal transfer complement resistance protein TraT -
LMH83_RS26660 (LMH83_26645) 38634..39371 + 738 WP_032246346 hypothetical protein -
LMH83_RS26665 (LMH83_26650) 39422..41629 + 2208 WP_228355618 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   1862 GenBank   NZ_JAJIZO010000009
Plasmid name   pB-9428-3 Incompatibility group   -
Plasmid size   51013 bp Coordinate of oriT [Strand]   12298..12421 [+]
Host baterium   Escherichia coli strain SCPM-O-B-9428

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -