Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103212
Name   oriT_FWSEC0088|unnamed2 in_silico
Organism   Escherichia coli strain FWSEC0088
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_RRFH01000138 (76039..76124 [+], 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_FWSEC0088|unnamed2
AATTACATGATTTAAAACGCAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2405 GenBank   WP_033815172
Name   traI_C9Z38_RS26825_FWSEC0088|unnamed2 insolico UniProt ID   A0A0P7RUT6
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191751.37 Da        Isoelectric Point: 5.7364

>WP_033815172.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMLT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVSRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKISLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKIPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVKMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDVREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVMAVSGDSVTLSDGQQTRVIRPGQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAISKAVQKGTAHDVL
EPGADREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVWIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAEEKPDQP
DGKTEQAVRAIAGQEQDRASSSERETALPESVLRESQRVQDAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-282)

AAA domain (AAA_30)

(968-1156)

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

(633-712)

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

(575-626)

DNA helicase TraI (TraI_C)

(1434-1557)


  Protein structure



No available structure.




Auxiliary protein

ID   1018 GenBank   WP_000089265
Name   WP_000089265_FWSEC0088|unnamed2 insolico UniProt ID   A0A1E5M428
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 8472.68 Da        Isoelectric Point: 9.9218

>WP_000089265.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacteriaceae]
MSRNIIRPAPGNKVLLVLDDATNHKLLGARERSGRTKTNEVLVRLRDHLSRFPDFYNLDAIKEGTGETDS
IIKDL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-60)


  Protein structure


Source ID Structure
AlphaFold DB A0A1E5M428

ID   1019 GenBank   WP_033802152
Name   WP_033802152_FWSEC0088|unnamed2 insolico UniProt ID   A0A0P7P9U0
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14535.47 Da        Isoelectric Point: 4.7116

>WP_033802152.1 conjugal transfer relaxosome DNA-binding protein TraM [Escherichia coli]
MARVILYISNDVYDKVNAIVEQRRQEGARDKDISVSGTASMLLELGLRVYEAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSELERFFQKNDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A0P7P9U0


T4CP

ID   2166 GenBank   WP_044809095
Name   traD_C9Z38_RS26830_FWSEC0088|unnamed2 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: 83686.34 Da        Isoelectric Point: 5.1711

>WP_044809095.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVSTGKSEVIRRLANYAR
KRGDMVVIYDRSCEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNVANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTYLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHSGESFTIRDWMRGVREDKQNGWLFISSNADTHASLKPVVSMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVLNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKEMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMTAYEAWQ
QENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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   2167 GenBank   WP_136769903
Name   traC_C9Z38_RS26950_FWSEC0088|unnamed2 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: 99550.31 Da        Isoelectric Point: 6.0813

>WP_136769903.1 type IV secretion system protein TraC [Escherichia coli]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEILGEMSFPQFSRLLPYRDYNQESGLFMNDTTLGFMLEAI
PINGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ETQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGAYITTQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRKSTARILNFHLARNPEIAF
LWNMADNYSNLLNPEMSISCPFILTLALVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLTRQNRARIDDVVDFLKNARDNDQYAESPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(468-772)

Family of unknown function (DUF5934) (DUF5934)

(291-447)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 46341..76692

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
C9Z38_RS26830 (C9Z38_26845) 46341..48548 - 2208 WP_044809095 type IV conjugative transfer system coupling protein TraD virb4
C9Z38_RS26835 (C9Z38_26850) 48604..49335 - 732 WP_054626809 hypothetical protein -
C9Z38_RS26840 (C9Z38_26855) 49503..49763 - 261 WP_001077900 hypothetical protein -
C9Z38_RS26845 (C9Z38_26860) 49823..50554 - 732 WP_033814940 conjugal transfer complement resistance protein TraT -
C9Z38_RS26850 (C9Z38_26865) 50586..51083 - 498 WP_033802149 entry exclusion protein -
C9Z38_RS26855 (C9Z38_26870) 51099..53921 - 2823 WP_033802129 conjugal transfer mating-pair stabilization protein TraG traG
C9Z38_RS26860 (C9Z38_26875) 53918..55291 - 1374 WP_033802130 conjugal transfer pilus assembly protein TraH traH
C9Z38_RS26865 (C9Z38_26880) 55278..55670 - 393 WP_000662210 F-type conjugal transfer protein TrbF -
C9Z38_RS26870 (C9Z38_26885) 55624..55938 - 315 WP_001244902 P-type conjugative transfer protein TrbJ -
C9Z38_RS26875 (C9Z38_26890) 55928..56482 - 555 WP_000059845 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
C9Z38_RS26880 (C9Z38_26895) 56469..56750 - 282 WP_000049684 type-F conjugative transfer system pilin chaperone TraQ -
C9Z38_RS26885 (C9Z38_26900) 56816..57217 - 402 WP_225394595 hypothetical protein -
C9Z38_RS26890 (C9Z38_26905) 57348..57713 - 366 WP_001009441 hypothetical protein -
C9Z38_RS26895 (C9Z38_26910) 57727..58470 - 744 WP_001030408 type-F conjugative transfer system pilin assembly protein TraF traF
C9Z38_RS26900 (C9Z38_26915) 58463..58720 - 258 WP_000864350 conjugal transfer protein TrbE -
C9Z38_RS26905 (C9Z38_26920) 58734..60584 - 1851 WP_033802133 type-F conjugative transfer system mating-pair stabilization protein TraN traN
C9Z38_RS26910 (C9Z38_26925) 60581..61003 - 423 WP_001229308 HNH endonuclease signature motif containing protein -
C9Z38_RS26915 (C9Z38_26930) 61029..61400 - 372 WP_000056336 hypothetical protein -
C9Z38_RS26920 (C9Z38_26935) 61397..62035 - 639 WP_000087538 type-F conjugative transfer system pilin assembly protein TrbC trbC
C9Z38_RS26925 (C9Z38_26940) 62062..62583 - 522 WP_000505571 hypothetical protein -
C9Z38_RS26935 (C9Z38_26950) 62988..63980 - 993 WP_032210964 conjugal transfer pilus assembly protein TraU traU
C9Z38_RS26940 (C9Z38_26955) 63977..64609 - 633 WP_021521304 type-F conjugative transfer system protein TraW traW
C9Z38_RS26945 (C9Z38_26960) 64606..64992 - 387 WP_021521305 type-F conjugative transfer system protein TrbI -
C9Z38_RS26950 (C9Z38_26965) 64989..67619 - 2631 WP_136769903 type IV secretion system protein TraC virb4
C9Z38_RS26955 (C9Z38_26970) 67746..68093 - 348 WP_000802783 hypothetical protein -
C9Z38_RS26965 (C9Z38_26980) 68278..68496 - 219 WP_033802135 hypothetical protein -
C9Z38_RS26970 (C9Z38_26985) 68576..69052 - 477 WP_032210967 hypothetical protein -
C9Z38_RS26975 (C9Z38_26990) 69045..69266 - 222 WP_001278689 conjugal transfer protein TraR -
C9Z38_RS26980 (C9Z38_26995) 69401..69916 - 516 WP_033802138 type IV conjugative transfer system lipoprotein TraV traV
C9Z38_RS26985 (C9Z38_27000) 69913..70185 - 273 WP_033802139 conjugal transfer protein TrbD -
C9Z38_RS26990 (C9Z38_27005) 70124..70684 - 561 WP_000232572 conjugal transfer pilus-stabilizing protein TraP -
C9Z38_RS26995 (C9Z38_27010) 70674..72128 - 1455 WP_032210972 F-type conjugal transfer pilus assembly protein TraB traB
C9Z38_RS27000 (C9Z38_27015) 72128..72856 - 729 WP_032210974 type-F conjugative transfer system secretin TraK traK
C9Z38_RS27005 (C9Z38_27020) 72843..73409 - 567 WP_033802141 type IV conjugative transfer system protein TraE traE
C9Z38_RS27010 (C9Z38_27025) 73431..73742 - 312 WP_033802142 type IV conjugative transfer system protein TraL traL
C9Z38_RS27015 (C9Z38_27030) 73757..74122 - 366 WP_000991522 type IV conjugative transfer system pilin TraA -
C9Z38_RS27020 (C9Z38_27035) 74155..74382 - 228 WP_000089265 conjugal transfer relaxosome protein TraY -
C9Z38_RS27025 (C9Z38_27040) 74519..75190 - 672 WP_054626810 conjugal transfer transcriptional regulator TraJ -
C9Z38_RS27030 (C9Z38_27045) 75384..75767 - 384 WP_033802152 conjugal transfer relaxosome DNA-binding protein TraM -
C9Z38_RS27040 (C9Z38_27055) 76102..76692 + 591 WP_284150284 transglycosylase SLT domain-containing protein virB1
C9Z38_RS27045 (C9Z38_27060) 76990..77811 - 822 WP_001562881 DUF932 domain-containing protein -
C9Z38_RS27050 (C9Z38_27065) 77930..78217 - 288 WP_000107543 hypothetical protein -
C9Z38_RS27060 (C9Z38_27075) 78373..78675 - 303 WP_001272235 hypothetical protein -
C9Z38_RS27955 78975..79148 + 174 Protein_94 hypothetical protein -

Host bacterium

ID   3655 GenBank   NZ_RRFH01000138
Plasmid name   FWSEC0088|unnamed2 Incompatibility group   ColRNAI
Plasmid size   79212 bp Coordinate of oriT [Strand]   76039..76124 [+]
Host baterium   Escherichia coli strain FWSEC0088

Cargo genes

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